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Sebastià C, Gallopin M, Ramayo-Caldas Y, Estellé J, Valdés-Hernández J, Castelló A, Sánchez A, Crespo-Piazuelo D, Folch JM. Gene co-expression network analysis for porcine intramuscular fatty acid composition. Animal 2024; 18:101259. [PMID: 39137614 DOI: 10.1016/j.animal.2024.101259] [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: 10/19/2023] [Revised: 07/08/2024] [Accepted: 07/09/2024] [Indexed: 08/15/2024] Open
Abstract
In pigs, meat quality depends markedly on the fatty acid (FA) content and composition of the intramuscular fat, which is partly determined by the gene expression in this tissue. The aim of this work was to identify the link between muscle gene expression and its FA composition. In an (Iberian × Duroc) × Duroc backcrossed pig population, we identified modules of co-expressed genes, and correlation analyses were performed for each of them versus the phenotypes, finding four relevant modules. Two of the modules were positively correlated with saturated FAs (SFAs) and monounsaturated FAs (MUFAs), while negatively correlated with polyunsaturated FAs (PUFAs) and the omega-6/omega-3 ratio. The gene-enrichment analysis showed that these modules had over-representation of pathways related with the biosynthesis of unsaturated FAs, the Peroxisome proliferator-activated receptor signalling pathway and FA elongation. The two other relevant modules were positively correlated with PUFA and the n-6/n-3 ratio, but negatively correlated with SFA and MUFA. In this case, they had an over-representation of pathways related with fatty and amino acid degradation, and with oxidative phosphorylation. Using a graphical Gaussian model, we inferred a network of connections between the genes within each module. The first module had 52 genes with 87 connections, and the most connected genes were ADIPOQ, which is related with FA oxidation, and ELOVL6 and FABP4, both involved in FA metabolism. The second module showed 196 genes connected by 263 edges, being FN1 and MAP3K11 the most connected genes. On the other hand, the third module had 161 genes connected by 251 edges and ATG13 was the top neighbouring gene, while the fourth module had 224 genes and 655 connections, and its most connected genes were related with mitochondrial pathways. Overall, this work successfully identified relevant muscle gene networks and modules linked with FA composition, providing further insights on how the physiology of the pigs influences FA composition.
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Affiliation(s)
- C Sebastià
- Plant and Animal Genomics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, C. de la Vall Moronta, 08193 Bellaterra, Spain; Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona (UAB), Edifici V, Travessera dels Turons, 08193 Bellaterra, Spain.
| | - M Gallopin
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 1, Avenue de la Terrasse, Bâtiment 21, 91190 Gif-sur-Yvette, France
| | - Y Ramayo-Caldas
- Departament de Genètica i Millora Animal, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Torre Marimon, 08140 Caldes de Montbui, Spain
| | - J Estellé
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Domaine de Vilvert, 78350 Jouy-en-Josas, France
| | - J Valdés-Hernández
- Plant and Animal Genomics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, C. de la Vall Moronta, 08193 Bellaterra, Spain; Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona (UAB), Edifici V, Travessera dels Turons, 08193 Bellaterra, Spain
| | - A Castelló
- Plant and Animal Genomics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, C. de la Vall Moronta, 08193 Bellaterra, Spain; Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona (UAB), Edifici V, Travessera dels Turons, 08193 Bellaterra, Spain
| | - A Sánchez
- Plant and Animal Genomics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, C. de la Vall Moronta, 08193 Bellaterra, Spain; Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona (UAB), Edifici V, Travessera dels Turons, 08193 Bellaterra, Spain
| | - D Crespo-Piazuelo
- Departament de Genètica i Millora Animal, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Torre Marimon, 08140 Caldes de Montbui, Spain; R&D Department, Cuarte S.L., Grupo Jorge, Autov. Zaragoza-Logroño, km.9, 50120 Monzalbarba, Spain
| | - J M Folch
- Plant and Animal Genomics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, C. de la Vall Moronta, 08193 Bellaterra, Spain; Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona (UAB), Edifici V, Travessera dels Turons, 08193 Bellaterra, Spain
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2
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Wang Y, Saelao P, Chanthavixay G, Gallardo RA, Wolc A, Fulton JE, Dekkers JM, Lamont SJ, Kelly TR, Zhou H. Genomic Regions and Candidate Genes Affecting Response to Heat Stress with Newcastle Virus Infection in Commercial Layer Chicks Using Chicken 600K Single Nucleotide Polymorphism Array. Int J Mol Sci 2024; 25:2640. [PMID: 38473888 DOI: 10.3390/ijms25052640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 02/19/2024] [Accepted: 02/22/2024] [Indexed: 03/14/2024] Open
Abstract
Heat stress results in significant economic losses to the poultry industry. Genetics plays an important role in chickens adapting to the warm environment. Physiological parameters such as hematochemical parameters change in response to heat stress in chickens. To explore the genetics of heat stress resilience in chickens, a genome-wide association study (GWAS) was conducted using Hy-Line Brown layer chicks subjected to either high ambient temperature or combined high temperature and Newcastle disease virus infection. Hematochemical parameters were measured during three treatment phases: acute heat stress, chronic heat stress, and chronic heat stress combined with NDV infection. Significant changes in blood parameters were recorded for 11 parameters (sodium (Na+, potassium (K+), ionized calcium (iCa2+), glucose (Glu), pH, carbon dioxide partial pressure (PCO2), oxygen partial pressure (PO2), total carbon dioxide (TCO2), bicarbonate (HCO3), base excess (BE), and oxygen saturation (sO2)) across the three treatments. The GWAS revealed 39 significant SNPs (p < 0.05) for seven parameters, located on Gallus gallus chromosomes (GGA) 1, 3, 4, 6, 11, and 12. The significant genomic regions were further investigated to examine if the genes within the regions were associated with the corresponding traits under heat stress. A candidate gene list including genes in the identified genomic regions that were also differentially expressed in chicken tissues under heat stress was generated. Understanding the correlation between genetic variants and resilience to heat stress is an important step towards improving heat tolerance in poultry.
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Affiliation(s)
- Ying Wang
- Genomics to Improve Poultry Innovation Lab, University of California, Davis, CA 95616, USA
- Department of Animal Science, University of California, Davis, CA 95616, USA
| | - Perot Saelao
- Genomics to Improve Poultry Innovation Lab, University of California, Davis, CA 95616, USA
- Department of Animal Science, University of California, Davis, CA 95616, USA
- Veterinary Pest Genetics Research Unit, United States Department of Agriculture U, Kerrville, TX 78006, USA
| | - Ganrea Chanthavixay
- Genomics to Improve Poultry Innovation Lab, University of California, Davis, CA 95616, USA
- Department of Animal Science, University of California, Davis, CA 95616, USA
| | - Rodrigo A Gallardo
- Genomics to Improve Poultry Innovation Lab, University of California, Davis, CA 95616, USA
- School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Anna Wolc
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA
- Hy-Line International, Dallas Center, IA 50063, USA
| | | | - Jack M Dekkers
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA
| | - Susan J Lamont
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA
| | - Terra R Kelly
- Genomics to Improve Poultry Innovation Lab, University of California, Davis, CA 95616, USA
- School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Huaijun Zhou
- Genomics to Improve Poultry Innovation Lab, University of California, Davis, CA 95616, USA
- Department of Animal Science, University of California, Davis, CA 95616, USA
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Schreurs G, Maudsley S, Nast C, Praet M, Da Silva Fernandes S, Boor P, D'Haese P, De Broe ME, Vervaet BA. Chronic dehydration induces injury pathways in rats, but does not mimic histopathology of chronic interstitial nephritis in agricultural communities. Sci Rep 2023; 13:18119. [PMID: 37872220 PMCID: PMC10593944 DOI: 10.1038/s41598-023-43567-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 09/26/2023] [Indexed: 10/25/2023] Open
Abstract
CINAC-patients present renal proximal tubular cell lysosomal lesions which are also observed in patients experiencing calcineurin inhibitor (CNI) nephrotoxicity, suggesting that CINAC is a toxin-induced nephropathy. An alternative hypothesis advocates chronic dehydration as a major etiological factor for CINAC. Here, we evaluated histological and molecular changes in dehydrated versus toxin exposed rats. Wistar rats were divided in 3 groups. Group 1 (n = 6) had free access to drinking water (control group). Group 2 (n = 8) was water deprived for 10 h per 24 h, 5 days/week and placed in an incubator (37 °C) for 30 min/h during water deprivation. Group 3 (n = 8) underwent daily oral gavage with cyclosporine (40 mg/kg body weight). After 28 days, renal function, histopathology and proteomic signatures were analysed. Cyclosporine-treated rats developed focal regions of atrophic proximal tubules with associated tubulo-interstitial fibrosis. PASM staining revealed enlarged argyrophilic granules in affected proximal tubules, identified as lysosomes by immunofluorescent staining. Electron microscopy confirmed the enlarged and dysmorphic phenotype of the lysosomes. Overall, these kidney lesions resemble those that have been previously documented in farmers with CINAC. Dehydration resulted in none of the above histopathological features. Proteomic analysis revealed that dehydration and cyclosporine both induce injury pathways, yet of a clear distinct nature with a signature of toxicity only for the cyclosporine group. In conclusion, both cyclosporine and dehydration are injurious to the kidney. However, dehydration alone does not result in kidney histopathology as observed in CINAC patients, whereas cyclosporine administration does. The histopathological analogy between CINAC and calcineurin inhibitor nephrotoxicity in rats and humans supports the involvement of an as-yet-unidentified environmental toxin in CINAC etiology.
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Affiliation(s)
- Gerd Schreurs
- Laboratory of Pathophysiology, University of Antwerp, Universiteitsplein 1, 2610, Antwerp, Belgium
| | - Stuart Maudsley
- Receptor Biology Lab, Department of Biomedical Science, University of Antwerp, Antwerp, Belgium
| | | | - Marleen Praet
- Department of Pathology, Ghent University Hospital, Ghent, Belgium
| | | | - Peter Boor
- Institute of Pathology, Electron Microscopy Facility and Division of Nephrology and Immunology, RWTH Aachen University Hospital, Aachen, Germany
| | - Patrick D'Haese
- Laboratory of Pathophysiology, University of Antwerp, Universiteitsplein 1, 2610, Antwerp, Belgium
| | - Marc E De Broe
- Laboratory of Pathophysiology, University of Antwerp, Universiteitsplein 1, 2610, Antwerp, Belgium
| | - Benjamin A Vervaet
- Laboratory of Pathophysiology, University of Antwerp, Universiteitsplein 1, 2610, Antwerp, Belgium.
