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Chilimoniuk J, Erol A, Rödiger S, Burdukiewicz M. Challenges and opportunities in processing NanoString nCounter data. Comput Struct Biotechnol J 2024; 23:1951-1958. [PMID: 38736697 PMCID: PMC11087919 DOI: 10.1016/j.csbj.2024.04.061] [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: 02/01/2024] [Revised: 04/25/2024] [Accepted: 04/25/2024] [Indexed: 05/14/2024] Open
Abstract
NanoString nCounter is a medium-throughput technology used in mRNA and miRNA differential expression studies. It offers several advantages, including the absence of an amplification step and the ability to analyze low-grade samples. Despite its considerable strengths, the popularity of the nCounter platform in experimental research stabilized in 2022 and 2023, and this trend may continue in the upcoming years. Such stagnation could potentially be attributed to the absence of a standardized analytical pipeline or the indication of optimal processing methods for nCounter data analysis. To standardize the description of the nCounter data analysis workflow, we divided it into five distinct steps: data pre-processing, quality control, background correction, normalization and differential expression analysis. Next, we evaluated eleven R packages dedicated to nCounter data processing to point out functionalities belonging to these steps and provide comments on their applications in studies of mRNA and miRNA samples.
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Affiliation(s)
| | - Anna Erol
- Clinical Research Centre, Medical University of Białystok, Białystok, Poland
| | - Stefan Rödiger
- Institute of Biotechnology, Faculty Environment and Natural Sciences, Brandenburg University of Technology Cottbus - Senftenberg, Senftenberg, Germany
| | - Michał Burdukiewicz
- Clinical Research Centre, Medical University of Białystok, Białystok, Poland
- Institute of Biotechnology and Biomedicine, Autonomous University of Barcelona, Barcelona, Spain
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2
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Ramzan F, Rong J, Roberts CT, O'Sullivan JM, Perry JK, Taylor R, McCowan L, Vickers MH. Maternal Plasma miRNAs as Early Biomarkers of Moderate-to-Late-Preterm Birth. Int J Mol Sci 2024; 25:9536. [PMID: 39273483 PMCID: PMC11394737 DOI: 10.3390/ijms25179536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2024] [Revised: 08/20/2024] [Accepted: 08/27/2024] [Indexed: 09/15/2024] Open
Abstract
Globally, preterm birth (PTB) is a primary cause of mortality and morbidity in infants, with PTB rates increasing worldwide over the last two decades. Biomarkers for accurate early prediction of PTB before the clinical event do not currently exist. Given their roles in the development and progression of many disease states, there has been increasing interest in the utility of microRNAs (miRNAs) as early biomarkers for pregnancy-related disorders, including PTB. The present study was designed to examine potential differences in miRNA abundances in maternal plasma from mothers with infants born following a moderate to late (28-36 weeks' gestation, n = 54) spontaneous PTB (SPTB) compared to mothers with matched term infants (n = 54). Maternal plasma collected at 15 weeks' gestation were utilised from the Auckland and Adelaide cohorts from the Screening for Pregnancy Endpoints (SCOPE) study. miRNAs in plasma were quantified using the NanoString nCounter expression panel (800 miRNAs). The top four most abundant miRNAs were significantly decreased in the plasma of mothers in the SPTB group with results consistent across both cohorts and pathway analysis was undertaken to examine the biological processes linked to the dysregulated miRNAs. The top candidate miRNAs (miRs-451a, -223-3p, let-7a-5p, and -126-3p) were linked to gene pathways associated with inflammation, apoptosis, and mitochondrial biogenesis. Moreover, miRNAs were consistently less abundant in the plasma of mothers of preterm infants across both sites, suggesting potential global dysregulation in miRNA biogenesis. This was supported by a significant downregulation in expression of key genes that are involved in miRNA biogenesis (DROSHA, DICER, and AGO2) across both sites in the SPTB group. In summary, the present study has identified miRNAs in maternal plasma that may provide predictive utility as early biomarkers for the risk of later SPTB. Importantly, these observations were conserved across two independent cohorts. Further, our data provide evidence for a persistent decrease in miRNA abundance in mothers who later experienced an SPTB, which is likely to have widespread consequences for gene regulation and epigenetic processes.
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Affiliation(s)
- Farha Ramzan
- Liggins Institute, University of Auckland, Auckland 1142, New Zealand
| | - Jing Rong
- Liggins Institute, University of Auckland, Auckland 1142, New Zealand
| | - Claire T Roberts
- Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Adelaide 5001, Australia
| | - Justin M O'Sullivan
- Liggins Institute, University of Auckland, Auckland 1142, New Zealand
- Maurice Wilkins Centre, University of Auckland, Auckland 1142, New Zealand
| | - Jo K Perry
- Liggins Institute, University of Auckland, Auckland 1142, New Zealand
- Maurice Wilkins Centre, University of Auckland, Auckland 1142, New Zealand
| | - Rennae Taylor
- Department of Obstetrics and Gynaecology, Faculty of Medical and Health Science, University of Auckland, Auckland 1142, New Zealand
| | - Lesley McCowan
- Department of Obstetrics and Gynaecology, Faculty of Medical and Health Science, University of Auckland, Auckland 1142, New Zealand
| | - Mark H Vickers
- Liggins Institute, University of Auckland, Auckland 1142, New Zealand
- Maurice Wilkins Centre, University of Auckland, Auckland 1142, New Zealand
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3
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Légaré C, Desgagné V, Thibeault K, White F, Clément AA, Poirier C, Luo ZC, Scott MS, Jacques PÉ, Perron P, Guérin R, Hivert MF, Bouchard L. First-Trimester Plasmatic microRNAs Are Associated with Fasting Glucose Levels in Late Second Trimester of Pregnancy. Biomedicines 2024; 12:1285. [PMID: 38927492 PMCID: PMC11201443 DOI: 10.3390/biomedicines12061285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 05/22/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024] Open
Abstract
Maternal blood glucose regulation adaptation to pregnancy aims to support fetal growth but may also lead to the development of gestational diabetes mellitus, the most common pregnancy complication. MiRNAs are small RNA molecules secreted and stable in the blood, where they could have paracrine hormone-like functions (ribo-hormone) and regulate metabolic processes including fetal growth and glucose metabolism. The objective of this study was to identify plasmatic microRNA (miRNAs) measured during the first trimester of pregnancy that were associated with glucose levels during a 75 g oral glucose tolerance test (OGTT) at ~26 weeks of pregnancy. miRNAs were quantified using next-generation sequencing in 444 pregnant women and replicated in an independent cohort of 106 pregnant women. MiRNAs associated with glucose levels were identified with the DESeq2 package. We identified 24 miRNAs associated with fasting glycemia, of which 18 were common to both cohorts (q-value < 0.1). However, no association was found between miRNAs and 1 h or 2 h post OGTT glycemia. To conclude, we identified 18 miRNAs early in pregnancy that were associated with fasting blood glucose measured 3 months later. Our findings offer new insights into the mechanisms involved in fasting glucose homeostasis regulation in pregnancy, which is critical to understanding how gestational diabetes develops.
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Affiliation(s)
- Cécilia Légaré
- RNA Institute, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA;
- Département des Sciences de La Santé, Université du Québec à Chicoutimi, Saguenay, QC G7H 2B1, Canada
| | - Véronique Desgagné
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences (FMHS), Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada; (V.D.); (K.T.); (A.-A.C.); (C.P.); (M.S.S.); (R.G.)
- Clinical Department of Laboratory Medicine, Centre Intégré Universitaire de Santé et de Services Sociaux (CIUSSS) du Saguenay–Lac-St-Jean, Hôpital Universitaire de Chicoutimi, Saguenay, QC G7H 5H6, Canada
| | - Kathrine Thibeault
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences (FMHS), Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada; (V.D.); (K.T.); (A.-A.C.); (C.P.); (M.S.S.); (R.G.)
| | - Frédérique White
- Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada; (F.W.); (P.-É.J.)
| | - Andrée-Anne Clément
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences (FMHS), Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada; (V.D.); (K.T.); (A.-A.C.); (C.P.); (M.S.S.); (R.G.)
| | - Cédrik Poirier
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences (FMHS), Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada; (V.D.); (K.T.); (A.-A.C.); (C.P.); (M.S.S.); (R.G.)
| | - Zhong-Cheng Luo
- Department of Obstetrics and Gynecology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Faculty of Medicine, Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON M5S 1A1, Canada;
| | - Michelle S. Scott
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences (FMHS), Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada; (V.D.); (K.T.); (A.-A.C.); (C.P.); (M.S.S.); (R.G.)
| | - Pierre-Étienne Jacques
- Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada; (F.W.); (P.-É.J.)
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CR-CHUS), Sherbrooke, QC J1H 5N4, Canada;
| | - Patrice Perron
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CR-CHUS), Sherbrooke, QC J1H 5N4, Canada;
- Department of Medicine, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada;
| | - Renée Guérin
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences (FMHS), Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada; (V.D.); (K.T.); (A.-A.C.); (C.P.); (M.S.S.); (R.G.)
- Clinical Department of Laboratory Medicine, Centre Intégré Universitaire de Santé et de Services Sociaux (CIUSSS) du Saguenay–Lac-St-Jean, Hôpital Universitaire de Chicoutimi, Saguenay, QC G7H 5H6, Canada
| | - Marie-France Hivert
- Department of Medicine, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada;
- Department of Population Medicine, Harvard Pilgrim Health Care Institute, Harvard Medical School, Boston, MA 02115, USA
- Diabetes Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Luigi Bouchard
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences (FMHS), Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada; (V.D.); (K.T.); (A.-A.C.); (C.P.); (M.S.S.); (R.G.)
- Clinical Department of Laboratory Medicine, Centre Intégré Universitaire de Santé et de Services Sociaux (CIUSSS) du Saguenay–Lac-St-Jean, Hôpital Universitaire de Chicoutimi, Saguenay, QC G7H 5H6, Canada
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CR-CHUS), Sherbrooke, QC J1H 5N4, Canada;
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Bahashwan S, Alsaadi M, Barefah A, Almahdi H, Alahwal H, Almohammadi A, Radhwi O, Daous Y, Idrees S, Almehdar H, Qadri I. Profiling of microRNAs by next-generation sequencing: Potential biomarkers for diffuse large B-cell lymphoma. J Taibah Univ Med Sci 2024; 19:619-627. [PMID: 38812724 PMCID: PMC11133910 DOI: 10.1016/j.jtumed.2024.04.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 03/27/2024] [Accepted: 04/28/2024] [Indexed: 05/31/2024] Open
Abstract
Background Lymphoma ranks fifth in prevalence among common cancer types worldwide. This lymphatic system cancer arises from T or B cells. Diffuse large B cell lymphomas (DLBCLs) are associated with most non-Hodgkin lymphomas. Non-coding microRNAs (miRNAs) greatly affect gene expression. A single miRNA can target numerous genes, thus largely influencing gene expression networks. MiRNAs can act as oncogenes or tumor suppressors in controlling DLBCL progression. This study investigated the roles of miRNAs in patients with DLBCL through next-generation sequencing, which was found to be sensitive, accurate, and robust. Methods The study involved seven patients with DLBCLs and three controls at a hematology-oncology clinic. MiRNA was extracted from existing formalin-fixed, paraffin-embedded (FFPE) tissue specimens. Illumina next-generation sequencing was used to sequence samples for miRNA profiling. Results Samples from patients showed expression of various hsa-mir miRNAs (1248, 3607, 21, 142, 1244, 182, 6516, 766, 1291, 4449, and 181a), whereas those from healthy individuals showed expression of hsa-mir 1248, 3607, 21, 142, and 877. Hsa-mir-877-3p is known to target multiple genes, and miRNAs such as hsa-mir-877-3p, hsa-mir-1291, and hsa-mir-181a-5p interact primarily with target genes. Conclusions MiRNA profiling in FFPE tissues from patients with DLBCL suggested that miRNA levels can distinguish patients with DLBCL from controls, and therefore may provide prognostic or diagnostic biomarkers for DLBCL. Altered genes and miRNAs may also be potential therapeutic targets.
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Affiliation(s)
- Salem Bahashwan
- Hematology Department, Faculty of Medicine, King Abdulaziz University, Jeddah, KSA
- Hematology Research Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, KSA
| | - Mohammed Alsaadi
- Hematology Research Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, KSA
- Department of Biological Science, Faculty of Science, King Abdulaziz University, Jeddah, KSA
| | - Ahmed Barefah
- Hematology Department, Faculty of Medicine, King Abdulaziz University, Jeddah, KSA
- Hematology Research Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, KSA
| | - Hadiah Almahdi
- Department of Biological Science, Faculty of Science, King Abdulaziz University, Jeddah, KSA
- Research and Development Unit, Al Borg Diagnostics, Jeddah, KSA
| | - Hatem Alahwal
- Hematology Department, Faculty of Medicine, King Abdulaziz University, Jeddah, KSA
- Hematology Research Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, KSA
| | - Abdullah Almohammadi
- Hematology Department, Faculty of Medicine, King Abdulaziz University, Jeddah, KSA
- Hematology Research Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, KSA
| | - Osman Radhwi
- Hematology Department, Faculty of Medicine, King Abdulaziz University, Jeddah, KSA
- Hematology Research Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, KSA
| | - Yara Daous
- Hematology Research Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, KSA
- Department of Pathology, Faculty of Medicine, King Abdulaziz University, Jeddah, KSA
| | - Sherif Idrees
- Department of Biological Science, Faculty of Science, King Abdulaziz University, Jeddah, KSA
- Research and Development Unit, Al Borg Diagnostics, Jeddah, KSA
| | - Hussien Almehdar
- Department of Biological Science, Faculty of Science, King Abdulaziz University, Jeddah, KSA
| | - Ishtiaq Qadri
- Department of Biological Science, Faculty of Science, King Abdulaziz University, Jeddah, KSA
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5
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Fattahi M, Rezaee D, Fakhari F, Najafi S, Aghaei-Zarch SM, Beyranvand P, Rashidi MA, Bagheri-Mohammadi S, Zamani-Rarani F, Bakhtiari M, Bakhtiari A, Falahi S, Kenarkoohi A, Majidpoor J, Nguyen PU. microRNA-184 in the landscape of human malignancies: a review to roles and clinical significance. Cell Death Discov 2023; 9:423. [PMID: 38001121 PMCID: PMC10673883 DOI: 10.1038/s41420-023-01718-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 11/05/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023] Open
Abstract
MicroRNAs (miRNAs) are a class of non-coding RNAs (ncRNAs) with a short length of 19-22 nucleotides. miRNAs are posttranscriptional regulators of gene expression involved in various biological processes like cell growth, apoptosis, and angiogenesis. miR-184 is a well-studied miRNA, for which most studies report its downregulation in cancer cells and tissues and experiments support its role as a tumor suppressor inhibiting malignant biological behaviors of cancer cells in vitro and in vivo. To exert its functions, miR-184 affects some signaling pathways involved in tumorigenesis like Wnt and β-catenin, and AKT/mTORC1 pathway, oncogenic factors (e.g., c-Myc) or apoptotic proteins, such as Bcl-2. Interestingly, clinical investigations have shown miR-184 with good performance as a prognostic/diagnostic biomarker for various cancers. Additionally, exogenous miR-184 in cell and xenograft animal studies suggest it as a therapeutic anticancer target. In this review, we outline the studies that evaluated the roles of miR-184 in tumorigenesis as well as its clinical significance.
