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Hykollari A, Malzl D, Eckmair B, Vanbeselaere J, Scheidl P, Jin C, Karlsson NG, Wilson IBH, Paschinger K. Isomeric Separation and Recognition of Anionic and Zwitterionic N-glycans from Royal Jelly Glycoproteins. Mol Cell Proteomics 2018; 17:2177-2196. [PMID: 30104209 DOI: 10.1074/mcp.ra117.000462] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 08/13/2018] [Indexed: 01/03/2023] Open
Abstract
Royal jelly has received attention because of its necessity for the development of queen honeybees as well as claims of benefits on human health; this product of the hypopharyngeal glands of worker bees contains a large number of proteins, some of which have been claimed to have various biological effects only in their glycosylated state. However, although there have been glycomic and glycoproteomic analyses in the past, none of the glycan structures previously defined would appear to have potential to trigger specific biological functions. In the current study, whole royal jelly as well as single protein bands were subject to off-line LC-MALDI-TOF MS glycomic analyses, complemented by permethylation, Western blotting and arraying data. Similarly to recent in-depth studies on other insect species, previously overlooked glucuronic acid termini, sulfation of mannose residues and core β-mannosylation of the N-glycans were found; additionally, a relatively rare zwitterionic modification with phosphoethanolamine is present, in contrast to the phosphorylcholine occurring in lepidopteran species. Indicative of tissue-specific remodelling of glycans in the Golgi apparatus of hypopharyngeal gland cells, only a low amount of fucosylated or paucimannosidic glycans were detected as compared with other insect samples or even bee venom. The unusual modifications of hybrid and multiantennary structures defined here may not only have a physiological role in honeybee development, but represent epitopes recognized by pentraxins with roles in animal innate immunity.
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Affiliation(s)
- Alba Hykollari
- From the ‡Department für Chemie, Universität für Bodenkultur, 1190 Wien, Austria
| | - Daniel Malzl
- From the ‡Department für Chemie, Universität für Bodenkultur, 1190 Wien, Austria
| | - Barbara Eckmair
- From the ‡Department für Chemie, Universität für Bodenkultur, 1190 Wien, Austria
| | - Jorick Vanbeselaere
- From the ‡Department für Chemie, Universität für Bodenkultur, 1190 Wien, Austria
| | - Patrick Scheidl
- From the ‡Department für Chemie, Universität für Bodenkultur, 1190 Wien, Austria
| | - Chunsheng Jin
- §Institutionen för Biomedicin, Göteborgs universitet, 405 30 Göteborg, Sweden
| | - Niclas G Karlsson
- §Institutionen för Biomedicin, Göteborgs universitet, 405 30 Göteborg, Sweden
| | - Iain B H Wilson
- From the ‡Department für Chemie, Universität für Bodenkultur, 1190 Wien, Austria
| | - Katharina Paschinger
- From the ‡Department für Chemie, Universität für Bodenkultur, 1190 Wien, Austria;
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Salpietro V, Manole A, Efthymiou S, Houlden H. A Review of Copy Number Variants in Inherited Neuropathies. Curr Genomics 2018; 19:412-419. [PMID: 30258273 PMCID: PMC6128387 DOI: 10.2174/1389202919666180330153316] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Revised: 11/23/2016] [Accepted: 03/13/2018] [Indexed: 11/22/2022] Open
Abstract
The rapid development in the last 10-15 years of microarray technologies, such as oligonucleotide array Comparative Genomic Hybridization (CGH) and Single Nucleotide Polymorphisms (SNP) genotyping array, has improved the identification of fine chromosomal structural variants, ranging in length from kilobases (kb) to megabases (Mb), as an important cause of genetic differences among healthy individuals and also as disease-susceptibility and/or disease-causing factors. Structural genomic variations due to unbalanced chromosomal rearrangements are known as Copy-Number Variants (CNVs) and these include variably sized deletions, duplications, triplications and translocations. CNVs can significantly contribute to human diseases and rearrangements in several dosage-sensitive genes have been identified as an important causative mechanism in the molecular aetiology of Charcot-Marie-Tooth (CMT) disease and of several CMT-related disorders, a group of inherited neuropathies with a broad range of clinical phenotypes, inheritance patterns and causative genes. Duplications or deletions of the dosage-sensitive gene PMP22 mapped to chromosome 17p12 represent the most frequent causes of CMT type 1A and Hereditary Neuropathy with liability to Pressure Palsies (HNPP), respectively. Additionally, CNVs have been identified in patients with other CMT types (e.g., CMT1X, CMT1B, CMT4D) and different hereditary poly- (e.g., giant axonal neuropathy) and focal- (e.g., hereditary neuralgic amyotrophy) neuropathies, supporting the notion of hereditary peripheral nerve diseases as possible genomic disorders and making crucial the identification of fine chromosomal rearrangements in the molecular assessment of such patients. Notably, the application of advanced computational tools in the analysis of Next-Generation Sequencing (NGS) data has emerged in recent years as a powerful technique for identifying a genome-wide scale complex structural variants (e.g., as the ones resulted from balanced rearrangements) and also smaller pathogenic (intragenic) CNVs that often remain beyond the detection limit of most conventional genomic microarray analyses; in the context of inherited neuropathies where more than 70 disease-causing genes have been identified to date, NGS and particularly Whole-Genome Sequencing (WGS) hold the potential to reduce the number of genomic assays required per patient to reach a diagnosis, analyzing with a single test all the Single Nucleotide Variants (SNVs) and CNVs in the genes possibly implicated in this heterogeneous group of disorders.
