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Turkoglu F, Calisir A, Ozturk B. Clinical importance of serum miRNA levels in breast cancer patients. Discov Oncol 2024; 15:19. [PMID: 38280134 PMCID: PMC10821853 DOI: 10.1007/s12672-024-00871-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 01/21/2024] [Indexed: 01/29/2024] Open
Abstract
There is limited data on the relationship of miRNAs with parameters that may affect surgical management or reflect tumour prognosis. It was aimed to evaluate serum miRNA levels in breast carcinoma cases and reveal the relationship between these levels and prognosis-related factors such as the histological type of the tumour, estrogen receptor, progesterone receptor, Ki-67 index, HER-2neu, E-cadherin, tumour size, CK5/6, CA15.3 levels, number of tumour foci, number of metastatic lymph nodes, and status of receiving neoadjuvant therapy. Thirty-five patients with a histopathologically confirmed breast carcinoma diagnosis in the case group and 35 healthy individuals in the control group were examined. miR-206, miR-17-5p, miR-125a, miR-125b, miR-200a, Let-7a, miR-34a, miR-31, miR-21, miR-155, miR-10b, miR-373, miR-520c, miR-210, miR-145, miR-139-5p, miR-195, miR-99a, miR-497 and miR-205 expression levels in the serum of participants were determined using the Polymerase Chain Reaction method. While serum miR-125b and Let-7a expression levels were significantly higher in breast cancer patients, miR-17-5p, miR-125a, miR-200a, miR-34a, miR-21, miR-99a and miR-497 levels were significantly lower in them. The Let-7a expression level had a statistically significant relationship with breast cancer histological type and HER-2neu parameters, miR-17-5p, miR-125b, Let-7a, miR-34a, miR-21 and miR-99a levels with E-cadherin, miR-34a, miR-99a and miR-497 with CA15.3, miR-125b, miR-200a and miR-34a with the number of metastatic lymph nodes, miR-125a with the number of tumour foci and miR-200a with the status of having the neoadjuvant therapy. Serum miR-17-5p, miR-125a, miR-125b, miR-200a, Let-7a, miR-34a, miR-21, miR-99a and miR-497 expression levels were determined to have predictive and prognostic importance in breast cancer.
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Affiliation(s)
- Fatih Turkoglu
- Department of General Surgery, Faculty of Medicine, Selcuk University, Akademi Mahallesi Yeni İstanbul Caddesi No:313, Selçuk Üniversitesi Alaeddin Keykubat Yerleşkesi, Selçuklu, Konya, 42130, Turkey.
| | - Akin Calisir
- Department of General Surgery, Faculty of Medicine, Selcuk University, Akademi Mahallesi Yeni İstanbul Caddesi No:313, Selçuk Üniversitesi Alaeddin Keykubat Yerleşkesi, Selçuklu, Konya, 42130, Turkey
| | - Bahadir Ozturk
- Department of Biochemistry, Faculty of Medicine, Selcuk University, Konya, Turkey
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2
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John MC, Quinn J, Hu ML, Cehajic-Kapetanovic J, Xue K. Gene-agnostic therapeutic approaches for inherited retinal degenerations. Front Mol Neurosci 2023; 15:1068185. [PMID: 36710928 PMCID: PMC9881597 DOI: 10.3389/fnmol.2022.1068185] [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: 10/12/2022] [Accepted: 12/12/2022] [Indexed: 01/11/2023] Open
Abstract
Inherited retinal diseases (IRDs) are associated with mutations in over 250 genes and represent a major cause of irreversible blindness worldwide. While gene augmentation or gene editing therapies could address the underlying genetic mutations in a small subset of patients, their utility remains limited by the great genetic heterogeneity of IRDs and the costs of developing individualised therapies. Gene-agnostic therapeutic approaches target common pathogenic pathways that drive retinal degeneration or provide functional rescue of vision independent of the genetic cause, thus offering potential clinical benefits to all IRD patients. Here, we review the key gene-agnostic approaches, including retinal cell reprogramming and replacement, neurotrophic support, immune modulation and optogenetics. The relative benefits and limitations of these strategies and the timing of clinical interventions are discussed.
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Affiliation(s)
- Molly C. John
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | - Joel Quinn
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | - Monica L. Hu
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | - Jasmina Cehajic-Kapetanovic
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Kanmin Xue
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
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3
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Ali Ahmed E, Abd El-Basit SA, Mohamed MA, Swellam M. Clinical role of MiRNA 29a and MiRNA 335 on breast cancer management: their relevance to MMP2 protein level. Arch Physiol Biochem 2022; 128:1058-1065. [PMID: 32267166 DOI: 10.1080/13813455.2020.1749085] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
BACKGROUND Circulating miRNAs are novel biomarkers, authors aimed to investigate the expression level of miR-29a and miR-335 and their relevance to CEA, CA15.3, and matrix metalloproteinase-2 (MMP2). MATERIALS AND METHODS Breast cancer (BC) patients (n = 44), benign breast lesion patients (n = 25), and healthy individuals (n = 19) were enrolled for detection of miRNA expression levels, MMP2 and biochemical markers using quantitative polymerase chain reaction (PCR) and ELISA, respectively. RESULTS Expression of miR-29a and miR-335 were significantly decreased in breast patients as compared to healthy individuals, while biochemical markers were high in BC patients as compared to the other two groups. The diagnostic efficacy for miR-29a, miR-335, and MMP2 were superior to both CEA and CA 15.3 for early detection of BC patients. CONCLUSIONS Detection of the miR-29a and miR335 expression levels in serum samples are significant promising biomarkers for BC diagnosis.
