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Paksoy A, Meller S, Schwotzer F, Moroder P, Trampuz A, Imiolczyk JP, Perka C, Hackl M, Plachel F, Akgün D. MicroRNA expression analysis in peripheral blood and soft-tissue of patients with periprosthetic hip infection. Bone Jt Open 2024; 5:479-488. [PMID: 38839054 PMCID: PMC11152758 DOI: 10.1302/2633-1462.56.bjo-2023-0172.r2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 06/07/2024] Open
Abstract
Aims Current diagnostic tools are not always able to effectively identify periprosthetic joint infections (PJIs). Recent studies suggest that circulating microRNAs (miRNAs) undergo changes under pathological conditions such as infection. The aim of this study was to analyze miRNA expression in hip arthroplasty PJI patients. Methods This was a prospective pilot study, including 24 patients divided into three groups, with eight patients each undergoing revision of their hip arthroplasty due to aseptic reasons, and low- and high-grade PJI, respectively. The number of intraoperative samples and the incidence of positive cultures were recorded for each patient. Additionally, venous blood samples and periarticular tissue samples were collected from each patient to determine miRNA expressions between the groups. MiRNA screening was performed by small RNA-sequencing using the miRNA next generation sequencing (NGS) discovery (miND) pipeline. Results Overall, several miRNAs in plasma and tissue were identified to be progressively deregulated according to ongoing PJI. When comparing the plasma samples, patients with a high-grade infection showed significantly higher expression levels for hsa-miR-21-3p, hsa-miR-1290, and hsa-miR-4488, and lower expression levels for hsa-miR-130a-3p and hsa-miR-451a compared to the aseptic group. Furthermore, the high-grade group showed a significantly higher regulated expression level of hsa-miR-1260a and lower expression levels for hsa-miR-26a-5p, hsa-miR-26b-5p, hsa-miR-148b-5p, hsa-miR-301a-3p, hsa-miR-451a, and hsa-miR-454-3p compared to the low-grade group. No significant differences were found between the low-grade and aseptic groups. When comparing the tissue samples, the high-grade group showed significantly higher expression levels for 23 different miRNAs and lower expression levels for hsa-miR-2110 and hsa-miR-3200-3p compared to the aseptic group. No significant differences were found in miRNA expression between the high- and low-grade groups, as well as between the low-grade and aseptic groups. Conclusion With this prospective pilot study, we were able to identify a circulating miRNA signature correlating with high-grade PJI compared to aseptic patients undergoing hip arthroplasty revision. Our data contribute to establishing miRNA signatures as potential novel diagnostic and prognostic biomarkers for PJI.
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Affiliation(s)
- Alp Paksoy
- Charité University Hospital, Center for Musculoskeletal Surgery, Berlin, Germany
| | - Sebastian Meller
- Charité University Hospital, Center for Musculoskeletal Surgery, Berlin, Germany
| | - Florian Schwotzer
- Charité University Hospital, Center for Musculoskeletal Surgery, Berlin, Germany
| | | | - Andrej Trampuz
- Charité University Hospital, Center for Musculoskeletal Surgery, Berlin, Germany
| | | | - Carsten Perka
- Charité University Hospital, Center for Musculoskeletal Surgery, Berlin, Germany
| | | | | | - Doruk Akgün
- Charité University Hospital, Center for Musculoskeletal Surgery, Berlin, Germany
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2
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Metcalf GAD. MicroRNAs: circulating biomarkers for the early detection of imperceptible cancers via biosensor and machine-learning advances. Oncogene 2024:10.1038/s41388-024-03076-3. [PMID: 38839942 DOI: 10.1038/s41388-024-03076-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 05/24/2024] [Accepted: 05/29/2024] [Indexed: 06/07/2024]
Abstract
This review explores the topic of microRNAs (miRNAs) for improved early detection of imperceptible cancers, with potential to advance precision medicine and improve patient outcomes. Historical research exploring miRNA's role in cancer detection collectively revealed initial hurdles in identifying specific miRNA signatures for early-stage and difficult-to-detect cancers. Early studies faced challenges in establishing robust biomarker panels and overcoming the heterogeneity of cancer types. Despite this, recent developments have supported the potential of miRNAs as sensitive and specific biomarkers for early cancer detection as well as having demonstrated remarkable potential as diagnostic tools for imperceptible cancers, such as those with elusive symptoms or challenging diagnostic criteria. This review discusses the advent of high-throughput technologies that have enabled comprehensive detection and profiling of unique miRNA signatures associated with early-stage cancers. Furthermore, advancements in bioinformatics and machine-learning techniques are considered, exploring the integration of multi-omics data which have potential to enhance both the accuracy and reliability of miRNA-based cancer detection assays. Finally, perspectives on the continuing development on technologies as well as discussion around challenges that remain, such as the need for standardised protocols and addressing the complex interplay of miRNAs in cancer biology are conferred.
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Affiliation(s)
- Gavin A D Metcalf
- School of Life Sciences, Faculty of Science and Engineering, Anglia Ruskin University, Cambridge, UK.
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3
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Weigl M, Krammer TL, Pultar M, Wieser M, Chaib S, Suda M, Diendorfer A, Khamina-Kotisch K, Giorgadze N, Pirtskhalava T, Johnson KO, Inman CL, Xue A, Lämmermann I, Meixner B, Wang L, Xu M, Grillari R, Ogrodnik M, Tchkonia T, Hackl M, Kirkland JL, Grillari J. Profiling microRNA expression during senescence and aging: mining for a diagnostic tool of senescent-cell burden. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.10.588794. [PMID: 38645053 PMCID: PMC11030445 DOI: 10.1101/2024.04.10.588794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
In the last decade cellular senescence, a hallmark of aging, has come into focus for pharmacologically targeting aging processes. Senolytics are one of these interventive strategies that have advanced into clinical trials, creating an unmet need for minimally invasive biomarkers of senescent cell load to identify patients at need for senotherapy. We created a landscape of miRNA and mRNA expression in five human cell types induced to senescence in-vitro and provide proof-of-principle evidence that miRNA expression can track senescence burden dynamically in-vivo using transgenic p21 high senescent cell clearance in HFD fed mice. Finally, we profiled miRNA expression in seven different tissues, total plasma, and plasma derived EVs of young and 25 months old mice. In a systematic analysis, we identified 22 candidate senomiRs with potential to serve as circulating biomarkers of senescence not only in rodents, but also in upcoming human clinical senolytic trials.