- Institute of Pathology, RWTH Aachen University Hospital, Aachen, Germany.
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Sneha NP, Dharshini SAP, Taguchi YH, Gromiha MM. Investigating Neuron Degeneration in Huntington's Disease Using RNA-Seq Based Transcriptome Study. Genes (Basel) 2023; 14:1801. [PMID: 37761940 PMCID: PMC10530489 DOI: 10.3390/genes14091801] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 09/02/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
Huntington's disease (HD) is a progressive neurodegenerative disorder caused due to a CAG repeat expansion in the huntingtin (HTT) gene. The primary symptoms of HD include motor dysfunction such as chorea, dystonia, and involuntary movements. The primary motor cortex (BA4) is the key brain region responsible for executing motor/movement activities. Investigating patient and control samples from the BA4 region will provide a deeper understanding of the genes responsible for neuron degeneration and help to identify potential markers. Previous studies have focused on overall differential gene expression and associated biological functions. In this study, we illustrate the relationship between variants and differentially expressed genes/transcripts. We identified variants and their associated genes along with the quantification of genes and transcripts. We also predicted the effect of variants on various regulatory activities and found that many variants are regulating gene expression. Variants affecting miRNA and its targets are also highlighted in our study. Co-expression network studies revealed the role of novel genes. Function interaction network analysis unveiled the importance of genes involved in vesicle-mediated transport. From this unified approach, we propose that genes expressed in immune cells are crucial for reducing neuron death in HD.
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Affiliation(s)
- Nela Pragathi Sneha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, Tamil Nadu, India; (N.P.S.); (S.A.P.D.)
| | - S. Akila Parvathy Dharshini
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, Tamil Nadu, India; (N.P.S.); (S.A.P.D.)
| | - Y.-h. Taguchi
- Department of Physics, Chuo University, Kasuga, Bunkyo-ku, Tokyo 112-8551, Japan;
| | - M. Michael Gromiha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, Tamil Nadu, India; (N.P.S.); (S.A.P.D.)
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5
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Feng S, Jia J, Lv G, Wang Y. Knockdown of ABCB7 inhibits esophageal cancer progression by inhibiting the TGF-β/Smad signaling. Arch Biochem Biophys 2023; 742:109620. [PMID: 37142077 DOI: 10.1016/j.abb.2023.109620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 04/10/2023] [Accepted: 05/01/2023] [Indexed: 05/06/2023]
Abstract
OBJECTIVES Esophageal cancer accounts for the seventh in human cancers, and the sixth in the global cancer death. ATP-binding cassette, sub-family B (MDR/TAP), member 7 (ABCB7) maintains intracellular iron homeostasis and involved in the regulation of tumor progression. However, the role and mechanism of ABCB7 in esophageal cancer remained unclear. METHODS Here, we investigated its role and regulatory mechanism by knocking down ABCB7 in Eca109 and KYSE30 cells. RESULTS ABCB7 was significantly upregulated in esophageal cancer tissues, and was strongly associated with metastasis and poor prognosis of patients. ABCB7 knockdown inhibits the proliferation, migration and invasion of esophageal cancer cells. Importantly, ABCB7 knockdown induces apoptosis and non-apoptotic cell death in flow cytometry analysis. Higher intracellular total iron concentration was observed in ABCB7 knockdown Eca109 and KYSE30 cells. We further analyzed ABCB7 expression related genes in esophageal cancer tissues. COX7B were positively correlated with the expression of ABCB7 in 440 esophageal cancer tissues. COX7B rescued the inhibition of cell proliferation and elevated total iron concentration induced by ABCB7 knockdown. In addition, Western blot results showed that ABCB7 knockdown reversed the epithelial-mesenchymal transition (EMT) process and inhibited the TGF-β signaling pathway in Eca109 and KYSE30 cells. CONCLUSION In conclusion, ABCB7 knockdown inhibits the TGF-β signaling pathway, inhibits the survival of esophageal cancer cells by inducing cell death, and reverses the EMT process. Targeting ABCB7 or COX7B could be a novel strategy for the treatment of esophageal cancer.
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Affiliation(s)
- Shiyun Feng
- Department of Thoracic Surgery, China-Japan Union Hospital of Jilin University, China; Department of Thoracic Surgery, The First Hospital of Jilin University, China
| | - Jiabao Jia
- Department of Thoracic Surgery, The First Hospital of Jilin University, China
| | - Guangchao Lv
- Department of Thoracic Surgery, The First Hospital of Jilin University, China
| | - Yue Wang
- Department of Thoracic Surgery, China-Japan Union Hospital of Jilin University, China.
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El-Masry OS. Gene expression profile and presentation of novel gene variants of <i>COX7B</i> and <i>COX7C</i> in a cohort of patients with chronic myeloid leukemia. ELECTRONIC JOURNAL OF GENERAL MEDICINE 2023. [DOI: 10.29333/ejgm/12939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Chronic myeloid leukemia (CML) is a common blood malignancy awaiting decisive cure. Understanding the genomic nature of the disease could help to improve treatment strategies and introduce novel therapeutic targets. The purpose of this study was to sequence the entire transcriptome of a cohort of CML patients to understand differences in gene expression profiles and gene variants compared to healthy controls. RNA was extracted from 10 CML and four healthy control subjects and sequenced by the DNBSEQ platform. Differential gene expression was evaluated and confirmed by the q-RT-PCR technique. Gene variants were also analyzed. The results showed that <i>COX7B</i> and <i>COX7C</i> were upregulated in CML patients than in controls; this was confirmed by quantitative PCR. In addition, novel single nucleotide and insertion/deletion variants were also found in both genes. In conclusion, the results of this study recommend further exploration of <i>COX7B</i> and <i>COX7C</i> and their novel variants in myeloid leukemogenesis.
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Affiliation(s)
- Omar S. El-Masry
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Imam Abdulrahman Bin Faisal University, Dammam, SAUDI ARABIA
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Chen Y, Yuan P, Gu L, Bai J, Ouyang S, Sun T, Liu K, Wang Z, Liu C. Constructing a seventeen-gene signature model for non-obstructive azoospermia based on integrated transcriptome analyses and WGCNA. Reprod Biol Endocrinol 2023; 21:30. [PMID: 36945018 PMCID: PMC10029246 DOI: 10.1186/s12958-023-01079-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 03/09/2023] [Indexed: 03/23/2023] Open
Abstract
BACKGROUND Non-obstructive azoospermia (NOA) affects approximately 1% of the male population worldwide. The underlying mechanism and gene transcription remain unclear. This study aims to explore the potential pathogenesis for the detection and management of NOA. METHODS Based on four microarray datasets from the Gene Expression Omnibus database, integrated analysis and weighted correlation network analysis (WGCNA) were used to obtain the intersected common differentially expressed genes (DESs). Differential signaling pathways were identified via GO and GSVA-KEGG analyses. We constructed a seventeen-gene signature model using least absolute shrinkage and selection operation (LASSO) regression, and validated its efficacy in another two GEO datasets. Three patients with NOA and three patients with obstructive azoospermia were recruited. The mRNA levels of seven key genes were measured in testicular samples, and the gene expression profile was evaluated in the Human Protein Atlas (HPA) database. RESULTS In total, 388 upregulated and 795 downregulated common DEGs were identified between the NOA and control groups. ATPase activity, tubulin binding, microtubule binding, and metabolism- and immune-associated signaling pathways were significantly enriched. A seventeen-gene signature predictive model was constructed, and receiver operating characteristic (ROC) analysis showed that the area under the curve (AUC) values were 1.000 (training group), 0.901 (testing group), and 0.940 (validation set). The AUCs of seven key genes (REC8, CPS1, DHX57, RRS1, GSTA4, SI, and COX7B) were all > 0.8 in both the testing group and the validation set. The qRT-PCR results showed that consistent with the sequencing data, the mRNA levels of RRS1, GSTA4, and COX7B were upregulated, while CPS1, DHX57, and SI were downregulated in NOA. Four genes (CPS1, DHX57, RRS1, and SI) showed significant differences. Expression data from the HPA database showed the localization characteristics and trajectories of seven key genes in spermatogenic cells, Sertoli cells, and Leydig cells. CONCLUSIONS Our findings suggest a novel seventeen-gene signature model with a favorable predictive power, and identify seven key genes with potential as NOA-associated marker genes. Our study provides a new perspective for exploring the underlying pathological mechanism in male infertility.
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Affiliation(s)
- Yinwei Chen
- Reproductive Medicine Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Penghui Yuan
- Department of Urology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450000, Henan, China
| | - Longjie Gu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Jian Bai
- Reproductive Medicine Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Song Ouyang
- Department of Urology, First Affiliated Hospital, School of Medicine, Shihezi University, Shihezi, 832008, Xinjiang, China
| | - Taotao Sun
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Kang Liu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Zhao Wang
- Department of Urology, Xiangya Hospital, Central South University, Changsha, 410000, Hunan, China.
| | - Chang Liu
- Reproductive Medicine Center, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, Jiangsu, China.