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Affiliation(s)
- Elham Ali Ahmed
- Zoology Department, Faculty of Science (Girls), Al-Azhar University, Cairo, Egypt
| | - Sohir A Abd El-Basit
- Zoology Department, Faculty of Science (Girls), Al-Azhar University, Cairo, Egypt
| | - Mona A Mohamed
- Biochemistry Division, Chemistry Department, Faculty of Science (Girls), Al-Azhar University, Cairo, Egypt
| | - Menha Swellam
- Biochemistry Department, Genetic Engineering and Biotechnology Research Division, Giza, Egypt
- High Throughput Molecular and Genetic Laboratory, Center for Excellences for Advanced Sciences, National Research Centre, Giza, Egypt
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4
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Electroacupuncture Alleviates Neuropathic Pain through Regulating miR-206-3p Targeting BDNF after CCI. Neural Plast 2022; 2022:1489841. [PMID: 35719137 PMCID: PMC9203241 DOI: 10.1155/2022/1489841] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 04/27/2022] [Indexed: 12/03/2022] Open
Abstract
Background Electroacupuncture (EA) has benefits for neuropathic pain. However, the underlying mechanisms are still unknown. The current study explores the underlying mechanisms of EA in neuropathic pain of chronic constriction injury (CCI) rats. Material/Methods. Overall, 126 Sprague-Dawley (200-250 g) rats were divided into nine groups randomly: the sham-operated, CCI, CCI+EA, CCI+sham EA, CCI+NS, CCI+AAV-NC, CCI+AAV-miR-206-3p, CCI+EA+NS, and CCI+EA+AAV-miR-206-3p groups. The animals were sacrificed 14 days postsurgery. Mechanical withdrawal threshold (MWT) and thermal withdrawal latency (TWL) tests were used to determine differences in neurobehavioral manifestations. qPCR, western blotting, and immunofluorescence (IF) were carried out to detect the expression levels of miR-206-3p, BDNF, BAX/Bcl-2, TNF-α, and IL-6. Nissl staining was measured to observe morphological changes in neurons. Transmission electron microscopy (TEM) was employed to evaluate microscopic changes in dorsal horn synapses. Results Hyperalgesia was reduced markedly by EA in the CCI model. The expression level of miR-206-3p was elevated, whereas the expression levels of BDNF, BAX/Bcl-2, TNF-α, and IL-6 were decreased in EA-treated CCI rats. However, a miR-206-3p inhibitor partially abrogated the analgesic effect of EA and resulted in poor behavioral performance and the BDNF, BAX/Bcl-2, TNF-α, and IL-6 expression was elevated as well. Conclusions EA can relieve neuropathic pain by regulating the miR-206-3p/BDNF pathway, thus exerting anti-inflammatory and antiapoptotic effect.
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Li X, Gong Y, Lin X, Lin Q, Luo J, Yu T, Xu J, Chen L, Xu L, Hu Y. Down-regulation of microRNA-155 suppressed Candida albicans induced acute lung injury by activating SOCS1 and inhibiting inflammation response. J Microbiol 2022; 60:402-410. [PMID: 35157222 PMCID: PMC8853013 DOI: 10.1007/s12275-022-1663-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/03/2022] [Accepted: 01/04/2022] [Indexed: 10/31/2022]
Abstract
Acute lung injury caused by Candida albicans could result in high mortality and morbidity. MicroRNA-155 (miR-155) and suppressor of cytokine signaling 1 (SOCS1) have been believed to play a key in the regulation of inflammatory response. Whether miR-155/SOCS1 axis could regulate the acute lung injury caused by C. albicans has not been reported. The acute lung injury animal model was established with acute infection of C. albicans. miR-155 inhibitor, miR-155 mimic, and sh-SOCS1 were constructed. The binding site between miR-155 and SOCS1 was identified with dual luciferase reporter assay. Knockdown of miR-155 markedly inhibited the germ tube formation of C. albicans. Knockdown of miR-155 significantly up-regulated the expression of SOCS1, and the binding site between miR-155 and SOCS1 was identified. Knockdown of miR-155 improved the acute lung injury, suppressed inflammatory factors and fungus loading through SOCS1. Knockdown of SOCS1 greatly reversed the influence of miR-155 inhibitor on the cell apoptosis in vitro. The improvement of acute lung injury caused by C. albicans, suppression of inflammatory response and C. albicans infection, and inhibitor of cell apoptosis were achieved by knocking down miR-155 through SOCS1. This research might provide a new thought for the prevention and treatment of acute lung injury caused by C. albicans through targeting miR-155/SOCS1 axis.
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Magdalena D, Magdalena G. Biological functions and diagnostic implications of microRNAs in Mycobacterium tuberculosis infection. Asian Pac J Trop Biomed 2022. [DOI: 10.4103/2221-1691.333208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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Smith NC, Umasuthan N, Kumar S, Woldemariam NT, Andreassen R, Christian SL, Rise ML. Transcriptome Profiling of Atlantic Salmon Adherent Head Kidney Leukocytes Reveals That Macrophages Are Selectively Enriched During Culture. Front Immunol 2021; 12:709910. [PMID: 34484211 PMCID: PMC8415484 DOI: 10.3389/fimmu.2021.709910] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 07/05/2021] [Indexed: 01/23/2023] Open
Abstract
The Atlantic salmon (Salmo salar) is an economically important fish, both in aquaculture and in the wild. In vertebrates, macrophages are some of the first cell types to respond to pathogen infection and disease. While macrophage biology has been characterized in mammals, less is known in fish. Our previous work identified changes in the morphology, phagocytic ability, and miRNA profile of Atlantic salmon adherent head kidney leukocytes (HKLs) from predominantly “monocyte-like” at Day 1 of in vitro culture to predominantly “macrophage-like” at Day 5 of culture. Therefore, to further characterize these two cell populations, we examined the mRNA transcriptome profile in Day 1 and Day 5 HKLs using a 44K oligonucleotide microarray. Large changes in the transcriptome were revealed, including changes in the expression of macrophage and immune-related transcripts (e.g. csf1r, arg1, tnfa, mx2), lipid-related transcripts (e.g. fasn, dhcr7, fabp6), and transcription factors involved in macrophage differentiation and function (e.g. klf2, klf9, irf7, irf8, stat1). The in silico target prediction analysis of differentially expressed genes (DEGs) using miRNAs known to change expression in Day 5 HKLs, followed by gene pathway enrichment analysis, supported that these miRNAs may be involved in macrophage maturation by targeting specific DEGs. Elucidating how immune cells, such as macrophages, develop and function is a key step in understanding the Atlantic salmon immune system. Overall, the results indicate that, without the addition of exogenous factors, the adherent HKL cell population differentiates in vitro to become macrophage-like.
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Affiliation(s)
- Nicole C Smith
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL, Canada
| | | | - Surendra Kumar
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Nardos T Woldemariam
- Department of Life Sciences and Health, OsloMet-Oslo Metropolitan University, Oslo, Norway
| | - Rune Andreassen
- Department of Life Sciences and Health, OsloMet-Oslo Metropolitan University, Oslo, Norway
| | - Sherri L Christian
- Department of Biochemistry, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Matthew L Rise
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL, Canada
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Desvignes T, Sydes J, Montfort J, Bobe J, Postlethwait JH. Evolution after Whole-Genome Duplication: Teleost MicroRNAs. Mol Biol Evol 2021; 38:3308-3331. [PMID: 33871629 PMCID: PMC8321539 DOI: 10.1093/molbev/msab105] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs (miRNAs) are important gene expression regulators implicated in many biological processes, but we lack a global understanding of how miRNA genes evolve and contribute to developmental canalization and phenotypic diversification. Whole-genome duplication events likely provide a substrate for species divergence and phenotypic change by increasing gene numbers and relaxing evolutionary pressures. To understand the consequences of genome duplication on miRNA evolution, we studied miRNA genes following the teleost genome duplication (TGD). Analysis of miRNA genes in four teleosts and in spotted gar, whose lineage diverged before the TGD, revealed that miRNA genes were retained in ohnologous pairs more frequently than protein-coding genes, and that gene losses occurred rapidly after the TGD. Genomic context influenced retention rates, with clustered miRNA genes retained more often than nonclustered miRNA genes and intergenic miRNA genes retained more frequently than intragenic miRNA genes, which often shared the evolutionary fate of their protein-coding host. Expression analyses revealed both conserved and divergent expression patterns across species in line with miRNA functions in phenotypic canalization and diversification, respectively. Finally, major strands of miRNA genes experienced stronger purifying selection, especially in their seeds and 3'-complementary regions, compared with minor strands, which nonetheless also displayed evolutionary features compatible with constrained function. This study provides the first genome-wide, multispecies analysis of the mechanisms influencing metazoan miRNA evolution after whole-genome duplication.