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4
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Erhart F, Widhalm G, Kiesel B, Hackl M, Diendorfer A, Preusser M, Rössler K, Thaler J, Pabinger I, Ay C, Riedl J. The plasma miRNome and venous thromboembolism in high-grade glioma: miRNA Sequencing of a nested case-control cohort. J Cell Mol Med 2024; 28:e18149. [PMID: 38613361 PMCID: PMC11015389 DOI: 10.1111/jcmm.18149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 12/31/2023] [Accepted: 01/05/2024] [Indexed: 04/14/2024] Open
Abstract
Patients with high-grade gliomas are at high risk of venous thromboembolism (VTE). MicroRNAs (miRNAs) are small non-coding RNAs with multiple roles in tumour biology, haemostasis and platelet function. Their association with VTE risk in high-grade glioma has not been comprehensively mapped so far. We thus conducted a nested case-control study within 152 patients with WHO grade IV glioma that had been part of a prospective cohort study on VTE risk factors. At inclusion a single blood draw was taken, and patients were thereafter followed for a maximum of 2 years. During that time, 24 patients (16%) developed VTE. Of the other 128 patients, we randomly selected 24 age- and sex-matched controls. After quality control, the final group size was 21 patients with VTE during follow-up and 23 without VTE. Small RNA next-generation sequencing of plasma was performed. We observed that hsa-miR-451a was globally the most abundant miRNA. Notably, 51% of all miRNAs showed a correlation with platelet count. The analysis of miRNAs differentially regulated in VTE patients-with and without platelet adjustment-identified potential VTE biomarker candidates such as has-miR-221-3p. Therewith, we here provide one of the largest and deepest peripheral blood miRNA datasets of high-grade glioma patients so far, in which we identified first VTE biomarker candidates that can serve as the starting point for future research.
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Affiliation(s)
- Friedrich Erhart
- Department of NeurosurgeryMedical University of ViennaViennaAustria
| | - Georg Widhalm
- Department of NeurosurgeryMedical University of ViennaViennaAustria
| | - Barbara Kiesel
- Department of NeurosurgeryMedical University of ViennaViennaAustria
| | | | | | - Matthias Preusser
- Clinical Division of OncologyDepartment of Medicine IMedical University of ViennaViennaAustria
| | - Karl Rössler
- Department of NeurosurgeryMedical University of ViennaViennaAustria
| | - Johannes Thaler
- Clinical Division of Haematology and HaemostaseologyDepartment of Medicine IMedical University of ViennaViennaAustria
| | - Ingrid Pabinger
- Clinical Division of Haematology and HaemostaseologyDepartment of Medicine IMedical University of ViennaViennaAustria
| | - Cihan Ay
- Clinical Division of Haematology and HaemostaseologyDepartment of Medicine IMedical University of ViennaViennaAustria
| | - Julia Riedl
- Clinical Division of Haematology and HaemostaseologyDepartment of Medicine IMedical University of ViennaViennaAustria
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5
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Sartorius K, Sartorius B, Winkler C, Chuturgoon A, Shen TW, Zhao Y, An P. Serum microRNA Profiles and Pathways in Hepatitis B-Associated Hepatocellular Carcinoma: A South African Study. Int J Mol Sci 2024; 25:975. [PMID: 38256049 PMCID: PMC10815595 DOI: 10.3390/ijms25020975] [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: 11/07/2023] [Revised: 12/28/2023] [Accepted: 12/29/2023] [Indexed: 01/24/2024] Open
Abstract
The incidence and mortality of hepatocellular carcinoma (HCC) in Sub-Saharan Africa is projected to increase sharply by 2040 against a backdrop of limited diagnostic and therapeutic options. Two large South African-based case control studies have developed a serum-based miRNome for Hepatitis B-associated hepatocellular carcinoma (HBV-HCC), as well as identifying their gene targets and pathways. Using a combination of RNA sequencing, differential analysis and filters including a unique molecular index count (UMI) ≥ 10 and log fold change (LFC) range > 2: <-0.5 (p < 0.05), 91 dysregulated miRNAs were characterized including 30 that were upregulated and 61 were downregulated. KEGG analysis, a literature review and other bioinformatic tools identified the targeted genes and HBV-HCC pathways of the top 10 most dysregulated miRNAs. The results, which are based on differentiating miRNA expression of cases versus controls, also develop a serum-based miRNA diagnostic panel that indicates 95.9% sensitivity, 91.0% specificity and a Youden Index of 0.869. In conclusion, the results develop a comprehensive African HBV-HCC miRNome that potentially can contribute to RNA-based diagnostic and therapeutic options.
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Affiliation(s)
- Kurt Sartorius
- Faculty of Commerce, Law and Management, University of the Witwatersrand, Johannesburg 2001, South Africa
- School of Laboratory Medicine and Molecular Sciences, University of Kwazulu-Natal, Durban 4041, South Africa;
- Africa Hepatopancreatobiliary Cancer Consortium (AHPBCC), Mayo Clinic, Jacksonville, FL 32224, USA
| | - Benn Sartorius
- School of Public Health, University of Queensland, Brisbane, QLD 4102, Australia
| | - Cheryl Winkler
- Centre for Cancer Research, Basic Research Laboratory, National Cancer Institute, Frederick Natifol Laboratory for Cancer Research, National Institute of Health, Frederick, MD 21701, USA
| | - Anil Chuturgoon
- School of Laboratory Medicine and Molecular Sciences, University of Kwazulu-Natal, Durban 4041, South Africa;
| | - Tsai-Wei Shen
- CCR-SF Bioinformatics Group, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Yongmei Zhao
- CCR-SF Bioinformatics Group, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Ping An
- Centre for Cancer Research, Basic Research Laboratory, National Cancer Institute, Frederick Natifol Laboratory for Cancer Research, National Institute of Health, Frederick, MD 21701, USA
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6
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Dobrzycka M, Sulewska A, Biecek P, Charkiewicz R, Karabowicz P, Charkiewicz A, Golaszewska K, Milewska P, Michalska-Falkowska A, Nowak K, Niklinski J, Konopińska J. miRNA Studies in Glaucoma: A Comprehensive Review of Current Knowledge and Future Perspectives. Int J Mol Sci 2023; 24:14699. [PMID: 37834147 PMCID: PMC10572595 DOI: 10.3390/ijms241914699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 09/25/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023] Open
Abstract
Glaucoma, a neurodegenerative disorder that leads to irreversible blindness, remains a challenge because of its complex nature. MicroRNAs (miRNAs) are crucial regulators of gene expression and are associated with glaucoma and other diseases. We aimed to review and discuss the advantages and disadvantages of miRNA-focused molecular studies in glaucoma through discussing their potential as biomarkers for early detection and diagnosis; offering insights into molecular pathways and mechanisms; and discussing their potential utility with respect to personalized medicine, their therapeutic potential, and non-invasive monitoring. Limitations, such as variability, small sample sizes, sample specificity, and limited accessibility to ocular tissues, are also addressed, underscoring the need for robust protocols and collaboration. Reproducibility and validation are crucial to establish the credibility of miRNA research findings, and the integration of bioinformatics tools for miRNA database creation is a valuable component of a comprehensive approach to investigate miRNA aberrations in patients with glaucoma. Overall, miRNA research in glaucoma has provided significant insights into the molecular mechanisms of the disease, offering potential biomarkers, diagnostic tools, and therapeutic targets. However, addressing challenges such as variability and limited tissue accessibility is essential, and further investigations and validation will contribute to a deeper understanding of the functional significance of miRNAs in glaucoma.