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Protein Transduction Domain-Mediated Delivery of Recombinant Proteins and In Vitro Transcribed mRNAs for Protein Replacement Therapy of Human Severe Genetic Mitochondrial Disorders: The Case of Sco2 Deficiency. Pharmaceutics 2023; 15:pharmaceutics15010286. [PMID: 36678915 PMCID: PMC9861957 DOI: 10.3390/pharmaceutics15010286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/31/2022] [Accepted: 01/09/2023] [Indexed: 01/19/2023] Open
Abstract
Mitochondrial disorders represent a heterogeneous group of genetic disorders with variations in severity and clinical outcomes, mostly characterized by respiratory chain dysfunction and abnormal mitochondrial function. More specifically, mutations in the human SCO2 gene, encoding the mitochondrial inner membrane Sco2 cytochrome c oxidase (COX) assembly protein, have been implicated in the mitochondrial disorder fatal infantile cardioencephalomyopathy with COX deficiency. Since an effective treatment is still missing, a protein replacement therapy (PRT) was explored using protein transduction domain (PTD) technology. Therefore, the human recombinant full-length mitochondrial protein Sco2, fused to TAT peptide (a common PTD), was produced (fusion Sco2 protein) and successfully transduced into fibroblasts derived from a SCO2/COX-deficient patient. This PRT contributed to effective COX assembly and partial recovery of COX activity. In mice, radiolabeled fusion Sco2 protein was biodistributed in the peripheral tissues of mice and successfully delivered into their mitochondria. Complementary to that, an mRNA-based therapeutic approach has been more recently considered as an innovative treatment option. In particular, a patented, novel PTD-mediated IVT-mRNA delivery platform was developed and applied in recent research efforts. PTD-IVT-mRNA of full-length SCO2 was successfully transduced into the fibroblasts derived from a SCO2/COX-deficient patient, translated in host ribosomes into a nascent chain of human Sco2, imported into mitochondria, and processed to the mature protein. Consequently, the recovery of reduced COX activity was achieved, thus suggesting the potential of this mRNA-based technology for clinical translation as a PRT for metabolic/genetic disorders. In this review, such research efforts will be comprehensibly presented and discussed to elaborate their potential in clinical application and therapeutic usefulness.
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Schwartz CE, Louie RJ, Toutain A, Skinner C, Friez MJ, Stevenson RE. X-Linked intellectual disability update 2022. Am J Med Genet A 2023; 191:144-159. [PMID: 36300573 DOI: 10.1002/ajmg.a.63008] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 07/28/2022] [Accepted: 09/29/2022] [Indexed: 12/14/2022]
Abstract
Genes that are involved in the transcription process, mitochondrial function, glycoprotein metabolism, and ubiquitination dominate the list of 21 new genes associated with X-linked intellectual disability since the last update in 2017. The new genes were identified by sequencing of candidate genes (2), the entire X-chromosome (2), the whole exome (15), or the whole genome (2). With these additions, 42 (21%) of the 199 named XLID syndromes and 27 (25%) of the 108 numbered nonsyndromic XLID families remain to be resolved at the molecular level. Although the pace of discovery of new XLID genes has slowed during the past 5 years, the density of genes on the X chromosome that cause intellectual disability still appears to be twice the density of intellectual disability genes on the autosomes.
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Affiliation(s)
| | | | - Annick Toutain
- Department of Medical Genetics, Centre Hospitalier Universitaire, Tours, France
| | - Cindy Skinner
- Greenwood Genetic Center, Greenwood, South Carolina, USA
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Mitochondrial Protein Cox7b Is a Metabolic Sensor Driving Brain-Specific Metastasis of Human Breast Cancer Cells. Cancers (Basel) 2022; 14:cancers14184371. [PMID: 36139533 PMCID: PMC9497206 DOI: 10.3390/cancers14184371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 08/29/2022] [Accepted: 09/05/2022] [Indexed: 11/16/2022] Open
Abstract
Distant metastases are detrimental for cancer patients, but the increasingly early detection of tumors offers a chance for metastasis prevention. Importantly, cancers do not metastasize randomly: depending on the type of cancer, metastatic progenitor cells have a predilection for well-defined organs. This has been theorized by Stephen Paget, who proposed the “seed-and-soil hypothesis”, according to which metastatic colonization occurs only when the needs of a given metastatic progenitor cell (the seed) match with the resources provided by a given organ (the soil). Here, we propose to explore the seed-and-soil hypothesis in the context of cancer metabolism, thus hypothesizing that metastatic progenitor cells must be capable of detecting the availability of metabolic resources in order to home in a secondary organ. If true, it would imply the existence of metabolic sensors. Using human triple-negative MDA-MB-231 breast cancer cells and two independent brain-seeking variants as models, we report that cyclooxygenase 7b (Cox7b), a structural component of Complex IV of the mitochondrial electron transport chain, belongs to a probably larger family of proteins responsible for breast cancer brain tropism in mice. For metastasis prevention therapy, this proof-of-principle study opens a quest for the identification of therapeutically targetable metabolic sensors that drive cancer organotropism.
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11
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Brischigliaro M, Cabrera‐Orefice A, Sturlese M, Elurbe DM, Frigo E, Fernandez‐Vizarra E, Moro S, Huynen MA, Arnold S, Viscomi C, Zeviani M. CG7630 is the
Drosophila melanogaster
homolog of the cytochrome
c
oxidase subunit COX7B. EMBO Rep 2022; 23:e54825. [PMID: 35699132 PMCID: PMC9346487 DOI: 10.15252/embr.202254825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 05/16/2022] [Accepted: 05/27/2022] [Indexed: 11/24/2022] Open
Abstract
The mitochondrial respiratory chain (MRC) is composed of four multiheteromeric enzyme complexes. According to the endosymbiotic origin of mitochondria, eukaryotic MRC derives from ancestral proteobacterial respiratory structures consisting of a minimal set of complexes formed by a few subunits associated with redox prosthetic groups. These enzymes, which are the “core” redox centers of respiration, acquired additional subunits, and increased their complexity throughout evolution. Cytochrome c oxidase (COX), the terminal component of MRC, has a highly interspecific heterogeneous composition. Mammalian COX consists of 14 different polypeptides, of which COX7B is considered the evolutionarily youngest subunit. We applied proteomic, biochemical, and genetic approaches to investigate the COX composition in the invertebrate model Drosophila melanogaster. We identified and characterized a novel subunit which is widely different in amino acid sequence, but similar in secondary and tertiary structures to COX7B, and provided evidence that this object is in fact replacing the latter subunit in virtually all protostome invertebrates. These results demonstrate that although individual structures may differ the composition of COX is functionally conserved between vertebrate and invertebrate species.
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Affiliation(s)
| | - Alfredo Cabrera‐Orefice
- Radboud Institute for Molecular Life Sciences Radboud University Medical Center Nijmegen The Netherlands
| | - Mattia Sturlese
- Molecular Modeling Section Department of Pharmaceutical and Pharmacological Sciences University of Padova Padova Italy
| | - Dei M Elurbe
- Centre for Molecular and Biomolecular Informatics Radboud University Medical Center Nijmegen The Netherlands
| | - Elena Frigo
- Department of Biomedical Sciences University of Padova Padova Italy
| | - Erika Fernandez‐Vizarra
- Department of Biomedical Sciences University of Padova Padova Italy
- Veneto Institute of Molecular Medicine Padova Italy
| | - Stefano Moro
- Molecular Modeling Section Department of Pharmaceutical and Pharmacological Sciences University of Padova Padova Italy
| | - Martijn A Huynen
- Centre for Molecular and Biomolecular Informatics Radboud University Medical Center Nijmegen The Netherlands
| | - Susanne Arnold
- Radboud Institute for Molecular Life Sciences Radboud University Medical Center Nijmegen The Netherlands
- Cologne Excellence Cluster on Cellular Stress Responses in Aging‐Associated Diseases (CECAD) University of Cologne Cologne Germany
| | - Carlo Viscomi
- Department of Biomedical Sciences University of Padova Padova Italy
| | - Massimo Zeviani
- Veneto Institute of Molecular Medicine Padova Italy
- Department of Neurosciences University of Padova Padova Italy
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12
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Molecular Mechanisms Contributing to the Etiology of Congenital Diaphragmatic Hernia: A Review and Novel Cases. J Pediatr 2022; 246:251-265.e2. [PMID: 35314152 DOI: 10.1016/j.jpeds.2022.03.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 03/01/2022] [Accepted: 03/15/2022] [Indexed: 12/25/2022]
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13
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Scott DA, Gofin Y, Berry AM, Adams AD. Underlying genetic etiologies of congenital diaphragmatic hernia. Prenat Diagn 2022; 42:373-386. [PMID: 35037267 PMCID: PMC8924940 DOI: 10.1002/pd.6099] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 01/11/2022] [Accepted: 01/12/2022] [Indexed: 11/09/2022]
Abstract
Congenital diaphragmatic hernia (CDH) is often detectable prenatally. Advances in genetic testing have made it possible to obtain a molecular diagnosis in many fetuses with CDH. Here, we review the aneuploidies, copy number variants (CNVs), and single genes that have been clearly associated with CDH. We suggest that array-based CNV analysis, with or without a chromosome analysis, is the optimal test for identifying chromosomal abnormalities and CNVs in fetuses with CDH. To identify causative sequence variants, whole exome sequencing (WES) is the most comprehensive strategy currently available. Whole genome sequencing (WGS) with CNV analysis has the potential to become the most efficient and effective means of identifying an underlying diagnosis but is not yet routinely available for prenatal diagnosis. We describe how to overcome and address the diagnostic and clinical uncertainty that may remain after genetic testing, and review how a molecular diagnosis may impact recurrence risk estimations, mortality rates, and the availability and outcomes of fetal therapy. We conclude that after the prenatal detection of CDH, patients should be counseled about the possible genetic causes of the CDH, and the genetic testing modalities available to them, in accordance with generally accepted guidelines for pretest counseling in the prenatal setting.
