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Vahidi S, Agah S, Mirzajani E, Asghari Gharakhyli E, Norollahi SE, Rahbar Taramsari M, Babaei K, Samadani AA. microRNAs, oxidative stress, and genotoxicity as the main inducers in the pathobiology of cancer development. Horm Mol Biol Clin Investig 2024; 45:55-73. [PMID: 38507551 DOI: 10.1515/hmbci-2023-0012] [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: 02/05/2023] [Accepted: 03/06/2024] [Indexed: 03/22/2024]
Abstract
Cancer is one of the most serious leading causes of death in the world. Many eclectic factors are involved in cancer progression including genetic and epigenetic alongside environmental ones. In this account, the performance and fluctuations of microRNAs are significant in cancer diagnosis and treatment, particularly as diagnostic biomarkers in oncology. So, microRNAs manage and control the gene expression after transcription by mRNA degradation, or also they can inhibit their translation. Conspicuously, these molecular structures take part in controlling the cellular, physiological and pathological functions, which many of them can accomplish as tumor inhibitors or oncogenes. Relatively, Oxidative stress is defined as the inequality between the creation of reactive oxygen species (ROS) and the body's ability to detoxify the reactive mediators or repair the resulting injury. ROS and microRNAs have been recognized as main cancer promoters and possible treatment targets. Importantly, genotoxicity has been established as the primary reason for many diseases as well as several malignancies. The procedures have no obvious link with mutagenicity and influence the organization, accuracy of the information, or fragmentation of DNA. Conclusively, mutations in these patterns can lead to carcinogenesis. In this review article, we report the impressive and practical roles of microRNAs, oxidative stress, and genotoxicity in the pathobiology of cancer development in conjunction with their importance as reliable cancer biomarkers and their association with circulating miRNA, exosomes and exosomal miRNAs, RNA remodeling, DNA methylation, and other molecular elements in oncology.
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Affiliation(s)
- Sogand Vahidi
- Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Shahram Agah
- Colorectal Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Ebrahim Mirzajani
- Department of Biochemistry and Biophysics, School of Medicine, 37554 Guilan University of Medical Sciences , Rasht, Iran
| | | | - Seyedeh Elham Norollahi
- Cancer Research Center and Department of Immunology, Semnan University of Medical Sciences, Semnan, Iran
| | - Morteza Rahbar Taramsari
- Department of Forensic Medicine, School of Medicine, 37554 Guilan University of Medical Sciences , Rasht, Iran
| | - Kosar Babaei
- Noncommunicable Diseases Research Center, Neyshabur University of Medical Sciences, Neyshabur, Iran
| | - Ali Akbar Samadani
- Guilan Road Trauma Research Center, Trauma Institute, Guilan University of Medical Sciences, Rasht, Iran
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Yabuki A, Muraoka A, Osuka S, Yokoi A, Yoshida K, Kitagawa M, Bayasura, Sonehara R, Miyake N, Nakanishi N, Nakamura T, Iwase A, Kajiyama H. Serum miRNA as a predictive biomarker for ovarian reserve after endometrioma-cystectomy. Reprod Biol 2024; 24:100821. [PMID: 37992589 DOI: 10.1016/j.repbio.2023.100821] [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: 07/29/2023] [Revised: 10/25/2023] [Accepted: 10/30/2023] [Indexed: 11/24/2023]
Abstract
Ovarian endometrioma (OE) is a common gynecological disease that is often treated with surgery and hormonal treatment. However, ovarian cystectomy can impair the ovarian reserve (OR). Previously, we showed that perioperative administration of dienogest (DNG) is an effective option for OR preservation. However, there were differences in the extent of OR preservation among patients following perioperative DNG treatment. In the current study, we performed a global examination of serum microRNAs (miRNAs) to identify accurate biomarkers that predict post-operative restoration of OR following perioperative DNG treatment. We also sought to identify specific miRNAs related to the anti-Müllerian hormone (AMH). miRNA sequencing was performed on serum samples obtained from twenty-seven patients who received perioperative DNG treatment. Candidate miRNAs were selected by comparing patients whose ORs were restored postoperatively (responder group, n = 7) with those whose ORs were not (non-responder group, n = 7). miR-370-3p and miR-1307-3p were significantly upregulated in the responder group, whereas miR-27b-3p was upregulated in the non-responder group. The pretreatment value of each miRNA could predict DNG responsiveness for OR following ovarian cystectomy (area under the curve [AUC] > 0.8). The quantitative polymerase chain reaction (qPCR) revealed only miR-1307-3p was found to be significantly upregulated in the responder group (P < 0.05). In addition, we identified miR-139-3p, miR-140-3p, and miR-629-5p as AMH-associated miRNAs. The transition of AMH showed a correlation with miR-139-3p (P < 0.05, r = -0.76). The miRNAs identified herein represent potential serum biomarkers of clinical value in predicting OR prior to DNG treatment.
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Affiliation(s)
- Atsushi Yabuki
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Ayako Muraoka
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan.
| | - Satoko Osuka
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Akira Yokoi
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan; Nagoya University Institute for Advanced Research, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan; Japan Science and Technology Agency (JST), FOREST, 4-1-8 Honcho, Kawaguchi, Saitama, Japan
| | - Kosuke Yoshida
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan; Nagoya University Institute for Advanced Research, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Masami Kitagawa
- Bell Research Center for Reproductive Health and Cancer, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Bayasura
- Bell Research Center for Reproductive Health and Cancer, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Reina Sonehara
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Natsuki Miyake
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Natsuki Nakanishi
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Tomoko Nakamura
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Akira Iwase
- Department of Obstetrics and Gynecology, Gunma University Graduate School of Medicine, 3-39-22, Showa-machi, Maebashi 371-8511, Japan
| | - Hiroaki Kajiyama
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
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Begum MIA, Chuan L, Hong ST, Chae HS. The Pathological Role of miRNAs in Endometriosis. Biomedicines 2023; 11:3087. [PMID: 38002087 PMCID: PMC10669455 DOI: 10.3390/biomedicines11113087] [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: 09/30/2023] [Revised: 11/13/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023] Open
Abstract
Association studies investigating miRNA in relation to diseases have consistently shown significant alterations in miRNA expression, particularly within inflammatory pathways, where they regulate inflammatory cytokines, transcription factors (such as NF-κB, STAT3, HIF1α), and inflammatory proteins (including COX-2 and iNOS). Given that endometriosis (EMS) is characterized as an inflammatory disease, albeit one influenced by estrogen levels, it is natural to speculate about the connection between EMS and miRNA. Recent research has indeed confirmed alterations in the expression levels of numerous microRNAs (miRNAs) in both endometriotic lesions and the eutopic endometrium of women with EMS, when compared to healthy controls. The undeniable association of miRNAs with EMS hints at the emergence of a new era in the study of miRNA in the context of EMS. This article reviews the advancements made in understanding the pathological role of miRNA in EMS and its association with EMS-associated infertility. These findings contribute to the ongoing pursuit of developing miRNA-based therapeutics and diagnostic markers for EMS.
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Affiliation(s)
- Mst Ismat Ara Begum
- Department of Biomedical Sciences, Institute for Medical Science, Jeonbuk National University Medical School, Jeonju 54907, Republic of Korea; (M.I.A.B.); (L.C.)
| | - Lin Chuan
- Department of Biomedical Sciences, Institute for Medical Science, Jeonbuk National University Medical School, Jeonju 54907, Republic of Korea; (M.I.A.B.); (L.C.)
| | - Seong-Tshool Hong
- Department of Biomedical Sciences, Institute for Medical Science, Jeonbuk National University Medical School, Jeonju 54907, Republic of Korea; (M.I.A.B.); (L.C.)
| | - Hee-Suk Chae
- Department of Obstetrics and Gynecology, Research Institute of Clinical Medicine, Jeonbuk National University, Jeonju 54907, Republic of Korea
- Biomedical Research Institute, Jeonbuk National University Hospital, Jeonbuk National University Medical School, Jeonju 54907, Republic of Korea
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Hon JX, Wahab NA, Karim AKA, Mokhtar NM, Mokhtar MH. MicroRNAs in Endometriosis: Insights into Inflammation and Progesterone Resistance. Int J Mol Sci 2023; 24:15001. [PMID: 37834449 PMCID: PMC10573326 DOI: 10.3390/ijms241915001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 10/03/2023] [Accepted: 10/05/2023] [Indexed: 10/15/2023] Open
Abstract
Endometriosis, a non-malignant gynecological disorder influenced by estrogen, involves the growth of endometrial tissue outside the uterus. Its development includes processes such as inflammation, progesterone resistance, angiogenesis, and cell proliferation. Epigenetic factors, particularly the dysregulation of microRNAs (miRNAs), have emerged as key factors in these mechanisms in endometriosis. This review aims to unveil the intricate molecular processes that control inflammation, progesterone resistance, and miRNA functions in endometriosis. In addition, it provides a comprehensive overview of the current understanding regarding the involvement of miRNAs in the inflammatory aspects of this condition. This synthesis encompasses research investigating the molecular underpinnings of inflammation, along with the biogenesis and roles of miRNAs in endometriosis. Furthermore, it examines human studies and functional analyses to establish the intricate connection between miRNAs, inflammation, and progesterone resistance in the context of endometriosis. The results highlight the significant impact of dysregulated miRNAs on the inflammatory pathways and hormonal imbalances characteristic of endometriosis. Consequently, miRNAs hold promise as potential non-invasive biomarkers and targeted therapeutic agents aimed at addressing inflammation and enhancing the response to progesterone treatment in individuals with endometriosis.
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Affiliation(s)
- Jing-Xian Hon
- Department of Physiology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur 56000, Malaysia
| | - Norhazlina Abdul Wahab
- Department of Physiology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur 56000, Malaysia
- GUT Research Group, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur 56000, Malaysia
| | - Abdul Kadir Abdul Karim
- Department of Obstetrics & Gynecology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur 56000, Malaysia
| | - Norfilza Mohd Mokhtar
- Department of Physiology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur 56000, Malaysia
- GUT Research Group, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur 56000, Malaysia
| | - Mohd Helmy Mokhtar
- Department of Physiology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur 56000, Malaysia
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Piscopo P, Grasso M, Manzini V, Zeni A, Castelluzzo M, Fontana F, Talarico G, Castellano AE, Rivabene R, Crestini A, Bruno G, Ricci L, Denti MA. Identification of miRNAs regulating MAPT expression and their analysis in plasma of patients with dementia. Front Mol Neurosci 2023; 16:1127163. [PMID: 37324585 PMCID: PMC10266489 DOI: 10.3389/fnmol.2023.1127163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 05/05/2023] [Indexed: 06/17/2023] Open
Abstract
Background Dementia is one of the most common diseases in elderly people and hundreds of thousand new cases per year of Alzheimer's disease (AD) are estimated. While the recent decade has seen significant advances in the development of novel biomarkers to identify dementias at their early stage, a great effort has been recently made to identify biomarkers able to improve differential diagnosis. However, only few potential candidates, mainly detectable in cerebrospinal fluid (CSF), have been described so far. Methods We searched for miRNAs regulating MAPT translation. We employed a capture technology able to find the miRNAs directly bound to the MAPT transcript in cell lines. Afterwards, we evaluated the levels of these miRNAs in plasma samples from FTD (n = 42) and AD patients (n = 33) and relative healthy controls (HCs) (n = 42) by using qRT-PCR. Results Firstly, we found all miRNAs that interact with the MAPT transcript. Ten miRNAs have been selected to verify their effect on Tau levels increasing or reducing miRNA levels by using cell transfections with plasmids expressing the miRNAs genes or LNA antagomiRs. Following the results obtained, miR-92a-3p, miR-320a and miR-320b were selected to analyse their levels in plasma samples of patients with FTD and AD respect to HCs. The analysis showed that the miR-92a-1-3p was under-expressed in both AD and FTD compared to HCs. Moreover, miR-320a was upregulated in FTD vs. AD patients, particularly in men when we stratified by sex. Respect to HC, the only difference is showed in men with AD who have reduced levels of this miRNA. Instead, miR-320b is up-regulated in both dementias, but only patients with FTD maintain this trend in both genders. Conclusions Our results seem to identify miR-92a-3p and miR-320a as possible good biomarkers to discriminate AD from HC, while miR-320b to discriminate FTD from HC, particularly in males. Combining three miRNAs improves the accuracy only in females, particularly for differential diagnosis (FTD vs. AD) and to distinguish FTD from HC.
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Affiliation(s)
- Paola Piscopo
- Department of Neuroscience, Istituto Superiore di Sanità, Rome, Italy
| | - Margherita Grasso
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Valeria Manzini
- Department of Neuroscience, Istituto Superiore di Sanità, Rome, Italy
- Department of Biology and Biotechnology Charles Darwin, University of Rome “Sapienza”, Rome, Italy
| | - Andrea Zeni
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | | | - Francesca Fontana
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Giuseppina Talarico
- Department of Human Neuroscience, University of Rome “Sapienza”, Rome, Italy
| | | | - Roberto Rivabene
- Department of Neuroscience, Istituto Superiore di Sanità, Rome, Italy
| | - Alessio Crestini
- Department of Neuroscience, Istituto Superiore di Sanità, Rome, Italy
| | - Giuseppe Bruno
- Department of Human Neuroscience, University of Rome “Sapienza”, Rome, Italy
| | - Leonardo Ricci
- Department of Physics, University of Trento, Trento, Italy
| | - Michela A. Denti
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
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Hicks SD, Onks C, Kim RY, Zhen KJ, Loeffert J, Loeffert AC, Olympia RP, Fedorchak G, DeVita S, Gagnon Z, McLoughlin C, Madeira MM, Zuckerman SL, Lee T, Heller M, Monteith C, Campbell TR, Neville C, Fengler E, Dretsch MN. Refinement of saliva microRNA biomarkers for sports-related concussion. JOURNAL OF SPORT AND HEALTH SCIENCE 2023; 12:369-378. [PMID: 34461327 DOI: 10.1016/j.jshs.2021.08.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 05/29/2021] [Accepted: 07/13/2021] [Indexed: 05/17/2023]
Abstract
BACKGROUND Recognizing sport-related concussion (SRC) is challenging and relies heavily on subjective symptom reports. An objective, biological marker could improve recognition and understanding of SRC. There is emerging evidence that salivary micro-ribonucleic acids (miRNAs) may serve as biomarkers of concussion; however, it remains unclear whether concussion-related miRNAs are impacted by exercise. We sought to determine whether 40 miRNAs previously implicated in concussion pathophysiology were affected by participation in a variety of contact and non-contact sports. Our goal was to refine a miRNA-based tool capable of identifying athletes with SRC without the confounding effects of exercise. METHODS This case-control study harmonized data from concussed and non-concussed athletes recruited across 10 sites. Levels of salivary miRNAs within 455 samples from 314 individuals were measured with RNA sequencing. Within-subjects testing was used to identify and exclude miRNAs that changed with either (a) a single episode of exercise (166 samples from 83 individuals) or (b) season-long participation in contact sports (212 samples from 106 individuals). The miRNAs that were not impacted by exercise were interrogated for SRC diagnostic utility using logistic regression (172 samples from 75 concussed and 97 non-concussed individuals). RESULTS Two miRNAs (miR-532-5p and miR-182-5p) decreased (adjusted p < 0.05) after a single episode of exercise, and 1 miRNA (miR-4510) increased only after contact sports participation. Twenty-three miRNAs changed at the end of a contact sports season. Two of these miRNAs (miR-26b-3p and miR-29c-3p) were associated (R > 0.50; adjusted p < 0.05) with the number of head impacts sustained in a single football practice. Among the 15 miRNAs not confounded by exercise or season-long contact sports participation, 11 demonstrated a significant difference (adjusted p < 0.05) between concussed and non-concussed participants, and 6 displayed moderate ability (area under curve > 0.70) to identify concussion. A single ratio (miR-27a-5p/miR-30a-3p) displayed the highest accuracy (AUC = 0.810, sensitivity = 82.4%, specificity = 73.3%) for differentiating concussed and non-concussed participants. Accuracy did not differ between participants with SRC and non-SRC (z = 0.5, p = 0.60). CONCLUSION Salivary miRNA levels may accurately identify SRC when not confounded by exercise. Refinement of this approach in a large cohort of athletes could eventually lead to a non-invasive, sideline adjunct for SRC assessment.
