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Diener C, Keller A, Meese E. The miRNA-target interactions: An underestimated intricacy. Nucleic Acids Res 2024; 52:1544-1557. [PMID: 38033323 PMCID: PMC10899768 DOI: 10.1093/nar/gkad1142] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 10/23/2023] [Accepted: 11/20/2023] [Indexed: 12/02/2023] Open
Abstract
MicroRNAs (miRNAs) play indispensable roles in posttranscriptional gene regulation. Their cellular regulatory impact is determined not solely by their sheer number, which likely amounts to >2000 individual miRNAs in human, than by the regulatory effectiveness of single miRNAs. Although, one begins to develop an understanding of the complex mechanisms underlying miRNA-target interactions (MTIs), the overall knowledge of MTI functionality is still rather patchy. In this critical review, we summarize key features of mammalian MTIs. We especially highlight latest insights on (i) the dynamic make-up of miRNA binding sites including non-canonical binding sites, (ii) the cooperativity between miRNA binding sites, (iii) the adaptivity of MTIs through sequence modifications, (iv) the bearing of intra-cellular miRNA localization changes and (v) the role of cell type and cell status specific miRNA interaction partners. The MTI biology is discussed against the background of state-of-the-art approaches with particular emphasis on experimental strategies for evaluating miRNA functionality.
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Affiliation(s)
- Caroline Diener
- Saarland University (USAAR), Institute of Human Genetics, 66421 Homburg, Germany
| | - Andreas Keller
- Saarland University (USAAR), Chair for Clinical Bioinformatics, 66123 Saarbrücken, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)–Helmholtz Centre for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany
| | - Eckart Meese
- Saarland University (USAAR), Institute of Human Genetics, 66421 Homburg, Germany
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2
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Vlachová M, Tran VN, Červený J, Dolníček F, Petrásková L, Pelantová H, Kundrát O, Cvačka J, Bosáková Z, Křen V, Lhoták P, Viktorová J, Bojarová P. Galectin-targeting glycocalix[4]arenes can enter the cells. Chem Commun (Camb) 2023; 59:10404-10407. [PMID: 37551910 DOI: 10.1039/d3cc02905k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/09/2023]
Abstract
Elevated levels of galectin-3 are associated with tumorigenesis. Its inhibition with high-affinity carbohydrate ligands opens new therapeutic routes. Targeting of intracellular galectin-3 is challenging for polar inhibitors like carbohydrates. We demonstrate the potential of novel biomedical research tools, glycocalix[4]arenes, to enter epithelial cells, which may allow their interaction with galectin-3.
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Affiliation(s)
- Miluše Vlachová
- Laboratory of Biotransformation, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-14220, Praha 4, Czech Republic.
| | - Van Nguyen Tran
- University of Chemistry and Technology Prague, Technická 5, CZ-16628 Praha 6, Czech Republic.
| | - Jakub Červený
- Laboratory of Biotransformation, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-14220, Praha 4, Czech Republic.
- Department of Analytical Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, CZ-12843 Praha 2, Czech Republic
| | - František Dolníček
- University of Chemistry and Technology Prague, Technická 5, CZ-16628 Praha 6, Czech Republic.
| | - Lucie Petrásková
- Laboratory of Biotransformation, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-14220, Praha 4, Czech Republic.
| | - Helena Pelantová
- Laboratory of Biotransformation, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-14220, Praha 4, Czech Republic.
| | - Ondřej Kundrát
- University of Chemistry and Technology Prague, Technická 5, CZ-16628 Praha 6, Czech Republic.
| | - Josef Cvačka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, CZ-16610 Praha 6, Czech Republic
| | - Zuzana Bosáková
- Department of Analytical Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, CZ-12843 Praha 2, Czech Republic
| | - Vladimír Křen
- Laboratory of Biotransformation, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-14220, Praha 4, Czech Republic.
| | - Pavel Lhoták
- University of Chemistry and Technology Prague, Technická 5, CZ-16628 Praha 6, Czech Republic.
| | - Jitka Viktorová
- University of Chemistry and Technology Prague, Technická 5, CZ-16628 Praha 6, Czech Republic.
| | - Pavla Bojarová
- Laboratory of Biotransformation, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-14220, Praha 4, Czech Republic.
