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Shetti D, Mallela VR, Ye W, Sharif M, Ambrozkiewicz F, Trailin A, Liška V, Hemminki K. Emerging role of circulating cell-free RNA as a non-invasive biomarker for hepatocellular carcinoma. Crit Rev Oncol Hematol 2024; 200:104391. [PMID: 38795877 DOI: 10.1016/j.critrevonc.2024.104391] [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: 03/14/2024] [Revised: 04/30/2024] [Accepted: 05/19/2024] [Indexed: 05/28/2024] Open
Abstract
Hepatocellular carcinoma (HCC) is a severe neoplastic disease associated with high morbidity and mortality rates. HCC is often detected at advanced stages leading to ineffective curative treatments. Recently, liquid biopsy has emerged as a non-invasive method to identify highly specific HCC biomarkers in bodily fluids such as blood, serum, urine, and saliva. Circulating cell-free nucleic acids (cfNAs), particularly cell-free DNA (cfDNA) and cell-free RNA (cfRNA), have become promising candidates for biomarkers in liquid biopsy applications. While cfDNA presented significant challenges, researchers have turned their attention to cfRNA, which can be efficiently identified through various methods and is considered a potential biomarker for cancer diagnosis and prognosis. This review primarily focuses on studies related to detecting various cfRNA in body fluids as biomarkers. The aim is to provide a summary of available information to assist researchers in their investigations and the development of new diagnostic and prognostic tools.
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Affiliation(s)
- Dattatrya Shetti
- Laboratory of Translational Cancer Genomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1665/76, Pilsen 323 00, Czech Republic.
| | - Venkata Ramana Mallela
- Laboratory of Translational Cancer Genomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1665/76, Pilsen 323 00, Czech Republic
| | - Wenjing Ye
- Laboratory of Translational Cancer Genomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1665/76, Pilsen 323 00, Czech Republic
| | - Mahyar Sharif
- Department of Histology and Embryology, Faculty of Medicine in Pilsen, Charles University,Alej Svobody 1665/76, Pilsen 323 00, Czech Republic
| | - Filip Ambrozkiewicz
- Laboratory of Translational Cancer Genomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1665/76, Pilsen 323 00, Czech Republic
| | - Andriy Trailin
- Laboratory of Translational Cancer Genomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1665/76, Pilsen 323 00, Czech Republic
| | - Václav Liška
- Laboratory of Cancer Treatment and Tissue Regeneration, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1665/76, Pilsen 323 00, Czech Republic; Department of Surgery, University Hospital in Pilsen and Faculty of Medicine in Pilsen, Charles University, Alej Svobody 80, Pilsen 323 00, Czech Republic
| | - Kari Hemminki
- Laboratory of Translational Cancer Genomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1665/76, Pilsen 323 00, Czech Republic; Department of Cancer Epidemiology, German Cancer Research Center, Im Neuenheimer Feld 280, Heidelberg 69120, 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; 43:2135-2142. [PMID: 38839942 PMCID: PMC11226400 DOI: 10.1038/s41388-024-03076-3] [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: 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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Zendjabil M. Preanalytical, analytical and postanalytical considerations in circulating microRNAs measurement. Biochem Med (Zagreb) 2024; 34:020501. [PMID: 38882585 PMCID: PMC11177657 DOI: 10.11613/bm.2024.020501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 03/08/2024] [Indexed: 06/18/2024] Open
Abstract
Microribonucleic acids (miRNAs) have emerged as a new category of biomarkers for many human diseases like cancer, cardiovascular and neurodegenerative disorders. MicroRNAs can be detected in various body fluids including blood, urine and cerebrospinal fluid. However, the literature contains conflicting results for circulating miRNAs, which is the main barrier to using miRNAs as non-invasive biomarkers. This variability in results is largely due to differences between studies in sample processing methodology, miRNA quantification and result normalization. The purpose of this review is to describe the various preanalytical, analytical and postanalytical factors that can impact miRNA detection accuracy and to propose recommendations for the standardization of circulating miRNAs measurement.
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Affiliation(s)
- Mustapha Zendjabil
- Faculty of Medicine, University of Oran 1 - Ahmed Ben Bella, Oran, Algeria
- Department of Biochemistry, Oran University Hospital, Oran, Algeria
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4
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Shinde DB, Mahore JG, Giram PS, Singh SL, Sharda A, Choyan D, Musale S. Microbiota of Saliva: A Non-invasive Diagnostic Tool. Indian J Microbiol 2024; 64:328-342. [PMID: 39010986 PMCID: PMC11246313 DOI: 10.1007/s12088-024-01219-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 01/30/2024] [Indexed: 07/17/2024] Open
Abstract
Potential of salivary microbiota as a non-invasive diagnostic tool for various diseases are explained in the present review. Traditional diagnostic methods rely on blood, which has limitations in terms of collection and biomarker specificity. We discuss the concept of normal flora and how disruptions in oral microbiota can be indicative of diseases. Saliva, harboring a diverse microbial community, offers promise as a diagnostic biomarker source for oral and non-oral conditions. We delve into the role of microbial dysbiosis in disease pathogenesis and the prospects of using biological indicators like dysbiosis for diagnosis, prediction, and monitoring. This review also emphasizes the significance of saliva microbiota in advancing early disease detection and timely intervention. We addressed the following research question and objectives: Can the microbiota of saliva serve as a non-invasive diagnostic tool for the early detection and monitoring of both oral and non-oral diseases? To achieve this, we will explore the normal flora of microorganisms in the oral cavity, the impact of microbial dysbiosis, and the potential of using specific pathogenic microorganisms as biomarkers. Additionally, we will investigate the correlation between oral and non-oral diseases by analyzing total saliva or site-specific dental biofilms for signs of symbiosis or dysbiosis. This research seeks to contribute valuable insights into the development of a non-invasive diagnostic approach with broad applications in healthcare.
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Affiliation(s)
- Dasharath B Shinde
- Symbiosis School of Biological Sciences (SSBS), Symbiosis International (Deemed University), Pune, 412115 India
| | - Jayashri G Mahore
- Dr. D. Y. Patil Institute of Pharmaceutical Sciences and Research, Pimpri, Pune, 411018 India
- Sinhgad College of Pharmacy, Vadgaon (Bk.), Pune, 411041 India
| | - Prabhanjan S Giram
- Dr. D. Y. Patil Institute of Pharmaceutical Sciences and Research, Pimpri, Pune, 411018 India
- Department of Pharmaceutical Sciences, The State University of New York, Buffalo, NY 14214 USA
| | - Shaktikumar L Singh
- Dr. D. Y. Patil Institute of Pharmaceutical Sciences and Research, Pimpri, Pune, 411018 India
| | - Aditi Sharda
- Dr. D. Y. Patil Institute of Pharmaceutical Sciences and Research, Pimpri, Pune, 411018 India
| | - Divya Choyan
- Dr. D. Y. Patil Institute of Pharmaceutical Sciences and Research, Pimpri, Pune, 411018 India
| | - Shubham Musale
- Dr. D. Y. Patil Institute of Pharmaceutical Sciences and Research, Pimpri, Pune, 411018 India
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5
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Grätz C, Schuster M, Brandes F, Meidert AS, Kirchner B, Reithmair M, Schelling G, Pfaffl MW. A pipeline for the development and analysis of extracellular vesicle-based transcriptomic biomarkers in molecular diagnostics. Mol Aspects Med 2024; 97:101269. [PMID: 38552453 DOI: 10.1016/j.mam.2024.101269] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 03/11/2024] [Accepted: 03/17/2024] [Indexed: 06/12/2024]
Abstract
Extracellular vesicles are shed by every cell type and can be found in any biofluid. They contain different molecules that can be utilized as biomarkers, including several RNA species which they protect from degradation. Here, we present a pipeline for the development and analysis of extracellular vesicle-associated transcriptomic biomarkers that our group has successfully applied multiple times. We highlight the key steps of the pipeline and give particular emphasis to the necessary quality control checkpoints, which are linked to numerous available guidelines that should be considered along the workflow. Our pipeline starts with patient recruitment and continues with blood sampling and processing. The purification and characterization of extracellular vesicles is explained in detail, as well as the isolation and quality control of extracellular vesicle-associated RNA. We point out the possible pitfalls during library preparation and RNA sequencing and present multiple bioinformatic tools to pinpoint biomarker signature candidates from the sequencing data. Finally, considerations and pitfalls during the validation of the biomarker signature using RT-qPCR will be elaborated.
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Affiliation(s)
- Christian Grätz
- Department of Animal Physiology and Immunology, School of Life Sciences, Technical University of Munich, Freising, Germany.
| | - Martina Schuster
- Institute of Human Genetics, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Florian Brandes
- Department of Anesthesiology, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Agnes S Meidert
- Department of Anesthesiology, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Benedikt Kirchner
- Department of Animal Physiology and Immunology, School of Life Sciences, Technical University of Munich, Freising, Germany; Institute of Human Genetics, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Marlene Reithmair
- Institute of Human Genetics, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Gustav Schelling
- Department of Anesthesiology, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Michael W Pfaffl
- Department of Animal Physiology and Immunology, School of Life Sciences, Technical University of Munich, Freising, Germany.
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6
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Rishan ST, Kline RJ, Rahman MS. New prospects of environmental RNA metabarcoding research in biological diversity, ecotoxicological monitoring, and detection of COVID-19: a critical review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:11406-11427. [PMID: 38183542 DOI: 10.1007/s11356-023-31776-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 12/26/2023] [Indexed: 01/08/2024]
Abstract
Ecosystems are multifaceted and complex systems and understanding their composition is crucial for the implementation of efficient conservation and management. Conventional approaches to biodiversity surveys can have limitations in detecting the complete range of species present. In contrast, the study of environmental RNA (eRNA) offers a non-invasive and comprehensive method for monitoring and evaluating biodiversity across different ecosystems. Similar to eDNA, the examination of genetic material found in environmental samples can identify and measure many species, including ones that pose challenges to traditional methods. However, eRNA is degraded quickly and therefore shows promise in detection of living organisms closer to their actual location than eDNA methods. This method provides a comprehensive perspective on the well-being of ecosystems, facilitating the development of focused conservation approaches to save at-risk species and uphold ecological equilibrium. Furthermore, eRNA has been recognized as a valuable method for the identification of COVID-19 in the environment, besides its established uses in biodiversity protection. The SARS-CoV-2 virus, which is accountable for the worldwide epidemic, releases RNA particles into the surrounding environment via human waste, providing insights into the feasibility of detecting it in wastewater and other samples taken from the environment. In this article, we critically reviewed the recent research activities that use the eRNA method, including its utilization in biodiversity conservation, ecological surveillance, and ecotoxicological monitoring as well as its innovative potential in identifying COVID-19. Through this review, the reader can understand the recent developments, prospects, and challenges of eRNA research in ecosystem management and biodiversity conservation.
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Affiliation(s)
- Sakib Tahmid Rishan
- Biochemistry and Molecular Biology Program, School of Integrative Biological and Chemical Sciences, University of Texas Rio Grande Valley, Brownsville, TX, USA
| | - Richard J Kline
- Biochemistry and Molecular Biology Program, School of Integrative Biological and Chemical Sciences, University of Texas Rio Grande Valley, Brownsville, TX, USA
- School of Earth, Environmental, and Marine Sciences, University of Texas Rio Grande Valley, Brownsville, TX, USA
| | - Md Saydur Rahman
- Biochemistry and Molecular Biology Program, School of Integrative Biological and Chemical Sciences, University of Texas Rio Grande Valley, Brownsville, TX, USA.
- School of Earth, Environmental, and Marine Sciences, University of Texas Rio Grande Valley, Brownsville, TX, USA.
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7
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Wagner V, Kern F, Hahn O, Schaum N, Ludwig N, Fehlmann T, Engel A, Henn D, Rishik S, Isakova A, Tan M, Sit R, Neff N, Hart M, Meese E, Quake S, Wyss-Coray T, Keller A. Characterizing expression changes in noncoding RNAs during aging and heterochronic parabiosis across mouse tissues. Nat Biotechnol 2024; 42:109-118. [PMID: 37106037 DOI: 10.1038/s41587-023-01751-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 03/15/2023] [Indexed: 04/29/2023]
Abstract
Molecular mechanisms of organismal and cell aging remain incompletely understood. We, therefore, generated a body-wide map of noncoding RNA (ncRNA) expression in aging (16 organs at ten timepoints from 1 to 27 months) and rejuvenated mice. We found molecular aging trajectories are largely tissue-specific except for eight broadly deregulated microRNAs (miRNAs). Their individual abundance mirrors their presence in circulating plasma and extracellular vesicles (EVs) whereas tissue-specific ncRNAs were less present. For miR-29c-3p, we observe the largest correlation with aging in solid organs, plasma and EVs. In mice rejuvenated by heterochronic parabiosis, miR-29c-3p was the most prominent miRNA restored to similar levels found in young liver. miR-29c-3p targets the extracellular matrix and secretion pathways, known to be implicated in aging. We provide a map of organism-wide expression of ncRNAs with aging and rejuvenation and identify a set of broadly deregulated miRNAs, which may function as systemic regulators of aging via plasma and EVs.
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Affiliation(s)
- Viktoria Wagner
- Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Fabian Kern
- Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Saarland University Campus, Saarbrücken, Germany
| | - Oliver Hahn
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Nicholas Schaum
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Nicole Ludwig
- Department of Human Genetics, Saarland University, Saarland, Germany
| | - Tobias Fehlmann
- Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Annika Engel
- Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Dominic Henn
- Department of Plastic Surgery, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Shusruto Rishik
- Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Alina Isakova
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Michelle Tan
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Rene Sit
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Norma Neff
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Martin Hart
- Department of Human Genetics, Saarland University, Saarland, Germany
| | - Eckart Meese
- Department of Human Genetics, Saarland University, Saarland, Germany
| | - Steve Quake
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Tony Wyss-Coray
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA.
- The Phil and Penny Knight Initiative for Brain Resilience, Stanford University, Stanford, CA, USA.
| | - Andreas Keller
- Clinical Bioinformatics, Saarland University, Saarbrücken, Germany.
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA.
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Saarland University Campus, Saarbrücken, Germany.