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Affiliation(s)
- Mehdi Fattahi
- Institute of Research and Development, Duy Tan University, Da Nang, Vietnam
- School of Engineering & Technology, Duy Tan University, Da Nang, Vietnam
| | - Delsuz Rezaee
- School of Allied Medical Sciences, Ilam University of Medical Sciences, Ilam, Iran
| | - Fatemeh Fakhari
- Department of Toxicology and Pharmacology, School of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Sajad Najafi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Seyed Mohsen Aghaei-Zarch
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Parisa Beyranvand
- Department of Molecular Genetics, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Mohammad Amin Rashidi
- Student Research Committee, Department of Occupational Health and Safety, School of Public Health and Safety, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Saeid Bagheri-Mohammadi
- Department of Physiology and Neurophysiology Research Center, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Fahimeh Zamani-Rarani
- Department of Anatomical Sciences, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | | | - Abbas Bakhtiari
- Anatomical Sciences Department, Medical Faculty, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Shahab Falahi
- Zoonotic Diseases Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Azra Kenarkoohi
- Zoonotic Diseases Research Center, Ilam University of Medical Sciences, Ilam, Iran
- Department of Microbiology, Faculty of Medicine, Ilam University of Medical Sciences, Ilam, Iran
| | - Jamal Majidpoor
- Department of Anatomy, Faculty of Medicine, Infectious Disease Research Center, Gonabad University of Medical Sciences, Gonabad, Iran
| | - P U Nguyen
- Institute of Research and Development, Duy Tan University, Da Nang, Vietnam
- School of Engineering & Technology, Duy Tan University, Da Nang, Vietnam
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Aravindraja C, Jeepipalli S, Duncan W, Vekariya KM, Bahadekar S, Chan EKL, Kesavalu L. Unique miRomics Expression Profiles in Tannerella forsythia-Infected Mandibles during Periodontitis Using Machine Learning. Int J Mol Sci 2023; 24:16393. [PMID: 38003583 PMCID: PMC10671577 DOI: 10.3390/ijms242216393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/01/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
T. forsythia is a subgingival periodontal bacterium constituting the subgingival pathogenic polymicrobial milieu during periodontitis (PD). miRNAs play a pivotal role in maintaining periodontal tissue homeostasis at the transcriptional, post-transcriptional, and epigenetic levels. The aim of this study was to characterize the global microRNAs (miRNA, miR) expression kinetics in 8- and 16-week-old T. forsythia-infected C57BL/6J mouse mandibles and to identify the miRNA bacterial biomarkers of disease process at specific time points. We examined the differential expression (DE) of miRNAs in mouse mandibles (n = 10) using high-throughput NanoString nCounter® miRNA expression panels, which provided significant advantages over specific candidate miRNA or pathway analyses. All the T. forsythia-infected mice at two specific time points showed bacterial colonization (100%) in the gingival surface, along with a significant increase in alveolar bone resorption (ABR) (p < 0.0001). We performed a NanoString analysis of specific miRNA signatures, miRNA target pathways, and gene network analysis. A total of 115 miRNAs were DE in the mandible tissue during 8 and 16 weeks The T. forsythia infection, compared with sham infection, and the majority (99) of DE miRNAs were downregulated. nCounter miRNA expression kinetics identified 67 downregulated miRNAs (e.g., miR-375, miR-200c, miR-200b, miR-34b-5p, miR-141) during an 8-week infection, whereas 16 upregulated miRNAs (e.g., miR-1902, miR-let-7c, miR-146a) and 32 downregulated miRNAs (e.g., miR-2135, miR-720, miR-376c) were identified during a 16-week infection. Two miRNAs, miR-375 and miR-200c, were highly downregulated with >twofold change during an 8-week infection. Six miRNAs in the 8-week infection (miR-200b, miR-141, miR-205, miR-423-3p, miR-141-3p, miR-34a-5p) and two miRNAs in the 16-week infection (miR-27a-3p, miR-15a-5p) that were downregulated have also been reported in the gingival tissue and saliva of periodontitis patients. This preclinical in vivo study identified T. forsythia-specific miRNAs (miR-let-7c, miR-210, miR-146a, miR-423-5p, miR-24, miR-218, miR-26b, miR-23a-3p) and these miRs have also been reported in the gingival tissues and saliva of periodontitis patients. Further, several DE miRNAs that are significantly upregulated (e.g., miR-101b, miR-218, miR-127, miR-24) are also associated with many systemic diseases such as atherosclerosis, Alzheimer's disease, rheumatoid arthritis, osteoarthritis, diabetes, obesity, and several cancers. In addition to DE analysis, we utilized the XGBoost (eXtreme Gradient boost) and Random Forest machine learning (ML) algorithms to assess the impact that the number of miRNA copies has on predicting whether a mouse is infected. XGBoost found that miR-339-5p was most predictive for mice infection at 16 weeks. miR-592-5p was most predictive for mice infection at 8 weeks and also when the 8-week and 16-week results were grouped together. Random Forest predicted miR-592 as most predictive at 8 weeks as well as the combined 8-week and 16-week results, but miR-423-5p was most predictive at 16 weeks. In conclusion, the expression levels of miR-375 and miR-200c family differed significantly during disease process, and these miRNAs establishes a link between T. forsythia and development of periodontitis genesis, offering new insights regarding the pathobiology of this bacterium.
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Affiliation(s)
- Chairmandurai Aravindraja
- Department of Periodontology, College of Dentistry, University of Florida, Gainesville, FL 32610, USA; (C.A.); (S.J.); (K.M.V.)
| | - Syam Jeepipalli
- Department of Periodontology, College of Dentistry, University of Florida, Gainesville, FL 32610, USA; (C.A.); (S.J.); (K.M.V.)
| | - William Duncan
- Department of Community Dentistry, College of Dentistry, University of Florida, Gainesville, FL 32610, USA;
| | - Krishna Mukesh Vekariya
- Department of Periodontology, College of Dentistry, University of Florida, Gainesville, FL 32610, USA; (C.A.); (S.J.); (K.M.V.)
| | - Sakshee Bahadekar
- Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL 32610, USA;
| | - Edward K. L. Chan
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL 32610, USA;
| | - Lakshmyya Kesavalu
- Department of Periodontology, College of Dentistry, University of Florida, Gainesville, FL 32610, USA; (C.A.); (S.J.); (K.M.V.)
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL 32610, USA;
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7
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Saviana M, Romano G, McElroy J, Nigita G, Distefano R, Toft R, Calore F, Le P, Morales DDV, Atmajoana S, Deppen S, Wang K, Lee LJ, Acunzo M, Nana-Sinkam P. A plasma miRNA-based classifier for small cell lung cancer diagnosis. Front Oncol 2023; 13:1255527. [PMID: 37869089 PMCID: PMC10585112 DOI: 10.3389/fonc.2023.1255527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 09/18/2023] [Indexed: 10/24/2023] Open
Abstract
Introduction Small cell lung cancer (SCLC) is characterized by poor prognosis and challenging diagnosis. Screening in high-risk smokers results in a reduction in lung cancer mortality, however, screening efforts are primarily focused on non-small cell lung cancer (NSCLC). SCLC diagnosis and surveillance remain significant challenges. The aberrant expression of circulating microRNAs (miRNAs/miRs) is reported in many tumors and can provide insights into the pathogenesis of tumor development and progression. Here, we conducted a comprehensive assessment of circulating miRNAs in SCLC with a goal of developing a miRNA-based classifier to assist in SCLC diagnoses. Methods We profiled deregulated circulating cell-free miRNAs in the plasma of SCLC patients. We tested selected miRNAs on a training cohort and created a classifier by integrating miRNA expression and patients' clinical data. Finally, we applied the classifier on a validation dataset. Results We determined that miR-375-3p can discriminate between SCLC and NSCLC patients, and between SCLC and Squamous Cell Carcinoma patients. Moreover, we found that a model comprising miR-375-3p, miR-320b, and miR-144-3p can be integrated with race and age to distinguish metastatic SCLC from a control group. Discussion This study proposes a miRNA-based biomarker classifier for SCLC that considers clinical demographics with specific cut offs to inform SCLC diagnosis.
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Affiliation(s)
- Michela Saviana
- Department of Internal Medicine, Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, Richmond, VA, United States
- Department of Molecular Medicine, University La Sapienza, Rome, Italy
| | - Giulia Romano
- Department of Internal Medicine, Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, Richmond, VA, United States
| | - Joseph McElroy
- Center for Biostatistics, The Ohio State University, Columbus, OH, United States
| | - Giovanni Nigita
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, United States
| | - Rosario Distefano
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, United States
| | - Robin Toft
- Department of Internal Medicine, Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, Richmond, VA, United States
| | - Federica Calore
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, United States
| | - Patricia Le
- Department of Internal Medicine, Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, Richmond, VA, United States
| | - Daniel Del Valle Morales
- Department of Internal Medicine, Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, Richmond, VA, United States
| | - Sarah Atmajoana
- Vanderbilt University Medical Center and Tennessee Valley Healthcare System, Nashville, TN, United States
| | - Stephen Deppen
- Vanderbilt University Medical Center and Tennessee Valley Healthcare System, Nashville, TN, United States
| | - Kai Wang
- Institute for System Biology, Seattle, WA, United States
| | - L. James Lee
- Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH, United States
| | - Mario Acunzo
- Department of Internal Medicine, Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, Richmond, VA, United States
| | - Patrick Nana-Sinkam
- Department of Internal Medicine, Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, Richmond, VA, United States
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8
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Aravindraja C, Jeepipalli S, Vekariya KM, Botello-Escalante R, Chan EKL, Kesavalu L. Oral Spirochete Treponema denticola Intraoral Infection Reveals Unique miR-133a, miR-486, miR-126-3p, miR-126-5p miRNA Expression Kinetics during Periodontitis. Int J Mol Sci 2023; 24:12105. [PMID: 37569480 PMCID: PMC10418472 DOI: 10.3390/ijms241512105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 07/25/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
miRNAs are major regulators of eukaryotic gene expression and host immunity, and play an important role in the inflammation-mediated pathways in periodontal disease (PD) pathogenesis. Expanding our previous observation with the global miRNA profiling using partial human mouth microbes, and lack of in vivo studies involving oral spirochete Treponema denticola-induced miRNAs, this study was designed to delineate the global miRNA expression kinetics during progression of periodontitis in mice infected with T. denticola by using NanoString nCounter® miRNA panels. All of the T. denticola-infected male and female mice at 8 and 16 weeks demonstrated bacterial colonization (100%) on the gingival surface, and an increase in alveolar bone resorption (p < 0.0001). A total of 70 miRNAs with at least 1.0-fold differential expression/regulation (DE) (26 upregulated and 44 downregulated) were identified. nCounter miRNA expression profiling identified 13 upregulated miRNAs (e.g., miR-133a, miR-378) and 25 downregulated miRNAs (e.g., miR-375, miR-34b-5p) in T. denticola-infected mouse mandibles during 8 weeks of infection, whereas 13 upregulated miRNAs (e.g., miR-486, miR-126-5p) and 19 downregulated miRNAs (miR-2135, miR-142-3p) were observed during 16 weeks of infection. One miRNA (miR-126-5p) showed significant difference between 8 and 16 weeks of infection. Interestingly, miR-126-5p has been presented as a potential biomarker in patients with periodontitis and coronary artery disease. Among the upregulated miRNAs, miR-486, miR-126-3p, miR-126-5p, miR-378a-3p, miR-22-3p, miR-151a-3p, miR-423-5p, and miR-221 were reported in human gingival plaques and saliva samples from periodontitis and with diabetes. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed various functional pathways of DE miRNAs, such as bacterial invasion of epithelial cells, Ras signaling, Fc gamma R-mediated phagocytosis, osteoclast differentiation, adherens signaling, and ubiquitin mediated proteolysis. This is the first study of DE miRNAs in mouse mandibles at different time-points of T. denticola infection; the combination of three specific miRNAs, miR-486, miR-126-3p, and miR-126-5p, may serve as an invasive biomarker of T. denticola in PD. These miRNAs may have a significant role in PD pathogenesis, and this research establishes a link between miRNA, periodontitis, and systemic diseases.
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Affiliation(s)
- Chairmandurai Aravindraja
- Department of Periodontology, College of Dentistry, University of Florida, Gainesville, FL 32610, USA; (C.A.)
| | - Syam Jeepipalli
- Department of Periodontology, College of Dentistry, University of Florida, Gainesville, FL 32610, USA; (C.A.)
| | - Krishna Mukesh Vekariya
- Department of Periodontology, College of Dentistry, University of Florida, Gainesville, FL 32610, USA; (C.A.)
| | - Ruben Botello-Escalante
- Department of Periodontology, College of Dentistry, University of Florida, Gainesville, FL 32610, USA; (C.A.)
| | - Edward K. L. Chan
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL 32610, USA
| | - Lakshmyya Kesavalu
- Department of Periodontology, College of Dentistry, University of Florida, Gainesville, FL 32610, USA; (C.A.)
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL 32610, USA
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9
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Fasoulakis Z, Kolialexi A, Mavreli D, Theodora M. MicroRnas in preeclampsia. Expert Rev Mol Diagn 2023; 23:1053-1055. [PMID: 37966969 DOI: 10.1080/14737159.2023.2284780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 11/14/2023] [Indexed: 11/17/2023]
Affiliation(s)
- Zacharias Fasoulakis
- 1st Department of Obstetrics and Gynecology, National and Kapodistrian University of Athens, Athens, Greece
| | | | - Danai Mavreli
- Department of Medical Genetics, National and Kapodistrian University of Athens Medical School, Athens, Greece
| | - Marianna Theodora
- 1st Department of Obstetrics and Gynecology, National and Kapodistrian University of Athens, Athens, Greece
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Stokes T, Cen HH, Kapranov P, Gallagher IJ, Pitsillides AA, Volmar C, Kraus WE, Johnson JD, Phillips SM, Wahlestedt C, Timmons JA. Transcriptomics for Clinical and Experimental Biology Research: Hang on a Seq. ADVANCED GENETICS (HOBOKEN, N.J.) 2023; 4:2200024. [PMID: 37288167 PMCID: PMC10242409 DOI: 10.1002/ggn2.202200024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Indexed: 06/09/2023]
Abstract
Sequencing the human genome empowers translational medicine, facilitating transcriptome-wide molecular diagnosis, pathway biology, and drug repositioning. Initially, microarrays are used to study the bulk transcriptome; but now short-read RNA sequencing (RNA-seq) predominates. Positioned as a superior technology, that makes the discovery of novel transcripts routine, most RNA-seq analyses are in fact modeled on the known transcriptome. Limitations of the RNA-seq methodology have emerged, while the design of, and the analysis strategies applied to, arrays have matured. An equitable comparison between these technologies is provided, highlighting advantages that modern arrays hold over RNA-seq. Array protocols more accurately quantify constitutively expressed protein coding genes across tissue replicates, and are more reliable for studying lower expressed genes. Arrays reveal long noncoding RNAs (lncRNA) are neither sparsely nor lower expressed than protein coding genes. Heterogeneous coverage of constitutively expressed genes observed with RNA-seq, undermines the validity and reproducibility of pathway analyses. The factors driving these observations, many of which are relevant to long-read or single-cell sequencing are discussed. As proposed herein, a reappreciation of bulk transcriptomic methods is required, including wider use of the modern high-density array data-to urgently revise existing anatomical RNA reference atlases and assist with more accurate study of lncRNAs.
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Affiliation(s)
- Tanner Stokes
- Faculty of ScienceMcMaster UniversityHamiltonL8S 4L8Canada
| | - Haoning Howard Cen
- Life Sciences InstituteUniversity of British ColumbiaVancouverV6T 1Z3Canada
| | | | - Iain J Gallagher
- School of Applied SciencesEdinburgh Napier UniversityEdinburghEH11 4BNUK
| | | | | | | | - James D. Johnson
- Life Sciences InstituteUniversity of British ColumbiaVancouverV6T 1Z3Canada
| | | | | | - James A. Timmons
- Miller School of MedicineUniversity of MiamiMiamiFL33136USA
- William Harvey Research InstituteQueen Mary University LondonLondonEC1M 6BQUK
- Augur Precision Medicine LTDStirlingFK9 5NFUK
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11
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Inagaki M, Uchiyama M, Yoshikawa-Kawabe K, Ito M, Murakami H, Gunji M, Minoshima M, Kohnoh T, Ito R, Kodama Y, Tanaka-Sakai M, Nakase A, Goto N, Tsushima Y, Mori S, Kozuka M, Otomo R, Hirai M, Fujino M, Yokoyama T. Comprehensive circulating microRNA profile as a supersensitive biomarker for early-stage lung cancer screening. J Cancer Res Clin Oncol 2023:10.1007/s00432-023-04728-9. [PMID: 37076642 PMCID: PMC10115369 DOI: 10.1007/s00432-023-04728-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 03/28/2023] [Indexed: 04/21/2023]
Abstract
PURPOSE Less-invasive early diagnosis of lung cancer is essential for improving patient survival rates. The purpose of this study is to demonstrate that serum comprehensive miRNA profile is high sensitive biomarker to early-stage lung cancer in direct comparison to the conventional blood biomarker using next-generation sequencing (NGS) technology combined with automated machine learning (AutoML). METHODS We first evaluated the reproducibility of our measurement system using Pearson's correlation coefficients between samples derived from a single pooled RNA sample. To generate comprehensive miRNA profile, we performed NGS analysis of miRNAs in 262 serum samples. Among the discovery set (57 patients with lung cancer and 57 healthy controls), 1123 miRNA-based diagnostic models for lung cancer detection were constructed and screened using AutoML technology. The diagnostic faculty of the best performance model was evaluated by inspecting the validation samples (74 patients with lung cancer and 74 healthy controls). RESULTS The Pearson's correlation coefficients between samples derived from the pooled RNA sample ≥ 0.98. In the validation analysis, the best model showed a high AUC score (0.98) and a high sensitivity for early stage lung cancer (85.7%, n = 28). Furthermore, in comparison to carcinoembryonic antigen (CEA), a conventional blood biomarker for adenocarcinoma, the miRNA-based model showed higher sensitivity for early-stage lung adenocarcinoma (CEA, 27.8%, n = 18; miRNA-based model, 77.8%, n = 18). CONCLUSION The miRNA-based diagnostic model showed a high sensitivity for lung cancer, including early-stage disease. Our study provides the experimental evidence that serum comprehensive miRNA profile can be a highly sensitive blood biomarker for early-stage lung cancer.