- Department of Health Care Disciplines and Population Protection, Faculty of Biomedical Engineering, Czech Technical University in Prague, nám. Sítná 3105, CZ-27201 Kladno, Czech Republic
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Meng S, Wang YU, Wang S, Qian W, Shao Q, Dou M, Zhao S, Wang J, Li M, An Y, He L, Zhang C. Establishment and characterization of an immortalized bovine intestinal epithelial cell line. J Anim Sci 2023; 101:skad215. [PMID: 37351870 PMCID: PMC10347977 DOI: 10.1093/jas/skad215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 06/22/2023] [Indexed: 06/24/2023] Open
Abstract
Primary bovine intestinal epithelial cells (PBIECs) are an important model for studying the molecular and pathogenic mechanisms of diseases affecting the bovine intestine. It is difficult to obtain and grow PBIECs stably, and their short lifespan greatly limits their application. Therefore, the purpose of this study was to create a cell line for exploring the mechanisms of pathogen infection in bovine intestinal epithelial cells in vitro. We isolated and cultured PBIECs and established an immortalized BIEC line by transfecting PBIECs with the pCI-neo-hTERT (human telomerase reverse transcriptase) recombinant plasmid. The immortalized cell line (BIECs-21) retained structure and function similar to that of the PBIECs. The marker proteins characteristic of epithelial cells, cytokeratin 18, occludin, zonula occludens protein 1 (ZO-1), E-cadherin and enterokinase, were all positive in the immortalized cell line, and the cell structure, growth rate, karyotype, serum dependence and contact inhibition were normal. The hTERT gene was successfully transferred into BIECs-21 where it remained stable and was highly expressed. The transport of short-chain fatty acids and glucose uptake by the BIECs-21 was consistent with PBIECs, and we showed that they could be infected with the intestinal parasite, Neospora caninum. The immortalized BIECs-21, which have exceeded 80 passages, were structurally and functionally similar to the primary BIECs and thus provide a valuable research tool for investigating the mechanism of pathogen infection of the bovine intestinal epithelium in vitro.
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Affiliation(s)
- Sudan Meng
- Henan International Joint Laboratory of Animal Welfare and Health Breeding, Henan University of Science and Technology, Luoyang 471023, China
- Innovative Research Team of Livestock Intelligent Breeding and Equipment, Longmen Laboratory, Luoyang 471023, China
| | - Y uexin Wang
- Henan International Joint Laboratory of Animal Welfare and Health Breeding, Henan University of Science and Technology, Luoyang 471023, China
| | - Shuai Wang
- Henan International Joint Laboratory of Animal Welfare and Health Breeding, Henan University of Science and Technology, Luoyang 471023, China
| | - Weifeng Qian
- Henan International Joint Laboratory of Animal Welfare and Health Breeding, Henan University of Science and Technology, Luoyang 471023, China
| | - Qi Shao
- Henan International Joint Laboratory of Animal Welfare and Health Breeding, Henan University of Science and Technology, Luoyang 471023, China
| | - Mengying Dou
- Henan International Joint Laboratory of Animal Welfare and Health Breeding, Henan University of Science and Technology, Luoyang 471023, China
| | - Shujuan Zhao
- Henan International Joint Laboratory of Animal Welfare and Health Breeding, Henan University of Science and Technology, Luoyang 471023, China
| | - Jianguo Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China
| | - Mengyun Li
