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Nakatsu K, Jijiwa M, Khadka V, Nasu M, Deng Y. sRNAfrag: a pipeline and suite of tools to analyze fragmentation in small RNA sequencing data. Brief Bioinform 2023; 25:bbad515. [PMID: 38243693 PMCID: PMC10796253 DOI: 10.1093/bib/bbad515] [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: 10/21/2023] [Revised: 11/25/2023] [Accepted: 12/13/2023] [Indexed: 01/21/2024] Open
Abstract
Fragments derived from small RNAs such as small nucleolar RNAs are biologically relevant but remain poorly understood. To address this gap, we developed sRNAfrag, a modular and interoperable tool designed to standardize the quantification and analysis of small RNA fragmentation across various biotypes. The tool outputs a set of tables forming a relational database, allowing for an in-depth exploration of biologically complex events such as multi-mapping and RNA fragment stability across different cell types. In a benchmark test, sRNAfrag was able to identify established loci of mature microRNAs solely based on sequencing data. Furthermore, the 5' seed sequence could be rediscovered by utilizing a visualization approach primarily applied in multi-sequence-alignments. Utilizing the relational database outputs, we detected 1411 snoRNA fragment conservation events between two out of four eukaryotic species, providing an opportunity to explore motifs through evolutionary time and conserved fragmentation patterns. Additionally, the tool's interoperability with other bioinformatics tools like ViennaRNA amplifies its utility for customized analyses. We also introduce a novel loci-level variance-score which provides insights into the noise around peaks and demonstrates biological relevance by distinctly separating breast cancer and neuroblastoma cell lines after dimension reduction when applied to small nucleolar RNAs. Overall, sRNAfrag serves as a versatile foundation for advancing our understanding of small RNA fragments and offers a functional foundation to further small RNA research. Availability: https://github.com/kenminsoo/sRNAfrag.
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Affiliation(s)
- Ken Nakatsu
- Emory College of Arts and Sciences, Emory University, 201 Dowman Dr, 30322, Georgia, United States of America
- Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine, 651 Ilalo St, 96813, Hawaii, United States of America
| | - Mayumi Jijiwa
- Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine, 651 Ilalo St, 96813, Hawaii, United States of America
| | - Vedbar Khadka
- Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine, 651 Ilalo St, 96813, Hawaii, United States of America
| | - Masaki Nasu
- Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine, 651 Ilalo St, 96813, Hawaii, United States of America
| | - Youping Deng
- Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine, 651 Ilalo St, 96813, Hawaii, United States of America
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2
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Padroni L, De Marco L, Fiano V, Milani L, Marmiroli G, Giraudo MT, Macciotta A, Ricceri F, Sacerdote C. Identifying MicroRNAs Suitable for Detection of Breast Cancer: A Systematic Review of Discovery Phases Studies on MicroRNA Expression Profiles. Int J Mol Sci 2023; 24:15114. [PMID: 37894794 PMCID: PMC10607026 DOI: 10.3390/ijms242015114] [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: 06/30/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
The analysis of circulating tumor cells and tumor-derived materials, such as circulating tumor DNA, circulating miRNAs (cfmiRNAs), and extracellular vehicles provides crucial information in cancer research. CfmiRNAs, a group of short noncoding regulatory RNAs, have gained attention as diagnostic and prognostic biomarkers. This review focuses on the discovery phases of cfmiRNA studies in breast cancer patients, aiming to identify altered cfmiRNA levels compared to healthy controls. A systematic literature search was conducted, resulting in 16 eligible publications. The studies included a total of 585 breast cancer cases and 496 healthy controls, with diverse sample types and different cfmiRNA assay panels. Several cfmiRNAs, including MIR16, MIR191, MIR484, MIR106a, and MIR193b, showed differential expressions between breast cancer cases and healthy controls. However, the studies had a high risk of bias and lacked standardized protocols. The findings highlight the need for robust study designs, standardized procedures, and larger sample sizes in discovery phase studies. Furthermore, the identified cfmiRNAs can serve as potential candidates for further validation studies in different populations. Improving the design and implementation of cfmiRNA research in liquid biopsies may enhance their clinical diagnostic utility in breast cancer patients.
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Affiliation(s)
- Lisa Padroni
- Unit of Cancer Epidemiology, Città Della Salute e Della Scienza University-Hospital and Center for Cancer Prevention (CPO), Via Santena 7, 10126 Turin, Italy; (L.P.); (L.D.M.); (G.M.)
| | - Laura De Marco
- Unit of Cancer Epidemiology, Città Della Salute e Della Scienza University-Hospital and Center for Cancer Prevention (CPO), Via Santena 7, 10126 Turin, Italy; (L.P.); (L.D.M.); (G.M.)
| | - Valentina Fiano
- Unit of Cancer Epidemiology, Department of Medical Sciences, University of Turin, 10126 Turin, Italy;
| | - Lorenzo Milani
- Centre for Biostatistics, Epidemiology and Public Health (C-BEPH), Department of Clinical and Biological Sciences, University of Turin, 10043 Orbassano, Italy; (L.M.); (M.T.G.); (A.M.); (F.R.)
| | - Giorgia Marmiroli
- Unit of Cancer Epidemiology, Città Della Salute e Della Scienza University-Hospital and Center for Cancer Prevention (CPO), Via Santena 7, 10126 Turin, Italy; (L.P.); (L.D.M.); (G.M.)
| | - Maria Teresa Giraudo
- Centre for Biostatistics, Epidemiology and Public Health (C-BEPH), Department of Clinical and Biological Sciences, University of Turin, 10043 Orbassano, Italy; (L.M.); (M.T.G.); (A.M.); (F.R.)
| | - Alessandra Macciotta
- Centre for Biostatistics, Epidemiology and Public Health (C-BEPH), Department of Clinical and Biological Sciences, University of Turin, 10043 Orbassano, Italy; (L.M.); (M.T.G.); (A.M.); (F.R.)
| | - Fulvio Ricceri
- Centre for Biostatistics, Epidemiology and Public Health (C-BEPH), Department of Clinical and Biological Sciences, University of Turin, 10043 Orbassano, Italy; (L.M.); (M.T.G.); (A.M.); (F.R.)
| | - Carlotta Sacerdote
- Unit of Cancer Epidemiology, Città Della Salute e Della Scienza University-Hospital and Center for Cancer Prevention (CPO), Via Santena 7, 10126 Turin, Italy; (L.P.); (L.D.M.); (G.M.)