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8
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Cherry AD, Chu CP, Cianciolo RE, Hokamp JA, Jacobson SA, Nabity MB. MicroRNA-126 in dogs with immune complex-mediated glomerulonephritis. J Vet Intern Med 2024; 38:216-227. [PMID: 38116844 PMCID: PMC10800198 DOI: 10.1111/jvim.16932] [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: 05/08/2023] [Accepted: 10/26/2023] [Indexed: 12/21/2023] Open
Abstract
BACKGROUND Most proteinuric dogs with naturally occurring chronic kidney disease have amyloidosis (AMYL), glomerulosclerosis (GS), or immune complex-mediated glomerulonephritis (ICGN), each with different treatment and prognosis. A noninvasive and disease-specific biomarker is lacking. HYPOTHESIS We hypothesized that the expression pattern of biofluid microRNA (miRNAs and miRs) would correlate with disease progression and categorization. ANIMALS Archived serum and urine samples from 18 dogs with glomerular disease and 6 clinically healthy dogs; archived urine samples from 49 dogs with glomerular disease and 13 clinically healthy dogs. METHODS Retrospective study. Archived biofluid samples from adult dogs with biopsy-confirmed glomerular disease submitted to the International Veterinary Renal Pathology Service between 2008 and 2016 were selected. Serum and urinary miRNAs were isolated and profiled using RNA sequencing. Urinary miR-126, miR-21, miR-182, and miR-486 were quantified using quantitative reverse transcription PCR. RESULTS When comparing more advanced disease with earlier disease, no serum miRNAs were differentially expressed, but urinary miR-21 and miR-182 were 1.63 (95% CI: .86-3.1) and 1.45 (95% CI: .82-2.6) times higher in azotemic dogs, respectively (adjusted P < .05) and weakly correlated with tubulointerstitial fibrosis (miR-21: r = .32, P = .03; miR-182: r = .28, P = .05). Expression of urinary miR-126 was 10.5 (95% CI: 4.1-26.7), 28.9 (95% CI: 10.5-79.8), and 126.2 (95% CI: 44.7-356.3) times higher in dogs with ICGN compared with dogs with GS, AMYL, and healthy controls, respectively (P < .001). CONCLUSIONS AND CLINICAL IMPORTANCE The miR-126 could help identify dogs that might benefit from immunosuppressive therapy in the absence of a biopsy. MiR-21 and miR-182 are potential markers of disease severity and fibrosis.
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Affiliation(s)
- Ariana D. Cherry
- Department of Veterinary Pathobiology, School of Veterinary Medicine & Biomedical SciencesTexas A&M UniversityCollege StationTexasUSA
| | - Candice P. Chu
- Department of Veterinary Pathobiology, School of Veterinary Medicine & Biomedical SciencesTexas A&M UniversityCollege StationTexasUSA
| | - Rachel E. Cianciolo
- Department of Veterinary Biosciences, College of Veterinary MedicineThe Ohio State UniversityColumbusOhioUSA
- Present address:
Niche Diagnostics, LLCColumbusOhioUSA
- Present address:
Zoetis Inc.ColumbusOhioUSA
| | - Jessica A. Hokamp
- Department of Veterinary Pathobiology, School of Veterinary Medicine & Biomedical SciencesTexas A&M UniversityCollege StationTexasUSA
| | - Sarah A. Jacobson
- Department of Veterinary Pathobiology, School of Veterinary Medicine & Biomedical SciencesTexas A&M UniversityCollege StationTexasUSA
| | - Mary B. Nabity
- Department of Veterinary Pathobiology, School of Veterinary Medicine & Biomedical SciencesTexas A&M UniversityCollege StationTexasUSA
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9
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Abou el qassim L, Martínez B, Rodríguez A, Dávalos A, López de las Hazas MC, Menéndez Miranda M, Royo LJ. Effects of Cow's Milk Processing on MicroRNA Levels. Foods 2023; 12:2950. [PMID: 37569218 PMCID: PMC10419269 DOI: 10.3390/foods12152950] [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: 07/05/2023] [Revised: 07/30/2023] [Accepted: 08/02/2023] [Indexed: 08/13/2023] Open
Abstract
MicroRNAs (miRNAs) regulate gene expression and might resist adverse physicochemical conditions, which makes them potential biomarkers. They are being investigated as biomarkers of dairy production systems, based on the variations in their levels in raw milk depending on animal diet and management. Whether miRNA levels can serve as biomarkers for dairy products remains unclear, since technological or culinary treatments, such as fermentation, may alter their levels. Here, 10 cow dairy farms were sampled in Asturias (north-west Spain) and milk samples were subjected to microwave heating or used to produce yogurt or cheese. Total RNA was isolated from raw milk and three derived products, and levels of seven miRNAs, selected based on previous studies as possible milk production system biomarkers, were assessed by RT-qPCR. The treatments decreased levels of all miRNAs to some extent. These results also imply that cheesemaking increases the concentration of miRNAs in this product; raw milk and cheese supposedly may provide similar concentrations of miRNAs, higher than those of yogurt and microwaved milk. They also indicate that the content of certain miRNAs in raw milk cannot necessarily be extrapolated to other dairy products.
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Affiliation(s)
- Loubna Abou el qassim
- Servicio Regional de Investigación y Desarrollo Agroalimentario (SERIDA), 33300 Villaviciosa, Spain;
| | - Beatriz Martínez
- Department of Technology and Biotechnology of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), 33300 Villaviciosa, Spain; (B.M.); (A.R.)
| | - Ana Rodríguez
- Department of Technology and Biotechnology of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), 33300 Villaviciosa, Spain; (B.M.); (A.R.)
| | - Alberto Dávalos
- Laboratory of Epigenetics of Lipid Metabolism, Madrid Institute for Advanced Studies (IMDEA)-Food, CEI UAM+CSIC, 28049 Madrid, Spain; (A.D.); (M.-C.L.d.l.H.)
| | - María-Carmen López de las Hazas
- Laboratory of Epigenetics of Lipid Metabolism, Madrid Institute for Advanced Studies (IMDEA)-Food, CEI UAM+CSIC, 28049 Madrid, Spain; (A.D.); (M.-C.L.d.l.H.)
| | - Mario Menéndez Miranda
- Servicio Regional de Investigación y Desarrollo Agroalimentario (SERIDA), 33300 Villaviciosa, Spain;
| | - Luis J. Royo
- Servicio Regional de Investigación y Desarrollo Agroalimentario (SERIDA), 33300 Villaviciosa, Spain;
- Department of Functional Biology, University of Oviedo, 33006 Oviedo, Spain
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10
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Kan CM, Pei XM, Yeung MHY, Jin N, Ng SSM, Tsang HF, Cho WCS, Yim AKY, Yu ACS, Wong SCC. Exploring the Role of Circulating Cell-Free RNA in the Development of Colorectal Cancer. Int J Mol Sci 2023; 24:11026. [PMID: 37446204 DOI: 10.3390/ijms241311026] [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: 05/21/2023] [Revised: 06/25/2023] [Accepted: 07/02/2023] [Indexed: 07/15/2023] Open
Abstract
Circulating tumor RNA (ctRNA) has recently emerged as a novel and attractive liquid biomarker. CtRNA is capable of providing important information about the expression of a variety of target genes noninvasively, without the need for biopsies, through the use of circulating RNA sequencing. The overexpression of cancer-specific transcripts increases the tumor-derived RNA signal, which overcomes limitations due to low quantities of circulating tumor DNA (ctDNA). The purpose of this work is to present an up-to-date review of current knowledge regarding ctRNAs and their status as biomarkers to address the diagnosis, prognosis, prediction, and drug resistance of colorectal cancer. The final section of the article discusses the practical aspects involved in analyzing plasma ctRNA, including storage and isolation, detection technologies, and their limitations in clinical applications.
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Affiliation(s)
- Chau-Ming Kan
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Xiao Meng Pei
- Department of Applied Biology & Chemical Technology, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Martin Ho Yin Yeung
- Department of Applied Biology & Chemical Technology, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Nana Jin
- Codex Genetics Limited, Shatin, Hong Kong SAR, China
| | - Simon Siu Man Ng
- Department of Surgery, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Hin Fung Tsang
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - William Chi Shing Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Kowloon, Hong Kong SAR, China
| | | | | | - Sze Chuen Cesar Wong
- Department of Applied Biology & Chemical Technology, The Hong Kong Polytechnic University, Hong Kong SAR, China
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11
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Yassin AM, AbuBakr HO, Abdelgalil AI, Farid OA, El-Behairy AM, Gouda EM. Circulating miR-146b and miR-27b are efficient biomarkers for early diagnosis of Equidae osteoarthritis. Sci Rep 2023; 13:7966. [PMID: 37198318 DOI: 10.1038/s41598-023-35207-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 05/14/2023] [Indexed: 05/19/2023] Open
Abstract
One of the most orthopedic problems seen in the equine is osteoarthritis (OA). The present study tracks some biochemical, epigenetic, and transcriptomic factors along different stages of monoiodoacetate (MIA) induced OA in donkeys in serum and synovial fluid. The aim of the study was the detection of sensitive noninvasive early biomarkers. OA was induced by a single intra-articular injection of 25 mg of MIA into the left radiocarpal joint of nine donkeys. Serum and synovial samples were taken at zero-day and different intervals for assessment of total GAGs and CS levels as well as miR-146b, miR-27b, TRAF-6, and COL10A1 gene expression. The results showed that the total GAGs and CS levels increased in different stages of OA. The level of expression of both miR-146b and miR-27b were upregulated as OA progressed and then downregulated at late stages. TRAF-6 gene was upregulated at the late stage while synovial fluid COL10A1 was over-expressed at the early stage of OA and then decreased at the late stages (P < 0.05). In conclusion, both miR-146b and miR-27b together with COL10A1 could be used as promising noninvasive biomarkers for the very early diagnosis of OA.
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Affiliation(s)
- Aya M Yassin
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Cairo University, Giza, 12211, Egypt.
| | - Huda O AbuBakr
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Cairo University, Giza, 12211, Egypt
| | - Ahmed I Abdelgalil
- Department of Surgery, Anesthesiology, and Radiology, Faculty of Veterinary Medicine, Cairo University, Giza, 12211, Egypt
| | - Omar A Farid
- Department of Physiology, National Organization for Drug Control and Research, Giza, Egypt
| | - Adel M El-Behairy
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Cairo University, Giza, 12211, Egypt
| | - Eman M Gouda
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Cairo University, Giza, 12211, Egypt
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12
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Reilly L, Seddighi S, Singleton AB, Cookson MR, Ward ME, Qi YA. Variant biomarker discovery using mass spectrometry-based proteogenomics. FRONTIERS IN AGING 2023; 4:1191993. [PMID: 37168844 PMCID: PMC10165118 DOI: 10.3389/fragi.2023.1191993] [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: 03/22/2023] [Accepted: 04/13/2023] [Indexed: 05/13/2023]
Abstract
Genomic diversity plays critical roles in risk of disease pathogenesis and diagnosis. While genomic variants-including single nucleotide variants, frameshift variants, and mis-splicing isoforms-are commonly detected at the DNA or RNA level, their translated variant protein or polypeptide products are ultimately the functional units of the associated disease. These products are often released in biofluids and could be leveraged for clinical diagnosis and patient stratification. Recent emergence of integrated analysis of genomics with mass spectrometry-based proteomics for biomarker discovery, also known as proteogenomics, have significantly advanced the understanding disease risk variants, precise medicine, and biomarker discovery. In this review, we discuss variant proteins in the context of cancers and neurodegenerative diseases, outline current and emerging proteogenomic approaches for biomarker discovery, and provide a comprehensive proteogenomic strategy for detection of putative biomarker candidates in human biospecimens. This strategy can be implemented for proteogenomic studies in any field of enquiry. Our review timely addresses the need of biomarkers for aging related diseases.
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Affiliation(s)
- Luke Reilly
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States
| | - Sahba Seddighi
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States
| | - Andrew B. Singleton
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, United States
| | - Mark R. Cookson
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, United States
| | - Michael E. Ward
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States
| | - Yue A. Qi
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States
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13
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Guedes PHG, Brussasco JG, Moço ACR, Moraes DD, Segatto M, Flauzino JMR, Mendes-Silva AP, Vieira CU, Madurro JM, Brito-Madurro AG. A highly reusable genosensor for late-life depression diagnosis based on microRNA 184 attomolar detection in human plasma. Talanta 2023; 258:124342. [PMID: 36940569 DOI: 10.1016/j.talanta.2023.124342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 02/08/2023] [Accepted: 02/09/2023] [Indexed: 02/12/2023]
Abstract
Late-Life Depression (LLD) is one of the most prevalent psychiatric disorders in elderly, causing significant functional impairments. MicroRNAs are small molecules involved in the post-transcriptional regulation of gene expression. Elderly individuals diagnosed with LLD present down regulation of miR-184 (hsa-miR-184) expression compared to healthy patients. Therefore, this miR-184 can be used as a biomarker to diagnose LLD. Current LLD diagnosis depends primarily on clinical subjective identification, based on symptoms and variable scales. This work introduces a novel and facile approach for the LLD diagnosis based on the development of an electrochemical genosensor for miR-184 detection in plasma, using differential pulse voltammetry (DPV) and electrochemical impedance spectroscopy (EIS). DPV results presented a 2-Fold increase in current value for healthy patients, compared to individuals with LLD when monitoring ethidium bromide oxidation peak. For EIS, a 1.5-fold increase in charge transfer resistance for healthy elderly subjects was observed in comparison with depressed patients. In addition, the analytical performance of the biosensor was evaluated using DPV, obtaining a linear response ranging from 10-9 mol L-1 to 10-17 mol L-1 of miR-184 in plasma and a detection limit of 10 atomoles L-1. The biosensor presented reusability, selectivity and stability, the current response remained 72% up to 50 days of storage. Thus, the genosensor proved to be efficient in the diagnosis of LLD, as well as the accurate quantification of miR-184 in real plasma samples of healthy and depressed patients.
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Affiliation(s)
- Pedro H G Guedes
- Institute of Biotecnology, Federal University of Uberlândia, Uberlândia, Brazil
| | - Jéssica G Brussasco
- Institute of Biotecnology, Federal University of Uberlândia, Uberlândia, Brazil
| | - Anna C R Moço
- Institute of Biotecnology, Federal University of Uberlândia, Uberlândia, Brazil
| | - Dayane D Moraes
- Institute of Biotecnology, Federal University of Uberlândia, Uberlândia, Brazil
| | - Monica Segatto
- Institute of Chemistry, Federal University of Uberlândia, Uberlândia, Brazil
| | - José M R Flauzino
- Institute of Biotecnology, Federal University of Uberlândia, Uberlândia, Brazil
| | - Ana P Mendes-Silva
- Institute of Biotecnology, Federal University of Uberlândia, Uberlândia, Brazil; Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Carlos U Vieira
- Institute of Biotecnology, Federal University of Uberlândia, Uberlândia, Brazil
| | - João M Madurro
- Institute of Chemistry, Federal University of Uberlândia, Uberlândia, Brazil
| | - Ana G Brito-Madurro
- Institute of Biotecnology, Federal University of Uberlândia, Uberlândia, Brazil.