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Affiliation(s)
- Daryl A. Scott
- Texas Children’s Hospital, Houston, TX, 77030,
USA,Department of Molecular and Human Genetics, Baylor College
of Medicine, Houston, TX, 77030, USA,Department of Molecular Physiology and Biophysics, Baylor
College of Medicine, Houston, TX, 77030, USA,Correspondence: Daryl A. Scott, R813, One Baylor
Plaza. BCM225, Houston, TX 77030, USA, Phone: +1 713-203-7242,
| | - Yoel Gofin
- Texas Children’s Hospital, Houston, TX, 77030,
USA,Department of Molecular and Human Genetics, Baylor College
of Medicine, Houston, TX, 77030, USA
| | - Aliska M. Berry
- Department of Molecular and Human Genetics, Baylor College
of Medicine, Houston, TX, 77030, USA
| | - April D. Adams
- Department of Molecular and Human Genetics, Baylor College
of Medicine, Houston, TX, 77030, USA,Department of Obstetrics and Gynecology, Division of
Maternal Fetal Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
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14
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Gayen Nee' Betal S, Urday P, Al-Kouatly HB, Solarin K, Chan JSY, Addya S, Boelig RC, Aghai ZH. COVID-19 Infection During Pregnancy Induces Differential Gene Expression in Human Cord Blood Cells From Term Neonates. Front Pediatr 2022; 10:834771. [PMID: 35547542 PMCID: PMC9084610 DOI: 10.3389/fped.2022.834771] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 03/24/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The COVID-19 pandemic continues worldwide with fluctuating case numbers in the United States. This pandemic has affected every segment of the population with more recent hospitalizations in the pediatric population. Vertical transmission of COVID-19 is uncommon, but reports show that there are thrombotic, vascular, and inflammatory changes in the placenta to which neonates are prenatally exposed. Individuals exposed in utero to influenza during the 1918 pandemic had increased risk for heart disease, kidney disease, diabetes, stomach disease and hypertension. Early exposure of COVID-19 during fetal life may lead to altered gene expression with potential long-term consequences. OBJECTIVE To determine if gene expression is altered in cord blood cells from term neonates who were exposed to COVID-19 during pregnancy and to identify potential gene pathways impacted by maternal COVID-19. METHODS Cord blood was collected from 16 term neonates (8 exposed to COVID-19 during pregnancy and 8 controls without exposure to COVID-19). Genome-wide gene expression screening was performed using Human Clariom S gene chips on total RNA extracted from cord blood cells. RESULTS We identified 510 differentially expressed genes (374 genes up-regulated, 136 genes down-regulated, fold change ≥1.5, p-value ≤ 0.05) in cord blood cells associated with exposure to COVID-19 during pregnancy. Ingenuity Pathway Analysis identified important canonical pathways associated with diseases such as cardiovascular disease, hematological disease, embryonic cancer and cellular development. Tox functions related to cardiotoxicity, hepatotoxicity and nephrotoxicity were also altered after exposure to COVID-19 during pregnancy. CONCLUSIONS Exposure to COVID-19 during pregnancy induces differential gene expression in cord blood cells. The differentially expressed genes may potentially contribute to cardiac, hepatic, renal and immunological disorders in offspring exposed to COVID-19 during pregnancy. These findings lead to a further understanding of the effects of COVID-19 exposure at an early stage of life and its potential long-term consequences as well as therapeutic targets.
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Affiliation(s)
| | - Pedro Urday
- Neonatology, Thomas Jefferson University/Nemours, Philadelphia, PA, United States
| | - Huda B Al-Kouatly
- Maternal Fetal Medicine, Thomas Jefferson University, Philadelphia, PA, United States
| | - Kolawole Solarin
- Neonatology, Thomas Jefferson University/Nemours, Philadelphia, PA, United States
| | - Joanna S Y Chan
- Department of Pathology, Thomas Jefferson University, Philadelphia, PA, United States
| | - Sankar Addya
- Laboratory of Cancer Genomics, Thomas Jefferson University, Philadelphia, PA, United States
| | - Rupsa C Boelig
- Maternal Fetal Medicine, Thomas Jefferson University, Philadelphia, PA, United States
| | - Zubair H Aghai
- Neonatology, Thomas Jefferson University/Nemours, Philadelphia, PA, United States
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15
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SINEUPs: a novel toolbox for RNA therapeutics. Essays Biochem 2021; 65:775-789. [PMID: 34623427 PMCID: PMC8564737 DOI: 10.1042/ebc20200114] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 07/22/2021] [Accepted: 08/23/2021] [Indexed: 12/17/2022]
Abstract
RNA molecules have emerged as a new class of promising therapeutics to expand the range of druggable targets in the genome. In addition to ‘canonical’ protein-coding mRNAs, the emerging richness of sense and antisense long non-coding RNAs (lncRNAs) provides a new reservoir of molecular tools for RNA-based drugs. LncRNAs are composed of modular structural domains with specific activities involving the recruitment of protein cofactors or directly interacting with nucleic acids. A single therapeutic RNA transcript can then be assembled combining domains with defined secondary structures and functions, and antisense sequences specific for the RNA/DNA target of interest. As the first representative molecules of this new pharmacology, we have identified SINEUPs, a new functional class of natural antisense lncRNAs that increase the translation of partially overlapping mRNAs. Their activity is based on the combination of two domains: an embedded mouse inverted SINEB2 element that enhances mRNA translation (effector domain) and an overlapping antisense region that provides specificity for the target sense transcript (binding domain). By genetic engineering, synthetic SINEUPs can potentially target any mRNA of interest increasing translation and therefore the endogenous level of the encoded protein. In this review, we describe the state-of-the-art knowledge of SINEUPs and discuss recent publications showing their potential application in diseases where a physiological increase of endogenous protein expression can be therapeutic.
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16
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Zanfardino P, Doccini S, Santorelli FM, Petruzzella V. Tackling Dysfunction of Mitochondrial Bioenergetics in the Brain. Int J Mol Sci 2021; 22:8325. [PMID: 34361091 PMCID: PMC8348117 DOI: 10.3390/ijms22158325] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/29/2021] [Accepted: 07/30/2021] [Indexed: 12/15/2022] Open
Abstract
Oxidative phosphorylation (OxPhos) is the basic function of mitochondria, although the landscape of mitochondrial functions is continuously growing to include more aspects of cellular homeostasis. Thanks to the application of -omics technologies to the study of the OxPhos system, novel features emerge from the cataloging of novel proteins as mitochondrial thus adding details to the mitochondrial proteome and defining novel metabolic cellular interrelations, especially in the human brain. We focussed on the diversity of bioenergetics demand and different aspects of mitochondrial structure, functions, and dysfunction in the brain. Definition such as 'mitoexome', 'mitoproteome' and 'mitointeractome' have entered the field of 'mitochondrial medicine'. In this context, we reviewed several genetic defects that hamper the last step of aerobic metabolism, mostly involving the nervous tissue as one of the most prominent energy-dependent tissues and, as consequence, as a primary target of mitochondrial dysfunction. The dual genetic origin of the OxPhos complexes is one of the reasons for the complexity of the genotype-phenotype correlation when facing human diseases associated with mitochondrial defects. Such complexity clinically manifests with extremely heterogeneous symptoms, ranging from organ-specific to multisystemic dysfunction with different clinical courses. Finally, we briefly discuss the future directions of the multi-omics study of human brain disorders.
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Affiliation(s)
- Paola Zanfardino
- Department of Medical Basic Sciences, Neurosciences and Sense Organs, University of Bari Aldo Moro, 70124 Bari, Italy;
| | - Stefano Doccini
- IRCCS Fondazione Stella Maris, Calambrone, 56128 Pisa, Italy;
| | | | - Vittoria Petruzzella
- Department of Medical Basic Sciences, Neurosciences and Sense Organs, University of Bari Aldo Moro, 70124 Bari, Italy;
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17
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Iaconis D, Crina C, Brillante S, Indrieri A, Morleo M, Franco B. The HOPS complex subunit VPS39 controls ciliogenesis through autophagy. Hum Mol Genet 2021; 29:1018-1029. [PMID: 32077937 PMCID: PMC7158379 DOI: 10.1093/hmg/ddaa029] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 02/12/2020] [Accepted: 02/13/2020] [Indexed: 12/12/2022] Open
Abstract
Primary cilia are microtubule-based organelles that assemble and protrude from the surface of most mammalian cells during quiescence. The biomedical relevance of cilia is indicated by disorders ascribed to cilia dysfunction, known as ciliopathies, that display distinctive features including renal cystic disease. In this report, we demonstrate that vacuolar protein sorting 39 (VPS39), a component of the homotypic fusion and vacuole protein sorting (HOPS) complex, acts as a negative regulator of ciliogenesis in human renal cells, by controlling the localization of the intraflagellar transport 20 protein at the base of cilia through autophagy. Moreover, we show that VPS39 controls ciliogenesis through autophagy also in vivo in renal tubules of medaka fish. These observations suggest a direct involvement of the HOPS complex in the regulation of autophagy-mediated ciliogenesis and eventually in target selection. Interestingly, we show that the impact of autophagy modulation on ciliogenesis is cell-type dependent and strictly related to environmental stimuli. This report adds a further tile to the cilia-autophagy connection and suggests that VPS39 could represent a new biological target for the recovery of the cilia-related phenotypes observed in the kidneys of patients affected by ciliopathies.
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Affiliation(s)
- Daniela Iaconis
- Telethon Institute of Genetics and Medicine, 80078 Pozzuoli, Italy
| | - Claudia Crina
- Telethon Institute of Genetics and Medicine, 80078 Pozzuoli, Italy
| | - Simona Brillante
- Telethon Institute of Genetics and Medicine, 80078 Pozzuoli, Italy
| | - Alessia Indrieri
- Telethon Institute of Genetics and Medicine, 80078 Pozzuoli, Italy.,Medical Genetics, Department of Translational Medical Sciences, University of Naples Federico II, 80131 Naples, Italy.,Institute for Genetic and Biomedical Research, National Research Council, 35 20122 Milan, Italy
| | - Manuela Morleo
- Telethon Institute of Genetics and Medicine, 80078 Pozzuoli, Italy.,Medical Genetics, Department of Translational Medical Sciences, University of Naples Federico II, 80131 Naples, Italy
| | - Brunella Franco
- Telethon Institute of Genetics and Medicine, 80078 Pozzuoli, Italy.,Medical Genetics, Department of Translational Medical Sciences, University of Naples Federico II, 80131 Naples, Italy
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18
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Blackout in the powerhouse: clinical phenotypes associated with defects in the assembly of OXPHOS complexes and the mitoribosome. Biochem J 2021; 477:4085-4132. [PMID: 33151299 PMCID: PMC7657662 DOI: 10.1042/bcj20190767] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 09/29/2020] [Accepted: 10/05/2020] [Indexed: 12/26/2022]
Abstract
Mitochondria produce the bulk of the energy used by almost all eukaryotic cells through oxidative phosphorylation (OXPHOS) which occurs on the four complexes of the respiratory chain and the F1–F0 ATPase. Mitochondrial diseases are a heterogenous group of conditions affecting OXPHOS, either directly through mutation of genes encoding subunits of OXPHOS complexes, or indirectly through mutations in genes encoding proteins supporting this process. These include proteins that promote assembly of the OXPHOS complexes, the post-translational modification of subunits, insertion of cofactors or indeed subunit synthesis. The latter is important for all 13 of the proteins encoded by human mitochondrial DNA, which are synthesised on mitochondrial ribosomes. Together the five OXPHOS complexes and the mitochondrial ribosome are comprised of more than 160 subunits and many more proteins support their biogenesis. Mutations in both nuclear and mitochondrial genes encoding these proteins have been reported to cause mitochondrial disease, many leading to defective complex assembly with the severity of the assembly defect reflecting the severity of the disease. This review aims to act as an interface between the clinical and basic research underpinning our knowledge of OXPHOS complex and ribosome assembly, and the dysfunction of this process in mitochondrial disease.
