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Tang S, Xie X, Li L, Zhou L, Xing Y, Chen Y, Cai K, Li F, Zhang J. High fidelity detection of miRNAs from complex physiological samples through electrochemical nanosensors empowered by proximity catalysis and magnetic separation. Biosens Bioelectron 2024; 260:116435. [PMID: 38820724 DOI: 10.1016/j.bios.2024.116435] [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: 12/07/2023] [Revised: 04/25/2024] [Accepted: 05/26/2024] [Indexed: 06/02/2024]
Abstract
Electrochemical detection of miRNA biomarkers in complex physiological samples holds great promise for accurate evaluation of tumor burden in the perioperative period, yet limited by reproducibility and bias issues. Here, nanosensors installed with hybrid probes that responsively release catalytic DNAzymes (G-quadruplexes/hemin) were developed to solve the fidelity challenge in an immobilization-free detection. miRNA targets triggered toehold-mediated strand displacement reactions on the sensor surface and resulted in amplified shedding of DNAzymes. Subsequently, the interference background was removed by Fe3O4 core-facilitated magnetic separation. Binding aptamers of the electrochemical reporter (dopamine) were tethered closely to the catalytic units for boosting H2O2-mediated oxidation through proximity catalysis. The one-to-many conversion by dual amplification from biological-chemical catalysis facilitated sufficient homogeneous sensing signals on electrodes. Thereby, the nanosensor exhibited a low detection limit (2.08 fM), and high reproducibility (relative standard deviation of 1.99%). Most importantly, smaller variations (RSD of 0.51-1.04%) of quantified miRNAs were observed for detection from cell lysates, multiplexed detection from unprocessed serum, and successful discrimination of small upregulations in lysates of tumor tissue samples. The nanosensor showed superior diagnostic performance with an area under curve (AUC) of 0.97 and 94% accuracy in classifying breast cancer patients and healthy donors. These findings demonstrated the synergy of signal amplification and interference removal in achieving high-fidelity miRNA detection for practical clinical applications.
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Affiliation(s)
- Shuqi Tang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, No. 174 Shazheng Road, Chongqing, 400044, China
| | - Xiyue Xie
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, No. 174 Shazheng Road, Chongqing, 400044, China
| | - Lin Li
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, No. 174 Shazheng Road, Chongqing, 400044, China
| | - Luoli Zhou
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, No. 174 Shazheng Road, Chongqing, 400044, China
| | - Yuxin Xing
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, No. 174 Shazheng Road, Chongqing, 400044, China
| | - Yuhua Chen
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, No. 174 Shazheng Road, Chongqing, 400044, China
| | - Kaiyong Cai
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, No. 174 Shazheng Road, Chongqing, 400044, China
| | - Fan Li
- Department of Breast and Thyroid Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, No.1 Youyi Road, Yuzhong District, Chongqing, 400016, China.
| | - Jixi Zhang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, No. 174 Shazheng Road, Chongqing, 400044, China.
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Sierra-Díaz DC, Cabrera R, Gonzalez-Vasquez LA, Angulo-Aguado M, Llinás-Caballero K, Fonseca-Mendoza DJ, Contreras-Bravo NC, Restrepo CM, Ortega-Recalde O, Morel A. Functional Analysis of BRCA1 3'UTR Variants Predisposing to Breast Cancer. Appl Clin Genet 2024; 17:57-62. [PMID: 38803352 PMCID: PMC11129763 DOI: 10.2147/tacg.s444546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 02/29/2024] [Indexed: 05/29/2024] Open
Abstract
Purpose Breast Cancer (BC) is the main female cancer diagnosed worldwide, and it has been described that few genes, such as BRCA1, have a high penetrance for this type of cancer. In this manuscript, we were interested in evaluating the effect of 3'UTR variants on BRCA1 expression. Patients and Methods To accomplish this objective, Whole Exome Sequencing (WES) data of 400 patients with unselected BC was used to filter variants located in the region of interest of BRCA1 gene, finding two of them (c.*36C>G and c.*369_373del). miRGate and miRanda in silico tools were used to predict microRNA (miRNA) interaction. Results The two variants (c.*36C>G, c.*369_373del) were predicted to affect miRNA interaction. After cloning of BRCA1 3'UTR into pMIR-Report vector, the construct was transfected into two BC cell lines (MDA-MB-231 and MCF-7), and the variant c.*36C>G evidenced overexpression of reporter gene luciferase, showing that the transcript was not being degraded by the miRNA in MDA-MB-231 cells. Conclusion The variant seems to protect against Triple Negative BC probably due to the expression level of miRNA in this particular cell line (MDA-MB-231). This is consistent with the clinical history of the patients who harbor BC Hormone Receptors positive (HR+).
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Affiliation(s)
- Diana Carolina Sierra-Díaz
- Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), School of Medicine and Health Sciences, Universidad Del Rosario, Bogotá, Colombia
| | - Rodrigo Cabrera
- Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), School of Medicine and Health Sciences, Universidad Del Rosario, Bogotá, Colombia
- Laboratorio de Biología Molecular y Pruebas Diagnósticas de Alta Complejidad, Fundación Cardioinfantil-Instituto de Cardiología, Bogotá, Colombia
| | - Laura Alejandra Gonzalez-Vasquez
- Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), School of Medicine and Health Sciences, Universidad Del Rosario, Bogotá, Colombia
| | - Mariana Angulo-Aguado
- Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), School of Medicine and Health Sciences, Universidad Del Rosario, Bogotá, Colombia
- Growth Factors, Nutrients and Cancer Group, Molecular Oncology Programme, Centro Nacional Investigaciones Oncológicas (CNIO), Madrid, Spain
| | - Kevin Llinás-Caballero
- Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), School of Medicine and Health Sciences, Universidad Del Rosario, Bogotá, Colombia
- Institute for Immunological Research, University of Cartagena, Cartagena, Colombia
| | - Dora Janeth Fonseca-Mendoza
- Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), School of Medicine and Health Sciences, Universidad Del Rosario, Bogotá, Colombia
| | - Nora Constanza Contreras-Bravo
- Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), School of Medicine and Health Sciences, Universidad Del Rosario, Bogotá, Colombia
| | - Carlos Martin Restrepo
- Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), School of Medicine and Health Sciences, Universidad Del Rosario, Bogotá, Colombia
| | - Oscar Ortega-Recalde
- Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), School of Medicine and Health Sciences, Universidad Del Rosario, Bogotá, Colombia
- Departamento de Morfología, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, D.C, Colombia
| | - Adrien Morel
- Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), School of Medicine and Health Sciences, Universidad Del Rosario, Bogotá, Colombia
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Mondal D, Shinde S, Sinha V, Dixit V, Paul S, Gupta RK, Thakur S, Vishvakarma NK, Shukla D. Prospects of liquid biopsy in the prognosis and clinical management of gastrointestinal cancers. Front Mol Biosci 2024; 11:1385238. [PMID: 38770216 PMCID: PMC11103528 DOI: 10.3389/fmolb.2024.1385238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 04/08/2024] [Indexed: 05/22/2024] Open
Abstract
Gastrointestinal (GI) cancers account for one-fourth of the global cancer incidence and are incriminated to cause one-third of cancer-related deaths. GI cancer includes esophageal, gastric, liver, pancreatic, and colorectal cancers, mostly diagnosed at advanced stages due to a lack of accurate markers for early stages. The invasiveness of diagnostic methods like colonoscopy for solid biopsy reduces patient compliance as it cannot be frequently used to screen patients. Therefore, minimally invasive approaches like liquid biopsy may be explored for screening and early identification of gastrointestinal cancers. Liquid biopsy involves the qualitative and quantitative determination of certain cancer-specific biomarkers in body fluids such as blood, serum, saliva, and urine to predict disease progression, therapeutic tolerance, toxicities, and recurrence by evaluating minimal residual disease and its correlation with other clinical features. In this review, we deliberate upon various tumor-specific cellular and molecular entities such as circulating tumor cells (CTCs), tumor-educated platelets (TEPs), circulating tumor DNA (ctDNA), cell-free DNA (cfDNA), exosomes, and exosome-derived biomolecules and cite recent advances pertaining to their use in predicting disease progression, therapy response, or risk of relapse. We also discuss the technical challenges associated with translating liquid biopsy into clinical settings for various clinical applications in gastrointestinal cancers.
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Affiliation(s)
- Deepankar Mondal
- Department of Biotechnology, Guru Ghasidas Vishwavidyalaya, Bilaspur, Chhattisgarh, India
| | - Sapnita Shinde
- Department of Biotechnology, Guru Ghasidas Vishwavidyalaya, Bilaspur, Chhattisgarh, India
| | - Vibha Sinha
- Department of Biotechnology, Guru Ghasidas Vishwavidyalaya, Bilaspur, Chhattisgarh, India
| | - Vineeta Dixit
- Department of Botany, Sri Sadguru Jagjit Singh Namdhari College, Garhwa, Jharkhand, India
| | - Souvik Paul
- Department of Surgical Gastroenterology, All India Institute of Medical Sciences, Raipur, Chhattisgarh, India
| | - Rakesh Kumar Gupta
- Department of Pathology and Lab Medicine, All India Institute of Medical Sciences, Raipur, Chhattisgarh, India
| | | | | | - Dhananjay Shukla
- Department of Biotechnology, Guru Ghasidas Vishwavidyalaya, Bilaspur, Chhattisgarh, India
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Watanabe Y, Yajima S, Koda M, Kinjou A, Koto A, Takamura E, Sakamoto H, Suye SI. Selective miR-21 detection technology based on photocrosslinkable artificial nucleic acid-modified magnetic particles and hybridization chain reaction. Biosens Bioelectron 2024; 247:115920. [PMID: 38091896 DOI: 10.1016/j.bios.2023.115920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 11/28/2023] [Accepted: 12/06/2023] [Indexed: 01/02/2024]
Abstract
Recently, microRNA (miRNA) detection in blood has attracted attention as a new early detection technology for cancer. The extraction of target miRNA is a necessary preliminary step for detection; however, currently, most extraction methods extract all RNA from the blood, which limits the detection selectivity. Therefore, a method for the selective extraction and detection of target miRNA from blood is very important. In this study, we utilized photocrosslinkable artificial nucleic acids and the hybridization chain reaction (HCR) in an attempt to improve upon the current standard method RT-qPCR, which is hampered by problems with primer design and enzymatic amplification. By introducing photocrosslinkable artificial nucleic acids to oligonucleotide probes modified with magnetic particles with a sequence complementary to that of the target miRNA and irradiating them with light, covalent bonds were formed between the target miRNA and the oligonucleotide probes. These tight covalent bonds enabled the capture of miRNA in blood, and intensive washing ensured that only the target miRNA were extracted. After extraction, two types of DNA (H1 and H2) modified with fluorescent dyes were added and the fluorescence signals were amplified by the HCR in the presence of the target miRNA bound to the photocrosslinkable artificial nucleic acids, allowing for isothermal and enzyme-free miRNA detection. The novel method is suitable for selective miRNA detection in real blood samples. Because the reaction proceeds isothermally and no specialized equipment is used for washing, this detection technology is simple and selective and suitable for application to point-of-care technology using microfluidic devices.
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Affiliation(s)
- Yui Watanabe
- University of Fukui, Faculty of Engineering, Graduate School of Engineering, Fukui, Japan
| | - Shuto Yajima
- University of Fukui, Faculty of Engineering, Graduate School of Engineering, Fukui, Japan
| | - Maho Koda
- University of Fukui, Faculty of Engineering, Graduate School of Engineering, Fukui, Japan
| | - Ayumu Kinjou
- University of Fukui, Faculty of Engineering, Graduate School of Engineering, Fukui, Japan
| | | | - Eiichiro Takamura
- University of Fukui, Faculty of Engineering, Graduate School of Engineering, Fukui, Japan
| | - Hiroaki Sakamoto
- University of Fukui, Faculty of Engineering, Graduate School of Engineering, Fukui, Japan.
| | - Shin-Ichiro Suye
- University of Fukui, Faculty of Engineering, Graduate School of Engineering, Fukui, Japan
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Soares S, Aires F, Monteiro A, Pinto G, Faria I, Sales G, Correa-Duarte MA, Guerreiro S, Fernandes R. Radiotherapy Metastatic Prostate Cancer Cell Lines Treated with Gold Nanorods Modulate miRNA Signatures. Int J Mol Sci 2024; 25:2754. [PMID: 38474003 DOI: 10.3390/ijms25052754] [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: 12/17/2023] [Revised: 02/21/2024] [Accepted: 02/24/2024] [Indexed: 03/14/2024] Open
Abstract
MicroRNA (miRNA) modulation has been identified as a promising strategy for improving the response of human prostate cancer (PCa) to radiotherapy (RT). Studies have shown that mimics or inhibitors of miRNAs could modulate the sensitivity of PCa cells to RT. In addition, pegylated gold nanoparticles have been studied as a therapeutic approach to treat PCa cells and/or vehicles for carrying miRNAs to the inside of cells. Therefore, we evaluated the capacity of hypofractionated RT and pegylated gold nanorods (AuNPr-PEG) to modulate the miRNA signature on PCa cells. Thus, RT-qPCR was used to analyze miRNA-95, miRNA-106-5p, miRNA-145-5p, and miRNA-541-3p on three human metastatic prostate cell lines (PC3, DU145, and LNCaP) and one human prostate epithelial cell line (HprEpiC, a non-tumor cell line) with and without treatment. Our results showed that miRNA expression levels depend on cell type and the treatment combination applied using RT and AuNPr-PEG. In addition, cells pre-treated with AuNPr-PEG and submitted to 2.5 Gy per day for 3 days decreased the expression levels of miRNA-95, miRNA-106, miRNA-145, and miRNA-541-3p. In conclusion, PCa patients submitted to hypofractionated RT could receive personalized treatment based on their metastatic cellular miRNA signature, and AuNPr-PEG could be used to increase metastatic cell radiosensitivity.