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Affiliation(s)
- Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA
| | - Jason Sydes
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA
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9
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Saleh AJ, Nothwang HG. Differential expression of microRNAs in the developing avian auditory hindbrain. J Comp Neurol 2021; 529:3477-3496. [PMID: 34180540 DOI: 10.1002/cne.25205] [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: 02/04/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 11/08/2022]
Abstract
The avian auditory hindbrain is a longstanding model for studying neural circuit development. Information on gene regulatory network (GRN) components underlying this process, however, is scarce. Recently, the spatiotemporal expression of 12 microRNAs (miRNAs) was investigated in the mammalian auditory hindbrain. As a comparative study, we here investigated the spatiotemporal expression of the orthologous miRNAs during development of the chicken auditory hindbrain. All miRNAs were expressed both at E13, an immature stage, and P14, a mature stage of the auditory system. In most auditory nuclei, a homogeneous expression pattern was observed at both stages, like the mammalian system. An exception was the nucleus magnocellularis (NM). There, at E13, nine miRNAs showed a differential expression pattern along the cochleotopic axis with high expression at the rostromedial pole. One of them showed a gradient expression whereas eight showed a spatially selective expression at the rostral pole that reflected the different rhombomeric origins of this composite nucleus. The miRNA differential expression persisted in the NM to the mature stage, with the selective expression changed to linear gradients. Bioinformatics analysis predicted mRNA targets that are associated with neuronal developmental processes such as neurite and synapse organization, calcium and ephrin-Eph signaling, and neurotransmission. Overall, this first analysis of miRNAs in the chicken central auditory system reveals shared and strikingly distinct features between chicken and murine orthologues. The embryonic gradient expression of these GRN elements in the NM adds miRNA patterns to the list of cochleotopic and developmental gradients in the central auditory system.
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Affiliation(s)
- Ali Jason Saleh
- Division of Neurogenetics and Cluster of Excellence Hearing4All, School of Medicine and Health Sciences, Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Hans Gerd Nothwang
- Division of Neurogenetics and Cluster of Excellence Hearing4All, School of Medicine and Health Sciences, Carl von Ossietzky University Oldenburg, Oldenburg, Germany.,Research Center for Neurosensory Science, Carl von Ossietzky University Oldenburg, Oldenburg, Germany
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10
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Marroquín-Flores RA, Bowden RM, Paitz RT. Brief exposure to warm temperatures reduces intron retention in Kdm6b in a species with temperature-dependent sex determination. Biol Lett 2021; 17:20210167. [PMID: 34102073 PMCID: PMC8187015 DOI: 10.1098/rsbl.2021.0167] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 05/13/2021] [Indexed: 12/14/2022] Open
Abstract
Animals with temperature-dependent sex determination (TSD) respond to thermal cues during early embryonic development to trigger gonadal differentiation. TSD has primarily been studied using constant temperature incubations, where embryos are exposed to constant male- or female-producing temperatures, and these studies have identified genes that display sex-specific expression in response to incubation temperature. Kdm6b, a histone demethylase gene, has received specific attention as it is among the initial genes to respond to incubation temperature and is necessary for testis development. Interestingly, Kdm6b retains an intron when eggs are incubated at a constant male-producing temperature, but the role of thermal variability in this developmental process is relatively understudied. Species with TSD regularly experience thermal cues that fluctuate between male- and female-producing temperatures throughout development but it is unclear how Kdm6b responds to such variable temperatures. In this study, we investigate temperature-sensitive splicing in Kdm6b by exposing embryos to male- and female-producing thermal conditions. We show a rapid decrease in levels of the intron retaining transcript of Kdm6b upon exposure to female-producing conditions. These results demonstrate that, under ecologically relevant conditions, temperature-sensitive splicing can differentially regulate genes critical to TSD.
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Affiliation(s)
| | - Rachel M. Bowden
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA
| | - Ryan T. Paitz
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA
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11
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Silencing lung cancer genes using miRNAs identified by 7mer-seed matching. Comput Biol Chem 2021; 92:107483. [PMID: 33932780 DOI: 10.1016/j.compbiolchem.2021.107483] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 03/19/2021] [Accepted: 04/03/2021] [Indexed: 12/20/2022]
Abstract
Lung cancer (LC) is the main cause of cancer-associated deaths in both men and women globally with a very high mortality rate. The microRNAs (miRNAs) are a class of noncoding RNAs consisting of 18-25 nucleotides. They inhibit translation of protein through binding to complementary target mRNAs. The non-coding miRNAs are recognized as potent biomarkers for detection, development and treatment of malignancy. In this study, we screened a set of 12 genes over expressed in small cell lung cancer, non small cell lung cancer and the genes involved in both categories and their binding sites for human miRNAs as no work was reported yet. Screening of human miRNAs revealed that a few genes showed numerous miRNA binding sites. Free energy values of mRNA sequences revealed that they might acquire compact folded structure causing complexity for miRNAs to interact. GC content in the target site was relatively higher than that of their flanks. It was observed through analysis of cosine similarity metric and compAI parameters that the genes related to lung cancer were encoded with non optimal codons and thus might be translationally less efficient for producing polypeptides. Gene ontology analysis was carried out to understand the diverse functions of these 12 genes.