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19
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Ramzan R, Kadenbach B, Vogt S. Multiple Mechanisms Regulate Eukaryotic Cytochrome C Oxidase. Cells 2021; 10:cells10030514. [PMID: 33671025 PMCID: PMC7997345 DOI: 10.3390/cells10030514] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/22/2021] [Accepted: 02/22/2021] [Indexed: 02/07/2023] Open
Abstract
Cytochrome c oxidase (COX), the rate-limiting enzyme of mitochondrial respiration, is regulated by various mechanisms. Its regulation by ATP (adenosine triphosphate) appears of particular importance, since it evolved early during evolution and is still found in cyanobacteria, but not in other bacteria. Therefore the "allosteric ATP inhibition of COX" is described here in more detail. Most regulatory properties of COX are related to "supernumerary" subunits, which are largely absent in bacterial COX. The "allosteric ATP inhibition of COX" was also recently described in intact isolated rat heart mitochondria.
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Affiliation(s)
- Rabia Ramzan
- Cardiovascular Research Laboratory, Biochemical-Pharmacological Center, Philipps-University Marburg, Karl-von-Frisch-Strasse 1, D-35043 Marburg, Germany;
| | - Bernhard Kadenbach
- Fachbereich Chemie, Philipps-University, D-35032 Marburg, Germany
- Correspondence:
| | - Sebastian Vogt
- Department of Heart Surgery, Campus Marburg, University Hospital of Giessen and Marburg, D-35043 Marburg, Germany;
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20
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Aly KA, Moutaoufik MT, Phanse S, Zhang Q, Babu M. From fuzziness to precision medicine: on the rapidly evolving proteomics with implications in mitochondrial connectivity to rare human disease. iScience 2021; 24:102030. [PMID: 33521598 PMCID: PMC7820543 DOI: 10.1016/j.isci.2020.102030] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Mitochondrial (mt) dysfunction is linked to rare diseases (RDs) such as respiratory chain complex (RCC) deficiency, MELAS, and ARSACS. Yet, how altered mt protein networks contribute to these ailments remains understudied. In this perspective article, we identified 21 mt proteins from public repositories that associate with RCC deficiency, MELAS, or ARSACS, engaging in a relatively small number of protein-protein interactions (PPIs), underscoring the need for advanced proteomic and interactomic platforms to uncover the complete scope of mt connectivity to RDs. Accordingly, we discuss innovative untargeted label-free proteomics in identifying RD-specific mt or other macromolecular assemblies and mapping of protein networks in complex tissue, organoid, and stem cell-differentiated neurons. Furthermore, tag- and label-based proteomics, genealogical proteomics, and combinatorial affinity purification-mass spectrometry, along with advancements in detecting and integrating transient PPIs with single-cell proteomics and transcriptomics, collectively offer seminal follow-ups to enrich for RD-relevant networks, with implications in RD precision medicine.
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Affiliation(s)
- Khaled A. Aly
- Department of Biochemistry, University of Regina, Regina, SK, Canada
| | | | - Sadhna Phanse
- Department of Biochemistry, University of Regina, Regina, SK, Canada
| | - Qingzhou Zhang
- Department of Biochemistry, University of Regina, Regina, SK, Canada
| | - Mohan Babu
- Department of Biochemistry, University of Regina, Regina, SK, Canada
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21
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Zhang HL, Xu Y, Ju JQ, Pan ZN, Liu JC, Sun SC. Increased Environment-Related Metabolism and Genetic Expression in the In Vitro Matured Mouse Oocytes by Transcriptome Analysis. Front Cell Dev Biol 2021; 9:642010. [PMID: 33681227 PMCID: PMC7928285 DOI: 10.3389/fcell.2021.642010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 01/18/2021] [Indexed: 12/28/2022] Open
Abstract
Infertility in humans at their reproductive age is a world-wide problem. Oocyte in vitro maturation (IVM) is generally used in such cases to acquire the embryo in assisted reproductive technology (ART). However, the differences between an in vivo (IVO) and IVM culture environment in the RNA expression profile in oocytes, remains unclear. In this study, we compared the global RNA transcription pattern of oocytes from in vitro and in vivo maturation. Our results showed that 1,864 genes differentially expressed between the IVO and IVM oocytes. Among these, 1,638 genes were up-regulated, and 226 genes were down-regulated, and these changes were mainly divided into environmental adaption, metabolism, and genetic expression. Our detailed analysis showed that the expression of genes that belonged to metabolism-related processes such as energy metabolism, nucleotide metabolism, and carbohydrate metabolism was changed; and these genes also belonged to organismal systems including environmental adaptation and the circulatory system; moreover, we also found that the relative gene expression of genetic expression processes, such as protein synthesis, modification, and DNA replication and repair were also altered. In conclusion, our data suggests that in vitro maturation of mouse oocyte resulted in metabolism and genetic expression changes due to environmental changes compared with in vivo matured oocytes.
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Affiliation(s)
- Hao-Lin Zhang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Yi Xu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Jia-Qian Ju
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Zhen-Nan Pan
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Jing-Cai Liu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Shao-Chen Sun
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
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22
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Indrieri A, Franco B. Linear Skin Defects with Multiple Congenital Anomalies (LSDMCA): An Unconventional Mitochondrial Disorder. Genes (Basel) 2021; 12:genes12020263. [PMID: 33670341 PMCID: PMC7918533 DOI: 10.3390/genes12020263] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/05/2021] [Accepted: 02/09/2021] [Indexed: 12/20/2022] Open
Abstract
Mitochondrial disorders, although heterogeneous, are traditionally described as conditions characterized by encephalomyopathy, hypotonia, and progressive postnatal organ failure. Here, we provide a systematic review of Linear Skin Defects with Multiple Congenital Anomalies (LSDMCA), a rare, unconventional mitochondrial disorder which presents as a developmental disease; its main clinical features include microphthalmia with different degrees of severity, linear skin lesions, and central nervous system malformations. The molecular basis of this disorder has been elusive for several years. Mutations were eventually identified in three X-linked genes, i.e., HCCS, COX7B, and NDUFB11, which are all endowed with defined roles in the mitochondrial respiratory chain. A peculiar feature of this condition is its inheritance pattern: X-linked dominant male-lethal. Only female or XX male individuals can be observed, implying that nullisomy for these genes is incompatible with normal embryonic development in mammals. All three genes undergo X-inactivation that, according to our hypothesis, may contribute to the extreme variable expressivity observed in this condition. We propose that mitochondrial dysfunction should be considered as an underlying cause in developmental disorders. Moreover, LSDMCA should be taken into consideration by clinicians when dealing with patients with microphthalmia with or without associated skin phenotypes.
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Affiliation(s)
- Alessia Indrieri
- Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei, 34, 80078 Pozzuoli, Naples, Italy;
- Institute for Genetic and Biomedical Research (IRGB), National Research Council (CNR), 20090 Milan, Italy
| | - Brunella Franco
- Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei, 34, 80078 Pozzuoli, Naples, Italy;
- Medical Genetics, Department of Translational Medical Sciences, University of Naples “Federico II”, Via Sergio Pansini 5, 80131 Naples, Italy
- Correspondence: ; Tel.: +39-081-1923-0615
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23
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Carli S, Chaabane L, Butti C, De Palma C, Aimar P, Salio C, Vignoli A, Giustetto M, Landsberger N, Frasca A. In vivo magnetic resonance spectroscopy in the brain of Cdkl5 null mice reveals a metabolic profile indicative of mitochondrial dysfunctions. J Neurochem 2021; 157:1253-1269. [PMID: 33448385 DOI: 10.1111/jnc.15300] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 10/24/2020] [Accepted: 01/07/2021] [Indexed: 12/12/2022]
Abstract
Mutations in the X-linked CDKL5 gene cause CDKL5 deficiency disorder (CDD), a severe neurodevelopmental condition mainly characterized by infantile epileptic encephalopathy, intellectual disability, and autistic features. The molecular mechanisms underlying the clinical symptoms remain largely unknown and the identification of reliable biomarkers in animal models will certainly contribute to increase our comprehension of CDD as well as to assess the efficacy of therapeutic strategies. Here, we used different Magnetic Resonance (MR) methods to disclose structural, functional, or metabolic signatures of Cdkl5 deficiency in the brain of adult mice. We found that loss of Cdkl5 does not cause cerebral atrophy but affects distinct brain areas, particularly the hippocampus. By in vivo proton-MR spectroscopy (MRS), we revealed in the Cdkl5 null brain a metabolic dysregulation indicative of mitochondrial dysfunctions. Accordingly, we unveiled a significant reduction in ATP levels and a decrease in the expression of complex IV of mitochondrial electron transport chain. Conversely, the number of mitochondria appeared preserved. Importantly, we reported a significant defect in the activation of one of the major regulators of cellular energy balance, the adenosine monophosphate-activated protein kinase (AMPK), that might contribute to the observed metabolic impairment and become an interesting therapeutic target for future preclinical trials. In conclusion, MRS revealed in the Cdkl5 null brain the presence of a metabolic dysregulation suggestive of a mitochondrial dysfunction that permitted to foster our comprehension of Cdkl5 deficiency and brought our interest towards targeting mitochondria as therapeutic strategy for CDD.