- Henan International Joint Laboratory of Animal Welfare and Health Breeding, Henan University of Science and Technology, Luoyang 471023, China
| | - Yongsheng An
- Henan International Joint Laboratory of Animal Welfare and Health Breeding, Henan University of Science and Technology, Luoyang 471023, China
| | - Lei He
- Henan International Joint Laboratory of Animal Welfare and Health Breeding, Henan University of Science and Technology, Luoyang 471023, China
| | - Cai Zhang
- Henan International Joint Laboratory of Animal Welfare and Health Breeding, Henan University of Science and Technology, Luoyang 471023, China
- Henan Engineering Research Center of Livestock and Poultry Eerging Disease Detection and Control, Luoyang 471023, China
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Müller L, Keuter L, Bücksteeg D, Uebel T, Wilken M, Schürmann L, Behrens M, Humpf HU, Esselen M. Metabolic conjugation reduces in vitro toxicity of the flavonoid nevadensin. Food Chem Toxicol 2022; 164:113006. [PMID: 35436549 DOI: 10.1016/j.fct.2022.113006] [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: 02/08/2022] [Revised: 03/18/2022] [Accepted: 04/07/2022] [Indexed: 02/07/2023]
Abstract
The present study focuses on the association between metabolic capacity and toxicity of the natural occurring flavonoid nevadensin in vitro. Human colon (HT29), liver (HepG2) and bone marrow (KG1) carcinoma cells were used and strong cell line dependent differences in toxic effect strength were found. HepG2 and KG1 cells were more sensitive against nevadensin treatment in comparison to HT29 cells. High resolution mass spectrometry experiments showed that nevadensin is rapidly glucuronidated in HT29 cells, whereas KG1 cells do not metabolize nevadensin, thus glucuronidation was supposed to be a crucial metabolic pathway in vitro. To proof this suggestion, nevadensin glucuronides were isolated from pig liver microsomes und structurally elucidated via NMR spectroscopy. In HepG2 cells a cellular enrichment of nevadensin itself as well as nevadensin-7-O-glucuronide was determined by tandem mass spectrometry. A proteomic screening of uridine 5'-diphospho (UDP)-glucuronosyltransferase (UGT) in HT29 and HepG2 cells provided first hints that the isoforms UGT1A6 and UGT1A1 are responsible for nevadensin glucuronidation. Additionally, nevadensin was found to be a potent SULT inhibitor in HepG2 cells. In sum, the present study clearly illustrates the importance of obtaining detailed information about metabolic competence of cell lines which should be considered in the evaluation of toxic endpoints.
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Affiliation(s)
- Lena Müller
- University of Münster, Institute of Food Chemistry, Corrensstraße 45, 48149, Münster, Germany
| | - Lucas Keuter
- University of Münster, Institute of Food Chemistry, Corrensstraße 45, 48149, Münster, Germany
| | - David Bücksteeg
- University of Münster, Institute of Food Chemistry, Corrensstraße 45, 48149, Münster, Germany
| | - Thomas Uebel
- University of Münster, Institute of Food Chemistry, Corrensstraße 45, 48149, Münster, Germany
| | - Markus Wilken
- University of Münster, Institute of Food Chemistry, Corrensstraße 45, 48149, Münster, Germany
| | - Lina Schürmann
- University of Münster, Institute of Food Chemistry, Corrensstraße 45, 48149, Münster, Germany
| | - Matthias Behrens
- University of Münster, Institute of Food Chemistry, Corrensstraße 45, 48149, Münster, Germany
| | - Hans-Ulrich Humpf
- University of Münster, Institute of Food Chemistry, Corrensstraße 45, 48149, Münster, Germany
| | - Melanie Esselen
- University of Münster, Institute of Food Chemistry, Corrensstraße 45, 48149, Münster, Germany.