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Affiliation(s)
- Margarita Dobrzycka
- Department of Ophthalmology, Medical University of Bialystok, 15-276 Bialystok, Poland; (M.D.); (K.G.)
| | - Anetta Sulewska
- Department of Clinical Molecular Biology, Medical University of Bialystok, 15-269 Bialystok, Poland; (A.S.); (A.C.); (J.N.)
| | - Przemyslaw Biecek
- Faculty of Mathematics and Information Science, Warsaw University of Technology, 00-662 Warsaw, Poland;
| | - Radoslaw Charkiewicz
- Center of Experimental Medicine, Medical University of Bialystok, 15-369 Bialystok, Poland;
- Biobank, Medical University of Bialystok, 15-269 Bialystok, Poland; (P.K.); (P.M.); (A.M.-F.)
| | - Piotr Karabowicz
- Biobank, Medical University of Bialystok, 15-269 Bialystok, Poland; (P.K.); (P.M.); (A.M.-F.)
| | - Angelika Charkiewicz
- Department of Clinical Molecular Biology, Medical University of Bialystok, 15-269 Bialystok, Poland; (A.S.); (A.C.); (J.N.)
| | - Kinga Golaszewska
- Department of Ophthalmology, Medical University of Bialystok, 15-276 Bialystok, Poland; (M.D.); (K.G.)
| | - Patrycja Milewska
- Biobank, Medical University of Bialystok, 15-269 Bialystok, Poland; (P.K.); (P.M.); (A.M.-F.)
| | | | - Karolina Nowak
- Department of Obstetrics and Gynecology, C.S. Mott Center for Human Growth and Development, School of Medicine, Wayne State University, Detroit, MI 48201, USA;
| | - Jacek Niklinski
- Department of Clinical Molecular Biology, Medical University of Bialystok, 15-269 Bialystok, Poland; (A.S.); (A.C.); (J.N.)
| | - Joanna Konopińska
- Department of Ophthalmology, Medical University of Bialystok, 15-276 Bialystok, Poland; (M.D.); (K.G.)
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7
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Grove JI, Stephens C, Lucena MI, Andrade RJ, Weber S, Gerbes A, Bjornsson ES, Stirnimann G, Daly AK, Hackl M, Khamina-Kotisch K, Marin JJG, Monte MJ, Paciga SA, Lingaya M, Forootan SS, Goldring CEP, Poetz O, Lombaard R, Stege A, Bjorrnsson HK, Robles-Diaz M, Li D, Tran TDB, Ramaiah SK, Samodelov SL, Kullak-Ublick GA, Aithal GP. Study design for development of novel safety biomarkers of drug-induced liver injury by the translational safety biomarker pipeline (TransBioLine) consortium: a study protocol for a nested case-control study. Diagn Progn Res 2023; 7:18. [PMID: 37697410 PMCID: PMC10496294 DOI: 10.1186/s41512-023-00155-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 08/08/2023] [Indexed: 09/13/2023] Open
Abstract
A lack of biomarkers that detect drug-induced liver injury (DILI) accurately continues to hinder early- and late-stage drug development and remains a challenge in clinical practice. The Innovative Medicines Initiative's TransBioLine consortium comprising academic and industry partners is developing a prospective repository of deeply phenotyped cases and controls with biological samples during liver injury progression to facilitate biomarker discovery, evaluation, validation and qualification.In a nested case-control design, patients who meet one of these criteria, alanine transaminase (ALT) ≥ 5 × the upper limit of normal (ULN), alkaline phosphatase ≥ 2 × ULN or ALT ≥ 3 ULN with total bilirubin > 2 × ULN, are enrolled. After completed clinical investigations, Roussel Uclaf Causality Assessment and expert panel review are used to adjudicate episodes as DILI or alternative liver diseases (acute non-DILI controls). Two blood samples are taken: at recruitment and follow-up. Sample size is as follows: 300 cases of DILI and 130 acute non-DILI controls. Additional cross-sectional cohorts (1 visit) are as follows: Healthy volunteers (n = 120), controls with chronic alcohol-related or non-alcoholic fatty liver disease (n = 100 each) and patients with psoriasis or rheumatoid arthritis (n = 100, 50 treated with methotrexate) are enrolled. Candidate biomarkers prioritised for evaluation include osteopontin, glutamate dehydrogenase, cytokeratin-18 (full length and caspase cleaved), macrophage-colony-stimulating factor 1 receptor and high mobility group protein B1 as well as bile acids, sphingolipids and microRNAs. The TransBioLine project is enabling biomarker discovery and validation that could improve detection, diagnostic accuracy and prognostication of DILI in premarketing clinical trials and for clinical healthcare application.