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3
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Nakatsu K, Jijiwa M, Khadka V, Nasu M, Huo M, Deng Y. sRNAfrag: A pipeline and suite of tools to analyze fragmentation in small RNA sequencing data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.19.553943. [PMID: 37662282 PMCID: PMC10473647 DOI: 10.1101/2023.08.19.553943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Fragments derived from small RNAs such as small nucleolar RNAs hold biological relevance. However, they remain poorly understood, calling for more comprehensive methods for analysis. We developed sRNAfrag, a standardized workflow and set of scripts to quantify and analyze sRNA fragmentation of any biotype. In a benchmark, it is able to detect loci of mature microRNAs fragmented from precursors and, utilizing multi-mapping events, the conserved 5' seed sequence of miRNAs which we believe may extraoplate to other small RNA fragments. The tool detected 1411 snoRNA fragment conservation events between 2/4 eukaryotic species, providing the opportunity to explore motifs and fragmentation patterns not only within species, but between. Availability: https://github.com/kenminsoo/sRNAfrag.
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Affiliation(s)
- Ken Nakatsu
- Emory College of Arts and Sciences, Emory University, 201 Dowman Dr, Atlanta, 30322, Georgia, United States of America
- Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine, 651 Ilalo St, Honolulu, 96813, Hawaii, United States of America
| | - Mayumi Jijiwa
- Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine, 651 Ilalo St, Honolulu, 96813, Hawaii, United States of America
| | - Vedbar Khadka
- Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine, 651 Ilalo St, Honolulu, 96813, Hawaii, United States of America
| | - Masaki Nasu
- Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine, 651 Ilalo St, Honolulu, 96813, Hawaii, United States of America
| | - Matthew Huo
- Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine, 651 Ilalo St, Honolulu, 96813, Hawaii, United States of America
- Krieger School of Arts and Sciences, Johns Hopkins University, 3400 N Charles St, Baltimore, 21218, Maryland, United States of America
| | - Youping Deng
- Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine, 651 Ilalo St, Honolulu, 96813, Hawaii, United States of America
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4
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Chiorino G, Petracci E, Sehovic E, Gregnanin I, Camussi E, Mello-Grand M, Ostano P, Riggi E, Vergini V, Russo A, Berrino E, Ortale A, Garena F, Venesio T, Gallo F, Favettini E, Frigerio A, Matullo G, Segnan N, Giordano L. Plasma microRNA ratios associated with breast cancer detection in a nested case-control study from a mammography screening cohort. Sci Rep 2023; 13:12040. [PMID: 37491482 PMCID: PMC10368693 DOI: 10.1038/s41598-023-38886-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 07/17/2023] [Indexed: 07/27/2023] Open
Abstract
Mammographic breast cancer screening is effective in reducing breast cancer mortality. Nevertheless, several limitations are known. Therefore, developing an alternative or complementary non-invasive tool capable of increasing the accuracy of the screening process is highly desirable. The objective of this study was to identify circulating microRNA (miRs) ratios associated with BC in women attending mammography screening. A nested case-control study was conducted within the ANDROMEDA cohort (women of age 46-67 attending BC screening). Pre-diagnostic plasma samples, information on life-styles and common BC risk factors were collected. Small-RNA sequencing was carried out on plasma samples from 65 cases and 66 controls. miR ratios associated with BC were selected by two-sample Wilcoxon test and lasso logistic regression. Subsequent assessment by RT-qPCR of the miRs contained in the selected miR ratios was carried out as a platform validation. To identify the most promising biomarkers, penalised logistic regression was further applied to candidate miR ratios alone, or in combination with non-molecular factors. Small-RNA sequencing yielded 20 candidate miR ratios associated with BC, which were further assessed by RT-qPCR. In the resulting model, penalised logistic regression selected seven miR ratios (miR-199a-3p_let-7a-5p, miR-26b-5p_miR-142-5p, let-7b-5p_miR-19b-3p, miR-101-3p_miR-19b-3p, miR-93-5p_miR-19b-3p, let-7a-5p_miR-22-3p and miR-21-5p_miR-23a-3p), together with body mass index (BMI), menopausal status (MS), the interaction term BMI * MS, life-style score and breast density. The ROC AUC of the model was 0.79 with a sensitivity and specificity of 71.9% and 76.6%, respectively. We identified biomarkers potentially useful for BC screening measured through a widespread and low-cost technique. This is the first study reporting circulating miRs for BC detection in a screening setting. Validation in a wider sample is warranted.Trial registration: The Andromeda prospective cohort study protocol was retrospectively registered on 27-11-2015 (NCT02618538).
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Affiliation(s)
- Giovanna Chiorino
- Cancer Genomics Lab, Fondazione Edo ed Elvo Tempia, Via Malta 3, 13900, Biella, Italy
| | - Elisabetta Petracci
- Unit of Biostatistics and Clinical Trials, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Emir Sehovic
- Cancer Genomics Lab, Fondazione Edo ed Elvo Tempia, Via Malta 3, 13900, Biella, Italy.