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5
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Valproic acid treatment rescues injured tissues after traumatic brain injury. J Trauma Acute Care Surg 2021; 89:1156-1165. [PMID: 32890344 DOI: 10.1097/ta.0000000000002918] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
BACKGROUND No agents that are specifically neuroprotective are currently approved to emergently treat patients with traumatic brain injury (TBI). The histone deacetylase inhibitor, high-dose valproic acid (VPA) has been shown to have cytoprotective potential in models of combined TBI and hemorrhagic shock, but it has not been tested in an isolated TBI model. We hypothesized that VPA, administered after isolated TBI, will penetrate the injured brain, attenuate the lesion size, and activate prosurvival pathways. METHODS Yorkshire swine were subjected to severe TBI by cortical impact. One hour later, animals were randomized to VPA treatment (150 mg/kg delivered intravenously for 1 hour; n = 4) or control (saline vehicle; n = 4) groups. Seven hours after injury, animals were sacrificed, and brain lesion size was measured. Mass spectrometry imaging was used to visualize and quantitate brain tissue distribution of VPA. Sequential serum samples were assayed for key biomarkers and subjected to proteomic and pathway analysis. RESULTS Brain lesion size was 50% smaller (p = 0.01) in the VPA-treated animals (3,837 ± 948 mm) compared with the controls (1,900 ± 614 mm). Endothelial regions had eightfold higher VPA concentrations than perivascular regions by mass spectrometry imaging, and it readily penetrated the injured brain tissues. Serum glial fibrillary acid protein was significantly lower in the VPA-treated compared with the control animals (p < 0.05). More than 500 proteins were differentially expressed in the brain, and pathway analysis revealed that VPA affected critical modulators of TBI response including calcium signaling pathways, mitochondria metabolism, and biosynthetic machinery. CONCLUSION Valproic acid penetrates injured brain tissues and exerts neuroprotective and prosurvival effects that resulted in a significant reduction in brain lesion size after isolated TBI. Levels of serum biomarkers reflect these changes, which could be useful for monitoring the response of TBI patients during clinical studies.
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6
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Wang F, Qin G, Liu J, Wang X, Ye B. Bio-analytical Identification of Key Genes that Could Contribute to the Progression and Metastasis of Osteosarcoma. Curr Bioinform 2021. [DOI: 10.2174/1574893615999200801014939] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Osteosarcoma (OS) is one of the most common primary malignant bone
tumors in children and adolescents. OS metastasis has been a challenge in the treatment of OS. The
present study screened progression related genes in OS by analyzing a public dataset GSE42352,
and identified 691 up-regulated and 945 down-regulated genes in advanced stage OS compared to
early-stage OS samples.
Methods:
Protein-protein interaction (PPI) networks were further employed to reveal the
interaction among these genes. Bioinformatics analysis showed that progression related differently
expressed genes (DEGs) were significantly associated with the regulation of cell proliferation and
metabolisms.
Results:
This study revealed that progression related DEGs were dysregulated in metastatic OS
compared to non-metastatic OS samples. Further analysis showed CSF1R, CASP1, CD163,
AP1B1, LAPTM5, PEX19, SLA, STAB1, YWHAH, PLCB2, and GPR84 were associated with the
metastasis-free survival time in patients with OS.
Conclusions:
These findings provided novel information for us to understand the mechanisms
underlying the progression and metastasis of OS.
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Affiliation(s)
- Fei Wang
- Department of Orthopedics, China-Japan Union Hospital Jilin University, Changchun, Jilin,China
| | - Guoqing Qin
- Department of Orthopedics, Jilin Disabled Persons' Rehabilitation Center, (Jilin Chunguang Rehabilitation Hospital), Changchun, Jilin,China
| | - Junzhi Liu
- Quality Control Department, China-Japan Union Hospital Jilin University, Changchun, Jilin,China
| | - Xiunan Wang
- Department of Orthopedics, The 964th Hospital of the PLA Joint Logistics Support Force, No. 4799 Xi 'an Road, Lvyuan District, Changchun City, Jilin Province,China