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Affiliation(s)
- Masayasu Inagaki
- Department of Respiratory Medicine, Japanese Red Cross Aichi Medical Center Nagoya Daiichi Hospital, 3-35 Michishita-Cho, Nakamura-Ku, Nagoya, Aichi, 453-8511, Japan
| | - Makoto Uchiyama
- Research and Development Division, ARKRAY, Inc., Yousuien-Nai, 59 Gansuin-Cho, Kamigyo-Ku, Kyoto, 602-0008, Japan.
| | - Kanae Yoshikawa-Kawabe
- Department of Pathology, Japanese Red Cross Aichi Medical Center Nagoya Daiichi Hospital, Nagoya, Aichi, 453-8511, Japan
| | - Masafumi Ito
- Department of Pathology, Japanese Red Cross Aichi Medical Center Nagoya Daiichi Hospital, Nagoya, Aichi, 453-8511, Japan
| | - Hideki Murakami
- Department of Pathology, Japanese Red Cross Aichi Medical Center Nagoya Daiichi Hospital, Nagoya, Aichi, 453-8511, Japan
| | - Masaharu Gunji
- Department of Cytology and Molecular Pathology, Japanese Red Cross Aichi Medical Center Nagoya Daiichi Hospital, Nagoya, Aichi, 453-8511, Japan
| | - Makoto Minoshima
- Department of Cytology and Molecular Pathology, Japanese Red Cross Aichi Medical Center Nagoya Daiichi Hospital, Nagoya, Aichi, 453-8511, Japan
| | - Takashi Kohnoh
- Department of Respiratory Medicine, Japanese Red Cross Aichi Medical Center Nagoya Daiichi Hospital, 3-35 Michishita-Cho, Nakamura-Ku, Nagoya, Aichi, 453-8511, Japan
| | - Ryota Ito
- Department of Respiratory Medicine, Japanese Red Cross Aichi Medical Center Nagoya Daiichi Hospital, 3-35 Michishita-Cho, Nakamura-Ku, Nagoya, Aichi, 453-8511, Japan
| | - Yuta Kodama
- Department of Respiratory Medicine, Japanese Red Cross Aichi Medical Center Nagoya Daiichi Hospital, 3-35 Michishita-Cho, Nakamura-Ku, Nagoya, Aichi, 453-8511, Japan
| | - Mari Tanaka-Sakai
- Department of Respiratory Medicine, Japanese Red Cross Aichi Medical Center Nagoya Daiichi Hospital, 3-35 Michishita-Cho, Nakamura-Ku, Nagoya, Aichi, 453-8511, Japan
| | - Atsushi Nakase
- Department of Respiratory Medicine, Japanese Red Cross Aichi Medical Center Nagoya Daiichi Hospital, 3-35 Michishita-Cho, Nakamura-Ku, Nagoya, Aichi, 453-8511, Japan
| | - Nozomi Goto
- Department of Respiratory Medicine, Japanese Red Cross Aichi Medical Center Nagoya Daiichi Hospital, 3-35 Michishita-Cho, Nakamura-Ku, Nagoya, Aichi, 453-8511, Japan
| | - Yusuke Tsushima
- Department of Respiratory Medicine, Japanese Red Cross Aichi Medical Center Nagoya Daiichi Hospital, 3-35 Michishita-Cho, Nakamura-Ku, Nagoya, Aichi, 453-8511, Japan
| | - Shoich Mori
- Department of Respiratory Surgery, Japanese Red Cross Aichi Medical Center Nagoya Daiichi Hospital, Nagoya, Aichi, 453-8511, Japan
| | - Masahiro Kozuka
- Research and Development Division, ARKRAY, Inc., Yousuien-Nai, 59 Gansuin-Cho, Kamigyo-Ku, Kyoto, 602-0008, Japan
| | - Ryo Otomo
- Research and Development Division, ARKRAY, Inc., Yousuien-Nai, 59 Gansuin-Cho, Kamigyo-Ku, Kyoto, 602-0008, Japan
| | - Mitsuharu Hirai
- Research and Development Division, ARKRAY, Inc., Yousuien-Nai, 59 Gansuin-Cho, Kamigyo-Ku, Kyoto, 602-0008, Japan
| | - Masahiko Fujino
- Department of Pathology, Japanese Red Cross Aichi Medical Center Nagoya Daiichi Hospital, Nagoya, Aichi, 453-8511, Japan
| | - Toshihiko Yokoyama
- Department of Respiratory Medicine, Japanese Red Cross Aichi Medical Center Nagoya Daiichi Hospital, 3-35 Michishita-Cho, Nakamura-Ku, Nagoya, Aichi, 453-8511, Japan.
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12
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Yaung KN, Yeo JG, Kumar P, Wasser M, Chew M, Ravelli A, Law AHN, Arkachaisri T, Martini A, Pisetsky DS, Albani S. Artificial intelligence and high-dimensional technologies in the theragnosis of systemic lupus erythematosus. THE LANCET. RHEUMATOLOGY 2023; 5:e151-e165. [PMID: 38251610 DOI: 10.1016/s2665-9913(23)00010-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 12/14/2022] [Accepted: 01/04/2023] [Indexed: 02/22/2023]
Abstract
Systemic lupus erythematosus is a complex, systemic autoimmune disease characterised by immune dysregulation. Pathogenesis is multifactorial, contributing to clinical heterogeneity and posing challenges for diagnosis and treatment. Although strides in treatment options have been made in the past 15 years, with the US Food and Drug Administration approval of belimumab in 2011, there are still many patients who have inadequate responses to therapy. A better understanding of underlying disease mechanisms with a holistic and multiparametric approach is required to improve clinical assessment and treatment. This Review discusses the evolution of genomics, epigenomics, transcriptomics, and proteomics in the study of systemic lupus erythematosus and ways to amalgamate these silos of data with a systems-based approach while also discussing ways to strengthen the overall process. These mechanistic insights will facilitate the discovery of functionally relevant biomarkers to guide rational therapeutic selection to improve patient outcomes.
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Affiliation(s)
- Katherine Nay Yaung
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore; Duke-NUS Medical School, Singapore.
| | - Joo Guan Yeo
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore; Duke-NUS Medical School, Singapore; Rheumatology and Immunology Service, KK Women's and Children's Hospital, Singapore
| | - Pavanish Kumar
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore
| | - Martin Wasser
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore
| | - Marvin Chew
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore
| | - Angelo Ravelli
- Direzione Scientifica, IRCCS Istituto Giannina Gaslini, Genoa, Italy; Dipartimento di Neuroscienze, Riabilitazione, Oftalmologia, Genetica e Scienze Materno-Infantili, Università degli Studi di Genova, Genoa, Italy
| | - Annie Hui Nee Law
- Duke-NUS Medical School, Singapore; Department of Rheumatology and Immunology, Singapore General Hospital, Singapore
| | - Thaschawee Arkachaisri
- Duke-NUS Medical School, Singapore; Rheumatology and Immunology Service, KK Women's and Children's Hospital, Singapore
| | | | - David S Pisetsky
- Department of Medicine and Department of Immunology, Duke University Medical Center, Durham, NC, USA; Medical Research Service, Veterans Administration Medical Center, Durham, NC, USA
| | - Salvatore Albani
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore; Duke-NUS Medical School, Singapore; Rheumatology and Immunology Service, KK Women's and Children's Hospital, Singapore
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13
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Beri D, Rodriguez M, Singh M, Liu Y, Rasquinha G, An X, Yazdanbakhsh K, Lobo CA. Identification and characterization of extracellular vesicles from red cells infected with Babesia divergens and Babesia microti. Front Cell Infect Microbiol 2022; 12:962944. [PMID: 36275032 PMCID: PMC9585353 DOI: 10.3389/fcimb.2022.962944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 09/05/2022] [Indexed: 11/21/2022] Open
Abstract
Babesiosis is a zoonosis and an important blood-borne human parasitic infection that has gained attention because of its growing infection rate in humans by transfer from animal reservoirs. Babesia represents a potential threat to the blood supply because asymptomatic infections in man are common, and blood from such donors can cause severe disease in certain recipients. Extracellular vesicles (EVs) are vesicles released by cells that contain a complex mixture of proteins, lipids, glycans, and genetic information that have been shown to play important roles in disease pathogenesis and susceptibility, as well as cell–cell communication and immune responses. In this article, we report on the identification and characterization of EVs released from red blood cells (RBCs) infected by two major human Babesia species—Babesia divergens from in vitro culture and those from an in vivo B. microti mouse infection. Using nanoparticle tracking analysis, we show that there is a range of vesicle sizes from 30 to 1,000 nm, emanating from the Babesia-infected RBC. The study of these EVs in the context of hemoparasite infection is complicated by the fact that both the parasite and the host RBC make and release vesicles into the extracellular environment. However, the EV frequency is 2- to 10-fold higher in Babesia-infected RBCs than uninfected RBCs, depending on levels of parasitemia. Using parasite-specific markers, we were able to show that ~50%–60% of all EVs contained parasite-specific markers on their surface and thus may represent the specific proportion of EVs released by infected RBCs within the EV population. Western blot analysis on purified EVs from both in vivo and in vitro infections revealed several parasite proteins that were targets of the host immune response. In addition, microRNA analysis showed that infected RBC EVs have different microRNA signature from uninfected RBC EVs, indicating a potential role as disease biomarkers. Finally, EVs were internalized by other RBCs in culture, implicating a potential role for these vesicles in cellular communication. Overall, our study points to the multiple functional implications of EVs in Babesia–host interactions and support the potential that EVs have as agents in disease pathogenesis.
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Affiliation(s)
- Divya Beri
- Department of Blood-Borne Parasites, Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY, United States
| | - Marilis Rodriguez
- Department of Blood-Borne Parasites, Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY, United States
| | - Manpreet Singh
- Department of Blood-Borne Parasites, Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY, United States
| | - Yunfeng Liu
- Department of Complement Biology, Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY, United States
| | - Giselle Rasquinha
- Department of Biology, Georgetown University, Washington, DC, United States
| | - Xiuli An
- Department of Membrane Biology, Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY, United States
| | - Karina Yazdanbakhsh
- Department of Complement Biology, Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY, United States
| | - Cheryl A. Lobo
- Department of Blood-Borne Parasites, Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY, United States
- *Correspondence: Cheryl A. Lobo,
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14
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Snoderly-Foster LJ, Olivas WM. Regulation of Parkinson's disease-associated genes by Pumilio proteins and microRNAs in SH-SY5Y neuronal cells. PLoS One 2022; 17:e0275235. [PMID: 36174040 PMCID: PMC9522289 DOI: 10.1371/journal.pone.0275235] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 09/12/2022] [Indexed: 11/18/2022] Open
Abstract
Parkinson's disease is the second most common age-related, neurodegenerative disease. A small collection of genes has been linked to Parkinson's disease including LRRK2, SAT1, and SNCA, the latter of which encodes the protein alpha-synuclein that aggregates in Lewy bodies as a hallmark of the disease. Overexpression of even wild-type versions of these genes can lead to pathogenesis, yet the regulatory mechanisms that control protein production of the genes are not fully understood. Pumilio proteins belong to the highly conserved PUF family of eukaryotic RNA-binding proteins that post-transcriptionally regulate gene expression through binding conserved motifs in the 3' untranslated region (UTR) of mRNA targets known as PUF Recognition Elements (PREs). The 3'UTRs of LRRK2, SNCA and SAT1 each contain multiple putative PREs. Knockdown (KD) of the two human Pumilio homologs (Pumilio 1 and Pumilio 2) in a neurodegenerative model cell line, SH-SY5Y, resulted in increased SNCA and LRRK2 mRNA, as well as alpha-synuclein levels, suggesting these genes are normally repressed by the Pumilio proteins. Some studies have indicated a relationship between Pumilio and microRNA activities on the same target, especially when their binding sites are close together. LRRK2, SNCA, and SAT1 each contain several putative microRNA-binding sites within the 3'UTR, some of which reside near PREs. Small RNA-seq and microRNA qPCR assays were performed in both wild type and Pumilio KD SH-SY5Y cells to analyze global and differential microRNA expression. One thousand four hundred and four microRNAs were detected across wild type and Pumilio KD cells. Twenty-one microRNAs were differentially expressed between treatments, six of which were previously established to be altered in Parkinson's disease patient samples or research models. Expression of ten miRs predicted to target LRRK2 and SNCA was verified by RT-qPCR. Collectively, our results demonstrate that Pumilios and microRNAs play a multi-faceted role in regulating Parkinson's disease-associated genes.
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Affiliation(s)
- Lisa J. Snoderly-Foster
- Department of Biology, University of Missouri-St. Louis, St. Louis, Missouri, United States of America
| | - Wendy M. Olivas
- Department of Biology, University of Missouri-St. Louis, St. Louis, Missouri, United States of America
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Thibeault K, Légaré C, Desgagné V, White F, Clément AA, Scott MS, Jacques PÉ, Guérin R, Perron P, Hivert MF, Bouchard L. Maternal Body Mass Index Is Associated with Profile Variation in Circulating MicroRNAs at First Trimester of Pregnancy. Biomedicines 2022; 10:1726. [PMID: 35885031 PMCID: PMC9313007 DOI: 10.3390/biomedicines10071726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/13/2022] [Accepted: 07/14/2022] [Indexed: 11/20/2022] Open
Abstract
Many women enter pregnancy with overweight and obesity, which are associated with complications for both the expectant mother and her child. MicroRNAs (miRNAs) are short non-coding RNAs that regulate many biological processes, including energy metabolism. Our study aimed to identify first trimester plasmatic miRNAs associated with maternal body mass index (BMI) in early pregnancy. We sequenced a total of 658 plasma samples collected between the 4th and 16th week of pregnancy from two independent prospective birth cohorts (Gen3G and 3D). In each cohort, we assessed associations between early pregnancy maternal BMI and plasmatic miRNAs using DESeq2 R package, adjusting for sequencing run and lane, gestational age, maternal age at the first trimester of pregnancy and parity. A total of 38 miRNAs were associated (FDR q < 0.05) with BMI in the Gen3G cohort and were replicated (direction and magnitude of the fold change) in the 3D cohort, including 22 with a nominal p-value < 0.05. Some of these miRNAs were enriched in fatty acid metabolism-related pathways. We identified first trimester plasmatic miRNAs associated with maternal BMI. These miRNAs potentially regulate fatty acid metabolism-related pathways, supporting the hypothesis of their potential contribution to energy metabolism regulation in early pregnancy.
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Affiliation(s)
- Kathrine Thibeault
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences (FMHS), Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada; (K.T.); (C.L.); (V.D.); (A.-A.C.); (M.S.S.); (R.G.)
| | - Cécilia Légaré
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences (FMHS), Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada; (K.T.); (C.L.); (V.D.); (A.-A.C.); (M.S.S.); (R.G.)
| | - Véronique Desgagné
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences (FMHS), Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada; (K.T.); (C.L.); (V.D.); (A.-A.C.); (M.S.S.); (R.G.)
- Clinical Department of Laboratory Medicine, Centre Intégré Universitaire de Santé et de Services Sociaux (CIUSSS) du Saguenay-Lac-Saint-Jean—Hôpital de Chicoutimi, Saguenay, QC G7H 5H6, Canada
| | - Frédérique White
- Département de Biologie, Faculté des Science, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada; (F.W.); (P.-É.J.)
| | - Andrée-Anne Clément
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences (FMHS), Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada; (K.T.); (C.L.); (V.D.); (A.-A.C.); (M.S.S.); (R.G.)
| | - Michelle S. Scott
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences (FMHS), Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada; (K.T.); (C.L.); (V.D.); (A.-A.C.); (M.S.S.); (R.G.)
| | - Pierre-Étienne Jacques
- Département de Biologie, Faculté des Science, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada; (F.W.); (P.-É.J.)
- Department of Medicine, FMHS, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada;
| | - Renée Guérin
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences (FMHS), Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada; (K.T.); (C.L.); (V.D.); (A.-A.C.); (M.S.S.); (R.G.)
- Clinical Department of Laboratory Medicine, Centre Intégré Universitaire de Santé et de Services Sociaux (CIUSSS) du Saguenay-Lac-Saint-Jean—Hôpital de Chicoutimi, Saguenay, QC G7H 5H6, Canada
| | - Patrice Perron
- Department of Medicine, FMHS, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada;
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CR-CHUS), Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada;
| | - Marie-France Hivert
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CR-CHUS), Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada;
- Department of Population Medicine, Harvard Medical School, Harvard Pilgrim Health Care Institute, Boston, MA 02115, USA
- Diabetes Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Luigi Bouchard
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences (FMHS), Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada; (K.T.); (C.L.); (V.D.); (A.-A.C.); (M.S.S.); (R.G.)
- Clinical Department of Laboratory Medicine, Centre Intégré Universitaire de Santé et de Services Sociaux (CIUSSS) du Saguenay-Lac-Saint-Jean—Hôpital de Chicoutimi, Saguenay, QC G7H 5H6, Canada
- Department of Medicine, FMHS, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada;
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Sabina S, Panico A, Mincarone P, Leo CG, Garbarino S, Grassi T, Bagordo F, De Donno A, Scoditti E, Tumolo MR. Expression and Biological Functions of miRNAs in Chronic Pain: A Review on Human Studies. Int J Mol Sci 2022; 23:ijms23116016. [PMID: 35682695 PMCID: PMC9181121 DOI: 10.3390/ijms23116016] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/24/2022] [Accepted: 05/26/2022] [Indexed: 02/01/2023] Open
Abstract
Chronic pain is a major public health problem and an economic burden worldwide. However, its underlying pathological mechanisms remain unclear. MicroRNAs (miRNAs) are a class of small noncoding RNAs that post-transcriptionally regulate gene expression and serve key roles in physiological and pathological processes. This review aims to synthesize the human studies examining miRNA expression in the pathogenesis of chronic primary pain and chronic secondary pain. Additionally, to understand the potential pathophysiological impact of miRNAs in these conditions, an in silico analysis was performed to reveal the target genes and pathways involved in primary and secondary pain and their differential regulation in the different types of chronic pain. The findings, methodological issues and challenges of miRNA research in the pathophysiology of chronic pain are discussed. The available evidence suggests the potential role of miRNA in disease pathogenesis and possibly the pain process, eventually enabling this role to be exploited for pain monitoring and management.