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Affiliation(s)
- Sílvia Soares
- (i3S), Instituto de Investigação e Inovação em Saúde, 4200-135 Porto, Portugal
- FP-I3ID, Instituto de Investigação, Inovação e Desenvolvimento, FP-BHS, Biomedical and Health Sciences, Universidade Fernando Pessoa (UFP), 4249-004 Porto, Portugal
- CECLIN, Centro de Estudos Clínicos, Hospital Escola Fernando Pessoa, 4420-096 Gondomar, Portugal
- Faculty of Chemistry, University of Vigo, 36310 Vigo, Spain
- CEB, Centre of Biological Engineering, Minho University, 4710-057 Braga, Portugal
- Biomark@UC/CEB-Centre of Biological Engineering of Minho University, Department of Chemical Engineering, Faculty of Sciences and Technology, Coimbra University, 3030-790 Coimbra, Portugal
- Radiotherapy Service, São João Hospital Center, 4200-319 Porto, Portugal
| | - Fátima Aires
- Radiotherapy Service, São João Hospital Center, 4200-319 Porto, Portugal
| | - Armanda Monteiro
- Radiotherapy Service, São João Hospital Center, 4200-319 Porto, Portugal
| | - Gabriela Pinto
- Radiotherapy Service, São João Hospital Center, 4200-319 Porto, Portugal
| | - Isabel Faria
- FP-I3ID, Instituto de Investigação, Inovação e Desenvolvimento, FP-BHS, Biomedical and Health Sciences, Universidade Fernando Pessoa (UFP), 4249-004 Porto, Portugal
- CECLIN, Centro de Estudos Clínicos, Hospital Escola Fernando Pessoa, 4420-096 Gondomar, Portugal
| | - Goreti Sales
- CEB, Centre of Biological Engineering, Minho University, 4710-057 Braga, Portugal
- Biomark@UC/CEB-Centre of Biological Engineering of Minho University, Department of Chemical Engineering, Faculty of Sciences and Technology, Coimbra University, 3030-790 Coimbra, Portugal
| | - Miguel A Correa-Duarte
- CINBIO, University of Vigo, 36310 Vigo, Spain
- Southern Galicia Institute of Health Research (IISGS), Biomedical Research Networking Center for Mental Health (CIBERSAM), 36310 Madrid, Spain
| | - Susana Guerreiro
- (i3S), Instituto de Investigação e Inovação em Saúde, 4200-135 Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto-IPATIMUP, 4200-465 Porto, Portugal
- Department of Biomedicine, Biochemistry Unit, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
- Faculty of Nutrition and Food Sciences, University of Porto, 4150-180 Porto, Portugal
| | - Rúben Fernandes
- (i3S), Instituto de Investigação e Inovação em Saúde, 4200-135 Porto, Portugal
- FP-I3ID, Instituto de Investigação, Inovação e Desenvolvimento, FP-BHS, Biomedical and Health Sciences, Universidade Fernando Pessoa (UFP), 4249-004 Porto, Portugal
- CECLIN, Centro de Estudos Clínicos, Hospital Escola Fernando Pessoa, 4420-096 Gondomar, Portugal
- UFP@RISE, Rede de Investigação em Saúde, Universidade Fernando Pessoa, 4249-004 Porto, Portugal
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Wang Y, Fang L, Wang Y, Xiong Z. Current Trends of Raman Spectroscopy in Clinic Settings: Opportunities and Challenges. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2300668. [PMID: 38072672 PMCID: PMC10870035 DOI: 10.1002/advs.202300668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 09/08/2023] [Indexed: 02/17/2024]
Abstract
Early clinical diagnosis, effective intraoperative guidance, and an accurate prognosis can lead to timely and effective medical treatment. The current conventional clinical methods have several limitations. Therefore, there is a need to develop faster and more reliable clinical detection, treatment, and monitoring methods to enhance their clinical applications. Raman spectroscopy is noninvasive and provides highly specific information about the molecular structure and biochemical composition of analytes in a rapid and accurate manner. It has a wide range of applications in biomedicine, materials, and clinical settings. This review primarily focuses on the application of Raman spectroscopy in clinical medicine. The advantages and limitations of Raman spectroscopy over traditional clinical methods are discussed. In addition, the advantages of combining Raman spectroscopy with machine learning, nanoparticles, and probes are demonstrated, thereby extending its applicability to different clinical phases. Examples of the clinical applications of Raman spectroscopy over the last 3 years are also integrated. Finally, various prospective approaches based on Raman spectroscopy in clinical studies are surveyed, and current challenges are discussed.
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Affiliation(s)
- Yumei Wang
- Department of NephrologyUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430022China
| | - Liuru Fang
- Hubei Province Key Laboratory of Systems Science in Metallurgical ProcessWuhan University of Science and TechnologyWuhan430081China
| | - Yuhua Wang
- Hubei Province Key Laboratory of Systems Science in Metallurgical ProcessWuhan University of Science and TechnologyWuhan430081China
| | - Zuzhao Xiong
- Hubei Province Key Laboratory of Systems Science in Metallurgical ProcessWuhan University of Science and TechnologyWuhan430081China
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Shrivastav D, Singh DD. Emerging roles of microRNAs as diagnostics and potential therapeutic interest in type 2 diabetes mellitus. World J Clin Cases 2024; 12:525-537. [PMID: 38322458 PMCID: PMC10841963 DOI: 10.12998/wjcc.v12.i3.525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/18/2023] [Accepted: 01/03/2024] [Indexed: 01/18/2024] Open
Abstract
BACKGROUND Type 2 diabetes mellitus (T2DM) is a metabolic disease of impaired glucose utilization. Uncontrolled high sugar levels lead to advanced glycation end products (AGEs), which affects several metabolic pathways by its receptor of advanced glycation end products (RAGE) and causes diabetic complication. MiRNAs are small RNA molecules which regulate genes linked to diabetes and affect AGEs pathogenesis, and target tissues, influencing health and disease processes. AIM To explore miRNA roles in T2DM's metabolic pathways for potential therapeutic and diagnostic advancements in diabetes complications. METHODS We systematically searched the electronic database PubMed using keywords. We included free, full-length research articles that evaluate the role of miRNAs in T2DM and its complications, focusing on genetic and molecular disease mechanisms. After assessing the full-length papers of the shortlisted articles, we included 12 research articles. RESULTS Several types of miRNAs are linked in metabolic pathways which are affected by AGE/RAGE axis in T2DM and its complications. miR-96-5p, miR-7-5p, miR-132, has_circ_0071106, miR-143, miR-21, miR-145-5p, and more are associated with various aspects of T2DM, including disease risk, diagnostic markers, complications, and gene regulation. CONCLUSION Targeting the AGE/RAGE axis, with a focus on miRNA regulation, holds promise for managing T2DM and its complications. MiRNAs have therapeutic potential as they can influence the metabolic pathways affected by AGEs and RAGE, potentially reducing inflammation, oxidative stress, and vascular complications. Additionally, miRNAs may serve as early diagnostic biomarkers for T2DM. Further research in this area may lead to innovative therapeutic strategies for diabetes and its associated complications.
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Affiliation(s)
| | - Desh Deepak Singh
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur 303002, India
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Wang C, Xie Y, Song X, Chao Z, Wu K, Fang Y, Zhao H, Ju H, Liu Y. A NIR Programmable In Vivo miRNA Magnifier for NIR-II Imaging of Early Stage Cancer. Angew Chem Int Ed Engl 2023; 62:e202312665. [PMID: 37903741 DOI: 10.1002/anie.202312665] [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: 08/28/2023] [Revised: 10/28/2023] [Accepted: 10/30/2023] [Indexed: 11/01/2023]
Abstract
Aberrant expressions of biomolecules occur much earlier than tumor visualized size and morphology change, but their common measurement strategies such as biopsy suffer from invasive sampling process. In vivo imaging of slight biomolecule expression difference is urgently needed for early cancer detection. Fluorescence of rare earth nanoparticles (RENPs) in second near-infrared (NIR-II) region makes them appropriate tool for in vivo imaging. However, the incapacity to couple with signal amplification strategies, especially programmable signal amplification strategies, limited their application in lowly expressed biomarkers imaging. Here we develop a 980/808 nm NIR programmed in vivo microRNAs (miRNAs) magnifier by conjugating activatable DNAzyme walker set to RENPs, which achieves more effective NIR-II imaging of early stage tumor than size monitoring imaging technique. Dye FD1080 (FD1080) modified substrate DNA quenches NIR-II downconversion emission of RENPs under 808 nm excitation. The miRNA recognition region in DNAzyme walker is sealed by a photo-cleavable strand to avoid "false positive" signal in systemic circulation. Upconversion emission of RENPs under 980 nm irradiation activates DNAzyme walker for miRNA recognition and amplifies NIR-II fluorescence recovery of RENPs via DNAzyme catalytic reaction to achieve in vivo miRNA imaging. This strategy demonstrates good application potential in the field of early cancer detection.
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Affiliation(s)
- Caixia Wang
- State Key Laboratory of Analytical Chemistry for Life Science Department, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Yuxin Xie
- State Key Laboratory of Analytical Chemistry for Life Science Department, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Xuefang Song
- State Key Laboratory of Analytical Chemistry for Life Science Department, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Zhicong Chao
- State Key Laboratory of Analytical Chemistry for Life Science Department, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Kun Wu
- State Key Laboratory of Analytical Chemistry for Life Science Department, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Yanyun Fang
- State Key Laboratory of Analytical Chemistry for Life Science Department, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Hongxia Zhao
- State Key Laboratory of Analytical Chemistry for Life Science Department, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science Department, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Ying Liu
- State Key Laboratory of Analytical Chemistry for Life Science Department, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
- Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing, 210023, China
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Banchelli M, Tombelli S, de Angelis M, D'Andrea C, Trono C, Baldini F, Giannetti A, Matteini P. Molecular beacon decorated silver nanowires for quantitative miRNA detection by a SERS approach. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:6165-6176. [PMID: 37961002 DOI: 10.1039/d3ay01661g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Advantages of biosensors based on surface enhanced Raman scattering (SERS) rely on improved sensitivity and specificity, and suited reproducibility in detecting a target molecule that is localized in close proximity to a SERS-active surface. Herein, a comprehensive study on the realization of a SERS biosensor designed for detecting miRNA-183, a miRNA biomarker that is specific for chronic obstructive pulmonary disease (COPD), is presented. The used strategy exploits a signal-off mechanism by means of a labelled molecular beacon (MB) as the oligonucleotide biorecognition element immobilized on a 2D SERS substrate, based on spot-on silver nanowires (AgNWs) and a multi-well low volume cell. The MB was properly designed by following a dedicated protocol to recognize the chosen miRNA. A limit of detection down to femtomolar concentration (3 × 10-16 M) was achieved and the specificity of the biosensor was proved. Furthermore, the possibility to regenerate the sensing system through a simple procedure is shown: with regeneration by using HCl 1 mM, two detection cycles were performed with a good recovery of the initial MB signal (83%) and a reproducible signal after hybridization.
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Affiliation(s)
- Martina Banchelli
- Istituto di Fisica Applicata Nello Carrara - CNR, Via Madonna del Piano 10, Sesto F.no (FI), Italy.
| | - Sara Tombelli
- Istituto di Fisica Applicata Nello Carrara - CNR, Via Madonna del Piano 10, Sesto F.no (FI), Italy.
| | - Marella de Angelis
- Istituto di Fisica Applicata Nello Carrara - CNR, Via Madonna del Piano 10, Sesto F.no (FI), Italy.
| | - Cristiano D'Andrea
- Istituto di Fisica Applicata Nello Carrara - CNR, Via Madonna del Piano 10, Sesto F.no (FI), Italy.
| | - Cosimo Trono
- Istituto di Fisica Applicata Nello Carrara - CNR, Via Madonna del Piano 10, Sesto F.no (FI), Italy.
| | - Francesco Baldini
- Istituto di Fisica Applicata Nello Carrara - CNR, Via Madonna del Piano 10, Sesto F.no (FI), Italy.
| | - Ambra Giannetti
- Istituto di Fisica Applicata Nello Carrara - CNR, Via Madonna del Piano 10, Sesto F.no (FI), Italy.
| | - Paolo Matteini
- Istituto di Fisica Applicata Nello Carrara - CNR, Via Madonna del Piano 10, Sesto F.no (FI), Italy.
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Samara M, Vlachostergios PJ, Thodou E, Zachos I, Mitrakas L, Evmorfopoulos K, Tzortzis V, Giakountis A. Characterization of a miRNA Signature with Enhanced Diagnostic and Prognostic Power for Patients with Bladder Carcinoma. Int J Mol Sci 2023; 24:16243. [PMID: 38003433 PMCID: PMC10671612 DOI: 10.3390/ijms242216243] [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: 10/12/2023] [Revised: 11/04/2023] [Accepted: 11/10/2023] [Indexed: 11/26/2023] Open
Abstract
Bladder carcinoma is globally among the most prevalent cancers and is associated with a high mortality rate at advanced stages. Its detection relies on invasive diagnostic methods that are unpleasant for the patient. Non-invasive molecular biomarkers, such as miRNAs, could serve as alternatives for early detection and prognosis of this malignancy. We designed a computational approach that combines transcriptome profiling, survival analyses, and calculation of diagnostic power in order to isolate miRNA signatures with high diagnostic and prognostic utility. Our analysis of TCGA-BLCA data from 429 patients yielded one miRNA signature, consisting of five upregulated and three downregulated miRNAs with cumulative diagnostic power that outperforms current diagnostic methods. The same miRNAs have a strong prognostic significance since their expression is associated with the overall survival of bladder cancer patients. We evaluated the expression of this signature in 19 solid cancer types, supporting its unique diagnostic utility for bladder carcinoma. We provide computational evidence regarding the functional implications of this miRNA signature in cell cycle regulation, demonstrating its abundance in body fluids, including peripheral blood and urine. Our study characterized a novel miRNA signature with the potential to serve as a non-invasive method for bladder cancer diagnosis and prognosis.