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Wei C, Xiang S, Yu Y, Song J, Zheng M, Lian F. miR-221-3p regulates apoptosis of ovarian granulosa cells via targeting FOXO1 in older women with diminished ovarian reserve (DOR). Mol Reprod Dev 2021; 88:251-260. [PMID: 33694202 PMCID: PMC8251591 DOI: 10.1002/mrd.23457] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 01/28/2021] [Accepted: 01/31/2021] [Indexed: 12/13/2022]
Abstract
In our earlier study, we showed that the expression of microRNA‐221‐3p (miR‐221‐3p) was significantly lower in women of advanced age with diminished ovarian reserve (DOR) compared with young women with normal ovarian reserve (NOR). Therefore, in this study, we aimed to explore how miR‐221‐3p regulates apoptosis of granulosa cells and the pathogenesis of DOR. Bioinformatics prediction and dual‐luciferase reporter assay were conducted to identify the target gene of miR‐221‐3p. miR‐221‐3p expression was manipulated by transfecting KGN cells with miR‐221‐3p mimics, inhibitor, and negative control. Following transfection, apoptosis of granulosa cells was determined by flow cytometry, and the expression of the target gene was measured by quantitative real‐time polymerase chain reaction (qRT‐PCR) and western blot analysis (WB). In addition, the expression of the target gene in granulosa cells of DOR patients and NOR patients was measured. miR‐221‐3p were found to directly bind the 3ʹ untranslated region of Forkhead box O1 (FOXO1). Transfection with miR‐221‐3p mimics significantly decreased the apoptosis rate of KGN cells compared with transfection with miR‐221‐3p inhibitors. The expression level of miR‐221‐3p was negatively correlated with the messenger RNA and protein levels of the FOXO1 gene. Besides, FOXO1 expression was upregulated in DOR patients. In conclusion, these results provide evidence that downregulation of miR‐221‐3p expression promotes apoptosis of granulosa cells by upregulating FOXO1 expression, thus serving an important role in DOR pathogenesis.
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Affiliation(s)
- Chaofeng Wei
- Master of Gynecology in Traditional Chinese Medicine, College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Shan Xiang
- First College of Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Yi Yu
- Integrative Medicine Research Centre of Reproduction and Heredity, The Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Jingyan Song
- First College of Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Mingming Zheng
- First College of Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Fang Lian
- Integrative Medicine Research Centre of Reproduction and Heredity, The Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
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Wang P, Zhang Y, Wang Z, Yang A, Li Y, Zhang Q. miR-128 regulates epilepsy sensitivity in mice by suppressing SNAP-25 and SYT1 expression in the hippocampus. Biochem Biophys Res Commun 2021; 545:195-202. [PMID: 33571908 DOI: 10.1016/j.bbrc.2021.01.079] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 01/23/2021] [Indexed: 10/22/2022]
Abstract
Epilepsy is accompanied by abnormal neurotransmission, and microRNAs, as versatile players in the modulation of gene expression, are important in epilepsy pathology. Here, we found that miR-128 expression was elevated in the acute seizure phase and decreased during the recurrent seizure phase after status epilepticus in mice. Both SNAP-25 and SYT1 are regulated by miR-128 in vitro and in vivo. Overexpressing miR-128 in cultured neurons decreased neurotransmitter released by suppressing SNAP-25 and SYT1 expression. Anti-miR-128 injection before kainic acid (KA) injection increased the sensitivity of mice to KA-induced seizures, while overexpressing miR-128 at the latent and recurrent phases had a neuroprotective effect in KA-induced seizures. Our study shows for the first time that miR-128, a key regulator of neurotransmission, plays an important role in epilepsy pathology and that miR-128 might be a potential candidate molecular target for epilepsy therapy.
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Affiliation(s)
- Peng Wang
- Medical Center for Human Reproduction, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100069, PR China
| | - Yanchufei Zhang
- Nanjing Drum Tower Hospital Center of Molecular Diagnostic and Therapy, Institute for Brain Sciences, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute of Life Sciences (NAILS), School of Life Sciences, Nanjing University, Nanjing, 210046, China
| | - Zihui Wang
- Nanjing Drum Tower Hospital Center of Molecular Diagnostic and Therapy, Institute for Brain Sciences, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute of Life Sciences (NAILS), School of Life Sciences, Nanjing University, Nanjing, 210046, China
| | - Anyong Yang
- Nanjing Drum Tower Hospital Center of Molecular Diagnostic and Therapy, Institute for Brain Sciences, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute of Life Sciences (NAILS), School of Life Sciences, Nanjing University, Nanjing, 210046, China
| | - Yuting Li
- Nanjing Drum Tower Hospital Center of Molecular Diagnostic and Therapy, Institute for Brain Sciences, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute of Life Sciences (NAILS), School of Life Sciences, Nanjing University, Nanjing, 210046, China
| | - Qipeng Zhang
- Nanjing Drum Tower Hospital Center of Molecular Diagnostic and Therapy, Institute for Brain Sciences, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute of Life Sciences (NAILS), School of Life Sciences, Nanjing University, Nanjing, 210046, China.
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14
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Krohs C, Bordeynik-Cohen M, Messika-Gold N, Elkon R, Avraham KB, Nothwang HG. Expression pattern of cochlear microRNAs in the mammalian auditory hindbrain. Cell Tissue Res 2021; 383:655-666. [PMID: 33156384 PMCID: PMC7904729 DOI: 10.1007/s00441-020-03290-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 08/24/2020] [Indexed: 12/28/2022]
Abstract
The auditory system comprises the auditory periphery, engaged in sound transduction and the central auditory system, implicated in auditory information processing and perception. Recently, evidence mounted that the mammalian peripheral and central auditory systems share a number of genes critical for proper development and function. This bears implication for auditory rehabilitation and evolution of the auditory system. To analyze to which extent microRNAs (miRNAs) belong to genes shared between both systems, we characterize the expression pattern of 12 cochlea-abundant miRNAs in the central auditory system. Quantitative real-time PCR (qRT-PCR) demonstrated expression of all 12 genes in the cochlea, the auditory hindbrain and the non-auditory prefrontal cortex (PFC) at embryonic stage (E)16 and postnatal stages (P)0 and P30. Eleven of them showed differences in expression between tissues and nine between the developmental time points. Hierarchical cluster analysis revealed that the temporal expression pattern in the auditory hindbrain was more similar to the PFC than to the cochlea. Spatiotemporal expression analysis by RNA in situ hybridization demonstrated widespread expression throughout the cochlear nucleus complex (CNC) and the superior olivary complex (SOC) during postnatal development. Altogether, our data indicate that miRNAs represent a relevant class of genetic factors functioning across the auditory system. Given the importance of gene regulatory network (GRN) components for development, physiology and evolution, the 12 miRNAs provide promising entry points to gain insights into their molecular underpinnings in the auditory system.
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Affiliation(s)
- Constanze Krohs
- Neurogenetics Group and Cluster of Excellence Hearing4All, School of Medicine and Health Sciences, Carl Von Ossietzky University Oldenburg, 26111, Oldenburg, Germany
| | - Mor Bordeynik-Cohen
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Naama Messika-Gold
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Ran Elkon
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Karen B Avraham
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Hans Gerd Nothwang
- Neurogenetics Group and Cluster of Excellence Hearing4All, School of Medicine and Health Sciences, Carl Von Ossietzky University Oldenburg, 26111, Oldenburg, Germany.
- Research Center for Neurosensory Science, Carl Von Ossietzky University Oldenburg, 26111, Oldenburg, Germany.
- Department of Neuroscience, Center of Excellence Hearing4All, Carl Von Ossietzky University Oldenburg, 26111, Oldenburg, Germany.