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy.
| | - Ilaria Gregnanin
- Cancer Genomics Lab, Fondazione Edo ed Elvo Tempia, Via Malta 3, 13900, Biella, Italy
| | - Elisa Camussi
- SSD Epidemiologia Screening, CPO-AOU Città della Salute e della Scienza di Torino, Via Camillo Benso Di Cavour 31, 10123, Turin, Italy
| | - Maurizia Mello-Grand
- Cancer Genomics Lab, Fondazione Edo ed Elvo Tempia, Via Malta 3, 13900, Biella, Italy
| | - Paola Ostano
- Cancer Genomics Lab, Fondazione Edo ed Elvo Tempia, Via Malta 3, 13900, Biella, Italy
| | - Emilia Riggi
- SSD Epidemiologia Screening, CPO-AOU Città della Salute e della Scienza di Torino, Via Camillo Benso Di Cavour 31, 10123, Turin, Italy
| | - Viviana Vergini
- SSD Epidemiologia Screening, CPO-AOU Città della Salute e della Scienza di Torino, Via Camillo Benso Di Cavour 31, 10123, Turin, Italy
| | - Alessia Russo
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Enrico Berrino
- Department of Medical Sciences, University of Turin, Turin, Italy
- Pathology Unit, Candiolo Cancer Institute, FPO IRCCS, Candiolo, Italy
| | - Andrea Ortale
- SSD Epidemiologia Screening, CPO-AOU Città della Salute e della Scienza di Torino, Via Camillo Benso Di Cavour 31, 10123, Turin, Italy
| | - Francesca Garena
- SSD Epidemiologia Screening, CPO-AOU Città della Salute e della Scienza di Torino, Via Camillo Benso Di Cavour 31, 10123, Turin, Italy
| | - Tiziana Venesio
- Pathology Unit, Candiolo Cancer Institute, FPO IRCCS, Candiolo, Italy
| | - Federica Gallo
- Epidemiology Unit, Staff Health Direction, Local Health Authority 1 of Cuneo, Cuneo, Italy
| | | | - Alfonso Frigerio
- SSD Epidemiologia Screening, CPO-AOU Città della Salute e della Scienza di Torino, Via Camillo Benso Di Cavour 31, 10123, Turin, Italy
| | - Giuseppe Matullo
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Nereo Segnan
- SSD Epidemiologia Screening, CPO-AOU Città della Salute e della Scienza di Torino, Via Camillo Benso Di Cavour 31, 10123, Turin, Italy.
| | - Livia Giordano
- SSD Epidemiologia Screening, CPO-AOU Città della Salute e della Scienza di Torino, Via Camillo Benso Di Cavour 31, 10123, Turin, Italy
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Yu Z, Chen S, Tang Z, Tang Y, Ling Z, Wang H, Gong T, Gao Z, Devendra G, Huang G, Chen W, Deng Y. Mitochondria-derived small RNAs as diagnostic biomarkers in lung cancer patients through a novel ratio-based expression analysis methodology. Genes Dis 2023; 10:1055-1061. [PMID: 37396544 PMCID: PMC10308114 DOI: 10.1016/j.gendis.2022.07.013] [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: 04/07/2022] [Revised: 07/01/2022] [Accepted: 07/16/2022] [Indexed: 10/15/2022] Open
Abstract
Small non-coding RNAs are potential diagnostic biomarkers for lung cancer. Mitochondria-derived small RNA (mtRNA) is a novel regulatory small non-coding RNA that only recently has been identified and cataloged. Currently, there are no reports of studies of mtRNA in human lung cancer. Currently, normalization methods are unstable, and they often fail to identify differentially expressed small non-coding RNAs (sncRNAs). In order to identify reliable biomarkers for lung cancer screening, we used a ratio-based method using mtRNAs newly discovered in human peripheral blood mononuclear cells. In the discovery cohort (AUC = 0.981) and independent validation cohort (AUC = 0.916) the prediction model of eight mtRNA ratios distinguished lung cancer patients from controls. The prediction model will provide reliable biomarkers that will allow blood-based screening to become more feasible and will help make lung cancer diagnosis more accurate in clinical practice.
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Affiliation(s)
- Zongtao Yu
- Department of Laboratory Medicine, Affiliated Taihe Hospital of Xi'an Jiaotong University Health Science Center, Shiyan, Hubei 710061, China
- Department of Internal Medicine, Rush University Cancer Center, Rush University Medical Center, Kidston House, Chicago, IL 60612, USA
| | - Shaoqiu Chen
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, USA
- Molecular Biosciences and Bioengineering Program, College of Tropical Agriculture and Human Resources, The University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Zhenming Tang
- Department of Pulmonary and Critical Care Medicine, The Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, Guangxi 545005, China
| | - Ying Tang
- Department of Pulmonary and Critical Care Medicine, The Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, Guangxi 545005, China
| | - Zhougui Ling
- Department of Pulmonary and Critical Care Medicine, The Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, Guangxi 545005, China
| | - Hongwei Wang
- Division of Research and Development, Decoding Therapeutics Corp, Mt Prospect, IL 60056, USA
| | - Ting Gong
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, USA
- Molecular Biosciences and Bioengineering Program, College of Tropical Agriculture and Human Resources, The University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Zitong Gao
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, USA
- Molecular Biosciences and Bioengineering Program, College of Tropical Agriculture and Human Resources, The University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Gehan Devendra
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, USA
- Division Chief Pulmonary & Critical Care Medicine, The Queen’s Medical Center, John A Burns School of Medicine, Honolulu, HI 96813, USA
| | - Gang Huang
- Shanghai Key Laboratory for Molecular Imaging, Shanghai University of Medicine and Health Sciences, Shanghai 201318, China
| | - Wei Chen
- Department of Laboratory Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Youping Deng
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, USA
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6
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Cen Z, Lu B, Ji Y, Chen J, Liu Y, Jiang J, Li X, Li X. Virus-induced breath biomarkers: A new perspective to study the metabolic responses of COVID-19 vaccinees. Talanta 2023; 260:124577. [PMID: 37116359 PMCID: PMC10122548 DOI: 10.1016/j.talanta.2023.124577] [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: 02/14/2023] [Revised: 04/15/2023] [Accepted: 04/18/2023] [Indexed: 04/30/2023]
Abstract
Coronavirus disease 2019 (COVID-19) vaccines can protect people from the infection; however, the action mechanism of vaccine-mediated metabolism remains unclear. Herein, we performed breath tests in COVID-19 vaccinees that revealed metabolic reprogramming induced by protective immune responses. In total, 204 breath samples were obtained from COVID-19 vaccinees and non-vaccinated controls, wherein numerous volatile organic compounds (VOCs) were detected by comprehensive two-dimensional gas chromatography and time-of-flight mass spectrometry system. Subsequently, 12 VOCs were selected as biomarkers to construct a signature panel using alveolar gradients and machine learning-based procedure. The signature panel could distinguish vaccinees from control group with a high prediction performance (AUC, 0.9953; accuracy, 94.42%). The metabolic pathways of these biomarkers indicated that the host-pathogen interactions enhanced enzymatic activity and microbial metabolism in the liver, lung, and gut, potentially constituting the dominant action mechanism of vaccine-driven metabolic regulation. Thus, our findings of this study highlight the potential of measuring exhaled VOCs as rapid, non-invasive biomarkers of viral infections. Furthermore, breathomics appears as an alternative for safety evaluation of biological agents and disease diagnosis.