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Affiliation(s)
- Saverio Sabina
- Institute of Clinical Physiology, National Research Council, Via Monteroni, 73100 Lecce, Italy; (S.S.); (C.G.L.); (M.R.T.)
| | - Alessandra Panico
- Department of Biological and Environmental Sciences and Technology, University of Salento, Via Monteroni, 73100 Lecce, Italy; (A.P.); (T.G.); (A.D.D.)
| | - Pierpaolo Mincarone
- Institute for Research on Population and Social Policies, National Research Council, c/o ex Osp. Di Summa, Piazza Di Summa, 72100 Brindisi, Italy;
| | - Carlo Giacomo Leo
- Institute of Clinical Physiology, National Research Council, Via Monteroni, 73100 Lecce, Italy; (S.S.); (C.G.L.); (M.R.T.)
| | - Sergio Garbarino
- Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics and Maternal/Child Sciences, University of Genoa, 16132 Genoa, Italy;
| | - Tiziana Grassi
- Department of Biological and Environmental Sciences and Technology, University of Salento, Via Monteroni, 73100 Lecce, Italy; (A.P.); (T.G.); (A.D.D.)
| | - Francesco Bagordo
- Department of Pharmacy-Pharmaceutical Science, University of Bari Aldo Moro, Via Edoardo Orabona, 70126 Bari, Italy;
| | - Antonella De Donno
- Department of Biological and Environmental Sciences and Technology, University of Salento, Via Monteroni, 73100 Lecce, Italy; (A.P.); (T.G.); (A.D.D.)
| | - Egeria Scoditti
- Institute of Clinical Physiology, National Research Council, Via Monteroni, 73100 Lecce, Italy; (S.S.); (C.G.L.); (M.R.T.)
- Correspondence: ; Tel.: +39-(08)-3229-8860
| | - Maria Rosaria Tumolo
- Institute of Clinical Physiology, National Research Council, Via Monteroni, 73100 Lecce, Italy; (S.S.); (C.G.L.); (M.R.T.)
- Department of Biological and Environmental Sciences and Technology, University of Salento, Via Monteroni, 73100 Lecce, Italy; (A.P.); (T.G.); (A.D.D.)
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Abstract
MicroRNAs (miRNAs) belong to a class of endogenous small noncoding RNAs that regulate gene expression at the posttranscriptional level, through both translational repression and mRNA destabilization. They are key regulators of kidney morphogenesis, modulating diverse biological processes in different renal cell lineages. Dysregulation of miRNA expression disrupts early kidney development and has been implicated in the pathogenesis of developmental kidney diseases. In this Review, we summarize current knowledge of miRNA biogenesis and function and discuss in detail the role of miRNAs in kidney morphogenesis and developmental kidney diseases, including congenital anomalies of the kidney and urinary tract and Wilms tumor. We conclude by discussing the utility of miRNAs as potentially novel biomarkers and therapeutic agents.
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Affiliation(s)
- Débora Malta Cerqueira
- Division of Nephrology, Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- John G. Rangos Sr. Research Center, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Maliha Tayeb
- Division of Nephrology, Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- John G. Rangos Sr. Research Center, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Jacqueline Ho
- Division of Nephrology, Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- John G. Rangos Sr. Research Center, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
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18
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Koh MZ, Ho WY, Yeap SK, Ali NM, Yong CY, Boo L, Alitheen NB. Exosomal-microRNA transcriptome profiling of Parental and CSC-like MDA-MB-231 cells in response to cisplatin treatment. Pathol Res Pract 2022; 233:153854. [PMID: 35398617 DOI: 10.1016/j.prp.2022.153854] [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: 09/14/2021] [Revised: 03/17/2022] [Accepted: 03/22/2022] [Indexed: 11/24/2022]
Abstract
Triple negative breast cancer (TNBC) is the most aggressive breast cancer subtype with higher risk of metastasis and cancer reoccurrence. Cisplatin is one of the potential anticancer drugs for treating TNBC, where its effectiveness remains challenged by frequent occurrence of cisplatin resistance. Since acquirement of drug resistance often being associated with presence of cancer stem cells (CSCs), investigation has been conducted, suggesting CSC-like subpopulation to be more resistant to cisplatin than their parental counterpart. On the other hand, plethora evidences showed the transmission of exosomal-miRNAs are capable of promoting drug resistance in breast cancers. In this study, we aim to elucidate the differential expression of exosomal-microRNAs profile and reveal the potential target genes in correlation to cisplatin resistance associated with CSC-like subpopulation by using TNBC cell line (MDA-MB-231). Utilizing next generation sequencing and Nanostring techniques, cisplatin-induced dysregulation of exosomal-miRNAs were evaluated in maximal for CSC-like subpopulation as compared to parental cells. Intriguingly, more oncogenic exosomal-miRNAs profile was detected from treated CSC-like subpopulation, which may correlate to enhancement of drug resistance and maintenance of CSCs. In treated CSC-like subpopulation, unique clusters of exosomal-miRNAs namely miR-221-3p, miR-196a-5p, miR-17-5p and miR-126-3p were predicted to target on six genes (ATXN1, LATS1, GSK3β, ITGA6, JAG1 and MYC), aligned with previous finding which demonstrated dysregulation of these genes in treated CSC-like subpopulation. Our results highlight the potential correlation of exosomal-miRNAs and their target genes as well as novel perspectives of the corresponding pathways that may be essential to contribute to the attenuated cytotoxicity of cisplatin in CSC-like subpopulation.
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Affiliation(s)
- May Zie Koh
- Faculty of Sciences and Engineering, University of Nottingham Malaysia, Semenyih 43500, Malaysia.
| | - Wan Yong Ho
- Faculty of Sciences and Engineering, University of Nottingham Malaysia, Semenyih 43500, Malaysia.
| | - Swee Keong Yeap
- China-ASEAN College of Marine Sciences, Xiamen University Malaysia, Sepang 43900, Malaysia.
| | - Norlaily Mohd Ali
- Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, Cheras 43000, Malaysia.
| | - Chean Yeah Yong
- Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia
| | - Lily Boo
- Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, Cheras 43000, Malaysia.
| | - Noorjahan Banu Alitheen
- Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia.
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Légaré C, Desgagné V, Poirier C, Thibeault K, White F, Clément AA, Scott MS, Jacques PÉ, Perron P, Guérin R, Hivert MF, Bouchard L. First trimester plasma microRNAs levels predict Matsuda Index-estimated insulin sensitivity between 24th and 29th week of pregnancy. BMJ Open Diabetes Res Care 2022; 10:e002703. [PMID: 35246451 PMCID: PMC8900031 DOI: 10.1136/bmjdrc-2021-002703] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 02/08/2022] [Indexed: 12/21/2022] Open
Abstract
INTRODUCTION Gestational diabetes mellitus (GDM) is a consequence of an imbalance between insulin sensitivity (IS) and secretion during pregnancy. MicroRNAs (miRNAs) are small and secreted RNA molecules stable in blood and known to regulate physiological processes including glucose homeostasis. The aim of this study was to identify plasmatic miRNAs detectable in early pregnancy predicting IS at 24th-29th week of pregnancy. RESEARCH DESIGN AND METHODS We quantified circulating miRNAs in 421 women in plasma collected at 9.6±2.2 weeks of pregnancy using next-generation sequencing. RESULTS we detected 2170 miRNAs: 39 (35 positively and 4 negatively) were associated with IS as estimated by the Matsuda Index at 26.4±1.0 weeks of pregnancy. Lasso regression identified 18 miRNAs independently predicting Matsuda Index-estimated IS. Together with gestational age, maternal age and body mass index at first trimester, they explain 36% of IS variance in late second trimester of pregnancy. These miRNAs regulate fatty acid biosynthesis and metabolism among other pathways. CONCLUSIONS In summary, we have identified first trimester plasmatic miRNAs predictive of Matsuda Index-estimated IS in late second trimester of pregnancy. These miRNAs could also contribute to initiate and support IS adaptation to pregnancy potentially through lipid metabolism regulation.
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Affiliation(s)
- Cécilia Légaré
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Véronique Desgagné
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec, Canada
- Clinical Department of Laboratory Medicine, Centre intégré universitaire de santé et de services sociaux (CIUSSS) du Saguenay-Lac-St-Jean-Hôpital Universitaire de Chicoutimi, Saguenay, Québec, Canada
| | - Cédrik Poirier
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Kathrine Thibeault
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Frédérique White
- Department of Biology, Faculty of Sciences, University of Sherbrooke, Sherbrooke, Québec, Canada
| | - Andrée-Anne Clément
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Michelle S Scott
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Pierre-Étienne Jacques
- Department of Biology, Faculty of Sciences, University of Sherbrooke, Sherbrooke, Québec, Canada
- Centre de Recherche du Centre hospitalier universitaire de Sherbrooke (CR-CHUS), Sherbrooke, Québec, Canada
| | - Patrice Perron
- Centre de Recherche du Centre hospitalier universitaire de Sherbrooke (CR-CHUS), Sherbrooke, Québec, Canada
- Department of Medicine, Faculty of Medicine and Health Sciences, University of Sherbrooke, Sherbrooke, Québec, Canada
| | - Renée Guérin
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec, Canada
- Clinical Department of Laboratory Medicine, Centre intégré universitaire de santé et de services sociaux (CIUSSS) du Saguenay-Lac-St-Jean-Hôpital Universitaire de Chicoutimi, Saguenay, Québec, Canada
| | - Marie-France Hivert
- Department of Medicine, Faculty of Medicine and Health Sciences, University of Sherbrooke, Sherbrooke, Québec, Canada
- Department of Population Medicine, Harvard Pilgrim Health Care Institute, Harvard Medical School, Boston, Massachusetts, USA
- Diabetes Unit, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Luigi Bouchard
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec, Canada
- Clinical Department of Laboratory Medicine, Centre intégré universitaire de santé et de services sociaux (CIUSSS) du Saguenay-Lac-St-Jean-Hôpital Universitaire de Chicoutimi, Saguenay, Québec, Canada
- Centre de Recherche du Centre hospitalier universitaire de Sherbrooke (CR-CHUS), Sherbrooke, Québec, Canada
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20
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Radfar S, Ghanbari R, Attaripour Isfahani A, Rezaei H, Kheirollahi M. A novel signal amplification tag to develop rapid and sensitive aptamer-based biosensors. Bioelectrochemistry 2022; 145:108087. [DOI: 10.1016/j.bioelechem.2022.108087] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 02/09/2022] [Accepted: 02/11/2022] [Indexed: 11/25/2022]
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21
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Légaré C, Clément AA, Desgagné V, Thibeault K, White F, Guay SP, Arsenault BJ, Scott MS, Jacques PÉ, Perron P, Guérin R, Hivert MF, Bouchard L. Human plasma pregnancy-associated miRNAs and their temporal variation within the first trimester of pregnancy. Reprod Biol Endocrinol 2022; 20:14. [PMID: 35031065 PMCID: PMC8759232 DOI: 10.1186/s12958-021-00883-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 12/20/2021] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND During pregnancy, maternal metabolism undergoes substantial changes to support the developing fetus. Such changes are finely regulated by different mechanisms carried out by effectors such as microRNAs (miRNAs). These small non-coding RNAs regulate numerous biological functions, mostly through post-transcriptional repression of gene expression. miRNAs are also secreted in circulation by numerous organs, such as the placenta. However, the complete plasmatic microtranscriptome of pregnant women has still not been fully described, although some miRNA clusters from the chromosome 14 (C14MC) and the chromosome 19 (C19MC and miR-371-3 cluster) have been proposed as being specific to pregnancy. Our aims were thus to describe the plasma microtranscriptome during the first trimester of pregnancy, by assessing the differences with non-pregnant women, and how it varies between the 4th and the 16th week of pregnancy. METHODS Plasmatic miRNAs from 436 pregnant (gestational week 4 to 16) and 15 non-pregnant women were quantified using Illumina HiSeq next-generation sequencing platform. Differentially abundant miRNAs were identified using DESeq2 package (FDR q-value ≤ 0.05) and their targeted biological pathways were assessed with DIANA-miRpath. RESULTS A total of 2101 miRNAs were detected, of which 191 were differentially abundant (fold change < 0.05 or > 2, FDR q-value ≤ 0.05) between pregnant and non-pregnant women. Of these, 100 miRNAs were less and 91 miRNAs were more abundant in pregnant women. Additionally, the abundance of 57 miRNAs varied according to gestational age at first trimester, of which 47 were positively and 10 were negatively associated with advancing gestational age. miRNAs from the C19MC were positively associated with both pregnancy and gestational age variation during the first trimester. Biological pathway analysis revealed that these 191 (pregnancy-specific) and 57 (gestational age markers) miRNAs targeted genes involved in fatty acid metabolism, ECM-receptor interaction and TGF-beta signaling pathways. CONCLUSION We have identified circulating miRNAs specific to pregnancy and/or that varied with gestational age in first trimester. These miRNAs target biological pathways involved in lipid metabolism as well as placenta and embryo development, suggesting a contribution to the maternal metabolic adaptation to pregnancy and fetal growth.
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Affiliation(s)
- Cécilia Légaré
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences (FMHS), Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Andrée-Anne Clément
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences (FMHS), Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Véronique Desgagné
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences (FMHS), Université de Sherbrooke, Sherbrooke, QC, Canada
- Clinical Department of Laboratory Medicine, Centre Intégré Universitaire de Santé et de Services Sociaux (CIUSSS) du Saguenay-Lac-St-Jean - Hôpital Universitaire de Chicoutimi, Pavillon des Augustines, 305 rue St-Vallier, Saguenay, QC, G7H 5H6, Canada
| | - Kathrine Thibeault
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences (FMHS), Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Frédérique White
- Department of Biology, FMHS, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Simon-Pierre Guay
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences (FMHS), Université de Sherbrooke, Sherbrooke, QC, Canada
- Department of Specialized Medicine, Division of Medical Genetics, McGill University Health Centre, Montreal, QC, Canada
| | - Benoit J Arsenault
- Centre de Recherche de L'Institut Universitaire de Cardiologie et de Pneumologie de Québec (IUCPQ), Québec, QC, Canada
- Department of Medicine, Faculty of Medicine, Université Laval, Québec, QC, Canada
| | - Michelle S Scott
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences (FMHS), Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Pierre-Étienne Jacques
- Department of Biology, FMHS, Université de Sherbrooke, Sherbrooke, QC, Canada
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CR-CHUS), Sherbrooke, QC, Canada
| | - Patrice Perron
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CR-CHUS), Sherbrooke, QC, Canada
- Department of Medicine, FMHS, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Renée Guérin
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences (FMHS), Université de Sherbrooke, Sherbrooke, QC, Canada
- Clinical Department of Laboratory Medicine, Centre Intégré Universitaire de Santé et de Services Sociaux (CIUSSS) du Saguenay-Lac-St-Jean - Hôpital Universitaire de Chicoutimi, Pavillon des Augustines, 305 rue St-Vallier, Saguenay, QC, G7H 5H6, Canada
| | - Marie-France Hivert
- Department of Population Medicine, Harvard Pilgrim Health Care Institute, Harvard Medical School, Boston, USA
- Diabetes Unit, Massachusetts General Hospital, Boston, USA
| | - Luigi Bouchard
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences (FMHS), Université de Sherbrooke, Sherbrooke, QC, Canada.
- Clinical Department of Laboratory Medicine, Centre Intégré Universitaire de Santé et de Services Sociaux (CIUSSS) du Saguenay-Lac-St-Jean - Hôpital Universitaire de Chicoutimi, Pavillon des Augustines, 305 rue St-Vallier, Saguenay, QC, G7H 5H6, Canada.
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CR-CHUS), Sherbrooke, QC, Canada.
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22
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Teerapakpinyo C, Areeruk W, Tantbirojn P, Phupong V, Shuangshoti S, Lertkhachonsuk R. MicroRNA Expression Profiling in Hydatidiform Mole for the Prediction of Postmolar GTN : MicroRNA Profile in Postmolar GTN. Technol Cancer Res Treat 2022; 21:15330338211067309. [PMID: 35023789 PMCID: PMC8785350 DOI: 10.1177/15330338211067309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Objectives: The primary aim of the study was to identify miRNAs that were differentially expressed between complete hydatidiform moles (CHMs) that turned out to be gestational trophoblastic neoplasia (GTN) [GTN moles] and CHMs that regressed spontaneously after evacuation [remission moles]. The secondary aim was to study the profiles of miRNA expressions in CHMs. Methods: A case-control study was conducted on GTN moles and remission moles. We quantitatively assessed the expression of 800 human miRNAs from molar tissues using Nanostring nCounter. Results: From a pilot study, 21 miRNAs were significantly downregulated in GTN moles compared to the remission moles. Five of them (miR-566, miR-608, miR-1226-3p, miR-548ar-3p and miR-514a-3p) were downregulated for >4 folds. MiR-608 was selected as a candidate for further analysis on 18 CHMs (9 remission moles and 9 GTN moles) due to its striking association with malignant formation. MiR-608 expression was slightly lower in GTN moles compared to the remission moles, that is, 2.22 folds change [p = 0.063]. Conclusion: We identified 21 miRNAs that were differentially expressed between GTN moles and remission moles suggesting that miRNA profiles can distinguish between the two groups. Although not reaching statistically significant, miR-608 expression was slightly lower in GTN moles compared to remission moles.
