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Payandeh Z, Tangruksa B, Synnergren J, Heydarkhan-Hagvall S, Nordin JZ, Andaloussi SE, Borén J, Wiseman J, Bohlooly-Y M, Lindfors L, Valadi H. Extracellular vesicles transport RNA between cells: Unraveling their dual role in diagnostics and therapeutics. Mol Aspects Med 2024; 99:101302. [PMID: 39094449 DOI: 10.1016/j.mam.2024.101302] [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: 10/30/2023] [Revised: 04/11/2024] [Accepted: 07/23/2024] [Indexed: 08/04/2024]
Abstract
Modern methods of molecular diagnostics and therapy have revolutionized the field of medicine in recent years by providing more precise and effective tools for detecting and treating diseases. This progress includes a growing exploration of the body's secreted vesicles, known as extracellular vesicles (EVs), for both diagnostic and therapeutic purposes. EVs are a heterogeneous population of lipid bilayer vesicles secreted by almost every cell type studied so far. They are detected in body fluids and conditioned culture media from living cells. EVs play a crucial role in communication between cells and organs, both locally and over long distances. They are recognized for their ability to transport endogenous RNA and proteins between cells, including messenger RNA (mRNA), microRNA (miRNA), misfolded neurodegenerative proteins, and several other biomolecules. This review explores the dual utilization of EVs, serving not only for diagnostic purposes but also as a platform for delivering therapeutic molecules to cells and tissues. Through an exploration of their composition, biogenesis, and selective cargo packaging, we elucidate the intricate mechanisms behind RNA transport between cells via EVs, highlighting their potential use for both diagnostic and therapeutic applications. Finally, it addresses challenges and outlines prospective directions for the clinical utilization of EVs.
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Affiliation(s)
- Zahra Payandeh
- Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, 41346, Sweden
| | - Benyapa Tangruksa
- Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, 41346, Sweden; Systems Biology Research Center, School of Bioscience, University of Skövde, 541 28, Skövde, Sweden
| | - Jane Synnergren
- Systems Biology Research Center, School of Bioscience, University of Skövde, 541 28, Skövde, Sweden; Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, 41345, Sweden
| | - Sepideh Heydarkhan-Hagvall
- Systems Biology Research Center, School of Bioscience, University of Skövde, 541 28, Skövde, Sweden; Global Patient Safety - Biopharma, AstraZeneca, 431 83, Gothenburg, Mölndal, Sweden
| | - Joel Z Nordin
- Division of Biomolecular and Cellular Medicine, Department of Laboratory Medicine, Karolinska Institutet, Huddinge, Sweden
| | | | - Jan Borén
- Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Sweden
| | - John Wiseman
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, 431 83, Gothenburg, Mölndal, Sweden
| | - Mohammad Bohlooly-Y
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, 431 83, Gothenburg, Mölndal, Sweden
| | - Lennart Lindfors
- Advanced Drug Delivery, Pharmaceutical Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, 431 83, Mölndal, Sweden
| | - Hadi Valadi
- Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, 41346, Sweden.
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Azam HMH, Rößling RI, Geithe C, Khan MM, Dinter F, Hanack K, Prüß H, Husse B, Roggenbuck D, Schierack P, Rödiger S. MicroRNA biomarkers as next-generation diagnostic tools for neurodegenerative diseases: a comprehensive review. Front Mol Neurosci 2024; 17:1386735. [PMID: 38883980 PMCID: PMC11177777 DOI: 10.3389/fnmol.2024.1386735] [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: 02/15/2024] [Accepted: 04/12/2024] [Indexed: 06/18/2024] Open
Abstract
Neurodegenerative diseases (NDs) are characterized by abnormalities within neurons of the brain or spinal cord that gradually lose function, eventually leading to cell death. Upon examination of affected tissue, pathological changes reveal a loss of synapses, misfolded proteins, and activation of immune cells-all indicative of disease progression-before severe clinical symptoms become apparent. Early detection of NDs is crucial for potentially administering targeted medications that may delay disease advancement. Given their complex pathophysiological features and diverse clinical symptoms, there is a pressing need for sensitive and effective diagnostic methods for NDs. Biomarkers such as microRNAs (miRNAs) have been identified as potential tools for detecting these diseases. We explore the pivotal role of miRNAs in the context of NDs, focusing on Alzheimer's disease, Parkinson's disease, Multiple sclerosis, Huntington's disease, and Amyotrophic Lateral Sclerosis. The review delves into the intricate relationship between aging and NDs, highlighting structural and functional alterations in the aging brain and their implications for disease development. It elucidates how miRNAs and RNA-binding proteins are implicated in the pathogenesis of NDs and underscores the importance of investigating their expression and function in aging. Significantly, miRNAs exert substantial influence on post-translational modifications (PTMs), impacting not just the nervous system but a wide array of tissues and cell types as well. Specific miRNAs have been found to target proteins involved in ubiquitination or de-ubiquitination processes, which play a significant role in regulating protein function and stability. We discuss the link between miRNA, PTM, and NDs. Additionally, the review discusses the significance of miRNAs as biomarkers for early disease detection, offering insights into diagnostic strategies.
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Affiliation(s)
- Hafiz Muhammad Husnain Azam
- Institute of Biotechnology, Faculty of Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Rosa Ilse Rößling
- German Center for Neurodegenerative Diseases (DZNE), Berlin, Germany
- Department of Neurology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Christiane Geithe
- Institute of Biotechnology, Faculty of Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
- Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus - Senftenberg, The Brandenburg Medical School Theodor Fontane and the University of Potsdam, Berlin, Germany
| | - Muhammad Moman Khan
- Institute of Biotechnology, Faculty of Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Franziska Dinter
- Institute of Biotechnology, Faculty of Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
- PolyAn GmbH, Berlin, Germany
| | - Katja Hanack
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Harald Prüß
- German Center for Neurodegenerative Diseases (DZNE), Berlin, Germany
- Department of Neurology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Britta Husse
- Institute of Biotechnology, Faculty of Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Dirk Roggenbuck
- Institute of Biotechnology, Faculty of Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Peter Schierack
- Institute of Biotechnology, Faculty of Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Stefan Rödiger
- Institute of Biotechnology, Faculty of Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
- Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus - Senftenberg, The Brandenburg Medical School Theodor Fontane and the University of Potsdam, Berlin, Germany
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3
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Miron RJ, Zhang Y. Understanding exosomes: Part 1-Characterization, quantification and isolation techniques. Periodontol 2000 2024; 94:231-256. [PMID: 37740431 DOI: 10.1111/prd.12520] [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: 05/16/2023] [Revised: 07/21/2023] [Accepted: 07/25/2023] [Indexed: 09/24/2023]
Abstract
Exosomes are the smallest subset of extracellular signaling vesicles secreted by most cells with a diameter in the range of 30-150 nm. Their use has gained great momentum recently due to their ability to be utilized as diagnostic tools with a vast array of therapeutic applications. Over 5000 publications are currently being published yearly on this topic, and this number is only expected to dramatically increase as novel therapeutic strategies continue to be investigated. This review article first focuses on understanding exosomes, including their cellular origin, biogenesis, function, and characterization. Thereafter, overviews of the quantification methods and isolation techniques are given with discussion over their potential use as novel therapeutics in regenerative medicine.
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Affiliation(s)
- Richard J Miron
- Department of Periodontology, University of Bern, Bern, Switzerland
| | - Yufeng Zhang
- Department of Oral Implantology, University of Wuhan, Wuhan, China
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Cai Y, Liu P, Xu Y, Xia Y, Peng X, Zhao H, Chen Q. Biomarkers of obesity-mediated insulin resistance: focus on microRNAs. Diabetol Metab Syndr 2023; 15:167. [PMID: 37537674 PMCID: PMC10401761 DOI: 10.1186/s13098-023-01137-3] [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: 05/04/2023] [Accepted: 07/09/2023] [Indexed: 08/05/2023] Open
Abstract
Obesity and metabolic syndromes are becoming increasingly prevalent worldwide. Insulin resistance (IR) is a common complication of obesity. However, IR occurrence varies across individuals with obesity and may involve epigenetic factors. To rationalize the allocation of healthcare resources, biomarkers for the early risk stratification of individuals with obesity should be identified. MicroRNAs (miRNAs) are closely associated with metabolic diseases and involved in epigenetic regulation. In this review, we have summarized the changes in miRNA expression in the peripheral circulation and tissues of patients and animals with obesity-associated IR over the last 5 years and identified several candidate biomarkers that predict obesity-related IR. There are areas for improvement in existing studies. First, more than the predictive validity of a single biomarker is required, and a biomarker panel needs to be formed. Second, miRNAs are often studied in isolation and do not form a network of signaling pathways. We believe that early biomarkers can help clinicians accurately predict individuals prone to obesity-related IR at an early stage. Epigenetic regulation may be one of the underlying causes of different clinical outcomes in individuals with obesity. Future studies should focus on objectively reflecting the differences in miRNA profile expression in individuals with obesity-related IR, which may help identify more reliable biomarkers. Understanding the metabolic pathways of these miRNAs can help design new metabolic risk prevention and management strategies, and support the development of drugs to treat obesity and metabolic disorders.
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Affiliation(s)
- Yichen Cai
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610072, Sichuan, China
- School of Clinical Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Pan Liu
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610072, Sichuan, China
- School of Clinical Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yumei Xu
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610072, Sichuan, China
- School of Clinical Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yuguo Xia
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610072, Sichuan, China
| | - Xiaowan Peng
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610072, Sichuan, China
- School of Clinical Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Haiyan Zhao
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610072, Sichuan, China
- School of Clinical Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Qiu Chen
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610072, Sichuan, China.
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Abdullah AL-maskri AA, Jin G, Li Y, Talap J, Almoiliqy M, Apu C, Zeng S, Zhou Y, Cai S. A self-assembly amplification strategy for ultra-sensitive detection of microRNA based on phosphorothioated probes. Talanta 2022; 249:123618. [DOI: 10.1016/j.talanta.2022.123618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 05/21/2022] [Accepted: 05/25/2022] [Indexed: 11/26/2022]
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6
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Mokhtari F, Kaboosi H, Mohebbi SR, Asadzadeh Aghdaei H, Zali MRZ. Evaluation of Circulating MicroRNA-222 in Patients with Chronic Hepatitis B virus Infection as a Potential Noninvasive Diagnostic Biomarker. IRANIAN JOURNAL OF MEDICAL MICROBIOLOGY 2022. [DOI: 10.30699/ijmm.16.6.543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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7
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Lai JJ, Chau ZL, Chen S, Hill JJ, Korpany KV, Liang N, Lin L, Lin Y, Liu JK, Liu Y, Lunde R, Shen W. Exosome Processing and Characterization Approaches for Research and Technology Development. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2103222. [PMID: 35332686 PMCID: PMC9130923 DOI: 10.1002/advs.202103222] [Citation(s) in RCA: 112] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 01/28/2022] [Indexed: 05/05/2023]
Abstract
Exosomes are extracellular vesicles that share components of their parent cells and are attractive in biotechnology and biomedical research as potential disease biomarkers as well as therapeutic agents. Crucial to realizing this potential is the ability to manufacture high-quality exosomes; however, unlike biologics such as proteins, exosomes lack standardized Good Manufacturing Practices for their processing and characterization. Furthermore, there is a lack of well-characterized reference exosome materials to aid in selection of methods for exosome isolation, purification, and analysis. This review informs exosome research and technology development by comparing exosome processing and characterization methods and recommending exosome workflows. This review also provides a detailed introduction to exosomes, including their physical and chemical properties, roles in normal biological processes and in disease progression, and summarizes some of the on-going clinical trials.