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14
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Sabbaghian A, Mussack V, Kirchner B, Bui MLU, Kalani MR, Pfaffl MW, Golalipour M. A panel of blood-derived miRNAs with a stable expression pattern as a potential pan-cancer detection signature. Front Mol Biosci 2022; 9:1030749. [PMID: 36589227 PMCID: PMC9798419 DOI: 10.3389/fmolb.2022.1030749] [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: 08/29/2022] [Accepted: 11/30/2022] [Indexed: 12/23/2022] Open
Abstract
Introduction: MicroRNAs have a significant role in the regulation of the transcriptome. Several miRNAs have been proposed as potential biomarkers in different malignancies. However, contradictory results have been reported on the capability of miRNA biomarkers in cancer detection. The human biological clock involves molecular mechanisms that regulate several genes over time. Therefore, the sampling time becomes one of the significant factors in gene expression studies. Method: In the present study, we have tried to find miRNAs with minimum fluctuation in expression levels at different time points that could be more accurate candidates as diagnostic biomarkers. The small RNA-seq raw data of ten healthy individuals across nine-time points were analyzed to identify miRNAs with stable expression. Results: We have found five oscillation patterns. The stable miRNAs were investigated in 779 small-RNA-seq datasets of eleven cancer types. All miRNAs with the highest differential expression were selected for further analysis. The selected miRNAs were explored for functional pathways. The predominantly enriched pathways were miRNA in cancer and the P53-signaling pathway. Finally, we have found seven miRNAs, including miR-142-3p, miR-199a-5p, miR-223-5p, let-7d-5p, miR-148b-3p, miR-340-5p, and miR-421. These miRNAs showed minimum fluctuation in healthy blood and were dysregulated in the blood of eleven cancer types. Conclusion: We have found a signature of seven stable miRNAs which dysregulate in several cancer types and may serve as potential pan-cancer biomarkers.
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Affiliation(s)
- Amir Sabbaghian
- Department of Molecular Medicine, Advanced Technologies Faculty, Golestan University of Medical Science, Gorgan, Iran
| | - Veronika Mussack
- Department of Animal Physiology and Immunology, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Benedikt Kirchner
- Department of Animal Physiology and Immunology, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Maria L. U. Bui
- Department of Animal Physiology and Immunology, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Mohammad Reza Kalani
- Department of Molecular Medicine, Advanced Technologies Faculty, Golestan University of Medical Science, Gorgan, Iran
| | - Michael W. Pfaffl
- Department of Animal Physiology and Immunology, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Masoud Golalipour
- Department of Molecular Medicine, Advanced Technologies Faculty, Golestan University of Medical Science, Gorgan, Iran,Cellular and Molecular Research Center, Golestan University of Medical Science, Gorgan, Iran,*Correspondence: Masoud Golalipour,
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15
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Hiskens MI, Mengistu TS, Li KM, Fenning AS. Systematic Review of the Diagnostic and Clinical Utility of Salivary microRNAs in Traumatic Brain Injury (TBI). Int J Mol Sci 2022; 23:13160. [PMID: 36361944 PMCID: PMC9654991 DOI: 10.3390/ijms232113160] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/18/2022] [Accepted: 10/27/2022] [Indexed: 07/29/2023] Open
Abstract
Research in traumatic brain injury (TBI) is an urgent priority, as there are currently no TBI biomarkers to assess the severity of injury, to predict outcomes, and to monitor recovery. Small non-coding RNAs (sncRNAs) including microRNAs can be measured in saliva following TBI and have been investigated as potential diagnostic markers. The aim of this systematic review was to investigate the diagnostic or prognostic ability of microRNAs extracted from saliva in human subjects. PubMed, Embase, Scopus, PsycINFO and Web of Science were searched for studies that examined the association of saliva microRNAs in TBI. Original studies of any design involving diagnostic capacity of salivary microRNAs for TBI were selected for data extraction. Nine studies met inclusion criteria, with a heterogeneous population involving athletes and hospital patients, children and adults. The studies identified a total of 188 differentially expressed microRNAs, with 30 detected in multiple studies. MicroRNAs in multiple studies involved expression change bidirectionality. The study design and methods involved significant heterogeneity that precluded meta-analysis. Early data indicates salivary microRNAs may assist with TBI diagnosis. Further research with consistent methods and larger patient populations is required to evaluate the diagnostic and prognostic potential of saliva microRNAs.
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Affiliation(s)
- Matthew I. Hiskens
- Mackay Institute of Research and Innovation, Mackay Hospital and Health Service, 475 Bridge Road, Mackay, QLD 4740, Australia
- School of Health, Medical and Applied Sciences, Central Queensland University, Bruce Highway, Rockhampton, QLD 4702, Australia
| | - Tesfaye S. Mengistu
- Mackay Institute of Research and Innovation, Mackay Hospital and Health Service, 475 Bridge Road, Mackay, QLD 4740, Australia
- Faculty of Medicine, School of Public Health, University of Queensland, 266 Herston Road, Herston, QLD 4006, Australia
| | - Katy M. Li
- School of Health, Medical and Applied Sciences, Central Queensland University, Bruce Highway, Rockhampton, QLD 4702, Australia
| | - Andrew S. Fenning
- School of Health, Medical and Applied Sciences, Central Queensland University, Bruce Highway, Rockhampton, QLD 4702, Australia
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16
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Bitaraf M, Mahmanzar M, Zafari N, Mohammadpour H, Vasei M, Moradi Matin L, Kajbafzadeh AM, Majidi Zolbin M. The potential key genes and pathways associated with Wilms tumor in quest of proper candidates for diagnostic and therapeutic purposes. Sci Rep 2022; 12:17906. [PMID: 36284226 PMCID: PMC9596724 DOI: 10.1038/s41598-022-22925-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 10/20/2022] [Indexed: 01/20/2023] Open
Abstract
To designate the probable most important differentially expressed genes and genetic pathways in Wilms tumor and assess their expression and diagnostic potential by RT-PCR and statistical analysis. Systematic review of the literature and various bioinformatics analysis was carried out to gather and narrow down data. The expression of end-resulting genes was compared in Wilms tumor and normal tissue samples using RT-PCR. Statistical tests reported the diagnostic accuracy of genes and their correlation with clinicopathological features. Four genes including CDH1, NCAM1, EGF, and IGF2 were designated. The panel combining them has 100% sensitivity and specificity in differentiating tumors from normal tissue. Eight pathways, most involved in cell-cell and cell-basal matrix junction interactions, were found to be associated with disease pathogenesis. The suggested genes should undergo further evaluation to be validated as diagnostic biomarkers. Further research on the eight proposed pathways is recommended.
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Affiliation(s)
- Masoud Bitaraf
- grid.411705.60000 0001 0166 0922Pediatric Urology and Regenerative Medicine Research Center, Gene, Cell and Tissue Research Institute, Children’s Medical Center, Tehran University of Medical Sciences, No. 62, Dr. Qarib’s St, Keshavarz Blvd, Tehran, 14194 33151 Iran
| | - Mohammadamin Mahmanzar
- grid.411705.60000 0001 0166 0922Pediatric Urology and Regenerative Medicine Research Center, Gene, Cell and Tissue Research Institute, Children’s Medical Center, Tehran University of Medical Sciences, No. 62, Dr. Qarib’s St, Keshavarz Blvd, Tehran, 14194 33151 Iran ,grid.46072.370000 0004 0612 7950Department of Bioinformatics, Kish International Campus, University of Tehran, Kish, Iran
| | - Narges Zafari
- grid.411705.60000 0001 0166 0922Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Hadiseh Mohammadpour
- grid.411705.60000 0001 0166 0922Dental Research Center, Dentistry Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Vasei
- grid.415646.40000 0004 0612 6034 Cell Therapy Based Research Center, Digestive Disease Research Institute, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Leyla Moradi Matin
- grid.411705.60000 0001 0166 0922Pediatric Urology and Regenerative Medicine Research Center, Gene, Cell and Tissue Research Institute, Children’s Medical Center, Tehran University of Medical Sciences, No. 62, Dr. Qarib’s St, Keshavarz Blvd, Tehran, 14194 33151 Iran
| | - Abdol-Mohammad Kajbafzadeh
- grid.411705.60000 0001 0166 0922Pediatric Urology and Regenerative Medicine Research Center, Gene, Cell and Tissue Research Institute, Children’s Medical Center, Tehran University of Medical Sciences, No. 62, Dr. Qarib’s St, Keshavarz Blvd, Tehran, 14194 33151 Iran
| | - Masoumeh Majidi Zolbin
- grid.411705.60000 0001 0166 0922Pediatric Urology and Regenerative Medicine Research Center, Gene, Cell and Tissue Research Institute, Children’s Medical Center, Tehran University of Medical Sciences, No. 62, Dr. Qarib’s St, Keshavarz Blvd, Tehran, 14194 33151 Iran
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17
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Variation of miRNA Content in Cow Raw Milk Depending on the Dairy Production System. Int J Mol Sci 2022; 23:ijms231911681. [PMID: 36232984 PMCID: PMC9569736 DOI: 10.3390/ijms231911681] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/22/2022] [Accepted: 09/27/2022] [Indexed: 11/23/2022] Open
Abstract
Pasture-based milk presents several advantages over milk from intensive industrial farming in terms of human health, the environment, animal welfare, and social aspects. This highlights the need for reliable methods to differentiate milk according to its origin on the market. Here, we explored whether miRNA profiles could serve as a marker of milk production systems. We compared levels of previously described miRNAs in milk from four production systems (altogether 112 milk samples): grazing, zero grazing, grass silage or corn silage. Total RNA was extracted from the fat phase, and miRNAs levels were quantified by real-time quantitative PCR. The levels of the miRNAs bta-miR-155 and bta-miR-103 were higher in the grazing system than in corn silage farms. The levels of bta-miR-532, bta-miR-103 and bta-miR-7863 showed differences between different farm managements. The miRNAs bta-miR-155 and bta-miR-103 were predicted to participate in common functions related to fat metabolism and fatty acid elongation. All four differentially expressed miRNAs were predicted to participate in transport, cell differentiation, and metabolism. These results suggest that the dairy production system influences the levels of some miRNAs in milk fat, and that bta-miR-155 and bta-miR-103 may be potential biomarkers to identify milk from pasture-managed systems.
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18
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Biomarker screening in preeclampsia: an RNA-sequencing approach based on data from multiple studies. J Hypertens 2022; 40:2022-2036. [PMID: 36052525 DOI: 10.1097/hjh.0000000000003226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE Biomarkers have become important in the prognosis and diagnosis of various diseases. High-throughput methods, such as RNA sequencing facilitate the detection of differentially expressed genes (DEGs), hence potential biomarker candidates. Individual studies suggest long lists of DEGs, hampering the identification of clinically relevant ones. Concerning preeclampsia - a major obstetric burden with high risk for adverse maternal and/or neonatal outcomes - limitations in diagnosis and prediction are still important issues. We, therefore, developed a workflow to facilitate the screening for biomarkers. METHODS On the basis of the tool DESeq2, a comprehensive workflow for identifying DEGs was established, analyzing data from several publicly available RNA-sequencing studies. We applied it to four RNA-sequencing datasets (one blood, three placenta) analyzing patients with preeclampsia and normotensive controls. We compared our results with other published approaches and evaluated their performance. RESULTS We identified 110 genes that are dysregulated in preeclampsia, observed in at least three of the studies analyzed, six even in all four studies. These included FLT-1, TREM-1, and FN1, which either represent established biomarkers at protein level, or promising candidates based on recent studies. For comparison, using a published meta-analysis approach, 5240 DEGs were obtained. CONCLUSION This study presents a data analysis workflow for preeclampsia biomarker screening, capable of identifying promising biomarker candidates, while drastically reducing the numbers of candidates. Moreover, we were also able to confirm its performance for heart failure. This approach can be applied to additional diseases for biomarker identification, and the set of DEGs identified in preeclampsia represents a resource for further studies.
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19
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Farschtschi S, Riedmaier-Sprenzel I, Phomvisith O, Gotoh T, Pfaffl MW. The successful use of -omic technologies to achieve the 'One Health' concept in meat producing animals. Meat Sci 2022; 193:108949. [PMID: 36029570 DOI: 10.1016/j.meatsci.2022.108949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 08/09/2022] [Accepted: 08/16/2022] [Indexed: 11/15/2022]
Abstract
Human health and wellbeing are closely linked to healthy domestic animals, a vital wildlife, and an intact ecosystem. This holistic concept is referred to as 'One Health'. In this review, we provide an overview of the potential and the challenges for the use of modern -omics technologies, especially transcriptomics and proteomics, to implement the 'One Health' idea for food-producing animals. These high-throughput studies offer opportunities to find new potential molecular biomarkers to monitor animal health, detect pharmacological interventions and evaluate the wellbeing of farm animals in modern intensive livestock systems.
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Affiliation(s)
- Sabine Farschtschi
- Division of Animal Physiology and Immunology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Irmgard Riedmaier-Sprenzel
- Division of Animal Physiology and Immunology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany; Eurofins Medigenomix Forensik GmbH, Anzinger Straße 7a, 85560 Ebersberg, Germany
| | - Ouanh Phomvisith
- Department of Agricultural Sciences and Natural Resources, Kagoshima University, Korimoto 1-21-24, Kagoshima 890-8580, Japan
| | - Takafumi Gotoh
- Department of Agricultural Sciences and Natural Resources, Kagoshima University, Korimoto 1-21-24, Kagoshima 890-8580, Japan
| | - Michael W Pfaffl
- Division of Animal Physiology and Immunology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany.
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20
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Current challenges and best practices for cell-free long RNA biomarker discovery. Biomark Res 2022; 10:62. [PMID: 35978416 PMCID: PMC9385245 DOI: 10.1186/s40364-022-00409-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/04/2022] [Indexed: 11/24/2022] Open
Abstract
The analysis of biomarkers in biological fluids, also known as liquid biopsies, is seen with great potential to diagnose complex diseases such as cancer with a high sensitivity and minimal invasiveness. Although it can target any biomolecule, most liquid biopsy studies have focused on circulating nucleic acids. Historically, studies have aimed at the detection of specific mutations on cell-free DNA (cfDNA), but recently, the study of cell-free RNA (cfRNA) has gained traction. Since 2020, a handful of cfDNA tests have been approved for therapy selection by the FDA, however, no cfRNA tests are approved to date. One of the main drawbacks in the field of RNA-based liquid biopsies is the low reproducibility of the results, often caused by technical and biological variability, a lack of standardized protocols and insufficient cohorts. In this review, we will identify the main challenges and biases introduced during the different stages of biomarker discovery in liquid biopsies with cfRNA and propose solutions to minimize them.
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21
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van Vliet EA, Hildebrand MS, Mills JD, Brennan GP, Eid T, Masino SA, Whittemore V, Bindila L, Wang KK, Patel M, Perucca P, Reid CA. A companion to the preclinical common data elements for genomics, transcriptomics, and epigenomics data in rodent epilepsy models. A report of the TASK3-WG4 omics working group of the ILAE/AES joint translational TASK force. Epilepsia Open 2022. [PMID: 35950645 DOI: 10.1002/epi4.12640] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 02/22/2022] [Indexed: 11/06/2022] Open
Abstract
The International League Against Epilepsy/American Epilepsy Society (ILAE/AES) Joint Translational Task Force established the TASK3 working groups to create common data elements (CDEs) for various preclinical epilepsy research disciplines. The aim of the CDEs is to improve the standardization of experimental designs across a range of epilepsy research-related methods. Here, we have generated CDE tables with key parameters and case report forms (CRFs) containing the essential contents of the study protocols for genomics, transcriptomics, and epigenomics in rodent models of epilepsy, with a specific focus on adult rats and mice. We discuss the important elements that need to be considered for genomics, transcriptomics, and epigenomics methodologies, providing a rationale for the parameters that should be collected. This is the first in a two-part series of omics papers with the second installment to cover proteomics, lipidomics, and metabolomics in adult rodents.