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Affiliation(s)
- Steven D Hicks
- Department of Pediatrics, College of Medicine, Pennsylvania State University, Hershey, PA 17033, USA.
| | - Cayce Onks
- Department of Orthopaedics and Rehabilitation, College of Medicine, Pennsylvania State University, Hershey, PA 17033, USA; Department of Family Medicine, College of Medicine, Pennsylvania State University, Hershey, PA 17033, USA
| | - Raymond Y Kim
- Department of Orthopaedics and Rehabilitation, College of Medicine, Pennsylvania State University, Hershey, PA 17033, USA
| | - Kevin J Zhen
- Department of Pediatrics, College of Medicine, Pennsylvania State University, Hershey, PA 17033, USA
| | - Jayson Loeffert
- Department of Orthopaedics and Rehabilitation, College of Medicine, Pennsylvania State University, Hershey, PA 17033, USA; Department of Family Medicine, College of Medicine, Pennsylvania State University, Hershey, PA 17033, USA
| | - Andrea C Loeffert
- Department of Pediatrics, College of Medicine, Pennsylvania State University, Hershey, PA 17033, USA
| | - Robert P Olympia
- Department of Emergency Medicine, College of Medicine, Pennsylvania State University, Hershey, PA 17033, USA
| | - Gregory Fedorchak
- Department of Research and Development, Quadrant Biosciences Inc., Syracuse, NY 13210, USA
| | - Samantha DeVita
- Department of Research and Development, Quadrant Biosciences Inc., Syracuse, NY 13210, USA
| | - Zofia Gagnon
- Department of Biology, Marist College, Poughkeepsie, NY 12601, USA
| | | | - Miguel M Madeira
- Department of Biology, Marist College, Poughkeepsie, NY 12601, USA
| | - Scott L Zuckerman
- Sports Concussion Center, College of Medicine, Vanderbilt University, Nashville, TN 37212, USA
| | - Timothy Lee
- Sports Concussion Center, College of Medicine, Vanderbilt University, Nashville, TN 37212, USA
| | - Matthew Heller
- Department of Family Medicine, College of Osteopathic Medicine, New York Institute of Technology, Old Westbury, NY 11568, USA
| | - Chuck Monteith
- Department of Athletic Training, Colgate University, Hamilton, NY 13346, USA
| | - Thomas R Campbell
- Department of Rehabilitation Sciences, Old Dominion University, Norfolk, VA 23529, USA
| | - Christopher Neville
- Department of Physical Therapy Education, Orthopedics, and Neuroscience, College of Medicine, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Elise Fengler
- Department of Exercise Science, Syracuse University, Syracuse, NY 13210, USA
| | - Michael N Dretsch
- Department of Medical Research-West, Walter Reed Army Institute of Research, US Army Joint Base Lewis-McChord, Hillhurst, WA 98433, USA
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Chen LH, Lo WC, Huang HY, Wu HM. A Lifelong Impact on Endometriosis: Pathophysiology and Pharmacological Treatment. Int J Mol Sci 2023; 24:ijms24087503. [PMID: 37108664 PMCID: PMC10139092 DOI: 10.3390/ijms24087503] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/06/2023] [Accepted: 04/16/2023] [Indexed: 04/29/2023] Open
Abstract
Endometriosis is a chronic inflammatory disease associated with bothersome symptoms in premenopausal women and is complicated with long-term systemic impacts in the post-menopausal stage. It is generally defined by the presence of endometrial-like tissue outside the uterine cavity, which causes menstrual disorders, chronic pelvic pain, and infertility. Endometriotic lesions can also spread and grow in extra-pelvic sites; the chronic inflammatory status can cause systemic effects, including metabolic disorder, immune dysregulation, and cardiovascular diseases. The uncertain etiologies of endometriosis and their diverse presentations limit the treatment efficacy. High recurrence risk and intolerable side effects result in poor compliance. Current studies for endometriosis have paid attention to the advances in hormonal, neurological, and immunological approaches to the pathophysiology and their potential pharmacological intervention. Here we provide an overview of the lifelong impacts of endometriosis and summarize the updated consensus on therapeutic strategies.
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Affiliation(s)
- Liang-Hsuan Chen
- Department of Obstetrics and Gynecology, Linkou Medical Center, Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Taoyuan 33305, Taiwan
- Graduate Institute of Clinical Medical Sciences, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
| | - Wei-Che Lo
- Department of Obstetrics and Gynecology, Linkou Medical Center, Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Taoyuan 33305, Taiwan
| | - Hong-Yuan Huang
- Department of Obstetrics and Gynecology, Linkou Medical Center, Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Taoyuan 33305, Taiwan
| | - Hsien-Ming Wu
- Department of Obstetrics and Gynecology, Linkou Medical Center, Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Taoyuan 33305, Taiwan
- Graduate Institute of Clinical Medical Sciences, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
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Putting the "mi" in omics: discovering miRNA biomarkers for pediatric precision care. Pediatr Res 2023; 93:316-323. [PMID: 35906312 PMCID: PMC9884316 DOI: 10.1038/s41390-022-02206-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 06/27/2022] [Indexed: 01/31/2023]
Abstract
In the past decade, growing interest in micro-ribonucleic acids (miRNAs) has catapulted these small, non-coding nucleic acids to the forefront of biomarker research. Advances in scientific knowledge have made it clear that miRNAs play a vital role in regulating cellular physiology throughout the human body. Perturbations in miRNA signaling have also been described in a variety of pediatric conditions-from cancer, to renal failure, to traumatic brain injury. Likewise, the number of studies across pediatric disciplines that pair patient miRNA-omics with longitudinal clinical data are growing. Analyses of these voluminous, multivariate data sets require understanding of pediatric phenotypic data, data science, and genomics. Use of machine learning techniques to aid in biomarker detection have helped decipher background noise from biologically meaningful changes in the data. Further, emerging research suggests that miRNAs may have potential as therapeutic targets for pediatric precision care. Here, we review current miRNA biomarkers of pediatric diseases and studies that have combined machine learning techniques, miRNA-omics, and patient health data to identify novel biomarkers and potential therapeutics for pediatric diseases. IMPACT: In the following review article, we summarized how recent developments in microRNA research may be coupled with machine learning techniques to advance pediatric precision care.
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9
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Bonavina G, Taylor HS. Endometriosis-associated infertility: From pathophysiology to tailored treatment. Front Endocrinol (Lausanne) 2022; 13:1020827. [PMID: 36387918 PMCID: PMC9643365 DOI: 10.3389/fendo.2022.1020827] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 10/06/2022] [Indexed: 11/13/2022] Open
Abstract
Despite the clinically recognized association between endometriosis and infertility, the mechanisms implicated in endometriosis-associated infertility are not fully understood. Endometriosis is a multifactorial and systemic disease that has pleiotropic direct and indirect effects on reproduction. A complex interaction between endometriosis subtype, pain, inflammation, altered pelvic anatomy, adhesions, disrupted ovarian reserve/function, and compromised endometrial receptivity as well as systemic effects of the disease define endometriosis-associated infertility. The population of infertile women with endometriosis is heterogeneous, and diverse patients' phenotypes can be observed in the clinical setting, thus making difficult to establish a precise diagnosis and a single mechanism of endometriosis related infertility. Moreover, clinical management of infertility associated with endometriosis can be challenging due to this heterogeneity. Innovative non-invasive diagnostic tools are on the horizon that may allow us to target the specific dysfunctional alteration in the reproduction process. Currently the treatment should be individualized according to the clinical situation and to the suspected level of impairment. Here we review the etiology of endometriosis related infertility as well as current treatment options, including the roles of surgery and assisted reproductive technologies.
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Affiliation(s)
- Giulia Bonavina
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale School of Medicine, New Haven, CT, United States
| | - Hugh S Taylor
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale School of Medicine, New Haven, CT, United States
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10
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Cheong JK, Rajgor D, Lv Y, Chung KY, Tang YC, Cheng H. Noncoding RNome as Enabling Biomarkers for Precision Health. Int J Mol Sci 2022; 23:ijms231810390. [PMID: 36142304 PMCID: PMC9499633 DOI: 10.3390/ijms231810390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 08/29/2022] [Accepted: 09/02/2022] [Indexed: 12/06/2022] Open
Abstract
Noncoding RNAs (ncRNAs), in the form of structural, catalytic or regulatory RNAs, have emerged to be critical effectors of many biological processes. With the advent of new technologies, we have begun to appreciate how intracellular and circulatory ncRNAs elegantly choreograph the regulation of gene expression and protein function(s) in the cell. Armed with this knowledge, the clinical utility of ncRNAs as biomarkers has been recently tested in a wide range of human diseases. In this review, we examine how critical factors govern the success of interrogating ncRNA biomarker expression in liquid biopsies and tissues to enhance our current clinical management of human diseases, particularly in the context of cancer. We also discuss strategies to overcome key challenges that preclude ncRNAs from becoming standard-of-care clinical biomarkers, including sample pre-analytics standardization, data cross-validation with closer attention to discordant findings, as well as correlation with clinical outcomes. Although harnessing multi-modal information from disease-associated noncoding RNome (ncRNome) in biofluids or in tissues using artificial intelligence or machine learning is at the nascent stage, it will undoubtedly fuel the community adoption of precision population health.
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Affiliation(s)
- Jit Kong Cheong
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore 117597, Singapore
- Precision Medicine Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore 117597, Singapore
- NUS Centre for Cancer Research, Singapore 117599, Singapore
- Correspondence: (J.K.C.); (H.C.)
| | | | - Yang Lv
- Precision Medicine Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore 117597, Singapore
| | | | | | - He Cheng
- MiRXES Lab, Singapore 138667, Singapore
- Correspondence: (J.K.C.); (H.C.)
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11
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Liu L, Zhou X, Chen J, Li X. Potential of ATP5MG to Treat Metabolic Syndrome-Associated Cardiovascular Diseases. Front Cardiovasc Med 2022; 9:921778. [PMID: 35935642 PMCID: PMC9355403 DOI: 10.3389/fcvm.2022.921778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 06/08/2022] [Indexed: 11/30/2022] Open
Abstract
Introduction Metabolic syndrome-associated cardiovascular disease (MetS-CVD) is a cluster of metabolism-immunity highly integrated diseases. Emerging evidence hints that mitochondrial energy metabolism may be involved in MetS-CVD development. The physiopathological role of ATP5MG, a subunit of the F0 ATPase complex, has not been fully elucidated. Methods In this study, we selected ATP5MG to identify the immunity-mediated pathway and mine drugs targeting this pathway for treating MetS-CVD. Using big data from public databases, we dissected co-expressed RNA (coRNA), competing endogenous RNA (ceRNA), and interacting RNA (interRNA) genes for ATP5MG. Results It was identified that ATP5MG may form ceRNA with COX5A through hsa-miR-142-5p and interplay with NDUFB8, SOD1, and MDH2 through RNA–RNA interaction under the immune pathway. We dug out 251 chemicals that may target this network and identified some of them as clinical drugs. We proposed five medicines for treating MetS-CVD. Interestingly, six drugs are being tested to treat COVID-19, which unexpectedly offers a new potential host-targeting antiviral strategy. Conclusion Collectively, we revealed the potential significance of the ATP5MG-centered network for developing drugs to treat MetS-CVD, which offers insights into the epigenetic regulation for metabolism-immunity highly integrated diseases.
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Affiliation(s)
- Lianyong Liu
- Department of Endocrinology and Metabolism, Punan Hospital, Shanghai, China
| | - Xinglu Zhou
- Department of Endocrinology and Metabolism, Gongli Hospital, Naval Medical University, Shanghai, China
| | - Juan Chen
- Department of Obstetrics and Gynecology, Gongli Hospital, Naval Medical University, Shanghai, China
| | - Xiangqi Li
- Department of Endocrinology and Metabolism, Gongli Hospital, Naval Medical University, Shanghai, China
- *Correspondence: Xiangqi Li
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12
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Saini VM, Liu KR, Surve AS, Gupta S, Gupta A. MicroRNAs as biomarkers for monitoring cardiovascular changes in Type II Diabetes Mellitus (T2DM) and exercise. J Diabetes Metab Disord 2022; 21:1819-1832. [PMID: 35818628 PMCID: PMC9261151 DOI: 10.1007/s40200-022-01066-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 05/10/2022] [Accepted: 05/27/2022] [Indexed: 11/21/2022]
Abstract
Introduction MicroRNAs (miRNAs) have been shown to be altered in both CVD and T2DM and can have an application as diagnostic and prognostic biomarkers. miRNAs are released into circulation when the cardiomyocyte is subjected to injury and damage. Objectives Measuring circulating miRNA levels in human plasma may be of great potential use for measuring the extent of damage to cardiomyocytes and response to exercise. This review is aimed to highlight the potential application of miRNAs as biomarkers of CVD progression in T2DM, and the impact of exercise on recovery. Methods The review aims to examine whether the health improvements following exercise in T2DM patients are reflective of changes in expression of plasma miRNAs. For this purpose, studies were identified from the literature that have established a correlation between diabetes, disease progression and plasma miRNA levels. We also reviewed studies which looked at the effect of exercise on plasma miRNA levels. Results The review identified miRNA signatures that are affected by T2DM and DHD and a subset of these miRNAs that are also affected by different types of exercise. This approach helped us to identify those miRNAs whose expression and function can be altered by regular bouts of exercise. Conclusions miRNAs identified as part of this review can serve as tools to monitor the cardio-protective, anti-inflammatory and metabolic effects of exercise in people suffering from T2DM. Future research should focus on regulation of these miRNAs in T2DM and how they can be altered by appropriate exercise interventions. Supplementary Information The online version contains supplementary material available at 10.1007/s40200-022-01066-4.