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Affiliation(s)
- Maria Samara
- Department of Pathology, Faculty of Medicine, School of Health Sciences, University of Thessaly, 41335 Larissa, Greece
| | - Panagiotis J. Vlachostergios
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Eleni Thodou
- Department of Pathology, Faculty of Medicine, School of Health Sciences, University of Thessaly, 41335 Larissa, Greece
| | - Ioannis Zachos
- Department of Urology, Faculty of Medicine, School of Health Sciences, University of Thessaly, University Hospital of Larissa, 41335 Larissa, Greece
| | - Lampros Mitrakas
- Department of Urology, Faculty of Medicine, School of Health Sciences, University of Thessaly, University Hospital of Larissa, 41335 Larissa, Greece
| | - Konstantinos Evmorfopoulos
- Department of Urology, Faculty of Medicine, School of Health Sciences, University of Thessaly, University Hospital of Larissa, 41335 Larissa, Greece
| | - Vassilios Tzortzis
- Department of Urology, Faculty of Medicine, School of Health Sciences, University of Thessaly, University Hospital of Larissa, 41335 Larissa, Greece
| | - Antonis Giakountis
- Department of Biochemistry and Biotechnology, University of Thessaly, 41335 Larissa, Greece
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11
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Gómez-Acebo I, Llorca J, Alonso-Molero J, Díaz-Martínez M, Pérez-Gómez B, Amiano P, Belmonte T, Molina AJ, Burgui R, Castaño-Vinyals G, Moreno V, Molina-Barceló A, Marcos-Gragera R, Kogevinas M, Pollán M, Dierssen-Sotos T. Circulating miRNAs signature on breast cancer: the MCC-Spain project. Eur J Med Res 2023; 28:480. [PMID: 37925534 PMCID: PMC10625260 DOI: 10.1186/s40001-023-01471-2] [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: 06/19/2023] [Accepted: 10/23/2023] [Indexed: 11/06/2023] Open
Abstract
PURPOSE To build models combining circulating microRNAs (miRNAs) able to identify women with breast cancer as well as different types of breast cancer, when comparing with controls without breast cancer. METHOD miRNAs analysis was performed in two phases: screening phase, with a total n = 40 (10 controls and 30 BC cases) analyzed by Next Generation Sequencing, and validation phase, which included 131 controls and 269 cases. For this second phase, the miRNAs were selected combining the screening phase results and a revision of the literature. They were quantified using RT-PCR. Models were built using logistic regression with LASSO penalization. RESULTS The model for all cases included seven miRNAs (miR-423-3p, miR-139-5p, miR-324-5p, miR-1299, miR-101-3p, miR-186-5p and miR-29a-3p); which had an area under the ROC curve of 0.73. The model for cases diagnosed via screening only took in one miRNA (miR-101-3p); the area under the ROC curve was 0.63. The model for disease-free cases in the follow-up had five miRNAs (miR-101-3p, miR-186-5p, miR-423-3p, miR-142-3p and miR-1299) and the area under the ROC curve was 0.73. Finally, the model for cases with active disease in the follow-up contained six miRNAs (miR-101-3p, miR-423-3p, miR-139-5p, miR-1307-3p, miR-331-3p and miR-21-3p) and its area under the ROC curve was 0.82. CONCLUSION We present four models involving eleven miRNAs to differentiate healthy controls from different types of BC cases. Our models scarcely overlap with those previously reported.
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Affiliation(s)
- Inés Gómez-Acebo
- Department of Preventive Medicine and Public Health, University of Cantabria, Santander, Spain.
- IDIVAL, Santander, Spain.
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Institute of Health Carlos III, Madrid, Spain.
| | - Javier Llorca
- Department of Preventive Medicine and Public Health, University of Cantabria, Santander, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Institute of Health Carlos III, Madrid, Spain
| | - Jessica Alonso-Molero
- Department of Preventive Medicine and Public Health, University of Cantabria, Santander, Spain
- IDIVAL, Santander, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Institute of Health Carlos III, Madrid, Spain
| | - Marta Díaz-Martínez
- Department of Preventive Medicine and Public Health, University of Cantabria, Santander, Spain
| | - Beatriz Pérez-Gómez
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Institute of Health Carlos III, Madrid, Spain
- National Centre for Epidemiology, Carlos III Institute of Health, Madrid, Spain
| | - Pilar Amiano
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Institute of Health Carlos III, Madrid, Spain
- Sub Directorate for Public Health and Addictions of Gipuzkoa, Ministry of Health of the Basque Government, San Sebastian, Spain
- Epidemiology of Chronic and Communicable Diseases Group, Biodonostia Health Research Institute, San Sebastián, Spain
| | - Thalía Belmonte
- IUOPA, University of Oviedo and ISPA (Health Research Institute of Asturias), Oviedo, Spain
| | - Antonio J Molina
- Grupo de Investigación en Interacción, Gen-Ambiente-Salud (GIIGAS), Instituto de Biomedicina (IBIOMED), Universidad de León, León, Spain
| | - Rosana Burgui
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Institute of Health Carlos III, Madrid, Spain
- Institute of Public and Occupational Health of Navarre (ISPLN), 31003, Pamplona, Spain
| | - Gemma Castaño-Vinyals
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Institute of Health Carlos III, Madrid, Spain
- Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Víctor Moreno
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Institute of Health Carlos III, Madrid, Spain
- Colorectal Cancer Group, ONCOBELL Program, Instituto de Investigación Biomédica de Bellvitge (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
- Oncology Data Analytics Program, Catalan Institute of Oncology, Hospitalet de Llobregat, Barcelona, Spain
- Department of Clinical Sciences, Faculty of Medicine and health Sciences and Universitat de Barcelona Institute of Complex Systems (UBICS), University of Barcelona, Barcelona, Spain
| | - Ana Molina-Barceló
- Cancer and Public Health UnitFoundation for the Promotion of Health and Biomedical Research (FISABIO-Salud Pública) in the Valencia Region, Valencia, Spain
| | - Rafael Marcos-Gragera
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Institute of Health Carlos III, Madrid, Spain
- Epidemiology Unit and Girona Cancer Registry, Oncology Coordination Plan, Department of Health, Autonomous Government of Catalonia, Catalan Institute of Oncology (ICO), Girona Biomedical Research Institute (IdiBGi), Girona, Spain
| | - Manolis Kogevinas
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Institute of Health Carlos III, Madrid, Spain
- Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Marina Pollán
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Institute of Health Carlos III, Madrid, Spain
- National Centre for Epidemiology, Carlos III Institute of Health, Madrid, Spain
| | - Trinidad Dierssen-Sotos
- Department of Preventive Medicine and Public Health, University of Cantabria, Santander, Spain
- IDIVAL, Santander, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Institute of Health Carlos III, Madrid, Spain
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12
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Smith DA, Redman JE, Fraser DJ, Bowen T. Identification and detection of microRNA kidney disease biomarkers in liquid biopsies. Curr Opin Nephrol Hypertens 2023; 32:515-521. [PMID: 37678380 DOI: 10.1097/mnh.0000000000000927] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
PURPOSE OF REVIEW MicroRNAs (miRNAs) are emerging rapidly as a novel class of biomarkers of major organ disorders, including kidney diseases. However, current PCR-based detection methods are not amenable to development for high-throughput, cost-effective miRNA biomarker quantification. RECENT FINDINGS MiRNA biomarkers show significant promise for diagnosis and prognosis of kidney diseases, including diabetic kidney disease, acute kidney injury, IgA nephropathy and delayed graft function following kidney transplantation. A variety of novel methods to detect miRNAs in liquid biopsies including urine, plasma and serum are being developed. As miRNAs are functional transcripts that regulate the expression of many protein coding genes, differences in miRNA profiles in disease also offer clues to underlying disease mechanisms. SUMMARY Recent findings highlight the potential of miRNAs as biomarkers to detect and predict progression of kidney diseases. Developing in parallel, novel methods for miRNA detection will facilitate the integration of these biomarkers into rapid routine clinical testing and existing care pathways. Validated kidney disease biomarkers also hold promise to identify novel therapeutic tools and targets. VIDEO ABSTRACT http://links.lww.com/CONH/A43.
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Affiliation(s)
- Daniel A Smith
- Division of Infection & Immunity
- Wales Kidney Research Unit
- Systems Immunity University Research Institute, School of Medicine, College of Biomedical and Life Sciences, Cardiff University, Heath Park, Cardiff
| | - James E Redman
- School of Chemistry, Cardiff University, Park Place, Cardiff, Wales, UK
| | - Donald J Fraser
- Division of Infection & Immunity
- Wales Kidney Research Unit
- Systems Immunity University Research Institute, School of Medicine, College of Biomedical and Life Sciences, Cardiff University, Heath Park, Cardiff
| | - Timothy Bowen
- Division of Infection & Immunity
- Wales Kidney Research Unit
- Systems Immunity University Research Institute, School of Medicine, College of Biomedical and Life Sciences, Cardiff University, Heath Park, Cardiff
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13
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Liu WJ, Wang LJ, Zhang CY. Progress in quantum dot-based biosensors for microRNA assay: A review. Anal Chim Acta 2023; 1278:341615. [PMID: 37709484 DOI: 10.1016/j.aca.2023.341615] [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: 05/04/2023] [Revised: 06/15/2023] [Accepted: 07/11/2023] [Indexed: 09/16/2023]
Abstract
MicroRNAs (miRNAs) are responsible for post-transcriptional gene regulation, and may function as valuable biomarkers for diseases diagnosis. Accurate and sensitive analysis of miRNAs is in great demand. Quantum dots (QDs) are semiconductor nanomaterials with superior optoelectronic features, such as high quantum yield and brightness, broad absorption and narrow emission, long fluorescence lifetime, and good photostability. Herein, we give a comprehensive review about QD-based biosensors for miRNA assay. Different QD-based biosensors for miRNA assay are classified by the signal types including fluorescent, electrochemical, electrochemiluminescent, and photoelectrochemical outputs. We highlight the features, principles, and performances of the emerging miRNA biosensors, and emphasize the challenges and perspectives in this field.
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Affiliation(s)
- Wen-Jing Liu
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China
| | - Li-Juan Wang
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China.
| | - Chun-Yang Zhang
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China.
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14
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Álvarez-Hilario LG, Salmerón-Bárcenas EG, Ávila-López PA, Hernández-Montes G, Aréchaga-Ocampo E, Herrera-Goepfert R, Albores-Saavedra J, Manzano-Robleda MDC, Saldívar-Cerón HI, Martínez-Frías SP, Thompson-Bonilla MDR, Vargas M, Hernández-Rivas R. Circulating miRNAs as Noninvasive Biomarkers for PDAC Diagnosis and Prognosis in Mexico. Int J Mol Sci 2023; 24:15193. [PMID: 37894871 PMCID: PMC10607652 DOI: 10.3390/ijms242015193] [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: 08/09/2023] [Revised: 09/20/2023] [Accepted: 10/08/2023] [Indexed: 10/29/2023] Open
Abstract
Among malignant neoplasms, pancreatic ductal adenocarcinoma (PDAC) has one of the highest fatality rates due to its late detection. Therefore, it is essential to discover a noninvasive, early, specific, and sensitive diagnostic method. MicroRNAs (miRNAs) are attractive biomarkers because they are accessible, highly specific, and sensitive. It is crucial to find miRNAs that could be used as possible biomarkers because PDAC is the eighth most common cause of cancer death in Mexico. With the help of microRNA microarrays, differentially expressed miRNAs (DEmiRNAs) were found in PDAC tissues. The presence of these DEmiRNAs in the plasma of Mexican patients with PDAC was determined using RT-qPCR. Receiver operating characteristic curve analysis was performed to determine the diagnostic capacity of these DEmiRNAs. Gene Expression Omnibus datasets (GEO) were employed to verify our results. The Prisma V8 statistical analysis program was used. Four DEmiRNAs in plasma from PDAC patients and microarray tissues were found. Serum samples from patients with PDAC were used to validate their overexpression in GEO databases. We discovered a new panel of the two miRNAs miR-222-3p and miR-221-3p that could be used to diagnose PDAC, and when miR-221-3p and miR-222-3p were overexpressed, survival rates decreased. Therefore, miR-222-3p and miR-221-3p might be employed as noninvasive indicators for the diagnosis and survival of PDAC in Mexican patients.
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Affiliation(s)
- Lissuly Guadalupe Álvarez-Hilario
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de Mexico C.P. 07360, Mexico; (L.G.Á.-H.); (E.G.S.-B.); (P.A.Á.-L.); (H.I.S.-C.); (M.V.)
| | - Eric Genaro Salmerón-Bárcenas
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de Mexico C.P. 07360, Mexico; (L.G.Á.-H.); (E.G.S.-B.); (P.A.Á.-L.); (H.I.S.-C.); (M.V.)
| | - Pedro Antonio Ávila-López
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de Mexico C.P. 07360, Mexico; (L.G.Á.-H.); (E.G.S.-B.); (P.A.Á.-L.); (H.I.S.-C.); (M.V.)
| | - Georgina Hernández-Montes
- Coordinación de la Investigación Científica, Red de Apoyo a la Investigación, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de Mexico C.P. 14080, Mexico;
| | - Elena Aréchaga-Ocampo
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana, Unidad Cuajimalpa, Ciudad de Mexico C.P. 05300, Mexico;
| | - Roberto Herrera-Goepfert
- Departamento de Patología, Instituto Nacional de Cancerología, Ciudad de Mexico C.P. 14080, Mexico;
| | - Jorge Albores-Saavedra
- Departamento de Patología, Medica Sur Clínica y Fundación, Ciudad de Mexico C.P. 14050, Mexico;
| | | | - Héctor Iván Saldívar-Cerón
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de Mexico C.P. 07360, Mexico; (L.G.Á.-H.); (E.G.S.-B.); (P.A.Á.-L.); (H.I.S.-C.); (M.V.)
| | - Sandra Paola Martínez-Frías
- Departamento de Infectología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán (INCMNSZ), Avenida Vasco de Quiroga No.15, Colonia Belisario Domínguez Sección XVI, Ciudad de Mexico C.P. 14080, Mexico
| | | | - Miguel Vargas
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de Mexico C.P. 07360, Mexico; (L.G.Á.-H.); (E.G.S.-B.); (P.A.Á.-L.); (H.I.S.-C.); (M.V.)
| | - Rosaura Hernández-Rivas
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de Mexico C.P. 07360, Mexico; (L.G.Á.-H.); (E.G.S.-B.); (P.A.Á.-L.); (H.I.S.-C.); (M.V.)