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Affiliation(s)
- Erwin A van Vliet
- Center for Neuroscience, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam UMC location University of Amsterdam, Department of (Neuro)Pathology, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Michael S Hildebrand
- Epilepsy Research Centre, Department of Medicine (Austin Health), The University of Melbourne, Heidelberg, Victoria, Australia
- Murdoch Children's Research Institute, The Royal Children's Hospital, Parkville, Victoria, Australia
| | - James D Mills
- Amsterdam UMC location University of Amsterdam, Department of (Neuro)Pathology, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Gary P Brennan
- UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin, Ireland
- FutureNeuro Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Tore Eid
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Susan A Masino
- Neuroscience Program and Psychology Department, Life Sciences Center, Trinity College, Hartford, Connecticut, USA
| | - Vicky Whittemore
- Division of Neuroscience, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Laura Bindila
- Clinical Lipidomics Unit, Institute of Physiological Chemistry, University Medical Center of the Johannes Gutenberg University of Mainz, Mainz, Germany
| | - Kevin K Wang
- Department of Emergency Medicine, Psychiatry and Neuroscience, University of Florida, Gainesville, Florida, USA
- Brain Rehabilitation Research Center, Malcom Randall VA Medical Center, North Florida/South Georgia Veterans Health System, Gainesville, Florida, USA
| | - Manisha Patel
- Department of Pharmaceutical Sciences, University of Colorado, Aurora, Colorado, USA
| | - Piero Perucca
- Epilepsy Research Centre, Department of Medicine (Austin Health), The University of Melbourne, Heidelberg, Victoria, Australia
- Bladin-Berkovic Comprehensive Epilepsy Program, Austin Health, Heidelberg, Victoria, Australia
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Victoria, Australia
- Department of Neurology, The Royal Melbourne Hospital, Melbourne, Victoria, Australia
- Department of Neurology, Alfred Health, Melbourne, Victoria, Australia
| | - Christopher A Reid
- Epilepsy Research Centre, Department of Medicine (Austin Health), The University of Melbourne, Heidelberg, Victoria, Australia
- Murdoch Children's Research Institute, The Royal Children's Hospital, Parkville, Victoria, Australia
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, Victoria, Australia
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22
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Abstract
Small RNAs are ubiquitous regulators of gene expression that participate in nearly all aspects of physiology in a wide range of organisms. There are many different classes of eukaryotic small RNAs that play regulatory roles at every level of gene expression, including transcription, RNA stability, and translation. While eukaryotic small RNAs display diverse functions across and within classes, they are generally grouped functionally based on the machinery required for their biogenesis, the effector proteins they associate with, and their molecular characteristics. The development of techniques to clone and sequence small RNAs has been critical for their identification, yet the ligation-dependent addition of RNA adapters and the use of reverse transcriptase to generate cDNA in traditional library preparation protocols can be unsuitable to detect certain small RNA subtypes. In particular, 3' or 5' chemical modifications that are characteristic of specific types of small RNAs can impede the ligation-dependent addition of RNA adapters, while internal RNA modifications can interfere with accurate reverse transcription. The inability to clone certain small RNA subtypes with traditional protocols results in an inaccurate assessment of small RNA abundance and diversity, where some RNAs appear over-represented and others are not detected. This overview aims to guide users on how to design small RNA cloning workflows in eukaryotes to more accurately capture specific small RNAs of interest. Hence, we discuss the molecular biology underlying the identification and quantitation of small RNAs, explore the limitations of commonly used protocols, and detail the alternative approaches that can be used to enrich specific small RNA classes. © 2022 Wiley Periodicals LLC.
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Affiliation(s)
- Olivia J Crocker
- Division of Neonatology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Departments of Genetics and Pediatrics - Penn Epigenetics Institute, Institute of Regenerative Medicine, and Center for Research on Reproduction and Women's Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Natalie A Trigg
- Division of Neonatology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Departments of Genetics and Pediatrics - Penn Epigenetics Institute, Institute of Regenerative Medicine, and Center for Research on Reproduction and Women's Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Colin C Conine
- Division of Neonatology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Departments of Genetics and Pediatrics - Penn Epigenetics Institute, Institute of Regenerative Medicine, and Center for Research on Reproduction and Women's Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
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23
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Dandapani MC, Venkatesan V, Charmine P, Geminiganesan S, Ekambaram S. Differential urinary microRNA expression analysis of miR-1, miR-215, miR-335, let-7a in childhood nephrotic syndrome. Mol Biol Rep 2022; 49:6591-6600. [PMID: 35553329 DOI: 10.1007/s11033-022-07500-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 04/21/2022] [Indexed: 10/18/2022]
Abstract
BACKGROUND Recently, urinary exosomal miRNAs are gaining increasing attention as their expression profiles are often associated with specific diseases and they exhibit great potential as noninvasive biomarkers for the diagnosis of various diseases. The present study was aimed to evaluate the expression status of selected miRNAs (miR-1, miR-215-5p, miR-335-5p and let-7a-5p) in urine samples from children with NS [steroid sensitive (SSNS)] and [steroid resistant (SRNS)] along with healthy control group. METHODS MicroRNA isolation was carried out in urine samples collected from SSNS (100 nos), SRNS (100 nos), and healthy controls (50 nos) using MiRNeasy Mini Kit, followed by cDNA conversion for all the four selected miRNAs using Taqman advanced miRNA cDNA synthesis kit and their expression was quantified by Taqman Advanced miRNA assay kits using Real Time PCR Machine and Rotogen-Q in SSNS and SRNS patients and healthy control subjects. RESULTS Quantification of all the four miRNAs (miR-1, mir-215, miR-335, let-7a) were found to be upregulated in both SSNS and SRNS as compared to control group. Further, the comparison of microRNAs within the case groups revealed significant downregulation of three microRNAs-miR-1, miR-215, miR- 335 and upregulation of let-7a in SRNS group as compared to SSNS. The t-test performed for all the four miRNAs was found to be statistically significant. CONCLUSIONS The aberrant expression of all the four microRNAs in both SSNS and SRNS as compared to healthy subjects may serve as novel biomarkers to distinguish between NS and healthy controls. The differential expression of microRNA let-7a is useful to discriminate SSNS and SRNS.
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Affiliation(s)
- Mohanapriya Chinambedu Dandapani
- Central Research Facility, Faculty of Clinical Research, Sri Ramachandra Institute of Higher Education and Research, No.1 Ramachandra Nagar, Porur, Chennai, Tamil Nadu, 600 116, India.
| | - Vettriselvi Venkatesan
- Department of Human Genetics, Sri Ramachandra Institute of Higher Education and Research, Porur, Chennai, 600 116, India
| | - Pricilla Charmine
- Central Research Facility, Faculty of Clinical Research, Sri Ramachandra Institute of Higher Education and Research, No.1 Ramachandra Nagar, Porur, Chennai, Tamil Nadu, 600 116, India
| | - Sangeetha Geminiganesan
- Department of Pediatric Medicine, Sri Ramachandra Institute of Higher Education and Research, Porur, Chennai, 600 116, India
| | - Sudha Ekambaram
- Department of Pediatric Nephrology, Dr. Mehta's Hospital, Chetpet, Chennai, 600031, India
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24
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Yan C, Zhang N, Wang Q, Fu Y, Zhao H, Wang J, Wu G, Wang F, Li X, Liao H. Full-length transcriptome sequencing reveals the molecular mechanism of potato seedlings responding to low-temperature. BMC PLANT BIOLOGY 2022; 22:125. [PMID: 35300606 PMCID: PMC8932150 DOI: 10.1186/s12870-022-03461-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 02/09/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Potato (Solanum tuberosum L.) is one of the world's most important crops, the cultivated potato is frost-sensitive, and low-temperature severely influences potato production. However, the mechanism by which potato responds to low-temperature stress is unclear. In this research, we apply a combination of second-generation sequencing and third-generation sequencing technologies to sequence full-length transcriptomes in low-temperature-sensitive cultivars to identify the important genes and main pathways related to low-temperature resistance. RESULTS In this study, we obtained 41,016 high-quality transcripts, which included 15,189 putative new transcripts. Amongst them, we identified 11,665 open reading frames, 6085 simple sequence repeats out of the potato dataset. We used public available genomic contigs to analyze the gene features, simple sequence repeat, and alternative splicing event of 24,658 non-redundant transcript sequences, predicted the coding sequence and identified the alternative polyadenylation. We performed cluster analysis, GO, and KEGG functional analysis of 4518 genes that were differentially expressed between the different low-temperature treatments. We examined 36 transcription factor families and identified 542 transcription factors in the differentially expressed genes, and 64 transcription factors were found in the AP2 transcription factor family which was the most. We measured the malondialdehyde, soluble sugar, and proline contents and the expression genes changed associated with low temperature resistance in the low-temperature treated leaves. We also tentatively speculate that StLPIN10369.5 and StCDPK16 may play a central coordinating role in the response of potatoes to low temperature stress. CONCLUSIONS Overall, this study provided the first large-scale full-length transcriptome sequencing of potato and will facilitate structure-function genetic and comparative genomics studies of this important crop.
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Affiliation(s)
- Chongchong Yan
- Anhui Academy of Agricultural Sciences, Hefei, 230031, Anhui, China.
| | - Nan Zhang
- Anhui Vocational College of City Management, Hefei, 231635, Anhui, China
| | - Qianqian Wang
- Anhui Academy of Agricultural Sciences, Hefei, 230031, Anhui, China
| | - Yuying Fu
- Anhui Academy of Agricultural Sciences, Hefei, 230031, Anhui, China
| | - Hongyuan Zhao
- Anhui Academy of Agricultural Sciences, Hefei, 230031, Anhui, China
| | - Jiajia Wang
- Anhui Academy of Agricultural Sciences, Hefei, 230031, Anhui, China
| | - Gang Wu
- Anhui Academy of Agricultural Sciences, Hefei, 230031, Anhui, China
| | - Feng Wang
- Jieshou County Agricultural Technology Promotion Center, Jieshou, 236500, Anhui, China
| | - Xueyan Li
- Funan County Agricultural Technology Promotion Center, Funan, 236300, Anhui, China
| | - Huajun Liao
- Anhui Academy of Agricultural Sciences, Hefei, 230031, Anhui, China.
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25
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Grätz C, Bui MLU, Thaqi G, Kirchner B, Loewe RP, Pfaffl MW. Obtaining Reliable RT-qPCR Results in Molecular Diagnostics—MIQE Goals and Pitfalls for Transcriptional Biomarker Discovery. Life (Basel) 2022; 12:life12030386. [PMID: 35330136 PMCID: PMC8953338 DOI: 10.3390/life12030386] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 02/15/2022] [Accepted: 03/02/2022] [Indexed: 11/16/2022] Open
Abstract
In this review, we discuss the development pipeline for transcriptional biomarkers in molecular diagnostics and stress the importance of a reliable gene transcript quantification strategy. Hence, a further focus is put on the MIQE guidelines and how to adapt them for biomarker discovery, from signature validation up to routine diagnostic applications. First, the advantages and pitfalls of the holistic RNA sequencing for biomarker development will be described to establish a candidate biomarker signature. Sequentially, the RT-qPCR confirmation process will be discussed to validate the discovered biomarker signature. Examples for the successful application of RT-qPCR as a fast and reproducible quantification method in routinemolecular diagnostics are provided. Based on the MIQE guidelines, the importance of “key steps” in RT-qPCR is accurately described, e.g., reverse transcription, proper reference gene selection and, finally, the application of automated RT-qPCR data analysis software. In conclusion, RT-qPCR proves to be a valuable tool in the establishment of a disease-specific transcriptional biomarker signature and will have a great future in molecular diagnostics or personalized medicine.
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Affiliation(s)
- Christian Grätz
- Department of Animal Physiology and Immunology, School of Life Sciences, Technical University of Munich, Weihenstephaner Berg 3, 85354 Freising, Germany; (C.G.); (M.L.U.B.); (G.T.); (B.K.)
- GeneSurge GmbH, Ottostr. 3, 80333 München, Germany;
| | - Maria L. U. Bui
- Department of Animal Physiology and Immunology, School of Life Sciences, Technical University of Munich, Weihenstephaner Berg 3, 85354 Freising, Germany; (C.G.); (M.L.U.B.); (G.T.); (B.K.)
- GeneSurge GmbH, Ottostr. 3, 80333 München, Germany;
| | - Granit Thaqi
- Department of Animal Physiology and Immunology, School of Life Sciences, Technical University of Munich, Weihenstephaner Berg 3, 85354 Freising, Germany; (C.G.); (M.L.U.B.); (G.T.); (B.K.)
| | - Benedikt Kirchner
- Department of Animal Physiology and Immunology, School of Life Sciences, Technical University of Munich, Weihenstephaner Berg 3, 85354 Freising, Germany; (C.G.); (M.L.U.B.); (G.T.); (B.K.)
- GeneSurge GmbH, Ottostr. 3, 80333 München, Germany;
| | | | - Michael W. Pfaffl
- Department of Animal Physiology and Immunology, School of Life Sciences, Technical University of Munich, Weihenstephaner Berg 3, 85354 Freising, Germany; (C.G.); (M.L.U.B.); (G.T.); (B.K.)
- Correspondence: or
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26
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A MicroRNA Next-Generation-Sequencing Discovery Assay (miND) for Genome-Scale Analysis and Absolute Quantitation of Circulating MicroRNA Biomarkers. Int J Mol Sci 2022; 23:ijms23031226. [PMID: 35163149 PMCID: PMC8835905 DOI: 10.3390/ijms23031226] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/19/2022] [Accepted: 01/19/2022] [Indexed: 12/13/2022] Open
Abstract
The plasma levels of tissue-specific microRNAs can be used as diagnostic, disease severity and prognostic biomarkers for chronic and acute diseases and drug-induced injury. Thereby, the combination of diverse microRNAs into biomarker signatures using multivariate statistics seems especially powerful from the perspective of tissue and condition specific microRNA shedding into the plasma. Although next-generation sequencing (NGS) technology enables one to analyse circulating microRNAs on a genome-scale level, it suffers from potential biases (e.g., adapter ligation bias) and lacks absolute transcript quantitation as well as tailor-made quality controls. In order to develop a robust NGS discovery assay for genome-scale quantitation of circulating microRNAs, we first evaluated the sensitivity, repeatability and ligation bias of four commercially available small RNA library preparation protocols. The protocol from RealSeq Biosciences was selected based on its performance and usability and coupled with a novel panel of exogenous small RNA spike-in controls to enable quality control and absolute quantitation, thus ensuring comparability of data across independent NGS experiments. The established microRNA Next-Generation-Sequencing Discovery Assay (miND) was validated for its relative accuracy, precision, analytical measurement range and sequencing bias and was considered fit-for-purpose for microRNA biomarker discovery. Summarized, all these criteria were met, and thus, our analytical platform is considered fit-for-purpose for microRNA biomarker discovery from biofluids in the setting of any diagnostic, prognostic or patient stratification need. The established miND assay was tested on serum, cerebrospinal fluid (CSF), synovial fluid (SF) and extracellular vesicles (EV) extracted from cell culture medium of primary cells and proved its potential to be used across different sample types.