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Affiliation(s)
- Jane I Grove
- Nottingham Digestive Diseases Centre, Translational Medical Sciences, School of Medicine, University of Nottingham, Nottingham, NG7 2UH, UK
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, UK
| | - Camilla Stephens
- Servicios de Aparato Digestivo Y Farmacologia Clínica, Instituto de Investigación Biomédica de Málaga-IBIMA Plataforma Bionand, Hospital Universitario Virgen de La Victoria, Universidad de Málaga, Malaga, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas Y Digestivas (CIBERehd), Madrid, Spain
| | - M Isabel Lucena
- Servicios de Aparato Digestivo Y Farmacologia Clínica, Instituto de Investigación Biomédica de Málaga-IBIMA Plataforma Bionand, Hospital Universitario Virgen de La Victoria, Universidad de Málaga, Malaga, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas Y Digestivas (CIBERehd), Madrid, Spain
| | - Raúl J Andrade
- Servicios de Aparato Digestivo Y Farmacologia Clínica, Instituto de Investigación Biomédica de Málaga-IBIMA Plataforma Bionand, Hospital Universitario Virgen de La Victoria, Universidad de Málaga, Malaga, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas Y Digestivas (CIBERehd), Madrid, Spain
| | - Sabine Weber
- Department of Medicine II, University Hospital, LMU Munich, Munich, Germany
| | - Alexander Gerbes
- Department of Medicine II, University Hospital, LMU Munich, Munich, Germany
| | - Einar S Bjornsson
- Department of Gastroenterology, Landspitali University Hospital Reykjavik, University of Iceland, Reykjavík, Iceland
- Faculty of Medicine, University of Iceland, Reykjavík, Iceland
| | - Guido Stirnimann
- University Clinic for Visceral Surgery and Medicine, University Hospital Inselspital and University of Bern, Bern, Switzerland
| | - Ann K Daly
- Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, NE2 4HH, UK
| | | | | | - Jose J G Marin
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas Y Digestivas (CIBERehd), Madrid, Spain
- Experimental Hepatology and Drug Targeting (HEVEPHARM), Institute of Biomedical Research of Salamanca (IBSAL), University of Salamanca, Salamanca, Spain
| | - Maria J Monte
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas Y Digestivas (CIBERehd), Madrid, Spain
- Experimental Hepatology and Drug Targeting (HEVEPHARM), Institute of Biomedical Research of Salamanca (IBSAL), University of Salamanca, Salamanca, Spain
| | - Sara A Paciga
- Worldwide Research Development and Medical, Pfizer, NY, USA
| | - Melanie Lingaya
- Nottingham Digestive Diseases Centre, Translational Medical Sciences, School of Medicine, University of Nottingham, Nottingham, NG7 2UH, UK
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, UK
| | - Shiva S Forootan
- Centre for Drug Safety Science, University of Liverpool, Liverpool, UK
| | | | | | - Rudolf Lombaard
- ABX-CRO Advanced Pharmaceutical Services, Forschungsgesellschaft mbH, Cape Town, 7441, South Africa
| | - Alexandra Stege
- Charité-Universitätsmedizin Berlin, Central Biobank Charité (ZeBanC), Berlin, Germany
| | - Helgi K Bjorrnsson
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Mercedes Robles-Diaz
- Servicios de Aparato Digestivo Y Farmacologia Clínica, Instituto de Investigación Biomédica de Málaga-IBIMA Plataforma Bionand, Hospital Universitario Virgen de La Victoria, Universidad de Málaga, Malaga, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas Y Digestivas (CIBERehd), Madrid, Spain
| | - Dingzhou Li
- Worldwide Research Development and Medical, Pfizer, NY, USA
| | | | | | - Sophia L Samodelov
- Department of Clinical Pharmacology and Toxicology, University Hospital Zurich, University of Zurich, 8006, Zurich, Switzerland
| | - Gerd A Kullak-Ublick
- Department of Clinical Pharmacology and Toxicology, University Hospital Zurich, University of Zurich, 8006, Zurich, Switzerland
- Mechanistic Safety, CMO & Patient Safety, Global Drug Development, Novartis Pharma, 4056, Basel, Switzerland
| | - Guruprasad P Aithal
- Nottingham Digestive Diseases Centre, Translational Medical Sciences, School of Medicine, University of Nottingham, Nottingham, NG7 2UH, UK.
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, UK.
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8
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Dongiovanni P, Meroni M, Casati S, Goldoni R, Thomaz DV, Kehr NS, Galimberti D, Del Fabbro M, Tartaglia GM. Salivary biomarkers: novel noninvasive tools to diagnose chronic inflammation. Int J Oral Sci 2023; 15:27. [PMID: 37386003 DOI: 10.1038/s41368-023-00231-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 05/23/2023] [Accepted: 06/05/2023] [Indexed: 07/01/2023] Open
Abstract
Several chronic disorders including type 2 diabetes (T2D), obesity, heart disease and cancer are preceded by a state of chronic low-grade inflammation. Biomarkers for the early assessment of chronic disorders encompass acute phase proteins (APP), cytokines and chemokines, pro-inflammatory enzymes, lipids and oxidative stress mediators. These substances enter saliva through the blood flow and, in some cases, there is a close relation between their salivary and serum concentration. Saliva can be easily collected and stored with non-invasive and cost-saving procedures, and it is emerging the concept to use it for the detection of inflammatory biomarkers. To this purpose, the present review aims to discuss the advantages and challenges of using standard and cutting-edge techniques to discover salivary biomarkers which may be used in diagnosis/therapy of several chronic diseases with inflammatory consequences with the pursuit to possibly replace conventional paths with detectable soluble mediators in saliva. Specifically, the review describes the procedures used for saliva collection, the standard approaches for the measurement of salivary biomarkers and the novel methodological strategies such as biosensors to improve the quality of care for chronically affected patients.
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Affiliation(s)
- Paola Dongiovanni
- Medicine and Metabolic Diseases, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Marica Meroni
- Medicine and Metabolic Diseases, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Sara Casati
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan, Italy.
| | - Riccardo Goldoni
- Department of Electronics, Information and Bioengineering (DEIB), Politecnico di Milano, Milan, Italy
- Istituto di Elettronica e di Ingegneria dell'Informazione e delle Telecomunicazioni, CNR, Pisa, Italy
| | - Douglas Vieira Thomaz
- Laboratory of Medicinal Pharmaceutical Chemistry, Faculty of Pharmacy, Federal University of Goiás, Goiânia, GO, Brazil
| | - Nermin Seda Kehr
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan, Italy
- Department of Chemistry, İzmir Institute of Technology, Gülbahçe Kampüsü, Urla İzmir, Turkey
| | - Daniela Galimberti
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan, Italy
- Neurology-Neurodegenerative Diseases, Fondazione IRCCS Cà Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Massimo Del Fabbro
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan, Italy
- UOC Maxillo-Facial Surgery and Dentistry Fondazione IRCCS Cà Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Gianluca M Tartaglia
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan, Italy
- UOC Maxillo-Facial Surgery and Dentistry Fondazione IRCCS Cà Granda, Ospedale Maggiore Policlinico, Milan, Italy
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9
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Liang LW, Hasegawa K, Maurer MS, Reilly MP, Fifer MA, Shimada YJ. Comprehensive Transcriptomics Profiling of MicroRNA Reveals Plasma Circulating Biomarkers of Hypertrophic Cardiomyopathy and Dysregulated Signaling Pathways. Circ Heart Fail 2023; 16:e010010. [PMID: 37305994 PMCID: PMC10293060 DOI: 10.1161/circheartfailure.122.010010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 03/20/2023] [Indexed: 06/13/2023]
Abstract
BACKGROUND Hypertrophic cardiomyopathy (HCM) is caused by mutations in genes coding for proteins essential for myocardial contraction. However, it remains unclear through which signaling pathways these gene mutations mediate HCM pathogenesis. Growing evidence indicates that microRNAs (miRNAs) play an important role in the regulation of gene expression. We hypothesized that transcriptomics profiling of plasma miRNAs would reveal circulating biomarkers and dysregulated signaling pathways in HCM. METHODS We conducted a multicenter case-control study of cases with HCM and controls with hypertensive left ventricular hypertrophy. We performed plasma transcriptomics profiling of miRNAs using RNA sequencing. We developed a transcriptomics-based discrimination model using samples retrieved during the first two-thirds of the study period at one institution (training set). We prospectively tested its discriminative ability in samples collected thereafter from the same institution (prospective test set). We also externally validated the model by applying it to samples collected from the other institutions (external test set). We executed pathway analysis of dysregulated miRNAs with univariable P<0.05. RESULTS This study included 555 patients (392 cases and 163 controls). One thousand one hundred forty-one miRNAs passed our quality control filters. The area under the receiver operating characteristic curve of the transcriptomics-based model derived from the training set was 0.86 (95% CI, 0.79-0.93) in the prospective test set and 0.94 (95% CI, 0.90-0.97) in the external test set. Pathway analysis revealed dysregulation of the Ras-MAPK (mitogen-activated protein kinase) pathway and pathways related to inflammation in HCM. CONCLUSIONS This study utilized comprehensive transcriptomics profiling with RNA sequencing in HCM, revealing circulating miRNA biomarkers and dysregulated pathways.