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15
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Yang H, Xun Y, Ke C, Tateishi K, You H. Extranodal lymphoma: pathogenesis, diagnosis and treatment. MOLECULAR BIOMEDICINE 2023; 4:29. [PMID: 37718386 PMCID: PMC10505605 DOI: 10.1186/s43556-023-00141-3] [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: 02/05/2023] [Accepted: 08/18/2023] [Indexed: 09/19/2023] Open
Abstract
Approximately 30% of lymphomas occur outside the lymph nodes, spleen, or bone marrow, and the incidence of extranodal lymphoma has been rising in the past decade. While traditional chemotherapy and radiation therapy can improve survival outcomes for certain patients, the prognosis for extranodal lymphoma patients remains unsatisfactory. Extranodal lymphomas in different anatomical sites often have distinct cellular origins, pathogenic mechanisms, and clinical manifestations, significantly influencing their diagnosis and treatment. Therefore, it is necessary to provide a comprehensive summary of the pathogenesis, diagnosis, and treatment progress of extranodal lymphoma overall and specifically for different anatomical sites. This review summarizes the current progress in the common key signaling pathways in the development of extranodal lymphomas and intervention therapy. Furthermore, it provides insights into the pathogenesis, diagnosis, and treatment strategies of common extranodal lymphomas, including gastric mucosa-associated lymphoid tissue (MALT) lymphoma, mycosis fungoides (MF), natural killer/T-cell lymphoma (nasal type, NKTCL-NT), and primary central nervous system lymphoma (PCNSL). Additionally, as PCNSL is one of the extranodal lymphomas with the worst prognosis, this review specifically summarizes prognostic indicators and discusses the challenges and opportunities related to its clinical applications. The aim of this review is to assist clinical physicians and researchers in understanding the current status of extranodal lymphomas, enabling them to make informed clinical decisions that contribute to improving patient prognosis.
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Affiliation(s)
- Hua Yang
- Department of Basic Medicine and Biomedical Engineering, School of Medicine, Foshan University, Foshan, 528000, China
| | - Yang Xun
- Department of Basic Medicine and Biomedical Engineering, School of Medicine, Foshan University, Foshan, 528000, China
| | - Chao Ke
- Department of Neurosurgery and Neuro-Oncology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060, China
| | - Kensuke Tateishi
- Department of Neurosurgery, Graduate School of Medicine, Yokohama City University, Yokohama, 2360004, Japan
| | - Hua You
- Laboratory for Excellence in Systems Biomedicine of Pediatric Oncology, Department of Pediatric Hematology and Oncology, Chongqing Key Laboratory of Pediatrics, Ministry of Education Key Laboratory of Child Development and Disorders, China International Science and Technology Cooperation base of Child development and Critical Disorders, National Clinical Research Center for Child Health and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, 401122, China.
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16
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Taghehchian N, Samsami Y, Maharati A, Zangouei AS, Boroumand-Noughabi S, Moghbeli M. Molecular biology of microRNA-342 during tumor progression and invasion. Pathol Res Pract 2023; 248:154672. [PMID: 37413875 DOI: 10.1016/j.prp.2023.154672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 07/02/2023] [Indexed: 07/08/2023]
Abstract
Cancer is considered as one of the main causes of human deaths and health challenges in the world. Various factors are involved in the high death rate of cancer patients, including late diagnosis and drug resistance that result in treatment failure and tumor recurrence. Invasive diagnostic methods are one of the main reasons of late tumor detection in cancer patients. Therefore, it is necessary to investigate the molecular tumor biology to introduce efficient non-invasive markers. MicroRNAs (miRNAs) are involved in regulation of the cellular mechanisms such as cell proliferation, apoptosis, and migration. MiRNAs deregulations have been also frequently shown in different tumor types. Here, we discussed the molecular mechanisms of miR-342 during tumor growth. MiR-342 mainly functions as a tumor suppressor by the regulation of transcription factors and signaling pathways such as WNT, PI3K/AKT, NF-kB, and MAPK. Therefore, miR-342 mimics can be used as a reliable therapeutic strategy to inhibit the tumor cells growth. The present review can also pave the way to introduce the miR-342 as a non-invasive diagnostic/prognostic marker in cancer patients.
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Affiliation(s)
- Negin Taghehchian
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Yalda Samsami
- Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amirhosein Maharati
- Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amir Sadra Zangouei
- Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Samaneh Boroumand-Noughabi
- Department of Hematology and Blood Bank, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Meysam Moghbeli
- Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
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17
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Kabzinski J, Kucharska-Lusina A, Majsterek I. RNA-Based Liquid Biopsy in Head and Neck Cancer. Cells 2023; 12:1916. [PMID: 37508579 PMCID: PMC10377854 DOI: 10.3390/cells12141916] [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: 06/26/2023] [Revised: 07/17/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023] Open
Abstract
Head and neck cancer (HNC) is a prevalent and diverse group of malignancies with substantial morbidity and mortality rates. Early detection and monitoring of HNC are crucial for improving patient outcomes. Liquid biopsy, a non-invasive diagnostic approach, has emerged as a promising tool for cancer detection and monitoring. In this article, we review the application of RNA-based liquid biopsy in HNC. Various types of RNA, including messenger RNA (mRNA), microRNA (miRNA), long non-coding RNA (lncRNA), small nuclear RNA (snRNA), small nucleolar RNA (snoRNA), circular RNA (circRNA) and PIWI-interacting RNA (piRNA), are explored as potential biomarkers in HNC liquid-based diagnostics. The roles of RNAs in HNC diagnosis, metastasis, tumor resistance to radio and chemotherapy, and overall prognosis are discussed. RNA-based liquid biopsy holds great promise for the early detection, prognosis, and personalized treatment of HNC. Further research and validation are necessary to translate these findings into clinical practice and improve patient outcomes.
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Affiliation(s)
- Jacek Kabzinski
- Department of Clinical Chemistry and Biochemistry, Medical University of Lodz, MolecoLAB A6, Mazowiecka 5, 92-215 Lodz, Poland
| | - Aleksandra Kucharska-Lusina
- Department of Clinical Chemistry and Biochemistry, Medical University of Lodz, MolecoLAB A6, Mazowiecka 5, 92-215 Lodz, Poland
| | - Ireneusz Majsterek
- Department of Clinical Chemistry and Biochemistry, Medical University of Lodz, MolecoLAB A6, Mazowiecka 5, 92-215 Lodz, Poland
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18
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Chan SF, Cheng H, Goh KKR, Zou R. Preanalytic Methodological Considerations and Sample Quality Control of Circulating miRNAs. J Mol Diagn 2023; 25:438-453. [PMID: 37030398 DOI: 10.1016/j.jmoldx.2023.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/24/2023] [Accepted: 03/22/2023] [Indexed: 04/10/2023] Open
Abstract
As miRNAs emerge as potential circulating biomarkers for the diagnosis or prognosis of a wide variety of diseases, the quantification of miRNA necessitates careful preanalytic considerations and sample quality control becomes crucial. This study comprehensively analyzed the profiles of 356 miRNAs by quantitative RT-PCR in various blood sample types, with various processing protocols. The comprehensive analysis investigated the correlations of individual miRNAs with certain confounding factors. On the basis of these profiles, a panel of 7 miRNAs was established for the quality control of samples corresponding to hemolysis and platelet contamination. The panel was used to investigate the confounding impacts based on the size of the blood collection tube, the centrifugation protocol, post-freeze-thaw spinning, and whole blood storage. A standard dual-spin workflow for the processing of blood had been established for optimal sample quality. The real-time stability of 356 miRNAs was also investigated with demonstration of the temperature and time-induced miRNA degradation profile. Stability-related miRNAs were identified from real-time stability study and further incorporated into the quality control panel. This quality control panel enables the assessment of sample quality for more robust and reliable detection of circulating miRNAs.
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Affiliation(s)
- Suit-Fong Chan
- Research and Development Lab, MiRXES Lab Pte. Ltd., Singapore.
| | - He Cheng
- Research and Development Lab, MiRXES Lab Pte. Ltd., Singapore
| | | | - Ruiyang Zou
- Research and Development Lab, MiRXES Lab Pte. Ltd., Singapore
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19
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González-Martínez C, Garrido-Navas C, Alcaide-Lucena M, Hidalgo JL, Ortega FG, Serrano MJ. microRNAs signature in relapse metastasis and de novo metastasis of breast cancer. A systematic review. Crit Rev Oncol Hematol 2023:104060. [PMID: 37353177 DOI: 10.1016/j.critrevonc.2023.104060] [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: 05/19/2023] [Revised: 06/12/2023] [Accepted: 06/19/2023] [Indexed: 06/25/2023] Open
Abstract
miRNAs have been widely identified as important players in cancer development and progression. Metastasis in breast cancer can occur as relapse of a treated primary tumour or at the time of diagnosis of the tumour. The aim of this review is to show if both metastasis are different molecular entities characterised by different miRNA signatures that could be studied as specific biomarkers for each entity. For this, we systematically searched the PubMed, Scopus and Web of Science databases. After searching and reviewing the literature, a total of 30 records were included in this review. Results showed a genetic signature including a total of 5 upregulated miRNAs in metastasis compared with early stages. Of them, miR-23b and miR-200c were exclusively present in relapse metastasis. Finally, we proposed a molecular signature for future studies that can be used as a complementary tool at clinical trials for the diagnosis and characterization of metastasis.
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Affiliation(s)
- Coral González-Martínez
- GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government. Avenida de la Ilustracion 114, 18016 Granada, Spain; IBS Granada, Institute of Biomedical Research. Avenida de Madrid 15, 18012 Granada, Spain; Department of Legal Medicine, University of Granada, Av. de la Investigación, 11, 18071 Granada, Spain
| | - Carmen Garrido-Navas
- GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government. Avenida de la Ilustracion 114, 18016 Granada, Spain; IBS Granada, Institute of Biomedical Research. Avenida de Madrid 15, 18012 Granada, Spain
| | - Miriam Alcaide-Lucena
- GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government. Avenida de la Ilustracion 114, 18016 Granada, Spain; General Surgery and Digestive System Unit, Hospital Clínico San Cecilio, 18016 Granada, Spain
| | - J López Hidalgo
- GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government. Avenida de la Ilustracion 114, 18016 Granada, Spain; IBS Granada, Institute of Biomedical Research. Avenida de Madrid 15, 18012 Granada, Spain; Pathological Anatomy Unit, Hospital Clínico San Cecilio, 18016 Granada, Spain
| | - Francisco Gabriel Ortega
- GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government. Avenida de la Ilustracion 114, 18016 Granada, Spain; IBS Granada, Institute of Biomedical Research. Avenida de Madrid 15, 18012 Granada, Spain.
| | - María José Serrano
- GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government. Avenida de la Ilustracion 114, 18016 Granada, Spain; IBS Granada, Institute of Biomedical Research. Avenida de Madrid 15, 18012 Granada, Spain; Integral Oncology Division, Hospital Virgen de las Nieves, 18014 Granada, Spain.
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20
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Compagnoni C, Capelli R, Zelli V, Corrente A, Vecchiotti D, Flati I, Di Vito Nolfi M, Angelucci A, Alesse E, Zazzeroni F, Tessitore A. MiR-182-5p Is Upregulated in Hepatic Tissues from a Diet-Induced NAFLD/NASH/HCC C57BL/6J Mouse Model and Modulates Cyld and Foxo1 Expression. Int J Mol Sci 2023; 24:ijms24119239. [PMID: 37298191 DOI: 10.3390/ijms24119239] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/15/2023] [Accepted: 05/23/2023] [Indexed: 06/12/2023] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) is considered a relevant liver chronic disease. Variable percentages of NAFLD cases progress from steatosis to steatohepatitis (NASH), cirrhosis and, eventually, hepatocellular carcinoma (HCC). In this study, we aimed to deepen our understanding of expression levels and functional relationships between miR-182-5p and Cyld-Foxo1 in hepatic tissues from C57BL/6J mouse models of diet-induced NAFL/NASH/HCC progression. A miR-182-5p increase was detected early in livers as NAFLD damage progressed, and in tumors compared to peritumor normal tissues. An in vitro assay on HepG2 cells confirmed Cyld and Foxo1, both tumor-suppressor, as miR-182-5p target genes. According to miR-182-5p expression, decreased protein levels were observed in tumors compared to peritumor tissues. Analysis of miR-182-5p, Cyld and Foxo1 expression levels, based on datasets from human HCC samples, showed results consistent with those from our mouse models, and also highlighted the ability of miR-182-5p to distinguish between normal and tumor tissues (AUC 0.83). Overall, this study shows, for the first time, miR-182-5p overexpression and Cyld-Foxo1 downregulation in hepatic tissues and tumors from a diet-induced NAFLD/HCC mouse model. These data were confirmed by the analysis of datasets from human HCC samples, highlighting miR-182-5p diagnostic accuracy and demonstrating the need for further studies to assess its potential role as a biomarker or therapeutic target.