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27
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Mogaka JJ, Chimbari MJ. Modeling factors critical for implementation of precision medicine at health systems-level: an IRT approach. Am J Transl Res 2021; 13:12557-12574. [PMID: 34956473 PMCID: PMC8661177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 12/13/2020] [Indexed: 06/14/2023]
Abstract
BACKGROUND Through recent advances in omics technologies, precision medicine (PM) promises to fundamentally change the way we approach health, disease and illness. Imperative applications of omics-based biomarkers are gradually moving from research to clinical settings, with huge long-term clinical and public health implications. Whereas much of research in PM is mainly focused on basic biomedical discoveries, currently there is little research on the clinical implementation of omics biomarkers, especially at health systems level. AIM AND METHODS This study investigated the application of multidimensional item response theory (IRT) models to validate a hypothesized PM implementation measurement model. This is a contribution to PM implementation at health systems level. Data obtained through an item-sort procedure involving 496 observations from 124 study participants formed the basis of a 22-item PMI measurement model. CONCLUSION Statistical significance of the bifactor model suggests PM implementation may have to be examined using factors that reflect a single common underlying implementation construct, as well as factors that reflect unique variances for the identified four content-specific factors.
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Affiliation(s)
- John Jo Mogaka
- Department of Public Health Medicine, University of KwaZulu-Natal Durban, South Africa
| | - Moses J Chimbari
- Department of Public Health Medicine, University of KwaZulu-Natal Durban, South Africa
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28
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Wu SC, Chi SY, Rau CS, Kuo PJ, Huang LH, Wu YC, Wu CJ, Lin HP, Hsieh CH. Identification of circulating biomarkers for differentiating patients with papillary thyroid cancers from benign thyroid tumors. J Endocrinol Invest 2021; 44:2375-2386. [PMID: 33646556 DOI: 10.1007/s40618-021-01543-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 02/25/2021] [Indexed: 11/26/2022]
Abstract
BACKGROUND This study aimed to identify the potential circulating biomarkers of protein, mRNAs, and long non-coding RNAs (lncRNAs) to differentiate the papillary thyroid cancers from benign thyroid tumors. METHODS The study population of 100 patients was classified into identification (10 patients with papillary thyroid cancers and 10 patients with benign thyroid tumors) and validation groups (45 patients with papillary thyroid cancers and 35 patients with benign thyroid tumors). The Sengenics Immunome Protein Array-combined data mining approach using the Open Targets Platform was used to identify the putative protein biomarkers, and their expression validated using the enzyme-linked immunosorbent assay. Next-generation sequencing by Illumina HiSeq was used for the detection of dysregulated mRNAs and lncRNAs. The website Timer v2.0 helped identify the putative mRNA biomarkers, which were significantly over-expressed in papillary thyroid cancers than in adjacent normal thyroid tissue. The mRNA and lncRNA biomarker expression was validated by a real-time polymerase chain reaction. RESULTS Although putative protein and mRNA biomarkers have been identified, their serum expression could not be confirmed in the validation cohorts. In addition, seven lncRNAs (TCONS_00516490, TCONS_00336559, TCONS_00311568, TCONS_00321917, TCONS_00336522, TCONS_00282483, and TCONS_00494326) were identified and validated as significantly downregulated in patients with papillary thyroid cancers compared to those with benign thyroid tumors. These seven lncRNAs showed moderate accuracy based on the area under the curve (AUC = 0.736) of receiver operating characteristic in predicting the occurrence of papillary thyroid cancers. CONCLUSIONS We identified seven downregulated circulating lncRNAs with the potential for predicting the occurrence of papillary thyroid cancers.
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Affiliation(s)
- S-C Wu
- Department of Anesthesiology, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung City, Taiwan
| | - S-Y Chi
- Department of General Surgery, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung City, Taiwan
| | - C-S Rau
- Department of Neurosurgery, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung City, Taiwan
| | - P-J Kuo
- Department of Plastic Surgery, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, No.123, Ta-Pei Road, Niao-Song District, Kaohsiung City 833, Taiwan
| | - L-H Huang
- Department of Plastic Surgery, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, No.123, Ta-Pei Road, Niao-Song District, Kaohsiung City 833, Taiwan
| | - Y-C Wu
- Department of Plastic Surgery, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, No.123, Ta-Pei Road, Niao-Song District, Kaohsiung City 833, Taiwan
| | - C-J Wu
- Department of Plastic Surgery, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, No.123, Ta-Pei Road, Niao-Song District, Kaohsiung City 833, Taiwan
| | - H-P Lin
- Department of Plastic Surgery, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, No.123, Ta-Pei Road, Niao-Song District, Kaohsiung City 833, Taiwan
| | - C-H Hsieh
- Department of Plastic Surgery, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, No.123, Ta-Pei Road, Niao-Song District, Kaohsiung City 833, Taiwan.
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29
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Hildebrandt A, Kirchner B, Meidert AS, Brandes F, Lindemann A, Doose G, Doege A, Weidenhagen R, Reithmair M, Schelling G, Pfaffl MW. Detection of Atherosclerosis by Small RNA-Sequencing Analysis of Extracellular Vesicle Enriched Serum Samples. Front Cell Dev Biol 2021; 9:729061. [PMID: 34712662 PMCID: PMC8546328 DOI: 10.3389/fcell.2021.729061] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 09/14/2021] [Indexed: 01/02/2023] Open
Abstract
Atherosclerosis can occur throughout the arterial vascular system and lead to various diseases. Early diagnosis of atherosclerotic processes and of individual disease patterns would be more likely to be successful if targeted therapies were available. For this, it is important to find reliable biomarkers that are easily accessible and with little inconvenience for patients. There are many cell culture, animal model or tissue studies that found biomarkers at the microRNA (miRNA) and mRNA level describing atherosclerotic processes. However, little is known about their potential as circulating and liquid biopsy markers in patients. In this study, we examined serum-derived miRNA - profiles from 129 patients and 28 volunteers to identify potential biomarkers. The patients had four different atherosclerotic manifestations: abdominal aneurysm (n = 35), coronary heart disease (n = 34), carotid artery stenosis (n = 24) and peripheral arterial disease (n = 36). The samples were processed with an extracellular vesicle enrichment protocol, total-RNA extraction and small RNA-sequencing were performed. A differential expression analysis was performed bioinformatically to find potentially regulated miRNA biomarkers. Resulting miRNA candidates served as a starting point for an overrepresentation analysis in which relevant target mRNAs were identified. The Gene Ontology database revealed relevant biological functions in relation to atherosclerotic processes. In patients, expression of specific miRNAs changed significantly compared to healthy volunteers; 27 differentially expressed miRNAs were identified. We were able to detect a group-specific miRNA fingerprint: miR-122-5p, miR-2110 and miR-483-5p for abdominal aortic aneurysm, miR-370-3p and miR-409-3p for coronary heart disease, miR-335-3p, miR-381-3p, miR493-5p and miR654-3p for carotid artery stenosis, miR-199a-5p, miR-215-5p, miR-3168, miR-582-3p and miR-769-5p for peripheral arterial disease. The results of the study show that some of the identified miRNAs have already been associated with atherosclerosis in previous studies. Overrepresentation analysis on this data detected biological processes that are clearly relevant for atherosclerosis, its development and progression showing the potential of these miRNAs as biomarker candidates. In a next step, the relevance of these findings on the mRNA level is to be investigated and substantiated.
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Affiliation(s)
- Alex Hildebrandt
- Division of Animal Physiology and Immunology, School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Benedikt Kirchner
- Division of Animal Physiology and Immunology, School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Agnes S Meidert
- Department of Anesthesiology, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Florian Brandes
- Department of Anesthesiology, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Anja Lindemann
- Institute of Human Genetics, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Gero Doose
- ecSeq Bioinformatics GmbH, Leipzig, Germany
| | - Alexander Doege
- Department of Anesthesiology, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Rolf Weidenhagen
- Department of Vascular Surgery, Klinikum Neuperlach, Muenchen-Kliniken, Munich, Germany
| | - Marlene Reithmair
- Institute of Human Genetics, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Gustav Schelling
- Department of Anesthesiology, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Michael W Pfaffl
- Division of Animal Physiology and Immunology, School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
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30
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Yan C, Zhang N, Wang Q, Fu Y, Wang F, Su Y, Xue B, Zhou L, Liao H. The Effect of Low Temperature Stress on the Leaves and MicroRNA Expression of Potato Seedlings. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.727081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
In recent years, with the wanton destruction of the ecological environment by humans and the frequent occurrence of extreme bad weather, many places that should have been warm and blooming in spring have instead experienced the phenomenon of the “April blizzard,” which has seriously affected China's crops, especially spring potato production in most areas. Potato cultivars, especially potato seedlings, are sensitive to frost, and low temperature frost has become one of the most important abiotic stresses affecting potato production. Potato cold tolerance is regulated by a complex gene network. Although some low temperature resistant microRNAs have been identified, little is known about the role of miRNAs in response to low temperature stress in potato. Therefore, the objective of this study is to clarify the influence of low temperature stress on the miRNA expression of potato by comparing the expression differences of miRNA in potato which was treated with different low temperatures. For the study, 307 known miRNAs belonging to 73 small RNA families and 211 novel miRNAs were obtained. When the temperature decreased, the number of both known and novel miRNA decreased, and the minimum temperature was −2°C. Most of the miRNAs respond to low temperature, drought, and disease stress; some conserved miRNAs were first found to respond to low temperature stress in potato, such as stu-miR530, stu-miR156d, and stu-miR167b. The Gene Ontology, Kyoto Encyclopedia of Genes, and Genomes pathway enrichment analysis of 442 different expression miRNAs target genes indicated that there existed diversified low temperature responsive pathways, but Abscisic Acid was found likely to play a central coordinating role in response to low temperature stress in many metabolism pathways. Quantitative real-time PCR assays indicated that the related targets were negatively regulated by the tested different expression miRNAs during low temperature stress. The results indicated that miRNAs may play an important coordination role in response to low temperature stress in many metabolic pathways by regulating abscisic acid and gibberellin, which provided insight into the roles of miRNAs during low temperature stress and would be helpful for alleviating low temperature stress and promoting low temperature resistant breeding in potatoes.
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31
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Nuñez-Borque E, Fernandez-Bravo S, Rodriguez Del Rio P, Alwashali EM, Lopez-Dominguez D, Gutierrez-Blazquez MD, Laguna JJ, Tome-Amat J, Gallego-Delgado J, Gomez-Lopez A, Betancor D, Cuesta-Herranz J, Ibañez-Sandin MD, Benito-Martin A, Esteban V. Increased miR-21-3p and miR-487b-3p serum levels during anaphylactic reaction in food allergic children. Pediatr Allergy Immunol 2021; 32:1296-1306. [PMID: 33876465 PMCID: PMC8453890 DOI: 10.1111/pai.13518] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 04/03/2021] [Accepted: 04/08/2021] [Indexed: 12/16/2022]
Abstract
BACKGROUND Anaphylaxis is the most severe manifestation of allergic disorders. The poor knowledge of its molecular mechanisms often leads to under-diagnosis. MicroRNAs (miRNA) regulate physiologic and pathologic processes, and they have been postulated as promising diagnostic markers. The main objectives of this study were to characterize the human miRNA profile during anaphylaxis and to assess their capacity as diagnostic markers and determine their participation in the molecular mechanisms of this event. METHODS The miRNA serum profiles from the acute and baseline phase of 5 oral food-challenged anaphylactic children (<18 years old) were obtained by next-generation sequencing (NGS). From the panel of statistically significant miRNAs obtained, several candidates were selected and analyzed in 19 anaphylactic children by qPCR. We performed system biology analysis (SBA) on their target genes to identify main functions and canonical pathways. A functional in vitro assay was carried out incubating endothelial cells (ECs) in anaphylactic conditions. RESULTS The NGS identified 389 miRNAs among which 41 were significantly different between acute and baseline samples. The high levels of miR-21-3p (fold change = 2.28, P = .006) and miR-487b-3p (fold change = 1.04, P = .039) observed by NGS in acute serum samples were confirmed in a larger group of 19 patients. The SBA revealed molecular pathways related to the inflammation and immune system regulation. miR-21-3p increased intracellularly and in acute phase serum after EC stimulation. CONCLUSIONS These findings provide, for the first time, some insights into the anaphylactic miRNA serum profile in children and point to miR-21-3p and miR-487b-3p as candidate biomarkers. Furthermore, the SBA revealed a possible implication of these molecules in the underlying molecular mechanisms. Moreover, ECs increased miR-21-3p intracellularly and released it to the environment in response to anaphylaxis.