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Affiliation(s)
- Sara Carli
- Neuroscience Division, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Linda Chaabane
- Institute of Experimental Neurology (INSPE) and Experimental Imaging Center (CIS), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Clarissa Butti
- Neuroscience Division, IRCCS San Raffaele Scientific Institute, Milan, Italy.,Molecular Nociception Group, Wolfson Institute for Biomedical Research (WIBR), University College London, London, UK
| | - Clara De Palma
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Segrate (Milan), Italy
| | - Patrizia Aimar
- Department of Veterinary Sciences, University of Turin, Grugliasco, Italy
| | - Chiara Salio
- Department of Veterinary Sciences, University of Turin, Grugliasco, Italy
| | - Aglaia Vignoli
- Epilepsy Center-Child Neuropsychiatric Unit, ASST Santi Paolo e Carlo, Department of Health Sciences, University of Milan, Milan, Italy
| | - Maurizio Giustetto
- Department of Neuroscience, University of Turin, Turin, Italy.,National Institute of Neuroscience-Italy, Turin, Italy
| | - Nicoletta Landsberger
- Neuroscience Division, IRCCS San Raffaele Scientific Institute, Milan, Italy.,Department of Medical Biotechnology and Translational Medicine, University of Milan, Segrate (Milan), Italy
| | - Angelisa Frasca
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Segrate (Milan), Italy
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24
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Hussain M, Krishnamurthy S, Patel J, Kim E, Baptiste BA, Croteau DL, Bohr VA. Skin Abnormalities in Disorders with DNA Repair Defects, Premature Aging, and Mitochondrial Dysfunction. J Invest Dermatol 2021; 141:968-975. [PMID: 33353663 DOI: 10.1016/j.jid.2020.10.019] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/25/2020] [Accepted: 10/08/2020] [Indexed: 02/06/2023]
Abstract
Defects in DNA repair pathways and alterations of mitochondrial energy metabolism have been reported in multiple skin disorders. More than 10% of patients with primary mitochondrial dysfunction exhibit dermatological features including rashes and hair and pigmentation abnormalities. Accumulation of oxidative DNA damage and dysfunctional mitochondria affect cellular homeostasis leading to increased apoptosis. Emerging evidence demonstrates that genetic disorders of premature aging that alter DNA repair pathways and cause mitochondrial dysfunction, such as Rothmund-Thomson syndrome, Werner syndrome, and Cockayne syndrome, also exhibit skin disease. This article summarizes recent advances in the research pertaining to these syndromes and molecular mechanisms underlying their skin pathologies.
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Affiliation(s)
- Mansoor Hussain
- Laboratory of Molecular Gerontology, National Institute on Aging, Baltimore, Maryland, USA
| | | | - Jaimin Patel
- Laboratory of Molecular Gerontology, National Institute on Aging, Baltimore, Maryland, USA
| | - Edward Kim
- Laboratory of Molecular Gerontology, National Institute on Aging, Baltimore, Maryland, USA
| | - Beverly A Baptiste
- Laboratory of Molecular Gerontology, National Institute on Aging, Baltimore, Maryland, USA
| | - Deborah L Croteau
- Laboratory of Molecular Gerontology, National Institute on Aging, Baltimore, Maryland, USA
| | - Vilhelm A Bohr
- Laboratory of Molecular Gerontology, National Institute on Aging, Baltimore, Maryland, USA.
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25
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Mitochondrial Structure and Bioenergetics in Normal and Disease Conditions. Int J Mol Sci 2021; 22:ijms22020586. [PMID: 33435522 PMCID: PMC7827222 DOI: 10.3390/ijms22020586] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/03/2021] [Accepted: 01/04/2021] [Indexed: 02/06/2023] Open
Abstract
Mitochondria are ubiquitous intracellular organelles found in almost all eukaryotes and involved in various aspects of cellular life, with a primary role in energy production. The interest in this organelle has grown stronger with the discovery of their link to various pathologies, including cancer, aging and neurodegenerative diseases. Indeed, dysfunctional mitochondria cannot provide the required energy to tissues with a high-energy demand, such as heart, brain and muscles, leading to a large spectrum of clinical phenotypes. Mitochondrial defects are at the origin of a group of clinically heterogeneous pathologies, called mitochondrial diseases, with an incidence of 1 in 5000 live births. Primary mitochondrial diseases are associated with genetic mutations both in nuclear and mitochondrial DNA (mtDNA), affecting genes involved in every aspect of the organelle function. As a consequence, it is difficult to find a common cause for mitochondrial diseases and, subsequently, to offer a precise clinical definition of the pathology. Moreover, the complexity of this condition makes it challenging to identify possible therapies or drug targets.
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26
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Fernandez-Vizarra E, Zeviani M. Mitochondrial disorders of the OXPHOS system. FEBS Lett 2020; 595:1062-1106. [PMID: 33159691 DOI: 10.1002/1873-3468.13995] [Citation(s) in RCA: 109] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 10/21/2020] [Accepted: 11/01/2020] [Indexed: 12/13/2022]
Abstract
Mitochondrial disorders are among the most frequent inborn errors of metabolism, their primary cause being the dysfunction of the oxidative phosphorylation system (OXPHOS). OXPHOS is composed of the electron transport chain (ETC), formed by four multimeric enzymes and two mobile electron carriers, plus an ATP synthase [also called complex V (cV)]. The ETC performs the redox reactions involved in cellular respiration while generating the proton motive force used by cV to synthesize ATP. OXPHOS biogenesis involves multiple steps, starting from the expression of genes encoded in physically separated genomes, namely the mitochondrial and nuclear DNA, to the coordinated assembly of components and cofactors building each individual complex and eventually the supercomplexes. The genetic cause underlying around half of the diagnosed mitochondrial disease cases is currently known. Many of these cases result from pathogenic variants in genes encoding structural subunits or additional factors directly involved in the assembly of the ETC complexes. Here, we review the historical and most recent findings concerning the clinical phenotypes and the molecular pathological mechanisms underlying this particular group of disorders.
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Affiliation(s)
- Erika Fernandez-Vizarra
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, UK
| | - Massimo Zeviani
- Venetian Institute of Molecular Medicine, Padova, Italy.,Department of Neurosciences, University of Padova, Italy
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27
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Hao Y, Reyes LT, Morris R, Xu Y, Wang Y, Cheng F. Changes of protein levels in human urine reflect the dysregulation of signaling pathways of chronic kidney disease and its complications. Sci Rep 2020; 10:20743. [PMID: 33247215 PMCID: PMC7699629 DOI: 10.1038/s41598-020-77916-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 11/18/2020] [Indexed: 11/30/2022] Open
Abstract
The increasing prevalence of chronic kidney disease (CKD) seriously is threatening human health and overall quality of life. The discovery of biomarkers of pathogenesis of CKD and the associated complications are very important for CDK diagnosis and treatment. In this paper, urine protein biomarkers were investigated because urine sample collection is convenient and non-invasive. We analyzed the protein concentrations in the urine of CKD patients and extracted abnormal protein signals comparing with the healthy control groups. The enriched signaling pathways that may characterize CKD pathology were identified from these proteins. We applied surface-enhanced laser desorption and ionization time of flight mass spectrometry technology to detect different protein peaks in urine samples from patients with CKD and healthy controls. We searched the proteins corresponding to protein peaks through the UniProt database and identified the signaling pathways of CKD and its complications by using the NIH DAVID database. 42 low abundance proteins and 46 high abundance proteins in the urine samples from CKD patients were found by comparing with healthy controls. Seven KEGG pathways related to CKD and its complications were identified from the regulated proteins. These pathways included chemokine signaling pathway, cytokine-cytokine receptor interaction, oxidative phosphorylation, cardiac muscle contraction, Alzheimer's disease, Parkinson's disease, and salivary secretion. In CKD stages 2, 3, 4, and 5, five proteins showed significantly differential abundances. The differential protein signals and regulated signaling pathways will provide new insight for the pathogenesis of CKD and its complications. These altered proteins may also be used as novel biomarkers for the noninvasive and convenient diagnosis methods of CKD and its complications through urine testing in the future.
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Affiliation(s)
- Yiming Hao
- Shanghai Key Laboratory of Health Identification and Assessment/Laboratory of TCM Four Diagnostic Information, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Luis Tanon Reyes
- Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, Tampa, FL, 33612, USA
| | - Robert Morris
- Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, Tampa, FL, 33612, USA
| | - Yifeng Xu
- Shanghai Key Laboratory of Health Identification and Assessment/Laboratory of TCM Four Diagnostic Information, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Yiqin Wang
- Shanghai Key Laboratory of Health Identification and Assessment/Laboratory of TCM Four Diagnostic Information, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
| | - Feng Cheng
- Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, Tampa, FL, 33612, USA.
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28
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Human Mitochondrial Pathologies of the Respiratory Chain and ATP Synthase: Contributions from Studies of Saccharomyces cerevisiae. Life (Basel) 2020; 10:life10110304. [PMID: 33238568 PMCID: PMC7700678 DOI: 10.3390/life10110304] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/18/2020] [Accepted: 11/19/2020] [Indexed: 12/14/2022] Open
Abstract
The ease with which the unicellular yeast Saccharomyces cerevisiae can be manipulated genetically and biochemically has established this organism as a good model for the study of human mitochondrial diseases. The combined use of biochemical and molecular genetic tools has been instrumental in elucidating the functions of numerous yeast nuclear gene products with human homologs that affect a large number of metabolic and biological processes, including those housed in mitochondria. These include structural and catalytic subunits of enzymes and protein factors that impinge on the biogenesis of the respiratory chain. This article will review what is currently known about the genetics and clinical phenotypes of mitochondrial diseases of the respiratory chain and ATP synthase, with special emphasis on the contribution of information gained from pet mutants with mutations in nuclear genes that impair mitochondrial respiration. Our intent is to provide the yeast mitochondrial specialist with basic knowledge of human mitochondrial pathologies and the human specialist with information on how genes that directly and indirectly affect respiration were identified and characterized in yeast.