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Affiliation(s)
| | - Wilasinee Areeruk
- Department of Obstetrics and Gynecology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Patou Tantbirojn
- Department of Obstetrics and Gynecology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Vorapong Phupong
- Department of Obstetrics and Gynecology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Shanop Shuangshoti
- Department of Pathology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Ruangsak Lertkhachonsuk
- Department of Obstetrics and Gynecology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
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23
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Leo CG, Mincarone P, Tumolo MR, Panico A, Guido M, Zizza A, Guarino R, De Santis G, Sedile R, Sabina S. MiRNA expression profiling in HIV pathogenesis, disease progression and response to treatment: a systematic review. Epigenomics 2021; 13:1653-1671. [PMID: 34693727 DOI: 10.2217/epi-2021-0237] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Aim: A systematic review was conducted to identify the association of miRNA expression with HIV pathogenesis, progression and treatment. Methods: A search of articles was conducted in MEDLINE®, Cochrane Central Register of Controlled Trials and Global Health. Results: 35 articles were included. Due to the heterogeneity of HIV phenotypes, a harmonization based on key progression parameters was proposed. The hsa-miR-29 family, hsa-miR-146b-5p and hsa-miR-150-5p, are the most frequently differentially expressed in HIV. Direct comparison of studies was not possible due to heterogeneity in biological samples and miRNA analysis techniques. Conclusion: This is the first attempt to systematically identify miRNA's different expression in well-defined patient phenotypes and could represent a helpful way to increase general knowledge in this field.
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Affiliation(s)
- Carlo Giacomo Leo
- Institute of Clinical Physiology National Research Council, Branch of Lecce, 73100, Italy
| | - Pierpaolo Mincarone
- Institute for Research on Population & Social Policies National Research Council, Research Unit of Brindisi, 72100, Italy
| | - Maria Rosaria Tumolo
- Institute for Research on Population & Social Policies National Research Council, Research Unit of Brindisi, 72100, Italy
| | - Alessandra Panico
- University of Salento, Department of Biological & Environmental Sciences & Technologies, Lecce, 73039, Italy
| | - Marcello Guido
- University of Salento, Department of Biological & Environmental Sciences & Technologies, Lecce, 73039, Italy
| | - Antonella Zizza
- Institute of Clinical Physiology National Research Council, Branch of Lecce, 73100, Italy
| | - Roberto Guarino
- Institute of Clinical Physiology National Research Council, Branch of Lecce, 73100, Italy
| | - Giuseppe De Santis
- Department of Neurology, Card. G. Panico Hospital, Tricase, 73039, Italy
| | - Raffaella Sedile
- Institute of Clinical Physiology National Research Council, Branch of Lecce, 73100, Italy
| | - Saverio Sabina
- Institute of Clinical Physiology National Research Council, Branch of Lecce, 73100, Italy
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24
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Mathew R, Mattei V, Al Hashmi M, Tomei S. Updates on the Current Technologies for microRNA Profiling. Microrna 2021; 9:17-24. [PMID: 31264553 DOI: 10.2174/2211536608666190628112722] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 05/16/2019] [Accepted: 05/31/2019] [Indexed: 12/21/2022]
Abstract
MicroRNAs are RNA molecules of ~22 nt length that regulate gene expression posttranscriptionally. The role of miRNAs has been reported in many cellular processes including apoptosis, cell differentiation, development and proliferation. The dysregulated expression of miRNAs has been proposed as a biomarker for the diagnosis, onset and prognosis of human diseases. The utility of miRNA profiles to identify and discriminate patients from healthy individuals is highly dependent on the sensitivity and specificity of the technologies used for their detection and the quantity and quality of starting material. In this review, we present an update of the current technologies for the extraction, QC assessment and detection of miRNAs with special focus to the most recent methods, discussing their advantages as well as their shortcomings.
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Affiliation(s)
- Rebecca Mathew
- Omics Core and Biorepository, Sidra Medicine, Out Patient Clinic, Doha, Qatar
| | - Valentina Mattei
- Omics Core and Biorepository, Sidra Medicine, Out Patient Clinic, Doha, Qatar
| | - Muna Al Hashmi
- Omics Core and Biorepository, Sidra Medicine, Out Patient Clinic, Doha, Qatar
| | - Sara Tomei
- Omics Core and Biorepository, Sidra Medicine, Out Patient Clinic, Doha, Qatar
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25
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Determination of a microRNA signature of protective kidney ischemic preconditioning originating from proximal tubules. Sci Rep 2021; 11:9862. [PMID: 33972622 PMCID: PMC8110756 DOI: 10.1038/s41598-021-89195-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 03/17/2021] [Indexed: 12/27/2022] Open
Abstract
Ischemic preconditioning (IPC) is effective in limiting subsequent ischemic acute kidney injury in experimental models. MicroRNAs are an important class of post-transcriptional regulator and show promise as biomarkers of kidney injury. We evaluated the time- and dose-dependence of benefit from IPC in a rat model of functional (bilateral) ischemia–reperfusion injury (IRI). We found optimal protection from subsequent injury following short, repetitive sequences of preconditioning insult. We subsequently used hybridization array and microRNA sequencing to characterize microRNA signatures of protective IPC and of IRI. These approaches identified a profile of microRNA changes consequent on IRI, that were limited by prior IPC. To localize these signals within the kidney, we used laser capture microdissection and RT-qPCR to measure microRNA abundance in nephron segments, pinpointing microRNA changes principally to glomeruli and proximal tubules. Our data describe a unique microRNA signature for IRI in the rat kidney. Pulsatile IPC reduces kidney damage following IRI and diminishes this microRNA signal. We have also identified candidate microRNAs that may act as biomarkers of injury and therapeutic targets in this context.
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26
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Wang L, Shang C, Pan H, Yang H, Zhu H, Gong F. MicroRNA Expression Profiles in the Subcutaneous Adipose Tissues of Morbidly Obese Chinese Women. Obes Facts 2021; 14:1-15. [PMID: 33550286 PMCID: PMC7983571 DOI: 10.1159/000511772] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 09/20/2020] [Indexed: 12/12/2022] Open
Abstract
INTRODUCTION Obesity is a main global health issue and an outstanding cause of morbidity and mortality. Exploring miRNA profiling may help further studies on obesity. METHODS Three morbidly obese and 5 normal-weight Chinese women were enrolled in the microarray testing group. Abdominal subcutaneous adipose tissue (SAT) samples were excised. Total RNAs including miRNAs were extracted. Affymetrix GeneChip miRNA 4.0 Array was used to compare the expression profiles of miRNAs between the 2 groups. Two algorithms, miRanda and TargetScan, were used to predict target messenger RNAs (mRNAs). Bioinformatics analysis was then done based on the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. The sample sizes were further expanded to 8 morbidly obese and 9 normal-weight subjects, and quantitative real-time PCR (qRT-PCR) was utilized to verify the expression of differential miRNAs and target genes. RESULTS As per the microarray assay, 58 miRNAs were differentially expressed in the SAT from the morbidly obese and normal-weight groups (Fold >4, p < 0.01, FDR <0.05); 54 of these were downregulated and 4 were upregulated in morbidly obese subjects. A total of 1,333 target genes were jointly predicted by miRanda and TargetScan. Further bioinformatics analysis showed that the differential miRNAs were involved in 269 significant biological functions and 89 significant signaling pathways. The validation experiment by qRT-PCR showed that the expression levels of miRNA-143-5p, miRNA-143-3p, miRNA-145-5p, and let-7a-5p were downregulated in morbidly obese subjects, consistent with the microarray detection. High-mobility group A2 (HMGA2), a target gene of the downregulated miRNA let-7a-5p, was first found to be upregulated 3.19-fold in the SAT of morbidly obese Chinese women when compared to normal-weight controls. CONCLUSIONS MiRNA downregulation is a hallmark of intact SAT in a morbidly obese state. Transcription (DNA-dependent), small-molecule metabolic processes, the MAPK signaling pathway, and cancer-related pathways may play important roles in the occurrence and development of obesity. For the first time, we proved that HMGA2, a target gene of let-7a-5p, is upregulated in the SAT of morbidly obese Chinese women.
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Affiliation(s)
- Linjie Wang
- Key Laboratory of Endocrinology of National Health Commission, Department of Endocrinology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Chen Shang
- Key Laboratory of Endocrinology of National Health Commission, Department of Endocrinology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Hui Pan
- Key Laboratory of Endocrinology of National Health Commission, Department of Endocrinology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Hongbo Yang
- Key Laboratory of Endocrinology of National Health Commission, Department of Endocrinology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Huijuan Zhu
- Key Laboratory of Endocrinology of National Health Commission, Department of Endocrinology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Fengying Gong
- Key Laboratory of Endocrinology of National Health Commission, Department of Endocrinology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China,
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Jet T, Gines G, Rondelez Y, Taly V. Advances in multiplexed techniques for the detection and quantification of microRNAs. Chem Soc Rev 2021; 50:4141-4161. [PMID: 33538706 DOI: 10.1039/d0cs00609b] [Citation(s) in RCA: 127] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
MicroRNA detection is currently a crucial analytical chemistry challenge: almost 2000 papers were referenced in PubMed in 2018 and 2019 for the keywords "miRNA detection method". MicroRNAs are potential biomarkers for multiple diseases including cancers, neurodegenerative and cardiovascular diseases. Since miRNAs are stably released in bodily fluids, they are of prime interest for the development of non-invasive diagnosis methods, such as liquid biopsies. Their detection is however challenging, as high levels of sensitivity, specificity and robustness are required. The analysis also needs to be quantitative, since the aim is to detect miRNA concentration changes. Moreover, a high multiplexing capability is also of crucial importance, since the clinical potential of miRNAs probably lays in our ability to perform parallel mapping of multiple miRNA concentrations and recognize typical disease signature from this profile. A plethora of biochemical innovative detection methods have been reported recently and some of them provide new solutions to the problem of sensitive multiplex detection. In this review, we propose to analyze in particular the new developments in multiplexed approaches to miRNA detection. The main aspects of these methods (including sensitivity and specificity) will be analyzed, with a particular focus on the demonstrated multiplexing capability and potential of each of these methods.
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Affiliation(s)
- Thomas Jet
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université de Paris, CNRS SNC5096, Equipe Labellisée Ligue Nationale Contre le Cancer, F-75006 Paris, France.
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Giuliani A, Londin E, Ferracin M, Mensà E, Prattichizzo F, Ramini D, Marcheselli F, Recchioni R, Rippo MR, Bonafè M, Rigoutsos I, Olivieri F, Sabbatinelli J. Long-term exposure of human endothelial cells to metformin modulates miRNAs and isomiRs. Sci Rep 2020; 10:21782. [PMID: 33311640 PMCID: PMC7732983 DOI: 10.1038/s41598-020-78871-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 12/01/2020] [Indexed: 02/07/2023] Open
Abstract
Increasing evidence suggest that the glucose-lowering drug metformin exerts a valuable anti-senescence role. The ability of metformin to affect the biogenesis of selected microRNAs (miRNAs) was recently suggested. MicroRNA isoforms (isomiRs) are distinct variations of miRNA sequences, harboring addition or deletion of one or more nucleotides at the 5′ and/or 3′ ends of the canonical miRNA sequence. We performed a comprehensive analysis of miRNA and isomiR profile in human endothelial cells undergoing replicative senescence in presence of metformin. Metformin treatment was associated with the differential expression of 27 miRNAs (including miR-100-5p, -125b-5p, -654-3p, -217 and -216a-3p/5p). IsomiR analysis revealed that almost 40% of the total miRNA pool was composed by non-canonical sequences. Metformin significantly affects the relative abundance of 133 isomiRs, including the non-canonical forms of the aforementioned miRNAs. Pathway enrichment analysis suggested that pathways associated with proliferation and nutrient sensing are modulated by metformin-regulated miRNAs and that some of the regulated isomiRs (e.g. the 5′ miR-217 isomiR) are endowed with alternative seed sequences and share less than half of the predicted targets with the canonical form. Our results show that metformin reshapes the senescence-associated miRNA/isomiR patterns of endothelial cells, thus expanding our insight into the cell senescence molecular machinery.
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Affiliation(s)
- Angelica Giuliani
- Department of Clinical and Molecular Sciences, Università Politecnica Delle Marche, Via Tronto 10/A, 60126, Ancona, Italy
| | - Eric Londin
- Computational Medicine Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Manuela Ferracin
- Department of Experimental, Diagnostic, and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Emanuela Mensà
- Department of Clinical and Molecular Sciences, Università Politecnica Delle Marche, Via Tronto 10/A, 60126, Ancona, Italy
| | | | - Deborah Ramini
- Department of Clinical and Molecular Sciences, Università Politecnica Delle Marche, Via Tronto 10/A, 60126, Ancona, Italy
| | | | - Rina Recchioni
- Center of Clinical Pathology and Innovative Therapy, IRCCS INRCA, Ancona, Italy
| | - Maria Rita Rippo
- Department of Clinical and Molecular Sciences, Università Politecnica Delle Marche, Via Tronto 10/A, 60126, Ancona, Italy
| | - Massimiliano Bonafè
- Department of Experimental, Diagnostic, and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Isidore Rigoutsos
- Computational Medicine Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Fabiola Olivieri
- Department of Clinical and Molecular Sciences, Università Politecnica Delle Marche, Via Tronto 10/A, 60126, Ancona, Italy. .,Center of Clinical Pathology and Innovative Therapy, IRCCS INRCA, Ancona, Italy.
| | - Jacopo Sabbatinelli
- Department of Clinical and Molecular Sciences, Università Politecnica Delle Marche, Via Tronto 10/A, 60126, Ancona, Italy
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Maternal plasma miRNAs as potential biomarkers for detecting risk of small-for-gestational-age births. EBioMedicine 2020; 62:103145. [PMID: 33260001 PMCID: PMC7708817 DOI: 10.1016/j.ebiom.2020.103145] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 11/02/2020] [Accepted: 11/11/2020] [Indexed: 12/20/2022] Open
Abstract
Background Small-for-gestational-age fetuses (SGA) (birthweight <10th centile) are at high risk for stillbirth or long-term adverse outcomes. Here, we investigate the ability of circulating maternal plasma miRNAs to determine the risk of SGA births. Methods Maternal plasma samples from 29 women of whom 16 subsequently delivered normally grown babies and 13 delivered SGA (birthweight <5th centile) were selected from a total of 511 women recruited to form a discovery cohort in which expression data for a total of 800 miRNAs was determined using the Nanostring nCounter miRNA assay. Validation by RT-qPCR was performed in an independent cohort. Findings Partial least-squares discriminant analysis (PLS-DA) of the Nanostring nCounter miRNA assay initially identified seven miRNAs at 12–14+6 weeks gestation, which discriminated between SGA cases and controls. Four of these were technically validated by RT-qPCR. Differential expression of two miRNA markers; hsa-miR-374a-5p (p = 0•0176) and hsa-let-7d-5p (p = 0•0036), were validated in an independent population of 95 women (SGA n = 12, Control n = 83). In the validation cohort, which was enriched for SGA cases, the ROC AUCs were 0•71 for hsa-miR-374a-5p, and 0•74 for hsa-let-7d-5p, and 0•77 for the two combined. Interpretation Whilst larger population-wide studies are required to validate their performance, these findings highlight the potential of circulating miRNAs to act as biomarkers for early prediction of SGA births. Funding This work was supported by Genesis Research Trust, March of Dimes, and the National Institute for Health Research Biomedical Research Centre (NIHR BRC) based at Imperial Healthcare NHS Trust and Imperial College London.
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Song Y, Xu Z, Wang F. Genetically Encoded Reporter Genes for MicroRNA Imaging in Living Cells and Animals. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 21:555-567. [PMID: 32721876 PMCID: PMC7390858 DOI: 10.1016/j.omtn.2020.06.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 06/12/2020] [Accepted: 06/24/2020] [Indexed: 12/13/2022]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression by base paring with the complementary sequences of the target mRNAs, and then exert their function through degrading mRNA or inhibiting protein translation. They play a significant role as a regulatory factor in biological processes of organism development, cell proliferation, differentiation, and cell death. Some of the traditional methods for studying miRNAs, such as northern blot, real-time PCR, or microarray, have been extensively used to investigate the biological properties and expression patterns of miRNAs. However, these methods often require considerable time, cell samples, and the design of effective primers or specific probes. Therefore, in order to gain a deeper understanding of the role of miRNAs in biological processes and accelerate the clinical application of miRNAs in the field of disease treatment, non-invasive, sensitive, and efficient imaging methods are needed to visualize the dynamic expression of miRNAs in living cells and animals. In this study, we reviewed the recent progress in the genetically encoded reporter genes for miRNA imaging.
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Affiliation(s)
- Yingzhuang Song
- Institute of Medical Research, Northwestern Polytechnical University, Xi'an, Shaanxi 710072, China
| | - Zhijing Xu
- Institute of Medical Research, Northwestern Polytechnical University, Xi'an, Shaanxi 710072, China
| | - Fu Wang
- Institute of Medical Research, Northwestern Polytechnical University, Xi'an, Shaanxi 710072, China; Engineering Research Center of Molecular and Neuro Imaging, Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an, Shaanxi 710071, China.