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Affiliation(s)
- Chiara Compagnoni
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, Via Vetoio, 67100 L'Aquila, Italy
| | - Roberta Capelli
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, Via Vetoio, 67100 L'Aquila, Italy
| | - Veronica Zelli
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, Via Vetoio, 67100 L'Aquila, Italy
- Center for Molecular Diagnostics and Advanced Therapies, University of L'Aquila, Via Petrini, 67100 L'Aquila, Italy
| | - Alessandra Corrente
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, Via Vetoio, 67100 L'Aquila, Italy
| | - Davide Vecchiotti
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, Via Vetoio, 67100 L'Aquila, Italy
| | - Irene Flati
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, Via Vetoio, 67100 L'Aquila, Italy
| | - Mauro Di Vito Nolfi
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, Via Vetoio, 67100 L'Aquila, Italy
| | - Adriano Angelucci
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, Via Vetoio, 67100 L'Aquila, Italy
| | - Edoardo Alesse
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, Via Vetoio, 67100 L'Aquila, Italy
| | - Francesca Zazzeroni
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, Via Vetoio, 67100 L'Aquila, Italy
| | - Alessandra Tessitore
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, Via Vetoio, 67100 L'Aquila, Italy
- Center for Molecular Diagnostics and Advanced Therapies, University of L'Aquila, Via Petrini, 67100 L'Aquila, Italy
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21
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Kayani FB, Rafique S, Akram R, Hussain M, Bashir S, Nasir R, Khan JS. A simple, sensitive, label-free electrochemical immunosensor based on the chitosan-coated silver/cerium oxide (CS@Ag/CeO 2) nanocomposites for the detection of alpha-fetoprotein (AFP). NANOTECHNOLOGY 2023; 34:265501. [PMID: 36996770 DOI: 10.1088/1361-6528/acc8d8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 03/30/2023] [Indexed: 06/19/2023]
Abstract
Metal oxide-based sensors have the benefit of inexpensive, quick response, and high sensitivity in detecting specific biological species. In this article, a simple electrochemical immunosensor was fabricated using antibody-chitosan coated silver/cerium oxide (Ab-CS@Ag/CeO2) nanocomposites on a gold electrode for sensitive alpha-fetoprotein (AFP) diagnosis in human serum samples. Successfully synthesis of AFP antibody-CS@Ag/CeO2conjugates was confirmed through Fourier transform infrared spectra of the prototype. The amine coupling bond chemistry was then used to immobilize the resultant conjugate on a gold electrode surface. It was observed that the interaction of the synthesized Ab-CS@Ag/CeO2nanocomposites with AFP prevented an electron transfer and reduced the voltammetric Fe(CN)63-/4-peak current, which was proportional to the amount of AFP. The linear ranges of AFP concentration were found from 10-12-10-6g.ml-1. The limit of detection was calculated using the calibration curve and came out to be 0.57 pg.ml-1. The designed label-free immunosensor successfully detected AFP in human serum samples. As a result, the resulting immunosensor is a promising sensor plate form for AFP detection and could be used in clinical bioanalysis.
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Affiliation(s)
| | - Saima Rafique
- Department of Physics, Air University, PAF Complex, E-9, Islamabad 44000, Pakistan
| | - Rizwan Akram
- Department of Physics, Air University, PAF Complex, E-9, Islamabad 44000, Pakistan
| | - Mozaffar Hussain
- Department of Physics, Air University, PAF Complex, E-9, Islamabad 44000, Pakistan
| | - Shazia Bashir
- Department of Physics & Applied Mathematics, Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad, 45650, Pakistan
| | - Rubina Nasir
- Department of Physics, Air University, PAF Complex, E-9, Islamabad 44000, Pakistan
| | - Jan Sher Khan
- Department of Physics, Air University, PAF Complex, E-9, Islamabad 44000, Pakistan
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22
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Ruiz-Pozo VA, Cadena-Ullauri S, Guevara-Ramírez P, Paz-Cruz E, Tamayo-Trujillo R, Zambrano AK. Differential microRNA expression for diagnosis and prognosis of papillary thyroid cancer. Front Med (Lausanne) 2023; 10:1139362. [PMID: 37089590 PMCID: PMC10113479 DOI: 10.3389/fmed.2023.1139362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 03/16/2023] [Indexed: 04/08/2023] Open
Abstract
Papillary thyroid cancer accounts for 85% of thyroid cancer. The diagnosis is based on ultrasound methods and tumor biopsies (FNA). In recent years, research has revealed the importance of miRNAs, non-coding RNA molecules that regulate gene expression and are involved in many diseases. The present mini review describes upregulated and downregulated miRNAs expression in papillary thyroid cancer patient samples (tissue, serum, plasma) and the genes regulated by these non-coding molecules. In addition, a bibliographic search was performed to identify the expression of miRNAs that are common in tumor tissue and blood. The miRNAs miR-146b, miR-221-3p, miRNA 222, miR-21, miR-296-5p, and miR-145 are common in both tissue and bloodstream of PTC patient samples. Furthermore, these miRNAs regulate genes involved in biological processes such as cell differentiation, proliferation, migration, invasion, and apoptosis. In conclusion, miRNAs could potentially become valuable biomarkers, which could help in the early diagnosis and prognosis of papillary thyroid cancer.
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23
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Manisekaran R, Chettiar ADR, Kandasamy G, Garcia-Contreras R, Acosta-Torres LS. State-of-the-art: MXene structures in nano-oncology. BIOMATERIALS ADVANCES 2023; 147:213354. [PMID: 36842245 DOI: 10.1016/j.bioadv.2023.213354] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 02/09/2023] [Accepted: 02/19/2023] [Indexed: 02/25/2023]
Abstract
Cancer nanomedicine has been investigated widely and boomed in the last two decades, resulting in designing nanostructures with biofunctionalization, giving rise to an "All-in-One" multifunctional platform. The development of rational design technology with extended functionalities brought interdisciplinary researchers to work continuously, aiming to find a prevent or effectively treat the deadly disease of the century. Thus, it led to some Food and Drug Administration (FDA)-approving nano-based formulations for cancer treatment and opening a vast area of promising discoveries by exploiting different nanomaterials. Two-dimensional (2D) materials have recently gained tremendous interest among scientists because of their outstanding structural, optical, electronic, thermal, and mechanical characteristics. Among various 2D nanomaterials, MXenes are a widely studied nanosystem because of their close similarity to graphene analogs. So, it is synthesized using multiple approaches and exploits their inherited properties. But in most cases, surface functionalization techniques are carried out for targeting, site-specific drug clearance, renal clearance, and biocompatible with healthy cells. Thus, fabricating a multimodal agent for mono or combined therapies is also an image-guided diagnostic agent. This review will explain the recent and emerging advancements of MXenes-based composites as a multifunctional theragnostic agent and discuss the possibilities of transferring laboratory research to clinical translation.
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Affiliation(s)
- Ravichandran Manisekaran
- Interdisciplinary Research Laboratory (LII), Nanostructures and Biomaterials Area, Escuela Nacional de Estudios Superiores Unidad León, Universidad Nacional Autónoma de México, Predio el Saucillo y el Potrero, Comunidad de los Tepetates, 37684 León, Mexico.
| | - Aruna-Devi Rasu Chettiar
- Facultad de Química, Materiales-Energía, Universidad Autónoma de Querétaro, 76010 Querétaro, Mexico
| | - Ganeshlenin Kandasamy
- Department of Biomedical Engineering, Vel Tech Rangarajan Dr Sagunthala R&D Institute of Science and Technology, Chennai, Tamil Nadu, India
| | - Rene Garcia-Contreras
- Interdisciplinary Research Laboratory (LII), Nanostructures and Biomaterials Area, Escuela Nacional de Estudios Superiores Unidad León, Universidad Nacional Autónoma de México, Predio el Saucillo y el Potrero, Comunidad de los Tepetates, 37684 León, Mexico
| | - Laura Susana Acosta-Torres
- Interdisciplinary Research Laboratory (LII), Nanostructures and Biomaterials Area, Escuela Nacional de Estudios Superiores Unidad León, Universidad Nacional Autónoma de México, Predio el Saucillo y el Potrero, Comunidad de los Tepetates, 37684 León, Mexico
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24
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Park W, Maeng SW, Mok JW, Choi M, Cha HJ, Joo CK, Hahn SK. Hydrogel Microneedles Extracting Exosomes for Early Detection of Colorectal Cancer. Biomacromolecules 2023; 24:1445-1452. [PMID: 36908257 DOI: 10.1021/acs.biomac.2c01449] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
There are several methods for early diagnosis of tumors, such as detecting circulating tumor DNAs, detecting circulating tumor cells, or imaging with tumor-targeting contrast agents. However, these assays are time-consuming and may cause patient discomfort during the biopsy collecting process. Here, we develop a facile method for early diagnosis of tumors by extracting exosomes from interstitial fluid (ISF) using hydrogel microneedles (MNs). The hydrogel MNs expand in the skin to absorb the ISF, and the tumor exosomes contained in the ISF bind with the glypican-1 antibodies inside the hydrogel of MNs. After removing the hydrogel on the MNs, exosomes are separately purified from the ISF to analyze tumor-related biomarkers. Finally, colorectal cancer can be diagnosed by ELISA for the colorectal cancer-induced model mice. This noninvasive hydrogel MN system to obtain the exosome samples would play an important role in early cancer diagnosis.
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Affiliation(s)
- Wonchan Park
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Seong-Woo Maeng
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Jee Won Mok
- CK St. Mary's Eye Center, CK Building, 559, Gangnam-daero, Seocho-gu, Seoul 06531, Republic of Korea
| | - Minji Choi
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Hyung Joon Cha
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Choun-Ki Joo
- CK St. Mary's Eye Center, CK Building, 559, Gangnam-daero, Seocho-gu, Seoul 06531, Republic of Korea
| | - Sei Kwang Hahn
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea
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25
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Ghamlouche F, Yehya A, Zeid Y, Fakhereddine H, Fawaz J, Liu YN, Al-Sayegh M, Abou-Kheir W. MicroRNAs as clinical tools for diagnosis, prognosis, and therapy in prostate cancer. Transl Oncol 2023; 28:101613. [PMID: 36608541 PMCID: PMC9827391 DOI: 10.1016/j.tranon.2022.101613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 12/05/2022] [Accepted: 12/24/2022] [Indexed: 01/06/2023] Open
Abstract
Prostate cancer (PCa) is one of the most commonly diagnosed cancers among men worldwide. Despite the presence of accumulated clinical strategies for PCa management, limited prognostic/sensitive biomarkers are available to follow up on disease occurrence and progression. MicroRNAs (miRNAs) are small non-coding RNAs that control gene expression through post-transcriptional regulation of their complementary target messenger RNA (mRNA). MiRNAs modulate fundamental biological processes and play crucial roles in the pathology of various diseases, including PCa. Multiple evidence proved an aberrant miRNA expression profile in PCa, which is actively involved in the carcinogenic process. The robust and pleiotropic impact of miRNAs on PCa suggests them as potential candidates to help more understand the molecular landscape of the disease, which is likely to provide tools for early diagnosis and prognosis as well as additional therapeutic strategies to manage prostate tumors. Here, we emphasize the most consistently reported dysregulated miRNAs and highlight the contribution of their altered downstream targets with PCa hallmarks. Also, we report the potential effectiveness of using miRNAs as diagnostic/prognostic biomarkers in PCa and the high-throughput profiling technologies that are being used in their detection. Another key aspect to be discussed in this review is the promising implication of miRNAs molecules as therapeutic tools and targets for fighting PCa.
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Affiliation(s)
- Fatima Ghamlouche
- Department of Anatomy, Cell Biology, and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut 1107-2020, Lebanon
| | - Amani Yehya
- Department of Anatomy, Cell Biology, and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut 1107-2020, Lebanon
| | - Yousef Zeid
- Department of Anatomy, Cell Biology, and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut 1107-2020, Lebanon
| | - Hiam Fakhereddine
- Department of Anatomy, Cell Biology, and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut 1107-2020, Lebanon
| | - Jhonny Fawaz
- Department of Anatomy, Cell Biology, and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut 1107-2020, Lebanon
| | - Yen-Nien Liu
- International Ph.D. Program in Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan.
| | - Mohamed Al-Sayegh
- Biology Division, New York University Abu Dhabi, Abu Dhabi 2460, United Arab Emirates.
| | - Wassim Abou-Kheir
- Department of Anatomy, Cell Biology, and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut 1107-2020, Lebanon.
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26
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Iacomino G. miRNAs: The Road from Bench to Bedside. Genes (Basel) 2023; 14:genes14020314. [PMID: 36833241 PMCID: PMC9957002 DOI: 10.3390/genes14020314] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 01/20/2023] [Accepted: 01/21/2023] [Indexed: 01/27/2023] Open
Abstract
miRNAs are small noncoding RNAs that control gene expression at the posttranscriptional level. It has been recognised that miRNA dysregulation reflects the state and function of cells and tissues, contributing to their dysfunction. The identification of hundreds of extracellular miRNAs in biological fluids has underscored their potential in the field of biomarker research. In addition, the therapeutic potential of miRNAs is receiving increasing attention in numerous conditions. On the other hand, many operative problems including stability, delivery systems, and bioavailability, still need to be solved. In this dynamic field, biopharmaceutical companies are increasingly engaged, and ongoing clinical trials point to anti-miR and miR-mimic molecules as an innovative class of molecules for upcoming therapeutic applications. This article aims to provide a comprehensive overview of current knowledge on several pending issues and new opportunities offered by miRNAs in the treatment of diseases and as early diagnostic tools in next-generation medicine.