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Affiliation(s)
- James J. Lai
- Department of BioengineeringUniversity of WashingtonSeattleWA98195USA
| | - Zoe L. Chau
- Department of BioengineeringUniversity of WashingtonSeattleWA98195USA
| | - Sheng‐You Chen
- Department of Mechanical EngineeringUniversity of WashingtonSeattleWA98195USA
| | - John J. Hill
- Department of BioengineeringUniversity of WashingtonSeattleWA98195USA
| | | | - Nai‐Wen Liang
- Department of Materials Science and EngineeringNational Tsing Hua UniversityHsinchu30013Taiwan
| | - Li‐Han Lin
- Department of Mechanical EngineeringNational Taiwan UniversityTaipei City10617Taiwan
| | - Yi‐Hsuan Lin
- Department of Engineering and System ScienceNational Tsing Hua UniversityHsinchu30013Taiwan
| | - Joanne K. Liu
- Department of BioengineeringUniversity of WashingtonSeattleWA98195USA
| | - Yu‐Chung Liu
- Department of Materials Science and EngineeringNational Tsing Hua UniversityHsinchu30013Taiwan
| | - Ruby Lunde
- Department of BioengineeringUniversity of WashingtonSeattleWA98195USA
| | - Wei‐Ting Shen
- Department of Biomedical Engineering and Environmental SciencesNational Tsing Hua UniversityHsinchu30013Taiwan
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8
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Ying S, Heung T, Zhang Z, Yuen RKC, Bassett AS. Schizophrenia Risk Mediated by microRNA Target Genes Overlapped by Genome-Wide Rare Copy Number Variation in 22q11.2 Deletion Syndrome. Front Genet 2022; 13:812183. [PMID: 35495153 PMCID: PMC9053669 DOI: 10.3389/fgene.2022.812183] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 02/25/2022] [Indexed: 11/13/2022] Open
Abstract
The 22q11.2 deletion is associated with >20-fold increased risk for schizophrenia. The presence of gene DGCR8 in the 22q11.2 deletion region has suggested microRNA (miRNA) dysregulation as possibly contributing to this risk. We therefore investigated the role of miRNA target genes in the context of previously identified genome-wide risk for schizophrenia conveyed by additional copy number variation (CNV) in 22q11.2 deletion syndrome (22q11.2DS). Using a cohort of individuals with 22q11.2DS and documented additional rare CNVs overlapping protein coding genes, we compared those with schizophrenia (n = 100) to those with no psychotic illness (n = 118), assessing for rare CNVs that overlapped experimentally supported miRNA target genes. We further characterized the contributing miRNA target genes using gene set enrichment analyses and identified the miRNAs most implicated. Consistent with our hypothesis, we found a significantly higher proportion of individuals in the schizophrenia than in the non-psychotic group to have an additional rare CNV that overlapped one or more miRNA target genes (odds ratio = 2.12, p = 0.0138). Gene set analyses identified an enrichment of FMRP targets and genes involved in nervous system development and postsynaptic density amongst these miRNA target genes in the schizophrenia group. The miRNAs most implicated included miR-17-5p, miR-34a-5p and miR-124-3p. These results provide initial correlational evidence in support of a possible role for miRNA perturbation involving genes affected by rare genome-wide CNVs in the elevated risk for schizophrenia in 22q11.2DS, consistent with the multi-hit and multi-layered genetic mechanisms implicated in this and other forms of schizophrenia.
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Affiliation(s)
- Shengjie Ying
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Tracy Heung
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, ON, Canada
- The Dalglish Family 22q Clinic, University Health Network, Toronto, ON, Canada
| | - Zhaolei Zhang
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
| | - Ryan K. C. Yuen
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Anne S. Bassett
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, ON, Canada
- The Dalglish Family 22q Clinic, University Health Network, Toronto, ON, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
- Toronto General Hospital Research Institute and Campbell Family Mental Health Research Institute, Toronto, ON, Canada
- *Correspondence: Anne S. Bassett,
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Gopcevic KR, Gkaliagkousi E, Nemcsik J, Acet Ö, Bernal-Lopez MR, Bruno RM, Climie RE, Fountoulakis N, Fraenkel E, Lazaridis A, Navickas P, Rochfort KD, Šatrauskienė A, Zupkauskienė J, Terentes-Printzios D. Pathophysiology of Circulating Biomarkers and Relationship With Vascular Aging: A Review of the Literature From VascAgeNet Group on Circulating Biomarkers, European Cooperation in Science and Technology Action 18216. Front Physiol 2021; 12:789690. [PMID: 34970157 PMCID: PMC8712891 DOI: 10.3389/fphys.2021.789690] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 11/17/2021] [Indexed: 12/14/2022] Open
Abstract
Impairment of the arteries is a product of sustained exposure to various deleterious factors and progresses with time; a phenomenon inherent to vascular aging. Oxidative stress, inflammation, the accumulation of harmful agents in high cardiovascular risk conditions, changes to the extracellular matrix, and/or alterations of the epigenetic modification of molecules, are all vital pathophysiological processes proven to contribute to vascular aging, and also lead to changes in levels of associated circulating molecules. Many of these molecules are consequently recognized as markers of vascular impairment and accelerated vascular aging in clinical and research settings, however, for these molecules to be classified as biomarkers of vascular aging, further criteria must be met. In this paper, we conducted a scoping literature review identifying thirty of the most important, and eight less important, biomarkers of vascular aging. Herein, we overview a selection of the most important molecules connected with the above-mentioned pathological conditions and study their usefulness as circulating biomarkers of vascular aging.
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Affiliation(s)
- Kristina R. Gopcevic
- Laboratory for Analytics of Biomolecules, Department of Chemistry in Medicine, Faculty of Medicine, Belgrade, Serbia
| | - Eugenia Gkaliagkousi
- 3rd Department of Internal Medicine, Papageorgiou Hospital, Faculty of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - János Nemcsik
- Department of Family Medicine, Semmelweis University, Budapest, Hungary
- Health Service of ZUGLO, Department of Family Medicine, Budapest, Hungary
| | - Ömür Acet
- Vocational School of Health Science, Pharmacy Services Program, Tarsus University, Tarsus, Turkey
| | - M. Rosa Bernal-Lopez
- Internal Medicine Department, Regional University Hospital of Malaga, Instituto de Investigacion Biomedica de Malaga, University of Malaga, CIBER Fisiopatología de la Obesidad y la Nutrición, Instituto de Salud Carlos III, Málaga, Spain
| | - Rosa M. Bruno
- Unversite de Paris, INSERM, U970, Paris Cardiovascular Research Center, Paris, France
| | - Rachel E. Climie
- Unversite de Paris, INSERM, U970, Paris Cardiovascular Research Center, Paris, France
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
- Sports Cardiology Lab, Clinical Research Domain, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
| | - Nikolaos Fountoulakis
- Faculty of Life Sciences and Medicine, King’s College London - Waterloo Campus, London, United Kingdom
| | - Emil Fraenkel
- 1st Department of Internal Medicine, University Hospital and Pavol Jozef Šafárik University in Košice, Košice, Slovakia
| | - Antonios Lazaridis
- 3rd Department of Internal Medicine, Papageorgiou Hospital, Faculty of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Petras Navickas
- Clinic of Cardiac and Vascular Diseases, Institute of Clinical Medicine, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Keith D. Rochfort
- School of Nursing, Psychotherapy and Community Health, Dublin City University, Dublin, Ireland
| | - Agnė Šatrauskienė
- Clinic of Cardiac and Vascular Diseases, Institute of Clinical Medicine, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
- Centre of Cardiology and Angiology, Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania
| | - Jūratė Zupkauskienė
- Clinic of Cardiac and Vascular Diseases, Institute of Clinical Medicine, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Dimitrios Terentes-Printzios
- First Department of Cardiology, Hippokration Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
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Na HK, Shon HK, Son HY, Jang E, Joh S, Huh YM, Castner DG, Lee TG. Utilization of chromogenic enzyme substrates for signal amplification in multiplexed detection of biomolecules using surface mass spectrometry. SENSORS AND ACTUATORS. B, CHEMICAL 2021; 332:129452. [PMID: 33519092 PMCID: PMC7845929 DOI: 10.1016/j.snb.2021.129452] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
MicroRNAs (miRNAs) are important post-transcriptional gene regulators and can serve as potential biomarkers for many diseases. Most of the current miRNA detection techniques require purification from biological samples, amplification, labeling, or tagging, which makes quantitative analysis of clinically relevant samples challenging. Here we present a new strategy for the detection of miRNAs with uniformity over a large area based on signal amplification using enzymatic reactions and measurements using time-of-flight secondary ion mass spectrometry (ToF-SIMS), a sensitive surface analysis tool. This technique has high sequence specificity through hybridization with a hairpin DNA probe and allows the identification of single-base mismatches that are difficult to distinguish by conventional mass spectrometry. We successfully detected target miRNAs in biological samples without purification, amplification, or labeling of target molecules. In addition, by adopting a well-known chromogenic enzymatic reaction from the field of biotechnology, we extended the use of enzyme-amplified signal enhancement ToF (EASE-ToF) to protein detection. Our strategy has advantages with respect to scope, quantification, and throughput over the currently available methods, and is amenable to multiplexing based on the outstanding molecular specificity of mass spectrometry (MS). Therefore, our technique not only has the potential for use in clinical diagnosis, but also provides evidence that MS can serve as a useful readout for biosensing to perform multiplexed analysis extending beyond the limitations of existing technology.
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Affiliation(s)
- Hee-Kyung Na
- Center for Nano-Bio Measurement, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Korea
| | - Hyun Kyong Shon
- Center for Nano-Bio Measurement, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Korea
| | - Hye Young Son
- Department of Radiology, College of Medicine, Yonsei University, Seoul 03722, Korea
| | - Eunji Jang
- Department of Radiology, College of Medicine, Yonsei University, Seoul 03722, Korea
| | - Sunho Joh
- Center for Nano-Bio Measurement, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Korea
- Department of Nano Science, University of Science and Technology (UST), Daejeon 34113, Korea
| | - Yong-Min Huh
- Department of Radiology, College of Medicine, Yonsei University, Seoul 03722, Korea
| | - David G. Castner
- National ESCA and Surface Analysis Center for Biomedical Problems, Departments of Bioengineering and Chemical Engineering, University of Washington, Seattle, WA 98195-1653, USA
| | - Tae Geol Lee
- Center for Nano-Bio Measurement, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Korea
- Department of Nano Science, University of Science and Technology (UST), Daejeon 34113, Korea
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11
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Sedlmeier EM, Meyer DM, Stecher L, Sailer M, Daniel H, Hauner H, Bader BL. Fetal sex modulates placental microRNA expression, potential microRNA-mRNA interactions, and levels of amino acid transporter expression and substrates: INFAT study subpopulation analysis of n-3 LCPUFA intervention during pregnancy and associations with offspring body composition. BMC Mol Cell Biol 2021; 22:15. [PMID: 33657992 PMCID: PMC7931339 DOI: 10.1186/s12860-021-00345-x] [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: 04/27/2020] [Accepted: 12/08/2020] [Indexed: 12/13/2022] Open
Abstract
Background Previously, we revealed sexually dimorphic mRNA expression and responsiveness to maternal dietary supplementation with n-3 long-chain polyunsaturated fatty acids (LCPUFA) in placentas from a defined INFAT study subpopulation. Here, we extended these analyses and explored the respective placental microRNA expression, putative microRNA-mRNA interactions, and downstream target processes as well as their associations with INFAT offspring body composition. Results We performed explorative placental microRNA profiling, predicted microRNA-mRNA interactions by bioinformatics, validated placental target microRNAs and their putative targets by RT-qPCR and western blotting, and measured amino acid levels in maternal and offspring cord blood plasma and placenta. microRNA, mRNA, protein, and amino acid levels were associated with each other and with offspring body composition from birth to 5 years of age. Forty-six differentially regulated microRNAs were found. Validations identified differential expression for microRNA-99a (miR-99a) and its predicted target genes mTOR, SLC7A5, encoding L-type amino acid transporter 1 (LAT1), and SLC6A6, encoding taurine transporter (TauT), and their prevailing significant sexually dimorphic regulation. Target mRNA levels were mostly higher in placentas from control male than from female offspring, whereas respective n-3 LCPUFA responsive target upregulation was predominantly found in female placentas, explaining the rather balanced expression levels between the sexes present only in the intervention group. LAT1 and TauT substrates tryptophan and taurine, respectively, were significantly altered in both maternal plasma at 32 weeks’ gestation and cord plasma following intervention, but not in the placenta. Several significant associations were observed for miR-99a, mTOR mRNA, SLC7A5 mRNA, and taurine and tryptophan in maternal and cord plasma with offspring body composition at birth, 1 year, 3 and 5 years of age. Conclusions Our data suggest that the analyzed targets may be part of a sexually dimorphic molecular regulatory network in the placenta, possibly modulating gene expression per se and/or counteracting n-3 LCPUFA responsive changes, and thereby stabilizing respective placental and fetal amino acid levels. Our data propose placental miR-99, SLC7A5 mRNA, and taurine and tryptophan levels in maternal and fetal plasma as potentially predictive biomarkers for offspring body composition. Supplementary Information The online version contains supplementary material available at 10.1186/s12860-021-00345-x.