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15
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Demircan T, Sibai M, Avşaroğlu ME, Altuntaş E, Ovezmyradov G. The first report on circulating microRNAs at Pre- and Post-metamorphic stages of axolotls. Gene 2020; 768:145258. [PMID: 33131713 DOI: 10.1016/j.gene.2020.145258] [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: 02/21/2020] [Revised: 10/01/2020] [Accepted: 10/20/2020] [Indexed: 02/07/2023]
Abstract
MicroRNAs (miRNAs) are endogenously coded small RNAs, implicated in post-transcriptional gene regulation by targeting messenger RNAs (mRNAs). Circulating miRNAs are cell-free molecules, found in body fluids, such as blood and saliva, and emerged recently as potential diagnostic biomarkers. Functions of circulating miRNAs and their roles in target tissues have been extensively investigated in mammals, and the reports on circulating miRNAs in non-mammalian clades are largely missing. Salamanders display remarkable regenerative potential, and the Mexican axolotl (Ambystoma mexicanum), a critically endangered aquatic salamander, has emerged as a powerful model organism in regeneration and developmental studies. This study aimed to explore the circulating miRNA signature in axolotl blood plasma. Small RNA sequencing on plasma samples revealed 16 differentially expressed (DE) circulating miRNAs between neotenic and metamorphic stages out of identified 164 conserved miRNAs. Bioinformatics predictions provided functional annotation of detected miRNAs for both stages and enrichment of DE miRNAs in cancer-related and developmental pathways was notable. Comparison with previous reports on axolotl miRNAs unraveled common and unique members of the axolotl circulating miRNome. Overall, this work provides novel insights into non-mammalian aspects of circulating miRNA biology and expands the multi-omics toolkit for this versatile model organism.
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Affiliation(s)
- Turan Demircan
- Department of Medical Biology, School of Medicine, Mugla Sitki Kocman University, Mugla, Turkey; Regenerative and Restorative Medicine Research Center, REMER, Istanbul Medipol University, Istanbul, Turkey.
| | - Mustafa Sibai
- Graduate School of Natural and Applied Sciences, Mugla Sitki Kocman University, Mugla, Turkey
| | - Mahmut Erhan Avşaroğlu
- Regenerative and Restorative Medicine Research Center, REMER, Istanbul Medipol University, Istanbul, Turkey
| | - Ebru Altuntaş
- Graduate School of Natural and Applied Sciences, Mugla Sitki Kocman University, Mugla, Turkey
| | - Guvanch Ovezmyradov
- Regenerative and Restorative Medicine Research Center, REMER, Istanbul Medipol University, Istanbul, Turkey; Department of Biostatistics and Medical Informatics, International School of Medicine, Istanbul Medipol University, Istanbul, Turkey
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16
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Yan Y, Zhang K, Zhou G, Hu W. MicroRNAs Responding to Space Radiation. Int J Mol Sci 2020; 21:ijms21186603. [PMID: 32917057 PMCID: PMC7555309 DOI: 10.3390/ijms21186603] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 09/02/2020] [Accepted: 09/07/2020] [Indexed: 12/15/2022] Open
Abstract
High-energy and high-atom-number (HZE) space radiation poses an inevitable potential threat to astronauts on deep space exploration missions. Compared with low-LET radiation, high-energy and high-LET radiation in space is more efficient in inducing clustered DNA damage with more serious biological consequences, such as carcinogenesis, central nervous system injury and degenerative disease. Space radiation also causes epigenetic changes in addition to inducing damage at the DNA level. Considering the important roles of microRNAs in the regulation of biological responses of radiation, we systematically reviewed both expression profiling and functional studies relating to microRNAs responding to space radiation as well as to space compound environment. Finally, the directions for improvement of the research related to microRNAs responding to space radiation are proposed. A better understanding of the functions and underlying mechanisms of the microRNAs responding to space radiation is of significance to both space radiation risk assessment and therapy development for lesions caused by space radiation.
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Affiliation(s)
| | | | - Guangming Zhou
- Correspondence: (G.Z.); (W.H.); Tel.: +86-512-65884829 (G.Z.); +86-512-65882451 (W.H.)
| | - Wentao Hu
- Correspondence: (G.Z.); (W.H.); Tel.: +86-512-65884829 (G.Z.); +86-512-65882451 (W.H.)
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17
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Guan ZX, Li SH, Zhang ZM, Zhang D, Yang H, Ding H. A Brief Survey for MicroRNA Precursor Identification Using Machine Learning Methods. Curr Genomics 2020; 21:11-25. [PMID: 32655294 PMCID: PMC7324890 DOI: 10.2174/1389202921666200214125102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 01/24/2020] [Accepted: 01/30/2020] [Indexed: 11/22/2022] Open
Abstract
MicroRNAs, a group of short non-coding RNA molecules, could regulate gene expression. Many diseases are associated with abnormal expression of miRNAs. Therefore, accurate identification of miRNA precursors is necessary. In the past 10 years, experimental methods, comparative genomics methods, and artificial intelligence methods have been used to identify pre-miRNAs. However, experimental methods and comparative genomics methods have their disadvantages, such as time-consuming. In contrast, machine learning-based method is a better choice. Therefore, the review summarizes the current advances in pre-miRNA recognition based on computational methods, including the construction of benchmark datasets, feature extraction methods, prediction algorithms, and the results of the models. And we also provide valid information about the predictors currently available. Finally, we give the future perspectives on the identification of pre-miRNAs. The review provides scholars with a whole background of pre-miRNA identification by using machine learning methods, which can help researchers have a clear understanding of progress of the research in this field.