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13
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Paschou M, Papazafiri P, Charalampous C, Zachariadis M, Dedos SG, Doxakis E. Neuronal microRNAs safeguard ER Ca 2+ homeostasis and attenuate the unfolded protein response upon stress. Cell Mol Life Sci 2022; 79:373. [PMID: 35727337 PMCID: PMC11073139 DOI: 10.1007/s00018-022-04398-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 04/23/2022] [Accepted: 05/21/2022] [Indexed: 11/30/2022]
Abstract
Ca2+ is a critical mediator of neurotransmitter release, synaptic plasticity, and gene expression, but also excitotoxicity. Ca2+ signaling and homeostasis are coordinated by an intricate network of channels, pumps, and calcium-binding proteins, which must be rapidly regulated at all expression levels. Τhe role of neuronal miRNAs in regulating ryanodine receptors (RyRs) and inositol 1,4,5-triphosphate receptors (IP3Rs) was investigated to understand the underlying mechanisms that modulate ER Ca2+ release. RyRs and IP3Rs are critical in mounting and propagating cytosolic Ca2+ signals by functionally linking the ER Ca2+ content, while excessive ER Ca2+ release via these receptors is central to the pathophysiology of a wide range of neurological diseases. Herein, two brain-restricted microRNAs, miR-124-3p and miR-153-3p, were found to bind to RyR1-3 and IP3R3 3'UTRs, and suppress their expression at both the mRNA and protein level. Ca2+ imaging studies revealed that overexpression of these miRNAs reduced ER Ca2+ release upon RyR/IP3R activation, but had no effect on [Ca2+]i under resting conditions. Interestingly, treatments that cause excessive ER Ca2+ release decreased expression of these miRNAs and increased expression of their target ER Ca2+ channels, indicating interdependence of miRNAs, RyRs, and IP3Rs in Ca2+ homeostasis. Furthermore, by maintaining the ER Ca2+ content, miR-124 and miR-153 reduced cytosolic Ca2+ overload and preserved protein-folding capacity by attenuating PERK signaling. Overall, this study shows that miR-124-3p and miR-153-3p fine-tune ER Ca2+ homeostasis and alleviate ER stress responses.
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Affiliation(s)
- Maria Paschou
- Center for Basic Research, Biomedical Research Foundation, Academy of Athens (BRFAA), Soranou Efesiou 4, 11527, Athens, Greece
- Department of Biology, National and Kapodistrian University of Athens (NKUA), Panepistimiopolis, 15784, Athens, Greece
| | - Panagiota Papazafiri
- Department of Biology, National and Kapodistrian University of Athens (NKUA), Panepistimiopolis, 15784, Athens, Greece
| | - Chrysanthi Charalampous
- Center for Basic Research, Biomedical Research Foundation, Academy of Athens (BRFAA), Soranou Efesiou 4, 11527, Athens, Greece
| | - Michael Zachariadis
- Department of Biology, National and Kapodistrian University of Athens (NKUA), Panepistimiopolis, 15784, Athens, Greece
- Material and Chemical Characterization Facility (MC2), Faculty of Science, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Skarlatos G Dedos
- Department of Biology, National and Kapodistrian University of Athens (NKUA), Panepistimiopolis, 15784, Athens, Greece.
| | - Epaminondas Doxakis
- Center for Basic Research, Biomedical Research Foundation, Academy of Athens (BRFAA), Soranou Efesiou 4, 11527, Athens, Greece.
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14
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del Saz-Lara A, López de las Hazas MC, Visioli F, Dávalos A. Nutri-Epigenetic Effects of Phenolic Compounds from Extra Virgin Olive Oil: A Systematic Review. Adv Nutr 2022; 13:2039-2060. [PMID: 35679085 PMCID: PMC9526845 DOI: 10.1093/advances/nmac067] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 04/14/2022] [Accepted: 06/02/2022] [Indexed: 01/28/2023] Open
Abstract
Dietary components can induce epigenetic changes through DNA methylation, histone modification, and regulation of microRNAs (miRNAs). Studies of diet-induced epigenetic regulation can inform anticipatory trials and fine-tune public health guidelines. We systematically reviewed data on the effect of extra virgin olive oil (EVOO) and its phenolic compounds (OOPCs) on the epigenetic landscape. We conducted a literature search using PubMed, Scopus, and Web of Science databases and scrutinized published evidence. After applying selection criteria (e.g., inclusion of in vitro, animal, or human studies supplemented with EVOO or its OOPCs), we thoroughly reviewed 51 articles, and the quality assessment was performed using the revised Cochrane risk of bias tool. The results show that both EVOO and its OOPCs can promote epigenetic changes capable of regulating the expression of genes and molecular targets involved in different metabolic processes. For example, oleuropein (OL) may be an epigenetic regulator in cancer, and hydroxytyrosol (HT) modulates the expression of miRNAs involved in the development of cancer, cardiovascular, and neurodegenerative diseases. We conclude that EVOO and its OOPCs can regulate gene expression by modifying epigenetic mechanisms that impact human pathophysiology. A full elucidation of the epigenetic effects of EVOO and its OOPCs may contribute to developing different pharma-nutritional strategies that exploit them as epigenetic agents. This study was registered in the International Prospective Register of Systematic Reviews (PROSPERO) as CRD42022320316.
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Affiliation(s)
- Andrea del Saz-Lara
- Laboratory of Epigenetics of Lipid Metabolism, Madrid Institute for Advanced Studies (IMDEA)-Food, Campus de Excelencia Internacional de la Universidad Autónoma de Madrid y el Consejo Superior de Investigaciones Científicas (CEI UAM + CSIC), Madrid, Spain,Laboratory of Functional Foods, Madrid Institute for Advanced Studies (IMDEA)-Food, CEI UAM + CSIC, Madrid, Spain
| | - María-Carmen López de las Hazas
- Laboratory of Epigenetics of Lipid Metabolism, Madrid Institute for Advanced Studies (IMDEA)-Food, Campus de Excelencia Internacional de la Universidad Autónoma de Madrid y el Consejo Superior de Investigaciones Científicas (CEI UAM + CSIC), Madrid, Spain
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15
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Ding H, Chen W, Chen X. Serum miR-96-5p is a novel and non-invasive marker of acute myocardial infarction associated with coronary artery disease. Bioengineered 2022; 13:3930-3943. [PMID: 35109756 PMCID: PMC8973839 DOI: 10.1080/21655979.2022.2031392] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Acute myocardial infarction (AMI) is a severe cardiovascular disease. AMI associated with coronary artery disease (AMI-CAD) is a subtype of AMI, composed of AMI patients caused by CAD. This study aimed to evaluate the diagnostic value of miR-96-5p in AMI induced by coronary artery disease. Expression of miR-96-5p and BCL2L13 was evaluated by serum samples and cells utilizing Western blot and RT-qPCR assays. The diagnostic value of miR-96-5p in AMI-CAD was analyzed with a receiver operating characteristic (ROC) curves. The correlation between miR-96-5p and BCL2L13 was examined by Spearman's correlation analysis. The level of oxidative stress and apoptosis were estimated via relative commercial kit, flow cytometry apoptosis assay and TUNEL staining assay. Our study discovered that miR-96-5p was down-regulated while BCL2L13 was up-regulated in patients with AMI-CAD. miR-96-5p was a potential diagnostic parameter, which may help distinguish AMI-CAD patients from healthy controls. In vitro experiments, miR-96-5p expression was down regulated while BCL2L13 was up-regulated in hypoxic cardiomyocytes. After confirming the targeted link of miR-96-5p to BCL2L13 using luciferase reporter and RNA pull down assays, we discovered that miR-96-5p overexpression may restore oxidative stress and cell apoptosis induced by hypoxia treatment in H9c2 cells; meanwhile, co-transfection with BCL2L13 overexpressing plasmid might partly countervail the ameliorative effects of miR-96-5p on oxidative stress and apoptosis. Collectively, miR-96-5p may function as a potential diagnostic biomarker for AMI-CAD patients, and the up-regulation of miR-96-5p would ameliorate AMI-associated cardiomyocytes injury by targeting BCL2L13, hence contributing to the clinical treatment of AMI-CAD.
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Affiliation(s)
- Hui Ding
- Department of Thoracic and Cardiovascular Surgery, School of Medicine, Southeast University, Nanjing, People's Republic of China.,Department of Cardiovascular Surgery, The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University, Huai'an, Jiangsu Province, China
| | - Wen Chen
- Department of Thoracic and Cardiovascular Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, People's Republic of China
| | - Xin Chen
- Department of Thoracic and Cardiovascular Surgery, School of Medicine, Southeast University, Nanjing, People's Republic of China.,Department of Thoracic and Cardiovascular Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, People's Republic of China
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16
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López de las Hazas MC, Boughanem H, Dávalos A. Untoward Effects of Micro- and Nanoplastics: An Expert Review of Their Biological Impact and Epigenetic Effects. Adv Nutr 2021; 13:1310-1323. [PMID: 34928307 PMCID: PMC9340974 DOI: 10.1093/advances/nmab154] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 11/17/2021] [Accepted: 12/16/2021] [Indexed: 12/22/2022] Open
Abstract
The production of plastic has dramatically increased in the last 50 y. Because of their stability and durability, plastics are ubiquitously incorporated in both marine and terrestrial ecosystems. Plastic is acted upon by biological, chemical, and physical agents, leading to fragmentation into small pieces [i.e., microplastics (MPs) or nanoplastics (NPs)], classified depending on their size. MPs range from 0.1 to 5000 μm and NPs are fragments between 0.001 to 0.1 μm. MPs and, especially NPs, are easily incorporated into living beings via ingestion. The penetration of MPs and NPs into the food system is an important issue, for both food security and health risk assessment. Ingestion of different MPs and NPs has been associated with different issues in the intestine, such as direct physical damage, increased intestinal permeability, diminished microbiota diversity, and increases in local inflammatory response. However, the potential harmful effects of low-dose dietary plastic are still unclear. Some evidence indicates that intestinal uptake of plastic particles is relatively low and is mostly dependent on the particle's size. However, other evidence highlights that NPs dysregulate key molecular signaling pathways, modify the gut microbiota composition, and may induce important epigenetic changes, including transgenerational effects that might be involved in the onset of many different metabolic disorders. Until now, experiments have been mostly performed on marine organisms, Caenorhabditis elegans, and mouse models, but some research indicates accidental plastic dietary consumption by humans, raising the issue of detrimental health effects of MPs and NPs. This review discusses the impact that MPs and NPs could have on the intestinal tract and the biodistribution and systemic, cellular, and molecular levels. Accumulated evidence of MPs' effects on the human gut suggests that large exposure to MPs and NPs may have phenotypical untoward effects in humans, calling for urgent research in this field.
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Affiliation(s)
- María-Carmen López de las Hazas
- Laboratory of Epigenetics of Lipid Metabolism, Madrid Institute for Advanced Studies (IMDEA)–Food, CEI UAM + CSIC, Madrid, Spain
| | - Hatim Boughanem
- Instituto de Investigación Biomédica de Málaga (IBIMA), Unidad de Gestión Clínica de Endocrinología y Nutrición del Hospital Virgen de la Victoria, Málaga, Spain
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17
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Monfared YK, Mirzaii-Dizgah MR, Khodabandehloo E, Sarookhani MR, Hashemipour S, Mirzaii-Dizgah I. Salivary microRNA-126 and 135a: a potentially non-invasive diagnostic biomarkers of type- 2 diabetes. J Diabetes Metab Disord 2021; 20:1631-1638. [PMID: 34900814 DOI: 10.1007/s40200-021-00914-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 10/04/2021] [Indexed: 12/27/2022]
Abstract
Purpose Emerging of miRNAs have illustrated the new mechanistic layer to regulate type 2 diabetes process and suggests a possible role of these RNAs in this defect. Thus, we designed this study to improve our understanding of salivary miRNA-126 and 135a expression utility as an easy of collection and non-invasive way in diabetic patients instead of blood sample. Methods This case-control study was done on T2D (n = 40) and healthy individuals (n = 40). The level of biochemical parameters were determined by enzymatic methods as well as glycosylated hemoglobin (HbA1c) was measured by immunoturbidimetry. We used the pooled whole stimulated saliva sample from cases and controls to assess the differentiation expression of miRNA 126 and 135-a with quantitative RT-PCR method. Unpaired Student's t test, Pearson's correlation coefficient and Receiver Operating Characteristic (ROC) analysis were used. Results A correlation was observed between the level of HbA1c, glucose and lipid profiles (TG, TC, and LDL) in serum and whole stimulated saliva samples in T2D patients compared to control (p < 0.001). miR-135a expression was considerably higher by 4.7-fold in T2D compared to the control group (1.8-fold) (p < 0.001) while the miR126 expression was significantly decreased by 3.9-fold in T2D compared to the controls (6.3-fold) (p < 0.001). Conclusions The results of this case and control study showed that miR-135a and miR126 expression in saliva fluid as a reliable biomarkers and non-invasive approach in combination by change of lipid profiles, glucose and HbA1c may be used to monitor diabetic and non-diabetic patients, while further research is needed to investigate the relationship of these salivary miRNAs (miR135a, miR126) levels change on shifting the levels of clinical laboratory outcomes.
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Affiliation(s)
- Yousef Khazaei Monfared
- Cellular and Molecular Research Center, Qazvin University of Medical Sciences, Qazvin, Iran.,Dip. Di Chimica, Università di Torino, Via P. Giuria 7, 10125 Torino, Italy
| | | | - Elham Khodabandehloo
- B.Sc of Medical Laboratory sciences, Dezful University of Medical Sciences, Dezful, Iran
| | | | - Sima Hashemipour
- Metabolic Diseases Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Iraj Mirzaii-Dizgah
- Department of Physiology, School of Medicine, Aja University of Medical Sciences, Tehran, Iran
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18
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Papa L, Johnson B, Walter AE, Wilkes JR, Knollmann-Ritschel B, Bhomia M, Slobounov SM. Decreases in Dorsal Cervical Spinal Cord White Matter Tract Integrity Are Associated with Elevated Levels of Serum MicroRNA Biomarkers in NCAA Division I Collegiate Football Players. Neurotrauma Rep 2021; 2:476-487. [PMID: 34901943 PMCID: PMC8655801 DOI: 10.1089/neur.2021.0036] [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] [Indexed: 11/07/2022] Open
Abstract
This prospective, controlled, observational cohort study assessed the performance of a novel panel of serum microRNA (miRNA) biomarkers relative to findings on cervical spinal cord magnetic resonance imaging (MRI) in collegiate football players. There were 44 participants included in the study: 30 non-athlete control subjects and 14 male collegiate football athletes participating in a Division I Football Bowl Subdivision of the National Collegiate Athletic Association. Diffuse tensor MRI and blood samples were acquired within the week before the athletic season began and within the week after the last game of the season. All miRNAs were significantly higher in athletes regardless of their fractional anisotropy (FA) values (p < 0.001), even those considered to be in the “normal” range of FA for white and gray matter integrity in the cervical spinal cord. miRNA biomarkers were most significantly correlated with FA of the white matter (WM) tracts of the dorsal (posterior) spinal cord; particularly, the fasciculus gracilis, fasciculus cuneatus, lateral corticospinal tract, rubrospinal tract, lateral reticulospinal tract, spinal lemniscus, and spinothalamic and -reticular tracts. Areas under the curve for miRNA biomarkers predicting lower FA of WM dorsal (posterior) cervical spinal tracts, therefore lower white matter integrity (connectivity), were miR-505* = 0.75 (0.54–0.96), miR-30d = 0.74 (0.52–0.95), and miR-92a = 0.75 (0.53–0.98). Should these findings be replicated in a larger cohort of athletes, these markers could potentially serve as measures of neuroimaging abnormalities in athletes at risk for concussion and subconcussive injuries to the cervical spinal cord.