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Affiliation(s)
- Eva-Maria Sedlmeier
- ZIEL-PhD Graduate School 'Epigenetics, Imprinting and Nutrition', ZIEL-Institute for Food and Health, School of Life Sciences Weihenstephan, Technical University of Munich, Gregor-Mendel-Straße 2, 85354, Freising, Germany.,Else Kröner-Fresenius-Center for Nutritional Medicine, School of Life Sciences Weihenstephan, Technical University of Munich, Gregor-Mendel-Straße 2, 85354, Freising, Germany
| | - Dorothy M Meyer
- Institute of Nutritional Medicine, School of Medicine, Technical University of Munich, Georg-Brauchle-Ring 62, 80992, Munich, Germany
| | - Lynne Stecher
- Institute of Nutritional Medicine, School of Medicine, Technical University of Munich, Georg-Brauchle-Ring 62, 80992, Munich, Germany
| | - Manuela Sailer
- Molecular Nutrition Unit, ZIEL-Institute for Food and Health, School of Life Sciences Weihenstephan, Technical University of Munich, Gregor-Mendel-Straße 2, 85354, Freising, Germany
| | - Hannelore Daniel
- Molecular Nutrition Unit, ZIEL-Institute for Food and Health, School of Life Sciences Weihenstephan, Technical University of Munich, Gregor-Mendel-Straße 2, 85354, Freising, Germany
| | - Hans Hauner
- Else Kröner-Fresenius-Center for Nutritional Medicine, School of Life Sciences Weihenstephan, Technical University of Munich, Gregor-Mendel-Straße 2, 85354, Freising, Germany.,Institute of Nutritional Medicine, School of Medicine, Technical University of Munich, Georg-Brauchle-Ring 62, 80992, Munich, Germany.,Clinical Nutritional Medicine Unit, ZIEL-Institute for Food and Health, School of Life Sciences Weihenstephan, Technical University of Munich, Gregor-Mendel-Straße 2, 85354, Freising, Germany
| | - Bernhard L Bader
- ZIEL-PhD Graduate School 'Epigenetics, Imprinting and Nutrition', ZIEL-Institute for Food and Health, School of Life Sciences Weihenstephan, Technical University of Munich, Gregor-Mendel-Straße 2, 85354, Freising, Germany. .,Else Kröner-Fresenius-Center for Nutritional Medicine, School of Life Sciences Weihenstephan, Technical University of Munich, Gregor-Mendel-Straße 2, 85354, Freising, Germany. .,Clinical Nutritional Medicine Unit, ZIEL-Institute for Food and Health, School of Life Sciences Weihenstephan, Technical University of Munich, Gregor-Mendel-Straße 2, 85354, Freising, Germany.
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Circulating MicroRNAs as Potential Biomarkers in the Diagnosis of Neurosyphilis: A Case Control Study. INTERNATIONAL JOURNAL OF DERMATOLOGY AND VENEREOLOGY 2021. [DOI: 10.1097/jd9.0000000000000127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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13
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Šatrauskienė A, Navickas R, Laucevičius A, Krilavičius T, Užupytė R, Zdanytė M, Ryliškytė L, Jucevičienė A, Holvoet P. Mir-1, miR-122, miR-132, and miR-133 Are Related to Subclinical Aortic Atherosclerosis Associated with Metabolic Syndrome. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18041483. [PMID: 33557426 PMCID: PMC7915826 DOI: 10.3390/ijerph18041483] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 01/08/2023]
Abstract
Previously, miR-1, miR-122, miR-126, miR-132, miR-133, and miR-370 were found to be related to coronary artery disease (CAD) progression. However, their relationship with subclinical atherosclerosis, especially in subjects with metabolic syndrome, is unknown. Therefore, our aim was to determine their relationship with arterial markers of subclinical atherosclerosis. Metabolic syndrome subjects (n = 182) with high cardiovascular risk but without overt cardiovascular disease (CVD) were recruited from the Lithuanian High Cardiovascular Risk (LitHiR) primary prevention program. The ardio-ankle vascular index (CAVI), augmentation index normalized to a heart rate of 75 bpm (AIxHR75), aortic pulse wave velocity (AoPWV), and carotid artery stiffness were assessed. MicroRNAs (miRs) were analyzed in serum. Pearson correlation and a univariate linear regression t-test showed that miR-1, miR-133b, and miR-133a were negatively associated with CAVI mean, whereas miR-122 was positively associated. MiR-1, miR-133b and miR-133a, and miR-145 were negatively associated with AIxHR75. MiR-122 correlated negatively with AoPWV. In multivariate linear regression models, miR-133b and miR-122 predicted CAVImean, miR-133 predicted AIxHR75, and miR-122 predicted AoPWV. MiR-132 predicted right carotid artery stiffness, and miR-1 predicted left carotid artery stiffness. The addition of smoking to miR-133b and miR-122 enhanced the prediction of CAVI. Age and triglycerides enhanced the prediction of AoPWV by miR-122. A cluster of four miRs are related to subclinical atherosclerosis in subjects with metabolic syndrome. Combined, they may have a more substantial diagnostic or prognostic value than any single miR. Future follow-up studies are needed to establish their clinical relevance.
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Affiliation(s)
- Agnė Šatrauskienė
- Clinic of Cardiac and Vascular Diseases, Institute of Clinical Medicine, Faculty of Medicine, Vilnius University, 08661 Vilnius, Lithuania; (A.Š.); (A.L.); (L.R.); (A.J.)
- Centre of Cardiology and Angiology, Vilnius University Hospital, Santaros Klinikos, 08410 Vilnius, Lithuania
| | - Rokas Navickas
- Clinic of Cardiac and Vascular Diseases, Institute of Clinical Medicine, Faculty of Medicine, Vilnius University, 08661 Vilnius, Lithuania; (A.Š.); (A.L.); (L.R.); (A.J.)
- Centre of Cardiology and Angiology, Vilnius University Hospital, Santaros Klinikos, 08410 Vilnius, Lithuania
- Correspondence:
| | - Aleksandras Laucevičius
- Clinic of Cardiac and Vascular Diseases, Institute of Clinical Medicine, Faculty of Medicine, Vilnius University, 08661 Vilnius, Lithuania; (A.Š.); (A.L.); (L.R.); (A.J.)
- Centre of Cardiology and Angiology, Vilnius University Hospital, Santaros Klinikos, 08410 Vilnius, Lithuania
- Experimental, Preventive, and Clinic Medicine Department, Centre for Innovative Medicine, 08406 Vilnius, Lithuania
| | - Tomas Krilavičius
- Informatics Faculty, Vytautas Magnus University, 44248 Kaunas, Lithuania; (T.K.); (R.U.)
- Baltic Institute of Advanced Technology, 01124 Vilnius, Lithuania
| | - Rūta Užupytė
- Informatics Faculty, Vytautas Magnus University, 44248 Kaunas, Lithuania; (T.K.); (R.U.)
- Baltic Institute of Advanced Technology, 01124 Vilnius, Lithuania
- Faculty of Mathematics and Informatics, Vilnius University, 03225 Vilnius, Lithuania
| | - Monika Zdanytė
- Department of Cardiology and Cardiovascular Medicine, Universität Tübingen, 72074 Tübingen, Germany;
| | - Ligita Ryliškytė
- Clinic of Cardiac and Vascular Diseases, Institute of Clinical Medicine, Faculty of Medicine, Vilnius University, 08661 Vilnius, Lithuania; (A.Š.); (A.L.); (L.R.); (A.J.)
- Centre of Cardiology and Angiology, Vilnius University Hospital, Santaros Klinikos, 08410 Vilnius, Lithuania
| | - Agnė Jucevičienė
- Clinic of Cardiac and Vascular Diseases, Institute of Clinical Medicine, Faculty of Medicine, Vilnius University, 08661 Vilnius, Lithuania; (A.Š.); (A.L.); (L.R.); (A.J.)
- Centre of Cardiology and Angiology, Vilnius University Hospital, Santaros Klinikos, 08410 Vilnius, Lithuania
| | - Paul Holvoet
- Experimental Cardiology, Department of Cardiovascular Sciences, KU Leuven, 3000 Leuven, Belgium;
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14
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Mokhtari F, Mohebbi SR, Sharifian A, Ramandi M, Razzaghi MR. Circulating non-coding RNAs as potential diagnostic biomarkers in liver diseases. GASTROENTEROLOGY AND HEPATOLOGY FROM BED TO BENCH 2021; 14:S10-S23. [PMID: 35154598 PMCID: PMC8817748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 08/23/2021] [Indexed: 11/07/2022]
Abstract
The liver plays a principal role in the human body as a metabolic and detoxifying unit. Liver diseases are the world's major health problems and affect millions of people worldwide. Early detection of liver diseases is certainly effective in timely treatment and prevention of their progression. Liver injury is associated with significant alterations in immune responses and pattern changes in various tissue-related gene expressions and cytokine production. Increasing or decreasing the specific spectrum of non-coding RNAs in different phases of liver disease can be a criterion for diagnosis. Novel diagnostic biomarkers are needed for liver diseases. Currently, micro-RNAs (miRNAs) are known to play important roles in the diagnosis of liver diseases. Circulating biomarkers such as miRNA-assisted diagnosis can conceivably be helpful for the early treatment of liver diseases. In this review, we look at miRNAs and their potential applications in liver diseases as diagnostic biomarkers were investigated.
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Affiliation(s)
- Fedra Mokhtari
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Seyed Reza Mohebbi
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Afsaneh Sharifian
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Marzieh Ramandi
- Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Razzaghi
- Laser Application in Medical Sciences Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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15
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Okuno J, Miyake T, Sota Y, Tanei T, Kagara N, Naoi Y, Shimoda M, Shimazu K, Kim SJ, Noguchi S. Development of Prediction Model Including MicroRNA Expression for Sentinel Lymph Node Metastasis in ER-Positive and HER2-Negative Breast Cancer. Ann Surg Oncol 2020; 28:310-319. [PMID: 32583195 DOI: 10.1245/s10434-020-08735-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Indexed: 11/18/2022]
Abstract
BACKGROUND The aim of our study is to find microRNAs (miRNAs) associated with sentinel lymph node metastasis (SLNM) and to develop a prediction model for SLNM in ER-positive and HER2-negative (ER+/HER2-) breast cancer. PATIENTS AND METHODS In the present study, only ER+/HER2- primary breast cancer was considered. The discovery set for SLNM-associated miRNAs included 10 tumors with and 10 tumors without SLNM. The training and validation sets both included 100 tumors. miRNA expression in tumors was examined comprehensively by miRNA microarray in the discovery set and by droplet digital PCR in the training and validation sets. RESULTS In the discovery set, miR-98, miR-22, and miR-223 were found to be significantly (P < 0.001, fold-change > 2.5) associated with SLNM. In the training set, we constructed the prediction model for SLNM using miR-98, tumor size, and lymphovascular invasion (LVI) with high accuracy (AUC, 0.877). The accuracy of this prediction model was confirmed in the validation set (AUC, 0.883), and it outperformed the conventional Memorial Sloan Kettering Cancer Center nomogram. In situ hybridization revealed the localization of miR-98 expression in tumor cells. CONCLUSIONS We developed a prediction model consisting of miR-98, tumor size, and LVI for SLNM with high accuracy in ER+/HER2- breast cancer. This model might help decide the indication for SLN biopsy in this subtype.