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Affiliation(s)
- Zhengnan Cen
- Department of Environmental Science & Engineering, Fudan University, Shanghai, 200438, PR China
| | - Bingqing Lu
- Department of Environmental Science & Engineering, Fudan University, Shanghai, 200438, PR China
| | - Yongyan Ji
- Department of Environmental Science & Engineering, Fudan University, Shanghai, 200438, PR China
| | - Jian Chen
- Department of Environmental Science & Engineering, Fudan University, Shanghai, 200438, PR China
| | - Yongqian Liu
- Department of Environmental Science & Engineering, Fudan University, Shanghai, 200438, PR China
| | - Jiakui Jiang
- Department of Environmental Science & Engineering, Fudan University, Shanghai, 200438, PR China
| | - Xue Li
- Institute of Mass Spectrometry and Atmospheric Environment, Jinan University, Guangzhou, 510632, PR China
| | - Xiang Li
- Department of Environmental Science & Engineering, Fudan University, Shanghai, 200438, PR China.
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7
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Shen B, Li L, Liu C, Li X, Li X, Cheng X, Wu H, Yang T, Cheng W, Ding S. Mesoporous Nanozyme-Enhanced DNA Tetrahedron Electrochemiluminescent Biosensor with Three-Dimensional Walking Nanomotor-Mediated CRISPR/Cas12a for Ultrasensitive Detection of Exosomal microRNA. Anal Chem 2023; 95:4486-4495. [PMID: 36802524 DOI: 10.1021/acs.analchem.2c05217] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Exosomal microRNAs (exomiRNAs) have emerged as ideal biomarkers for early clinical diagnostics. The accurate detection of exomiRNAs plays a crucial role in facilitating clinical applications. Herein, an ultrasensitive electrochemiluminescent (ECL) biosensor was constructed using three-dimensional (3D) walking nanomotor-mediated CRISPR/Cas12a and tetrahedral DNA nanostructures (TDNs)-modified nanoemitters (TCPP-Fe@HMUiO@Au-ABEI) for exomiR-155 detection. Initially, the 3D walking nanomotor-mediated CRISPR/Cas12a strategy could effectively convert the target exomiR-155 into amplified biological signals for improving the sensitivity and specificity. Then, TCPP-Fe@HMUiO@Au nanozymes with excellent catalytic performance were used to amplify ECL signals because of the enhanced mass transfer and increased catalytic active sites, originating from its high surface areas (601.83 m2/g), average pore size (3.46 nm), and large pore volumes (0.52 cm3/g). Meanwhile, the TDNs as the scaffold to fabricate "bottom-up" anchor bioprobes could improve the trans-cleavage efficiency of Cas12a. Consequently, this biosensor achieved the limit of detection down to 273.20 aM ranging from 1.0 fM to 1.0 nM. Furthermore, the biosensor could discriminate breast cancer patients evidently by analyzing exomiR-155, and these results conformed to that of qRT-PCR. Thus, this work provides a promising tool for early clinical diagnostics.