| | - Baoguo Ye
- Department of Anesthesiology, China-Japan Union Hospital Jilin University, Changchun, Jilin,China
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Eosinophil microRNAs Play a Regulatory Role in Allergic Diseases Included in the Atopic March. Int J Mol Sci 2020; 21:ijms21239011. [PMID: 33260893 PMCID: PMC7730597 DOI: 10.3390/ijms21239011] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 11/23/2020] [Accepted: 11/25/2020] [Indexed: 12/11/2022] Open
Abstract
(1) Background: The atopic march is defined by the increased prevalence of allergic diseases after atopic dermatitis onset. In fact, atopic dermatitis is believed to play an important role in allergen sensitization via the damaged skin barrier, leading to allergic diseases such as allergic asthma and allergic rhinitis. The eosinophil, a pro-inflammatory cell that contributes to epithelial damage, is one of the various cells recruited in the inflammatory reactions characterizing these diseases. Few studies were conducted on the transcriptome of this cell type and even less on their specific microRNA (miRNA) profile, which could modulate pathogenesis of allergic diseases and clinical manifestations post-transcriptionally. Actually, their implication in allergic diseases is not fully understood, but they are believed to play a role in inflammation-related patterns and epithelial cell proliferation. (2) Methods: Next-generation sequencing was performed on RNA samples from eosinophils of individuals with atopic dermatitis, atopy, allergic rhinitis and asthma to obtain differential counts of primary miRNA (pri-miRNA); these were also analyzed for asthma-related phenotypes such as forced expiratory volume in one second (FEV1), immunoglobulin E (IgE) and provocative concentration of methacholine inducing a 20% fall in forced expiratory volume in 1 s (PC20) levels, as well as FEV1 to forced vital capacity (FEV1/FVC) ratio. (3) Results: Eighteen miRNAs from eosinophils were identified to be significantly different between affected individuals and unaffected ones. Based on counts from these miRNAs, individuals were then clustered into groups using Ward's method on Euclidian distances. Groups were found to be explained by asthma diagnosis, familial history of respiratory diseases and allergic rhinitis as well as neutrophil counts. (4) Conclusions: The 18 differential miRNA counts for the studying phenotypes allow a better understanding of the epigenetic mechanisms underlying the development of the allergic diseases included in the atopic march.
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8
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Functional omics analyses reveal only minor effects of microRNAs on human somatic stem cell differentiation. Sci Rep 2020; 10:3284. [PMID: 32094412 PMCID: PMC7040006 DOI: 10.1038/s41598-020-60065-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 01/30/2020] [Indexed: 01/12/2023] Open
Abstract
The contribution of microRNA-mediated posttranscriptional regulation on the final proteome in differentiating cells remains elusive. Here, we evaluated the impact of microRNAs (miRNAs) on the proteome of human umbilical cord blood-derived unrestricted somatic stem cells (USSC) during retinoic acid (RA) differentiation by a systemic approach using next generation sequencing analysing mRNA and miRNA expression and quantitative mass spectrometry-based proteome analyses. Interestingly, regulation of mRNAs and their dedicated proteins highly correlated during RA-incubation. Additionally, RA-induced USSC demonstrated a clear separation from native USSC thereby shifting from a proliferating to a metabolic phenotype. Bioinformatic integration of up- and downregulated miRNAs and proteins initially implied a strong impact of the miRNome on the XXL-USSC proteome. However, quantitative proteome analysis of the miRNA contribution on the final proteome after ectopic overexpression of downregulated miR-27a-5p and miR-221-5p or inhibition of upregulated miR-34a-5p, respectively, followed by RA-induction revealed only minor proportions of differentially abundant proteins. In addition, only small overlaps of these regulated proteins with inversely abundant proteins in non-transfected RA-treated USSC were observed. Hence, mRNA transcription rather than miRNA-mediated regulation is the driving force for protein regulation upon RA-incubation, strongly suggesting that miRNAs are fine-tuning regulators rather than active primary switches during RA-induction of USSC.