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Affiliation(s)
- Jun Okuno
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Suita City, Osaka, Japan
| | - Tomohiro Miyake
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Suita City, Osaka, Japan.
| | - Yoshiaki Sota
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Suita City, Osaka, Japan
| | - Tomonori Tanei
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Suita City, Osaka, Japan
| | - Naofumi Kagara
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Suita City, Osaka, Japan
| | - Yasuto Naoi
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Suita City, Osaka, Japan
| | - Masafumi Shimoda
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Suita City, Osaka, Japan
| | - Kenzo Shimazu
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Suita City, Osaka, Japan
| | - Seung Jin Kim
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Suita City, Osaka, Japan
| | - Shinzaburo Noguchi
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Suita City, Osaka, Japan
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16
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Valihrach L, Androvic P, Kubista M. Circulating miRNA analysis for cancer diagnostics and therapy. Mol Aspects Med 2020; 72:100825. [DOI: 10.1016/j.mam.2019.10.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 10/01/2019] [Accepted: 10/07/2019] [Indexed: 12/12/2022]
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17
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Zheng YY, Fei Y, Wang Z, Chen Y, Qiu C, Li FR. Tissue microRNAs in non-small cell lung cancer detected with a new kind of liquid bead array detection system. J Transl Med 2020; 18:108. [PMID: 32122370 PMCID: PMC7053089 DOI: 10.1186/s12967-020-02280-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 10/31/2019] [Indexed: 12/15/2022] Open
Abstract
Background Commonly used miRNA detection methods cannot be applied for high-throughput analyses. However, this study was aimed to performed a liquid bead array detection system (LBAS) to detect tissue 6 miRNAs in non-small cell lung cancer (NSCLC). Methods In this study, evaluation of LBAS was performed to observe the precision, specificity, limitation and stability. Then, a total of 52 primary NSCLC patients who received resection operation without preoperative radiotherapy and chemotherapy between June 2013 and March 2014 were selected, and then the total RNA of the tissues were extracted. We prepared six NSCLC-related miRNAs for LBAS. After optimization and evaluation, LBAS was verified by detecting the relative expression levels of 6 microRNAs in the pathological tissues and corresponding normal tissues of 52 NSCLC patients. Results The results of evaluation of LBAS showed that the Mean Fluorescence Intensity (MFI) of the reaction only added with chimeric probes and beads showed no significant change after 180 days (P > 0.05). And the intra-assay Coefficient of Variation (CV) was between 1.57 and 3.5%, while the inter-assay CV was between 4.24 and 11.27%, indicating this system was ideal for diagnostic reagents. In addition, only the beads corresponding to the additional miRNAs showed high MFIs from 8426 to 18,769, whereas the fluorescence values of the other beads were under background levels (MFIs = 20 to 55) in each reaction, indicating no cross reactivity among the miRNAs. The limit of detection of miR-21, miR-210, miR-125b, miR-155, miR-375, and miR-31 were 5.27, 1.39, 1.85, 2.01, 1.34, and 2.73 amol/μL, respectively, showing that the lowest detection limit of miRNA by this system was under pM level. Then, the relative expression levels of miR-21, miR-210, miR-125b, miR-155, miR-375, and miR-31 by using this system were significantly correlated with NSCLC (P < 0.05). And the results of AUC method indicated that specific of the LBAS system was 94.2%. Conclusions Our findings suggest that LBAS was simple, high-throughput, and freely combined with absolute quantification. Thus, this system could be applied for tumor miRNAs detection.
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Affiliation(s)
- Yuan-Yuan Zheng
- Department of Pathophysiology, The Basic Medical School, Jinan University, Guangzhou, China.,Translational Medicine Collaborative Innovation Center, The Second Clinical Medical College (Shenzhen People's Hospital), Jinan University, No. 1017 Dongmen North Road, Shenzhen, 518020, China
| | - Yun Fei
- Department of Clinical Diagnosis Laboratory, The Second Clinical Medical College (Shenzhen People's Hospital), Jinan University, Shenzhen, China
| | - Zheng Wang
- Department of Surgery, The Second Clinical Medical College (Shenzhen People's Hospital), Jinan University, Shenzhen, China
| | - Yue Chen
- Department of Clinical Diagnosis Laboratory, The Second Clinical Medical College (Shenzhen People's Hospital), Jinan University, Shenzhen, China
| | - Cheng Qiu
- Institute of Respiratory Diseases, The Second Clinical Medical College (Shenzhen People's Hospital), Jinan University, Shenzhen, China
| | - Fu-Rong Li
- Translational Medicine Collaborative Innovation Center, The Second Clinical Medical College (Shenzhen People's Hospital), Jinan University, No. 1017 Dongmen North Road, Shenzhen, 518020, China. .,Institute of Respiratory Diseases, The Second Clinical Medical College (Shenzhen People's Hospital), Jinan University, Shenzhen, China.
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18
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Hu L, Anand M, Krylova SM, Yang BB, Liu SK, Yousef GM, Krylov SN. Direct Quantitative Analysis of Multiple microRNAs (DQAMmiR) with Peptide Nucleic Acid Hybridization Probes. Anal Chem 2018; 90:14610-14615. [PMID: 30451492 DOI: 10.1021/acs.analchem.8b04793] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Direct quantitative analysis of multiple miRNAs (DQAMmiR) is a hybridization-based assay, in which the excess of the DNA hybridization probes is separated from the miRNA-probe hybrids, and the hybrids are separated from each other in gel-free capillary electrophoresis (CE) using two types of mobility shifters: single-strand DNA binding protein (SSB) added to the CE running buffer and peptide drag tags conjugated with the probes. Here we introduce the second-generation DQAMmiR, which utilizes peptide nucleic acid (PNA) rather than DNA hybridization probes and requires no SSB in the CE running buffer. PNA probes are electrically neutral, while PNA-miRNA hybrids are negatively charged, and this difference in charge can be a basis for separation of the hybrids from the probes. In this proof-of-principle work, we first experimentally confirmed that the PNA-RNA hybrid was separable from the excess of the PNA probe without SSB in the running buffer, resulting in a near 10 min time window, which would allow, theoretically, separation of up to 30 hybrids. Then, we adapted to PNA-RNA hybrids our previously developed theoretical model for predicting hybrid mobilities. The calculation performed with the modified theoretical model indicated that PNA-RNA hybrids of slightly different lengths could be separated from each other without drag tags. Accordingly, we designed a simple experimental model capable of confirming: (i) separation of tag-free hybrids of different lengths and (ii) separation of same-length hybrids due to a drag tag on the PNA probe. The experimental model included three miRNAs: 20-nt miR-147a, 20-nt miR-378g, and 22-nt miR-21. The three complementary PNA probes had lengths matching those of the corresponding target miRNAs. The probe for miR-147a had a short five-amino-acid drag tag; the other two had no drag tags. We were able to achieve baseline separation of the three hybrids from each other. The LOQ of 14 pM along with the high accuracy (recovery >90%) and precision (RSD ≈ 10%) of the assay at picomolar target concentrations suggest that PNA-facilitated DQAMmiR could potentially support practical miRNA analysis of clinical samples.
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Affiliation(s)
- Liang Hu
- Department of Chemistry and Centre for Research on Biomolecular Interactions , York University , Toronto , Ontario M3J 1P3 , Canada
| | - Mansi Anand
- Department of Chemistry and Centre for Research on Biomolecular Interactions , York University , Toronto , Ontario M3J 1P3 , Canada
| | - Svetlana M Krylova
- Department of Chemistry and Centre for Research on Biomolecular Interactions , York University , Toronto , Ontario M3J 1P3 , Canada
| | - Burton B Yang
- Sunnybrook Research Institute and Department of Laboratory Medicine and Pathobiology, Faculty of Medicine , University of Toronto , Toronto , Ontario M5S 1A8 , Canada
| | - Stanley K Liu
- Department of Radiation Oncology , Sunnybrook-Odette Cancer Centre , 2075 Bayview Avenue , Toronto , Ontario M4N 3M5 , Canada
| | - George M Yousef
- Keenan Research Centre , St. Michael's Hospital , 30 Bond Street , Toronto , Ontario M5B 1W8 , Canada
| | - Sergey N Krylov
- Department of Chemistry and Centre for Research on Biomolecular Interactions , York University , Toronto , Ontario M3J 1P3 , Canada
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19
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Gholaminejad A, Abdul Tehrani H, Gholami Fesharaki M. Identification of candidate microRNA biomarkers in renal fibrosis: a meta-analysis of profiling studies. Biomarkers 2018; 23:713-724. [DOI: 10.1080/1354750x.2018.1488275] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Alieh Gholaminejad
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Hossein Abdul Tehrani
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
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Nagarajan MB, Tentori AM, Zhang WC, Slack FJ, Doyle PS. Nonfouling, Encoded Hydrogel Microparticles for Multiplex MicroRNA Profiling Directly from Formalin-Fixed, Paraffin-Embedded Tissue. Anal Chem 2018; 90:10279-10285. [PMID: 30106558 DOI: 10.1021/acs.analchem.8b02010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
MicroRNAs (miRNA) are short, noncoding RNAs that have been implicated in many diseases, including cancers. Because miRNAs are dysregulated in disease, miRNAs show promise as highly stable biomarkers. Formalin-fixed, paraffin-embedded (FFPE) tissue is a valuable sample type to assay for biomolecules because it is a convenient storage method and is often used by pathologists for histological staining. However, extracting biomolecules from FFPE tissue is challenging because of the presence of cellular and extracellular proteins, formaldehyde cross-links, and paraffin. Moreover, most protocols to measure miRNA in FFPE tissue are time-consuming and laborious. Here, we report a simple protocol to directly measure miRNA from formalin-fixed cells, FFPE tissue sections after paraffin is removed, and FFPE tissue sections using encoded hydrogel microparticles fabricated using stop flow lithography. Measurements by these particles show agreement between formalin-fixed cells and fresh cells, and measurement of FFPE tissue with paraffin is 10% less than FFPE tissue when paraffin is removed before the assay. When normal and tumor FFPE tissue are compared using this microparticle assay, we observe differential miRNA signal for oncogenic miRNAs and tumor suppressing miRNAs. This approach reduces assay times, reduces the use of hazardous chemicals to remove paraffin, and provides a sensitive, quantitative, and multiplexed measurement of miRNA in FFPE tissue.
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Affiliation(s)
- Maxwell B Nagarajan
- Department of Chemical Engineering , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Augusto M Tentori
- Department of Chemical Engineering , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Wen Cai Zhang
- HMS Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center , Harvard Medical School , 330 Brookline Avenue , Boston , Massachusetts 02215 , United States
| | - Frank J Slack
- HMS Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center , Harvard Medical School , 330 Brookline Avenue , Boston , Massachusetts 02215 , United States
| | - Patrick S Doyle
- Department of Chemical Engineering , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
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Cui L, Markou A, Stratton CW, Lianidou E. Diagnosis and Assessment of Microbial Infections with Host and Microbial MicroRNA Profiles. ADVANCED TECHNIQUES IN DIAGNOSTIC MICROBIOLOGY 2018. [PMCID: PMC7119978 DOI: 10.1007/978-3-319-95111-9_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
MicroRNAs (miRNAs) encoded by viral genome or host have been found participating in host-microbe interactions. Differential expression profiles of miRNAs were shown linking to specific disease pathologies which indicated its potency as diagnostic/prognostic biomarkers of infectious disease. This was emphasized by the discovery of circulating miRNAs which were found to be remarkably stable in mammalian biofluids. Standardized methods of miRNA quantification including RNA isolation should be established before they will be ready for use in clinical practice.
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Darvasi O, Szabo PM, Nemeth K, Szabo K, Spisak S, Liko I, Czirjak S, Racz K, Igaz P, Patocs A, Butz H. Limitations of high throughput methods for miRNA expression profiles in non-functioning pituitary adenomas. Pathol Oncol Res 2017; 25:169-182. [PMID: 29043608 DOI: 10.1007/s12253-017-0330-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 10/02/2017] [Indexed: 12/24/2022]
Abstract
Microarray, RT-qPCR based arrays and next-generation-sequencing (NGS) are available high-throughput methods for miRNA profiling (miRNome). Analytical and biological performance of these methods were tested in identification of biologically relevant miRNAs in non-functioning pituitary adenomas (NFPA). miRNome of 4 normal pituitary (NP) and 8 NFPA samples was determined by these platforms and expression of 21 individual miRNAs was measured on 30 (20 NFPA and 10 NP) independent samples. Complex bioinformatics was used. 132 and 137 miRNAs were detected by all three platforms in NP and NFPA, respectively, of which 25 were differentially expressed (fold change > 2). The strongest correlation was observed between microarray and TaqMan-array, while the data obtained by NGS were the most discordant despite of various bioinformatics settings. As a technical validation we measured the expression of 21 selected miRNAs by individual RT-qPCR and we were able to validate 35.1%, 76.2% and 71.4% of the miRNAs revealed by SOLiD, TLDA and microarray result, respectively. We performed biological validation using an extended number of samples (20 NFPAs and 8 NPs). Technical and biological validation showed high correlation (p < 0.001; R = 0.96). Pathway and network analysis revealed several common pathways but no pathway showed the same activation score. Using the 25 platform-independent miRNAs developmental pathways were the top functional categories relevant for NFPA genesis. The difference among high-throughput platforms is of great importance and selection of screening method can influence experimental results. Validation by another platform is essential in order to avoid or to minimalize the platform specific errors.