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31
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microRNA neural networks improve diagnosis of acute coronary syndrome (ACS). J Mol Cell Cardiol 2020; 151:155-162. [PMID: 32305360 DOI: 10.1016/j.yjmcc.2020.04.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/06/2020] [Accepted: 04/11/2020] [Indexed: 11/20/2022]
Abstract
BACKGROUND Cardiac troponins are the preferred biomarkers of acute myocardial infarction. Despite superior sensitivity, serial testing of Troponins to identify patients suffering acute coronary syndromes is still required in many cases to overcome limited specificity. Moreover, unstable angina pectoris relies on reported symptoms in the troponin-negative group. In this study, we investigated genome-wide miRNA levels in a prospective cohort of patients with clinically suspected ACS and determined their diagnostic value by applying an in silico neural network. METHODS PAXgene blood and serum samples were drawn and hsTnT was measured in patients at initial presentation to our Chest-Pain Unit. After clinical and diagnostic workup, patients were adjudicated by senior cardiologists in duty to their final diagnosis: STEMI, NSTEMI, unstable angina pectoris and non-ACS patients. ACS patients and a cohort of healthy controls underwent deep transcriptome sequencing. Machine learning was implemented to construct diagnostic miRNA classifiers. RESULTS We developed a neural network model which incorporates 34 validated ACS miRNAs, showing excellent classification results. By further developing additional machine learning models and selecting the best miRNAs, we achieved an accuracy of 0.96 (95% CI 0.96-0.97), sensitivity of 0.95, specificity of 0.96 and AUC of 0.99. The one-point hsTnT value reached an accuracy of 0.89, sensitivity of 0.82, specificity of 0.96, and AUC of 0.96. CONCLUSIONS Here we show the concept of neural network based biomarkers for ACS. This approach also opens the possibility to include multi-modal data points to further increase precision and perform classification of other ACS differential diagnoses.
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32
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Mejia-Vilet JM, Parikh SV, Song H, Fadda P, Shapiro JP, Ayoub I, Yu L, Zhang J, Uribe-Uribe N, Rovin BH. Immune gene expression in kidney biopsies of lupus nephritis patients at diagnosis and at renal flare. Nephrol Dial Transplant 2020; 34:1197-1206. [PMID: 29800348 DOI: 10.1093/ndt/gfy125] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Up to 50% of lupus nephritis (LN) patients experience renal flares after their initial episode of LN. These flares contribute to poor renal outcomes. We postulated that intrarenal immune gene expression is different in flares compared with de novo LN, and conducted these studies to test this hypothesis. METHODS Glomerular and tubulointerstitial immune gene expression was evaluated in 14 patients who had a kidney biopsy to diagnose LN and another biopsy at their first LN flare. Ten healthy living kidney donors were included as controls. RNA was extracted from laser microdissected formalin-fixed paraffin-embedded kidney biopsies. Gene expression was analyzed using the Nanostring nCounter® platform and validated by quantitative real-time polymerase chain reaction. Differentially expressed genes were analyzed by the Ingenuity Pathway Analysis and Panther Gene Ontology tools. RESULTS Over 110 genes were differentially expressed between LN and healthy control kidney biopsies. Although there was considerable molecular heterogeneity between LN biopsies at diagnosis and flare, for about half the LN patients gene expression from the first LN biopsy clustered with the repeated LN biopsy. However, in all patients, a set of eight interferon alpha-controlled genes had a significantly higher expression in the diagnostic biopsy compared with the flare biopsy. In contrast, nine tumor necrosis factor alpha-controlled genes had higher expression in flare biopsies. CONCLUSIONS There is significant heterogeneity in immune-gene expression of kidney tissue from LN patients. There are limited but important differences in gene expression between LN flares, which may influence treatment decisions.
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Affiliation(s)
- Juan M Mejia-Vilet
- Division of Nephrology, Department of Internal Medicine, Davis Heart and Lung Research Institute, Ohio State University Medical Center, Columbus, OH, USA.,Department of Nephrology and Mineral Metabolism, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Samir V Parikh
- Division of Nephrology, Department of Internal Medicine, Davis Heart and Lung Research Institute, Ohio State University Medical Center, Columbus, OH, USA
| | - Huijuan Song
- Division of Nephrology, Department of Internal Medicine, Davis Heart and Lung Research Institute, Ohio State University Medical Center, Columbus, OH, USA
| | - Paolo Fadda
- Genomics Shared Resource (GSR)-Comprehensive Cancer Center (CCC)
| | - John P Shapiro
- Division of Nephrology, Department of Internal Medicine, Davis Heart and Lung Research Institute, Ohio State University Medical Center, Columbus, OH, USA
| | - Isabelle Ayoub
- Division of Nephrology, Department of Internal Medicine, Davis Heart and Lung Research Institute, Ohio State University Medical Center, Columbus, OH, USA
| | - Lianbo Yu
- Center for Biostatistics, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Jianying Zhang
- Center for Biostatistics, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Norma Uribe-Uribe
- Department of Nephrology and Mineral Metabolism, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Brad H Rovin
- Division of Nephrology, Department of Internal Medicine, Davis Heart and Lung Research Institute, Ohio State University Medical Center, Columbus, OH, USA
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Kiliszek M, Maciak K, Maciejak A, Krzyżanowski K, Wierzbowski R, Gora M, Burzynska B, Segiet A, Skrobowski A. Serum microRNA in patients undergoing atrial fibrillation ablation. Sci Rep 2020; 10:4424. [PMID: 32157193 PMCID: PMC7064599 DOI: 10.1038/s41598-020-61322-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 01/29/2020] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs mediate posttranscriptional gene regulation. The aim of the study was to find a microRNA predictor of successful atrial fibrillation (AF) ablation. A total of 109 patients undergoing first-time AF ablation were included. Nineteen patients were selected to undergo serum microRNA sequencing (study group). The sequencing data were used to select several microRNAs that correlated with 12-month recurrences after AF ablation. Those microRNAs were validated by digital droplet PCR in samples from remaining 90 patients. All patients underwent pulmonary vein isolation (RF ablation, contact force catheter, electroanatomical system). The endpoint of the study was the 12-month AF recurrence rate; the overall recurrence rate was 42.5%. In total, levels of 34 miRNAs were significantly different in sera from patients with AF recurrence compared to patients without AF recurrence. Six microRNAs (miR-183-5p, miR-182-5p, miR-32-5p, miR-107, miR-574-3p, and miR-144-3p) were validated in the whole group. Data from the validation group did not confirm the observations from the study group, as no significant differences were found between miRNAs serum levels in patients with and without recurrences 12 months after AF ablation.
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Affiliation(s)
- Marek Kiliszek
- Department of Cardiology and Internal Diseases, Military Institute of Medicine, Warsaw, Poland.
| | - Karolina Maciak
- Institute of Biochemistry and Biophysics, PAS, Warsaw, Poland
| | - Agata Maciejak
- Department of Clinical Chemistry and Laboratory Diagnostics, Medical University of Warsaw, Warsaw, Poland
| | - Krystian Krzyżanowski
- Department of Cardiology and Internal Diseases, Military Institute of Medicine, Warsaw, Poland
| | - Robert Wierzbowski
- Department of Cardiology and Internal Diseases, Military Institute of Medicine, Warsaw, Poland
| | - Monika Gora
- Institute of Biochemistry and Biophysics, PAS, Warsaw, Poland
| | - Beata Burzynska
- Institute of Biochemistry and Biophysics, PAS, Warsaw, Poland
| | - Agnieszka Segiet
- Chair and Department of Experimental and Clinical Physiology, Medical University of Warsaw, Warsaw, Poland
| | - Andrzej Skrobowski
- Department of Cardiology and Internal Diseases, Military Institute of Medicine, Warsaw, Poland
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van der Sijde F, Vietsch EE, Mustafa DAM, Li Y, van Eijck CHJ. Serum miR-338-3p and miR-199b-5p are associated with the absolute neutrophil count in patients with resectable pancreatic cancer. Clin Chim Acta 2020; 505:183-189. [PMID: 32145274 DOI: 10.1016/j.cca.2020.03.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 02/27/2020] [Accepted: 03/03/2020] [Indexed: 01/18/2023]
Abstract
BACKGROUND Several peripheral blood cell counts and immune ratios, such as the systemic immune-inflammation index (SII = platelet x neutrophil count/lymphocyte count) have prognostic value in patients with resectable pancreatic cancer (PDAC). Circulating microRNAs (miRNAs) are involved in various aspects of cancer and inflammation. We aimed to identify measurable circulating miRNAs in PDAC patients correlating with systemic inflammation parameters. METHODS A total of 42 PDAC patients was included in this study: twelve in the discovery (n = 6 SII low; n = 6 SII high) and 30 patients in the validation cohort (n = 19 SII low, n = 11 SII high). MiRNAs isolated from preoperative serum samples were measured with a 352 miRNA panel in the discovery cohort and individual miRNA primers in the validation cohort, using RT-qPCR (ID3EAL assays, MiRXES). RESULTS Only in the discovery cohort miR-328-3p, miR-338-3p, miR-1258 and miR-199b-5p were upregulated in high compared to low SII patients (fold difference ≥ 2, P<0.05). In the total cohort (n = 42) correlations were found between miR-338-3p (r = 0.48, P = 0.002) and miR-199b-5p (r = 0.44, P = 0.005) and the absolute neutrophil count. CONCLUSION Circulating miR-338-3p and miR-199b-5p are correlated to the neutrophil count in the blood of PDAC patients, suggesting a potential role of circulating miRNAs in cancer immune evasion and systemic inflammation.
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Affiliation(s)
- Fleur van der Sijde
- Department of Surgery, Erasmus MC, University Medical Center Rotterdam, the Netherlands
| | - Eveline E Vietsch
- Department of Surgery, Erasmus MC, University Medical Center Rotterdam, the Netherlands
| | - Dana A M Mustafa
- Department of Pathology, Tumor Immuno-Pathology Laboratory, Erasmus MC, University Medical Center Rotterdam, the Netherlands
| | - Yunlei Li
- Department of Pathology and Clinical Bioinformatics, Erasmus MC, University Medical Center Rotterdam, the Netherlands
| | - Casper H J van Eijck
- Department of Surgery, Erasmus MC, University Medical Center Rotterdam, the Netherlands.
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Soda N, Rehm BHA, Sonar P, Nguyen NT, Shiddiky MJA. Advanced liquid biopsy technologies for circulating biomarker detection. J Mater Chem B 2019; 7:6670-6704. [PMID: 31646316 DOI: 10.1039/c9tb01490j] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Liquid biopsy is a new diagnostic concept that provides important information for monitoring and identifying tumor genomes in body fluid samples. Detection of tumor origin biomolecules like circulating tumor cells (CTCs), circulating tumor specific nucleic acids (circulating tumor DNA (ctDNA), circulating tumor RNA (ctRNA), microRNAs (miRNAs), long non-coding RNAs (lnRNAs)), exosomes, autoantibodies in blood, saliva, stool, urine, etc. enables cancer screening, early stage diagnosis and evaluation of therapy response through minimally invasive means. From reliance on painful and hazardous tissue biopsies or imaging depending on sophisticated equipment, cancer management schemes are witnessing a rapid evolution towards minimally invasive yet highly sensitive liquid biopsy-based tools. Clinical application of liquid biopsy is already paving the way for precision theranostics and personalized medicine. This is achieved especially by enabling repeated sampling, which in turn provides a more comprehensive molecular profile of tumors. On the other hand, integration with novel miniaturized platforms, engineered nanomaterials, as well as electrochemical detection has led to the development of low-cost and simple platforms suited for point-of-care applications. Herein, we provide a comprehensive overview of the biogenesis, significance and potential role of four widely known biomarkers (CTCs, ctDNA, miRNA and exosomes) in cancer diagnostics and therapeutics. Furthermore, we provide a detailed discussion of the inherent biological and technical challenges associated with currently available methods and the possible pathways to overcome these challenges. The recent advances in the application of a wide range of nanomaterials in detecting these biomarkers are also highlighted.
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Affiliation(s)
- Narshone Soda
- School of Environment and Science, Griffith University, Nathan Campus, QLD 4111, Australia. and Queensland Micro- and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, QLD 4111, Australia
| | - Bernd H A Rehm
- Centre for Cell Factories and Biopolymers (CCFB), Griffith Institute for Drug Discovery (GRIDD), Griffith University, Nathan, QLD 4111, Australia
| | - Prashant Sonar
- School of Chemistry, Physics and Mechanical Engineering, Molecular Design and Synthesis, Queensland University of Technology (QUT), Brisbane, Australia
| | - Nam-Trung Nguyen
- Queensland Micro- and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, QLD 4111, Australia
| | - Muhammad J A Shiddiky
- School of Environment and Science, Griffith University, Nathan Campus, QLD 4111, Australia. and Queensland Micro- and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, QLD 4111, Australia
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Forero DA, González-Giraldo Y, Castro-Vega LJ, Barreto GE. qPCR-based methods for expression analysis of miRNAs. Biotechniques 2019; 67:192-199. [PMID: 31560239 DOI: 10.2144/btn-2019-0065] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Several approaches for miRNA expression analysis have been developed in recent years. In this article, we provide an updated and comprehensive review of available qPCR-based methods for miRNA expression analysis and discuss their advantages and disadvantages. Existing techniques involve the use of stem-loop reverse transcriptase-PCR, polyadenylation of RNAs, ligation of adapters or RT with complex primers, using universal or miRNA-specific qPCR primers and/or probes. Many of these methods are oriented towards the expression analysis of mature miRNAs and few are designed for the study of pre-miRNAs and pri-miRNAs. We also discuss findings from articles that compare results from existing methods. Finally, we suggest key points for the improvement of available techniques and for the future development of additional methods.
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Affiliation(s)
- Diego A Forero
- Laboratory of NeuroPsychiatric Genetics, Biomedical Sciences Research Group, School of Medicine, Universidad Antonio Nariño, Bogotá, Colombia.,PhD Program in Health Sciences, School of Medicine, Universidad Antonio Nariño, Bogotá, Colombia
| | - Yeimy González-Giraldo
- Departamento de Nutrición y Bioquímica, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Luis J Castro-Vega
- INSERM, UMR970, Paris-Cardiovascular Research Center, Equipe Labellisée par la Ligue contre le Cancer, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Faculté de Médecine, Paris, France
| | - George E Barreto
- Departamento de Nutrición y Bioquímica, Pontificia Universidad Javeriana, Bogotá, Colombia
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Li J, Fu W, Wang Z, Dai Z. Substrate specificity-enabled terminal protection for direct quantification of circulating MicroRNA in patient serums. Chem Sci 2019; 10:5616-5623. [PMID: 31293746 PMCID: PMC6552989 DOI: 10.1039/c8sc05240a] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Accepted: 04/28/2019] [Indexed: 12/12/2022] Open
Abstract
Currently, reported affinity pairings still lack in diversity, and thus terminal protection relying on steric hindrance is restricted in designing nucleic acid-based analytical systems. In this work, resistance to exonuclease is testified by group modification or backbone replacement, and the 3'-phosphate group (P) reveals the strongest exonuclease I-resistant capability. Due to the substrate specificity of enzymatic catalysis, this 3'-P protection works in a "direct mode". By introducing DNA templated copper nanoparticles, an alkaline phosphatase assay is performed to confirm the 3'-P protection. To display the application of this novel terminal protection, a multifunctional DNA is designed to quantify the model circulating microRNA (hsa-miR-21-5p) in serums from different cancer patients. According to our data, hsa-miR-21-5p-correlated cancers can be evidently distinguished from non-correlated cancers. Meanwhile, the effect of chemotherapy and radiotherapy on breast cancer is evaluated from the perspective of hsa-miR-21-5p residue in serums. Since greatly reducing the limitations of DNA design, this P-induced terminal protection can be facilely integrated with other DNA manipulations, thereby constructing more advanced biosensors with improved analytical performances for clinical applications.
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Affiliation(s)
- Junyao Li
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials , Jiangsu Key Laboratory of Biofunctional Materials , School of Chemistry and Materials Science , Nanjing Normal University , Nanjing , 210023 , P. R. China . ; ; Tel: +86-25-85891051
| | - Wenxin Fu
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials , Jiangsu Key Laboratory of Biofunctional Materials , School of Chemistry and Materials Science , Nanjing Normal University , Nanjing , 210023 , P. R. China . ; ; Tel: +86-25-85891051
| | - Zhaoyin Wang
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials , Jiangsu Key Laboratory of Biofunctional Materials , School of Chemistry and Materials Science , Nanjing Normal University , Nanjing , 210023 , P. R. China . ; ; Tel: +86-25-85891051
| | - Zhihui Dai
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials , Jiangsu Key Laboratory of Biofunctional Materials , School of Chemistry and Materials Science , Nanjing Normal University , Nanjing , 210023 , P. R. China . ; ; Tel: +86-25-85891051
- Nanjing Normal University Center for Analysis and Testing , Nanjing , 210023 , P. R. China
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38
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Thibord F, Perret C, Roux M, Suchon P, Germain M, Deleuze JF, Morange PE, Trégouët DA. OPTIMIR, a novel algorithm for integrating available genome-wide genotype data into miRNA sequence alignment analysis. RNA (NEW YORK, N.Y.) 2019; 25:657-668. [PMID: 30819774 PMCID: PMC6521604 DOI: 10.1261/rna.069708.118] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 02/21/2019] [Indexed: 06/09/2023]
Abstract
Next-generation sequencing is an increasingly popular and efficient approach to characterize the full set of microRNAs (miRNAs) present in human biosamples. MiRNAs' detection and quantification still remain a challenge as they can undergo different posttranscriptional modifications and might harbor genetic variations (polymiRs) that may impact on the alignment step. We present a novel algorithm, OPTIMIR, that incorporates biological knowledge on miRNA editing and genome-wide genotype data available in the processed samples to improve alignment accuracy. OPTIMIR was applied to 391 human plasma samples that had been typed with genome-wide genotyping arrays. OPTIMIR was able to detect genotyping errors, suggested the existence of novel miRNAs and highlighted the allelic imbalance expression of polymiRs in heterozygous carriers. OPTIMIR is written in python, and freely available on the GENMED website (http://www.genmed.fr/index.php/fr/) and on Github (github.com/FlorianThibord/OptimiR).