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Affiliation(s)
- Zheng-Xing Guan
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu610054, China
| | - Shi-Hao Li
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu610054, China
| | - Zi-Mei Zhang
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu610054, China
| | - Dan Zhang
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu610054, China
| | - Hui Yang
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu610054, China
| | - Hui Ding
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu610054, China
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18
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Chen X, Jiang M, Li H, Wang Y, Shen H, Li X, Zhang Y, Wu J, Yu Z, Chen G. CX3CL1/CX3CR1 axis attenuates early brain injury via promoting the delivery of exosomal microRNA-124 from neuron to microglia after subarachnoid hemorrhage. J Neuroinflammation 2020; 17:209. [PMID: 32664984 PMCID: PMC7362528 DOI: 10.1186/s12974-020-01882-6] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 06/25/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Microglial activation-mediated neuroinflammation is a major contributor to early brain injury (EBI) after subarachnoid hemorrhage (SAH). MicroRNA-124 (miR-124) is the most abundant miRNAs in the central nervous system (CNS) and plays a vital role in microglial activation by targeting protein CCAAT-enhancer-binding protein α (C/EBPα). It has been reported that the CX3CL1/CX3CR1 axis is involved in the delivery of miR-124 from neurons to microglia. METHODS An experimental rat SAH model was established by injecting autologous arterial blood into the prechiasmatic cistern, and cultured primary neurons and microglia were exposed to oxyhemoglobin to mimic SAH in vitro. We additionally exploited specific expression plasmids encoding CX3CL1 and CX3CR1. RESULTS We observed significant decreases in CX3CL1 and CX3CR1 in the brain tissues of SAH patients. We also observed decreases in the levels of CX3CL1 in neurons and CX3CR1 in microglia after SAH in rats. Moreover, microglia exhibited an activated phenotype with macrophage-like morphology and high levels of CD45 and major histocompatibility complex (MHC) class II after SAH. After overexpression of CX3CL1/CX3CR1, the level of CD45 and MHC class II and the release of inflammatory factors tumor necrosis factor α, interleukin 1α and complement 1q were significantly decreased. There was also increased neuronal degeneration and behavior dysfunction after SAH, both of which were inhibited by CX3CL1/CX3CR1 overexpression. Additionally, we found that the delivery of exosomal miR-124 from neurons to microglia was significantly reduced after SAH, accompanied by an increase in C/EBPα expression, and was inhibited by CX3CL1/CX3CR1 overexpression. In conclusion, the CX3CL1/CX3CR1 axis may play protective roles after SAH by promoting the delivery of exosomal miR-124 to microglia and attenuate microglial activation and neuroinflammation. CONCLUSIONS CX3CL1/CX3CR1 axis may be a potential intervention target for the inhibition of SAH-induced EBI by promoting exosome transport of miR-124 to microglia.
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Affiliation(s)
- Xiao Chen
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, 188 Shizi Street, Suzhou, 215006, China
| | - Ming Jiang
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, 188 Shizi Street, Suzhou, 215006, China
| | - Haiying Li
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, 188 Shizi Street, Suzhou, 215006, China
| | - Yang Wang
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, 188 Shizi Street, Suzhou, 215006, China.,Department of Neurosurgery, The First Affiliated Hospital of University of Science and Technology of China, 17 Lujiang Road, Hefei, 230001, China
| | - Haitao Shen
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, 188 Shizi Street, Suzhou, 215006, China
| | - Xiang Li
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, 188 Shizi Street, Suzhou, 215006, China
| | - Yunhai Zhang
- Jiangsu Key Laboratory of Medical Optics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Jiang Wu
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, 188 Shizi Street, Suzhou, 215006, China
| | - Zhengquan Yu
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, 188 Shizi Street, Suzhou, 215006, China.
| | - Gang Chen
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, 188 Shizi Street, Suzhou, 215006, China.
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19
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Lyons KE, Ryan CA, Dempsey EM, Ross RP, Stanton C. Breast Milk, a Source of Beneficial Microbes and Associated Benefits for Infant Health. Nutrients 2020; 12:E1039. [PMID: 32283875 PMCID: PMC7231147 DOI: 10.3390/nu12041039] [Citation(s) in RCA: 236] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 04/03/2020] [Accepted: 04/04/2020] [Indexed: 12/27/2022] Open
Abstract
Human breast milk is considered the optimum feeding regime for newborn infants due to its ability to provide complete nutrition and many bioactive health factors. Breast feeding is associated with improved infant health and immune development, less incidences of gastrointestinal disease and lower mortality rates than formula fed infants. As well as providing fundamental nutrients to the growing infant, breast milk is a source of commensal bacteria which further enhance infant health by preventing pathogen adhesion and promoting gut colonisation of beneficial microbes. While breast milk was initially considered a sterile fluid and microbes isolated were considered contaminants, it is now widely accepted that breast milk is home to its own unique microbiome. The origins of bacteria in breast milk have been subject to much debate, however, the possibility of an entero-mammary pathway allowing for transfer of microbes from maternal gut to the mammary gland is one potential pathway. Human milk derived strains can be regarded as potential probiotics; therefore, many studies have focused on isolating strains from milk for subsequent use in infant health and nutrition markets. This review aims to discuss mammary gland development in preparation for lactation as well as explore the microbial composition and origins of the human milk microbiota with a focus on probiotic development.
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Affiliation(s)
- Katríona E. Lyons
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork P61 C996, Ireland
- School of Microbiology, University College Cork, Cork T12 YN60, Ireland
| | - C. Anthony Ryan
- APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland
- Department of Neonatology, Cork University Maternity Hospital, Cork T12 YE02, Ireland
| | - Eugene M. Dempsey
- APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland
- Department of Neonatology, Cork University Maternity Hospital, Cork T12 YE02, Ireland
- INFANT Research Centre, University College Cork, Cork T12 DFK4, Ireland
| | - R. Paul Ross
- APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland
| | - Catherine Stanton
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork P61 C996, Ireland
- APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland
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20
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Ferro E, Enrico Bena C, Grigolon S, Bosia C. microRNA-mediated noise processing in cells: A fight or a game? Comput Struct Biotechnol J 2020; 18:642-649. [PMID: 32257047 PMCID: PMC7103774 DOI: 10.1016/j.csbj.2020.02.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 02/27/2020] [Accepted: 02/27/2020] [Indexed: 12/17/2022] Open
Abstract
In the past decades, microRNAs (miRNA) have much attracted the attention of researchers at the interface between life and theoretical sciences for their involvement in post-transcriptional regulation and related diseases. Thanks to the always more sophisticated experimental techniques, the role of miRNAs as "noise processing units" has been further elucidated and two main ways of miRNA noise-control have emerged by combinations of theoretical and experimental studies. While on one side miRNAs were thought to buffer gene expression noise, it has recently been suggested that miRNAs could also increase the cell-to-cell variability of their targets. In this Mini Review, we focus on the role of miRNAs in molecular noise processing and on the advantages as well as current limitations of theoretical modelling.
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Affiliation(s)
- Elsi Ferro
- Italian Institute for Genomic Medicine, Italy
| | | | - Silvia Grigolon
- The Francis Crick Institute, 1, Midland Road, London NW1 1AT, UK
| | - Carla Bosia
- Italian Institute for Genomic Medicine, Italy
- Department of Applied Science and Technology, Politecnico di Torino, Italy
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21
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Chandan K, Gupta M, Sarwat M. Role of Host and Pathogen-Derived MicroRNAs in Immune Regulation During Infectious and Inflammatory Diseases. Front Immunol 2020; 10:3081. [PMID: 32038627 PMCID: PMC6992578 DOI: 10.3389/fimmu.2019.03081] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 12/17/2019] [Indexed: 12/11/2022] Open
Abstract
MicroRNAs (miRNAs, miRs) are short, endogenously initiated, non-coding RNAs that bind to target mRNAs, leading to the degradation or translational suppression of respective mRNAs. They have been reported as key players in physiological processes like differentiation, cellular proliferation, development, and apoptosis. They have gained importance as gene expression regulators in the immune system. They control antibody production and release various inflammatory mediators. Abnormal expression and functioning of miRNA in the immune system is linked to various diseases like inflammatory disorders, allergic diseases, cancers etc. As compared to the average human genome, miRNA targets the genes of immune system quite differently. miRNA appeared to regulate the responses related to both acquired and innate immunity of the humans. Several miRNAs importantly regulate the transcription and even, dysregulation of inflammation-related mediators. Many miRNAs are either upregulated or downregulated in various inflammatory and infectious diseases. Hence, modifying or targeting the expression of miRNAs might serve as a novel strategy for the diagnosis, prevention, and treatment of various inflammatory and infectious conditions.