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Affiliation(s)
- O Darvasi
- Hereditary Endocrine Tumors Research Group, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary
| | - P M Szabo
- Molecular Medicine Research Group, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary
| | - K Nemeth
- 2nd Department of Medicine, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - K Szabo
- 2nd Department of Medicine, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - S Spisak
- Molecular Medicine Research Group, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary
| | - I Liko
- Hereditary Endocrine Tumors Research Group, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary
| | - S Czirjak
- National Institute of Neurosurgery, Budapest, Hungary
| | - K Racz
- Molecular Medicine Research Group, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary
- 2nd Department of Medicine, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - P Igaz
- Molecular Medicine Research Group, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary
- 2nd Department of Medicine, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - A Patocs
- Hereditary Endocrine Tumors Research Group, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary
- Semmelweis University, Department of Laboratory Medicine, 46 Szentkirályi Str, Budapest, H-1088, Hungary
| | - Henriett Butz
- Molecular Medicine Research Group, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary.
- Semmelweis University, Department of Laboratory Medicine, 46 Szentkirályi Str, Budapest, H-1088, Hungary.
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Li S, Zhang F, Cui Y, Wu M, Lee C, Song J, Cao C, Chen H. Modified high-throughput quantification of plasma microRNAs in heparinized patients with coronary artery disease using heparinase. Biochem Biophys Res Commun 2017; 493:556-561. [PMID: 28867189 DOI: 10.1016/j.bbrc.2017.08.153] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 08/31/2017] [Indexed: 12/24/2022]
Abstract
Heparin, a widely used anticoagulant in cardiovascular diseases, is notorious for its inhibitory effect on qRT-PCR-based detection. Heparinase I could degrade heparin in RNA. qRT-PCR-based TaqMan Low Density Array (TLDA) technology is commonly used for circulating microRNAs (miRNAs) profiling analysis. However, the effect of heparin contamination on inhibition of miRNAs TLDA amplification, as well as the method for removing heparin during this process, are not yet well investigated. We obtained the plasma RNA samples from patients undergoing percutaneous coronary intervention (PCI) before and after heparinization (n = 26). We found that heparin suppressed the miRNAs amplification by ∼8 cycles in the TLDA assay, which was absolutely reversed after treating the RNA samples with heparinase I using the components from TLDA reverse transcription system. We further observed that heparin inhibited the miRNAs amplification by ∼4 cycles in the qRT-PCR assay, which was also reversed by heparinase I using the similar method. Furthermore, we demonstrated that plasma miR-92a and miR-155 were differentially expressed in the patients undergoing PCI tested by TLDA assay, which was validated by qRT-PCR. In conclusion, we present a simple method for the removal of heparin with heparinase I, and for the subsequent successful miRNAs TLDA or RT-qPCR amplification.
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Affiliation(s)
- Sufang Li
- Department of Cardiology, Peking University People's Hospital, Beijing, 100044, China; Beijing Key Laboratory of Early Prediction and Intervention of Acute Myocardial Infarction, Peking University People's Hospital, Beijing, 100044, China; Center for Cardiovascular Translational Research, Peking University People's Hospital, Beijing, 100044, China
| | - Feng Zhang
- Department of Cardiology, Peking University People's Hospital, Beijing, 100044, China; Beijing Key Laboratory of Early Prediction and Intervention of Acute Myocardial Infarction, Peking University People's Hospital, Beijing, 100044, China; Center for Cardiovascular Translational Research, Peking University People's Hospital, Beijing, 100044, China
| | - Yuxia Cui
- Department of Cardiology, Peking University People's Hospital, Beijing, 100044, China; Beijing Key Laboratory of Early Prediction and Intervention of Acute Myocardial Infarction, Peking University People's Hospital, Beijing, 100044, China; Center for Cardiovascular Translational Research, Peking University People's Hospital, Beijing, 100044, China
| | - Manyan Wu
- Department of Cardiology, Peking University People's Hospital, Beijing, 100044, China; Beijing Key Laboratory of Early Prediction and Intervention of Acute Myocardial Infarction, Peking University People's Hospital, Beijing, 100044, China; Center for Cardiovascular Translational Research, Peking University People's Hospital, Beijing, 100044, China
| | - Chongyou Lee
- Department of Cardiology, Peking University People's Hospital, Beijing, 100044, China; Beijing Key Laboratory of Early Prediction and Intervention of Acute Myocardial Infarction, Peking University People's Hospital, Beijing, 100044, China; Center for Cardiovascular Translational Research, Peking University People's Hospital, Beijing, 100044, China
| | - Junxian Song
- Department of Cardiology, Peking University People's Hospital, Beijing, 100044, China; Beijing Key Laboratory of Early Prediction and Intervention of Acute Myocardial Infarction, Peking University People's Hospital, Beijing, 100044, China; Center for Cardiovascular Translational Research, Peking University People's Hospital, Beijing, 100044, China
| | - Chengfu Cao
- Department of Cardiology, Peking University People's Hospital, Beijing, 100044, China; Beijing Key Laboratory of Early Prediction and Intervention of Acute Myocardial Infarction, Peking University People's Hospital, Beijing, 100044, China; Center for Cardiovascular Translational Research, Peking University People's Hospital, Beijing, 100044, China
| | - Hong Chen
- Department of Cardiology, Peking University People's Hospital, Beijing, 100044, China; Beijing Key Laboratory of Early Prediction and Intervention of Acute Myocardial Infarction, Peking University People's Hospital, Beijing, 100044, China; Center for Cardiovascular Translational Research, Peking University People's Hospital, Beijing, 100044, China.
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Patnaik SK, Kannisto ED, Mallick R, Vachani A, Yendamuri S. Whole blood microRNA expression may not be useful for screening non-small cell lung cancer. PLoS One 2017; 12:e0181926. [PMID: 28742859 PMCID: PMC5526508 DOI: 10.1371/journal.pone.0181926] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 06/28/2017] [Indexed: 12/17/2022] Open
Abstract
At least seven studies have suggested that microRNA levels in whole blood can be diagnostic for lung cancer. We conducted a large bi-institutional study to validate this. Qiagen® PAXgene™ Blood miRNA System was used to collect blood and extract RNA from it for 85 pathologic stage I-IV non-small cell lung cancer (NSCLC) cases and 76 clinically-relevant controls who had a benign pulmonary mass, or a high risk of developing lung cancer because of a history of cigarette smoking or age >60 years. Cases and controls were similar for age, gender, race, and blood hemoglobin and leukocyte but not platelet levels (0.23 and 0.26 million/μl, respectively; t test P = 0.01). Exiqon® MiRCURY™ microarrays were used to quantify microRNAs in RNA isolates. Quantification was also performed using Taqman™ microRNA reverse transcription (RT)-PCR assays for five microRNAs whose lung cancer-diagnostic potential had been suggested in seven published studies. Of the 1,941 human mature microRNAs detectable with the microarray platform, 598 (31%) were identified as expressed and reliably quantified among the study's subjects. However, none of the microRNAs was differentially expressed between cases and controls (P >0.05 at false discovery rate <5% in test using empirical Bayes-moderated t statistics). In classification analyses with leave-one-out internal cross-validation, cases and controls could be identified by microRNA expression with 47% and 50% accuracy with support vector machines and top-scoring pair methods, respectively. Cases and controls did not differ for RT-PCR-based measurements of any of the five microRNAs whose biomarker potential had been suggested by seven previous studies. Additionally, no difference for microRNA expression was noticed in microarray-based microRNA profiles of whole blood of 12 stage IA-IIIB NSCLC cases before and three-four weeks after tumor resection. These findings show that whole blood microRNA expression profiles lack diagnostic value for high-risk screening of NSCLC, though such value may exist for selective sub-groups of NSCLC and control populations.
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Affiliation(s)
- Santosh K. Patnaik
- Department of Thoracic Surgery, Roswell Park Cancer Institute, Buffalo, New York, United States of America
- Department of Surgery, State University of New York, Buffalo, New York, United States of America
- * E-mail: (SY); (SP)
| | - Eric D. Kannisto
- Department of Thoracic Surgery, Roswell Park Cancer Institute, Buffalo, New York, United States of America
| | - Reema Mallick
- Department of Surgery, University of Minnesota, Minneapolis, United States of America
| | - Anil Vachani
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Sai Yendamuri
- Department of Thoracic Surgery, Roswell Park Cancer Institute, Buffalo, New York, United States of America
- Department of Surgery, State University of New York, Buffalo, New York, United States of America
- * E-mail: (SY); (SP)
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25
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Kappel A, Keller A. miRNA assays in the clinical laboratory: workflow, detection technologies and automation aspects. Clin Chem Lab Med 2017; 55:636-647. [PMID: 27987355 DOI: 10.1515/cclm-2016-0467] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 11/01/2016] [Indexed: 12/27/2022]
Abstract
microRNAs (miRNAs) are short non-coding RNA molecules that regulate gene expression in eukaryotes. Their differential abundance is indicative or even causative for a variety of pathological processes including cancer or cardiovascular disorders. Due to their important biological function, miRNAs represent a promising class of novel biomarkers that may be used to diagnose life-threatening diseases, and to monitor disease progression. Further, they may guide treatment selection or dosage of drugs. miRNAs from blood or derived fractions are particularly interesting candidates for routine laboratory applications, as they can be measured in most clinical laboratories already today. This assures a good accessibility of respective tests. Albeit their great potential, miRNA-based diagnostic tests have not made their way yet into the clinical routine, and hence no standardized workflows have been established to measure miRNAs for patients' benefit. In this review we summarize the detection technologies and workflow options that exist to measure miRNAs, and we describe the advantages and disadvantages of each of these options. Moreover, we also provide a perspective on data analysis aspects that are vital for translation of raw data into actionable diagnostic test results.
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Affiliation(s)
- Andreas Kappel
- Siemens Healthcare GmbH, Guenther-Scharowsky-Str.1, Erlangen
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, University Hospital, Saarbruecken
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26
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Rebustini IT. A Functional MicroRNA Screening Method for Organ Morphogenesis. CURRENT PROTOCOLS IN CELL BIOLOGY 2017; 74:19.19.1-19.19.17. [PMID: 28256721 DOI: 10.1002/cpcb.15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The increasing repertoire of microRNAs expressed during organ development and their role in regulating organ morphogenesis provide a compelling need to develop methods to assess microRNA function using various in vitro and in vivo experimental models. Methods to assess microRNA function during organ morphogenesis include transfection of microRNA inhibitors (antagomirs) and activators (mimics) into mouse embryonic explanted organs using liposomes, which can potentially result in low efficiency of transfection and off-target effects. We devised a method to assess microRNA function in explanted organs by transfecting antagomirs and mimics using peptide-based nanoparticles, increasing functional microRNA targeting efficiency, and decreasing off-target effects. Our method can be applied to a variety of embryonic organs that can be explanted and provides an alternative to efficiently and functionally prioritize microRNAs during organ morphogenesis for further in vivo genetic approaches. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Ivan T Rebustini
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
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27
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Fujimoto S, Ishikawa M, Nagano M, Sakamoto A. Influence of neonatal sevoflurane exposure on nerve development-related microRNAs and behavior of rats. Biomed Res 2016; 36:347-55. [PMID: 26700589 DOI: 10.2220/biomedres.36.347] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Commonly used anesthetics adversely affect the developing brain, but the mechanisms remain unknown. We previously showed that the expressions of microRNAs (miRNAs) in major organs are affected by anesthetics. Therefore, we used TaqMan low-density array (TLDA) to analyze gene expression in the hippocampus of neonatal rats exposed to sevoflurane and performed behavioral tests after they reached adulthood to evaluate cognitive and memory function. Rat male pups at postnatal day 7 were exposed to 1.9% sevoflurane for 3 h, and the hippocampus-miRNA expression profile on postnatal day 8 was determined. Open field and fear conditioning tests conducted during postnatal weeks 7 and 8 indicated that sevoflurane-exposed rats, but not controls, exhibited anxiety-like disorders. TLDA analysis identified 20 differentially expressed miRNAs, which were not shared between postnatally and maturely sevoflurane-exposed rats. The level of rno-miR-632, which targets brain-derived neurotrophic factor and calcium channel, voltage-dependent, alpha 2/delta subunit 2, increased by 10-fold, indicating that exposure to sevoflurane during early neural development alters hippocampus-miRNA expression and may induce subsequent behavioral disorders.