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Affiliation(s)
- Lusha W. Liang
- Division of Cardiology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Kohei Hasegawa
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Mathew S. Maurer
- Division of Cardiology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Muredach P. Reilly
- Division of Cardiology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Irving Institute for Clinical and Translational Research, Columbia University Irving Medical Center, New York, NY, USA
| | - Michael A. Fifer
- Cardiology Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Yuichi J. Shimada
- Division of Cardiology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Cardiology Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
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10
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Gómez-Martín C, Aparicio-Puerta E, van Eijndhoven MA, Medina JM, Hackenberg M, Pegtel DM. Reassessment of miRNA variant (isomiRs) composition by small RNA sequencing. CELL REPORTS METHODS 2023; 3:100480. [PMID: 37323569 PMCID: PMC10261927 DOI: 10.1016/j.crmeth.2023.100480] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 03/07/2023] [Accepted: 04/21/2023] [Indexed: 06/17/2023]
Abstract
IsomiRs, sequence variants of mature microRNAs, are usually detected and quantified using high-throughput sequencing. Many examples of their biological relevance have been reported, but sequencing artifacts identified as artificial variants might bias biological inference and therefore need to be ideally avoided. We conducted a comprehensive evaluation of 10 different small RNA sequencing protocols, exploring both a theoretically isomiR-free pool of synthetic miRNAs and HEK293T cells. We calculated that, with the exception of two protocols, less than 5% of miRNA reads can be attributed to library preparation artifacts. Randomized-end adapter protocols showed superior accuracy, with 40% of true biological isomiRs. Nevertheless, we demonstrate concordance across protocols for selected miRNAs in non-templated uridyl additions. Notably, NTA-U calling and isomiR target prediction can be inaccurate when using protocols with poor single-nucleotide resolution. Our results highlight the relevance of protocol choice for biological isomiRs detection and annotation, which has key potential implications for biomedical applications.
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Affiliation(s)
- Cristina Gómez-Martín
- Amsterdam UMC Location Vrije Universiteit Amsterdam, Pathology, De Boelelaan, 1117 Amsterdam, the Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, the Netherlands
| | | | - Monique A.J. van Eijndhoven
- Amsterdam UMC Location Vrije Universiteit Amsterdam, Pathology, De Boelelaan, 1117 Amsterdam, the Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, the Netherlands
| | - José M. Medina
- Department of Genetics, Faculty of Science, University of Granada, 18071 Granada, Spain
- Bioinformatics Laboratory, Biotechnology Institute, Centro de Investigación Biomédica, PTS, Avda. del Conocimiento s/n, 18100 Granada, Spain
| | - Michael Hackenberg
- Department of Genetics, Faculty of Science, University of Granada, 18071 Granada, Spain
- Bioinformatics Laboratory, Biotechnology Institute, Centro de Investigación Biomédica, PTS, Avda. del Conocimiento s/n, 18100 Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, University of Granada, 18071 Granada, Spain
- Excellence Research Unit “Modelling Nature” (MNat), University of Granada, 18071 Granada, Spain
| | - D. Michiel Pegtel
- Amsterdam UMC Location Vrije Universiteit Amsterdam, Pathology, De Boelelaan, 1117 Amsterdam, the Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, the Netherlands
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11
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Zhang J, Campion S, Catlin N, Reagan WJ, Palyada K, Ramaiah SK, Ramanathan R. Circulating microRNAs as promising testicular translatable safety biomarkers: current state and future perspectives. Arch Toxicol 2023; 97:947-961. [PMID: 36795116 PMCID: PMC9933818 DOI: 10.1007/s00204-023-03460-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 02/07/2023] [Indexed: 02/17/2023]
Abstract
Drug-induced testicular injury (DITI) is one of the often-observed and challenging safety issues seen during drug development. Semen analysis and circulating hormones currently utilized have significant gaps in their ability to detect testicular damage accurately. In addition, no biomarkers enable a mechanistic understanding of the damage to the different regions of the testis, such as seminiferous tubules, Sertoli, and Leydig cells. MicroRNAs (miRNAs) are a class of non-coding RNAs that modulate gene expression post-transcriptionally and have been indicated to regulate a wide range of biological pathways. Circulating miRNAs can be measured in the body fluids due to tissue-specific cell injury/damage or toxicant exposure. Therefore, these circulating miRNAs have become attractive and promising non-invasive biomarkers for assessing drug-induced testicular injury, with several reports on their use as safety biomarkers for monitoring testicular damage in preclinical species. Leveraging emerging tools such as 'organs-on-chips' that can emulate the human organ's physiological environment and function is starting to enable biomarker discovery, validation, and clinical translation for regulatory qualification and implementation in drug development.
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Affiliation(s)
- Jiangwei Zhang
- Drug Safety Research & Development, Pfizer Worldwide Research, Development & Medical, 10777 Science Center Dr, San Diego, CA, USA
| | - Sarah Campion
- Drug Safety Research & Development, Pfizer Worldwide Research, Development & Medical, 445 Eastern Point Rd., Groton, CT, USA
| | - Natasha Catlin
- Drug Safety Research & Development, Pfizer Worldwide Research, Development & Medical, 445 Eastern Point Rd., Groton, CT, USA
| | - William J Reagan
- Drug Safety Research & Development, Pfizer Worldwide Research, Development & Medical, 445 Eastern Point Rd., Groton, CT, USA
| | - Kiran Palyada
- Drug Safety Research & Development, Pfizer Worldwide Research, Development & Medical, 10777 Science Center Dr, San Diego, CA, USA
| | - Shashi K Ramaiah
- Drug Safety Research & Development, Pfizer Worldwide Research, Development & Medical, 1 Portland St., Cambridge, MA, 02139, USA
| | - Ragu Ramanathan
- Drug Safety Research & Development, Pfizer Worldwide Research, Development & Medical, 445 Eastern Point Rd., Groton, CT, USA.