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Affiliation(s)
- Giuseppe Iacomino
- Institute of Food Sciences, National Research Council, Via Roma, 64, 83100 Avellino, Italy
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27
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Chalutz Ben-Gal H. Artificial intelligence (AI) acceptance in primary care during the coronavirus pandemic: What is the role of patients' gender, age and health awareness? A two-phase pilot study. Front Public Health 2023; 10:931225. [PMID: 36699881 PMCID: PMC9868720 DOI: 10.3389/fpubh.2022.931225] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 12/15/2022] [Indexed: 01/11/2023] Open
Abstract
Background Artificial intelligence (AI) is steadily entering and transforming the health care and Primary Care (PC) domains. AI-based applications assist physicians in disease detection, medical advice, triage, clinical decision-making, diagnostics and digital public health. Recent literature has explored physicians' perspectives on the potential impact of digital public health on key tasks in PC. However, limited attention has been given to patients' perspectives of AI acceptance in PC, specifically during the coronavirus pandemic. Addressing this research gap, we administered a pilot study to investigate criteria for patients' readiness to use AI-based PC applications by analyzing key factors affecting the adoption of digital public health technology. Methods The pilot study utilized a two-phase mixed methods approach. First, we conducted a qualitative study with 18 semi-structured interviews. Second, based on the Technology Readiness and Acceptance Model (TRAM), we conducted an online survey (n = 447). Results The results indicate that respondents who scored high on innovativeness had a higher level of readiness to use AI-based technology in PC during the coronavirus pandemic. Surprisingly, patients' health awareness and sociodemographic factors, such as age, gender and education, were not significant predictors of AI-based technology acceptance in PC. Conclusions This paper makes two major contributions. First, we highlight key social and behavioral determinants of acceptance of AI-enabled health care and PC applications. Second, we propose that to increase the usability of digital public health tools and accelerate patients' AI adoption, in complex digital public health care ecosystems, we call for implementing adaptive, population-specific promotions of AI technologies and applications.
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28
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Wang Z, Xie W, Guan H. The diagnostic, prognostic role and molecular mechanism of miR-328 in human cancer. Biomed Pharmacother 2023; 157:114031. [PMID: 36413837 DOI: 10.1016/j.biopha.2022.114031] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 11/06/2022] [Accepted: 11/17/2022] [Indexed: 11/20/2022] Open
Abstract
MicroRNA are non-coding small RNAs that bind to their target mRNA and cause mRNA degradation or translation inhibition. MiRNA dysregulation is linked to a variety of human cancers and has a role in the genesis and development of cancer pathology. MiR-328 has been reported to be involved in various human cancers. And miR-328 is considered a key regulator in human cancer. It participates in biological processes such as proliferation, apoptosis, invasion, migration, and EMT. The present review will combine the basic and clinical studies to find that miR-328 promotes tumorigenesis and metastasis in human cancer. And we will describe the diagnostic, prognostic, and therapeutic value of miR-328 in various human cancers.
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Affiliation(s)
- Zhichao Wang
- Department of Clinical Laboratory, The Affiliated Hospital of Qingdao University, 16 Jiangsu Road, Qingdao 266003, China.
| | - Wenjie Xie
- Department of Clinical Laboratory, The Affiliated Hospital of Qingdao University, 16 Jiangsu Road, Qingdao 266003, China.
| | - Hongzai Guan
- Department of Clinical Laboratory, The Affiliated Hospital of Qingdao University, 16 Jiangsu Road, Qingdao 266003, China.
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29
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Tavakoli Pirzaman A, Ebrahimi P, Hasanpour AH, Shakeri M, Babajani B, Pourali Ganji Z, Babaei H, Rahmati A, Hosseinzadeh R, Doostmohamadian S, Kazemi S. miRNAs and Multiple Myeloma: Focus on the Pathogenesis, Prognosis, and Drug Resistance. Technol Cancer Res Treat 2023; 22:15330338231202391. [PMID: 37728167 PMCID: PMC10515583 DOI: 10.1177/15330338231202391] [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: 05/08/2023] [Revised: 08/30/2023] [Accepted: 09/04/2023] [Indexed: 09/21/2023] Open
Abstract
Multiple myeloma (MM) produces clonal plasma cells and aberrant monoclonal antibody accumulation in patients' bone marrow (BM). Around 1% of all cancers and 13% of hematological malignancies are caused by MM, making it one of the most common types of cancer. Diagnostic and therapeutic methods for managing MM are currently undergoing extensive research. MicroRNAs (miRNAs) are short noncoding RNAs that reduce or inhibit the translation of their target mRNA after transcription. Because miRNAs play an influential role in how myeloma develops, resources, and becomes resistant to drugs, miRNA signatures may be used to diagnose, do prognosis, and treat the myeloma response. Consequently, researchers have investigated the levels of miRNA in plasma cells from MM patients and developed tools to test whether they directly impacted tumor growth. This review discusses the latest discoveries in miRNA science and their role in the development of MM. We also emphasize the potential applications of miRNAs to diagnose, prognosticate, and treat MM in the future.
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Affiliation(s)
| | - Pouyan Ebrahimi
- Student Research Committee, Babol University of Medical Sciences, Babol, Iran
| | | | - Mahdi Shakeri
- Student Research Committee, Babol University of Medical Sciences, Babol, Iran
| | - Bahareh Babajani
- Student Research Committee, Babol University of Medical Sciences, Babol, Iran
| | - Zahra Pourali Ganji
- Student Research Committee, Babol University of Medical Sciences, Babol, Iran
| | - Hedye Babaei
- Student Research Committee, Babol University of Medical Sciences, Babol, Iran
| | - Amirhossein Rahmati
- Student Research Committee, Babol University of Medical Sciences, Babol, Iran
| | - Rezvan Hosseinzadeh
- Student Research Committee, Babol University of Medical Sciences, Babol, Iran
| | | | - Sohrab Kazemi
- Cellular and Molecular Biology Research Center, Health Research Center, Babol University of Medical Sciences, Babol, Iran
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30
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Rosso AD, Aguilera P, Quesada S, Mascardi F, Mascuka SN, Cimolai MC, Cerezo J, Spiazzi R, Conlon C, Milano C, Iraola GM, Penas-Steinhardt A, Belforte FS. Comprehensive Phenotyping in Inflammatory Bowel Disease: Search for Biomarker Algorithms in the Transkingdom Interactions Context. Microorganisms 2022; 10:microorganisms10112190. [PMID: 36363782 PMCID: PMC9698371 DOI: 10.3390/microorganisms10112190] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/27/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022] Open
Abstract
Inflammatory bowel disease (IBD) is the most common form of intestinal inflammation associated with a dysregulated immune system response to the commensal microbiota in a genetically susceptible host. IBD includes ulcerative colitis (UC) and Crohn’s disease (CD), both of which are remarkably heterogeneous in their clinical presentation and response to treatment. This translates into a notable diagnostic challenge, especially in underdeveloped countries where IBD is on the rise and access to diagnosis or treatment is not always accessible for chronic diseases. The present work characterized, for the first time in our region, epigenetic biomarkers and gut microbial profiles associated with UC and CD patients in the Buenos Aires Metropolitan area and revealed differences between non-IBD controls and IBD patients. General metabolic functions associated with the gut microbiota, as well as core microorganisms within groups, were also analyzed. Additionally, the gut microbiota analysis was integrated with relevant clinical, biochemical and epigenetic markers considered in the follow-up of patients with IBD, with the aim of generating more powerful diagnostic tools to discriminate phenotypes. Overall, our study provides new insights into data analysis algorithms to promote comprehensive phenotyping tools using quantitative and qualitative analysis in a transkingdom interactions network context.
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Affiliation(s)
- Ayelén D. Rosso
- Laboratorio de Genómica Computacional (GeC-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján 6700, Argentina
- Programa del Estudio de Comunicación y Señalización Interreino (PECSI-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján 6700, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires C1425FQB, Argentina
- Instituto de Ecología y Desarrollo Sustentable (INEDES-CONICET-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján 6700, Argentina
| | - Pablo Aguilera
- Programa del Estudio de Comunicación y Señalización Interreino (PECSI-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján 6700, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires C1425FQB, Argentina
| | - Sofía Quesada
- Laboratorio de Genómica Computacional (GeC-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján 6700, Argentina
- Programa del Estudio de Comunicación y Señalización Interreino (PECSI-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján 6700, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires C1425FQB, Argentina
| | - Florencia Mascardi
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires C1425FQB, Argentina
- Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB), CONICET, Instituto Universitario del Hospital Italiano (IUHI), Hospital Italiano de Buenos Aires (HIBA), Ciudad Autónoma de Buenos Aires C1199, Argentina
| | - Sebastian N. Mascuka
- Laboratorio de Genómica Computacional (GeC-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján 6700, Argentina
- Programa del Estudio de Comunicación y Señalización Interreino (PECSI-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján 6700, Argentina
| | - María C. Cimolai
- Laboratorio de Genómica Computacional (GeC-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján 6700, Argentina
- Programa del Estudio de Comunicación y Señalización Interreino (PECSI-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján 6700, Argentina
| | - Jimena Cerezo
- Servicio de Gastroenterología, Hospital Nacional Prof. Alejandro Posadas, Ciudad Autónoma de Buenos Aires 1704, Argentina
| | - Renata Spiazzi
- Servicio de Gastroenterología, Hospital Nacional Prof. Alejandro Posadas, Ciudad Autónoma de Buenos Aires 1704, Argentina
| | - Carolina Conlon
- Servicio de Gastroenterología, Hospital Nacional Prof. Alejandro Posadas, Ciudad Autónoma de Buenos Aires 1704, Argentina
| | - Claudia Milano
- Servicio de Gastroenterología, Hospital Nacional Prof. Alejandro Posadas, Ciudad Autónoma de Buenos Aires 1704, Argentina
| | - Gregorio M. Iraola
- Laboratorio de Genómica Microbiana, Institut Pasteur Montevideo, Montevideo 11400, Uruguay
- Centro de Biología Integrativa, Universidad Mayor, Santiago 7510041, Chile
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridgeshire CB10 1SA, UK
| | - Alberto Penas-Steinhardt
- Laboratorio de Genómica Computacional (GeC-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján 6700, Argentina
- Programa del Estudio de Comunicación y Señalización Interreino (PECSI-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján 6700, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires C1425FQB, Argentina
- Instituto Universitario de Ciencias de la Salud, Fundación H.A. Barceló, Ciudad Autónoma de Buenos Aires 1127, Argentina
| | - Fiorella S. Belforte
- Laboratorio de Genómica Computacional (GeC-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján 6700, Argentina
- Programa del Estudio de Comunicación y Señalización Interreino (PECSI-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján 6700, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires C1425FQB, Argentina
- Instituto de Ecología y Desarrollo Sustentable (INEDES-CONICET-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján 6700, Argentina
- Correspondence: ; Tel.: +54-91153114059
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Noncoding RNAs Emerging as Drugs or Drug Targets: Their Chemical Modification, Bio-Conjugation and Intracellular Regulation. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27196717. [PMID: 36235253 PMCID: PMC9573214 DOI: 10.3390/molecules27196717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 10/06/2022] [Accepted: 10/07/2022] [Indexed: 11/07/2022]
Abstract
With the increasing understanding of various disease-related noncoding RNAs, ncRNAs are emerging as novel drugs and drug targets. Nucleic acid drugs based on different types of noncoding RNAs have been designed and tested. Chemical modification has been applied to noncoding RNAs such as siRNA or miRNA to increase the resistance to degradation with minimum influence on their biological function. Chemical biological methods have also been developed to regulate relevant noncoding RNAs in the occurrence of various diseases. New strategies such as designing ribonuclease targeting chimeras to degrade endogenous noncoding RNAs are emerging as promising approaches to regulate gene expressions, serving as next-generation drugs. This review summarized the current state of noncoding RNA-based theranostics, major chemical modifications of noncoding RNAs to develop nucleic acid drugs, conjugation of RNA with different functional biomolecules as well as design and screening of potential molecules to regulate the expression or activity of endogenous noncoding RNAs for drug development. Finally, strategies of improving the delivery of noncoding RNAs are discussed.
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Cheong JK, Rajgor D, Lv Y, Chung KY, Tang YC, Cheng H. Noncoding RNome as Enabling Biomarkers for Precision Health. Int J Mol Sci 2022; 23:ijms231810390. [PMID: 36142304 PMCID: PMC9499633 DOI: 10.3390/ijms231810390] [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: 08/11/2022] [Revised: 08/29/2022] [Accepted: 09/02/2022] [Indexed: 12/06/2022] Open
Abstract
Noncoding RNAs (ncRNAs), in the form of structural, catalytic or regulatory RNAs, have emerged to be critical effectors of many biological processes. With the advent of new technologies, we have begun to appreciate how intracellular and circulatory ncRNAs elegantly choreograph the regulation of gene expression and protein function(s) in the cell. Armed with this knowledge, the clinical utility of ncRNAs as biomarkers has been recently tested in a wide range of human diseases. In this review, we examine how critical factors govern the success of interrogating ncRNA biomarker expression in liquid biopsies and tissues to enhance our current clinical management of human diseases, particularly in the context of cancer. We also discuss strategies to overcome key challenges that preclude ncRNAs from becoming standard-of-care clinical biomarkers, including sample pre-analytics standardization, data cross-validation with closer attention to discordant findings, as well as correlation with clinical outcomes. Although harnessing multi-modal information from disease-associated noncoding RNome (ncRNome) in biofluids or in tissues using artificial intelligence or machine learning is at the nascent stage, it will undoubtedly fuel the community adoption of precision population health.
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Affiliation(s)
- Jit Kong Cheong
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore 117597, Singapore
- Precision Medicine Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore 117597, Singapore
- NUS Centre for Cancer Research, Singapore 117599, Singapore
- Correspondence: (J.K.C.); (H.C.)
| | | | - Yang Lv
- Precision Medicine Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore 117597, Singapore
| | | | | | - He Cheng
- MiRXES Lab, Singapore 138667, Singapore
- Correspondence: (J.K.C.); (H.C.)