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Affiliation(s)
- Bo Shen
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, P. R. China.,Chongqing Key Laboratory of Sichuan-Chongqing Co-construction for Diagnosis and Treatment of Infectious Diseases Integrated Traditional Chinese and Western Medicine, Chongqing Hospital of Traditional Chinese Medicine, Chongqing 400021, P. R. China
| | - Li Li
- Department of Laboratory Medicine, Chongqing General Hospital, Chongqing 401147, P. R. China
| | - Changjin Liu
- Department of Laboratory Medicine, The Fifth People's Hospital of Chongqing, Chongqing 400062, P. R. China
| | - Xinmin Li
- Chongqing Key Laboratory of Sichuan-Chongqing Co-construction for Diagnosis and Treatment of Infectious Diseases Integrated Traditional Chinese and Western Medicine, Chongqing Hospital of Traditional Chinese Medicine, Chongqing 400021, P. R. China
| | - Xinyu Li
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, P. R. China
| | - Xiaoxue Cheng
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P. R. China
| | - Haiping Wu
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, P. R. China
| | - Tiantian Yang
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P. R. China
| | - Wei Cheng
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P. R. China
| | - Shijia Ding
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, P. R. China
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8
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Sehovic E, Urru S, Chiorino G, Doebler P. Meta-analysis of diagnostic cell-free circulating microRNAs for breast cancer detection. BMC Cancer 2022; 22:634. [PMID: 35681127 PMCID: PMC9178880 DOI: 10.1186/s12885-022-09698-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 05/24/2022] [Indexed: 01/17/2023] Open
Abstract
Background Breast cancer (BC) is the most frequently diagnosed cancer among women. Numerous studies explored cell-free circulating microRNAs as diagnostic biomarkers of BC. As inconsistent and rarely intersecting microRNA panels have been reported thus far, we aim to evaluate the overall diagnostic performance as well as the sources of heterogeneity between studies. Methods Based on the search of three online search engines performed up to March 21st 2022, 56 eligible publications that investigated diagnostic circulating microRNAs by utilizing Real-Time Quantitative Reverse Transcription PCR (qRT-PCR) were obtained. Primary studies’ potential for bias was evaluated with the revised tool for the quality assessment of diagnostic accuracy studies (QUADAS-2). A bivariate generalized linear mixed-effects model was applied to obtain pooled sensitivity and specificity. A novel methodology was utilized in which the sample and study models’ characteristics were analysed to determine the potential preference of studies for sensitivity or specificity. Results Pooled sensitivity and specificity of 0.85 [0.81—0.88] and 0.83 [0.79—0.87] were obtained, respectively. Subgroup analysis showed a significantly better performance of multiple (sensitivity: 0.90 [0.86—0.93]; specificity: 0.86 [0.80—0.90]) vs single (sensitivity: 0.82 [0.77—0.86], specificity: 0.83 [0.78—0.87]) microRNA panels and a comparable pooled diagnostic performance between studies using serum (sensitivity: 0.87 [0.81—0.91]; specificity: 0.83 [0.78—0.87]) and plasma (sensitivity: 0.83 [0.77—0.87]; specificity: 0.85 [0.78—0.91]) as specimen type. In addition, based on bivariate and univariate analyses, miRNA(s) based on endogenous normalizers tend to have a higher diagnostic performance than miRNA(s) based on exogenous ones. Moreover, a slight tendency of studies to prefer specificity over sensitivity was observed. Conclusions In this study the diagnostic ability of circulating microRNAs to diagnose BC was reaffirmed. Nonetheless, some subgroup analyses showed between-study heterogeneity. Finally, lack of standardization and of result reproducibility remain the biggest issues regarding the diagnostic application of circulating cell-free microRNAs. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-09698-8.
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Affiliation(s)
- Emir Sehovic
- Cancer Genomics Lab, Fondazione Edo ed Elvo Tempia, 13900, Biella, Italy. .,Department of Life Sciences and Systems Biology, University of Turin, 10100, Turin, Italy.
| | - Sara Urru
- Cancer Genomics Lab, Fondazione Edo ed Elvo Tempia, 13900, Biella, Italy.,Unit of Biostatistics, Epidemiology and Public Health, Department of Cardiac, Thoracic, Vascular Sciences, and Public Health, University of Padova, 35121, Padova, Italy
| | - Giovanna Chiorino
- Cancer Genomics Lab, Fondazione Edo ed Elvo Tempia, 13900, Biella, Italy
| | - Philipp Doebler
- Department of Statistics, TU Dortmund University, 44227, Dortmund, Germany
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Ling Z, Huang S, Wen Z, Tang Z, Huang Y, Wei N, Liu M, Wu J. mtTB: A Web-Based R/Shiny App for Pulmonary Tuberculosis Screening. Front Cell Infect Microbiol 2022; 12:850279. [PMID: 35392603 PMCID: PMC8982078 DOI: 10.3389/fcimb.2022.850279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 02/18/2022] [Indexed: 11/13/2022] Open
Abstract
Pulmonary tuberculosis caused by Mycobacterium tuberculosis remains a global issue. However, the diagnosis of active pulmonary tuberculosis (TB) remains a challenge in the clinic. Small non-coding RNAs are potential diagnostic biomarkers for pulmonary tuberculosis. However, the current normalization methods are not stable and usually fail to reliably detect differentially expressed sncRNAs. To identify reliable biomarkers for pulmonary tuberculosis screening, we utilized the ratio-based method on the newly discovered mitochondria-derived small RNAs in human peripheral blood mononuclear cells. The prediction model of seven mtRNA biomarkers noteworthily enables the discrimination between pulmonary tuberculosis patients and controls in discovery (AUC = 0.906, 23 patients) and independent validation cohort (AUC = 0.968, 20 patients). Moreover, we present mtTB (https://tuberculosis.shinyapps.io/mtTB/), a novel R Graphical User Interface (GUI) that provides reliable biomarkers for the feasibility of blood-based screening, and produce a more accurate tool for pulmonary tuberculosis diagnosis in real clinical practice.
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10
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Zhu Y, Chen S, Ling Z, Winnicki A, Xu L, Xu S, Gong T, Jiang B, Huang G, Deng Y. Comprehensive Analysis of a tRNA-Derived Small RNA in Colorectal Cancer. Front Oncol 2021; 11:701440. [PMID: 34422655 PMCID: PMC8371552 DOI: 10.3389/fonc.2021.701440] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 07/01/2021] [Indexed: 12/12/2022] Open
Abstract
Colorectal cancer often presents as a highly variable disease with myriad forms that are at times difficult to detect in early screenings with sufficient accuracy, for which novel diagnostic methods are an attractive and valuable area of improvement. To improve colorectal cancer diagnosis and prognosis, new biomarkers that can be assembled into a diagnostic panel must be identified, and tRNA-derived small RNAs (tsRNAs) are a particularly interesting and increasingly visible new class of molecules to examine. In this study, small RNA-seq data were profiled for the expression of 104 human tsRNAs in tumor tissue and adjacent normal tissue samples, and a diagnostic model was built based on four differentially expressed tsRNAs: tRF-22-WB86Q3P92, tRF-22-WE8SPOX52, tRF-22-WE8S68L52, tRF-18-8R1546D2. Furthermore, the diagnostic model was validated by two independent validation datasets (AUC was 0.97 and 0.99), and a LASSO model was applied to develop a seven-tsRNA-based risk score model for colorectal cancer prognosis. Finally, a tsRNA-mRNA interaction network was established according to potential mRNA targets predicted by bioinformatic methods. In conclusion, the results suggest that abnormal expression of tsRNA in colorectal cancer may have a functional effect on tumor action and moreover, that some of the tsRNAs identified in this study with diagnostic and prognostic potential could be of clinical significance.