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Affiliation(s)
- Linda Papa
- Department of Emergency Medicine, Orlando Regional Medical Center, Orlando, Florida, USA.,Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
| | - Brian Johnson
- Department of Radiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Alexa E Walter
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - James R Wilkes
- Department of Kinesiology, Pennsylvania State University, University Park, Pennsylvania, USA
| | | | - Manish Bhomia
- Department of Pathology, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Semyon M Slobounov
- Department of Kinesiology, Pennsylvania State University, University Park, Pennsylvania, USA
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Pinilla L, Benitez ID, González J, Torres G, Barbé F, de Gonzalo-Calvo D. Peripheral blood microRNAs and the COVID-19 patient: methodological considerations, technical challenges and practice points. RNA Biol 2021; 18:688-695. [PMID: 33530819 PMCID: PMC8078525 DOI: 10.1080/15476286.2021.1885188] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 01/30/2021] [Indexed: 02/06/2023] Open
Abstract
The COVID-19 emergency pandemic resulting from infection with SARS-CoV-2 represents a major threat to public health worldwide. There is an urgent clinical demand for easily accessible tools to address weaknesses and gaps in the management of COVID-19 patients. In this context, transcriptomic profiling of liquid biopsies, especially microRNAs (miRNAs), has recently emerged as a robust source of potential clinical indicators for medical decision-making. Nevertheless, the analysis of the circulating miRNA signature and its translation to clinical practice requires strict control of a wide array of methodological details. In this review, we indicate the main methodological aspects that should be addressed when evaluating the circulating miRNA profiles in COVID-19 patients, from preanalytical and analytical variables to the experimental design, impact of confounding, analysis of the data and interpretation of the findings, among others. Additionally, we provide practice points to ensure the rigour and reproducibility of miRNA-based biomarker investigations of this condition.Abbreviations: ACE: angiotensin-converting enzyme; ARDS: acute respiratory distress syndrome; COVID-19: coronavirus disease 2019; ERDN: early Detection Research Network; LMWH: low molecular weight heparin; miRNA: microRNA; ncRNA: noncoding RNA; SARS-CoV-2: severe acute respiratory syndrome coronavirus-2; SOP: standard operating procedure.
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Affiliation(s)
- Lucía Pinilla
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Ivan D. Benitez
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Jessica González
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
- Respiratory Department, University Hospital Arnau de Vilanova-Santa María, Translational Research in Respiratory Medicine, IRBLleida, University of Lleida, Lleida, Spain
| | - Gerard Torres
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
- Respiratory Department, University Hospital Arnau de Vilanova-Santa María, Translational Research in Respiratory Medicine, IRBLleida, University of Lleida, Lleida, Spain
| | - Ferran Barbé
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
- Respiratory Department, University Hospital Arnau de Vilanova-Santa María, Translational Research in Respiratory Medicine, IRBLleida, University of Lleida, Lleida, Spain
| | - David de Gonzalo-Calvo
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
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Raissi V, Zibaei M, Raiesi O, Samani Z, Yarahmadi M, Etemadi S, Istiqomah A, Alizadeh Z, Shadabi S, Sohrabi N, Ibrahim A. Parasite-derived microRNAs as a diagnostic biomarker: potential roles, characteristics, and limitations. J Parasit Dis 2021; 45:546-556. [PMID: 34295053 DOI: 10.1007/s12639-021-01395-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 04/12/2021] [Indexed: 12/25/2022] Open
Abstract
MicroRNAs (miRNAs), a subclass of small regulatory RNAs that present from ancient unicellular protozoans to parasitic helminths and parasitic arthropods. MiRNAs' mode of action has attracted wide attention as a result of their unique functional importance. MiRNAs play a role in diverse physiological and pathological processes ranging from organ development, immune function to apoptosis and cancer at the post-transcription gene expression. Thus, miRNAs are known to be targets for clinical treatment and therapy. The discovery of the high stability of circulating miRNA in various types of host body fluids, such as whole blood, serum, plasma, saliva, and urine has increased great interest among researchers in the potential of circulating miRNA as a prognosis/diagnosis of infectious. Some circulating miRNAs biomarkers advanced to clinical applications related to human diseases. However, this idea starts to come only in the fields of infectious disease. The goal of this review is to enhance the current understanding of these molecules and their applicability in the field of medicine. A detailed review of the available literature consulting tools performed in online repositories such as NCBI, PubMed, Medline, ScienceDirect, and UpToDate. This review summarizes an overview of preclinical studies using circulating miRNAs biomarkers against infectious diseases affecting humans. The use of miRNA as a safe and potential tool is encouraging news, considering that until now, guidelines for the use of miRNA in clinical practice are still lacking.
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Affiliation(s)
- Vahid Raissi
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
- Department of Medical Parasitology and Mycology, Faculty of Medicine, Lorestan University of Medical Sciences, Khorramabad, Iran
| | - Mohammad Zibaei
- Department of Parasitology and Mycology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Omid Raiesi
- Department of Parasitology, School of Allied Medical Sciences, Ilam University of Medical Sciences, Ilam, Iran
| | - Zahra Samani
- DVM Student At Faculty of Veterinary Medicine, Shahrekord University, Shahrekord, Iran
| | - Mohammad Yarahmadi
- Department of Medical Parasitology and Mycology, Faculty of Medicine, Lorestan University of Medical Sciences, Khorramabad, Iran
| | - Soudabeh Etemadi
- Department of Medical Parasitology and Mycology, Faculty of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Afrida Istiqomah
- West Java Animal Health and Veterinary Public Health, Jakarta, Indonesia
| | - Zahra Alizadeh
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Shahrzad Shadabi
- Hepatitis Research Center, Lorestan University of Medical Sciences, Khorramabad, Iran
| | - Nasrin Sohrabi
- Department of Medical Genetics, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Asmaa Ibrahim
- Genetic Engineering and Biotechnology Research Institute, University of Sadat City, Sadat, Egypt
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21
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Hirschfeld M, Rücker G, Weiß D, Berner K, Ritter A, Jäger M, Erbes T. Urinary Exosomal MicroRNAs as Potential Non-invasive Biomarkers in Breast Cancer Detection. Mol Diagn Ther 2021; 24:215-232. [PMID: 32112368 DOI: 10.1007/s40291-020-00453-y] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Breast cancer (BC) is the most frequent malignant disease in women worldwide and is therefore challenging for the healthcare system. Early BC detection remains a leading factor that improves overall outcome and disease management. Aside from established screening procedures, there is a constant demand for additional BC detection methods. Routine BC screening via non-invasive liquid biopsy biomarkers is one auspicious approach to either complete or even replace the current state-of-the-art diagnostics. The study explores the diagnostic potential of urinary exosomal microRNAs with specific BC biomarker characteristics to initiate the potential prospective application of non-invasive BC screening as routine practice. METHODS Based on a case-control study (69 BC vs. 40 healthy controls), expression level quantification and subsequent biostatistical computation of 13 urine-derived microRNAs were performed to evaluate their diagnostic relevance in BC. RESULTS Multilateral statistical assessment determined and repeatedly confirmed a specific panel of four urinary microRNA types (miR-424, miR-423, miR-660, and let7-i) as a highly specific combinatory biomarker tool discriminating BC patients from healthy controls, with 98.6% sensitivity and 100% specificity. DISCUSSION Urine-based BC diagnosis may be achieved through the analysis of distinct microRNA panels with proven biomarker abilities. Subject to further validation, the implementation of urinary BC detection in routine screening offers a promising non-invasive alternative in women's healthcare.
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Affiliation(s)
- Marc Hirschfeld
- Department of Obstetrics and Gynecology, Medical Center, University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Institute of Veterinary Medicine, Georg-August-University Goettingen, Goettingen, Germany
| | - Gerta Rücker
- Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Institute of Medical Biometry and Statistics, Medical Center, University of Freiburg, Freiburg, Germany
| | - Daniela Weiß
- Department of Obstetrics and Gynecology, Medical Center, University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Kai Berner
- Department of Obstetrics and Gynecology, Medical Center, University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Andrea Ritter
- Department of Obstetrics and Gynecology, Medical Center, University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Markus Jäger
- Department of Obstetrics and Gynecology, Medical Center, University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Thalia Erbes
- Department of Obstetrics and Gynecology, Medical Center, University of Freiburg, Freiburg, Germany. .,Faculty of Medicine, University of Freiburg, Freiburg, Germany.
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22
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Charting Extracellular Transcriptomes in The Human Biofluid RNA Atlas. Cell Rep 2020; 33:108552. [PMID: 33378673 DOI: 10.1016/j.celrep.2020.108552] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 10/14/2020] [Accepted: 12/03/2020] [Indexed: 02/06/2023] Open
Abstract
Extracellular RNAs present in biofluids have emerged as potential biomarkers for disease. Where most studies focus on blood-derived fluids, other biofluids may be more informative. We present an atlas of messenger, circular, and small RNA transcriptomes of a comprehensive collection of 20 human biofluids. By means of synthetic spike-in controls, we compare RNA content across biofluids, revealing a 10,000-fold difference in concentration. The circular RNA fraction is increased in most biofluids compared to tissues. Each biofluid transcriptome is enriched for RNA molecules derived from specific tissues and cell types. Our atlas enables an informed selection of the most relevant biofluid to monitor particular diseases. To verify the biomarker potential in these biofluids, four validation cohorts representing a broad spectrum of diseases were profiled, revealing numerous differential RNAs between case and control subjects. Spike-normalized data are publicly available in the R2 web portal for further exploration.
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23
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Fehlmann T, Lehallier B, Schaum N, Hahn O, Kahraman M, Li Y, Grammes N, Geffers L, Backes C, Balling R, Kern F, Krüger R, Lammert F, Ludwig N, Meder B, Fromm B, Maetzler W, Berg D, Brockmann K, Deuschle C, von Thaler AK, Eschweiler GW, Milman S, Barziliai N, Reichert M, Wyss-Coray T, Meese E, Keller A. Common diseases alter the physiological age-related blood microRNA profile. Nat Commun 2020; 11:5958. [PMID: 33235214 PMCID: PMC7686493 DOI: 10.1038/s41467-020-19665-1] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 10/16/2020] [Indexed: 02/07/2023] Open
Abstract
Aging is a key risk factor for chronic diseases of the elderly. MicroRNAs regulate post-transcriptional gene silencing through base-pair binding on their target mRNAs. We identified nonlinear changes in age-related microRNAs by analyzing whole blood from 1334 healthy individuals. We observed a larger influence of the age as compared to the sex and provide evidence for a shift to the 5' mature form of miRNAs in healthy aging. The addition of 3059 diseased patients uncovered pan-disease and disease-specific alterations in aging profiles. Disease biomarker sets for all diseases were different between young and old patients. Computational deconvolution of whole-blood miRNAs into blood cell types suggests that cell intrinsic gene expression changes may impart greater significance than cell abundance changes to the whole blood miRNA profile. Altogether, these data provide a foundation for understanding the relationship between healthy aging and disease, and for the development of age-specific disease biomarkers.
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Affiliation(s)
- Tobias Fehlmann
- Chair for Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
| | - Benoit Lehallier
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, 94305, USA
| | - Nicholas Schaum
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, 94305, USA
| | - Oliver Hahn
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, 94305, USA
| | - Mustafa Kahraman
- Chair for Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
| | - Yongping Li
- Chair for Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
| | - Nadja Grammes
- Chair for Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
| | - Lars Geffers
- Luxembourg Center for Systems Biomedicine, 4362, Esch-sur-Alzette, Luxemburg
| | - Christina Backes
- Chair for Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
| | - Rudi Balling
- Luxembourg Center for Systems Biomedicine, 4362, Esch-sur-Alzette, Luxemburg
- Transversal Translational Medicine, Luxembourg Institute of Health (LIH), 1445, Strassen, Luxemburg
- Parkinson Research Clinic, Centre Hospitalier de Luxembourg, 1210, Luxembourg, Luxemburg
| | - Fabian Kern
- Chair for Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
| | - Rejko Krüger
- Luxembourg Center for Systems Biomedicine, 4362, Esch-sur-Alzette, Luxemburg
- Transversal Translational Medicine, Luxembourg Institute of Health (LIH), 1445, Strassen, Luxemburg
- Parkinson Research Clinic, Centre Hospitalier de Luxembourg, 1210, Luxembourg, Luxemburg
| | - Frank Lammert
- Internal Medicine, Saarland University, 66421, Homburg, Germany
| | - Nicole Ludwig
- Human Genetics, Saarland University, 66421, Homburg, Germany
| | - Benjamin Meder
- Internal Medicine, University Hospital Heidelberg, 69120, Heidelberg, Germany
| | - Bastian Fromm
- Department of Molecular Biosciences, Stockholm University, 11418, Stockholm, Sweden
| | - Walter Maetzler
- Department of Neurology, Christian-Albrechts-Universität zu Kiel, 24105, Kiel, Germany
| | - Daniela Berg
- Department of Neurology, Christian-Albrechts-Universität zu Kiel, 24105, Kiel, Germany
| | | | | | | | - Gerhard W Eschweiler
- Geriatric Center and the Department of Psychiatry and Psychotherapy, University Hospital Tübingen, 72076, Tübingen, Germany
| | - Sofiya Milman
- The Institute for Aging Research, Albert Einstein College of Medicine, New York, NY, 10461, USA
| | - Nir Barziliai
- The Institute for Aging Research, Albert Einstein College of Medicine, New York, NY, 10461, USA
| | | | - Tony Wyss-Coray
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, 94305, USA
| | - Eckart Meese
- Human Genetics, Saarland University, 66421, Homburg, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany.
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, 94305, USA.
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, 66123, Saarbrücken, Germany.