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MicroRNAs as Potential Tools for Predicting Cancer Patients’ Susceptibility to SARS-CoV-2 Infection and Vaccination Response. Cells 2022; 11:cells11152279. [PMID: 35892576 PMCID: PMC9332853 DOI: 10.3390/cells11152279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/18/2022] [Accepted: 07/21/2022] [Indexed: 11/16/2022] Open
Abstract
Coronavirus disease (COVID-19) is an infectious disease that is caused by a highly contagious and severe acute respiratory syndrome—coronavirus 2 (SARS-CoV-2). This infection started to spread across the world in 2019 and rapidly turned into a global pandemic, causing an urgent necessity for treatment strategies development. The mRNA vaccines against SARS-CoV-2 can trigger an immune response, providing genetic information that allows the production of spike glycoproteins. MiRNAs play a crucial role in diverse key cellular processes, including antiviral defense. Several miRNAs are described as key factors in SARS-CoV-2 human infection through the regulation of ACE2 levels and by the inhibition of SARS-CoV-2 replication and spike expression. Consequently, these molecules have been considered as highly promising biomarkers. In numerous human malignancies, it has been recognized that miRNAs expression is dysregulated. Since miRNAs can target SARS-CoV-2-associated mRNAs, in cancer patients, the deregulation of these molecules can impair the immune response to the vaccines. Therefore, in this review, we propose a miRNA profile of seven SARS-CoV-2-related miRNAs, namely miR-214, miR-98-5p, miR-7-5p, miR-24-3p, miR-145-5p, miR-223-3p and miR-15b-5p, that are deregulated in a high number of cancers and have the potential to be used as prognostic biomarkers to stratify cancer patients.
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Chen JW, Dhahbi J. Identification of four serum miRNAs as potential markers to screen for thirteen cancer types. PLoS One 2022; 17:e0269554. [PMID: 35687572 PMCID: PMC9187062 DOI: 10.1371/journal.pone.0269554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 05/23/2022] [Indexed: 02/07/2023] Open
Abstract
Introduction Cancer consistently remains one of the top causes of death in the United States every year, with many cancer deaths preventable if detected early. Circulating serum miRNAs are a promising, minimally invasive supplement or even an alternative to many current screening procedures. Many studies have shown that different serum miRNAs can discriminate healthy individuals from those with certain types of cancer. Although many of those miRNAs are often reported to be significant in one cancer type, they are also altered in other cancer types. Currently, very few studies have investigated serum miRNA biomarkers for multiple cancer types for general cancer screening purposes. Method To identify serum miRNAs that would be useful in screening multiple types of cancers, microarray cancer datasets were curated, yielding 13 different types of cancer with a total of 3352 cancer samples and 2809 non-cancer samples. The samples were divided into training and validation sets. One hundred random forest models were built using the training set to select candidate miRNAs. The selected miRNAs were then used in the validation set to see how well they differentiate cancer from normal samples in an independent dataset. Furthermore, the interactions between these miRNAs and their target mRNAs were investigated. Result The random forest models achieved an average of 97% accuracy in the training set with 95% bootstrap confidence interval of 0.9544 to 0.9778. The selected miRNAs were hsa-miR-663a, hsa-miR-6802-5p, hsa-miR-6784-5p, hsa-miR-3184-5p, and hsa-miR-8073. Each miRNA exhibited high area under the curve (AUC) value using receiver operating characteristic analysis. Moreover, the combination of four out of five miRNAs achieved the highest AUC value of 0.9815 with high sensitivity of 0.9773, indicating that these miRNAs have a high potential for cancer screening. miRNA-mRNA and protein-protein interaction analysis provided insights into how these miRNAs play a role in cancer.
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Affiliation(s)
- Joe W. Chen
- California University of Science and Medicine, Colton, CA, United States of America
| | - Joseph Dhahbi
- California University of Science and Medicine, Colton, CA, United States of America
- * E-mail:
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Abstract
Quantum dots (QDs) possess exceptional optoelectronic properties that enable their use in the most diverse applications, namely, in the medical field. The prevalence of cancer has increased and has been considered the major cause of death worldwide. Thus, there has been a great demand for new methodologies for diagnosing and monitoring cancer in cells to provide an earlier prognosis of the disease and contribute to the effectiveness of treatment. Several molecules in the human body can be considered relevant as cancer markers. Studies published over recent years have revealed that micro ribonucleic acids (miRNAs) play a crucial role in this pathology, since they are responsible for some physiological processes of the cell cycle and, most important, they are overexpressed in cancer cells. Thus, the analytical sensing of miRNA has gained importance to provide monitoring during cancer treatment, allowing the evaluation of the disease's evolution. Recent methodologies based on nanochemistry use fluorescent quantum dots for sensing of the miRNA. Combining the unique characteristics of QDs, namely, their fluorescence capacity, and the fact that miRNA presents an aberrant expression in cancer cells, the researchers created diverse strategies for miRNA monitoring. This review aims to present an overview of the recent use of QDs as biosensors in miRNA detection, also highlighting some tutorial descriptions of the synthesis methods of QDs, possible surface modification, and functionalization approaches.
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Affiliation(s)
- Catarina
S. M. Martins
- International
Iberian Nanotechnology Laboratory, 4715-330 Braga, Portugal,LAQV,
REQUIMTE, Laboratory of Applied Chemistry, Department of Chemical
Sciences, Faculty of Pharmacy, University
of Porto, Rua de Jorge Viterbo Ferreira, No. 228, 4050-313 Porto, Portugal
| | - Alec P. LaGrow
- International
Iberian Nanotechnology Laboratory, 4715-330 Braga, Portugal
| | - João A. V. Prior
- LAQV,
REQUIMTE, Laboratory of Applied Chemistry, Department of Chemical
Sciences, Faculty of Pharmacy, University
of Porto, Rua de Jorge Viterbo Ferreira, No. 228, 4050-313 Porto, Portugal,
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Koh Y, Bustos MA, Moon J, Gross R, Ramos RI, Ryu S, Choe J, Lin SY, Allen WM, Krasne DL, Wilson TG, Hoon DSB. Urine Cell-Free MicroRNAs in Localized Prostate Cancer Patients. Cancers (Basel) 2022; 14:cancers14102388. [PMID: 35625992 PMCID: PMC9139357 DOI: 10.3390/cancers14102388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/05/2022] [Accepted: 05/10/2022] [Indexed: 02/01/2023] Open
Abstract
Prostate cancer (PCa) is the most common cancer in men. Prostate-specific antigen screening is recommended for the detection of PCa. However, its specificity is limited. Thus, there is a need to find more reliable biomarkers that allow non-invasive screening for early-stage PCa. This study aims to explore urine microRNAs (miRs) as diagnostic biomarkers for PCa. We assessed cell-free miR (cfmiR) profiles of urine and plasma samples from pre- and post-operative PCa patients (n = 11) and normal healthy donors (16 urine and 24 plasma) using HTG EdgeSeq miRNA Whole Transcriptome Assay based on next-generation sequencing. Furthermore, tumor-related miRs were detected in formalin-fixed paraffin-embedded tumor tissues obtained from patients with localized PCa. Specific cfmiRs signatures were found in urine samples of localized PCa patients using differential expression analysis. Forty-two cfmiRs that were detected were common to urine, plasma, and tumor samples. These urine cfmiRs may have potential utility in diagnosing early-stage PCa and complementing or improving currently available PCa screening assays. Future studies may validate the findings.
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Affiliation(s)
- Yoko Koh
- Department of Translational Molecular Medicine, Saint John’s Cancer Institute (SJCI), Providence Saint John’s Health Center (SJHC), Santa Monica, CA 90404, USA; (Y.K.); (M.A.B.); (J.M.); (R.G.); (R.I.R.)
- Department of Urology and Urologic Oncology, Saint John’s Cancer Institute (SJCI), Providence Saint John’s Health Center (SJHC), Santa Monica, CA 90404, USA; (J.C.); (T.G.W.)
| | - Matias A. Bustos
- Department of Translational Molecular Medicine, Saint John’s Cancer Institute (SJCI), Providence Saint John’s Health Center (SJHC), Santa Monica, CA 90404, USA; (Y.K.); (M.A.B.); (J.M.); (R.G.); (R.I.R.)
| | - Jamie Moon
- Department of Translational Molecular Medicine, Saint John’s Cancer Institute (SJCI), Providence Saint John’s Health Center (SJHC), Santa Monica, CA 90404, USA; (Y.K.); (M.A.B.); (J.M.); (R.G.); (R.I.R.)
| | - Rebecca Gross
- Department of Translational Molecular Medicine, Saint John’s Cancer Institute (SJCI), Providence Saint John’s Health Center (SJHC), Santa Monica, CA 90404, USA; (Y.K.); (M.A.B.); (J.M.); (R.G.); (R.I.R.)
- Department of Urology and Urologic Oncology, Saint John’s Cancer Institute (SJCI), Providence Saint John’s Health Center (SJHC), Santa Monica, CA 90404, USA; (J.C.); (T.G.W.)
| | - Romela Irene Ramos
- Department of Translational Molecular Medicine, Saint John’s Cancer Institute (SJCI), Providence Saint John’s Health Center (SJHC), Santa Monica, CA 90404, USA; (Y.K.); (M.A.B.); (J.M.); (R.G.); (R.I.R.)
| | - Suyeon Ryu
- Genome Sequencing Center, Saint John’s Cancer Institute (SJCI), Providence Saint John’s Health Center (SJHC), Santa Monica, CA 90404, USA;
| | - Jane Choe
- Department of Urology and Urologic Oncology, Saint John’s Cancer Institute (SJCI), Providence Saint John’s Health Center (SJHC), Santa Monica, CA 90404, USA; (J.C.); (T.G.W.)
| | | | - Warren M. Allen
- Division of Surgical Pathology, Providence Saint John’s Health Center (SJHC), Santa Monica, CA 90404, USA; (W.M.A.); (D.L.K.)
| | - David L. Krasne
- Division of Surgical Pathology, Providence Saint John’s Health Center (SJHC), Santa Monica, CA 90404, USA; (W.M.A.); (D.L.K.)
| | - Timothy G. Wilson
- Department of Urology and Urologic Oncology, Saint John’s Cancer Institute (SJCI), Providence Saint John’s Health Center (SJHC), Santa Monica, CA 90404, USA; (J.C.); (T.G.W.)
| | - Dave S. B. Hoon
- Department of Translational Molecular Medicine, Saint John’s Cancer Institute (SJCI), Providence Saint John’s Health Center (SJHC), Santa Monica, CA 90404, USA; (Y.K.); (M.A.B.); (J.M.); (R.G.); (R.I.R.)
- Genome Sequencing Center, Saint John’s Cancer Institute (SJCI), Providence Saint John’s Health Center (SJHC), Santa Monica, CA 90404, USA;
- Correspondence:
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de Assis JV, Coutinho LA, Oyeyemi IT, Oyeyemi OT, Grenfell RFEQ. Diagnostic and therapeutic biomarkers in colorectal cancer: a review. Am J Cancer Res 2022; 12:661-680. [PMID: 35261794 PMCID: PMC8900002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 01/22/2022] [Indexed: 06/14/2023] Open
Abstract
Colorectal cancer (CRC) is a public health concern and the second most common type of cancer among men and women causing a significant mortality. Biomarkers closely linked to the disease morbidity could holds potential as diagnostic and/or prognostic biomarker for the disease. This review provides an overview of recent advances in the search for colorectal cancer biomarkers through genomics and proteomics according to clinical function and application. Specifically, a number of biomarkers were identified and discussed. Emphasis was placed on their clinical applications relative to the diagnosis and prognosis of CRC. The discovery of more sensitive and specific markers for CRC is an urgent need, and the study of molecular targets is extremely important in this process, as they will allow for a better understanding of colorectal carcinogenesis, identification and validation of potential genetic signatures.
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Affiliation(s)
- Jéssica Vieira de Assis
- Diagnosis and Therapy of Infectious Diseases and Cancer, René Rachou Institute, Oswaldo Cruz Foundation (Fiocruz)Belo Horizonte, Minas Gerais, Brazil
| | - Lucélia Antunes Coutinho
- Diagnosis and Therapy of Infectious Diseases and Cancer, René Rachou Institute, Oswaldo Cruz Foundation (Fiocruz)Belo Horizonte, Minas Gerais, Brazil
| | | | - Oyetunde Timothy Oyeyemi
- Diagnosis and Therapy of Infectious Diseases and Cancer, René Rachou Institute, Oswaldo Cruz Foundation (Fiocruz)Belo Horizonte, Minas Gerais, Brazil
- Department of Biological Sciences, University of Medical SciencesOndo, Ondo State, Nigeria
| | - Rafaella Fortini e Queiroz Grenfell
- Diagnosis and Therapy of Infectious Diseases and Cancer, René Rachou Institute, Oswaldo Cruz Foundation (Fiocruz)Belo Horizonte, Minas Gerais, Brazil
- Department of Infectious Diseases, College of Veterinary Medicine, University of GeorgiaAthens, Georgia, United States of America
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The Landscape of Circulating miRNAs in the Post-Genomic Era. Genes (Basel) 2021; 13:genes13010094. [PMID: 35052434 PMCID: PMC8774581 DOI: 10.3390/genes13010094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/07/2021] [Accepted: 12/15/2021] [Indexed: 02/06/2023] Open
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Xie S, Jin L, Yin T, Ren J, Liu W. Microarray analysis and functional prediction of differentially expressed circular RNAs in acquired middle ear cholesteatoma. Biomed Eng Online 2021; 20:129. [PMID: 34922560 PMCID: PMC8684697 DOI: 10.1186/s12938-021-00960-x] [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: 09/28/2021] [Accepted: 11/16/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Middle ear cholesteatoma is characterized by hyper-proliferation of keratinocytes. Circular RNA (circRNA) plays an essential role in the pathogenesis of many proliferative diseases. However, the role of circRNA in the etiopathogenesis of middle ear cholesteatoma is rarely investigated so far. We aimed to investigate the differential expression profiling of circRNAs between acquired middle ear cholesteatoma and normal skin, and to identify potential circRNAs contributing to the etiopathogenesis of middle ear cholesteatoma. Microarray analysis and functional prediction were performed to investigate the circRNA expression profiling between middle ear cholesteatoma and normal skin. Validation of differentially expressed circRNAs was conducted by qRT-PCR. Prediction of m6A modification was also carried out. RESULTS Microarray analysis displayed that totally 93 up-regulated and 85 down-regulated circRNAs were identified in middle ear cholesteatoma. Through validation, expressions of hsa_circRNA_104327 and hsa_circRNA_404655 were significantly higher, while hsa_circRNA_000319 was significantly down-regulated in cholesteatoma. GO classification, KEGG pathway, and ceRNA network analyses suggested that these differentially expressed circRNAs might play important roles in the etiopathogenesis of middle ear cholesteatoma. Prediction of m6A modification exhibited that hsa_circRNA_000319 possessed 4 m6A sites with very high confidence, and hsa_circRNA_404655 had 3 m6A sites with high confidence. CONCLUSIONS Our study revealed that these differentially expressed circRNAs might contribute to the etiopathogenesis of middle ear cholesteatoma. Further researches should be conducted to investigate the exact mechanism of these differentially expressed circRNAs in the etiopathogenesis of middle ear cholesteatoma. Targeting on these circRNAs may provide a new strategy for middle ear cholesteatoma therapy in the future.