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Affiliation(s)
- Yong Zhu
- National Medical Centre of Colorectal Disease, The Third Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
- Department of Cell & Molecular Medicine, Rush University Medical Center, Chicago, IL, United States
| | - Shaoqiu Chen
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI, United States
- Molecular Biosciences and Bioengineering Program, College of Tropical Agriculture and Human Resources, University of Hawaii at Manoa, Honolulu, HI, United States
| | - Zhougui Ling
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI, United States
- Department of Pulmonary and Critical Care Medicine, The Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, China
| | - Andrew Winnicki
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI, United States
| | - Lilly Xu
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI, United States
| | - Shaun Xu
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI, United States
| | - Ting Gong
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI, United States
| | - Bin Jiang
- National Medical Centre of Colorectal Disease, The Third Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Gang Huang
- Shanghai Key Laboratory for Molecular Imaging, Shanghai University of Medicine and Health Sciences, Shanghai, China
| | - Youping Deng
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI, United States
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11
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Mu Y, McManus DP, Gordon CA, Cai P. Parasitic Helminth-Derived microRNAs and Extracellular Vesicle Cargos as Biomarkers for Helminthic Infections. Front Cell Infect Microbiol 2021; 11:708952. [PMID: 34249784 PMCID: PMC8267863 DOI: 10.3389/fcimb.2021.708952] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 06/14/2021] [Indexed: 12/11/2022] Open
Abstract
As an adaption to their complex lifecycles, helminth parasites garner a unique repertoire of genes at different developmental stages with subtle regulatory mechanisms. These parasitic worms release differential components such as microRNAs (miRNAs) and extracellular vesicles (EVs) as mediators which participate in the host-parasite interaction, immune regulation/evasion, and in governing processes associated with host infection. MiRNAs are small (~ 22-nucleotides) non-coding RNAs that regulate gene expression at the post-transcriptional level, and can exist in stable form in bodily fluids such as serum/plasma, urine, saliva and bile. In addition to reports focusing on the identification of miRNAs or in the probing of differentially expressed miRNA profiles in different development stages/sexes or in specific tissues, a number of studies have focused on the detection of helminth-derived miRNAs in the mammalian host circulatory system as diagnostic biomarkers. Extracellular vesicles (EVs), small membrane-surrounded structures secreted by a wide variety of cell types, contain rich cargos that are important in cell-cell communication. EVs have attracted wide attention due to their unique functional relevance in host-parasite interactions and for their potential value in translational applications such as biomarker discovery. In the current review, we discuss the status and potential of helminth parasite-derived circulating miRNAs and EV cargos as novel diagnostic tools.
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Affiliation(s)
- Yi Mu
- Molecular Parasitology Laboratory, Infectious Diseases Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Donald P McManus
- Molecular Parasitology Laboratory, Infectious Diseases Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Catherine A Gordon
- Molecular Parasitology Laboratory, Infectious Diseases Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Pengfei Cai
- Molecular Parasitology Laboratory, Infectious Diseases Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
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12
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Qin D, Guo Q, Wei R, Liu S, Zhu S, Zhang S, Min L. Predict Colon Cancer by Pairing Plasma miRNAs: Establishment of a Normalizer-Free, Cross-Platform Model. Front Oncol 2021; 11:561763. [PMID: 33968711 PMCID: PMC8101326 DOI: 10.3389/fonc.2021.561763] [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: 09/10/2020] [Accepted: 03/29/2021] [Indexed: 01/12/2023] Open
Abstract
Background Plasma miRNAs are emerging biomarkers for colon cancer (CC) diagnosis. However, the lack of robust internal references largely limits their clinical application. Here we propose a ratio-based, normalizer-free algorithm to quantitate plasma miRNA for CC diagnosis. Methods A miRNA-pair matrix was established by pairing differentially expressed miRNAs in the training group from GSE106817. LASSO regression was performed to select variables. To maximize the performance, four algorithms (LASSO regression, random forest, logistic regression, and SVM) were tested for each biomarker combination. Data from GSE106817 and GSE112264 were used for internal and external verification. RT-qPCR data acquired from another cohort were also used for external validation. Results After validation through four algorithms, we obtained a 4-miRNA pair model (miR-1246 miR-451a; miR-1246 miR-4514; miR-654-5p miR-575; miR-4299 miR-575) that showed good performance in differentiating CC from normal controls with a maximum AUC of 1.00 in internal verification and 0.93 in external verification. Tissue validation showed a maximum AUC of 0.81. Further external validation using RT-qPCR data exhibited good classifier ability with an AUC of 0.88. Conclusion We established a cross-platform prediction model robust against sample-specific disturbance, which is not only well-performed in predicting CC but also promising in the diagnosis of other diseases.