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Affiliation(s)
- Emilio Nuñez-Borque
- Department of Allergy and Immunology, IIS-Fundación Jiménez Díaz, UAM, Madrid, Spain
| | | | - Pablo Rodriguez Del Rio
- Allergy Department, Foundation for Biomedical Research, Niño Jesus University Children's Hospital, Madrid, Spain.,Instituto de Salud Carlos III, ARADyAL Network, Madrid, Spain
| | - Ebrahim Mohammed Alwashali
- CAI Genomics and Proteomics, Proteomic Unit, Faculty of Pharmacy, Complutense University of Madrid, Madrid, Spain
| | - David Lopez-Dominguez
- Clinical Biostatistics Unit, Instituto de Investigación Puerta de Hierro (IDIPHIM), Puerta de Hierro Majadahonda University Hospital, Madrid, Spain
| | | | - Jose Julio Laguna
- Instituto de Salud Carlos III, ARADyAL Network, Madrid, Spain.,Allergy Unit, Allergo-Anaesthesia Unit, Faculty of Medicine, Hospital Central de la Cruz Roja, Alfonso X El Sabio University, Madrid, Spain
| | - Jaime Tome-Amat
- Instituto de Salud Carlos III, ARADyAL Network, Madrid, Spain.,Centro de Biotecnología y Genómica de Plantas (UPM-INIA), Universidad Politécnica de Madrid, Madrid, Spain
| | - Julio Gallego-Delgado
- Department of Biological Sciences, Lehman College, City University of New York, New York, NY, USA.,Program in Biology, The Graduate Center, The City University of New York, New York, NY, USA
| | | | | | - Javier Cuesta-Herranz
- Department of Allergy and Immunology, IIS-Fundación Jiménez Díaz, UAM, Madrid, Spain.,Instituto de Salud Carlos III, ARADyAL Network, Madrid, Spain.,Hospital Fundación Jiménez Díaz, Madrid, Spain
| | - Maria Dolores Ibañez-Sandin
- Allergy Department, Foundation for Biomedical Research, Niño Jesus University Children's Hospital, Madrid, Spain.,Instituto de Salud Carlos III, ARADyAL Network, Madrid, Spain
| | | | - Vanesa Esteban
- Department of Allergy and Immunology, IIS-Fundación Jiménez Díaz, UAM, Madrid, Spain.,Instituto de Salud Carlos III, ARADyAL Network, Madrid, Spain.,Faculty of Biomedicine and Medicine, Alfonso X El Sabio University, Madrid, Spain
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32
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Badimon L, Robinson EL, Jusic A, Carpusca I, deWindt LJ, Emanueli C, Ferdinandy P, Gu W, Gyöngyösi M, Hackl M, Karaduzovic-Hadziabdic K, Lustrek M, Martelli F, Nham E, Potočnjak I, Satagopam V, Schneider R, Thum T, Devaux Y. Cardiovascular RNA markers and artificial intelligence may improve COVID-19 outcome: a position paper from the EU-CardioRNA COST Action CA17129. Cardiovasc Res 2021; 117:1823-1840. [PMID: 33839767 PMCID: PMC8083253 DOI: 10.1093/cvr/cvab094] [Citation(s) in RCA: 9] [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: 09/16/2020] [Accepted: 04/08/2021] [Indexed: 02/06/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has been as unprecedented as unexpected, affecting more than 105 million people worldwide as of 8 February 2020 and causing more than 2.3 million deaths according to the World Health Organization (WHO). Not only affecting the lungs but also provoking acute respiratory distress, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is able to infect multiple cell types including cardiac and vascular cells. Hence a significant proportion of infected patients develop cardiac events, such as arrhythmias and heart failure. Patients with cardiovascular comorbidities are at highest risk of cardiac death. To face the pandemic and limit its burden, health authorities have launched several fast-track calls for research projects aiming to develop rapid strategies to combat the disease, as well as longer-term projects to prepare for the future. Biomarkers have the possibility to aid in clinical decision-making and tailoring healthcare in order to improve patient quality of life. The biomarker potential of circulating RNAs has been recognized in several disease conditions, including cardiovascular disease. RNA biomarkers may be useful in the current COVID-19 situation. The discovery, validation, and marketing of novel biomarkers, including RNA biomarkers, require multi-centre studies by large and interdisciplinary collaborative networks, involving both the academia and the industry. Here, members of the EU-CardioRNA COST Action CA17129 summarize the current knowledge about the strain that COVID-19 places on the cardiovascular system and discuss how RNA biomarkers can aid to limit this burden. They present the benefits and challenges of the discovery of novel RNA biomarkers, the need for networking efforts, and the added value of artificial intelligence to achieve reliable advances.
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Affiliation(s)
- Lina Badimon
- Cardiovascular Science Program-ICCC, IR-Hospital de la Santa Creu i Santa Pau, Ciber CV, Autonomous University of Barcelona, Barcelona, Spain
| | - Emma L Robinson
- Department of Cardiology, School for Cardiovascular Diseases, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, the Netherlands
- Division of Cardiology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Amela Jusic
- Cardiovascular Research Unit, Department of Population Health, Luxembourg Institute of Health, 1A-B rue Edison, L-1445 Strassen, Luxembourg
| | - Irina Carpusca
- Cardiovascular Research Unit, Department of Population Health, Luxembourg Institute of Health, 1A-B rue Edison, L-1445 Strassen, Luxembourg
| | - Leon J deWindt
- Department of Molecular Genetics, Faculty of Science and Engineering, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, the Netherlands
| | - Costanza Emanueli
- National Heart & Lung Institute, Faculty of Medicine, Imperial College London, London, UK
| | - Péter Ferdinandy
- Cardiometabolic Research Group and MTA-SE System Pharmacology Research Group, Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest,Hungary
- Pharmahungary Group, Szeged, Hungary
| | - Wei Gu
- Luxembourg Center for Systems Biomedicine, University of Luxembourg, Esch sur Alzette, Luxembourg
| | - Mariann Gyöngyösi
- Department of Cardiology, Medical University of Vienna, Vienna, Austria
| | | | | | - Mitja Lustrek
- Department of Intelligent Systems, Jozef Stefan Institute, Ljubljana, Slovenia
| | - Fabio Martelli
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, San Donato Milanese, Milan 20097, Italy
| | - Eric Nham
- University of Zagreb School of Medicine, Zagreb, Croatia
| | - Ines Potočnjak
- Institute for Clinical Medical Research and Education, University Hospital Centre Sisters of Charity, Zagreb, Croatia
| | - Venkata Satagopam
- Luxembourg Center for Systems Biomedicine, University of Luxembourg, Esch sur Alzette, Luxembourg
| | - Reinhard Schneider
- Luxembourg Center for Systems Biomedicine, University of Luxembourg, Esch sur Alzette, Luxembourg
| | - Thomas Thum
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Fraunhofer Institute for Toxicology and Experimental Medicine, Hannover,Germany
- REBIRTH Center for Translational Regenerative Medicine, Hannover Medical School, Hannover, Germany
| | - Yvan Devaux
- Cardiovascular Research Unit, Department of Population Health, Luxembourg Institute of Health, 1A-B rue Edison, L-1445 Strassen, Luxembourg
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Jia J, Yang S, Huang J, Zheng H, He Y, Wang L. Distinct Extracellular RNA Profiles in Different Plasma Components. Front Genet 2021; 12:564780. [PMID: 34234804 PMCID: PMC8256274 DOI: 10.3389/fgene.2021.564780] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 05/17/2021] [Indexed: 01/08/2023] Open
Abstract
Circulating extracellular RNAs (exRNAs) have great potential to serve as biomarkers for a wide range of diagnostic, therapeutic, and prognostic applications. So far, knowledge of the difference among different sources of exRNAs is limited. To address this issue, we performed a sequential physical and biochemical precipitation to collect four fractions (platelets and cell debris, the thrombin-induced precipitates, extracellular vesicles, and supernatant) from each of 10 plasma samples. From total RNAs of the 40 fractions, we prepared ligation-free libraries to profile full spectrum of all RNA species, without size selection and rRNA reduction. Due to complicated RNA composition in these libraries, we utilized a successive stepwise alignment strategy to map the RNA sequences to different RNA categories, including miRNAs, piwi-interacting RNAs, tRNAs, rRNAs, lincRNAs, snoRNAs, snRNAs, other ncRNAs, protein coding RNAs, and circRNAs. Our data showed that each plasma fraction had its own unique distribution of RNA species. Hierarchical cluster analyses using transcript abundance demonstrated similarities in the same plasma fraction and significant differences between different fractions. In addition, we observed various unique transcripts, and novel predicted miRNAs among these plasma fractions. These results demonstrate that the distribution of RNA species and functional RNA transcripts is plasma fraction-dependent. Appropriate plasma preparation and thorough inspection of different plasma fractions are necessary for an exRNA-based biomarker study.
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Affiliation(s)
- Jing Jia
- Department of Medical Genetics & Cell Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China.,Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | - Shangdong Yang
- Department of Medical Genetics & Cell Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Jinyong Huang
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | - Hong Zheng
- Department of Medical Genetics & Cell Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Ying He
- Department of Medical Genetics & Cell Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Liang Wang
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States.,Department of Pathology, Medical College of Wisconsin, Milwaukee, WI, United States
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miREV: An Online Database and Tool to Uncover Potential Reference RNAs and Biomarkers in Small-RNA Sequencing Data Sets from Extracellular Vesicles Enriched Samples. J Mol Biol 2021; 433:167070. [PMID: 34052284 DOI: 10.1016/j.jmb.2021.167070] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 05/11/2021] [Accepted: 05/22/2021] [Indexed: 02/06/2023]
Abstract
Extracellular vesicles (EVs) are nano-sized, membrane-enclosed vesicles released by cells for intercellular communication. EVs are involved in pathological processes and miRNAs in EVs have gained interest as easily accessible biomolecules in liquid biopsies for diagnostic purposes. To validate potential miRNA biomarker, transcriptome analyses must be carried out to detect suitable reference miRNAs. miREV is a database with over 400 miRNA sequencing data sets and helps the researcher to find suitable reference miRNAs for their individual experimental setup. The researcher can put together a specific sample set in miREV, which is similar to his own experimental concept in order to find the most suitable references. This allows to run validation experiments without having to carry out a complex and costly transcriptome analysis priorly. Additional read count tables of each generated sample set are downloadable for further analysis. miREV is freely available at https://www.physio.wzw.tum.de/mirev/.
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Benesova S, Kubista M, Valihrach L. Small RNA-Sequencing: Approaches and Considerations for miRNA Analysis. Diagnostics (Basel) 2021; 11:964. [PMID: 34071824 PMCID: PMC8229417 DOI: 10.3390/diagnostics11060964] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/21/2021] [Accepted: 05/24/2021] [Indexed: 01/15/2023] Open
Abstract
MicroRNAs (miRNAs) are a class of small RNA molecules that have an important regulatory role in multiple physiological and pathological processes. Their disease-specific profiles and presence in biofluids are properties that enable miRNAs to be employed as non-invasive biomarkers. In the past decades, several methods have been developed for miRNA analysis, including small RNA sequencing (RNA-seq). Small RNA-seq enables genome-wide profiling and analysis of known, as well as novel, miRNA variants. Moreover, its high sensitivity allows for profiling of low input samples such as liquid biopsies, which have now found applications in diagnostics and prognostics. Still, due to technical bias and the limited ability to capture the true miRNA representation, its potential remains unfulfilled. The introduction of many new small RNA-seq approaches that tried to minimize this bias, has led to the existence of the many small RNA-seq protocols seen today. Here, we review all current approaches to cDNA library construction used during the small RNA-seq workflow, with particular focus on their implementation in commercially available protocols. We provide an overview of each protocol and discuss their applicability. We also review recent benchmarking studies comparing each protocol's performance and summarize the major conclusions that can be gathered from their usage. The result documents variable performance of the protocols and highlights their different applications in miRNA research. Taken together, our review provides a comprehensive overview of all the current small RNA-seq approaches, summarizes their strengths and weaknesses, and provides guidelines for their applications in miRNA research.
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Affiliation(s)
- Sarka Benesova
- Laboratory of Gene Expression, Institute of Biotechnology, CAS, BIOCEV, 252 50 Vestec, Czech Republic; (S.B.); (M.K.)
- Laboratory of Informatics and Chemistry, Faculty of Chemical Technology, University of Chemistry and Technology, 166 28 Prague, Czech Republic
| | - Mikael Kubista
- Laboratory of Gene Expression, Institute of Biotechnology, CAS, BIOCEV, 252 50 Vestec, Czech Republic; (S.B.); (M.K.)
- TATAA Biocenter AB, 411 03 Gothenburg, Sweden
| | - Lukas Valihrach
- Laboratory of Gene Expression, Institute of Biotechnology, CAS, BIOCEV, 252 50 Vestec, Czech Republic; (S.B.); (M.K.)
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Identification of plasma miRNA biomarkers for pregnancy detection in dairy cattle. JOURNAL OF ANIMAL REPRODUCTION AND BIOTECHNOLOGY 2021. [DOI: 10.12750/jarb.36.1.35] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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Abstract
Progress in genomic analytical technologies has improved our possibilities to obtain information regarding DNA, RNA, and their dynamic changes that occur over time or in response to specific challenges. This information describes the blueprint for cells, tissues, and organisms and has fundamental importance for all living organisms. This review focuses on the technological challenges to analyze the transcriptome and what is the impact of transcriptomics on precision medicine. The transcriptome is a term that covers all RNA present in cells and a substantial part of it will never be translated into protein but is nevertheless functional in determining cell phenotype. Recent developments in transcriptomics have challenged the fundamentals of the central dogma of biology by providing evidence of pervasive transcription of the genome. Such massive transcriptional activity is challenging the definition of a gene and especially the term "pseudogene" that has now been demonstrated in many examples to be both transcribed and translated. We also review the common sources of biomaterials for transcriptomics and justify the suitability of whole blood RNA as the current optimal analyte for clinical transcriptomics. At the end of the review, a brief overview of the clinical implications of transcriptomics in clinical trial design and clinical diagnosis is given. Finally, we introduce the transcriptome as a target for modern drug development as a tool for extending our capacity for precision medicine in multiple diseases.
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Affiliation(s)
| | - Abigail L Pfaff
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch 6150, Australia
- Perron Institute for Neurological and Translational Science, Nedlands 6009, Australia
| | - Vivien J Bubb
- Department of Pharmacology and Therapeutics, University of Liverpool, Liverpool L69 3BX, UK
| | - John P Quinn
- Department of Pharmacology and Therapeutics, University of Liverpool, Liverpool L69 3BX, UK
| | - Sulev Koks
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch 6150, Australia
- Perron Institute for Neurological and Translational Science, Nedlands 6009, Australia
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Castanheira C, Balaskas P, Falls C, Ashraf-Kharaz Y, Clegg P, Burke K, Fang Y, Dyer P, Welting TJM, Peffers MJ. Equine synovial fluid small non-coding RNA signatures in early osteoarthritis. BMC Vet Res 2021; 17:26. [PMID: 33422071 PMCID: PMC7796526 DOI: 10.1186/s12917-020-02707-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 12/02/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Osteoarthritis remains one of the greatest causes of morbidity and mortality in the equine population. The inability to detect pre-clinical changes in osteoarthritis has been a significant impediment to the development of effective therapies against this disease. Synovial fluid represents a potential source of disease-specific small non-coding RNAs (sncRNAs) that could aid in the understanding of the pathogenesis of osteoarthritis. We hypothesised that early stages of osteoarthritis would alter the expression of sncRNAs, facilitating the understanding of the underlying pathogenesis and potentially provide early biomarkers. METHODS Small RNA sequencing was performed using synovial fluid from the metacarpophalangeal joints of both control and early osteoarthritic horses. A group of differentially expressed sncRNAs was selected for further validation through qRT-PCR using an independent cohort of synovial fluid samples from control and early osteoarthritic horses. Bioinformatic analysis was performed in order to identify putative targets of the differentially expressed microRNAs and to explore potential associations with specific biological processes. RESULTS Results revealed 22 differentially expressed sncRNAs including 13 microRNAs; miR-10a, miR-223, let7a, miR-99a, miR-23b, miR-378, miR-143 (and six novel microRNAs), four small nuclear RNAs; U2, U5, U11, U12, three small nucleolar RNAs; U13, snoR38, snord96, and one small cajal body-specific RNA; scarna3. Five sncRNAs were validated; miR-223 was significantly reduced in early osteoarthritis and miR-23b, let-7a-2, snord96A and snord13 were significantly upregulated. Significant cellular actions deduced by the differentially expressed microRNAs included apoptosis (P < 0.0003), necrosis (P < 0.0009), autophagy (P < 0.0007) and inflammation (P < 0.00001). A conservatively filtered list of 57 messenger RNA targets was obtained; the top biological processes associated were regulation of cell population proliferation (P < 0.000001), cellular response to chemical stimulus (P < 0.000001) and cell surface receptor signalling pathway (P < 0.000001). CONCLUSIONS Synovial fluid sncRNAs may be used as molecular biomarkers for early disease in equine osteoarthritic joints. The biological processes they regulate may play an important role in understanding early osteoarthritis pathogenesis. Characterising these dynamic molecular changes could provide novel insights on the process and mechanism of early osteoarthritis development and is critical for the development of new therapeutic approaches.