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Affiliation(s)
- Shumin Xie
- Department of Otolaryngology-Head and Neck Surgery, The Xiangya Hospital, Central South University, Hunan Provincial Key Lab, Otolaryngology Institute of Major Diseases, Changsha, 410008, Hunan, China
| | - Li Jin
- Department of Otolaryngology-Head and Neck Surgery, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
| | - Tuanfang Yin
- Department of Otolaryngology-Head and Neck Surgery, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
| | - Jihao Ren
- Department of Otolaryngology-Head and Neck Surgery, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
| | - Wei Liu
- Department of Otolaryngology-Head and Neck Surgery, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China.
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Qiu P, Guo Q, Yao Q, Chen J, Lin J. Hsa-mir-3163 and CCNB1 may be potential biomarkers and therapeutic targets for androgen receptor positive triple-negative breast cancer. PLoS One 2021; 16:e0254283. [PMID: 34797837 PMCID: PMC8604295 DOI: 10.1371/journal.pone.0254283] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 11/02/2021] [Indexed: 12/02/2022] Open
Abstract
Breast cancer (BC) is the most common malignancy in female, but the role of androgen receptor (AR) in triple-negative breast cancer (TNBC) is still unclear. This study aimed to exam the performance of innovative biomarkers for AR positive TNBC in diagnosis and therapies. Four datasets (GSE42568, GSE45827, GSE54002 and GSE76124) were analyzed by bioinformatic methods and the differential expression genes (DEGs) between the AR positive TNBC tissues and normal tissues were firstly identified by limma package and Venn diagrams. Next, Gene Ontologies (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were performed to explore the relationship between these DEGs. Then, the Protein-protein interaction (PPI) network was constructed. CytoHubba and bioinformatic approaches including Molecular Complex Detection (MCODE), Gene Expression Profiling Interactive Analysis (GEPIA), the Kaplan–Meier (KM) plotter and The Human Pro-tein Atlas (THPA) were used to identify the hub genes. Lastly, a miRNA-hub-gene regulatory axis was constructed by use of Target Scan database and ENCORI database. As a result, a total of 390 common DEGs were identified, including 250 up-regulated and 140 down-regulated. GO and KEGG enrichment analysis showed that the up-regulated DEGs were mostly enriched in the cell division, mitotic nuclear division, nucleosome, midbody, protein heterodimerization activity, cadherin binding involved in cell−cell adhesion, systemic lupus erythematosus and alcoholism, while the down-regulated DEGs were mainly enriched in carbohydrate metabolic process, extracellular space, extracellular region, zinc ion binding and microRNAs in cancer. Then, 13 hub genes (CCNB2, FOXM1, HMMR, MAD2L1, RRM2, TPX2, TYMS, CEP55, AURKA, CCNB1, CDK1, TOP2A, PBK) were selected. The survival analysis revealed that only CCNB1 was associated with significantly poor survival (P <0.05) in TNBC patients. Finally, we found that hsa-miR-3163 took part in the regulation of CCNB1 and constructed a potential hsa-miR-3163-CCNB1 regulatory axis. The results of current study suggest that CCNB1 and hsa-miR-3163 may serve as highly potential prognostic markers and therapeutic targets for AR positive TNBC. Our findings may make contributions to the diagnosis and therapies of AR positive TNBC.
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Affiliation(s)
- Pengjun Qiu
- Thyroid & Breast Surgery, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
| | - Qiaonan Guo
- Thyroid & Breast Surgery, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
| | - Qingzhi Yao
- Thyroid & Breast Surgery, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
| | - Jianpeng Chen
- Thyroid & Breast Surgery, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
| | - Jianqing Lin
- Thyroid & Breast Surgery, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
- * E-mail:
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Rincón-Riveros A, Morales D, Rodríguez JA, Villegas VE, López-Kleine L. Bioinformatic Tools for the Analysis and Prediction of ncRNA Interactions. Int J Mol Sci 2021; 22:11397. [PMID: 34768830 PMCID: PMC8583695 DOI: 10.3390/ijms222111397] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 09/30/2021] [Accepted: 09/30/2021] [Indexed: 12/16/2022] Open
Abstract
Noncoding RNAs (ncRNAs) play prominent roles in the regulation of gene expression via their interactions with other biological molecules such as proteins and nucleic acids. Although much of our knowledge about how these ncRNAs operate in different biological processes has been obtained from experimental findings, computational biology can also clearly substantially boost this knowledge by suggesting possible novel interactions of these ncRNAs with other molecules. Computational predictions are thus used as an alternative source of new insights through a process of mutual enrichment because the information obtained through experiments continuously feeds through into computational methods. The results of these predictions in turn shed light on possible interactions that are subsequently validated experimentally. This review describes the latest advances in databases, bioinformatic tools, and new in silico strategies that allow the establishment or prediction of biological interactions of ncRNAs, particularly miRNAs and lncRNAs. The ncRNA species described in this work have a special emphasis on those found in humans, but information on ncRNA of other species is also included.
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Affiliation(s)
- Andrés Rincón-Riveros
- Bioinformatics and Systems Biology Group, Universidad Nacional de Colombia, Bogotá 111221, Colombia;
| | - Duvan Morales
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111221, Colombia;
| | - Josefa Antonia Rodríguez
- Grupo de Investigación en Biología del Cáncer, Instituto Nacional de Cancerología, Bogotá 111221, Colombia;
| | - Victoria E. Villegas
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111221, Colombia;
| | - Liliana López-Kleine
- Department of Statistics, Faculty of Science, Universidad Nacional de Colombia, Bogotá 111221, Colombia
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Zhang S, Chen J, Liu D, Hu B, Luo G, Huang Z. A novel microfluidic RNA chip for direct, single-nucleotide specific, rapid and partially-degraded RNA detection. Talanta 2021; 239:122974. [PMID: 34920889 DOI: 10.1016/j.talanta.2021.122974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/31/2021] [Accepted: 09/02/2021] [Indexed: 10/20/2022]
Abstract
Direct RNA detection is critical for providing the RNA insights into gene expression profiling, noncoding RNAs, RNA-associated diseases and pathogens, without reverse transcription. However, classical RNA analysis usually requires RT-PCR, which can cause bias amplification and quantitation errors. To address this challenge, herein we report a microfluidic RNA chip (the microchip prototype) for direct RNA detection, which is primarily based on RNA extension and labeling with DNA polymerase. This detection strategy is of high specificity (discriminating against single-nucleotide differences), rapidity, accuracy, nuclease resistance, and reusability. Further, we have successfully detected disease-associated RNAs in clinical samples, demonstrating its great potentials in biomedical research and clinical diagnosis.
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Affiliation(s)
- Shun Zhang
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610064, PR China; SeNA Research Institute and Szostak-CDHT Large Nucleic Acids Institute, Chengdu, Sichuan, PR China
| | - Jiuyi Chen
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610064, PR China
| | - Dan Liu
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610064, PR China
| | - Bei Hu
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610064, PR China
| | - Guangcheng Luo
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610064, PR China
| | - Zhen Huang
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610064, PR China; SeNA Research Institute and Szostak-CDHT Large Nucleic Acids Institute, Chengdu, Sichuan, PR China.
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Wang L, Wu J, Ye N, Li F, Zhan H, Chen S, Xu J. Plasma-Derived Exosome MiR-19b Acts as a Diagnostic Marker for Pancreatic Cancer. Front Oncol 2021; 11:739111. [PMID: 34589435 PMCID: PMC8473875 DOI: 10.3389/fonc.2021.739111] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 08/23/2021] [Indexed: 12/18/2022] Open
Abstract
Background Diagnosis of pancreatic cancer (Pca) is challenging. This study investigated the value of plasma-derived exosome miR-19b (Exo-miR-19b) in diagnosing patients with Pca. Methods Plasma was collected from 62 patients with Pca, 30 patients with other pancreatic tumor (OPT), 23 patients with chronic pancreatitis (CP), and 53 healthy volunteers. MiR-19b levels in plasma-derived exosomes were detected. Results Plasma-derived Exo-miR-19b levels normalized using miR-1228 were significantly lower in Pca patients than in patients with OPT, CP patients, and healthy volunteers. The diagnostic values of Exo-miR-19b normalized using miR-1228 were superior to those of serum cancer antigen 19-9 (CA19-9) in differentiating Pca patients from healthy volunteers (area under the curve (AUC): 0.942 vs. 0.813, p = 0.0054), potentially better than those of CA19-9 in differentiating Pca patients from CP patients (AUC: 0.898 vs. 0.792, p = 0.0720), and equivalent to those of CA19-9 in differentiating Pca patients from patients with OPT (AUC: 0.810 vs. 0.793, p = 0.8206). When normalized using Caenorhabditis elegans miR-39 (cel-miR-39), Exo-miR-19b levels in Pca patients were significantly higher than those in patients with OPT, CP patients, and healthy volunteers. The diagnostic values of Exo-miR-19b normalized using cel-miR-39 were equivalent to those of CA19-9 in differentiating Pca patients from healthy volunteers (AUC: 0.781 vs. 0.813, p = 0.6118) and CP patients (AUC: 0.672 vs. 0.792, p = 0.1235), while they were inferior to those of CA19-9 in differentiating Pca patients from patients with OPT (AUC: 0.631 vs. 0.793, p = 0.0353). Conclusion Plasma-derived Exo-miR-19b is a promising diagnostic marker for Pca. The diagnostic value of plasma-derived Exo-miR-19b normalized using miR-1228 is superior to that of serum CA19-9 in differentiating patients with Pca from healthy volunteers.
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Affiliation(s)
- Lei Wang
- Department of Pancreatic Surgery, General Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Jinxiang Wu
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Naikuan Ye
- Department of Pancreatic Surgery, General Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Feng Li
- Department of Pancreatic Surgery, General Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Hanxiang Zhan
- Department of Pancreatic Surgery, General Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Shihong Chen
- Department of Pancreatic Surgery, General Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Jianwei Xu
- Department of Pancreatic Surgery, General Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,School of Medicine, Cheeloo College of Medicine, Shandong University, Jinan, China
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Liang G, Ling Y, Lin Q, Shi Y, Luo Q, Cen Y, Mehrpour M, Hamai A, Li J, Gong C. MiR-92b-3p Inhibits Proliferation of HER2-Positive Breast Cancer Cell by Targeting circCDYL. Front Cell Dev Biol 2021; 9:707049. [PMID: 34395434 PMCID: PMC8358302 DOI: 10.3389/fcell.2021.707049] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 07/02/2021] [Indexed: 12/24/2022] Open
Abstract
Objectives Circular RNA (circRNA) is a novel class of RNA, which exhibits powerful biological function in regulating cellular fate of various tumors. Previously, we had demonstrated that over-expression of circRNA circCDYL promoted progression of HER2-negative (HER2–) breast cancer via miR-1275-ULK1/ATG7-autophagic axis. However, the role of circCDYL in HER2-positive (HER2+) breast cancer, in particular its role in modulating cell proliferation, one of the most important characteristics of cellular fate, is unclear. Materials and methods qRT-PCR and in situ hybridization analyses were performed to examine the expression of circCDYL and miR-92b-3p in breast cancer tissues or cell lines. The biological function of circCDYL and miR-92b-3p were assessed by plate colony formation and cell viability assays and orthotopic animal models. In mechanistic study, circRNAs pull-down, RNA immunoprecipitation, dual luciferase report, western blot, immunohistochemical and immunofluorescence staining assays were performed. Results CircCDYL was high-expressed in HER2+ breast cancer tissue, similar with that in HER2– breast cancer tissue. Silencing HER2 gene had no effect on expression of circCDYL in HER2+ breast cancer cells. Over-expression of circCDYL promoted proliferation of HER2+ breast cancer cells but not through miR-1275-ULK1/ATG7-autophagic axis. CircRNA pull down and miRNA deep-sequencing demonstrated the binding of miR-92b-3p and circCDYL. Interestingly, circCDYL did not act as miR-92b-3p sponge, but was degraded in miR-92b-3p-dependent silencing manner. Clinically, expression of circCDYL and miR-92b-3p was associated with clinical outcome of HER2+ breast cancer patients. Conclusion MiR-92b-3p-dependent cleavage of circCDYL was an essential mechanism in regulating cell proliferation of HER2+ breast cancer cells. CircCDYL was proved to be a potential therapeutic target for HER2+ breast cancer, and both circCDYL and miR-92b-3p might be potential biomarkers in predicting clinical outcome of HER2+ breast cancer patients.
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Affiliation(s)
- Gehao Liang
- Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.,Department of Breast Oncology, Sun Yat-sen University Cancer Center, Sun Yat-sen University, Guangzhou, China
| | - Yun Ling
- Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.,Department of Breast Surgery, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Qun Lin
- Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yu Shi
- Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Qing Luo
- Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yinghuan Cen
- Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Maryam Mehrpour
- Institut Necker-Enfants Malades (INEM), Inserm U1151-CNRS UMR 8253, Paris, France
| | - Ahmed Hamai
- Institut Necker-Enfants Malades (INEM), Inserm U1151-CNRS UMR 8253, Paris, France
| | - Jun Li
- Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Chang Gong
- Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
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