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Affiliation(s)
- Florian Thibord
- Sorbonne Universités, Université Pierre et Marie Curie (UPMC Univ Paris 06), Institut National pour la Santé et la Recherche Médicale (INSERM), Unité Mixte de Recherche en Santé (UMR_S) 1166, Team Genomics and Pathophysiology of Cardiovascular Diseases, 75013 Paris, France
- Institute for Cardiometabolism and Nutrition (ICAN), 75013 Paris, France
- INSERM UMR_S 1219, Bordeaux Population Health Research Center, University of Bordeaux, 33076 Bordeaux, France
| | - Claire Perret
- Sorbonne Universités, Université Pierre et Marie Curie (UPMC Univ Paris 06), Institut National pour la Santé et la Recherche Médicale (INSERM), Unité Mixte de Recherche en Santé (UMR_S) 1166, Team Genomics and Pathophysiology of Cardiovascular Diseases, 75013 Paris, France
- Institute for Cardiometabolism and Nutrition (ICAN), 75013 Paris, France
| | - Maguelonne Roux
- Sorbonne Universités, Université Pierre et Marie Curie (UPMC Univ Paris 06), Institut National pour la Santé et la Recherche Médicale (INSERM), Unité Mixte de Recherche en Santé (UMR_S) 1166, Team Genomics and Pathophysiology of Cardiovascular Diseases, 75013 Paris, France
- Institute for Cardiometabolism and Nutrition (ICAN), 75013 Paris, France
| | - Pierre Suchon
- Laboratory of Haematology, La Timone Hospital, 13885 Marseille, France
- Institut National pour la Santé et la Recherche Médicale (INSERM), Unité Mixte de Recherche en Santé (UMR_S) 1062, Nutrition Obesity and Risk of Thrombosis, Center for CardioVascular and Nutrition Research (C2VN), Aix-Marseille University, 13885 Marseille, France
| | - Marine Germain
- Sorbonne Universités, Université Pierre et Marie Curie (UPMC Univ Paris 06), Institut National pour la Santé et la Recherche Médicale (INSERM), Unité Mixte de Recherche en Santé (UMR_S) 1166, Team Genomics and Pathophysiology of Cardiovascular Diseases, 75013 Paris, France
- Institute for Cardiometabolism and Nutrition (ICAN), 75013 Paris, France
- INSERM UMR_S 1219, Bordeaux Population Health Research Center, University of Bordeaux, 33076 Bordeaux, France
| | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine, Direction de la Recherche Fondamentale, CEA, 91057 Evry, France
- CEPH, Fondation Jean Dausset, 75011 Paris, France
| | - Pierre-Emmanuel Morange
- Laboratory of Haematology, La Timone Hospital, 13885 Marseille, France
- Institut National pour la Santé et la Recherche Médicale (INSERM), Unité Mixte de Recherche en Santé (UMR_S) 1062, Nutrition Obesity and Risk of Thrombosis, Center for CardioVascular and Nutrition Research (C2VN), Aix-Marseille University, 13885 Marseille, France
| | - David-Alexandre Trégouët
- Sorbonne Universités, Université Pierre et Marie Curie (UPMC Univ Paris 06), Institut National pour la Santé et la Recherche Médicale (INSERM), Unité Mixte de Recherche en Santé (UMR_S) 1166, Team Genomics and Pathophysiology of Cardiovascular Diseases, 75013 Paris, France
- Institute for Cardiometabolism and Nutrition (ICAN), 75013 Paris, France
- INSERM UMR_S 1219, Bordeaux Population Health Research Center, University of Bordeaux, 33076 Bordeaux, France
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39
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Rosato AJ, Chen X, Tanaka Y, Farrer LA, Kranzler HR, Nunez YZ, Henderson DC, Gelernter J, Zhang H. Salivary microRNAs identified by small RNA sequencing and machine learning as potential biomarkers of alcohol dependence. Epigenomics 2019; 11:739-749. [PMID: 31140863 DOI: 10.2217/epi-2018-0177] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Aim: Salivary miRNA can be easily accessible biomarkers of alcohol dependence (AD). Materials & methods: The miRNA transcriptome in the saliva of 56 African-Americans (AAs; 28 AD patients/28 controls) and 64 European-Americans (EAs; 32 AD patients/32 controls) was profiled using small RNA sequencing. Differentially expressed miRNAs were identified. Salivary miRNAs were used to predict the AD presence using machine learning with Random Forests. Results: Seven miRNAs were differentially expressed in AA AD patients, and five miRNAs were differentially expressed in EA AD patients. The AD prediction accuracy based on top five miRNAs (ranked by Gini index) was 79.1 and 72.2% in AAs and EAs, respectively. Conclusion: This study provided the first evidence that salivary miRNAs are AD biomarkers.
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Affiliation(s)
- Andrew J Rosato
- Department of Psychiatry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Xiaochun Chen
- Department of Psychiatry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Yoshiaki Tanaka
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Lindsay A Farrer
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA 02118, USA.,Department of Neurology, Boston University School of Medicine, Boston, MA 02118, USA.,Department of Ophthalmology, Boston University School of Medicine, Boston, MA 02118, USA.,Department of Epidemiology & Boston University School of Public Health, Boston, MA 02118, USA.,Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA
| | - Henry R Kranzler
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania & VISN4 MIRECC, Crescenz VAMC, Philadelphia, PA 19104, USA
| | - Yaira Z Nunez
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA
| | - David C Henderson
- Department of Psychiatry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Joel Gelernter
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA.,Department of Psychiatry, Yale University School of Medicine, New Haven, CT 06511, USA.,Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06510, USA.,VA Connecticut Healthcare System, West Haven, CT 06516, USA
| | - Huiping Zhang
- Department of Psychiatry, Boston University School of Medicine, Boston, MA 02118, USA.,Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA 02118, USA
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40
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de Kerckhove M, Tanaka K, Umehara T, Okamoto M, Kanematsu S, Hayashi H, Yano H, Nishiura S, Tooyama S, Matsubayashi Y, Komatsu T, Park S, Okada Y, Takahashi R, Kawano Y, Hanawa T, Iwasaki K, Nozaki T, Torigoe H, Ikematsu K, Suzuki Y, Tanaka K, Martin P, Shimokawa I, Mori R. Targeting miR-223 in neutrophils enhances the clearance of Staphylococcus aureus in infected wounds. EMBO Mol Med 2019; 10:emmm.201809024. [PMID: 30171089 PMCID: PMC6180296 DOI: 10.15252/emmm.201809024] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Argonaute 2 bound mature microRNA (Ago2-miRNA) complexes are key regulators of the wound inflammatory response and function in the translational processing of target mRNAs. In this study, we identified four wound inflammation-related Ago2-miRNAs (miR-139-5p, miR-142-3p, miR-142-5p, and miR-223) and show that miR-223 is critical for infection control. miR-223 Y/- mice exhibited delayed sterile healing with prolonged neutrophil activation and interleukin-6 expression, and markedly improved repair of Staphylococcus aureus-infected wounds. We also showed that the expression of miR-223 was regulated by CCAAT/enhancer binding protein alpha in human neutrophils after exposure to S. aureus peptides. Treatment with miR-223 Y/--derived neutrophils, or miR-223 antisense oligodeoxynucleotides in S. aureus-infected wild-type wounds markedly improved the healing of these otherwise chronic, slow healing wounds. This study reveals how miR-223 regulates the bactericidal capacity of neutrophils at wound sites and indicates that targeting miR-223 might be of therapeutic benefit for infected wounds in the clinic.
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Affiliation(s)
- Maiko de Kerckhove
- Department of Pathology, Nagasaki University School of Medicine and Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Katsuya Tanaka
- Department of Pathology, Nagasaki University School of Medicine and Graduate School of Biomedical Sciences, Nagasaki, Japan.,Department of Plastic and Reconstructive Surgery, Nagasaki University School of Medicine and Graduate School of Biomedical Sciences, Nagasaki, Japan.,Department of Plastic and Reconstructive Surgery, Ehime Prefectural Center Hospital, Ehime, Japan
| | - Takahiro Umehara
- Department of Forensic Pathology and Science, Nagasaki University School of Medicine and Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Momoko Okamoto
- Department of Pathology, Nagasaki University School of Medicine and Graduate School of Biomedical Sciences, Nagasaki, Japan.,Department of Immunology and Rheumatology, Nagasaki University School of Medicine and Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Sotaro Kanematsu
- Laboratory of Functional Genomics, Department of Medical Genome Science, Graduate of Frontier Science, The University of Tokyo, Tokyo, Japan
| | - Hiroko Hayashi
- Department of Pathology, Nagasaki University School of Medicine and Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Hiroki Yano
- Department of Plastic and Reconstructive Surgery, Nagasaki University School of Medicine and Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Soushi Nishiura
- Department of Pathology, Nagasaki University School of Medicine and Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Shiho Tooyama
- Department of Pathology, Nagasaki University School of Medicine and Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Yutaka Matsubayashi
- Schools of Biochemistry and Physiology, Pharmacology & Neuroscience, Faculty of Biomedical Sciences, University of Bristol, Bristol, UK.,Randall Division of Cell and Molecular Biophysics, King's College London, London, UK
| | - Toshimitsu Komatsu
- Department of Pathology, Nagasaki University School of Medicine and Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Seongjoon Park
- Department of Pathology, Nagasaki University School of Medicine and Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Yuka Okada
- Department of Ophthalmology, Wakayama Medical University, Wakayama, Japan
| | - Rina Takahashi
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, Chiba, Japan
| | - Yayoi Kawano
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, Chiba, Japan
| | - Takehisa Hanawa
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, Chiba, Japan
| | - Keisuke Iwasaki
- Department of Pathology, Sasebo City General Hospital, Sasebo Nagasaki, Japan
| | - Tadashige Nozaki
- Department of Pharmacology, Faculty of Dentistry, Osaka Dental University, Hirakata Osaka, Japan
| | - Hidetaka Torigoe
- Department of Applied Chemistry, Faculty of Science, Tokyo University of Science, Tokyo, Japan
| | - Kazuya Ikematsu
- Department of Forensic Pathology and Science, Nagasaki University School of Medicine and Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Yutaka Suzuki
- Laboratory of Functional Genomics, Department of Medical Genome Science, Graduate of Frontier Science, The University of Tokyo, Tokyo, Japan
| | - Katsumi Tanaka
- Department of Plastic and Reconstructive Surgery, Nagasaki University School of Medicine and Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Paul Martin
- Schools of Biochemistry and Physiology, Pharmacology & Neuroscience, Faculty of Biomedical Sciences, University of Bristol, Bristol, UK
| | - Isao Shimokawa
- Department of Pathology, Nagasaki University School of Medicine and Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Ryoichi Mori
- Department of Pathology, Nagasaki University School of Medicine and Graduate School of Biomedical Sciences, Nagasaki, Japan
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41
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Gruzdev SK, Yakovlev AA, Druzhkova TA, Guekht AB, Gulyaeva NV. The Missing Link: How Exosomes and miRNAs can Help in Bridging Psychiatry and Molecular Biology in the Context of Depression, Bipolar Disorder and Schizophrenia. Cell Mol Neurobiol 2019; 39:729-750. [PMID: 31089834 DOI: 10.1007/s10571-019-00684-6] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 05/03/2019] [Indexed: 12/21/2022]
Abstract
MicroRNAs (miRNAs) only recently have been recognized as promising molecules for both fundamental and clinical neuroscience. We provide a literature review of miRNA biomarker studies in three most prominent psychiatric disorders (depression, bipolar disorder and schizophrenia) with the particular focus on depression due to its social and healthcare importance. Our search resulted in 191 unique miRNAs across 35 human studies measuring miRNA levels in blood, serum or plasma. 30 miRNAs replicated in more than one study. Most miRNAs targeted neuroplasticity and neurodevelopment pathways. Various limitations do not allow us to make firm conclusions on clinical potential of studied miRNAs. Based on our results we discuss the rationale for future research investigations of exosomal mechanisms to overcome methodological caveats both in studying etiology and pathogenesis, and providing an objective back-up for clinical decisions.
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Affiliation(s)
- S K Gruzdev
- Institute of Medicine, RUDN University, Miklukho-Maklaya Str. 6, Moscow, Russia, 117198.
| | - A A Yakovlev
- Institute of Higher Nervous Activity and Neurophysiology, Russian Academy of Sciences, Butlerova Str., 5A, Moscow, Russia, 117485.,Moscow Research & Clinical Center for Neuropsychiatry, Moscow Healthcare Department, Donskaya Str., 43, Moscow, Russia, 115419
| | - T A Druzhkova
- Moscow Research & Clinical Center for Neuropsychiatry, Moscow Healthcare Department, Donskaya Str., 43, Moscow, Russia, 115419
| | - A B Guekht
- Moscow Research & Clinical Center for Neuropsychiatry, Moscow Healthcare Department, Donskaya Str., 43, Moscow, Russia, 115419.,Russian National Research Medical University, Ostrovitianov Str. 1, Moscow, Russia, 117997
| | - N V Gulyaeva
- Institute of Higher Nervous Activity and Neurophysiology, Russian Academy of Sciences, Butlerova Str., 5A, Moscow, Russia, 117485.,Moscow Research & Clinical Center for Neuropsychiatry, Moscow Healthcare Department, Donskaya Str., 43, Moscow, Russia, 115419
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42
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Lindberg T, Forreryd A, Bergendorff O, Lindstedt M, Zeller KS. In vitro assessment of mechanistic events induced by structurally related chemical rubber sensitizers. Toxicol In Vitro 2019; 60:144-153. [PMID: 31082492 DOI: 10.1016/j.tiv.2019.05.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 04/30/2019] [Accepted: 05/09/2019] [Indexed: 10/26/2022]
Abstract
Allergic contact dermatitis (ACD) is one of the most common forms of immunotoxicity, and increased understanding of how chemicals trigger these adverse reactions is needed in order to treat or design testing strategies to identify and subsequently avoid exposure to such substances. In this study, we investigated the cellular response induced by rubber chemicals in a dendritic cell (DC) model, focusing on the structurally similar chemicals diethylthiocarbamylbenzothiazole sulfide and dimethylthiocarbamylbenzothiazole sulfide, with regard to regulation of microRNA, and messenger RNA expression. Only a few miRNAs were found to be commonly regulated by both rubber chemicals, among them miR1973, while the overall miRNA expression profiles were diverse. Similarly, out of approximately 500 differentially regulated transcripts for each chemical, about 60% overlapped, while remaining were unique. The pathways predicted to be enriched in the cell model by stimulation with the rubber chemicals were linked to immunological events, relevant in the context of ACD. These results suggest that small structural differences can trigger specific activation of the immune system in response to chemicals. The here presented mechanistic data can be valuable in explaining the immunotoxicological events in DC activation after exposure to skin sensitizing chemicals, and can contribute to understanding, preventing and treating ACD.
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Affiliation(s)
- Tim Lindberg
- Department of Immunotechnology, Medicon Village (406), 22381 Lund, Sweden.
| | - Andy Forreryd
- Department of Immunotechnology, Medicon Village (406), 22381 Lund, Sweden.
| | - Ola Bergendorff
- Department of Occupational and Environmental Dermatology, Skåne University Hospital, Lund University, 20502 Malmö, Sweden.
| | - Malin Lindstedt
- Department of Immunotechnology, Medicon Village (406), 22381 Lund, Sweden.
| | - Kathrin S Zeller
- Department of Immunotechnology, Medicon Village (406), 22381 Lund, Sweden.
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43
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Guo WJ, Wu Z, Yang XY, Pang DW, Zhang ZL. Ultrasensitive electrochemical detection of microRNA-21 with wide linear dynamic range based on dual signal amplification. Biosens Bioelectron 2019; 131:267-273. [DOI: 10.1016/j.bios.2019.02.026] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 01/18/2019] [Accepted: 02/11/2019] [Indexed: 12/18/2022]
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44
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Basiri B, Sutton JM, Hooshfar S, Byrnes CC, Murph MM, Bartlett MG. Direct identification of microribonucleic acid miR-451 from plasma using liquid chromatography mass spectrometry. J Chromatogr A 2019; 1584:97-105. [PMID: 30502920 DOI: 10.1016/j.chroma.2018.11.029] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 10/16/2018] [Accepted: 11/15/2018] [Indexed: 12/12/2022]
Abstract
In recent years, small endogenous RNAs have come to the forefront of both basic and translational research. For example, many studies have pointed to the potential role of microRNAs (miRNAs) as disease biomarkers. However, precise quantitative methods for the analysis of miRNAs are still lacking. In this study, we report the first mass spectrometry-based quantitation of miR-451, a circulatory microRNA. Using a highly selective sample preparation method with an average recovery of 83.6% and a novel mobile phase chemistry, we were able to reach an LOQ of 0.5 ng/mL. Because of such high sensitivity, we could detect and quantify the endogenous miR-451 from both human and rat plasma. Considering the increased precision of LC-MS compared to other methods, these results usher in a new era of miRNA biomarker discovery and validation.