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Affiliation(s)
- Saiko Fujimoto
- Department of Anesthesiology and Pain Medicine, Graduate School of Medicine, Nippon Medical School
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28
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Petrova A, Capalbo A, Jacquet L, Hazelwood-Smith S, Dafou D, Hobbs C, Arno M, Farcomeni A, Devito L, Badraiq H, Simpson M, McGrath JA, Di WL, Cheng JB, Mauro TM, Ilic D. Induced Pluripotent Stem Cell Differentiation and Three-Dimensional Tissue Formation Attenuate Clonal Epigenetic Differences in Trichohyalin. Stem Cells Dev 2016; 25:1366-75. [PMID: 27460132 PMCID: PMC5035378 DOI: 10.1089/scd.2016.0156] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 07/26/2016] [Indexed: 11/13/2022] Open
Abstract
The epigenetic background of pluripotent stem cells can influence transcriptional and functional behavior. Most of these data have been obtained in standard monolayer cell culture systems. In this study, we used exome sequencing, array comparative genomic hybridization (CGH), miRNA array, DNA methylation array, three-dimensional (3D) tissue engineering, and immunostaining to conduct a comparative analysis of two induced pluripotent stem cell (iPSC) lines used in engineering of 3D human epidermal equivalent (HEE), which more closely approximates epidermis. Exome sequencing and array CGH suggested that their genome was stable following 3 months of feeder-free culture. While the miRNAome was also not affected, ≈7% of CpG sites were differently methylated between the two lines. Analysis of the epidermal differentiation complex, a region on chromosome 1 that contains multiple genes involved in skin barrier maturation (including trichohyalin, TCHH), found that in one of the iPSC clones (iKCL004), TCHH retained a DNA methylation signature characteristic of the original somatic cells, whereas in other iPSC line (iKCL011), the TCHH methylation signature matched that of the human embryonic stem cell line KCL034. The difference between the two iPSC clones in TCHH methylation did not have an obvious effect on its expression in 3D HEE, suggesting that differentiation and tissue formation may mitigate variations in the iPSC methylome.
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Affiliation(s)
- Anastasia Petrova
- Assisted Conception Unit, Stem Cell Laboratory, Division of Women's Health, Women's Health Academic Centre, King's College London, London, United Kingdom
- St John's Institute of Dermatology, King's College London, London, United Kingdom
- Immunobiology Unit, Institute of Child Health, University College London, London, United Kingdom
| | | | - Laureen Jacquet
- Assisted Conception Unit, Stem Cell Laboratory, Division of Women's Health, Women's Health Academic Centre, King's College London, London, United Kingdom
| | - Simon Hazelwood-Smith
- Division of Genetics and Molecular Medicine, King's College London, London, United Kingdom
| | - Dimitra Dafou
- Division of Genetics and Molecular Medicine, King's College London, London, United Kingdom
| | - Carl Hobbs
- Histology Laboratory, Wolfson Centre for Age-Related Diseases, King's College London, London, United Kingdom
| | - Matthew Arno
- Genomics Centre, King's College London, London, United Kingdom
| | - Alessio Farcomeni
- Statistics Section, Department of Public Health and Infectious Diseases, Sapienza–University of Rome, Rome, Italy
| | - Liani Devito
- Assisted Conception Unit, Stem Cell Laboratory, Division of Women's Health, Women's Health Academic Centre, King's College London, London, United Kingdom
| | - Heba Badraiq
- Assisted Conception Unit, Stem Cell Laboratory, Division of Women's Health, Women's Health Academic Centre, King's College London, London, United Kingdom
| | - Michael Simpson
- Division of Genetics and Molecular Medicine, King's College London, London, United Kingdom
| | - John A McGrath
- St John's Institute of Dermatology, King's College London, London, United Kingdom
| | - Wei-Li Di
- Immunobiology Unit, Institute of Child Health, University College London, London, United Kingdom
| | - Jeffrey B Cheng
- Department of Dermatology, Veteran Affairs Medical Center, University of California San Francisco, San Francisco, California
| | - Theodora M Mauro
- Department of Dermatology, Veteran Affairs Medical Center, University of California San Francisco, San Francisco, California
| | - Dusko Ilic
- Assisted Conception Unit, Stem Cell Laboratory, Division of Women's Health, Women's Health Academic Centre, King's College London, London, United Kingdom
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29
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Abstract
Microarray is a high throughput discovery tool that has been broadly used for genomic research. Probe-target hybridization is the central concept of this technology to determine the relative abundance of nucleic acid sequences through fluorescence-based detection. In microarray experiments, variations of expression measurements can be attributed to many different sources that influence the stability and reproducibility of microarray platforms. Normalization is an essential step to reduce non-biological errors and to convert raw image data from multiple arrays (channels) to quality data for further analysis. In general, for the traditional microarray analysis, most established normalization methods are based on two assumptions: (1) the total number of target genes is large enough (>10,000); and (2) the expression level of the majority of genes is kept constant. However, microRNA (miRNA) arrays are usually spotted in low density, due to the fact that the total number of miRNAs is less than 2,000 and the majority of miRNAs are weakly or not expressed. As a result, normalization methods based on the above two assumptions are not applicable to miRNA profiling studies. In this review, we discuss a few representative microarray platforms on the market for miRNA profiling and compare the traditional methods with a few novel strategies specific for miRNA microarrays.
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Affiliation(s)
- Bin Wang
- Department of Mathematics and Statistics, University of South Alabama, 411 University BLVD N, Room 325, Mobile, AL 36688, USA; E-Mail:
| | - Yaguang Xi
- Mitchell Cancer Institute, University of South Alabama, 1660 Springhill Avenue, Mobile, AL 36604, USA
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: 1-251-445-9857; Fax: 1-251-460-6994
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30
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Noveski P, Popovska-Jankovic K, Kubelka-Sabit K, Filipovski V, Lazarevski S, Plaseski T, Plaseska-Karanfilska D. MicroRNA expression profiles in testicular biopsies of patients with impaired spermatogenesis. Andrology 2016; 4:1020-1027. [DOI: 10.1111/andr.12246] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 06/02/2016] [Accepted: 06/03/2016] [Indexed: 12/21/2022]
Affiliation(s)
- P. Noveski
- Research Center for Genetic Engineering and Biotechnology ‘Georgi D. Efremov’; Macedonian Academy of Science and Arts; Skopje Republic of Macedonia
| | - K. Popovska-Jankovic
- Research Center for Genetic Engineering and Biotechnology ‘Georgi D. Efremov’; Macedonian Academy of Science and Arts; Skopje Republic of Macedonia
| | - K. Kubelka-Sabit
- Clinical Hospital ‘Acibadem Sistina’; Skopje Republic of Macedonia
| | - V. Filipovski
- Clinical Hospital ‘Acibadem Sistina’; Skopje Republic of Macedonia
| | - S. Lazarevski
- Clinical Hospital ‘Acibadem Sistina’; Skopje Republic of Macedonia
| | - T. Plaseski
- Faculty of Medicine; Clinic of Endocrinology and Metabolic Disorders; Skopje Republic of Macedonia
| | - D. Plaseska-Karanfilska
- Research Center for Genetic Engineering and Biotechnology ‘Georgi D. Efremov’; Macedonian Academy of Science and Arts; Skopje Republic of Macedonia
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31
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Hu Y, Wang H, Chen E, Xu Z, Chen B, Lu G. Candidate microRNAs as biomarkers of thyroid carcinoma: a systematic review, meta-analysis, and experimental validation. Cancer Med 2016; 5:2602-14. [PMID: 27465286 PMCID: PMC5055193 DOI: 10.1002/cam4.811] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 06/01/2016] [Accepted: 06/04/2016] [Indexed: 01/17/2023] Open
Abstract
Thyroid cancer is one of the most common carcinomas of the endocrine system with an increasing incidence. A growing number of studies have focused on the diagnostic and prognostic values of dysregulated microRNAs (miRNAs) in thyroid carcinoma. However, differences in the measurement platforms, variations in lab protocols, and small sample sizes can make gene profiling data incomparable. A meta-review of the published studies that compared miRNA expression data of thyroid carcinoma and paired normal tissues was performed to identify potential miRNA biomarkers of thyroid carcinoma with the vote-counting strategy. Two hundred and thirty-six aberrantly expressed miRNAs were reported in 19 microRNA expression profiling studies. Among them, 138 miRNAs were reported in at least two studies. We also provided a meta-signature of differentially expressed miRNAs between individual histological types of thyroid carcinoma and normal tissues. The experimental validation with qRT-PCR analysis verified that the profiles identified with the meta-review approach could effectively discriminate papillary thyroid carcinoma tissues from paired noncancer tissues. The meta-review of miRNA expression profiling studies of thyroid carcinoma would provide information on candidate miRNAs that could potentially be used as biomarkers in thyroid carcinoma.
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Affiliation(s)
- Yiren Hu
- Department of General Surgery, The Third Clinical College of Wenzhou Medical University, Wenzhou People's Hospital, Wenzhou, China
| | - Hui Wang
- Department of General Surgery, Ningbo Yinzhou People's Hospital, Ningbo, China
| | - Ende Chen
- Department of General Surgery, The Third Clinical College of Wenzhou Medical University, Wenzhou People's Hospital, Wenzhou, China
| | - Zhifeng Xu
- Department of General Surgery, The Third Clinical College of Wenzhou Medical University, Wenzhou People's Hospital, Wenzhou, China
| | - Bi Chen
- Department of Oncological Surgery, Wenzhou People's Hospital, The Third Clinical College of Wenzhou Medical University, Wenzhou, China
| | - Guowen Lu
- Department of Thyroid and breast mininally invasive surgery, Ningbo Yinzhou People's Hospital, Ningbo, China.
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32
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How to interpret epigenetic association studies: a guide for clinicians. BONEKEY REPORTS 2016; 5:797. [PMID: 27195108 DOI: 10.1038/bonekey.2016.24] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 03/15/2016] [Indexed: 01/23/2023]
Abstract
Epigenetic mechanisms are able to alter gene expression, without altering DNA sequence, in a stable manner through cell divisions. They include, among others, the methylation of DNA cytosines and microRNAs and allow the cells to adapt to changing environmental conditions. In recent years, epigenetic association studies are providing new insights into the pathogenesis of complex disorders including prevalent skeletal disorders. Unlike the genome, the epigenome is cell and tissue specific and may change with age and a number of acquired factors. This poses particular difficulties for the design and interpretation of epigenetic studies, particularly those exploring the association of genome-wide epigenetic marks with disease phenotypes. In this report, we propose a framework to help in the critical appraisal of epigenetic association studies. In line with previous suggestions, we focus on the questions critical to appraise the validity of the study, to interpret the results and to assess the generalizability and relevance of the information.
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33
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Kichukova TM, Popov NT, Ivanov HY, Vachev TI. Circulating microRNAs as a Novel Class of Potential Diagnostic Biomarkers in Neuropsychiatric Disorders. Folia Med (Plovdiv) 2016; 57:159-72. [DOI: 10.1515/folmed-2015-0035] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 12/28/2015] [Indexed: 02/06/2023] Open
Abstract
AbstractNeuropsychiatric diseases, such as schizophrenia, bipolar disorder (BD), major depressive disorder (MDD) and autism spectrum disorder (ASD), are a huge burden on society, impairing the health of those affected, as well as their ability to learn and work. Biomarkers that reflect the dysregulations linked to neuropsychiatric diseases may potentially assist the diagnosis of these disorders. Most of these biomarkers are found in the brain tissue, which is not easily accessible. This is the challenge for the search of novel biomarkers that are present in various body fluids, including serum or plasma. As a group of important endogenous small noncoding RNAs that regulate gene expression at post-transcriptional level, microRNAs (miRNAs) play a crucial role in many physiological and pathological processes. Previously, researchers discovered that miRNAs contribute to the neurodevelopment and maturation, including neurite outgrowth, dendritogenesis and dendritic spine formation. These developments underline the significance of miRNAs as potential biomarkers for diagnosing and prognosing central nervous system diseases. Accumulated evidence indicates that there are considerable differences between the cell-free miRNA expression profiles of healthy subjects and those of patients. Therefore, circulating miRNAs are likely to become a new class of noninvasive, sensitive biomarkers. Despite the fact that little is known about the origin and functions of circulating miRNAs, their essential roles in the clinical diagnosis and prognosis of neuropsychiatric diseases make them attractive biomarkers. In this review we cover the increasing amounts of dataset that have accumulated in the last years on the use of circulating miRNAs and their values as potential biomarkers in most areas of neuropsychiatric diseases.