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Affiliation(s)
- Catarina Castanheira
- Department of Musculoskeletal and Ageing Science, Institute of Life Course and Medical Sciences, William Henry Duncan Building, 6 West Derby Street, Liverpool, L7 8TX UK
| | - Panagiotis Balaskas
- Department of Musculoskeletal and Ageing Science, Institute of Life Course and Medical Sciences, William Henry Duncan Building, 6 West Derby Street, Liverpool, L7 8TX UK
| | - Charlotte Falls
- Department of Musculoskeletal and Ageing Science, Institute of Life Course and Medical Sciences, William Henry Duncan Building, 6 West Derby Street, Liverpool, L7 8TX UK
| | - Yalda Ashraf-Kharaz
- Department of Musculoskeletal and Ageing Science, Institute of Life Course and Medical Sciences, William Henry Duncan Building, 6 West Derby Street, Liverpool, L7 8TX UK
| | - Peter Clegg
- Department of Musculoskeletal and Ageing Science, Institute of Life Course and Medical Sciences, William Henry Duncan Building, 6 West Derby Street, Liverpool, L7 8TX UK
| | - Kim Burke
- Institute of Veterinary Science, University of Liverpool, Chester High Road, Neston, CH64 7TE UK
| | - Yongxiang Fang
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool, L69 7ZB UK
| | - Philip Dyer
- Institute of Infection and Global Health, University of Liverpool, 8 West Derby Street, Liverpool, L7 3EA UK
| | - Tim J. M. Welting
- Department of Orthopaedic Surgery, Maastricht University Medical Centre, Maastricht, AZ 6202 The Netherlands
| | - Mandy J. Peffers
- Department of Musculoskeletal and Ageing Science, Institute of Life Course and Medical Sciences, William Henry Duncan Building, 6 West Derby Street, Liverpool, L7 8TX UK
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Molecular Signature of Extracellular Vesicular Small Non-Coding RNAs Derived from Cerebrospinal Fluid of Leptomeningeal Metastasis Patients: Functional Implication of miR-21 and Other Small RNAs in Cancer Malignancy. Cancers (Basel) 2021; 13:cancers13020209. [PMID: 33430103 PMCID: PMC7828086 DOI: 10.3390/cancers13020209] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/23/2020] [Accepted: 12/30/2020] [Indexed: 02/06/2023] Open
Abstract
Simple Summary Leptomeningeal metastasis (LM) is a lethal complication in which cancer metastasizes to the meninges. Currently, there are neither definitive treatments nor diagnosis methods for LM patients. In this study, we suggest the examination of small non-coding RNA (smRNA) populations of extracellular vesicles (EVs) derived from the cerebrospinal fluid (CSF) as a potential vehicle for diagnosis and treatment strategies. Systemic and quantitative analysis of smRNA subpopulations from LM CSF EVs showed unique expression patterns between LM patients and healthy donors. In addition, LM CSF EVs smRNAs appeared to be associated with LM pathogenesis suggesting they may be viable targets for novel diagnostic and treatment strategies. Abstract Leptomeningeal metastasis (LM) is a fatal and rare complication of cancer in which the cancer spreads via the cerebrospinal fluid (CSF). At present, there is no definitive treatment or diagnosis for this deleterious disease. In this study, we systemically and quantitatively investigated biased expression of key small non-coding RNA (smRNA) subpopulations from LM CSF extracellular vesicles (EVs) via a unique smRNA sequencing method. The analyzed subpopulations included microRNA (miRNA), Piwi-interacting RNA (piRNA), Y RNA, small nuclear RNA (snRNA), small nucleolar RNAs (snoRNA), vault RNA (vtRNA), novel miRNA, etc. Here, among identified miRNAs, miR-21, which was already known to play an essential oncogenic role in tumorigenesis, was thoroughly investigated via systemic biochemical, miR-21 sensor, and physiological cell-based approaches, with the goal of confirming its functionality and potential as a biomarker for the pathogenesis and diagnosis of LM. We herein uncovered LM CSF extravesicular smRNAs that may be associated with LM-related complications and elucidated plausible pathways that may mechanistically contribute to LM progression. In sum, the analyzed smRNA subpopulations will be useful as targets for the development of therapeutic and diagnostic strategies for LM and LM-related complications.
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Inokuchi K, Ochiya T, Matsuzaki J. Extracellular miRNAs for the Management of Barrett's Esophagus and Esophageal Adenocarcinoma: A Systematic Review. J Clin Med 2020; 10:E117. [PMID: 33396321 PMCID: PMC7795564 DOI: 10.3390/jcm10010117] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 12/26/2020] [Accepted: 12/28/2020] [Indexed: 02/06/2023] Open
Abstract
Esophageal adenocarcinoma (EAC), the major histologic type of esophageal cancer (EC) in Western countries, is a disease with a poor prognosis, primarily due to usual diagnosis at an advanced stage. The prevalence of EAC has increased in recent years, both in Western countries and in Asia. Barrett's esophagus (BE) is a precursor lesion of EAC. Therefore, early detection and proper management of BE and EAC is important to improve prognosis. Here, we systematically summarize current knowledge about the potential utility of extracellular microRNAs (miRNAs), which are thought to be non-invasive biomarkers for many diseases, for these purposes. A search of the PubMed and Embase databases identified 22 papers about extracellular miRNAs that have potential utility for management of EAC. Among them, 19 were EAC-related and ten were BE-related; some of these dealt with both conditions. The articles included studies reporting diagnosis, prognosis, and treatment responses. Multiple papers report dysregulation of miR-194-5p in BE and miR-21-5p, -25-3p, and -93-5p in EAC. Although it will take time to utilize these miRNAs in clinical practice, they are likely to be useful non-invasive markers in the future.
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Affiliation(s)
- Kazumi Inokuchi
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan;
| | - Takahiro Ochiya
- Department of Molecular and Cellular Medicine, Tokyo Medical University, 6-7-1 Nishishinjuku, Shinjuku-ku, Tokyo 160-0023, Japan;
| | - Juntaro Matsuzaki
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan;
- Department of Molecular and Cellular Medicine, Tokyo Medical University, 6-7-1 Nishishinjuku, Shinjuku-ku, Tokyo 160-0023, Japan;
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Nguyen L, Schilling D, Dobiasch S, Raulefs S, Santiago Franco M, Buschmann D, Pfaffl MW, Schmid TE, Combs SE. The Emerging Role of miRNAs for the Radiation Treatment of Pancreatic Cancer. Cancers (Basel) 2020; 12:cancers12123703. [PMID: 33317198 PMCID: PMC7763922 DOI: 10.3390/cancers12123703] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/17/2020] [Accepted: 12/04/2020] [Indexed: 12/11/2022] Open
Abstract
Simple Summary Pancreatic cancer is an aggressive disease with a high mortality rate. Radiotherapy is one treatment option within a multimodal therapy approach for patients with locally advanced, non-resectable pancreatic tumors. However, radiotherapy is only effective in about one-third of the patients. Therefore, biomarkers that can predict the response to radiotherapy are of utmost importance. Recently, microRNAs, small non-coding RNAs regulating gene expression, have come into focus as there is growing evidence that microRNAs could serve as diagnostic, predictive and prognostic biomarkers in various cancer entities, including pancreatic cancer. Moreover, their high stability in body fluids such as serum and plasma render them attractive candidates for non-invasive biomarkers. This article describes the role of microRNAs as suitable blood biomarkers and outlines an overview of radiation-induced microRNAs changes and the association with radioresistance in pancreatic cancer. Abstract Today, pancreatic cancer is the seventh leading cause of cancer-related deaths worldwide with a five-year overall survival rate of less than 7%. Only 15–20% of patients are eligible for curative intent surgery at the time of diagnosis. Therefore, neoadjuvant treatment regimens have been introduced in order to downsize the tumor by chemotherapy and radiotherapy. To further increase the efficacy of radiotherapy, novel molecular biomarkers are urgently needed to define the subgroup of pancreatic cancer patients who would benefit most from radiotherapy. MicroRNAs (miRNAs) could have the potential to serve as novel predictive and prognostic biomarkers in patients with pancreatic cancer. In the present article, the role of miRNAs as blood biomarkers, which are associated with either radioresistance or radiation-induced changes of miRNAs in pancreatic cancer, is discussed. Furthermore, the manuscript provides own data of miRNAs identified in a pancreatic cancer mouse model as well as radiation-induced miRNA changes in the plasma of tumor-bearing mice.
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Affiliation(s)
- Lily Nguyen
- Institute of Radiation Medicine (IRM), Department of Radiation Sciences (DRS), Helmholtz Zentrum München, 85764 Neuherberg, Germany; (L.N.); (D.S.); (S.D.); (S.R.); (M.S.F.); (T.E.S.)
- Department of Radiation Oncology, School of Medicine, Technical University of Munich (TUM), Klinikum rechts der Isar, 81675 Munich, Germany
| | - Daniela Schilling
- Institute of Radiation Medicine (IRM), Department of Radiation Sciences (DRS), Helmholtz Zentrum München, 85764 Neuherberg, Germany; (L.N.); (D.S.); (S.D.); (S.R.); (M.S.F.); (T.E.S.)
- Department of Radiation Oncology, School of Medicine, Technical University of Munich (TUM), Klinikum rechts der Isar, 81675 Munich, Germany
| | - Sophie Dobiasch
- Institute of Radiation Medicine (IRM), Department of Radiation Sciences (DRS), Helmholtz Zentrum München, 85764 Neuherberg, Germany; (L.N.); (D.S.); (S.D.); (S.R.); (M.S.F.); (T.E.S.)
- Department of Radiation Oncology, School of Medicine, Technical University of Munich (TUM), Klinikum rechts der Isar, 81675 Munich, Germany
- Deutsches Konsortium für Translationale Krebsforschung (DKTK), Partner Site Munich, 81675 Munich, Germany
| | - Susanne Raulefs
- Institute of Radiation Medicine (IRM), Department of Radiation Sciences (DRS), Helmholtz Zentrum München, 85764 Neuherberg, Germany; (L.N.); (D.S.); (S.D.); (S.R.); (M.S.F.); (T.E.S.)
- Department of Radiation Oncology, School of Medicine, Technical University of Munich (TUM), Klinikum rechts der Isar, 81675 Munich, Germany
| | - Marina Santiago Franco
- Institute of Radiation Medicine (IRM), Department of Radiation Sciences (DRS), Helmholtz Zentrum München, 85764 Neuherberg, Germany; (L.N.); (D.S.); (S.D.); (S.R.); (M.S.F.); (T.E.S.)
| | - Dominik Buschmann
- Division of Animal Physiology and Immunology, TUM School of Life Sciences Weihenstephan, Technical University of Munich (TUM), 85354 Freising, Germany; (D.B.); (M.W.P.)
| | - Michael W. Pfaffl
- Division of Animal Physiology and Immunology, TUM School of Life Sciences Weihenstephan, Technical University of Munich (TUM), 85354 Freising, Germany; (D.B.); (M.W.P.)
| | - Thomas E. Schmid
- Institute of Radiation Medicine (IRM), Department of Radiation Sciences (DRS), Helmholtz Zentrum München, 85764 Neuherberg, Germany; (L.N.); (D.S.); (S.D.); (S.R.); (M.S.F.); (T.E.S.)
- Department of Radiation Oncology, School of Medicine, Technical University of Munich (TUM), Klinikum rechts der Isar, 81675 Munich, Germany
| | - Stephanie E. Combs
- Institute of Radiation Medicine (IRM), Department of Radiation Sciences (DRS), Helmholtz Zentrum München, 85764 Neuherberg, Germany; (L.N.); (D.S.); (S.D.); (S.R.); (M.S.F.); (T.E.S.)
- Department of Radiation Oncology, School of Medicine, Technical University of Munich (TUM), Klinikum rechts der Isar, 81675 Munich, Germany
- Deutsches Konsortium für Translationale Krebsforschung (DKTK), Partner Site Munich, 81675 Munich, Germany
- Correspondence: ; Tel.: +49-89-4140-4501
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Fan S, Yin Q, Li D, Ma J, Li L, Chai S, Guo H, Yang Z. Anti-neuroinflammatory effects of Eucommia ulmoides Oliv. In a Parkinson's mouse model through the regulation of p38/JNK-Fosl2 gene expression. JOURNAL OF ETHNOPHARMACOLOGY 2020; 260:113016. [PMID: 32464317 DOI: 10.1016/j.jep.2020.113016] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 05/15/2020] [Accepted: 05/24/2020] [Indexed: 06/11/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Eucommia ulmoides Oliv., a Chinese medicinal herb called "Duzhong" from the bark of Eucommia ulmoides Oliv., has been shown to possess significant protective effects in Parkinson's disease (PD). However, the molecular mechanism remains unclear. AIM OF THE STUDY In this study, we explored the anti-neuroinflammatory mechanisms of Duzhong on the 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-induced PD mouse model to elucidate the traditional medical theories with modern pharmacological methods and to provide a reference for further clarifying its mechanisms of action. MATERIALS AND METHODS The representative components in Duzhong extract were identified by UPLC-Q-TOF/MS. Male C57BL/6J mice were intraperitoneally injected with MPTP to establish an in vivo PD model. The pole, rotarod, and grip strength tests were performed to evaluate the motor coordination ability of the PD mice. HPLC-ECD was used to detect the striatal levels of dopamine (DA), 3,4- dihydroxyphenylacetic acid (DOPAC) and homovanillic acid (HVA). The expression of tyrosine hydroxylase (TH) was studied by immunohistochemistry (IHC) and Western blot assays. ELISA and Q-PCR were used examined the levels of proinflammatory cytokines in the serum and midbrain, respectively. Whole-transcriptome analysis of the midbrain was performed to explore the therapeutic effect of Duzhong on PD mice, and Q-PCR was then used to validate the differential gene expression changes in the PD mice treated with Duzhong. RESULTS Ten compounds were identified from Duzhong extract. Duzhong significantly alleviated the behavioral impairments and dopaminergic neuron degeneration of PD mice, and inhibited the expression of proinflammatory cytokines. Whole-transcriptome analysis revealed nine oppositely regulated genes, and the Fosl2 gene was consistent with the trend of observed by RNA-seq. Furthermore, Duzhong downregulated mRNA expression of p38 and JNK, which are key upstream genes of Fosl2. CONCLUSIONS Duzhong has promising therapeutic potential in PD mice, and its molecular mechanism is mediated by downregulating p38/JNK-Fosl2 gene expression to alleviate neuroinflammation.