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Affiliation(s)
| | | | - Maryam Sarwat
- Amity Institute of Pharmacy, Amity University, Noida, India
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22
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Yan J, Lu X, Zhu X, Hu X, Wang L, Qian J, Zhang F, Liu M. Effects of miR-26a on Osteogenic Differentiation of Bone Marrow Mesenchymal Stem Cells by a Mesoporous Silica Nanoparticle - PEI - Peptide System. Int J Nanomedicine 2020; 15:497-511. [PMID: 32158207 PMCID: PMC6986258 DOI: 10.2147/ijn.s228797] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 12/28/2019] [Indexed: 12/14/2022] Open
Abstract
INTRODUCTION RNA-based therapy for bone repair and regeneration is a highly safe and effective approach, which has been extensively investigated in recent years. However, the molecular stability of RNA agents still remains insufficient for clinical application. High porosity, tunable size, and ideal biodegradability and biosafety are a few of the characters of mesoporous silicon nanoparticles (MSNs) that render them a promising biomaterial carrier for RNA treatment. MATERIALS AND METHODS In this study, a novel miR-26a delivery system was constructed based on MSNs. Next, we assessed the miRNA protection of the delivery vehicles. Then, rat bone marrow mesenchymal stem cells (rBMSCs) were incubated with the vectors, and the transfection efficiency, cellular uptake, and effects on cell viability and osteogenic differentiation were evaluated. RESULTS The results demonstrated that the vectors protected miR-26a from degradation in vitro and delivered it into the cytoplasm. A relatively low concentration of the delivery systems significantly increased osteogenic differentiation of rBMSCs. CONCLUSION The vectors constructed in our study provide new methods and strategies for the delivery of microRNAs in bone tissue engineering.
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Affiliation(s)
- Jia Yan
- Jiangsu Key Laboratory of Oral Diseases, Department of Prosthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing210029, People’s Republic of China
| | - Xiaoli Lu
- Jiangsu Key Laboratory of Oral Diseases, Department of Prosthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing210029, People’s Republic of China
| | - Xinchen Zhu
- Jiangsu Key Laboratory of Oral Diseases, Department of Prosthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing210029, People’s Republic of China
| | - Xiaokun Hu
- Jiangsu Key Laboratory of Oral Diseases, Department of Prosthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing210029, People’s Republic of China
| | - Lili Wang
- Jiangsu Key Laboratory of Oral Diseases, Department of Prosthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing210029, People’s Republic of China
| | - Jun Qian
- Jiangsu Key Laboratory of Oral Diseases, Department of Prosthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing210029, People’s Republic of China
| | - Feimin Zhang
- Jiangsu Key Laboratory of Oral Diseases, Department of Prosthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing210029, People’s Republic of China
| | - Mei Liu
- Jiangsu Key Laboratory of Oral Diseases, Department of Prosthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing210029, People’s Republic of China
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23
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Qian T, Shi S, Xie L, Zhu Y. miR-938 promotes cell proliferation by regulating RBM5 in lung adenocarcinoma cells. Cell Biol Int 2020; 44:295-305. [PMID: 31498514 DOI: 10.1002/cbin.11233] [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] [Received: 04/30/2019] [Accepted: 08/31/2019] [Indexed: 01/24/2023]
Abstract
A growing body of research suggests that microRNAs (miRNAs) may play a key part in the progression of various cancers, including lung adenocarcinoma (LUAD). However, the expression and mechanism of miR-938 (microRNA-938) in LUAD have not been defined. Compared with adjacent tissues, the level of miR-938 was up-regulated in LUAD tissues. miR-938 expression was significantly associated with tumor size. In vitro assays indicated that miR-938 expression was also increased in the LUAD cell lines. Overexpression of miR-938 promoted LUAD cell proliferation, whereas down-regulation of miR-938 had the opposite effect. We identified RNA-binding protein 5 (RBM5) as a potential target gene of miR-938 in LUAD. Expression of RBM5 was down-regulated in LUAD tumor tissues and negatively correlated with expression of miR-938. Up-regulation of RBM5 reversed cell proliferation by inhibition of miR-938 expression in LUAD cells. These results showed that miR-938 may act as an oncogenic miRNA by targeting RBM5 in LUAD, indicating that miR-938 could be used as a potential therapeutic target for LUAD patients.
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Affiliation(s)
- Taotao Qian
- Department of Thoracic Surgery, Suzhou Ninth People's Hospital, 2666 Ludang Road, Taihu New City, Wujiang District, Suzhou, Jiangsu Province, 215000, China.,Department of Thoracic Surgery, Wujiang People's Hospital Affiliated to Nantong University, 2666 Ludang Road, Taihu New City, Wujiang District, Suzhou, Jiangsu Province, 215000, China
| | - Shunbin Shi
- Department of Thoracic Surgery, Suzhou Ninth People's Hospital, 2666 Ludang Road, Taihu New City, Wujiang District, Suzhou, Jiangsu Province, 215000, China.,Department of Thoracic Surgery, Wujiang People's Hospital Affiliated to Nantong University, 2666 Ludang Road, Taihu New City, Wujiang District, Suzhou, Jiangsu Province, 215000, China
| | - Lincen Xie
- Department of Thoracic Surgery, Suzhou Ninth People's Hospital, 2666 Ludang Road, Taihu New City, Wujiang District, Suzhou, Jiangsu Province, 215000, China.,Department of Thoracic Surgery, Wujiang People's Hospital Affiliated to Nantong University, 2666 Ludang Road, Taihu New City, Wujiang District, Suzhou, Jiangsu Province, 215000, China
| | - Yong Zhu
- Department of Thoracic Surgery, Suzhou Ninth People's Hospital, 2666 Ludang Road, Taihu New City, Wujiang District, Suzhou, Jiangsu Province, 215000, China.,Department of Thoracic Surgery, Wujiang People's Hospital Affiliated to Nantong University, 2666 Ludang Road, Taihu New City, Wujiang District, Suzhou, Jiangsu Province, 215000, China
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24
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Ferro E, Enrico Bena C, Grigolon S, Bosia C. From Endogenous to Synthetic microRNA-Mediated Regulatory Circuits: An Overview. Cells 2019; 8:E1540. [PMID: 31795372 PMCID: PMC6952906 DOI: 10.3390/cells8121540] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 11/22/2019] [Accepted: 11/25/2019] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs are short non-coding RNAs that are evolutionarily conserved and are pivotal post-transcriptional mediators of gene regulation. Together with transcription factors and epigenetic regulators, they form a highly interconnected network whose building blocks can be classified depending on the number of molecular species involved and the type of interactions amongst them. Depending on their topology, these molecular circuits may carry out specific functions that years of studies have related to the processing of gene expression noise. In this review, we first present the different over-represented network motifs involving microRNAs and their specific role in implementing relevant biological functions, reviewing both theoretical and experimental studies. We then illustrate the recent advances in synthetic biology, such as the construction of artificially synthesised circuits, which provide a controlled tool to test experimentally the possible microRNA regulatory tasks and constitute a starting point for clinical applications.