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29
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Cytochrome c oxidase deficiency. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1862:148335. [PMID: 33171185 DOI: 10.1016/j.bbabio.2020.148335] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/31/2020] [Accepted: 11/03/2020] [Indexed: 12/23/2022]
Abstract
Cytochrome c oxidase (COX) deficiency is characterized by a high degree of genetic and phenotypic heterogeneity, partly reflecting the extreme structural complexity, multiple post-translational modification, variable, tissue-specific composition, and the high number of and intricate connections among the assembly factors of this enzyme. In fact, decreased COX specific activity can manifest with different degrees of severity, affect the whole organism or specific tissues, and develop a wide spectrum of disease natural history, including disease onsets ranging from birth to late adulthood. More than 30 genes have been linked to COX deficiency, but the list is still incomplete and in fact constantly updated. We here discuss the current knowledge about COX in health and disease, focusing on genetic aetiology and link to clinical manifestations. In addition, information concerning either fundamental biological features of the enzymes or biochemical signatures of its defects have been provided by experimental in vivo models, including yeast, fly, mouse and fish, which expanded our knowledge on the functional features and the phenotypical consequences of different forms of COX deficiency.
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30
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Čunátová K, Reguera DP, Houštěk J, Mráček T, Pecina P. Role of cytochrome c oxidase nuclear-encoded subunits in health and disease. Physiol Res 2020; 69:947-965. [PMID: 33129245 DOI: 10.33549/physiolres.934446] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Cytochrome c oxidase (COX), the terminal enzyme of mitochondrial electron transport chain, couples electron transport to oxygen with generation of proton gradient indispensable for the production of vast majority of ATP molecules in mammalian cells. The review summarizes current knowledge of COX structure and function of nuclear-encoded COX subunits, which may modulate enzyme activity according to various conditions. Moreover, some nuclear-encoded subunits posess tissue-specific and development-specific isoforms, possibly enabling fine-tuning of COX function in individual tissues. The importance of nuclear-encoded subunits is emphasized by recently discovered pathogenic mutations in patients with severe mitopathies. In addition, proteins substoichiometrically associated with COX were found to contribute to COX activity regulation and stabilization of the respiratory supercomplexes. Based on the summarized data, a model of three levels of quaternary COX structure is postulated. Individual structural levels correspond to subunits of the i) catalytic center, ii) nuclear-encoded stoichiometric subunits and iii) associated proteins, which may constitute several forms of COX with varying composition and differentially regulated function.
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Affiliation(s)
- K Čunátová
- Department of Bioenergetics, Institute of Physiology CAS, Prague, Czech Republic. ,
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31
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Abstract
Maternally mitochondrial dysfunction includes a heterogeneous group of genetic disorders which leads to the impairment of the final common pathway of energy metabolism. Coronary heart disease and coronary venous disease are two important clinical manifestations of mitochondrial dysfunction due to abnormality in the setting of underlying pathways. Mitochondrial dysfunction can lead to cardiomyopathy, which is involved in the onset of acute cardiac and pulmonary failure. Mitochondrial diseases present other cardiac manifestations such as left ventricular noncompaction and cardiac conduction disease. Different clinical findings from mitochondrial dysfunction originate from different mtDNA mutations, and this variety of clinical symptoms poses a diagnostic challenge for cardiologists. Heart transplantation may be a good treatment, but it is not always possible, and other complications of the disease, such as mitochondrial encephalopathy, lactic acidosis, and stroke-like syndrome, should be considered. To diagnose and treat most mitochondrial disorders, careful cardiac, neurological, and molecular studies are needed. In this study, we looked at molecular genetics of MIDs and cardiac manifestations in patients with mitochondrial dysfunction.
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32
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Sreedhar A, Aguilera-Aguirre L, Singh KK. Mitochondria in skin health, aging, and disease. Cell Death Dis 2020; 11:444. [PMID: 32518230 PMCID: PMC7283348 DOI: 10.1038/s41419-020-2649-z] [Citation(s) in RCA: 134] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 05/22/2020] [Accepted: 05/25/2020] [Indexed: 02/08/2023]
Abstract
The skin is a high turnover organ, and its constant renewal depends on the rapid proliferation of its progenitor cells. The energy requirement for these metabolically active cells is met by mitochondrial respiration, an ATP generating process driven by a series of protein complexes collectively known as the electron transport chain (ETC) that is located on the inner membrane of the mitochondria. However, reactive oxygen species (ROS) like superoxide, singlet oxygen, peroxides are inevitably produced during respiration and disrupt macromolecular and cellular structures if not quenched by the antioxidant system. The oxidative damage caused by mitochondrial ROS production has been established as the molecular basis of multiple pathophysiological conditions, including aging and cancer. Not surprisingly, the mitochondria are the primary organelle affected during chronological and UV-induced skin aging, the phenotypic manifestations of which are the direct consequence of mitochondrial dysfunction. Also, deletions and other aberrations in the mitochondrial DNA (mtDNA) are frequent in photo-aged skin and skin cancer lesions. Recent studies have revealed a more innate role of the mitochondria in maintaining skin homeostasis and pigmentation, which are affected when the essential mitochondrial functions are impaired. Some common and rare skin disorders have a mitochondrial involvement and include dermal manifestations of primary mitochondrial diseases as well as congenital skin diseases caused by damaged mitochondria. With studies increasingly supporting the close association between mitochondria and skin health, its therapeutic targeting in the skin-either via an ATP production boost or free radical scavenging-has gained attention from clinicians and aestheticians alike. Numerous bioactive compounds have been identified that improve mitochondrial functions and have proved effective against aged and diseased skin. In this review, we discuss the essential role of mitochondria in regulating normal and abnormal skin physiology and the possibility of targeting this organelle in various skin disorders.
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Affiliation(s)
| | | | - Keshav K Singh
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.
- Integartive Center For Aging Research and O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.
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33
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La Morgia C, Maresca A, Caporali L, Valentino ML, Carelli V. Mitochondrial diseases in adults. J Intern Med 2020; 287:592-608. [PMID: 32463135 DOI: 10.1111/joim.13064] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/07/2020] [Accepted: 02/21/2020] [Indexed: 02/07/2023]
Abstract
Mitochondrial medicine is a field that expanded exponentially in the last 30 years. Individually rare, mitochondrial diseases as a whole are probably the most frequent genetic disorder in adults. The complexity of their genotype-phenotype correlation, in terms of penetrance and clinical expressivity, natural history and diagnostic algorithm derives from the dual genetic determination. In fact, in addition to the about 1.500 genes encoding mitochondrial proteins that reside in the nuclear genome (nDNA), we have the 13 proteins encoded by the mitochondrial genome (mtDNA), for which 22 specific tRNAs and 2 rRNAs are also needed. Thus, besides Mendelian genetics, we need to consider all peculiarities of how mtDNA is inherited, maintained and expressed to fully understand the pathogenic mechanisms of these disorders. Yet, from the initial restriction to the narrow field of oxidative phosphorylation dysfunction, the landscape of mitochondrial functions impinging on cellular homeostasis, driving life and death, is impressively enlarged. Finally, from the clinical standpoint, starting from the neuromuscular field, where brain and skeletal muscle were the primary targets of mitochondrial dysfunction as energy-dependent tissues, after three decades virtually any subspecialty of medicine is now involved. We will summarize the key clinical pictures and pathogenic mechanisms of mitochondrial diseases in adults.
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Affiliation(s)
- C La Morgia
- From the, Dipartimento di Scienze Biomediche e Neuromotorie, Università di Bologna, Bologna, Italy.,IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna, Italy
| | - A Maresca
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna, Italy
| | - L Caporali
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna, Italy
| | - M L Valentino
- From the, Dipartimento di Scienze Biomediche e Neuromotorie, Università di Bologna, Bologna, Italy.,IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna, Italy
| | - V Carelli
- From the, Dipartimento di Scienze Biomediche e Neuromotorie, Università di Bologna, Bologna, Italy.,IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna, Italy
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34
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Oláh A, Alam M, Chéret J, Kis NG, Hegyi Z, Szöllősi AG, Vidali S, Bíró T, Paus R. Mitochondrial energy metabolism is negatively regulated by cannabinoid receptor 1 in intact human epidermis. Exp Dermatol 2020; 29:616-622. [PMID: 32367548 DOI: 10.1111/exd.14110] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 04/21/2020] [Accepted: 04/28/2020] [Indexed: 12/28/2022]
Abstract
Epidermal energy metabolism is relevant to skin physiology, ageing and photodamage. While selected hormones stimulate epidermal keratinocyte mitochondrial activity, its negative regulation remains unknown. In several cell types, cannabinoid receptor 1 (CB1 ) is expressed both on the cell membrane (cmCB1 ) and on the mitochondrial outer membrane (mtCB1 ), where its stimulation directly suppresses mitochondrial functions. In the current pilot study, we investigated if CB1 is a negative regulator of human epidermal energy metabolism under physiological conditions. Using organ-cultured full-thickness human skin specimens of healthy individuals, we showed that antagonizing the homeostatic CB1 signalling by the administration of the CB1 inverse agonist AM251 increased respiratory chain complex I and II/IV activity. The effect was CB1 -dependent, since the CB1 -selective agonist arachidonyl-2'-chloroethylamide could prevent the effect. Moreover, the phenomenon was also reproduced by siRNA-mediated down-regulation of CB1 . As revealed by the unaltered expression of several relevant markers (TFAM, VDAC1, MTCO1 and NDUFS4), modulation of CB1 signalling had no effect on the epidermal mitochondrial mass. Next, by using immunoelectron microscopy, we found that human epidermal keratinocytes express both cmCB1 and mtCB1 . Finally, by using equipotent extracellularly restricted (hemopressin) as well as cell-permeable (AM251) inverse agonists, we found that mitochondrial activity is most likely exclusively regulated by mtCB1 . Thus, our data identify mtCB1 as a novel negative regulator of keratinocyte mitochondrial activity in intact human epidermis, and raise the question, whether topical therapeutic interventions capable of selectively activating mtCB1 can reduce excessive mitochondrial ROS production resulting from dysregulated mitochondrial activity during skin ageing or photodamage.