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Schira-Heinen J, Grube L, Waldera-Lupa DM, Baberg F, Langini M, Etemad-Parishanzadeh O, Poschmann G, Stühler K. Pitfalls and opportunities in the characterization of unconventionally secreted proteins by secretome analysis. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:140237. [DOI: 10.1016/j.bbapap.2019.06.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 06/04/2019] [Accepted: 06/06/2019] [Indexed: 02/07/2023]
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Emery-Corbin SJ, Grüttner J, Svärd S. Transcriptomic and proteomic analyses of Giardia intestinalis: Intestinal epithelial cell interactions. ADVANCES IN PARASITOLOGY 2019; 107:139-171. [PMID: 32122528 DOI: 10.1016/bs.apar.2019.11.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Giardia intestinalis is a unicellular protozoan parasite that infects the small intestines of humans and animals. Giardiasis, the disease caused by the parasite, occurs globally across socioeconomic boundaries but is mainly endemic in developing countries and particularly within young children, where pronounced effects manifests in a failure to thrive condition. The molecular pathogenesis of Giardia has been studied using in vitro models of human and rat intestinal epithelial cells (IECs) and parasites from the two major human genotypes or assemblages (A and B). High-quality, genome sequencing of representative isolates from assemblages A (WB) and B (GS) has enabled exploration of these host-parasite models using 'omics' technologies, allowing deep and quantitative analyses of global gene expression changes in IECs and parasites during their interactions, cross-talk and competition. These include a major up-regulation of immune-related genes in the IECs early after the start of interactions, as well as competition between host cells and parasites for nutrients like sugars, amino acids and lipids, which is also reflected in their secretome interactions. Unique parasite proteins dominate these interactions, with many major up-regulated genes being either hypothetical proteins or members of Giardia-specific gene families like the high-cysteine-rich membrane proteins (HCMPs), variable surface proteins (VSPs), alpha-giardins and cysteine proteases. Furthermore, these proteins also dominate in the secretomes, suggesting that they are important virulence factors in Giardia and crucial molecular effectors at the host-parasite interface.
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Affiliation(s)
- Samantha J Emery-Corbin
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, VIC, Australia
| | - Jana Grüttner
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Staffan Svärd
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.
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Murphy S, Zweyer M, Raucamp M, Henry M, Meleady P, Swandulla D, Ohlendieck K. Proteomic profiling of the mouse diaphragm and refined mass spectrometric analysis of the dystrophic phenotype. J Muscle Res Cell Motil 2019; 40:9-28. [PMID: 30888583 DOI: 10.1007/s10974-019-09507-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 03/08/2019] [Indexed: 12/11/2022]
Abstract
The diaphragm is a crucial muscle involved in active inspiration and whole body homeostasis. Previous biochemical, immunochemical and cell biological investigations have established the distribution and fibre type-specific expression of key diaphragm proteins. Building on these findings, it was of interest to establish the entire experimentally assessable diaphragm proteome and verify the presence of specific protein isoforms within this specialized subtype of skeletal muscle. A highly sensitive Orbitrap Fusion Tribrid mass spectrometer was used for the systematic identification of the mouse diaphragm-associated protein population. Proteomics established 2925 proteins by high confidence peptide identification. Bioinformatics was used to determine the distribution of the main protein classes, biological processes and subcellular localization within the diaphragm proteome. Following the establishment of the respiratory muscle proteome with special emphasis on protein isoform expression in the contractile apparatus, the extra-sarcomeric cytoskeleton, the extracellular matrix and the excitation-contraction coupling apparatus, the mass spectrometric analysis of the diaphragm was extended to the refined identification of proteome-wide changes in X-linked muscular dystrophy. The comparative mass spectrometric profiling of the dystrophin-deficient diaphragm from the mdx-4cv mouse model of Duchenne muscular dystrophy identified 289 decreased and 468 increased protein species. Bioinformatics was employed to analyse the clustering of changes in protein classes and potential alterations in interaction patterns of proteins involved in metabolism, the contractile apparatus, proteostasis and the extracellular matrix. The detailed pathoproteomic profiling of the mdx-4cv diaphragm suggests highly complex alterations in a variety of crucial cellular processes due to deficiency in the membrane cytoskeletal protein dystrophin.
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Affiliation(s)
- Sandra Murphy
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland.,Newcastle Fibrosis Research Group, Institute of Cellular Medicine, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Margit Zweyer
- Institute of Physiology II, University of Bonn, 53115, Bonn, Germany
| | - Maren Raucamp
- Institute of Physiology II, University of Bonn, 53115, Bonn, Germany
| | - Michael Henry
- National Institute for Cellular Biotechnology, Dublin City University, Dublin 9, Ireland
| | - Paula Meleady
- National Institute for Cellular Biotechnology, Dublin City University, Dublin 9, Ireland
| | - Dieter Swandulla
- Institute of Physiology II, University of Bonn, 53115, Bonn, Germany
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland.