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Affiliation(s)
- Vincenzo Salpietro
- Department of Molecular Neuroscience, Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Andreea Manole
- Department of Molecular Neuroscience, Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Stephanie Efthymiou
- Department of Molecular Neuroscience, Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Henry Houlden
- Department of Molecular Neuroscience, Institute of Neurology, University College London, London WC1N 3BG, UK
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Yamaura Y, Tatsumi N, Takagi S, Tokumitsu S, Fukami T, Tajiri K, Minemura M, Yokoi T, Nakajima M. Serum microRNA profiles in patients with chronic hepatitis B, chronic hepatitis C, primary biliary cirrhosis, autoimmune hepatitis, nonalcoholic steatohepatitis, or drug-induced liver injury. Clin Biochem 2017; 50:1034-1039. [PMID: 28823616 DOI: 10.1016/j.clinbiochem.2017.08.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 07/24/2017] [Accepted: 08/16/2017] [Indexed: 02/08/2023]
Abstract
PURPOSE Some blood biomarkers or histological examination by liver biopsy are used for the diagnosis of liver diseases in clinics. However, conventional blood biomarkers show poor specificity and sensitivity, and liver biopsy is highly invasiveness. Therefore, to overcome such disadvantages, specific/sensitive and noninvasive options are desirable. In recent years, circulating microRNAs (miRNAs) have been acknowledged for their potential as disease markers. Actually, several miRNAs have been reported to be biomarker candidates of liver diseases. However, these earlier studies were performed for one disease. Therefore, the specificity as biomarkers was not guaranteed, because they didn't study for the other types of liver injury. In this study, we examined if circulating miRNA could distinguish different types of liver diseases. METHODS Serum miRNA profiles in 28 patients with chronic hepatitis B, chronic hepatitis C, primary biliary cirrhosis, autoimmune hepatitis, nonalcoholic steatohepatitis or drug-induced liver injury as well as 4 control subjects were determined by TaqMan MicroRNA Array analysis. Principal component analysis (PCA) of selected miRNAs was performed. RESULTS We identified 37 miRNAs whose levels were significantly different between any of the groups. Although individual miRNAs could not distinguish different types of liver diseases, probably because of similar liver pathology, their profiling by PCA could classify different liver disease groups. CONCLUSIONS The profiling of the selected miRNAs can be useful to distinguish different types of liver diseases.
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Affiliation(s)
- Yu Yamaura
- Drug Metabolism and Toxicology, Faculty of Pharmaceutical Sciences, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Naoyuki Tatsumi
- Drug Metabolism and Toxicology, Faculty of Pharmaceutical Sciences, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Shingo Takagi
- Drug Metabolism and Toxicology, Faculty of Pharmaceutical Sciences, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Shinsaku Tokumitsu
- Drug Metabolism and Toxicology, Faculty of Pharmaceutical Sciences, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Tatsuki Fukami
- Drug Metabolism and Toxicology, Faculty of Pharmaceutical Sciences, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Kazuto Tajiri
- Graduate School of Medicine and Pharmaceutical Science, University of Toyama, Sugitani, Toyama 930-0194, Japan
| | - Masami Minemura
- Graduate School of Medicine and Pharmaceutical Science, University of Toyama, Sugitani, Toyama 930-0194, Japan
| | - Tsuyoshi Yokoi
- Drug Metabolism and Toxicology, Faculty of Pharmaceutical Sciences, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Miki Nakajima
- Drug Metabolism and Toxicology, Faculty of Pharmaceutical Sciences, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan.