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24
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Extracellular MicroRNAs as Intercellular Mediators and Noninvasive Biomarkers of Cancer. Cancers (Basel) 2020; 12:cancers12113455. [PMID: 33233600 PMCID: PMC7699762 DOI: 10.3390/cancers12113455] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/11/2020] [Accepted: 11/18/2020] [Indexed: 02/06/2023] Open
Abstract
Simple Summary There are an extensive number of publications regarding the role of endogenous miRNAs as regulators of gene expression in cancer. However, extracellular miRNAs have emerged as a novel mechanism of cell-to-cell communication in normal conditions and disease and have drawn a large amount of interest as regulators of gene expression and as potential non-invasive biomarkers in cancer. Despite this high interest and the abundance of research on the biology and role of extracellular miRNAs in cancer, they are not yet completely understood. The aim of this review is to highlight the relevant biological characteristics of extracellular miRNAs that enable them to function as intercellular mediators of gene expression regulation and provide the recently published evidence of the specific role of extracellular miRNAs in tumor development and progression. Abstract MicroRNAs (miRNAs) are released by different types of cells through highly regulated mechanisms under normal and pathological conditions. These extracellular miRNAs can be delivered into recipient cells for functional purposes, acting as cell-to-cell signaling mediators. It has been discovered that cancer cells release miRNAs into their surroundings, targeting normal cells or other cancer cells, presumably to promote tumor development and progression. These extracellular miRNAs are associated with oncogenic mechanisms and, because they can be quantified in blood and other bodily fluids, may be suitable noninvasive biomarkers for cancer detection. This review summarizes recent evidence of the role of extracellular miRNAs as intercellular mediators, with an emphasis on their role in the mechanisms of tumor development and progression and their potential value as biomarkers in solid tumors. It also highlights the biological characteristics of extracellular miRNAs that enable them to function as regulators of gene expression, such as biogenesis, gene silencing mechanisms, subcellular compartmentalization, and the functions and mechanisms of release.
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25
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Bjorkman S, Taylor HS. MicroRNAs in endometriosis: biological function and emerging biomarker candidates†. Biol Reprod 2020; 100:1135-1146. [PMID: 30721951 DOI: 10.1093/biolre/ioz014] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 12/21/2018] [Accepted: 01/31/2019] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs (miRNAs), a class of small noncoding RNA molecules, have been recognized as key post-transcriptional regulators associated with a multitude of human diseases. Global expression profiling studies have uncovered hundreds of miRNAs that are dysregulated in several diseases, and yielded many candidate biomarkers. This review will focus on miRNAs in endometriosis, a common chronic disease affecting nearly 10% of reproductive-aged women, which can cause pelvic pain, infertility, and a myriad of other symptoms. Endometriosis has delayed time to diagnosis when compared to other chronic diseases, as there is no current accurate, easily accessible, and noninvasive tool for diagnosis. Specific miRNAs have been identified as potential biomarkers for this disease in multiple studies. These and other miRNAs have been linked to target genes and functional pathways in disease-specific pathophysiology. Highlighting investigations into the roles of tissue and circulating miRNAs in endometriosis, published through June 2018, this review summarizes new connections between miRNA expression and the pathophysiology of endometriosis, including impacts on fertility. Future applications of miRNA biomarkers for precision medicine in diagnosing and managing endometriosis treatment are also discussed.
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Affiliation(s)
- Sarah Bjorkman
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale School of Medicine, New Haven, Connecticut, USA
| | - Hugh S Taylor
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale School of Medicine, New Haven, Connecticut, USA
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26
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Keller A, Fehlmann T, Backes C, Kern F, Gislefoss R, Langseth H, Rounge TB, Ludwig N, Meese E. Competitive learning suggests circulating miRNA profiles for cancers decades prior to diagnosis. RNA Biol 2020; 17:1416-1426. [PMID: 32456538 DOI: 10.1080/15476286.2020.1771945] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs are regulators of gene expressionand may be key markers in liquid biopsy.Early diagnosis is an effective means to increase patients' overall survival. We generated genome-wide miRNA profiles from serum of patients and controls from the population-based Janus Serum Bank (JSB) and analysed them by bioinformatics and artificial intelligence approaches. JSB contains sera from 318,628 originally healthy persons, more than 96,000 of whom developed cancer. We selected 210 serum samples from patients with lung, colon or breast cancer at three time points prior to diagnosis (up to 32 years prior to diagnosis with median 5 years interval between TPs), one time-point after diagnosis and from individually matched controls. The controls were matched on age and year of all pre-diagnostic sampling time-points for the corresponding case. Using ANOVA we report 70 significantly deregulated markers (adjusted p-value<0.05). The driver for the significance was the diagnostic time point (miR-575, miR-6821-5p, miR-630 with adjusted p-values<10-10). Further, 91miRNAs were differently expressed in pre-diagnostic samples as compared to controls (nominal p < 0.05). Self-organized maps (SOMs)indicated larges effects in lung cancer samples while breast cancer samples showed the least pronounced changes. SOMsalsohighlighted cancer and time point specific miRNA dys-regulation. Intriguingly, a detailed breakdown of the results highlighted that 51% of all miRNAs were highly specific, either for a time-point or a cancer entity. Pathway analysis highlighted 12 pathways including Hipo signalling and ABC transporters.Our results indicate that tumours may be indicated by serum miRNAs decades prior the clinical manifestation.
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Affiliation(s)
- Andreas Keller
- Department of Clinical Bioinformatics, Saarland University , Saarbrücken, Germany.,Department of Neurology and Neurological Sciences, Stanford University School of Medicine , Stanford, CA, USA
| | - Tobias Fehlmann
- Department of Clinical Bioinformatics, Saarland University , Saarbrücken, Germany
| | - Christina Backes
- Department of Clinical Bioinformatics, Saarland University , Saarbrücken, Germany
| | - Fabian Kern
- Department of Clinical Bioinformatics, Saarland University , Saarbrücken, Germany
| | - Randi Gislefoss
- Department of Research, Cancer Registry of Norway , Oslo, Norway
| | - Hilde Langseth
- Department of Research, Cancer Registry of Norway , Oslo, Norway.,Department of Epidemiology and Biostatistics, Imperial College London , London, UK
| | - Trine B Rounge
- Department of Research, Cancer Registry of Norway , Oslo, Norway.,Department of Informatics, University of Oslo , Oslo, Norway
| | - Nicole Ludwig
- Department of Human Genetics, Saarland University , Homburg/Saar, Germany
| | - Eckart Meese
- Department of Human Genetics, Saarland University , Homburg/Saar, Germany
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27
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Liu S, Xin W, Tang X, Qiu J, Zhang Y, Hua K. LncRNA H19 Overexpression in Endometriosis and its Utility as a Novel Biomarker for Predicting Recurrence. Reprod Sci 2020; 27:1687-1697. [DOI: 10.1007/s43032-019-00129-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 11/05/2019] [Indexed: 02/07/2023]
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28
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La T, Jin L, Liu XY, Song ZH, Farrelly M, Feng YC, Yan XG, Zhang YY, Thorne RF, Zhang XD, Teng L. Cylindromatosis Is Required for Survival of a Subset of Melanoma Cells. Oncol Res 2020; 28:385-398. [PMID: 32252875 PMCID: PMC7851542 DOI: 10.3727/096504020x15861709922491] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The deubiquitinase cylindromatosis (CYLD) functions as a tumor suppressor inhibiting cell proliferation in many cancer types including melanoma. Here we present evidence that a proportion of melanoma cells are nonetheless addicted to CYLD for survival. The expression levels of CYLD varied widely in melanoma cell lines and melanomas in vivo, with a subset of melanoma cell lines and melanomas displaying even higher levels of CYLD than melanocyte lines and nevi, respectively. Strikingly, although short hairpin RNA (shRNA) knockdown of CYLD promoted, as anticipated, cell proliferation in some melanoma cell lines, it reduced cell viability in a fraction of melanoma cell lines with relatively high levels of CYLD expression and did not impinge on survival and proliferation in a third type of melanoma cell lines. The decrease in cell viability caused by CYLD knockdown was due to induction of apoptosis, as it was associated with activation of the caspase cascade and was abolished by treatment with a general caspase inhibitor. Mechanistic investigations demonstrated that induction of apoptosis by CYLD knockdown was caused by upregulation of receptor-interacting protein kinase 1 (RIPK1) that was associated with elevated K63-linked polyubiquitination of the protein, indicating that CYLD is critical for controlling RIPK1 expression in these cells. Of note, microRNA (miR) profiling showed that miR-99b-3p that was predicted to target the 3′-untranslated region (3′-UTR) of the CYLD mRNA was reduced in melanoma cell lines with high levels of CYLD compared with melanocyte lines. Further functional studies confirmed that the reduction in miR-99b-3p expression was responsible for the increased expression of CYLD in a highly cell line-specific manner. Taken together, these results reveal an unexpected role of CYLD in promoting survival of a subset of melanoma cells and uncover the heterogeneity of CYLD expression and its biological significance in melanoma.
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Affiliation(s)
- Ting La
- Translational Research Institute, Henan Provincial Peoples Hospital, Academy of Medical Science, Zhengzhou UniversityZhengzhouP.R. China
| | - Lei Jin
- Translational Research Institute, Henan Provincial Peoples Hospital, Academy of Medical Science, Zhengzhou UniversityZhengzhouP.R. China
| | - Xiao Ying Liu
- Translational Research Institute, Henan Provincial Peoples Hospital, Academy of Medical Science, Zhengzhou UniversityZhengzhouP.R. China
| | - Ze Hua Song
- Translational Research Institute, Henan Provincial Peoples Hospital, Academy of Medical Science, Zhengzhou UniversityZhengzhouP.R. China
| | - Margaret Farrelly
- School of Biomedical Sciences and Pharmacy, The University of NewcastleCallaghan, NSWAustralia
| | - Yu Chen Feng
- School of Biomedical Sciences and Pharmacy, The University of NewcastleCallaghan, NSWAustralia
| | - Xu Guang Yan
- School of Biomedical Sciences and Pharmacy, The University of NewcastleCallaghan, NSWAustralia
| | - Yuan Yuan Zhang
- School of Biomedical Sciences and Pharmacy, The University of NewcastleCallaghan, NSWAustralia
| | - Rick F Thorne
- Translational Research Institute, Henan Provincial Peoples Hospital, Academy of Medical Science, Zhengzhou UniversityZhengzhouP.R. China
| | - Xu Dong Zhang
- Translational Research Institute, Henan Provincial Peoples Hospital, Academy of Medical Science, Zhengzhou UniversityZhengzhouP.R. China
| | - Liu Teng
- Translational Research Institute, Henan Provincial Peoples Hospital, Academy of Medical Science, Zhengzhou UniversityZhengzhouP.R. China
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29
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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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30
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Doxakis E. Cell-free microRNAs in Parkinson's disease: potential biomarkers that provide new insights into disease pathogenesis. Ageing Res Rev 2020; 58:101023. [PMID: 32001380 DOI: 10.1016/j.arr.2020.101023] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 01/21/2020] [Accepted: 01/21/2020] [Indexed: 02/07/2023]
Abstract
MicroRNAs (miRNAs) are master post-transcriptional regulators of gene expression and their specific footprints reflect disease conditions. Over the last few years, several primary reports have described the deregulation of cell-free miRNAs in Parkinson's disease (PD), however, results have been rather inconsistent due to preanalytical and analytical challenges. This study integrated the data across twenty-four reports to identify steadily deregulated miRNAs that may assist in the path towards biomarker development and molecular characterization of the underlying pathology. Stringent KEGG pathway analysis of the miRNA targets revealed FoxO, Prolactin, TNF, and ErbB signaling pathways as the most significantly enriched categories while Gene Ontology analysis revealed that the protein targets are mostly associated with transcription. Chromosomal location of the consistently deregulated miRNAs revealed that over a third of them were clustered at the same location at Chr14q32 suggesting that they are co-regulated by specific transcription factors. This genomic region is inherently unstable due to expanded TGG repeats and responsible for human abnormalities. Stringent analysis of transcription factor sites surrounding the deregulated miRNAs revealed that CREB1, CEBPB and MAZ sites existed in approximately half of the miRNAs, including all of the miRNAs located at Chr14q32. Additional studies are now needed to determine the biomarker potential of the consistently deregulated miRNAs in PD and the therapeutic implications of these bioinformatics insights.
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31
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Bushel PR, Caiment F, Wu H, O'Lone R, Day F, Calley J, Smith A, Li J, Harrill AH. RATEmiRs: the rat atlas of tissue-specific and enriched miRNAs for discerning baseline expression exclusivity of candidate biomarkers. RNA Biol 2020; 17:630-636. [PMID: 32009518 DOI: 10.1080/15476286.2020.1724715] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs (miRNAs) are small RNAs that regulate mRNA expression and have been targeted as biomarkers of organ damage and disease. To explore the utility of miRNAs to assess injury to specific tissues, a tissue atlas of miRNA abundance was constructed. The Rat Atlas of Tissue-specific and Enriched miRNAs (RATEmiRs) catalogues miRNA sequencing data from 21 and 23 tissues in male and female Sprague-Dawley rats, respectively. RATEmiRs identifies tissue-enriched (TE), tissue-specific (TS), or organ-specific (OS) miRNAs via comparisons of one or more tissue or organ vs others. We provide a brief overview of RATEmiRs and present how to use it to detect miRNA expression abundance of candidate biomarkers as well as to compare the expression of miRNAs between rat and human. The database is available at https://www.niehs.nih.gov/ratemirs/.
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Affiliation(s)
- Pierre R Bushel
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC, USA.,Microarray and Genome Informatics Group, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC, USA
| | - Florian Caiment
- Department of Toxicogenomics, Maastricht University, Maastricht, The Netherlands
| | - Han Wu
- Department of Discovery and Development Statistics, Lilly Research Laboratories, Lilly Corporate Center, Indianapolis, IN, USA
| | - Raegan O'Lone
- eSTAR, Health and Environmental Sciences Institute, Washington, DC, USA
| | - Frank Day
- Office of Scientific Computing, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC, USA
| | - John Calley
- Department of TTX Bioinformatics, Lilly Research Laboratories, Lilly Corporate Center, Indianapolis, IN, USA
| | - Aaron Smith
- Department of Investigative Toxicology, Non-Clinical Safety Assessment and Pathology, Lilly Research Laboratories, Lilly Corporate Center, Indianapolis, IN, USA
| | - Jianying Li
- Microarray and Genome Informatics Group, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC, USA.,Integrative Bioinformatics, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC, USA.,Kelly Government Solutions, Research Triangle Park, Durham, NC, USA
| | - Alison H Harrill
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC, USA
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32
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Paschou M, Maier L, Papazafiri P, Selescu T, Dedos SG, Babes A, Doxakis E. Neuronal microRNAs modulate TREK two-pore domain K + channel expression and current density. RNA Biol 2020; 17:651-662. [PMID: 31994436 DOI: 10.1080/15476286.2020.1722450] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The TREK family of leak potassium channels has been found to play critical roles in nociception, sensitivity to general anaesthetics, neuroprotection, and memory. The three members of the family, TREK1, TREK2 and TRAAK establish the resting potential and modify the duration, frequency and amplitude of action potentials. Despite their apparent importance, the repertoire of regulatory interactions utilized by cells to control their expression is poorly understood. Herein, the contribution of miRNAs in the regulation of their post-transcriptional gene expression has been examined. Using different assays, miR-124 and to a lesser extent miR-128 and miR-183 were found to reduce TREK1 and TREK2 levels through specific binding to their 3'UTRs. In contrast, miR-9 which was predicted to bind to TRAAK 3'UTR, did not alter its expression. Expression of miR-124, miR-128 and miR-183 was found to mirror that of Trek1 and Trek2 mRNAs during brain development. Moreover, application of proinflammatory mediators in dorsal root ganglion (DRG) neurons revealed an inverse correlation between miR-124 and Trek1 and Trek2 mRNA expression. Voltage clamp recordings of TREK2-mediated currents showed that miR-124 reduced the sensitivity of TREK2-expressing cells to non-aversive warmth stimulation. Overall, these findings reveal a significant regulatory mechanism by which TREK1 and TREK2 expression and hence activity are controlled in neurons and uncover new druggable targets for analgesia and neuroprotection.Abbreviations: microRNA: miRNA; UTR: untranslated region; K2p channels: two-pore domain K+channels; DRG: dorsal root ganglion; CNS: central nervous system; FBS: fetal bovine serum; TuD: Tough Decoy; TREK: tandem P-domain weak inward rectifying K+ (TWIK)-related K+ channel 1; TRAAK: TWIK-related arachidonic acid K+.