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12
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Wu YZ, Chan KYY, Leung KT, Lam HS, Tam YH, Lee KH, Li K, Ng PC. Dysregulation of miR-431 and target gene FOXA1 in intestinal tissues of infants with necrotizing enterocolitis. FASEB J 2019; 33:5143-5152. [PMID: 30624964 DOI: 10.1096/fj.201801470r] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The level of microRNA (miR)-431 was found to be markedly up-regulated in intestinal tissue of necrotizing enterocolitis (NEC). The objective of this study was to identify the target gene of miR-431 and to investigate the role of the miR-431-FOXA1 axis in the pathophysiology of NEC. The target gene of miR-431 was identified by in silico target prediction bioinformatics, luciferase assay, and Western blotting. Effects of miR-431 on downstream expression signals, cell proliferation, and apoptosis were investigated by overexpression in Caco-2 cells upon stimulation by LPS or lipoteichoic acid (LTA). FOXA1 was identified as the target gene of miR-431. Overexpression of miR-431 in Caco-2 cells significantly inhibited FOXA1, ESRRG, and HNF4A and activated IL-6, LGR5, NFKB2, PLA2G2A, PRKCZ, and TNF. IL-8 and - 10 were enhanced when costimulated with LPS or LTA. These potential downstream genes were also significantly dysregulated in primary NEC tissues compared with surgical-control tissues. Overexpression of miR-431 significantly decreased proliferation and increased apoptosis of Caco-2 cells. A proposed network of miR-431-FOXA1 interaction with LPS and LTA receptors demonstrates dysregulation of transcription factors, inflammatory mediators, epithelium tight junction regulators, and cell proliferation and apoptosis signals. The miR-431-FOXA1 axis could in part be responsible for the intensification of the inflammatory response in NEC tissues and contribute to the proinflammatory pathophysiology.-Wu, Y. Z., Chan, K. Y. Y., Leung, K. T., Lam, H. S., Tam, Y. H., Lee, K. H., Li, K., Ng, P. C. Dysregulation of miR-431 and target gene FOXA1 in intestinal tissues of infants with necrotizing enterocolitis.
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Affiliation(s)
- Yu Zheng Wu
- Department of Paediatrics, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong; and
| | - Kathy Yuen Yee Chan
- Department of Paediatrics, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong; and
| | - Kam Tong Leung
- Department of Paediatrics, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong; and
| | - Hugh Simon Lam
- Department of Paediatrics, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong; and
| | - Yuk Him Tam
- Department of Surgery, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Kim Hung Lee
- Department of Surgery, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Karen Li
- Department of Paediatrics, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong; and
| | - Pak Cheung Ng
- Department of Paediatrics, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong; and
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Murphy S, Zweyer M, Henry M, Meleady P, Mundegar RR, Swandulla D, Ohlendieck K. Proteomic profiling of liver tissue from the mdx- 4cv mouse model of Duchenne muscular dystrophy. Clin Proteomics 2018; 15:34. [PMID: 30386187 PMCID: PMC6205794 DOI: 10.1186/s12014-018-9212-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 10/23/2018] [Indexed: 12/30/2022] Open
Abstract
Background Duchenne muscular dystrophy is a highly complex multi-system disease caused by primary abnormalities in the membrane cytoskeletal protein dystrophin. Besides progressive skeletal muscle degeneration, this neuromuscular disorder is also associated with pathophysiological perturbations in many other organs including the liver. To determine potential proteome-wide alterations in liver tissue, we have used a comparative and mass spectrometry-based approach to study the dystrophic mdx-4cv mouse model of dystrophinopathy. Methods The comparative proteomic profiling of mdx-4cv versus wild type liver extracts was carried out with an Orbitrap Fusion Tribrid mass spectrometer. The distribution of identified liver proteins within protein families and potential protein interaction patterns were analysed by systems bioinformatics. Key findings on fatty acid binding proteins were confirmed by immunoblot analysis and immunofluorescence microscopy. Results The proteomic analysis revealed changes in a variety of protein families, affecting especially fatty acid, carbohydrate and amino acid metabolism, biotransformation, the cellular stress response and ion handling in the mdx-4cv liver. Drastically increased protein species were identified as fatty acid binding protein FABP5, ferritin and calumenin. Decreased liver proteins included phosphoglycerate kinase, apolipoprotein and perilipin. The drastic change in FABP5 was independently verified by immunoblotting and immunofluorescence microscopy. Conclusions The proteomic results presented here indicate that the intricate and multifaceted pathogenesis of the mdx-4cv model of dystrophinopathy is associated with secondary alterations in the liver affecting especially fatty acid transportation. Since FABP5 levels were also shown to be elevated in serum from dystrophic mice, this protein might be a useful indicator for monitoring liver changes in X-linked muscular dystrophy.