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12
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Reiss AB, Ahmed S, Johnson M, Saeedullah U, De Leon J. Exosomes in Cardiovascular Disease: From Mechanism to Therapeutic Target. Metabolites 2023; 13:479. [PMID: 37110138 PMCID: PMC10142472 DOI: 10.3390/metabo13040479] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/22/2023] [Accepted: 03/24/2023] [Indexed: 03/29/2023] Open
Abstract
Cardiovascular disease (CVD) is the leading cause of morbidity and mortality globally. In recent decades, clinical research has made significant advances, resulting in improved survival and recovery rates for patients with CVD. Despite this progress, there is substantial residual CVD risk and an unmet need for better treatment. The complex and multifaceted pathophysiological mechanisms underlying the development of CVD pose a challenge for researchers seeking effective therapeutic interventions. Consequently, exosomes have emerged as a new focus for CVD research because their role as intercellular communicators gives them the potential to act as noninvasive diagnostic biomarkers and therapeutic nanocarriers. In the heart and vasculature, cell types such as cardiomyocytes, endothelial cells, vascular smooth muscle, cardiac fibroblasts, inflammatory cells, and resident stem cells are involved in cardiac homeostasis via the release of exosomes. Exosomes encapsulate cell-type specific miRNAs, and this miRNA content fluctuates in response to the pathophysiological setting of the heart, indicating that the pathways affected by these differentially expressed miRNAs may be targets for new treatments. This review discusses a number of miRNAs and the evidence that supports their clinical relevance in CVD. The latest technologies in applying exosomal vesicles as cargo delivery vehicles for gene therapy, tissue regeneration, and cell repair are described.
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Affiliation(s)
- Allison B. Reiss
- Department of Medicine and Biomedical Research Institute, NYU Long Island School of Medicine, Mineola, NY 11501, USA
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13
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Ratre P, Nazeer N, Kumari R, Thareja S, Jain B, Tiwari R, Kamthan A, Srivastava RK, Mishra PK. Carbon-Based Fluorescent Nano-Biosensors for the Detection of Cell-Free Circulating MicroRNAs. BIOSENSORS 2023; 13:226. [PMID: 36831992 PMCID: PMC9953975 DOI: 10.3390/bios13020226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 02/02/2023] [Accepted: 02/02/2023] [Indexed: 06/18/2023]
Abstract
Currently, non-communicable diseases (NCDs) have emerged as potential risks for humans due to adopting a sedentary lifestyle and inaccurate diagnoses. The early detection of NCDs using point-of-care technologies significantly decreases the burden and will be poised to transform clinical intervention and healthcare provision. An imbalance in the levels of circulating cell-free microRNAs (ccf-miRNA) has manifested in NCDs, which are passively released into the bloodstream or actively produced from cells, improving the efficacy of disease screening and providing enormous sensing potential. The effective sensing of ccf-miRNA continues to be a significant technical challenge, even though sophisticated equipment is needed to analyze readouts and expression patterns. Nanomaterials have come to light as a potential solution as they provide significant advantages over other widely used diagnostic techniques to measure miRNAs. Particularly, CNDs-based fluorescence nano-biosensors are of great interest. Owing to the excellent fluorescence characteristics of CNDs, developing such sensors for ccf-microRNAs has been much more accessible. Here, we have critically examined recent advancements in fluorescence-based CNDs biosensors, including tools and techniques used for manufacturing these biosensors. Green synthesis methods for scaling up high-quality, fluorescent CNDs from a natural source are discussed. The various surface modifications that help attach biomolecules to CNDs utilizing covalent conjugation techniques for multiple applications, including self-assembly, sensing, and imaging, are analyzed. The current review will be of particular interest to researchers interested in fluorescence-based biosensors, materials chemistry, nanomedicine, and related fields, as we focus on CNDs-based nano-biosensors for ccf-miRNAs detection applications in the medical field.
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Affiliation(s)
- Pooja Ratre
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal 462030, India
| | - Nazim Nazeer
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal 462030, India
| | - Roshani Kumari
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal 462030, India
| | - Suresh Thareja
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda 151401, India
| | - Bulbul Jain
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal 462030, India
| | - Rajnarayan Tiwari
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal 462030, India
| | - Arunika Kamthan
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal 462030, India
| | - Rupesh K. Srivastava
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Pradyumna Kumar Mishra
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal 462030, India
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14
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Messner Z, Carro-Vazquez D, Haschka J, Grillari J, Resch H, Muschitz C, Pietschmann P, Zwerina J, Hackl M, Kocijan R. Circulating miRNAs Respond to Denosumab Treatment after Two Years in Postmenopausal Women with Osteoporosis. J Clin Endocrinol Metab 2022; 108:1154-1165. [PMID: 36408612 PMCID: PMC10099174 DOI: 10.1210/clinem/dgac667] [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: 07/19/2022] [Revised: 10/19/2022] [Accepted: 11/14/2022] [Indexed: 11/22/2022]
Abstract
CONTEXT MicroRNAs (miRNAs) are short, single-stranded, non-coding RNAs which regulate gene expression. They originate from various tissues including bone and regulate different biological mechanisms including bone metabolism. OBJECTIVE The aim of this project was to investigate circulating miRNAs as promising biomarkers for treatment monitoring in women with postmenopausal osteoporosis on denosumab (DMAB) therapy. DESIGN, SETTING AND PATIENTS In this prospective, observational, single-centre study twenty-one postmenopausal women treated with DMAB were included for a longitudinal follow-up of two years. INTERVENTIONS AND MAIN OUTCOME MEASURES Next-generation sequencing (NGS) was performed to screen for serological miRNAs at defined time points (baseline, month 6 and month 24). Reverse transcription quantitative polymerase chain reaction (RT-qPCR) was used to confirm NGS findings in the entire cohort. Bone turnover markers (BTM) P1NP and CTX, and bone mineral density (BMD) by Dual X-Ray absorptiometry (DXA) were assessed and correlated to miRNAs. RESULTS BMD at the hip (5,5%, p = 0.0006) and lumbar spine significantly increased (11,4%, p-value = 0.017) and CTX (64,1%, p < 0.0001) and P1NP (69,3%, p < 0.0001) significantly decreased during treatment. NGS analysis revealed significant changes in miRNAs after 2-years of DMAB treatment, but not after 6-months. Seven miRNAs were confirmed by RT-qPCR to be significantly changed during a 2-year course of DMAB treatment compared to baseline. Four of these were found to be mainly transcribed in blood cells including monocytes. Correlation analysis identified a significant correlation between change in miRNA and change in BTMs as well as BMD. Based on effect size and correlation strength, miR-454-3p, miR-26b-5p and miR-584-5p were defined as top biomarker candidates with the strongest association to the sustained effect of denosumab on bone in osteoporotic patients. CONCLUSIONS Two years of DMAB-treatment resulted in the upregulation of 7 miRNAs, four of which are mainly transcribed in monocytes indicating a potential impact of DMAB on circulating osteoclast precursor cells. These changes were associated to BMD gain and BTM suppression and could therefore be useful for monitoring DMAB-treatment response.