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Affiliation(s)
- Maria Paschou
- Center for Basic Research, Biomedical Research Foundation, Academy of Athens, Athens, Greece.,Department of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Larisa Maier
- Department of Anatomy, Physiology and Biophysics, Faculty of Biology, University of Bucharest, Bucharest, Romania
| | - Panagiota Papazafiri
- Department of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Tudor Selescu
- Department of Anatomy, Physiology and Biophysics, Faculty of Biology, University of Bucharest, Bucharest, Romania
| | - Skarlatos G Dedos
- Department of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Alexandru Babes
- Department of Anatomy, Physiology and Biophysics, Faculty of Biology, University of Bucharest, Bucharest, Romania
| | - Epaminondas Doxakis
- Center for Basic Research, Biomedical Research Foundation, Academy of Athens, Athens, Greece
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Ventriglia G, Mancarella F, Sebastiani G, Cook DP, Mallone R, Mathieu C, Gysemans C, Dotta F. miR-409-3p is reduced in plasma and islet immune infiltrates of NOD diabetic mice and is differentially expressed in people with type 1 diabetes. Diabetologia 2020; 63:124-136. [PMID: 31659408 DOI: 10.1007/s00125-019-05026-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 08/30/2019] [Indexed: 02/07/2023]
Abstract
AIMS/HYPOTHESIS MicroRNAs (miRNAs) are a novel class of potential biomarkers emerging in many diseases, including type 1 diabetes. Here, we aim to analyse a panel of circulating miRNAs in non-obese diabetic (NOD) mice and individuals with type 1 diabetes. METHODS We adopted standardised methodologies for extracting miRNAs from small sample volumes to evaluate a profiling panel of mature miRNAs in paired plasma and laser-captured microdissected immune-infiltrated islets of recently diabetic and normoglycaemic NOD mice. Moreover, we validated the findings during disease progression and remission after anti-CD3 therapy in NOD mice, as well as in individuals with type 1 diabetes. RESULTS Plasma levels of five miRNAs were downregulated in diabetic vs normoglycaemic mice. Of those, miR-409-3p was also downregulated in situ in the immune islet infiltrates of diabetic mice, suggesting an association with disease pathogenesis. Target-prediction tools linked miR-409-3p to immune- and metabolism-related signalling molecules. In situ miR-409-3p expression correlated with insulitis severity, and CD8+ central memory T cells were found to be enriched in miR-409-3p. Plasma miR-409-3p levels gradually decreased during diabetes development and improved with disease remission after anti-CD3 antibody therapy. Finally, plasma miR-409-3p levels were lower in people recently diagnosed with type 1 diabetes compared with a non-diabetic control group, and levels were inversely correlated with HbA1c levels. CONCLUSIONS/INTERPRETATION We propose that miR-409-3p may represent a new circulating biomarker of islet inflammation and type 1 diabetes severity.
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Affiliation(s)
- Giuliana Ventriglia
- Diabetes Unit, Department of Medicine, Surgery and Neurosciences, University of Siena, V.le Bracci, 16 - 53100, Siena, Italy
- Fondazione Umberto Di Mario ONLUS c/o Toscana Life Sciences, Siena, Italy
- Clinical and Experimental Endocrinology (CEE), Katholieke Universiteit Leuven (KU LEUVEN), Leuven, Belgium
| | - Francesca Mancarella
- Diabetes Unit, Department of Medicine, Surgery and Neurosciences, University of Siena, V.le Bracci, 16 - 53100, Siena, Italy
- Fondazione Umberto Di Mario ONLUS c/o Toscana Life Sciences, Siena, Italy
| | - Guido Sebastiani
- Diabetes Unit, Department of Medicine, Surgery and Neurosciences, University of Siena, V.le Bracci, 16 - 53100, Siena, Italy
- Fondazione Umberto Di Mario ONLUS c/o Toscana Life Sciences, Siena, Italy
| | - Dana P Cook
- Clinical and Experimental Endocrinology (CEE), Katholieke Universiteit Leuven (KU LEUVEN), Leuven, Belgium
| | - Roberto Mallone
- Inserm, U1016, CNRS, UMR8104, Paris Descartes University, Sorbonne Paris Cité, Cochin Institute, Paris, France
| | - Chantal Mathieu
- Clinical and Experimental Endocrinology (CEE), Katholieke Universiteit Leuven (KU LEUVEN), Leuven, Belgium
| | - Conny Gysemans
- Clinical and Experimental Endocrinology (CEE), Katholieke Universiteit Leuven (KU LEUVEN), Leuven, Belgium
| | - Francesco Dotta
- Diabetes Unit, Department of Medicine, Surgery and Neurosciences, University of Siena, V.le Bracci, 16 - 53100, Siena, Italy.
- Fondazione Umberto Di Mario ONLUS c/o Toscana Life Sciences, Siena, Italy.
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Ravanidis S, Bougea A, Papagiannakis N, Maniati M, Koros C, Simitsi AM, Bozi M, Pachi I, Stamelou M, Paraskevas GP, Kapaki E, Moraitou M, Michelakakis H, Stefanis L, Doxakis E. Circulating Brain-enriched MicroRNAs for detection and discrimination of idiopathic and genetic Parkinson's disease. Mov Disord 2019; 35:457-467. [PMID: 31799764 DOI: 10.1002/mds.27928] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 10/13/2019] [Accepted: 10/30/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND A minimally invasive test for early detection and monitoring of Parkinson's disease (PD) is a highly unmet need for drug development and planning of patient care. Blood plasma represents an attractive source of biomarkers. MicroRNAs (miRNAs) are conserved noncoding RNA molecules that serve as posttranscriptional regulators of gene expression. As opposed to ubiquitously expressed miRNAs that control house-keeping processes, brain-enriched miRNAs regulate diverse aspects of neuron development and function. These include neuron-subtype specification, axonal growth, dendritic morphogenesis, and spine density. Backed by a large number of studies, we now know that the differential expression of neuron-enriched miRNAs leads to brain dysfunction. OBJECTIVES The aim was to identify subsets of brain-enriched miRNAs with diagnostic potential for familial and idiopathic PD as well as specify the molecular pathways deregulated in PD. METHODS Initially, brain-enriched miRNAs were selected based on literature review and validation studies in human tissues. Subsequently, real-time reverse transcription polymerase chain reaction was performed in the plasma of 100 healthy controls and 99 idiopathic and 53 genetic (26 alpha-synucleinA53T and 27 glucocerebrosidase) patients. Statistical and bioinformatics analyses were carried out to pinpoint the diagnostic biomarkers and deregulated pathways, respectively. RESULTS An explicit molecular fingerprint for each of the 3 PD cohorts was generated. Although the idiopathic PD fingerprint was different from that of genetic PD, the molecular pathways deregulated converged between all PD subtypes. CONCLUSIONS The study provides a group of brain-enriched miRNAs that may be used for the detection and differentiation of PD subtypes. It has also identified the molecular pathways deregulated in PD. © 2019 International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Stylianos Ravanidis
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | - Anastasia Bougea
- Center of Clinical Research, Experimental Surgery and Translational Research, Biomedical Research Foundation, Academy of Athens, Athens, Greece.,1st Department of Neurology, National and Kapodistrian University of Athens Medical School, Eginition Hospital, Athens, Greece
| | - Nikolaos Papagiannakis
- Center of Clinical Research, Experimental Surgery and Translational Research, Biomedical Research Foundation, Academy of Athens, Athens, Greece.,1st Department of Neurology, National and Kapodistrian University of Athens Medical School, Eginition Hospital, Athens, Greece
| | - Matina Maniati
- Center of Clinical Research, Experimental Surgery and Translational Research, Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | - Christos Koros
- 1st Department of Neurology, National and Kapodistrian University of Athens Medical School, Eginition Hospital, Athens, Greece.,2nd Department of Neurology, National and Kapodistrian University of Athens Medical School, Athens, Greece
| | - Athina-Maria Simitsi
- 1st Department of Neurology, National and Kapodistrian University of Athens Medical School, Eginition Hospital, Athens, Greece
| | - Maria Bozi
- 2nd Department of Neurology, National and Kapodistrian University of Athens Medical School, Athens, Greece
| | - Ioanna Pachi
- 1st Department of Neurology, National and Kapodistrian University of Athens Medical School, Eginition Hospital, Athens, Greece
| | - Maria Stamelou
- 1st Department of Neurology, National and Kapodistrian University of Athens Medical School, Eginition Hospital, Athens, Greece.,Parkinson's disease and Movement disorders department, HYGEIA Hospital, Athens, Greece
| | - George P Paraskevas
- 1st Department of Neurology, National and Kapodistrian University of Athens Medical School, Eginition Hospital, Athens, Greece
| | - Elisabeth Kapaki
- 1st Department of Neurology, National and Kapodistrian University of Athens Medical School, Eginition Hospital, Athens, Greece
| | - Marina Moraitou
- Department of Enzymology and Cellular Function, Institute of Child Health, Athens, Greece
| | - Helen Michelakakis
- Department of Enzymology and Cellular Function, Institute of Child Health, Athens, Greece
| | - Leonidas Stefanis
- Center of Clinical Research, Experimental Surgery and Translational Research, Biomedical Research Foundation, Academy of Athens, Athens, Greece.,1st Department of Neurology, National and Kapodistrian University of Athens Medical School, Eginition Hospital, Athens, Greece
| | - Epaminondas Doxakis
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, Athens, Greece
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35
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Gholami M, Larijani B, Zahedi Z, Mahmoudian F, Bahrami S, Omran SP, Saadatian Z, Hasani-Ranjbar S, Taslimi R, Bastami M, Amoli MM. Inflammation related miRNAs as an important player between obesity and cancers. J Diabetes Metab Disord 2019; 18:675-692. [PMID: 31890692 PMCID: PMC6915181 DOI: 10.1007/s40200-019-00459-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 10/23/2019] [Indexed: 12/13/2022]
Abstract
The growing trend in addition to their burden, prevalence, and death has made obesity and cancer two of the most concerning diseases worldwide. Obesity is an important risk factor for common types of cancers where the risk of some cancers is directly related to the obesity. Various inflammatory mechanisms and increased level of pro-inflammatory cytokines have been investigated in many previous studies, which play key roles in the pathophysiology and development of both of these conditions. On the other hand, in the recent years, many studies have individually focused on the biomarker's role and therapeutic targeting of microRNAs (miRNAs) in different types of cancers and obesity including newly discovered small noncoding RNAs (sncRNAs) which regulate gene expression and RNA silencing. This study is a comprehensive review of the main inflammation related miRNAs in obesity/obesity related traits. For the first time, the main roles of miRNAs in obesity related cancers have been discussed in response to the question raised in the following hypothesis; do the main inflammatory miRNAs link obesity with obesity-related cancers regarding their role as biomarkers? Graphical abstractConceptual design of inflammatory miRNAs which provide link between obesity and cancers.
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Affiliation(s)
- Morteza Gholami
- Obesity and Eating Habits Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Bagher Larijani
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Zhila Zahedi
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Fatemeh Mahmoudian
- Department of Molecular Medicine, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Samira Bahrami
- Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sima Parvizi Omran
- Metabolic Disorders Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, 5th floor, Shariati Hospital, North Kargar Ave, Tehran, Iran
| | - Zahra Saadatian
- Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shirin Hasani-Ranjbar
- Obesity and Eating Habits Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Reza Taslimi
- Department of Gastroenterology, Imam Khomeini Hospital, Tehran University of Medical Sciences, Tehran, IR Iran
| | - Milad Bastami
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mahsa M. Amoli
- Metabolic Disorders Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, 5th floor, Shariati Hospital, North Kargar Ave, Tehran, Iran
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Fehlmann T, Backes C, Pirritano M, Laufer T, Galata V, Kern F, Kahraman M, Gasparoni G, Ludwig N, Lenhof HP, Gregersen HA, Francke R, Meese E, Simon M, Keller A. The sncRNA Zoo: a repository for circulating small noncoding RNAs in animals. Nucleic Acids Res 2019; 47:4431-4441. [PMID: 30937442 PMCID: PMC6511844 DOI: 10.1093/nar/gkz227] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 03/29/2019] [Indexed: 12/12/2022] Open
Abstract
The repertoire of small noncoding RNAs (sncRNAs), particularly miRNAs, in animals is considered to be evolutionarily conserved. Studies on sncRNAs are often largely based on homology-based information, relying on genomic sequence similarity and excluding actual expression data. To obtain information on sncRNA expression (including miRNAs, snoRNAs, YRNAs and tRNAs), we performed low-input-volume next-generation sequencing of 500 pg of RNA from 21 animals at two German zoological gardens. Notably, none of the species under investigation were previously annotated in any miRNA reference database. Sequencing was performed on blood cells as they are amongst the most accessible, stable and abundant sources of the different sncRNA classes. We evaluated and compared the composition and nature of sncRNAs across the different species by computational approaches. While the distribution of sncRNAs in the different RNA classes varied significantly, general evolutionary patterns were maintained. In particular, miRNA sequences and expression were found to be even more conserved than previously assumed. To make the results available for other researchers, all data, including expression profiles at the species and family levels, and different tools for viewing, filtering and searching the data are freely available in the online resource ASRA (Animal sncRNA Atlas) at https://www.ccb.uni-saarland.de/asra/.