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34
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An integrated miRNA functional screening and target validation method for organ morphogenesis. Sci Rep 2016; 6:23215. [PMID: 26980315 PMCID: PMC4793243 DOI: 10.1038/srep23215] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 02/26/2016] [Indexed: 12/20/2022] Open
Abstract
The relative ease of identifying microRNAs and their increasing recognition as important regulators of organogenesis motivate the development of methods to efficiently assess microRNA function during organ morphogenesis. In this context, embryonic organ explants provide a reliable and reproducible system that recapitulates some of the important early morphogenetic processes during organ development. Here we present a method to target microRNA function in explanted mouse embryonic organs. Our method combines the use of peptide-based nanoparticles to transfect specific microRNA inhibitors or activators into embryonic organ explants, with a microRNA pulldown assay that allows direct identification of microRNA targets. This method provides effective assessment of microRNA function during organ morphogenesis, allows prioritization of multiple microRNAs in parallel for subsequent genetic approaches, and can be applied to a variety of embryonic organs.
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35
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Baldwin DA, Horan AD, Hesketh PJ, Mehta S. Combined RT-qPCR of mRNA and microRNA Targets within One Fluidigm Integrated Fluidic Circuit. J Biomol Tech 2016; 27:75-83. [PMID: 26977138 DOI: 10.7171/jbt.16-2702-003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The ability to profile expression levels of a large number of mRNAs and microRNAs (miRNAs) within the same sample, using a single assay method, would facilitate investigations of miRNA effects on mRNA abundance and streamline biomarker screening across multiple RNA classes. A protocol is described for reverse transcription of long RNA and miRNA targets, followed by preassay amplification of the pooled cDNAs and quantitative PCR (qPCR) detection for a mixed panel of candidate RNA biomarkers. The method provides flexibility for designing custom target panels, is robust over a range of input RNA amounts, and demonstrated a high assay success rate.
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Affiliation(s)
- Don A Baldwin
- 1 MSK/dx LLC, Philadelphia, Pennsylvania, USA; and 2 Department of Orthopaedic Surgery, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Annamarie D Horan
- 1 MSK/dx LLC, Philadelphia, Pennsylvania, USA; and 2 Department of Orthopaedic Surgery, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Patrick J Hesketh
- 1 MSK/dx LLC, Philadelphia, Pennsylvania, USA; and 2 Department of Orthopaedic Surgery, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Samir Mehta
- 1 MSK/dx LLC, Philadelphia, Pennsylvania, USA; and 2 Department of Orthopaedic Surgery, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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36
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Lee H, Shapiro SJ, Chapin SC, Doyle PS. Encoded Hydrogel Microparticles for Sensitive and Multiplex microRNA Detection Directly from Raw Cell Lysates. Anal Chem 2016; 88:3075-81. [DOI: 10.1021/acs.analchem.5b03902] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Hyewon Lee
- Department
of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Synthetic Biology & Bioengineering Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon 34141, South Korea
| | - Sarah J. Shapiro
- Department
of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Stephen C. Chapin
- Department
of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Patrick S. Doyle
- Department
of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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37
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Kiseleva Y, Ptitsyn K, Radko S, Zgoda V, Archakov A. Digital droplet PCR - a prospective technological approach to quantitative profiling of microRNA. ACTA ACUST UNITED AC 2016; 62:403-10. [DOI: 10.18097/pbmc20166204403] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
MicroRNA is a special type of regulatory molecules governing gene expression. Circulating microRNAs found in blood and other biological fluids are considered today as potential biomarkers of human pathology. Presently, quantitative alterations of particular microRNAs are revealed for a large number of oncological diseases and other disorders. The recently emerged method of digital droplet PCR (ddPCR) possesses a number of advantages making this method the most suitable for verification and validation of perspective microRNA markers of human pathologies. Among these advantages are the high accuracy and reproducibility of microRNA quantification as well as the capability to directly measure the absolute number of microRNA copies with the large dynamic range and a high throughput. The paper reviews microRNA biogenesis, the origin of circulating microRNAs, and methods used for their quantification. The special technical features of ddPCR, which make it an attractive method both for studying microRNAs as biomarkers of human pathologies and for basic research devoted to aspects of gene regulation by microRNA molecules, are also discussed.
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Affiliation(s)
| | - K.G. Ptitsyn
- Institute of Biomedical Chemistry, Moscow, Russia
| | - S.P. Radko
- Institute of Biomedical Chemistry, Moscow, Russia
| | - V.G. Zgoda
- Institute of Biomedical Chemistry, Moscow, Russia
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38
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Hofmann S, Huang Y, Paulicka P, Kappel A, Katus HA, Keller A, Meder B, Stähler CF, Gumbrecht W. Double-Stranded Ligation Assay for the Rapid Multiplex Quantification of MicroRNAs. Anal Chem 2015; 87:12104-11. [DOI: 10.1021/acs.analchem.5b02850] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Stefan Hofmann
- Department
of Bioinformatics, University of Würzburg, Würzburg, 97074, Germany
| | - Yiwei Huang
- Technology Center,
Siemens Healthcare, Erlangen, 91058, Germany
| | - Peter Paulicka
- Technology Center,
Siemens Healthcare, Erlangen, 91058, Germany
| | - Andreas Kappel
- Technology Center,
Siemens Healthcare, Erlangen, 91058, Germany
| | - Hugo A. Katus
- Internal
Medicine III, University Hospital Heidelberg, Heidelberg, 69120, Germany
| | - Andreas Keller
- Clinical
Bioinformatics, Medical Faculty, Saarland University, Saarbrücken, 66123, Germany
| | - Benjamin Meder
- Internal
Medicine III, University Hospital Heidelberg, Heidelberg, 69120, Germany
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39
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A cross comparison of technologies for the detection of microRNAs in clinical FFPE samples of hepatoblastoma patients. Sci Rep 2015; 5:10438. [PMID: 26039282 PMCID: PMC4453922 DOI: 10.1038/srep10438] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 04/13/2015] [Indexed: 01/01/2023] Open
Abstract
Although formalin fixed paraffin embedded (FFPE) tissue is a major biological source in cancer research, it is challenging to work with due to macromolecular fragmentation and nucleic acid crosslinking. Therefore, it is important to characterise the quality of data that can be obtained from FFPE samples. We have compared three independent platforms (next generation sequencing, microarray and NanoString) for profiling microRNAs (miRNAs) using clinical FFPE samples from hepatoblastoma (HB) patients. The number of detected miRNAs ranged from 228 to 345 (median=294) using the next generation sequencing platform, whereas 79 to 125 (median=112) miRNAs were identified using microarrays in three HB samples, including technical replicates. NanoString identified 299 to 372 miRNAs in two samples. Between the platforms, we observed high reproducibility and significant levels of shared detection. However, for commonly detected miRNAs, a strong correlation between platforms was not observed. Analysis of 10 additional HB samples with NanoString identified significantly overlapping miRNA expression profiles, and an alternative pattern was identified in a poorly differentiated HB with an aggressive phenotype. This investigation serves as a roadmap for future studies investigating miRNA expression in clinical FFPE samples, and as a guideline for the selection of an appropriate platform.
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40
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Wong W, Farr R, Joglekar M, Januszewski A, Hardikar A. Probe-based Real-time PCR Approaches for Quantitative Measurement of microRNAs. J Vis Exp 2015:52586. [PMID: 25938938 PMCID: PMC4541571 DOI: 10.3791/52586] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Probe-based quantitative PCR (qPCR) is a favoured method for measuring transcript abundance, since it is one of the most sensitive detection methods that provides an accurate and reproducible analysis. Probe-based chemistry offers the least background fluorescence as compared to other (dye-based) chemistries. Presently, there are several platforms available that use probe-based chemistry to quantitate transcript abundance. qPCR in a 96 well plate is the most routinely used method, however only a maximum of 96 samples or miRNAs can be tested in a single run. This is time-consuming and tedious if a large number of samples/miRNAs are to be analyzed. High-throughput probe-based platforms such as microfluidics (e.g. TaqMan Array Card) and nanofluidics arrays (e.g. OpenArray) offer ease to reproducibly and efficiently detect the abundance of multiple microRNAs in a large number of samples in a short time. Here, we demonstrate the experimental setup and protocol for miRNA quantitation from serum or plasma-EDTA samples, using probe-based chemistry and three different platforms (96 well plate, microfluidics and nanofluidics arrays) offering increasing levels of throughput.
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Affiliation(s)
- Wilson Wong
- Diabetes and Islet Biology Group, NHMRC Clinical Trials Centre, Faculty of Medicine, The University of Sydney
| | - Ryan Farr
- Diabetes and Islet Biology Group, NHMRC Clinical Trials Centre, Faculty of Medicine, The University of Sydney
| | - Mugdha Joglekar
- Diabetes and Islet Biology Group, NHMRC Clinical Trials Centre, Faculty of Medicine, The University of Sydney
| | - Andrzej Januszewski
- Biomarkers Laboratory, NHMRC Clinical Trials Centre, Faculty of Medicine, The University of Sydney
| | - Anandwardhan Hardikar
- Diabetes and Islet Biology Group, NHMRC Clinical Trials Centre, Faculty of Medicine, The University of Sydney;
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41
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Geraci NS, Tan JC, McDowell MA. Characterization of microRNA expression profiles in Leishmania-infected human phagocytes. Parasite Immunol 2015; 37:43-51. [PMID: 25376316 DOI: 10.1111/pim.12156] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 10/29/2014] [Indexed: 12/14/2022]
Abstract
Leishmania are intracellular protozoa that influence host immune responses eliciting parasite species-specific pathologies. MicroRNAs (miRNAs) are short single-stranded ribonucleic acids that complement gene transcripts to block protein translation and have been shown to regulate immune system molecular mechanisms. Human monocyte-derived dendritic cells (DC) and macrophages (MP) were infected in vitro with Leishmania major or Leishmania donovani parasites. Small RNAs were isolated from total RNA and sequenced to identify mature miRNAs associated with leishmanial infections. Normalized sequence read count profiles revealed a global downregulation in miRNA expression among host cells following infection. Most identified miRNAs were expressed at higher levels in L. donovani-infected cells relative to L. major-infected cells. Pathway enrichments using in silico-predicted gene targets of differentially expressed miRNAs showed evidence of potentially universal MAP kinase signalling pathway effects. Whereas JAK-STAT and TGF-β signalling pathways were more highly enriched using targets of miRNAs upregulated in L. donovani-infected cells, these data provide evidence in support of a selective influence on host cell miRNA expression and regulation in response to differential Leishmania infections.
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Affiliation(s)
- N S Geraci
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, USA
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42
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Butz H, Patócs A. Technical Aspects Related to the Analysis of Circulating microRNAs. EXPERIENTIA SUPPLEMENTUM (2012) 2015; 106:55-71. [PMID: 26608199 DOI: 10.1007/978-3-0348-0955-9_3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Specific and sensitive noninvasive biofluid-based biomarkers are always needed in the laboratory diagnosis of diseases. Biomarkers are applied not only for diagnostic purposes but for stratifying a disease and for assessing the therapy response or disease progression. MicroRNAs (miRNAs) are short noncoding RNA molecules regulating gene expression posttranscriptionally. They are frequently dysregulated in many physiological and pathophysiological conditions. miRNAs are present in the circulation and in other biofluids that are common matrices for clinical laboratory testing that has raised the possibility that miRNAs may serve as novel biomarkers. Their excellent stability also supports the possibility that miRNAs once will be routinely used biomarkers in clinical practice. From an analytical point of view, there are many factors (starting material, sample storage and processing, different RNA extraction and detection methods, intra- and interassay variability, and assay interferences) to consider if a miRNA as biomarker is aimed to be introduced as a clinical laboratory test. Despite several pre-analytical and analytical factors that still need standardization, a significant number of studies have been published about the potential role of circulating miRNAs as biomarkers. Due to the lack of standardization of methods, there are a lot of discrepancies among results. In this chapter, we aimed to summarize the current findings about circulating miRNAs focusing on the analytical points related to miRNAs measurements from biofluids.
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Affiliation(s)
- Henriett Butz
- Molecular Medicine Research Group, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary
- Hungarian Academy of Sciences and Semmelweis University "Lendület" Hereditary Endocrine Tumors Research Group, Budapest, Hungary
- Department of Laboratory Medicine, Semmelweis University, 46 Szentkirályi Str., 1088, Budapest, Hungary
| | - Attila Patócs
- Hungarian Academy of Sciences and Semmelweis University "Lendület" Hereditary Endocrine Tumors Research Group, Budapest, Hungary.
- Department of Laboratory Medicine, Semmelweis University, 46 Szentkirályi Str., 1088, Budapest, Hungary.