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Affiliation(s)
- Zora Messner
- St. Vincent Hospital Vienna, 2nd Department of Internal Medicine - VINFORCE
| | - David Carro-Vazquez
- University of Natural Resources and Life Sciences Vienna (Department of Biotechnology)
- TAmiRNA GmbH, Vienna, Austria
| | - Judith Haschka
- Ludwig Boltzmann Institute of Osteology at Hanusch Hospital of OEGK and AUVA
| | - Johannes Grillari
- Trauma Centre Meidling, 1st Med. Dept. Hanusch Hospital, Heinrich Collin-Str. 30, Vienna
| | - Heinrich Resch
- St. Vincent Hospital Vienna, 2nd Department of Internal Medicine - VINFORCE
- Sigmund Freud University Vienna, School of medicine, Metabolic bone diseases unit
| | - Christian Muschitz
- St. Vincent Hospital Vienna, 2nd Department of Internal Medicine - VINFORCE
| | - Peter Pietschmann
- Medical University of Vienna, Center for Pathophysiology, Infectiology and Immunology, Institute of Pathophysiology and Allergy Research
| | - Jochen Zwerina
- Ludwig Boltzmann Institute of Osteology at Hanusch Hospital of OEGK and AUVA
| | | | - Roland Kocijan
- Ludwig Boltzmann Institute of Osteology at Hanusch Hospital of OEGK and AUVA
- Sigmund Freud University Vienna, School of medicine, Metabolic bone diseases unit
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15
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Wijesinghe SN, Anderson J, Brown TJ, Nanus DE, Housmans B, Green JA, Hackl M, Choi KK, Arkill KP, Welting T, James V, Jones SW, Peffers MJ. The role of extracellular vesicle miRNAs and tRNAs in synovial fibroblast senescence. Front Mol Biosci 2022; 9:971621. [PMID: 36213127 PMCID: PMC9537453 DOI: 10.3389/fmolb.2022.971621] [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: 06/17/2022] [Accepted: 09/06/2022] [Indexed: 11/24/2022] Open
Abstract
Extracellular vesicles are mediators of intercellular communication with critical roles in cellular senescence and ageing. In arthritis, senescence is linked to the activation of a pro-inflammatory phenotype contributing to chronic arthritis pathogenesis. We hypothesised that senescent osteoarthritic synovial fibroblasts induce senescence and a pro-inflammatory phenotype in non-senescent osteoarthritic fibroblasts, mediated through extracellular vesicle cargo. Small RNA-sequencing and mass spectrometry proteomics were performed on extracellular vesicles isolated from the secretome of non-senescent and irradiation-induced senescent synovial fibroblasts. β-galactosidase staining confirmed senescence in SFs. RNA sequencing identified 17 differentially expressed miRNAs, 11 lncRNAs, 14 tRNAs and one snoRNA and, 21 differentially abundant proteins were identified by mass spectrometry. Bioinformatics analysis of miRNAs identified fibrosis, cell proliferation, autophagy, and cell cycle as significant pathways, tRNA analysis was enriched for signaling pathways including FGF, PI3K/AKT and MAPK, whilst protein analysis identified PAX3-FOXO1, MYC and TFGB1 as enriched upstream regulators involved in senescence and cell cycle arrest. Finally, treatment of non-senescent synovial fibroblasts with senescent extracellular vesicles confirmed the bystander effect, inducing senescence in non-senescent cells potentially through down regulation of NF-κβ and cAMP response element signaling pathways thus supporting our hypothesis. Understanding the exact composition of EV-derived small RNAs of senescent cells in this way will inform our understanding of their roles in inflammation, intercellular communication, and as active molecules in the senescence bystander effect.
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Affiliation(s)
- Susanne N. Wijesinghe
- Institute of Inflammation and Ageing, MRC- Versus Arthritis Centre for Musculoskeletal Ageing Research, University of Birmingham, Birmingham, United Kingdom
| | - James Anderson
- Institute of Life Course and Medical Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Thomas J. Brown
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, United Kingdom
| | - Dominika E. Nanus
- Institute of Inflammation and Ageing, MRC- Versus Arthritis Centre for Musculoskeletal Ageing Research, University of Birmingham, Birmingham, United Kingdom
| | - Bas Housmans
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University Medical Center, Maastricht, Netherlands
| | | | | | - Katie K. Choi
- School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Kenton P. Arkill
- School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Tim Welting
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University Medical Center, Maastricht, Netherlands
| | - Victoria James
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, United Kingdom
| | - Simon W. Jones
- Institute of Inflammation and Ageing, MRC- Versus Arthritis Centre for Musculoskeletal Ageing Research, University of Birmingham, Birmingham, United Kingdom
| | - Mandy J. Peffers
- Institute of Life Course and Medical Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, United Kingdom
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16
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Carro Vázquez D, Emini L, Rauner M, Hofbauer C, Grillari J, Diendorfer AB, Eastell R, Hofbauer LC, Hackl M. Effect of Anti-Osteoporotic Treatments on Circulating and Bone MicroRNA Patterns in Osteopenic ZDF Rats. Int J Mol Sci 2022; 23:6534. [PMID: 35742976 PMCID: PMC9224326 DOI: 10.3390/ijms23126534] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/03/2022] [Accepted: 06/08/2022] [Indexed: 02/05/2023] Open
Abstract
Bone fragility is an adverse outcome of type 2 diabetes mellitus (T2DM). The underlying molecular mechanisms have, however, remained largely unknown. MicroRNAs (miRNAs) are short non-coding RNAs that control gene expression in health and disease states. The aim of this study was to investigate the genome-wide regulation of miRNAs in T2DM bone disease by analyzing serum and bone tissue samples from a well-established rat model of T2DM, the Zucker Diabetic Fatty (ZDF) model. We performed small RNA-sequencing analysis to detect dysregulated miRNAs in the serum and ulna bone of the ZDF model under placebo and also under anti-sclerostin, PTH, and insulin treatments. The dysregulated circulating miRNAs were investigated for their cell-type enrichment to identify putative donor cells and were used to construct gene target networks. Our results show that unique sets of miRNAs are dysregulated in the serum (n = 12, FDR < 0.2) and bone tissue (n = 34, FDR < 0.2) of ZDF rats. Insulin treatment was found to induce a strong dysregulation of circulating miRNAs which are mainly involved in metabolism, thereby restoring seven circulating miRNAs in the ZDF model to normal levels. The effects of anti-sclerostin treatment on serum miRNA levels were weaker, but affected miRNAs were shown to be enriched in bone tissue. PTH treatment did not produce any effect on circulating or bone miRNAs in the ZDF rats. Altogether, this study provides the first comprehensive insights into the dysregulation of bone and serum miRNAs in the context of T2DM and the effect of insulin, PTH, and anti-sclerostin treatments on circulating miRNAs.