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Pan F, You J, Liu Y, Qiu X, Yu W, Ma J, Pan L, Zhang A, Zhang Q. Differentially expressed microRNAs in the corpus cavernosum from a murine model with type 2 diabetes mellitus-associated erectile dysfunction. Mol Genet Genomics 2016; 291:2215-2224. [PMID: 27681254 DOI: 10.1007/s00438-016-1250-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 09/19/2016] [Indexed: 01/14/2023]
Abstract
To better understand the molecular aetiology of type 2 diabetes mellitus-associated erectile dysfunction (T2DMED) and to provide candidates for further study of its diagnosis and treatment, this study was designed to investigate differentially expressed microRNAs (miRNAs) in the corpus cavernosum (CC) of mice with T2DMED using GeneChip array techniques (Affymetrix miRNA 4.0 Array) and to predict target genes and signalling pathways regulated by these miRNAs based on bioinformatic analysis using TargetScan, the DAIAN web platform and DAVID. In the initial screening, 21 miRNAs appeared distinctly expressed in the T2DMED group (fold change ≥3, p ≤ 0.01). Among them, the differential expression of miR-18a, miR-206, miR-122, and miR-133 were confirmed by qRT-PCR (p < 0.05 and FDR <5 %). According to bioinformatic analysis, the four miRNAs were speculated to play potential roles in the mechanisms of T2DMED via regulating 28 different genes and several pathways, including apoptosis, fibrosis, eNOS/cGMP/PKG, and vascular smooth muscle contraction processes, which mainly focused on influencing the functions of the endothelium and smooth muscle in the CC. IGF-1, as one of the target genes, was verified to decrease in the CCs of T2DMED animals via ELISA and was confirmed as the target of miR-18a or miR-206 via luciferase assay. Finally, these four miRNAs deserve further confirmation as biomarkers of T2DMED in larger studies. Additionally, miR-18a and/or miR-206 may provide new preventive/therapeutic targets for ED management by targeting IGF-1.
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Affiliation(s)
- Feng Pan
- State Key Laboratory of Reproductive Medicine, Department of Andrology, Maternity Hospital Affiliated to Nanjing Medical University, Nanjing, China
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Jiangsu Engineering Research Center for microRNA Biology and Biotechnology, Nanjing University, Nanjing, China
| | - Jinwei You
- State Key Laboratory of Reproductive Medicine, Department of Andrology, Maternity Hospital Affiliated to Nanjing Medical University, Nanjing, China
- Department of Comparative Medicine, Jinling Hospital, School of Clinical Medicine, Nanjing University, Nanjing, China
| | - Yuan Liu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Jiangsu Engineering Research Center for microRNA Biology and Biotechnology, Nanjing University, Nanjing, China
| | - Xuefeng Qiu
- Department of Andrology, Affiliated Drum Tower Hospital, School of Medicine, Nanjing University, Nanjing, China
| | - Wen Yu
- Department of Andrology, Affiliated Drum Tower Hospital, School of Medicine, Nanjing University, Nanjing, China
| | - Jiehua Ma
- State Key Laboratory of Reproductive Medicine, Department of Andrology, Maternity Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Lianjun Pan
- State Key Laboratory of Reproductive Medicine, Department of Andrology, Maternity Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Aixia Zhang
- State Key Laboratory of Reproductive Medicine, Department of Andrology, Maternity Hospital Affiliated to Nanjing Medical University, Nanjing, China.
| | - Qipeng Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Jiangsu Engineering Research Center for microRNA Biology and Biotechnology, Nanjing University, Nanjing, China.
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Falaleeva M, Surface J, Shen M, de la Grange P, Stamm S. SNORD116 and SNORD115 change expression of multiple genes and modify each other's activity. Gene 2015; 572:266-73. [PMID: 26220404 DOI: 10.1016/j.gene.2015.07.023] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The loss of two gene clusters encoding small nucleolar RNAs, SNORD115 and SNORD116 contribute to Prader-Willi syndrome (PWS), the most common syndromic form of obesity in humans. SNORD115 and SNORD116 are considered to be orphan C/D box snoRNAs (SNORDs) as they do not target rRNAs or snRNAs. SNORD115 exhibits sequence complementarity towards the serotonin receptor 2C, but SNORD116 shows no extended complementarities to known RNAs. To identify molecular targets, we performed genome-wide array analysis after overexpressing SNORD115 and SNORD116 in HEK 293T cells, either alone or together. We found that SNORD116 changes the expression of over 200 genes. SNORD116 mainly changed mRNA expression levels. Surprisingly, we found that SNORD115 changes SNORD116's influence on gene expression. In similar experiments, we compared gene expression in post-mortem hypothalamus between individuals with PWS and aged-matched controls. The synopsis of these experiments resulted in 23 genes whose expression levels were influenced by SNORD116. Together our results indicate that SNORD115 and SNORD116 influence expression levels of multiple genes and modify each other activity.