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Affiliation(s)
- Elsi Ferro
- IIGM—Italian Institute for Genomic Medicine, c/o IRCCS, 10060 Candiolo (Torino), Italy
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo (Torino), Italy
| | - Chiara Enrico Bena
- IIGM—Italian Institute for Genomic Medicine, c/o IRCCS, 10060 Candiolo (Torino), Italy
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo (Torino), Italy
| | - Silvia Grigolon
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Carla Bosia
- IIGM—Italian Institute for Genomic Medicine, c/o IRCCS, 10060 Candiolo (Torino), Italy
- Department of Applied Science and Technology, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy
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25
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Yang T, Yuan P, Yang Y, Liang N, Wang Q, Li J, Lu R, Zhang H, Mu J, Yan Z, Chang H. NPAS2 Contributes to Liver Fibrosis by Direct Transcriptional Activation of Hes1 in Hepatic Stellate Cells. MOLECULAR THERAPY. NUCLEIC ACIDS 2019; 18:1009-1022. [PMID: 31778954 PMCID: PMC6889679 DOI: 10.1016/j.omtn.2019.10.025] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 10/23/2019] [Indexed: 12/29/2022]
Abstract
Recently, emerging evidence shows that dysregulation of circadian genes is closely associated with liver fibrosis. However, how dysregulation of circadian genes promotes liver fibrosis is unknown. In this study, we show that neuronal PAS domain protein 2 (NPAS2), one of the core circadian molecules that has been shown to promote hepatocarcinoma cell proliferation, significantly contributed to liver fibrogenesis. NPAS2 is upregulated in hepatic stellate cells (HSCs) after fibrogenic injury, which subsequently contributes to the activation of HSCs. Mechanistically, NPAS2 plays a profibrotic role via direct transcriptional activation of hairy and enhancer of split 1 (Hes1), a critical transcriptor of Notch signaling for the fibrogenesis process, in HSCs. Our findings demonstrate that NPAS2 plays a critical role in liver fibrosis through direct transcriptional activation of Hes1, indicating that NPAS2 may serve as an important therapeutic target to reverse the progression of liver fibrosis.
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Affiliation(s)
- Tao Yang
- Department of Pain Treatment, Tangdu Hospital, The Fourth Military Medical University, Xi'an, Shaanxi 710038, China
| | - Peng Yuan
- State Key Laboratory of Cancer Biology and Experimental Teaching Center of Basic Medicine, The Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Yi Yang
- Department of Pain Treatment, Tangdu Hospital, The Fourth Military Medical University, Xi'an, Shaanxi 710038, China
| | - Ning Liang
- Department of General Surgery, The 75th Group Army Hospital, Dali, Yunnan 671000, China
| | - Qian Wang
- Department of General Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Jing Li
- College and Hospital of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004, China
| | - Rui Lu
- Department of Pain Treatment, Tangdu Hospital, The Fourth Military Medical University, Xi'an, Shaanxi 710038, China
| | - Hongxin Zhang
- Department of Pain Treatment, Tangdu Hospital, The Fourth Military Medical University, Xi'an, Shaanxi 710038, China
| | - Jiao Mu
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China; Department of Hematology, Xi'an Central Hospital, Xi'an, Shaanxi 710003, China.
| | - Zhaoyong Yan
- Department of Pain Treatment, Tangdu Hospital, The Fourth Military Medical University, Xi'an, Shaanxi 710038, China.
| | - Hulin Chang
- Department of Hepatobiliary Surgery, Shaanxi Provincial People's Hospital, Xi'an 710068, China.
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26
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Franchini P, Xiong P, Fruciano C, Schneider RF, Woltering JM, Hulsey CD, Meyer A. MicroRNA Gene Regulation in Extremely Young and Parallel Adaptive Radiations of Crater Lake Cichlid Fish. Mol Biol Evol 2019; 36:2498-2511. [PMID: 31397871 DOI: 10.1093/molbev/msz168] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 07/03/2019] [Accepted: 07/17/2019] [Indexed: 12/20/2022] Open
Abstract
AbstractCichlid fishes provide textbook examples of explosive phenotypic diversification and sympatric speciation, thereby making them ideal systems for studying the molecular mechanisms underlying rapid lineage divergence. Despite the fact that gene regulation provides a critical link between diversification in gene function and speciation, many genomic regulatory mechanisms such as microRNAs (miRNAs) have received little attention in these rapidly diversifying groups. Therefore, we investigated the posttranscriptional regulatory role of miRNAs in the repeated sympatric divergence of Midas cichlids (Amphilophus spp.) from Nicaraguan crater lakes. Using miRNA and mRNA sequencing of embryos from five Midas species, we first identified miRNA binding sites in mRNAs and highlighted the presences of a surprising number of novel miRNAs in these adaptively radiating species. Then, through analyses of expression levels, we identified putative miRNA/gene target pairs with negatively correlated expression level that were consistent with the role of miRNA in downregulating mRNA. Furthermore, we determined that several miRNA/gene pairs show convergent expression patterns associated with the repeated benthic/limnetic sympatric species divergence implicating these miRNAs as potential molecular mechanisms underlying replicated sympatric divergence. Finally, as these candidate miRNA/gene pairs may play a central role in phenotypic diversification in these cichlids, we characterized the expression domains of selected miRNAs and their target genes via in situ hybridization, providing further evidence that miRNA regulation likely plays a role in the Midas cichlid adaptive radiation. These results provide support for the hypothesis that extremely quickly evolving miRNA regulation can contribute to rapid evolutionary divergence even in the presence of gene flow.
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Affiliation(s)
- Paolo Franchini
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Peiwen Xiong
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Carmelo Fruciano
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany
- Institut de biologie de l’Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, PSL Université Paris, Paris, France
| | - Ralf F Schneider
- Marine Ecology, Helmholtz-Zentrum für Ozeanforschung Kiel (GEOMAR), Düsternbrooker Weg 20, Kiel, Germany
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Joost M Woltering
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Christopher Darrin Hulsey
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Axel Meyer
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany
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