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Affiliation(s)
- Da Qin
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, China
| | - Qingdong Guo
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, China
| | - Rui Wei
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, China
| | - Si Liu
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, China
| | - Shengtao Zhu
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, China
| | - Shutian Zhang
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, China
| | - Li Min
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, China
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13
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Unraveling Molecular Pathways Altered in MeCP2-Related Syndromes, in the Search for New Potential Avenues for Therapy. Biomedicines 2021; 9:biomedicines9020148. [PMID: 33546327 PMCID: PMC7913493 DOI: 10.3390/biomedicines9020148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/25/2021] [Accepted: 01/30/2021] [Indexed: 12/27/2022] Open
Abstract
Methyl-CpG-binding protein 2 (MeCP2) is an X-linked epigenetic modulator whose dosage is critical for neural development and function. Loss-of-function mutations in MECP2 cause Rett Syndrome (RTT, OMIM #312750) while duplications in the Xq28 locus containing MECP2 and Interleukin-1 receptor-associated kinase 1 (IRAK1) cause MECP2 duplication syndrome (MDS, OMIM #300260). Both are rare neurodevelopmental disorders that share clinical symptoms, including intellectual disability, loss of speech, hand stereotypies, vasomotor deficits and seizures. The main objective of this exploratory study is to identify novel signaling pathways and potential quantitative biomarkers that could aid early diagnosis and/or the monitoring of disease progression in clinical trials. We analyzed by RT-PCR gene expression in whole blood and microRNA (miRNA) expression in plasma, in a cohort of 20 females with Rett syndrome, 2 males with MECP2 duplication syndrome and 28 healthy controls, and correlated RNA expression with disease and clinical parameters. We have identified a set of potential biomarker panels for RTT diagnostic and disease stratification of patients with microcephaly and vasomotor deficits. Our study sets the basis for larger studies leading to the identification of specific miRNA signatures for early RTT detection, stratification, disease progression and segregation from other neurodevelopmental disorders. Nevertheless, these data will require verification and validation in further studies with larger sample size including a whole range of ages.
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14
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Qin D, Zhao Y, Guo Q, Zhu S, Zhang S, Min L. Detection of Pancreatic Ductal Adenocarcinoma by A qPCR-based Normalizer-free Circulating Extracellular Vesicles RNA Signature. J Cancer 2021; 12:1445-1454. [PMID: 33531989 PMCID: PMC7847660 DOI: 10.7150/jca.50716] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 10/25/2020] [Indexed: 12/17/2022] Open
Abstract
Background: Pancreatic ductal adenocarcinoma (PDAC) is difficult to diagnose and many efforts have been made to evaluate EVs-derived RNAs as biomarkers to predict PDAC. However, lack of robust internal references largely limited their clinical application. Here we proposed an RNA ratio-based, normalizer-free algorithm to quantitate EVs-derived RNAs in PDAC. Methods: Differentially expressed RNAs in the training group were identified using "limma" package. The ratio of any two candidate RNAs in the same sample was calculated and used as a new biomarker. LASSO regression was performed to build prediction models based on those RNA ratios. RNA-seq data of 116 plasma samples and RT-qPCR data of 111 plasma samples were used for internal and external validation, separately. Three algorithms (lasso regression, logistic regression, and SVM) were compared to improve the performance of this RNA signature. Results: We developed an RNA-ratio based prediction model which comprised eight EVs-derived RNAs, including FBXO7, MORF4L1, DDX17, TALDO1, AHNAK, TUBA1B, CD44, and SETD3. This model could well differentiate PDAC patients with a minimal AUC of 0.86 in internal verification using testing group. External validation using RT-qPCR data also exhibited a good classifier ability with an AUC of 0.89 when distinguishing PDAC from healthy controls. Conclusion: We've developed a qPCR-based, normalizer-free circulating EVs RNA classifier, which could well distinguish PDAC patients from noncancerous controls.
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Affiliation(s)
- Da Qin
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, 100050, P. R. China
| | - Yu Zhao
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, 100050, P. R. China
| | - Qingdong Guo
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, 100050, P. R. China
| | - Shengtao Zhu
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, 100050, P. R. China
| | - Shutian Zhang
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, 100050, P. R. China
| | - Li Min
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, 100050, P. R. China
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15
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Chen X, Zhu Y, Jijiwa M, Nasu M, Ai J, Dai S, Jiang B, Zhang J, Huang G, Deng Y. Identification of plasma lipid species as promising diagnostic markers for prostate cancer. BMC Med Inform Decis Mak 2020; 20:223. [PMID: 32967667 PMCID: PMC7513490 DOI: 10.1186/s12911-020-01242-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 09/02/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Prostate cancer is a very common and highly fatal in men. Current non-invasive detection methods like serum biomarker are unsatisfactory. Biomarkers with high accuracy for diagnostic of prostate cancer are urgently needed. Many lipid species have been found related to various cancers. The purpose of our study is to explore the diagnostic value of lipids for prostate cancer. RESULTS Using triple quadruple liquid chromatography electrospray ionization tandem mass spectrometry, we performed lipidomics profiling of 367 lipids on a total 114 plasma samples from 30 patients with prostate cancer, 38 patients with benign prostatic hyperplasia (BPH), and 46 male healthy controls to evaluate the lipids as potential biomarkers in the diagnosis of prostate cancer. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database was used to construct the potential mechanism pathway. After statistical analysis, five lipids were identified as a panel of potential biomarkers for the detection of prostate cancer between prostate cancer group and the BPH group; the sensitivity, specificity, and area under curve (AUC) of the combination of these five lipids were 73.3, 81.6%, and 0.800, respectively. We also identified another panel of five lipids in distinguishing between prostate cancer group and the control group with predictive values of sensitivity at 76.7%, specificity at 80.4%, and AUC at 0.836, respectively. The glycerophospholipid metabolism pathway of the selected lipids was considered as the target pathway. CONCLUSIONS Our study indicated that the identified plasma lipid biomarkers have potential in the diagnosis of prostate cancer.