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Affiliation(s)
- Tobias Fehlmann
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Christina Backes
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Marcello Pirritano
- Molecular Cell Dynamics, Center for Human and Molecular Biology, Saarland University, 66123 Saarbrücken, Germany.,Molecular Cell Biology and Microbiology, University of Wuppertal, 42097 Wuppertal, Germany
| | - Thomas Laufer
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany.,Hummingbird Diagnostics GmbH, 69120 Heidelberg, Germany
| | - Valentina Galata
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Fabian Kern
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Mustafa Kahraman
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany.,Hummingbird Diagnostics GmbH, 69120 Heidelberg, Germany
| | - Gilles Gasparoni
- Department of Genetics, Center for Human and Molecular Biology, Saarland University, 66123 Saarbrücken, Germany
| | - Nicole Ludwig
- Department of Human Genetics, Saarland University Hospital, 66421 Homburg, Germany
| | - Hans-Peter Lenhof
- Chair for Bioinformatics, Saarland University, 66123 Saarbrücken, Germany.,Center for Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | | | | | - Eckart Meese
- Department of Human Genetics, Saarland University Hospital, 66421 Homburg, Germany
| | - Martin Simon
- Molecular Cell Dynamics, Center for Human and Molecular Biology, Saarland University, 66123 Saarbrücken, Germany.,Molecular Cell Biology and Microbiology, University of Wuppertal, 42097 Wuppertal, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany.,Center for Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
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37
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Burns KE, Deane-Alder KD, Bellissima BL, Tingle MD. Circulating microRNA as biomarkers of clozapine-induced cardiotoxicity. Biomarkers 2019; 25:76-85. [PMID: 31722571 DOI: 10.1080/1354750x.2019.1693631] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Purpose: This work investigated the utility of circulating microRNA (miRNA) as biomarkers of clozapine (CLZ)-induced cardiotoxicities: serious adverse events with an unusually high incidence in Australia and New Zealand.Methods: Global plasma miRNA expression was analysed by microarray in patients taking CLZ, to investigate differential expression between CLZ-induced cardiotoxicity cases (n = 6) and matched control patients (n = 12). The results were validated by RT-qPCR using a panel of 17 miRNA, and their expression was examined in both CLZ-naïve healthy volunteers (n = 12) and an expanded cohort of CLZ-taking patients (n = 21). Temporal changes were also examined in two healthy volunteers and two CLZ-induced cardiotoxicity patients.Results: No miRNA were differentially expressed between cases of CLZ-induced cardiotoxicity and control patients. Circulating levels of several miRNA were significantly altered in CLZ-taking patients compared to healthy volunteers, with miR-16-5p, miR-25-3p, miR-92a-3p, miR-320a-3p, and miR-486-3p upregulated and miR-22-3p, miR-126-3p, and miR-142-3p downregulated in the patients. Five of these (miR-16-5p, miR-22-3p, miR-92a-3p, miR-126-3p, miR-142-3p) were stably expressed over time in both CLZ-induced cardiotoxicity patients and CLZ-naïve healthy volunteers.Conclusions: Plasma miRNA are not useful biomarkers of CLZ-induced cardiotoxicity, however patients taking CLZ have significantly altered circulating miRNA compared to healthy volunteers.
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Affiliation(s)
- Kathryn E Burns
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | - Kieran D Deane-Alder
- Department of Pharmacology and Clinical Pharmacology, University of Auckland, Auckland, New Zealand
| | - Brandi L Bellissima
- Department of Pharmacology and Clinical Pharmacology, University of Auckland, Auckland, New Zealand
| | - Malcolm D Tingle
- Department of Pharmacology and Clinical Pharmacology, University of Auckland, Auckland, New Zealand
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38
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Ning J, Li P, Zhang B, Han B, Su X, Wang Q, Wang X, Li B, Kang H, Zhou L, Chu C, Zhang N, Pang Y, Niu Y, Zhang R. miRNAs deregulation in serum of mice is associated with lung cancer related pathway deregulation induced by PM2.5. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 254:112875. [PMID: 31377334 DOI: 10.1016/j.envpol.2019.07.043] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 06/23/2019] [Accepted: 07/09/2019] [Indexed: 05/28/2023]
Abstract
Ambient fine particulate matter (PM2.5) as an environmental pollution has been associated with the lung cancer. However, the mechanism of epigenetics such as miRNAs deregulation between PM2.5-exposure and lung cancer has not been elucidated clearly. Twenty C57BL/6 mice were divided randomly into 2 groups and exposed to the filtered air (FA) and the concentrated air (CA), respectively. The FA mice were exposed to filtered air in chambers with a high-efficient particulate air filter (HEPA-filter), and the CA mice were exposed to concentration ambient PM2.5. The total duration of exposure was performed 6 h per day from December 1st, 2017 to January 27th, 2018. The mice exposed 900.21 μg/m3 PM2.5 for 6 h per day in CA chamber, which was nearly equaled to 225.05 μg/m3 for 24-h calculatingly. After exposure, the serum miRNAs levels were detected by microarray. Genetic and pathological alterations in lung of mice with/without PM2.5 exposure were detected. 38 differential miRNAs in serum of mice were found after PM2.5 exposure for 8 weeks. Among of them, 13 miRNAs related with lung cancer were consistent in serum and lung of mice. The target genes of 13 deregulated miRNAs including CRK, NR2F2, VIM, RASSF1, CCND2, PRKCA, SIRT1, CDK6, MAP3K7, HIF1A, UBE2V2, ATG10, BAX, E2F1, RASSF5 and CTNNB1, could involve in the pathway of lung cancer developing. Compared with the FA group, the significantly increases of histopathological changes, ROS and DNA damage were observed in lung of mice in CA group. Our study suggested that miRNAs in serum could be identified as candidate biomarkers to predict the lung cancer development during early PM2.5 exposure.
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Affiliation(s)
- Jie Ning
- Department of Toxicology, School of Public Health, Hebei Medical University, Shijiazhuang, 050017, PR China
| | - Peiyuan Li
- Department of Toxicology, School of Public Health, Hebei Medical University, Shijiazhuang, 050017, PR China
| | - Boyuan Zhang
- Department of Toxicology, School of Public Health, Hebei Medical University, Shijiazhuang, 050017, PR China
| | - Bin Han
- Department of Toxicology, School of Public Health, Hebei Medical University, Shijiazhuang, 050017, PR China
| | - Xuan Su
- Department of Toxicology, School of Public Health, Hebei Medical University, Shijiazhuang, 050017, PR China
| | - Qian Wang
- Experimental Center, School of Public Health, Hebei Medical University, Shijiazhuang, 050017, PR China
| | - Xiurong Wang
- Department of Immunology, School of Basic Medicine, Hebei Medical University, Shijiazhuang, 050017, PR China
| | - Binghua Li
- Department of Occupation Health and Environmental Health, School of Public Health, Hebei Medical University, Shijiazhuang, 050051, PR China
| | - Hui Kang
- Department of Occupation Health and Environmental Health, School of Public Health, Hebei Medical University, Shijiazhuang, 050051, PR China
| | - Lixiao Zhou
- Department of Toxicology, School of Public Health, Hebei Medical University, Shijiazhuang, 050017, PR China
| | - Chen Chu
- Department of Toxicology, School of Public Health, Hebei Medical University, Shijiazhuang, 050017, PR China
| | - Ning Zhang
- Department of Toxicology, School of Public Health, Hebei Medical University, Shijiazhuang, 050017, PR China
| | - Yaxian Pang
- Department of Toxicology, School of Public Health, Hebei Medical University, Shijiazhuang, 050017, PR China
| | - Yujie Niu
- Department of Occupation Health and Environmental Health, School of Public Health, Hebei Medical University, Shijiazhuang, 050051, PR China; Hebei Key Laboratory of Environment and Human Health, Shijiazhuang, 050017, PR China
| | - Rong Zhang
- Department of Toxicology, School of Public Health, Hebei Medical University, Shijiazhuang, 050017, PR China; Hebei Key Laboratory of Environment and Human Health, Shijiazhuang, 050017, PR China.
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Role of cell free microRNA-19a and microRNA-19b in gestational diabetes mellitus patients. 3 Biotech 2019; 9:406. [PMID: 31687318 DOI: 10.1007/s13205-019-1952-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 10/11/2019] [Indexed: 10/25/2022] Open
Abstract
Gestational diabetes mellitus (GDM) is associated with adverse pregnancy outcomes in pregnant women and it's prevalence is increasing worldwide. A total 100 cases of GDM and 100 healthy controls were included in a study and blood samples were collected in plain vials from all study participant. Difference among several variables which included BMI, glycemia, insulinaemia, HbA1c, total cholesterol, triglycerides, urinary albumin were compared between GDM cases and controls and were found to be statistically significant (p < 0.0001). Additionally, GDM cases showed 4.0 fold increase in miRNA-19a and 4.7 mean increase in miRNA-19b expression compared to healthy control individuals. A positive correlation was observed between miRNA-19a and miRNA-19b among GDM cases. However the correlation coefficient was 0.13 between miRNA-19a and miRNA-19b. This suggested that with the increase in miRNA-19a, miRNA-19b also increased. The findings of this study concludes that an increase in microRNA-19a and microRNA-19b is observed in GDM cases and could be linked with increased risk factor for worsening of the disease. MicroRNA-19a and 19b have been linked to alcoholism and smoking and could also be the factors in GDM.
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40
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Meistertzheim M, Fehlmann T, Drews F, Pirritano M, Gasparoni G, Keller A, Simon M. Comparative Analysis of Biochemical Biases by Ligation- and Template-Switch-Based Small RNA Library Preparation Protocols. Clin Chem 2019; 65:1581-1591. [PMID: 31645340 DOI: 10.1373/clinchem.2019.305045] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Accepted: 09/18/2019] [Indexed: 01/06/2023]
Abstract
BACKGROUND Small RNAs are key players in the regulation of gene expression and differentiation. However, many different classes of small RNAs (sRNAs) have been described with distinct biogenesis pathways and, as a result, with different biochemical properties. To analyze sRNAs by deep sequencing, complementary DNA synthesis requires manipulation of the RNA molecule itself. Thus, enzymatic activities during library preparation bias the library content owing to biochemical criteria. METHODS We compared 4 different manipulations of RNA for library preparation: (a) a ligation-based procedure allowing only 5'-mono-phosphorylated RNA to enter the library, (b) a ligation-based procedure allowing additional 5'-triphosphates and Cap structures, (c) a ligation-independent, template-switch-based library preparation, and (d) a template-switch-based library preparation allowing 3'-phosphorylated RNAs to enter the library. RESULTS Our data show large differences between ligation-dependent and ligation-independent libraries in terms of their preference for individual sRNA classes such as microRNAs (miRNAs), Piwi-interacting RNAs (piRNAs), and transfer RNA fragments. Moreover, the miRNA composition is different between both procedures, and more microRNA isoforms (isomiRs) can be identified after pyrophosphatase treatment. piRNAs are enriched in template-switch libraries, and this procedure apparently includes more different RNA species. CONCLUSIONS Our data indicate that miRNAomics from both methods will hardly be comparable. Ligation-based libraries enrich for canonical miRNAs, which thus may be suitable methods for miRNAomics. Template-switch libraries contain increased numbers and different compositions of fragments and long RNAs. Following different interests for other small RNA species, ligation-independent libraries appear to show a more realistic sRNA landscape with lower bias against biochemical modifications.
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Affiliation(s)
- Morgane Meistertzheim
- Molecular Cell Dynamics, Centre for Human and Molecular Biology, Saarland University, Saarbruecken, Germany
| | - Tobias Fehlmann
- Clinical Bioinformatics, Center for Bioinformatics, Saarland University, Saarbruecken, Germany
| | - Franziska Drews
- Molecular Cell Dynamics, Centre for Human and Molecular Biology, Saarland University, Saarbruecken, Germany.,Molecular Cell Biology and Microbiology, Wuppertal University, Wuppertal, Germany
| | - Marcello Pirritano
- Molecular Cell Dynamics, Centre for Human and Molecular Biology, Saarland University, Saarbruecken, Germany.,Molecular Cell Biology and Microbiology, Wuppertal University, Wuppertal, Germany
| | - Gilles Gasparoni
- Epigenetics, Centre for Human and Molecular Biology, Saarland University, Saarbruecken, Germany
| | - Andreas Keller
- Clinical Bioinformatics, Center for Bioinformatics, Saarland University, Saarbruecken, Germany
| | - Martin Simon
- Molecular Cell Dynamics, Centre for Human and Molecular Biology, Saarland University, Saarbruecken, Germany; .,Molecular Cell Biology and Microbiology, Wuppertal University, Wuppertal, Germany
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41
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Current Evidence on Potential Uses of MicroRNA Biomarkers for Migraine: From Diagnosis to Treatment. Mol Diagn Ther 2019; 23:681-694. [DOI: 10.1007/s40291-019-00428-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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42
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Chen L, Heikkinen L, Wang C, Yang Y, Sun H, Wong G. Trends in the development of miRNA bioinformatics tools. Brief Bioinform 2019; 20:1836-1852. [PMID: 29982332 PMCID: PMC7414524 DOI: 10.1093/bib/bby054] [Citation(s) in RCA: 344] [Impact Index Per Article: 68.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 05/18/2018] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression via recognition of cognate sequences and interference of transcriptional, translational or epigenetic processes. Bioinformatics tools developed for miRNA study include those for miRNA prediction and discovery, structure, analysis and target prediction. We manually curated 95 review papers and ∼1000 miRNA bioinformatics tools published since 2003. We classified and ranked them based on citation number or PageRank score, and then performed network analysis and text mining (TM) to study the miRNA tools development trends. Five key trends were observed: (1) miRNA identification and target prediction have been hot spots in the past decade; (2) manual curation and TM are the main methods for collecting miRNA knowledge from literature; (3) most early tools are well maintained and widely used; (4) classic machine learning methods retain their utility; however, novel ones have begun to emerge; (5) disease-associated miRNA tools are emerging. Our analysis yields significant insight into the past development and future directions of miRNA tools.
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Affiliation(s)
- Liang Chen
- Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R, China
| | - Liisa Heikkinen
- Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R, China
| | - Changliang Wang
- Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R, China
| | - Yang Yang
- Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R, China
| | - Huiyan Sun
- Key Laboratory of Symbolic Computation and Knowledge Engineering of the Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, China
| | - Garry Wong
- Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R, China
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43
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Ries J, Baran C, Wehrhan F, Weber M, Motel C, Kesting M, Nkenke E. The altered expression levels of miR-186, miR-494 and miR-3651 in OSCC tissue vary from those of the whole blood of OSCC patients. Cancer Biomark 2019; 24:19-30. [DOI: 10.3233/cbm-180032] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Jutta Ries
- Department of Oral and Maxillofacial Surgery, Erlangen University Hospital, Erlangen 91054, Germany
| | - Christoph Baran
- Department of Oral and Maxillofacial Surgery, Erlangen University Hospital, Erlangen 91054, Germany
| | - Falk Wehrhan
- Department of Oral and Maxillofacial Surgery, Erlangen University Hospital, Erlangen 91054, Germany
| | - Manuel Weber
- Department of Oral and Maxillofacial Surgery, Erlangen University Hospital, Erlangen 91054, Germany
| | - Constantin Motel
- Department of Prosthodontics, Erlangen University Hospital, Erlangen 91054, Germany
| | - Marco Kesting
- Department of Oral and Maxillofacial Surgery, Erlangen University Hospital, Erlangen 91054, Germany
| | - Emeka Nkenke
- Department of Oral and Maxillofacial Surgery, Medical University of Vienna, Vienna 1090, Austria
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44
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Bär C, Thum T, de Gonzalo-Calvo D. Circulating miRNAs as mediators in cell-to-cell communication. Epigenomics 2019; 11:111-113. [PMID: 30638052 DOI: 10.2217/epi-2018-0183] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Christian Bär
- Institute of Molecular & Translational Therapeutic Strategies (IMTTS), Hannover Medical School, 30625, Hannover, Germany
| | - Thomas Thum
- Institute of Molecular & Translational Therapeutic Strategies (IMTTS), Hannover Medical School, 30625, Hannover, Germany.,National Heart & Lung Institute, Imperial College London, London, SW7 2AZ, UK
| | - David de Gonzalo-Calvo
- Institute of Molecular & Translational Therapeutic Strategies (IMTTS), Hannover Medical School, 30625, Hannover, Germany.,Institute of Biomedical Research of Barcelona (IIBB) - Spanish National Research Council (CSIC), 08036, Barcelona, Spain.,CIBERCV, Institute of Health Carlos III, 28029, Madrid, Spain.,Biomedical Research Institute Sant Pau (IIB Sant Pau), 08025, Barcelona, Spain
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45
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Fadaka AO, Pretorius A, Klein A. Biomarkers for Stratification in Colorectal Cancer: MicroRNAs. Cancer Control 2019; 26:1073274819862784. [PMID: 31431043 PMCID: PMC6704426 DOI: 10.1177/1073274819862784] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 06/08/2019] [Accepted: 06/13/2019] [Indexed: 12/18/2022] Open
Abstract
Colorectal cancer (CRC) is one of the most widely recognized and deadly malignancies worldwide. In spite of the fact that the death rates have declined over the previous decade, particularly because of enhanced screening or potential treatment alternatives, CRC still remains the third leading cause of cancer-related mortality in the world, with an estimated incidence of over 1 million new cases and approximately 600 000 deaths estimated yearly. Unlike prostate and lung cancer, CRC is not easily detectable in its early stage, which may also account for its high mortality rate. MicroRNAs (miRNAs) are a class of noncoding RNAs. The roles of these noncoding RNAs have been implicated in cancer pathogenesis, most especially CRC, due to their ability to posttranscriptionally regulate the expression of oncogenes and tumor suppressor genes. Dysregulated expression of many miRNAs regulates the expression of hundreds of growth regulatory genes and pathways that are important in the multistep model of colorectal carcinogenesis. If CRC is detected early, it is a largely treatable disease. Early diagnosis, including the identification of premalignant adenomas, is regarded a major concept for improving patient survival in CRC treatment. Several lines of research suggest that miRNAs are closely implicated in the metastatic process in CRC and some of these miRNAs could be useful as promising clinical tools for identifying specific stages of CRC due to their differential expression. This review discusses the correlation between CRC staging relative to the specific expression of miRNA for early detection, treatment, and disease management.