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Affiliation(s)
- Babak Basiri
- Department of Pharmaceutical and Biomedical Sciences, The University of Georgia College of Pharmacy, 250 W. Green Street, Athens, GA 30602-2352, USA
| | - J Michael Sutton
- Department of Pharmaceutical and Biomedical Sciences, The University of Georgia College of Pharmacy, 250 W. Green Street, Athens, GA 30602-2352, USA
| | - Shirin Hooshfar
- Department of Pharmaceutical and Biomedical Sciences, The University of Georgia College of Pharmacy, 250 W. Green Street, Athens, GA 30602-2352, USA
| | - Charnel C Byrnes
- Department of Pharmaceutical and Biomedical Sciences, The University of Georgia College of Pharmacy, 250 W. Green Street, Athens, GA 30602-2352, USA
| | - Mandi M Murph
- Department of Pharmaceutical and Biomedical Sciences, The University of Georgia College of Pharmacy, 250 W. Green Street, Athens, GA 30602-2352, USA
| | - Michael G Bartlett
- Department of Pharmaceutical and Biomedical Sciences, The University of Georgia College of Pharmacy, 250 W. Green Street, Athens, GA 30602-2352, USA.
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45
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Barberán-Soler S, Vo JM, Hogans RE, Dallas A, Johnston BH, Kazakov SA. Decreasing miRNA sequencing bias using a single adapter and circularization approach. Genome Biol 2018; 19:105. [PMID: 30173660 PMCID: PMC6120088 DOI: 10.1186/s13059-018-1488-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 07/18/2018] [Indexed: 12/22/2022] Open
Abstract
The ability to accurately quantify all the microRNAs (miRNAs) in a sample is important for understanding miRNA biology and for development of new biomarkers and therapeutic targets. We develop a new method for preparing miRNA sequencing libraries, RealSeq®-AC, that involves ligating the miRNAs with a single adapter and circularizing the ligation products. When compared to other methods, RealSeq®-AC provides greatly reduced miRNA sequencing bias and allows the identification of the largest variety of miRNAs in biological samples. This reduced bias also allows robust quantification of miRNAs present in samples across a wide range of RNA input levels.
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Affiliation(s)
| | - Jenny M. Vo
- SomaGenics, Inc., Santa Cruz, California, USA
| | | | - Anne Dallas
- SomaGenics, Inc., Santa Cruz, California, USA
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46
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Chiam K, Mayne GC, Watson DI, Woodman RJ, Bright TF, Michael MZ, Karapetis CS, Irvine T, Phillips WA, Hummel R, Wang T, Pimlott LK, Marri S, Astill DS, Ruszkiewicz AR, Thompson SK, Hussey DJ. Identification of microRNA Biomarkers of Response to Neoadjuvant Chemoradiotherapy in Esophageal Adenocarcinoma Using Next Generation Sequencing. Ann Surg Oncol 2018; 25:2731-2738. [PMID: 29987600 DOI: 10.1245/s10434-018-6626-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Indexed: 12/13/2022]
Abstract
BACKGROUND Clinical trials report improved overall survival following neoadjuvant chemoradiotherapy in patients undergoing surgery for esophageal adenocarcinoma, with a 10-15% survival improvement. MicroRNAs (miRNAs) are small noncoding RNAs that are known to direct the behavior of cancers, including response to treatment. We investigated the ability of miRNAs to predict outcomes after neoadjuvant chemoradiotherapy. METHODS Endoscopic biopsies from esophageal adenocarcinomas were obtained before neoadjuvant chemoradiotherapy and esophagectomy. miRNA levels were measured in the biopsies using next generation sequencing and compared with pathological response in the surgical resection, and subsequent survival. miRNA ratios that predicted pathological response were identified by Lasso regression and leave-one-out cross-validation. Association between miRNA ratio candidates and relapse-free survival was assessed using Kaplan-Meier analysis. Cox regression and Harrell's C analyses were performed to assess the predictive performance of the miRNAs. RESULTS Two miRNA ratios (miR-4521/miR-340-5p and miR-101-3p/miR-451a) that predicted the pathological response to neoadjuvant chemoradiotherapy were found to be associated with relapse-free survival. Pretreatment expression of these two miRNA ratios, pretreatment tumor differentiation, posttreatment AJCC histopathological tumor regression grading, and posttreatment tumor clearance/margins were significant factors associated with survival in Cox regression analysis. Multivariate analysis of the two ratios together with pretherapy factors resulted in a risk prediction accuracy of 85% (Harrell's C), which was comparable with the prediction accuracy of the AJCC treatment response grading (77%). CONCLUSIONS miRNA-ratio biomarkers identified using next generation sequencing can be used to predict disease free survival following neoadjuvant chemoradiotherapy and esophagectomy in patients with esophageal adenocarcinoma.
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Affiliation(s)
- Karen Chiam
- Cancer Research Division, Cancer Council New South Wales, Sydney, Australia.,Discipline of Surgery, College of Medicine and Public Health, Flinders University of South Australia, Adelaide, SA, Australia
| | - George C Mayne
- Discipline of Surgery, College of Medicine and Public Health, Flinders University of South Australia, Adelaide, SA, Australia.,Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - David I Watson
- Discipline of Surgery, College of Medicine and Public Health, Flinders University of South Australia, Adelaide, SA, Australia.,Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - Richard J Woodman
- Flinders Centre for Epidemiology and Biostatistics, College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - Tim F Bright
- Discipline of Surgery, College of Medicine and Public Health, Flinders University of South Australia, Adelaide, SA, Australia.,Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - Michael Z Michael
- Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - Christos S Karapetis
- Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - Tanya Irvine
- Discipline of Surgery, College of Medicine and Public Health, Flinders University of South Australia, Adelaide, SA, Australia.,Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - Wayne A Phillips
- Cancer Biology and Surgical Oncology Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
| | - Richard Hummel
- Discipline of Surgery, College of Medicine and Public Health, Flinders University of South Australia, Adelaide, SA, Australia.,Department of Surgery, University Hospital Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Tingting Wang
- Discipline of Surgery, College of Medicine and Public Health, Flinders University of South Australia, Adelaide, SA, Australia.,Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - Letitia K Pimlott
- Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - Shashikanth Marri
- Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - David StJ Astill
- Department of Anatomical Pathology, Flinders Medical Centre, Adelaide, SA, Australia
| | - Andrew R Ruszkiewicz
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
| | - Sarah K Thompson
- Department of Surgery, University of Adelaide, Royal Adelaide Hospital, Adelaide, SA, Australia
| | - Damian J Hussey
- Discipline of Surgery, College of Medicine and Public Health, Flinders University of South Australia, Adelaide, SA, Australia. .,Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia.
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47
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Chen W, Zhang L, Shi C, Ren G, Kong Q, Qin C. Comprehensive analysis of hippocampal miRNAomes in humans and mice. Epigenomics 2018; 10:813-828. [PMID: 29979109 DOI: 10.2217/epi-2017-0161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM This study aims to explore the similarity and difference of hippocampal miRNAomes between humans and mice. MATERIALS & METHODS A systematic comparison of the miRNAomes between healthy human and mouse hippocampi was performed using high-throughput sequencing followed by bioinformatic analyses. RESULTS A novel miRNA termed novel-21-5p and a human-specific miR-656-3p were identified in human hippocampi, which were expressed ubiquitously and predicted to be associated with neural activities. Compared with mouse, abundantly expressed miRNAs in human hippocampus were notably enriched in pathways pertaining to neural activities, such as neurotrophin TRK receptor signaling pathway, axon guidance and synaptic transmission. Expression pattern of orthologous miRNAs between human and mouse hippocampi was conserved. Meanwhile, the expression conservation was positively correlated with the sequence conservation. CONCLUSION Hippocampal miRNAomes between humans and mice were overall comparable; the differences in expression or function across species should be considered when constructing mouse models.
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Affiliation(s)
- Wei Chen
- Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences (CAMS) & Comparative Medicine Centre, Peking Union Medical Collage (PUMC), Beijing, PR China.,Experimental & Translational Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing, PR China
| | - Ling Zhang
- Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences (CAMS) & Comparative Medicine Centre, Peking Union Medical Collage (PUMC), Beijing, PR China
| | - Changhua Shi
- Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences (CAMS) & Comparative Medicine Centre, Peking Union Medical Collage (PUMC), Beijing, PR China
| | - Guanhua Ren
- Library of Peking University First Hospital, Beijing, PR China
| | - Qi Kong
- Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences (CAMS) & Comparative Medicine Centre, Peking Union Medical Collage (PUMC), Beijing, PR China
| | - Chuan Qin
- Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences (CAMS) & Comparative Medicine Centre, Peking Union Medical Collage (PUMC), Beijing, PR China
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48
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Kanda P, Alarcon EI, Yeuchyk T, Parent S, de Kemp RA, Variola F, Courtman D, Stewart DJ, Davis DR. Deterministic Encapsulation of Human Cardiac Stem Cells in Variable Composition Nanoporous Gel Cocoons To Enhance Therapeutic Repair of Injured Myocardium. ACS NANO 2018; 12:4338-4350. [PMID: 29660269 DOI: 10.1021/acsnano.7b08881] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Although cocooning explant-derived cardiac stem cells (EDCs) in protective nanoporous gels (NPGs) prior to intramyocardial injection boosts long-term cell retention, the number of EDCs that finally engraft is trivial and unlikely to account for salutary effects on myocardial function and scar size. As such, we investigated the effect of varying the NPG content within capsules to alter the physical properties of cocoons without influencing cocoon dimensions. Increasing NPG concentration enhanced cell migration and viability while improving cell-mediated repair of injured myocardium. Given that the latter occurred with NPG content having no detectable effect on the long-term engraftment of transplanted cells, we found that changing the physical properties of cocoons prompted explant-derived cardiac stem cells to produce greater amounts of cytokines, nanovesicles, and microRNAs that boosted the generation of new blood vessels and new cardiomyocytes. Thus, by altering the physical properties of cocoons by varying NPG content, the paracrine signature of encapsulated cells can be enhanced to promote greater endogenous repair of injured myocardium.
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Affiliation(s)
- Pushpinder Kanda
- University of Ottawa Heart Institute, Division of Cardiology, Department of Medicine , University of Ottawa , Ottawa , Canada K1Y4W7
| | - Emilio I Alarcon
- Division of Cardiac Surgery, Department of Surgery, University of Ottawa Heart Institute , University of Ottawa , Ottawa , Canada K1Y4W7
- Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine , University of Ottawa , Ottawa , Canada K1H8M5
| | - Tanya Yeuchyk
- University of Ottawa Heart Institute, Division of Cardiology, Department of Medicine , University of Ottawa , Ottawa , Canada K1Y4W7
| | - Sandrine Parent
- University of Ottawa Heart Institute, Division of Cardiology, Department of Medicine , University of Ottawa , Ottawa , Canada K1Y4W7
| | - Robert A de Kemp
- University of Ottawa Heart Institute, Division of Cardiology, Department of Medicine , University of Ottawa , Ottawa , Canada K1Y4W7
| | - Fabio Variola
- Department of Mechanical Engineering , University of Ottawa , Ottawa , Canada K1N6N5
- Department of Cellular and Molecular Medicine , University of Ottawa , Ottawa , Canada K1H8M5
| | - David Courtman
- Regenerative Medicine Program , Ottawa Hospital Research Institute , Ottawa , Canada K1H8L6
| | - Duncan J Stewart
- University of Ottawa Heart Institute, Division of Cardiology, Department of Medicine , University of Ottawa , Ottawa , Canada K1Y4W7
- Department of Cellular and Molecular Medicine , University of Ottawa , Ottawa , Canada K1H8M5
- Regenerative Medicine Program , Ottawa Hospital Research Institute , Ottawa , Canada K1H8L6
| | - Darryl R Davis
- University of Ottawa Heart Institute, Division of Cardiology, Department of Medicine , University of Ottawa , Ottawa , Canada K1Y4W7
- Department of Cellular and Molecular Medicine , University of Ottawa , Ottawa , Canada K1H8M5
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49
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Guelfi G, Cochetti G, Stefanetti V, Zampini D, Diverio S, Boni A, Mearini E. Next Generation Sequencing of urine exfoliated cells: an approach of prostate cancer microRNAs research. Sci Rep 2018; 8:7111. [PMID: 29740090 PMCID: PMC5940782 DOI: 10.1038/s41598-018-24236-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 03/22/2018] [Indexed: 12/24/2022] Open
Abstract
There is emerging evidence that microRNAs (miRNAs) dysregulation is involved in the genesis and the progression of Prostate Cancer (PCa), thus potentially increasing their use in urological clinical practice. This is the first pilot study which utilizes Illumina Deep Sequencing to examine the entire miRNAs spectrum existent in urine exfoliated prostate cells (UEPCs) of PCa patients. A total of 11 male patients with histological diagnosis of PCa were enrolled in the present study. First-catch urine (30 mL) was collected following a prostate massage. Total RNA was extracted from urine and sequenced using an HiSeq2500 System (Illumina). QPCR assay was used to validate the highest NGS results in PCA patients and in age-matched, caucasian men. Remarkably, PCA let-7 family was down-regulated (P < 0.01), compared to the controls. The results of our study support the notion of a relatively high diagnostic value of miRNA family for PCa detection, especially in the let-7 family. The present research confirmed the potential use of miRNAs as non-invasive biomarkers in the diagnosis of PCa, potentially reducing the invasiveness of actual clinical strategy.
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Affiliation(s)
- Gabriella Guelfi
- Department of Veterinary Medicine, University of Perugia, Via S. Costanzo n.4, 06126, Perugia, PG, Italy.
| | - Giovanni Cochetti
- Department of Surgical and Biomedical Sciences, Section of Urological, Andrological and Minimally invasive techniques, University of Perugia, Piazza Lucio Severi 1, 06132, Perugia, PG, Italy
| | - Valentina Stefanetti
- Department of Veterinary Medicine, University of Perugia, Via S. Costanzo n.4, 06126, Perugia, PG, Italy
| | - Danilo Zampini
- Department of Veterinary Medicine, University of Perugia, Via S. Costanzo n.4, 06126, Perugia, PG, Italy
| | - Silvana Diverio
- Department of Veterinary Medicine, University of Perugia, Via S. Costanzo n.4, 06126, Perugia, PG, Italy
| | - Andrea Boni
- Department of Surgical and Biomedical Sciences, Section of Urological, Andrological and Minimally invasive techniques, University of Perugia, Piazza Lucio Severi 1, 06132, Perugia, PG, Italy
| | - Ettore Mearini
- Department of Surgical and Biomedical Sciences, Section of Urological, Andrological and Minimally invasive techniques, University of Perugia, Piazza Lucio Severi 1, 06132, Perugia, PG, Italy
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50
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Loudig O, Liu C, Rohan T, Ben-Dov IZ. Retrospective MicroRNA Sequencing: Complementary DNA Library Preparation Protocol Using Formalin-fixed Paraffin-embedded RNA Specimens. J Vis Exp 2018. [PMID: 29781987 DOI: 10.3791/57471] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
-Archived, clinically classified formalin-fixed paraffin-embedded (FFPE) tissues can provide nucleic acids for retrospective molecular studies of cancer development. By using non-invasive or pre-malignant lesions from patients who later develop invasive disease, gene expression analyses may help identify early molecular alterations that predispose to cancer risk. It has been well described that nucleic acids recovered from FFPE tissues have undergone severe physical damage and chemical modifications, which make their analysis difficult and generally requires adapted assays. MicroRNAs (miRNAs), however, which represent a small class of RNA molecules spanning only up to ~18-24 nucleotides, have been shown to withstand long-term storage and have been successfully analyzed in FFPE samples. Here we present a 3' barcoded complementary DNA (cDNA) library preparation protocol specifically optimized for the analysis of small RNAs extracted from archived tissues, which was recently demonstrated to be robust and highly reproducible when using archived clinical specimens stored for up to 35 years. This library preparation is well adapted to the multiplex analysis of compromised/degraded material where RNA samples (up to 18) are ligated with individual 3' barcoded adapters and then pooled together for subsequent enzymatic and biochemical preparations prior to analysis. All purifications are performed by polyacrylamide gel electrophoresis (PAGE), which allows size-specific selections and enrichments of barcoded small RNA species. This cDNA library preparation is well adapted to minute RNA inputs, as a pilot polymerase chain reaction (PCR) allows determination of a specific amplification cycle to produce optimal amounts of material for next-generation sequencing (NGS). This approach was optimized for the use of degraded FFPE RNA from specimens archived for up to 35 years and provides highly reproducible NGS data.
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Affiliation(s)
- Olivier Loudig
- Department of Research, Hackensack University Medical Center; Department of Medical Sciences, Seton Hall University; Department of Epidemiology and Population Health, Albert Einstein College of Medicine;
| | - Christina Liu
- Department of Research, Hackensack University Medical Center; Department of Medical Sciences, Seton Hall University
| | - Thomas Rohan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine
| | - Iddo Z Ben-Dov
- Department of Nephrology and Hypertension, Hadassah - Hebrew University Medical Center
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