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Affiliation(s)
- David Carro Vázquez
- TAmiRNA GmbH, Department of Research, Leberstrasse 20, 1110 Vienna, Austria; (D.C.V.); (A.B.D.)
| | - Lejla Emini
- Center for Healthy Aging and Department of Medicine III, Technische Universität Dresden, 01069 Dresden, Germany; (L.E.); (M.R.); (C.H.); (L.C.H.)
| | - Martina Rauner
- Center for Healthy Aging and Department of Medicine III, Technische Universität Dresden, 01069 Dresden, Germany; (L.E.); (M.R.); (C.H.); (L.C.H.)
| | - Christine Hofbauer
- Center for Healthy Aging and Department of Medicine III, Technische Universität Dresden, 01069 Dresden, Germany; (L.E.); (M.R.); (C.H.); (L.C.H.)
| | - Johannes Grillari
- Ludwig Boltzmann Institute for Traumatology in Cooperation with AUVA, Ludwig Boltzmann Society, 1200 Vienna, Austria;
- Institute of Molecular Biotechnology, University of Natural Resources and Life Sciences, 1180 Vienna, Austria
- Austrian Cluster for Tissue Regeneration, 1200 Vienna, Austria
| | - Andreas B. Diendorfer
- TAmiRNA GmbH, Department of Research, Leberstrasse 20, 1110 Vienna, Austria; (D.C.V.); (A.B.D.)
| | - Richard Eastell
- Academic Unit of Bone Metabolism and Mellanby Centre for Bone Research, University of Sheffield, Sheffield S10 2RX, UK;
| | - Lorenz C. Hofbauer
- Center for Healthy Aging and Department of Medicine III, Technische Universität Dresden, 01069 Dresden, Germany; (L.E.); (M.R.); (C.H.); (L.C.H.)
| | - Matthias Hackl
- TAmiRNA GmbH, Department of Research, Leberstrasse 20, 1110 Vienna, Austria; (D.C.V.); (A.B.D.)
- Austrian Cluster for Tissue Regeneration, 1200 Vienna, Austria
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17
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Almatroudi A. Non-Coding RNAs in Tuberculosis Epidemiology: Platforms and Approaches for Investigating the Genome's Dark Matter. Int J Mol Sci 2022; 23:ijms23084430. [PMID: 35457250 PMCID: PMC9024992 DOI: 10.3390/ijms23084430] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/05/2022] [Accepted: 04/14/2022] [Indexed: 02/07/2023] Open
Abstract
A growing amount of information about the different types, functions, and roles played by non-coding RNAs (ncRNAs) is becoming available, as more and more research is done. ncRNAs have been identified as potential therapeutic targets in the treatment of tuberculosis (TB), because they may be essential regulators of the gene network. ncRNA profiling and sequencing has recently revealed significant dysregulation in tuberculosis, primarily due to aberrant processes of ncRNA synthesis, including amplification, deletion, improper epigenetic regulation, or abnormal transcription. Despite the fact that ncRNAs may have a role in TB characteristics, the detailed mechanisms behind these occurrences are still unknown. The dark matter of the genome can only be explored through the development of cutting-edge bioinformatics and molecular technologies. In this review, ncRNAs' synthesis and functions are discussed in detail, with an emphasis on the potential role of ncRNAs in tuberculosis. We also focus on current platforms, experimental strategies, and computational analyses to explore ncRNAs in TB. Finally, a viewpoint is presented on the key challenges and novel techniques for the future and for a wide-ranging therapeutic application of ncRNAs.
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Affiliation(s)
- Ahmad Almatroudi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
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18
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Diendorfer A, Khamina K, Pultar M, Hackl M. miND (miRNA NGS Discovery pipeline): a small RNA-seq analysis pipeline and report generator for microRNA biomarker discovery studies. F1000Res 2022. [DOI: 10.12688/f1000research.94159.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
In contrast to traditional methods like real-time polymerase chain reaction, next-generation sequencing (NGS), and especially small RNA-seq, enables the untargeted investigation of the whole small RNAome, including microRNAs (miRNAs) but also a multitude of other RNA species. With the promising application of small RNAs as biofluid-based biomarkers, small RNA-seq is the method of choice for an initial discovery study. However, the presentation of specific quality aspects of small RNA-seq data varies significantly between laboratories and is lacking a common (minimal) standard. The miRNA NGS Discovery pipeline (miND) aims to bridge the gap between wet lab scientist and bioinformatics with an easy to setup configuration sheet and an automatically generated comprehensive report that contains all essential qualitative and quantitative results that should be reported. Besides the standard steps like preprocessing, mapping, visualization, and quantification of reads, the pipeline also incorporates differential expression analysis when given the appropriate information regarding sample groups. Although miND has a focus on miRNAs, other RNA species like tRNAs, piRNA, snRNA, or snoRNA are included and mapping statistics are available for further analysis. miND has been developed and tested on a multitude of data sets with various RNA sources (tissue, plasma, extracellular vesicles, urine, etc.) and different species. miND is a Snakemake based pipeline and thus incorporates all advantages using a flexible workflow management system. Reference databases are downloaded, prepared and built with an included (but separate) workflow and thus can easily be updated to the most recent version but also stored for reproducibility. In conclusion, the miND pipeline aims to streamline the bioinformatics processing of small RNA-seq data by standardizing the processing from raw data to a final, comprehensive and reproducible report.
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19
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Maguire S, Guan S. Rolling circle reverse transcription enables high fidelity nanopore sequencing of small RNA. PLoS One 2022; 17:e0275471. [PMID: 36215256 PMCID: PMC9550094 DOI: 10.1371/journal.pone.0275471] [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: 07/06/2022] [Accepted: 09/17/2022] [Indexed: 11/07/2022] Open
Abstract
Small RNAs (sRNAs) are an important group of non-coding RNAs that have great potential as diagnostic and prognostic biomarkers for treatment of a wide variety of diseases. The portability and affordability of nanopore sequencing technology makes it ideal for point of care and low resource settings. Currently sRNAs can't be reliably sequenced on the nanopore platform due to the short size of sRNAs and high error rate of the nanopore sequencer. Here, we developed a highly efficient nanopore-based sequencing strategy for sRNAs (SR-Cat-Seq) in which sRNAs are ligated to an adapter, circularized, and undergo rolling circle reverse transcription to generate concatemeric cDNA. After sequencing, the resulting tandem repeat sequences within the individual cDNA can be aligned to generate highly accurate consensus sequences. We compared our sequencing strategy with other sRNA sequencing methods on a short-read sequencing platform and demonstrated that SR-Cat-Seq can obtain low bias and highly accurate sRNA transcriptomes. Therefore, our method could enable nanopore sequencing for sRNA-based diagnostics and other applications.
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Affiliation(s)
- Sean Maguire
- New England Biolabs, Inc., Beverly, MA, United States of America
| | - Shengxi Guan
- New England Biolabs, Inc., Beverly, MA, United States of America
- * E-mail:
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