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Affiliation(s)
- Xiaoli Chen
- Medical Science Laboratory, the Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, Guangxi China
- Department of Medicine, Rush University Medical Center, Chicago, IL USA
| | - Yong Zhu
- Department of Medicine, Rush University Medical Center, Chicago, IL USA
- National Medical Centre of Colorectal Disease, The Third Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, P. R. China
| | - Mayumi Jijiwa
- Bioinformatics Core, Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine, Honolulu, HI USA
| | - Masaki Nasu
- Bioinformatics Core, Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine, Honolulu, HI USA
| | - Junmei Ai
- Department of Medicine, Rush University Medical Center, Chicago, IL USA
| | - Shengming Dai
- Medical Science Laboratory, the Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, Guangxi China
- Bioinformatics Core, Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine, Honolulu, HI USA
| | - Bin Jiang
- National Medical Centre of Colorectal Disease, The Third Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, P. R. China
| | - Jicai Zhang
- Department of Laboratory Medicine, Shiyan Taihe Hospital, College of Biomedical Engineering, Hubei University of Medicine, Shiyan, Hubei 442000 P. R. China
| | - Gang Huang
- Shanghai Key Laboratory for Molecular Imaging, Shanghai University of Medicine and Health Sciences, Shanghai, 201318 P. R. China
| | - Youping Deng
- Bioinformatics Core, Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine, Honolulu, HI USA
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16
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Ando Y, Yamazaki M, Yamada H, Munetsuna E, Fujii R, Mizuno G, Ichino N, Osakabe K, Sugimoto K, Ishikawa H, Ohashi K, Teradaira R, Ohta Y, Hamajima N, Hashimoto S, Suzuki K. Association of circulating miR-20a, miR-27a, and miR-126 with non-alcoholic fatty liver disease in general population. Sci Rep 2019; 9:18856. [PMID: 31827150 PMCID: PMC6906495 DOI: 10.1038/s41598-019-55076-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Accepted: 11/22/2019] [Indexed: 02/07/2023] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) is closely associated with obesity, metabolic syndrome, and type II diabetes mellitus. Recently, circulating microRNAs (miRNAs) have been proposed as useful disease biomarkers. We examined whether circulating miRNAs, such as miR-20a, miR-27a, and miR-126, were useful biomarkers for NAFLD. We conducted a cross-sectional analysis of 527 subjects aged 39 years or older who had undergone a health examination in the Yakumo Study. Of the residents, 92 were diagnosed with NAFLD using a registered medical sonographer. Serum miR-20a, miR-27a and miR-126 levels were measured by quantitative real-time PCR. We then calculated the odds ratios for serum miRNA level changes according to the severity of NAFLD using normal liver status as the reference group. Serum levels of miR-20a and 27a, but not miR-126, were significantly lower in NAFLD subjects than normal subjects. Serum miR-20a and miR-27a levels were significantly lower in both male and female severe NAFLD subjects. Logistic regression analysis showed a significant relationship between low circulating miR-20a and 27a levels and severe NAFLD. Down-regulated circulating miR-20a and 27a levels were significantly associated with severe NAFLD in the general population. Circulating miR-20a and miR-27a may be useful biomarkers for severe NAFLD.
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Affiliation(s)
- Yoshitaka Ando
- Department of Biomedical and Analytical Sciences, Fujita Health University School of Medical Sciences, 1-98, Dengakugakubo, Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan
| | - Mirai Yamazaki
- Department of Medical Technology, Kagawa Prefectural University of Health Sciences, 281-1, Murechohara, Takamatsu, Kagawa, 761-0123, Japan
| | - Hiroya Yamada
- Department of Hygiene, Fujita Health University School of Medicine, 1-98, Dengakugakubo, Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan.
| | - Eiji Munetsuna
- Department of Biochemistry, Fujita Health University School of Medicine, 1-98, Dengakugakubo, Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan
| | - Ryosuke Fujii
- Department of Preventive Medical Sciences, Fujita Health University School of Medical Sciences, 1-98, Dengakugakubo, Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan
| | - Genki Mizuno
- Department of Joint Research Laboratory of Clinical Medicine, Fujita Health University Hospital, 1-98, Dengakugakubo, Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan
| | - Naohiro Ichino
- Department of Clinical Physiology and Functional Imaging, Fujita Health University School of Medical Sciences, 1-98, Dengakugakubo, Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan
| | - Keisuke Osakabe
- Department of Clinical Physiology and Functional Imaging, Fujita Health University School of Medical Sciences, 1-98, Dengakugakubo, Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan
| | - Keiko Sugimoto
- Department of Clinical Physiology and Functional Imaging, Fujita Health University School of Medical Sciences, 1-98, Dengakugakubo, Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan
| | - Hiroaki Ishikawa
- Department of Biomedical and Analytical Sciences, Fujita Health University School of Medical Sciences, 1-98, Dengakugakubo, Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan
| | - Koji Ohashi
- Department of Biomedical and Analytical Sciences, Fujita Health University School of Medical Sciences, 1-98, Dengakugakubo, Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan
| | - Ryoji Teradaira
- Department of Biomedical and Analytical Sciences, Fujita Health University School of Medical Sciences, 1-98, Dengakugakubo, Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan
| | - Yoshiji Ohta
- Department of Chemistry, Fujita Health University School of Medicine, 1-98, Dengakugakubo, Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan
| | - Nobuyuki Hamajima
- Department of Healthcare Administration, Nagoya University Graduate School of Medicine, 65, Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8550, Japan
| | - Shuji Hashimoto
- Department of Hygiene, Fujita Health University School of Medicine, 1-98, Dengakugakubo, Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan
| | - Koji Suzuki
- Department of Preventive Medical Sciences, Fujita Health University School of Medical Sciences, 1-98, Dengakugakubo, Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan.
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