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Affiliation(s)
- Shanshan Fan
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin Key Laboratory of Traditional Chinese Medicine Pharmacology, Tianjin University of Traditional Chinese Medicine, #10 Boyanghu Road, Jinghai District, Tianjin, 301617, China
| | - Qingsheng Yin
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin Key Laboratory of Traditional Chinese Medicine Pharmacology, Tianjin University of Traditional Chinese Medicine, #10 Boyanghu Road, Jinghai District, Tianjin, 301617, China
| | - Dongna Li
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin Key Laboratory of Traditional Chinese Medicine Pharmacology, Tianjin University of Traditional Chinese Medicine, #10 Boyanghu Road, Jinghai District, Tianjin, 301617, China; Key Laboratory of Pharmacology of Traditional Chinese Medical Formulae, Ministry of Education, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Jing Ma
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin Key Laboratory of Traditional Chinese Medicine Pharmacology, Tianjin University of Traditional Chinese Medicine, #10 Boyanghu Road, Jinghai District, Tianjin, 301617, China
| | - Lili Li
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin Key Laboratory of Traditional Chinese Medicine Pharmacology, Tianjin University of Traditional Chinese Medicine, #10 Boyanghu Road, Jinghai District, Tianjin, 301617, China; Key Laboratory of Pharmacology of Traditional Chinese Medical Formulae, Ministry of Education, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Shiwei Chai
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, 300193, China
| | - Hong Guo
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin Key Laboratory of Traditional Chinese Medicine Pharmacology, Tianjin University of Traditional Chinese Medicine, #10 Boyanghu Road, Jinghai District, Tianjin, 301617, China; Key Laboratory of Pharmacology of Traditional Chinese Medical Formulae, Ministry of Education, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China.
| | - Zhen Yang
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin Key Laboratory of Traditional Chinese Medicine Pharmacology, Tianjin University of Traditional Chinese Medicine, #10 Boyanghu Road, Jinghai District, Tianjin, 301617, China.
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An LF, Li ZD, Li L, Li H, Yu J. Pharmacological Effects of Novel Peptide Drugs on Allergic Rhinitis at the Small Ribonucleic Acids Level. Front Genet 2020; 11:560812. [PMID: 33061944 PMCID: PMC7517717 DOI: 10.3389/fgene.2020.560812] [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: 05/10/2020] [Accepted: 08/24/2020] [Indexed: 11/30/2022] Open
Abstract
Using an allergic rhinitis (AR) model, we evaluated the pharmacological effects of novel peptide drugs (P-ONE and P-TWO) at the small RNA (sRNA) level. Using high-throughput sequencing, we assessed the sRNA expression profile of the negative control, AR antagonist (positive control), P-ONE, and P-TWO groups. By functional clustering and Gene Ontology and KEGG pathway analyses, we found that sRNA target genes have a specific enrichment pattern and may contribute to the effects of the novel peptides. Small RNA sequencing confirmed the biological foundations of novel and traditional AR treatments and suggested unique pharmacological effects. Our findings will facilitate evaluation of the pathogenesis of AR and of the pharmacological mechanisms of novel peptide drugs.
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Affiliation(s)
- Li-Feng An
- Department of Otorhinolaryngology Head and Neck Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Zhan-Dong Li
- College of Food Engineering, Jilin Engineering Normal University, Changchun, China
- Measurement Biotechnique Research Center, Jilin Engineering Normal University, Changchun, China
| | - Lin Li
- Department of Otorhinolaryngology Head and Neck Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Hao Li
- College of Food Engineering, Jilin Engineering Normal University, Changchun, China
| | - Jian Yu
- College of Food Engineering, Jilin Engineering Normal University, Changchun, China
- Measurement Biotechnique Research Center, Jilin Engineering Normal University, Changchun, China
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Avendaño-Vázquez SE, Flores-Jasso CF. Stumbling on elusive cargo: how isomiRs challenge microRNA detection and quantification, the case of extracellular vesicles. J Extracell Vesicles 2020; 9:1784617. [PMID: 32944171 PMCID: PMC7480573 DOI: 10.1080/20013078.2020.1784617] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Affiliation(s)
- S Eréndira Avendaño-Vázquez
- Consorcio de Metabolismo de RNA y Vesículas Extracelulares, Instituto Nacional de Medicina Genómica, INMEGEN, Ciudad de México, México
| | - C Fabián Flores-Jasso
- Consorcio de Metabolismo de RNA y Vesículas Extracelulares, Instituto Nacional de Medicina Genómica, INMEGEN, Ciudad de México, México
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45
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Ghosh RD, Pattatheyil A, Roychoudhury S. Functional Landscape of Dysregulated MicroRNAs in Oral Squamous Cell Carcinoma: Clinical Implications. Front Oncol 2020; 10:619. [PMID: 32547936 PMCID: PMC7274490 DOI: 10.3389/fonc.2020.00619] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 04/03/2020] [Indexed: 12/24/2022] Open
Abstract
MicroRNA (miRNA) dysregulation is associated with the pathogenesis of oral squamous cell carcinoma (OSCC), and its elucidation could potentially provide information on patient outcome. A growing body of translational research on miRNA biology is focusing on precision oncology, aiming to decode the miRNA regulatory network in the development and progression of cancer. Tissue-specific expression and stable presence in all body fluids are unique features of miRNAs, which could be potentially exploited in the clinical setting. Recent understanding of miRNA properties has led them to be useful, attractive, and potential tools either as biomarkers (distinct miRNA expression signature) for diagnosis and prognostic outcomes or as targets for novel therapeutic entities, enabling personalized treatment for OSCC. In this review, we discuss recent research on different aspects of alterations in miRNA profiles along with their clinical significance and strive to identify probable potential miRNA biomarkers for diagnosis and prognosis of OSCC. We also discuss the current understanding and scope of development of miRNA-based therapeutics against OSCC.
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Affiliation(s)
- Ruma Dey Ghosh
- Tata Translational Cancer Research Center, Tata Medical Center, Kolkata, India
| | - Arun Pattatheyil
- Department of Head and Neck Surgical Oncology, Tata Medical Center, Kolkata, India
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46
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Valihrach L, Androvic P, Kubista M. Circulating miRNA analysis for cancer diagnostics and therapy. Mol Aspects Med 2020; 72:100825. [DOI: 10.1016/j.mam.2019.10.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 10/01/2019] [Accepted: 10/07/2019] [Indexed: 12/12/2022]
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47
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Weiser DA, West-Szymanski DC, Fraint E, Weiner S, Rivas MA, Zhao CWT, He C, Applebaum MA. Progress toward liquid biopsies in pediatric solid tumors. Cancer Metastasis Rev 2020; 38:553-571. [PMID: 31836951 DOI: 10.1007/s10555-019-09825-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Pediatric solid tumors have long been known to shed tumor cells, DNA, RNA, and proteins into the blood. Recent technological advances have allowed for improved capture and analysis of these typically scant circulating materials. Efforts are ongoing to develop "liquid biopsy" assays as minimally invasive tools to address diagnostic, prognostic, and disease monitoring needs in childhood cancer care. Applying these highly sensitive technologies to serial liquid biopsies is expected to advance understanding of tumor biology, heterogeneity, and evolution over the course of therapy, thus opening new avenues for personalized therapy. In this review, we outline the latest technologies available for liquid biopsies and describe the methods, pitfalls, and benefits of the assays that are being developed for children with extracranial solid tumors. We discuss what has been learned in several of the most common pediatric solid tumors including neuroblastoma, sarcoma, Wilms tumor, and hepatoblastoma and highlight promising future directions for the field.
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Affiliation(s)
- Daniel A Weiser
- Department of Pediatrics, Albert Einstein College of Medicine and Children's Hospital at Montefiore, Bronx, NY, USA
| | | | - Ellen Fraint
- Department of Pediatrics, Albert Einstein College of Medicine and Children's Hospital at Montefiore, Bronx, NY, USA
| | - Shoshana Weiner
- Department of Pediatrics, Weill Cornell Medical Center, New York, NY, USA
| | - Marco A Rivas
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
| | - Carolyn W T Zhao
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Mark A Applebaum
- Department of Pediatrics, The University of Chicago, 900 E. 57th St., KCBD 5116, Chicago, IL, 60637, USA.
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48
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Propofol and Sevoflurane Differentially Impact MicroRNAs in Circulating Extracellular Vesicles during Colorectal Cancer Resection. Anesthesiology 2020; 132:107-120. [DOI: 10.1097/aln.0000000000002986] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Abstract
Editor’s Perspective
What We Already Know about This Topic
What This Article Tells Us That Is New
Background
Extracellular vesicles and their microRNA cargo are crucial facilitators of malignant cell communication and could mediate effects of anesthetics on tumor biology during cancer resection. The authors performed a proof-of-concept study to demonstrate that propofol and sevoflurane have differential effects on vesicle-associated microRNAs that influence signaling pathways involved in tumor progression and metastasis.
Methods
Circulating vesicles were investigated in a prospective, matched-case pilot study in two cohorts of colorectal cancer patients receiving either propofol (n = 8) or sevoflurane (n = 9), matched for tumor stage and location. Serum was sampled before anesthesia and after tumor resection. Vesicular microRNA profiles were analyzed by next generation sequencing and confirmed by real-time polymerase chain reaction. Next, we assessed perioperative changes in microRNA expression induced by either anesthetic and compared their biologic effects on tumor-relevant pathways. Additionally, vesicles from pre- and postoperative sera were biologic characterized.
Results
Postoperative microRNA profiles were shifted in both groups with overlap in the perioperative response. A total of 64 (48 up, range of log2 fold change 1.07 to 3.76; 16 down, −1.00 to −1.55) and 33 (32 up, 1.02 to 2.98; 1 down, −1.36) microRNAs were significantly regulated (adjusted P value less than 0.05) by propofol and sevoflurane, respectively. Thirty-six (propofol) and five (sevoflurane) microRNAs were specifically responsive to either anesthetic agent. In silico target analyses of microRNA expression patterns indicated an inhibitory effect of propofol on crucial carcinoma-related pathways such as proliferation (z-score, −1.73) and migration (z-score, −1.97), as well as enhanced apoptosis (z-score, 1.19). While size distribution and protein markers of circulating vesicles were not affected by anesthesia, their concentration was reduced after surgery using both anesthetic procedures.
Conclusions
This proof-of-concept study provides preliminary evidence that anesthetic agents have specific effects on microRNA profiles in circulating vesicles. These findings could form the basis for larger and mechanistically oriented outcome studies in cancer patients.
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Mussack V, Hermann S, Buschmann D, Kirchner B, Pfaffl MW. MIQE-Compliant Validation of MicroRNA Biomarker Signatures Established by Small RNA Sequencing. Methods Mol Biol 2020; 2065:23-38. [PMID: 31578685 DOI: 10.1007/978-1-4939-9833-3_3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
MicroRNAs (miRNAs), a class of small non-coding RNAs that modulate gene expression at the post-transcriptional level, are attractive targets in many academic and diagnostic applications. Among them, assessing miRNA biomarkers in minimally invasive liquid biopsies was shown to be a promising tool for managing diseases, particularly cancer. The initial screening of disease-relevant transcripts is often performed by high-throughput next-generation sequencing (NGS), in here RNA sequencing (RNA-Seq). After complex processing of small RNA-Seq data, differential gene expression analysis is performed to evaluate miRNA biomarker signatures. To ensure experimental validity, biomarker candidates are commonly validated by an orthogonal technology such as reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR). This chapter outlines in detail the material and methods one can apply to reproducibly identify miRNA biomarker signatures from blood total RNA. After screening miRNA profiles by small RNA-Seq, resulting data is validated in compliance with the "Minimum Information for Publication of Quantitative Real-Time PCR Experiments" (MIQE) guidelines.
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Affiliation(s)
- Veronika Mussack
- Animal Physiology and Immunology, School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
| | - Stefanie Hermann
- Animal Physiology and Immunology, School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
| | - Dominik Buschmann
- Animal Physiology and Immunology, School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
| | - Benedikt Kirchner
- Animal Physiology and Immunology, School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
| | - Michael W Pfaffl
- Animal Physiology and Immunology, School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany.
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50
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Yong YK, Tan HY, Saeidi A, Wong WF, Vignesh R, Velu V, Eri R, Larsson M, Shankar EM. Immune Biomarkers for Diagnosis and Treatment Monitoring of Tuberculosis: Current Developments and Future Prospects. Front Microbiol 2019; 10:2789. [PMID: 31921004 PMCID: PMC6930807 DOI: 10.3389/fmicb.2019.02789] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 11/18/2019] [Indexed: 12/22/2022] Open
Abstract
Tuberculosis (TB) treatment monitoring is paramount to clinical decision-making and the host biomarkers appears to play a significant role. The currently available diagnostic technology for TB detection is inadequate. Although GeneXpert detects total DNA present in the sample regardless live or dead bacilli present in clinical samples, all the commercial tests available thus far have low sensitivity. Humoral responses against Mycobacterium tuberculosis (Mtb) antigens are generally low, which precludes the use of serological tests for TB diagnosis, prognosis, and treatment monitoring. Mtb-specific CD4+ T cells correlate with Mtb antigen/bacilli burden and hence might serve as good biomarkers for monitoring treatment progress. Omics-based techniques are capable of providing a more holistic picture for disease mechanisms and are more accurate in predicting TB disease outcomes. The current review aims to discuss some of the recent advances on TB biomarkers, particularly host biomarkers that have the potential to diagnose and differentiate active TB and LTBI as well as their use in disease prognosis and treatment monitoring.
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Affiliation(s)
- Yean K Yong
- Laboratory Center, Xiamen University Malaysia, Sepang, Malaysia
| | - Hong Y Tan
- Laboratory Center, Xiamen University Malaysia, Sepang, Malaysia.,Department of Traditional Chinese Medicine, Xiamen University Malaysia, Sepang, Malaysia
| | - Alireza Saeidi
- Department of Pediatrics, Emory Vaccine Center, Atlanta, GA, United States
| | - Won F Wong
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | | | - Vijayakumar Velu
- Department of Microbiology and Immunology, Emory Vaccine Center, Atlanta, GA, United States
| | - Rajaraman Eri
- School of Health Sciences, College of Health and Medicine, University of Tasmania, Launceston, TAS, Australia
| | - Marie Larsson
- Division of Molecular Virology, Department of Clinical and Experimental Medicine, Linkoping University, Linkoping, Sweden
| | - Esaki M Shankar
- Division of Infection Biology and Medical Microbiology, Department of Life Sciences, Central University of Tamil Nadu (CUTN), Thiruvarur, India
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