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Xia H, Yamada S, Aoyama M, Sato F, Masaki A, Ge Y, Ri M, Ishida T, Ueda R, Utsunomiya A, Asai K, Inagaki H. Prognostic impact of microRNA-145 down-regulation in adult T-cell leukemia/lymphoma. Hum Pathol 2014; 45:1192-8. [PMID: 24745613 DOI: 10.1016/j.humpath.2014.01.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 01/16/2014] [Accepted: 01/24/2014] [Indexed: 01/07/2023]
Abstract
Adult T-cell leukemia/lymphoma (ATL) is a highly aggressive tumor caused by human T-cell leukemia virus type 1. MicroRNAs (miRNAs) are closely involved in the development and progression of various tumors. Here we investigated the dysregulation of miRNAs in ATL and its clinical significance. Studies using miRNA arrays and subsequent real-time reverse transcription polymerase chain reaction showed that, in the 9 ATL cell lines examined, 1 miRNA was consistently up-regulated, whereas another 3 were consistently down-regulated, compared with normal CD4-positive lymphocytes. Next, we analyzed the prognostic impact of these 4 miRNAs in patients with aggressive-type ATL (n = 40). Of the 4 dysregulated miRNAs selected, 3 (miR-130b higher expression, miR-145 lower expression, and miR-223 lower expression) were significantly associated with a worsened overall patient survival. We found that expressions of these 3 miRNAs were correlated with each other. To clarify which of the 3 had the most significant impact on overall survival, we performed a multivariate prognostic analysis that included these 3 miRNAs, and only miR-145 lower expression was selected as an independent risk factor (P = .0005). When overexpressed in an ATL cell line in vitro, miR-145 specifically inhibited tumor cell growth. In conclusion, our study suggests that miR-145 down-regulation provides a growth advantage in ATL and is highly associated with a worsened prognosis for patients with ALT. Hence, miR-145 may be a useful prognostic marker and a potential therapeutic target for ATL.
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Affiliation(s)
- Hongjing Xia
- Department of Anatomic Pathology and Molecular Diagnostics, Nagoya City University Graduate School of Medical Sciences, Nagoya 467-8601, Japan
| | - Seiji Yamada
- Department of Anatomic Pathology and Molecular Diagnostics, Nagoya City University Graduate School of Medical Sciences, Nagoya 467-8601, Japan
| | - Mineyoshi Aoyama
- Department of Molecular Neurobiology, Nagoya City University Graduate School of Medical Sciences, Nagoya 467-8601, Japan
| | - Fumihiko Sato
- Department of Anatomic Pathology and Molecular Diagnostics, Nagoya City University Graduate School of Medical Sciences, Nagoya 467-8601, Japan
| | - Ayako Masaki
- Department of Anatomic Pathology and Molecular Diagnostics, Nagoya City University Graduate School of Medical Sciences, Nagoya 467-8601, Japan
| | - Yan Ge
- Department of Anatomic Pathology and Molecular Diagnostics, Nagoya City University Graduate School of Medical Sciences, Nagoya 467-8601, Japan
| | - Masaki Ri
- Department of Medical Oncology and Immunology, Nagoya City University Graduate School of Medical Sciences, Nagoya 467-8601, Japan
| | - Takashi Ishida
- Department of Medical Oncology and Immunology, Nagoya City University Graduate School of Medical Sciences, Nagoya 467-8601, Japan
| | - Ryuzo Ueda
- Department of Medical Oncology and Immunology, Nagoya City University Graduate School of Medical Sciences, Nagoya 467-8601, Japan; Department of Tumor Immunology, Aichi Medical University School of Medicine, Nagakute 480-1195, Japan
| | - Atae Utsunomiya
- Department of Hematology, Imamura Bun-in Hospital, Kagoshima 890-0064, Japan
| | - Kiyofumi Asai
- Department of Molecular Neurobiology, Nagoya City University Graduate School of Medical Sciences, Nagoya 467-8601, Japan
| | - Hiroshi Inagaki
- Department of Anatomic Pathology and Molecular Diagnostics, Nagoya City University Graduate School of Medical Sciences, Nagoya 467-8601, Japan.
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Abstract
Development of the genitourinary tract requires spatiotemporal expression of a myriad of genes involved in various cascades and signaling events. To date, researchers have put great efforts into defining the etiology of these malformations. However, many aspects remain unsolved. This paper reviews the most recent progress in identifying causally related genes and novel loci assumed to harbor genes involved in the formation of urogenital malformations. These investigations have been considerately accelerated by the implementation of molecular karyotyping using array techniques and next generation sequencing strategies.
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Affiliation(s)
- Michael Ludwig
- Department of Clinical Chemistry and Clinical Pharmacology, University of Bonn, Bonn, Germany
| | - Heiko Reutter
- Institute of Human Genetics, University of Bonn, Bonn, Germany; Department of Neonatology, Children's Hospital, University of Bonn, Bonn, Germany
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