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Affiliation(s)
- Sandra Murphy
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland
| | - Margit Zweyer
- 2Institute of Physiology II, University of Bonn, 53115 Bonn, Germany
| | - Michael Henry
- 3National Institute for Cellular Biotechnology, Dublin City University, Dublin 9, Ireland
| | - Paula Meleady
- 3National Institute for Cellular Biotechnology, Dublin City University, Dublin 9, Ireland
| | - Rustam R Mundegar
- 2Institute of Physiology II, University of Bonn, 53115 Bonn, Germany
| | - Dieter Swandulla
- 2Institute of Physiology II, University of Bonn, 53115 Bonn, Germany
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland
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Murphy S, Henry M, Meleady P, Ohlendieck K. Utilization of dried and long-term stored polyacrylamide gels for the advanced proteomic profiling of mitochondrial contact sites from rat liver. Biol Methods Protoc 2018; 3:bpy008. [PMID: 32161802 PMCID: PMC6994098 DOI: 10.1093/biomethods/bpy008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 06/07/2018] [Accepted: 07/24/2018] [Indexed: 11/25/2022] Open
Abstract
Following subcellular fractionation, the complexity of proteins derived from a particular cellular compartment is often evaluated by gel electrophoretic analysis. For the proteomic cataloguing of these distinct protein populations and their biochemical characterization, gel electrophoretic protein separation can be conveniently combined with liquid chromatography mass spectrometry. Here we describe a gel-enhanced liquid chromatography mass spectrometry (GeLC-MS)/MS approach with a new bioanalytical focus on the proteomic profiling of mitochondrial contact sites from rat liver using the highly sensitive Orbitrap Fusion Tribrid mass spectrometer for optimum protein identification following extraction from dried and long-term stored gels. Mass spectrometric analysis identified 964 protein species in the mitochondrial contact site fraction, whereby 459 proteins were identified by ≥3 unique peptides. This included mitochondrial components of the supramolecular complexes that form the ATP synthase, the respiratory chain, ribosomal subunits and the cytochrome P450 system, as well as crucial components of the translocase complexes translocase of the inner membrane (TIM) and translocase of the outer membrane (TOM) of the two mitochondrial membranes. Proteomics also identified contact site markers, such as glutathione transferase, monoamine oxidase and the pore protein voltage dependent anion channel (VDAC)-1. Hence, this report demonstrates that the GeLC-MS/MS method can be used to study complex mixtures of proteins that have been embedded and stored in dried polyacrylamide gels for a long period of time. Careful re-swelling and standard in-gel digestion is suitable to produce peptide profiles from old gels that can be used to extract sophisticated proteomic maps and enable the subsequent bioinformatics analysis of the distribution of protein function and the determination of potential protein clustering within the contact site system.
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Affiliation(s)
- Sandra Murphy
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland
| | - Michael Henry
- National Institute for Cellular Biotechnology, Dublin City University, Dublin 9, Ireland
| | - Paula Meleady
- National Institute for Cellular Biotechnology, Dublin City University, Dublin 9, Ireland
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland
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