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Døssing KBV, Binderup T, Kaczkowski B, Jacobsen A, Rossing M, Winther O, Federspiel B, Knigge U, Kjær A, Friis-Hansen L. Down-Regulation of miR-129-5p and the let-7 Family in Neuroendocrine Tumors and Metastases Leads to Up-Regulation of Their Targets Egr1, G3bp1, Hmga2 and Bach1. Genes (Basel) 2014; 6:1-21. [PMID: 25546138 PMCID: PMC4377830 DOI: 10.3390/genes6010001] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 12/09/2014] [Indexed: 01/12/2023] Open
Abstract
Expression of miRNAs in Neuroendocrine Neoplasms (NEN) is poorly characterized. We therefore wanted to examine the miRNA expression in Neuroendocrine Tumors (NETs), and identify their targets and importance in NET carcinogenesis. miRNA expression in six NEN primary tumors, six NEN metastases and four normal intestinal tissues was characterized using miRNA arrays, and validated by in-situ hybridization and qPCR. Among the down-regulated miRNAs miR-129-5p and the let-7f/let-7 family, were selected for further characterization. Transfection of miR-129-5p inhibited growth of a pulmonary and an intestinal carcinoid cell line. Analysis of mRNA expression changes identified EGR1 and G3BP1 as miR-129-5p targets. They were validated by luciferase assay and western blotting, and found robustly expressed in NETs by immunohistochemistry. Knockdown of EGR1 and G3BP1 mimicked the growth inhibition induced by miR-129-5p. let-7 overexpression inhibited growth of carcinoid cell lines, and let-7 inhibition increased protein content of the transcription factor BACH1 and its targets MMP1 and HMGA2, all known to promote bone metastases. Immunohistochemistry analysis revealed that let-7 targets are highly expressed in NETs and metastases. We found down-regulation of miR-129-5p and the let-7 family, and identified new neuroendocrine specific targets for these miRNAs, which contributes to the growth and metastatic potential of these tumors.
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Affiliation(s)
- Kristina B V Døssing
- Center for Genomic Medicine, Rigshospitalet, Blegdamsvej 9, 2100 Copenhagen, Denmark.
| | - Tina Binderup
- Department of Clinical Physiology, Nuclear Medicine and PET, Rigshospitalet, Blegdamsvej 9, 2100 Copenhagen, Denmark.
| | - Bogumil Kaczkowski
- The Bioinformatics Center, Department of Biology and Biotech and Research Innovation Centre, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark.
| | - Anders Jacobsen
- The Bioinformatics Center, Department of Biology and Biotech and Research Innovation Centre, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark.
| | - Maria Rossing
- Center for Genomic Medicine, Rigshospitalet, Blegdamsvej 9, 2100 Copenhagen, Denmark.
| | - Ole Winther
- DTU Informatics, Technical University of Denmark, Anker Engelunds Vej 1, 2800 Kongens Lyngby, Denmark.
| | - Birgitte Federspiel
- Department of Pathology, Rigshospitalet, Blegdamsvej 9, 2100 Copenhagen, Denmark.
| | - Ulrich Knigge
- Cluster for Molecular Imaging, Faculty of Health Sciences, Blegdamsvej 3B, 2100 Copenhagen, Denmark.
| | - Andreas Kjær
- Department of Clinical Physiology, Nuclear Medicine and PET, Rigshospitalet, Blegdamsvej 9, 2100 Copenhagen, Denmark.
| | - Lennart Friis-Hansen
- Center for Genomic Medicine, Rigshospitalet, Blegdamsvej 9, 2100 Copenhagen, Denmark.
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Vescovo VD, Grasso M, Barbareschi M, Denti MA. MicroRNAs as lung cancer biomarkers. World J Clin Oncol 2014; 5:604-620. [PMID: 25302165 PMCID: PMC4129526 DOI: 10.5306/wjco.v5.i4.604] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 02/28/2014] [Accepted: 05/08/2014] [Indexed: 02/06/2023] Open
Abstract
Lung cancer is the leading cause of cancer mortality worldwide. Its high mortality is due to the poor prognosis of the disease caused by a late disease presentation, tumor heterogeneities within histological subtypes, and the relatively limited understanding of tumor biology. Importantly, lung cancer histological subgroups respond differently to some chemotherapeutic substances and side effects of some therapies appear to vary between subgroups. Biomarkers able to stratify for the subtype of lung cancer, prognosticate the course of disease, or predict the response to treatment are in high demand. In the last decade, microRNAs (miRNAs), measured in resected tumor samples or in fine needle aspirate samples have emerged as biomarkers for tumor diagnosis, prognosis and prediction of response to treatment, due to the ease of their detection and in their extreme specificity. Moreover, miRNAs present in sputum, in plasma, in serum or in whole blood have increasingly been explored in the last five years as less invasive biomarkers for the early detection of cancers. In this review we cover the increasing amounts of data that have accumulated in the last ten years on the use of miRNAs as lung cancer biomarkers.
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45
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Wang Y, Chen T, Tong W. miRNAs and their application in drug-induced liver injury. Biomark Med 2014; 8:161-72. [PMID: 24521012 DOI: 10.2217/bmm.13.147] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The complex miRNA regulatory network plays an important role in diverse biological activities of physiopathological processes. In addition to the discovery of and research on the extracellular miRNAs detected in multiple biofluids, the properties of tissue specificity and high stability underlie the great potential of these small miRNAs to serve as translational biomarkers for various diseases in the clinical setting, including in drug-induced liver injury. In this review, we describe the major technologies currently used and challenges in miRNA measurement and provide information on major bioinformatics resources available for current miRNA research. We also discuss novel findings in liver disease and highlight the potential of miRNAs for clinical and basic research as translational biomarkers for drug-induced liver injury.
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Affiliation(s)
- Yuping Wang
- Division of Bioinformatics & Biostatistics, National Center for Toxicological Research, US FDA, 3900 NCTR Road, Jefferson, AR 72079, USA
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46
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De Sarkar N, Roy R, Mitra JK, Ghose S, Chakraborty A, Paul RR, Mukhopadhyay I, Roy B. A quest for miRNA bio-marker: a track back approach from gingivo buccal cancer to two different types of precancers. PLoS One 2014; 9:e104839. [PMID: 25126847 PMCID: PMC4134240 DOI: 10.1371/journal.pone.0104839] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2014] [Accepted: 07/15/2014] [Indexed: 12/19/2022] Open
Abstract
Deregulation of miRNA expression may contribute to tumorigenesis and other patho-physiology associated with cancer. Using TLDA, expression of 762 miRNAs was checked in 18 pairs of gingivo buccal cancer-adjacent control tissues. Expression of significantly deregulated miRNAs was further validated in cancer and examined in two types of precancer (leukoplakia and lichen planus) tissues by primer-specific TaqMan assays. Biological implications of these miRNAs were assessed bioinformatically. Expression of hsa-miR-1293, hsa-miR-31, hsa-miR-31* and hsa-miR-7 were significantly up-regulated and those of hsa-miR-206, hsa-miR-204 and hsa-miR-133a were significantly down-regulated in all cancer samples. Expression of only hsa-miR-31 was significantly up-regulated in leukoplakia but none in lichen planus samples. Analysis of expression heterogeneity divided 18 cancer samples into clusters of 13 and 5 samples and revealed that expression of 30 miRNAs (including the above-mentioned 7 miRNAs), was significantly deregulated in the cluster of 13 samples. From database mining and pathway analysis it was observed that these miRNAs can significantly target many of the genes present in different cancer related pathways such as “proteoglycans in cancer”, PI3K-AKT etc. which play important roles in expression of different molecular features of cancer. Expression of hsa-miR-31 was significantly up-regulated in both cancer and leukoplakia tissues and, thus, may be one of the molecular markers of leukoplakia which may progress to gingivo-buccal cancer.
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Affiliation(s)
| | - Roshni Roy
- Human Genetics Unit, Indian Statistical Institute, Kolkata, India
| | - Jit Kumar Mitra
- Human Genetics Unit, Indian Statistical Institute, Kolkata, India
| | - Sandip Ghose
- Oral Pathology Department, Guru Nanak Institute of Dental Science & Research, Panihati, Kokata, India
| | | | - Ranjan Rashmi Paul
- Oral Pathology Department, Guru Nanak Institute of Dental Science & Research, Panihati, Kokata, India
| | | | - Bidyut Roy
- Human Genetics Unit, Indian Statistical Institute, Kolkata, India
- * E-mail:
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47
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Degliangeli F, Pompa PP, Fiammengo R. Nanotechnology-based strategies for the detection and quantification of microRNA. Chemistry 2014; 20:9476-92. [PMID: 24989446 DOI: 10.1002/chem.201402649] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
MicroRNAs (miRNAs) are important regulators of gene expression, and many pathological conditions, including cancer, are characterized by altered miRNA expression levels. Therefore, accurate and sensitive quantification of miRNAs may result in correct disease diagnosis establishing these small noncoding RNA transcripts as valuable biomarkers. Aiming at overcoming some limitations of conventional quantification strategies, nanotechnology is currently providing numerous significant alternatives to miRNA sensing. In this review an up-to-date account of nanotechnology-based strategies for miRNA detection and quantification is given. The topics covered are: nanoparticle-based approaches in solution, sensing based on nanostructured surfaces, combined nanoparticle/surface sensing approaches, and single-molecule approaches.
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Affiliation(s)
- Federica Degliangeli
- Center for Biomolecular Nanotechnologies@UniLe, Istituto Italiano di Tecnologia (IIT), Via Barsanti, 73010 Arnesano (Lecce) (Italy)
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48
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Evaluation of quantitative miRNA expression platforms in the microRNA quality control (miRQC) study. Nat Methods 2014; 11:809-15. [PMID: 24973947 DOI: 10.1038/nmeth.3014] [Citation(s) in RCA: 468] [Impact Index Per Article: 46.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 05/22/2014] [Indexed: 11/08/2022]
Abstract
MicroRNAs are important negative regulators of protein-coding gene expression and have been studied intensively over the past years. Several measurement platforms have been developed to determine relative miRNA abundance in biological samples using different technologies such as small RNA sequencing, reverse transcription-quantitative PCR (RT-qPCR) and (microarray) hybridization. In this study, we systematically compared 12 commercially available platforms for analysis of microRNA expression. We measured an identical set of 20 standardized positive and negative control samples, including human universal reference RNA, human brain RNA and titrations thereof, human serum samples and synthetic spikes from microRNA family members with varying homology. We developed robust quality metrics to objectively assess platform performance in terms of reproducibility, sensitivity, accuracy, specificity and concordance of differential expression. The results indicate that each method has its strengths and weaknesses, which help to guide informed selection of a quantitative microRNA gene expression platform for particular study goals.
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49
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Colombo S, Zeng X, Ragelle H, Foged C. Complexity in the therapeutic delivery of RNAi medicines: an analytical challenge. Expert Opin Drug Deliv 2014; 11:1481-95. [DOI: 10.1517/17425247.2014.927439] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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50
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Waldron PR, Holodniy M. MicroRNA and hepatitis C virus--challenges in investigation and translation: a review of the literature. Diagn Microbiol Infect Dis 2014; 80:1-12. [PMID: 24996839 DOI: 10.1016/j.diagmicrobio.2014.05.024] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 05/22/2014] [Accepted: 05/27/2014] [Indexed: 12/25/2022]
Abstract
Investigations into the role of microRNA (miRNA) in hepatitis C virus (HCV) infection, disease pathogenesis and host immune and treatment response have potential to produce innovations in diagnosis, prognosis and therapy. However, investigational challenges remain in generating clinically useful and reproducible results. We review the literature with a primary emphasis on methods and technologies used to construct our current understanding of miRNA and HCV disease. A second emphasis is to understand potential clinical research applications and provide clarification of previous study results. Many miRNA have key roles in viral and immunopathogenesis of HCV infection across multiple tissue compartments. Controversy exists among published studies regarding relative measurements, temporal changes and biological significance of specific miRNA and HCV infection. To reconcile diverging data, additional research into optimal sample processing, in vitro models, techniques for microarray differential expression of miRNAs, practices for sample result normalization, and effect of HCV genotype variation on expression are all necessary. Microarray and miRNA isolation techniques should be selected based on ability to generate reproducible results in the sample type of interest. More direct comparisons of efficacy and reliability of various multiplex microarrays and an improved consensus around miRNA normalization and quantitation are necessary so that data can be compared across studies.
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Affiliation(s)
- Paul Ravi Waldron
- Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA.
| | - Mark Holodniy
- Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA; Office of Public Health, Department of Veterans Affairs, Washington, DC
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