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Affiliation(s)
- Adewale Oluwaseun Fadaka
- Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Cape Town, South Africa
| | - Ashley Pretorius
- Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Cape Town, South Africa
| | - Ashwil Klein
- Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Cape Town, South Africa
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46
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Fehlmann T, Laufer T, Backes C, Kahramann M, Alles J, Fischer U, Minet M, Ludwig N, Kern F, Kehl T, Galata V, Düsterloh A, Schrörs H, Kohlhaas J, Bals R, Huwer H, Geffers L, Krüger R, Balling R, Lenhof HP, Meese E, Keller A. Large-scale validation of miRNAs by disease association, evolutionary conservation and pathway activity. RNA Biol 2018; 16:93-103. [PMID: 30567465 DOI: 10.1080/15476286.2018.1559689] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The validation of microRNAs (miRNAs) identified by next generation sequencing involves amplification-free and hybridization-based detection of transcripts as criteria for confirming valid miRNAs. Since respective validation is frequently not performed, miRNA repositories likely still contain a substantial fraction of false positive candidates while true miRNAs are not stored in the repositories yet. Especially if downstream analyses are performed with these candidates (e.g. target or pathway prediction), the results may be misleading. In the present study, we evaluated 558 mature miRNAs from miRBase and 1,709 miRNA candidates from next generation sequencing experiments by amplification-free hybridization and investigated their distributions in patients with various disease conditions. Notably, the most significant miRNAs in diseases are often not contained in the miRBase. However, these candidates are evolutionary highly conserved. From the expression patterns, target gene and pathway analyses and evolutionary conservation analyses, we were able to shed light on the complexity of miRNAs in humans. Our data also highlight that a more thorough validation of miRNAs identified by next generation sequencing is required. The results are available in miRCarta ( https://mircarta.cs.uni-saarland.de ).
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Affiliation(s)
- Tobias Fehlmann
- a Chair for Clinical Bioinformatics , Saarland University , Saarbrücken , Germany
| | - Thomas Laufer
- b Department of Human Genetics , Saarland University , Homburg , Germany.,c Hummingbird Diagnostics GmbH , Heidelberg , Germany
| | - Christina Backes
- a Chair for Clinical Bioinformatics , Saarland University , Saarbrücken , Germany
| | - Mustafa Kahramann
- a Chair for Clinical Bioinformatics , Saarland University , Saarbrücken , Germany.,c Hummingbird Diagnostics GmbH , Heidelberg , Germany
| | - Julia Alles
- b Department of Human Genetics , Saarland University , Homburg , Germany
| | - Ulrike Fischer
- b Department of Human Genetics , Saarland University , Homburg , Germany
| | - Marie Minet
- a Chair for Clinical Bioinformatics , Saarland University , Saarbrücken , Germany.,b Department of Human Genetics , Saarland University , Homburg , Germany
| | - Nicole Ludwig
- b Department of Human Genetics , Saarland University , Homburg , Germany
| | - Fabian Kern
- a Chair for Clinical Bioinformatics , Saarland University , Saarbrücken , Germany
| | - Tim Kehl
- d Center for Bioinformatics , Saarland Informatics Campus , Saarbrücken , Germany
| | - Valentina Galata
- a Chair for Clinical Bioinformatics , Saarland University , Saarbrücken , Germany
| | | | | | | | - Robert Bals
- e Department of Internal Medicine V - Pulmonology, Allergology, Intensive Care Medicine , Saarland University Hospital , Homburg , Germany
| | - Hanno Huwer
- f Department of Thoracic Surgery , SHG Clinics , Völklingen , Germany
| | - Lars Geffers
- g LCSB, Luxembourg Centre for Systems Biomedicine , University of Luxembourg , Esch-Sur-Alzette , Luxembourg
| | - Rejko Krüger
- g LCSB, Luxembourg Centre for Systems Biomedicine , University of Luxembourg , Esch-Sur-Alzette , Luxembourg
| | - Rudi Balling
- g LCSB, Luxembourg Centre for Systems Biomedicine , University of Luxembourg , Esch-Sur-Alzette , Luxembourg
| | - Hans-Peter Lenhof
- d Center for Bioinformatics , Saarland Informatics Campus , Saarbrücken , Germany
| | - Eckart Meese
- b Department of Human Genetics , Saarland University , Homburg , Germany
| | - Andreas Keller
- a Chair for Clinical Bioinformatics , Saarland University , Saarbrücken , Germany.,d Center for Bioinformatics , Saarland Informatics Campus , Saarbrücken , Germany
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47
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Papa L, Slobounov SM, Breiter HC, Walter A, Bream T, Seidenberg P, Bailes JE, Bravo S, Johnson B, Kaufman D, Molfese DL, Talavage TM, Zhu DC, Knollmann-Ritschel B, Bhomia M. Elevations in MicroRNA Biomarkers in Serum Are Associated with Measures of Concussion, Neurocognitive Function, and Subconcussive Trauma over a Single National Collegiate Athletic Association Division I Season in Collegiate Football Players. J Neurotrauma 2018; 36:1343-1351. [PMID: 30343622 DOI: 10.1089/neu.2018.6072] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
This prospective controlled observational cohort study assessed the performance of a novel panel of serum microRNA (miRNA) biomarkers on indicators of concussion, subconcussive impacts, and neurocognitive function in collegiate football players over the playing season. Male collegiate student football athletes participating in a Division I Football Bowl Subdivision of the National Collegiate Athletic Association (NCAA) were enrolled. There were a total of 53 participants included in the study, 30 non-athlete control subjects and 23 male collegiate student football athletes. Neurocognitive assessments and blood samples were taken within the week before the athletic season began and within the week after the last game of the season and measured for a panel of pre-selected miRNA biomarkers. All the athletes had elevated levels of circulating miRNAs at the beginning of the season compared with control subjects (p < 0.001). Athletes with the lowest standard assessment of concussion (SAC) scores at the beginning of the season had the highest levels of miRNAs. The area under the curve (AUC) for predicting pre-season SAC scores were miR-195 (0.90), miR-20a (0.89), miR-151-5p (0.86), miR-505* (0.85), miR-9-3p (0.77), and miR-362-3p (0.76). In athletes with declining neurocognitive function over the season, concentrations of miRNAs increased over same period. There were significant negative correlations with miR-505* (p = 0.011), miR-30d (p = 0.007), miR-92 (p = 0.033), and (p = 0.008). The miRNAs correlating with balance problems were miR-505* (p = 0.007), miR-30d (p = 0.028), and miR-151-5p (p = 0.023). Those correlating with poor reaction times were miR-20a (0.043), miR-505* (p = 0.049), miR-30d (p = 0.031), miR-92 (p = 0.015), and miR-151-5p (p = 0.044). Select miRNAs were associated with baseline concussion assessments at the beginning of the season and with neurocognitive changes from pre to post-season in collegiate football players. Should these findings be replicated in a larger cohort of athletes, these markers could potentially serve as measures of neurocognitive status in athletes at risk for concussion and subconcussive injuries.
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Affiliation(s)
- Linda Papa
- 1 Department of Emergency Medicine, Orlando Regional Medical Center, Orlando, Florida.,2 Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
| | - Semyon M Slobounov
- 3 Department of Kinesiology, Pennsylvania State University, University Park, Pennsylvania
| | - Hans C Breiter
- 4 Department of Psychiatry and Behavioral Sciences, Warren Wright Adolescent Center, Northwestern University, Chicago, Illinois
| | - Alexa Walter
- 3 Department of Kinesiology, Pennsylvania State University, University Park, Pennsylvania
| | - Tim Bream
- 5 Athletic Department, Pennsylvania State University, University Park, Pennsylvania
| | - Peter Seidenberg
- 6 Department of Orthopaedics and Rehabilitation, Penn State College of Medicine, University Park, Pennsylvania.,7 Department of Family and Community Medicine, Penn State College of Medicine, University Park, Pennsylvania
| | - Julian E Bailes
- 8 Department of Neurosurgery, Northshore University Health System, University of Chicago Pritzker School of Medicine, Chicago, Illinois
| | | | - Brian Johnson
- 3 Department of Kinesiology, Pennsylvania State University, University Park, Pennsylvania
| | - David Kaufman
- 10 Department of Neurology and Ophthalmology, Michigan State University, East Lansing, Michigan
| | - Dennis L Molfese
- 11 Department of Psychology, University of Nebraska-Lincoln, Lincoln, Nebraska
| | - Thomas M Talavage
- 12 School of Electrical and Computer Engineering, Purdue University, West Lafayette, Indiana
| | - David C Zhu
- 13 Department of Radiology and Psychology, Michigan State University, East Lansing, Michigan
| | | | - Manish Bhomia
- 14 Department of Pathology, Uniformed Services University of the Health Sciences, Bethesda, Maryland
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48
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Zhao C, Tolkach Y, Schmidt D, Muders M, Kristiansen G, Müller SC, Ellinger J. tRNA-halves are prognostic biomarkers for patients with prostate cancer. Urol Oncol 2018; 36:503.e1-503.e7. [DOI: 10.1016/j.urolonc.2018.08.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 07/05/2018] [Accepted: 08/04/2018] [Indexed: 01/25/2023]
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49
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Pirritano M, Fehlmann T, Laufer T, Ludwig N, Gasparoni G, Li Y, Meese E, Keller A, Simon M. Next Generation Sequencing Analysis of Total Small Noncoding RNAs from Low Input RNA from Dried Blood Sampling. Anal Chem 2018; 90:11791-11796. [DOI: 10.1021/acs.analchem.8b03557] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Marcello Pirritano
- Molecular Cell Dynamics, Centre for Human and Molecular Biology, Campus A2.4, Saarland University, 66123 Saarbrücken, Germany
- Molecular Cell Biology and Microbiology, Wuppertal University, Building V12.070, 42097 Wuppertal, Germany
| | - Tobias Fehlmann
- Clinical Bioinformatics, Center for Bioinformatics, Campus E2.1, Saarland University, 66123 Saarbruecken, Germany
| | - Thomas Laufer
- Institute of Human Genetics, Medical School, Saarland University, Building 60, 66421 Homburg Germany
- Hummingbird Diagnostics GmbH, Im Neuenheimer Feld 583, 69120 Heidelberg, Germany
| | - Nicole Ludwig
- Institute of Human Genetics, Medical School, Saarland University, Building 60, 66421 Homburg Germany
| | - Gilles Gasparoni
- Epigenetics, Centere for Human and Molecular Biology, Campus A2.4, Saarland University, 66123 Saarbruecken, Germany
| | - Yongping Li
- Clinical Bioinformatics, Center for Bioinformatics, Campus E2.1, Saarland University, 66123 Saarbruecken, Germany
- BGI, Building No.7, BGI Park, No.12 Hongan Third Street, Yantian District, Shenzhen, 518083 China
| | - Eckart Meese
- Institute of Human Genetics, Medical School, Saarland University, Building 60, 66421 Homburg Germany
| | - Andreas Keller
- Clinical Bioinformatics, Center for Bioinformatics, Campus E2.1, Saarland University, 66123 Saarbruecken, Germany
- Hummingbird Diagnostics GmbH, Im Neuenheimer Feld 583, 69120 Heidelberg, Germany
| | - Martin Simon
- Molecular Cell Dynamics, Centre for Human and Molecular Biology, Campus A2.4, Saarland University, 66123 Saarbrücken, Germany
- Molecular Cell Biology and Microbiology, Wuppertal University, Building V12.070, 42097 Wuppertal, Germany
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50
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MicroRNA in diagnosis and therapy monitoring of early-stage triple-negative breast cancer. Sci Rep 2018; 8:11584. [PMID: 30072748 PMCID: PMC6072710 DOI: 10.1038/s41598-018-29917-2] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 07/09/2018] [Indexed: 11/12/2022] Open
Abstract
Breast cancer is a heterogeneous disease with distinct molecular subtypes including the aggressive subtype triple-negative breast cancer (TNBC). We compared blood-borne miRNA signatures of early-stage basal-like (cytokeratin-CK5-positive) TNBC patients to age-matched controls. The miRNAs of TNBC patients were assessed prior to and following platinum-based neoadjuvant chemotherapy (NCT). After an exploratory genome-wide study on 21 cases and 21 controls using microarrays, the identified signatures were verified independently in two laboratories on the same and a new cohort by RT-qPCR. We differentiated the blood of TNBC patients before NCT from controls with 84% sensitivity. The most significant miRNA for this diagnostic classification was miR-126-5p (two tailed t-test p-value of 1.4 × 10−5). Validation confirmed the microarray results for all tested miRNAs. Comparing cancer patients prior to and post NCT highlighted 321 significant miRNAs (among them miR-34a, p-value of 1.2 × 10−23). Our results also suggest that changes in miRNA expression during NCT may have predictive potential to predict pathological complete response (pCR). In conclusion we report that miRNA expression measured from blood facilitates early and minimally-invasive diagnosis of basal-like TNBC. We also demonstrate that NCT has a significant influence on miRNA expression. Finally, we show that blood-borne miRNA profiles monitored over time have potential to predict pCR.
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