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Affiliation(s)
- Attila Oláh
- Department of Physiology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Majid Alam
- Monasterium Laboratory Skin & Hair Research Solutions GmbH, Münster, Germany.,Department of Dermatology and Venereology, Hamad Medical Corporation, Doha, Qatar.,Translational Research Institute, Hamad Medical Corporation, Doha, Qatar
| | - Jérémy Chéret
- Monasterium Laboratory Skin & Hair Research Solutions GmbH, Münster, Germany.,Dr. Phillip Frost Department of Dermatology & Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Nikolett Gréta Kis
- Department of Anatomy, Embryology and Histology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Zoltán Hegyi
- Department of Anatomy, Embryology and Histology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Attila Gábor Szöllősi
- Department of Immunology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Silvia Vidali
- Research Program for Receptor Biochemistry and Tumor Metabolism, Department of Pediatrics, Paracelsus Medical University, Salzburg, Austria
| | - Tamás Bíró
- Department of Immunology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Ralf Paus
- Monasterium Laboratory Skin & Hair Research Solutions GmbH, Münster, Germany.,Dr. Phillip Frost Department of Dermatology & Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, FL, USA.,Centre for Dermatology Research, NIHR Manchester Biomedical Research Centre, University of Manchester, Manchester, UK
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35
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A Novel 4-Gene Score to Predict Survival, Distant Metastasis and Response to Neoadjuvant Therapy in Breast Cancer. Cancers (Basel) 2020; 12:cancers12051148. [PMID: 32370309 PMCID: PMC7281399 DOI: 10.3390/cancers12051148] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 04/24/2020] [Accepted: 04/28/2020] [Indexed: 12/15/2022] Open
Abstract
We generated a 4-gene score with genes upregulated in LM2-4, a metastatic variant of MDA-MB-231 (DOK 4, HCCS, PGF, and SHCBP1) that was strongly associated with disease-free survival (DFS) in TCGA cohort (hazard ratio [HR]>1.2, p < 0.02). The 4-gene score correlated with overall survival of TCGA (HR = 1.44, p < 0.001), which was validated with DFS and disease-specific survival of METABRIC cohort. The 4-gene score was able to predict worse survival or clinically aggressive tumors, such as high Nottingham pathological grade and advanced cancer staging. High score was associated with worse survival in the hormonal receptor (HR)-positive/Her2-negative subtype. High score enriched cell proliferation-related gene sets in GSEA. The score was high in primary tumors that originated, in and metastasized to, brain and lung, and it predicted worse progression-free survival for metastatic tumors. Good tumor response to neoadjuvant chemotherapy or hormonal therapy was accompanied by score reduction. High scores were also predictive of response to neoadjuvant chemotherapy for HR-positive/Her2-negative subtype. High score tumors had increased expression of T cell exhaustion marker genes, suggesting that the score may also be a biomarker for immunotherapy response. Our novel 4-gene score with both prognostic and predictive values may, therefore, be clinically useful particularly in HR-positive breast cancer.
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36
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Jiao N, Xu D, Qiu K, Wang L, Wang L, Piao X, Yin J. Restoring mitochondrial function and normalizing ROS-JNK/MAPK pathway exert key roles in glutamine ameliorating bisphenol A-induced intestinal injury. FASEB J 2020; 34:7442-7461. [PMID: 32285985 DOI: 10.1096/fj.201902503r] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 03/02/2020] [Accepted: 03/17/2020] [Indexed: 12/30/2022]
Abstract
Bisphenol A (BPA) is toxic to the reproductive and nervous system, even carcinogenetic in humans and animals. However, few studies focused on effects of BPA on the intestinal tract. Here, we detected BPA-induced injuries on intestinal mucosa and explored a reliable approach to counteract BPA effects. C57BL/6J mice were gavage BPA or BPA accompanied with ingestion of 4% (w/w) of glutamine for 4-wks. In vitro, IEC-6 cells were treated with 0.4 mmol/L BPA for 6 hours mimicking acute injury and 0.2 mmol/L BPA for 12 hours followed with or without the inclusion of 4 mmol/L glutamine for 12 hours to determine cell renewal, mitochondrial function and ROS-JNK/MAPK pathway upon moderate BPA exposure. As results, BPA exposure caused severe intestinal injury, and disturbed intestinal epithelial cell proliferation and apoptosis, accompanied with mitochondrial malfunction and activated JNK/MAPK pathway as well. Notably, glutathione metabolism was implicated in BPA-induce injury. Glutamine could well rescue cell renewal and mitochondrial function from BPA exposure-induced injuries. In conclusion, we demonstrated impaired effect of BPA exposure on intestinal functions, which could be well counteracted by glutamine partly via restoring mitochondrial function and normalizing ROS-JNK/MAPK pathway. Thereby, we provided a novel application of glutamine to rescue intestinal injury.
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Affiliation(s)
- Ning Jiao
- State Key Lab of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Doudou Xu
- State Key Lab of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Kai Qiu
- State Key Lab of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Liqi Wang
- State Key Lab of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Lu Wang
- State Key Lab of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xiangshu Piao
- State Key Lab of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jingdong Yin
- State Key Lab of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
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37
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Indrieri A, Carrella S, Carotenuto P, Banfi S, Franco B. The Pervasive Role of the miR-181 Family in Development, Neurodegeneration, and Cancer. Int J Mol Sci 2020; 21:ijms21062092. [PMID: 32197476 PMCID: PMC7139714 DOI: 10.3390/ijms21062092] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/13/2020] [Accepted: 03/16/2020] [Indexed: 12/21/2022] Open
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs playing a fundamental role in the regulation of gene expression. Evidence accumulating in the past decades indicate that they are capable of simultaneously modulating diverse signaling pathways involved in a variety of pathophysiological processes. In the present review, we provide a comprehensive overview of the function of a highly conserved group of miRNAs, the miR-181 family, both in physiological as well as in pathological conditions. We summarize a large body of studies highlighting a role for this miRNA family in the regulation of key biological processes such as embryonic development, cell proliferation, apoptosis, autophagy, mitochondrial function, and immune response. Importantly, members of this family have been involved in many pathological processes underlying the most common neurodegenerative disorders as well as different solid tumors and hematological malignancies. The relevance of this miRNA family in the pathogenesis of these disorders and their possible influence on the severity of their manifestations will be discussed. A better understanding of the miR-181 family in pathological conditions may open new therapeutic avenues for devasting disorders such as neurodegenerative diseases and cancer.
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Affiliation(s)
- Alessia Indrieri
- Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei 34, 80078 Pozzuoli, Naples, Italy; (S.C.); (P.C.)
- Medical Genetics, Department of Translational Medical Sciences, University of Naples “Federico II”, Via Sergio Pansini 5, 80131 Naples, Italy
- Institute for Genetic and Biomedical Research (IRGB), National Research Council (CNR), 20090 Milan, Italy
- Correspondence: (A.I.); (S.B.); (B.F.); Tel.: +39-081-19230655 (A.I.); +39-081-19230606 (S.B.); +39-081-19230615 (B.F.)
| | - Sabrina Carrella
- Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei 34, 80078 Pozzuoli, Naples, Italy; (S.C.); (P.C.)
- Medical Genetics, Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy
| | - Pietro Carotenuto
- Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei 34, 80078 Pozzuoli, Naples, Italy; (S.C.); (P.C.)
- The Institute of Cancer Research, Cancer Therapeutics Unit 15 Cotswold Road, Sutton, London SM2 5NG, UK
| | - Sandro Banfi
- Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei 34, 80078 Pozzuoli, Naples, Italy; (S.C.); (P.C.)
- Medical Genetics, Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy
- Correspondence: (A.I.); (S.B.); (B.F.); Tel.: +39-081-19230655 (A.I.); +39-081-19230606 (S.B.); +39-081-19230615 (B.F.)
| | - Brunella Franco
- Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei 34, 80078 Pozzuoli, Naples, Italy; (S.C.); (P.C.)
- Medical Genetics, Department of Translational Medical Sciences, University of Naples “Federico II”, Via Sergio Pansini 5, 80131 Naples, Italy
- Correspondence: (A.I.); (S.B.); (B.F.); Tel.: +39-081-19230655 (A.I.); +39-081-19230606 (S.B.); +39-081-19230615 (B.F.)
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38
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Vendramini-Pittoli S, Candido-Souza RM, Quiezi RG, Zechi-Ceide RM, Kokitsu-Nakata NM, Jehee FS, Ribeiro-Bicudo LA, FitzPatrick DR, Guion-Almeida ML, Richieri-Costa A. Microphthalmia, Linear Skin Defects, Callosal Agenesis, and Cleft Palate in a Patient with Deletion at Xp22.3p22.2. J Pediatr Genet 2020; 9:258-262. [PMID: 32765930 DOI: 10.1055/s-0039-3402047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 11/07/2019] [Indexed: 01/23/2023]
Abstract
The authors describe the clinical findings observed in a Brazilian girl that are suggestive of microphthalmia and linear skin defects (MLS) also known as MIDAS syndrome (OMIM #309801). She also presented with short stature, agenesis of corpus callosum, cleft palate, enamel defects, and genitourinary anomalies, which are rarely reported within the clinical spectrum of MLS. The 11,5 Mb deletion in Xp22.3p22.2 observed in the patient includes the entire HCCS gene (responsible for the MLS phenotype) and also encompasses several other genes involved with behavioral phenotypes, craniofacial and central nervous system development such as MID1, NLGN4X, AMELX , ARHGAP6, and TBL1X. The whole clinical features of our proband possibly represents an unusual MLS syndromic phenotype caused by an Xp22.3p22.2 continuous gene deletion.
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Affiliation(s)
- Siulan Vendramini-Pittoli
- Department of Clinical Genetics, Hospital for Rehabilitation of Craniofacial Anomalies, University of São Paulo, Bauru, São Paulo, Brazil
| | - Rosana Maria Candido-Souza
- Department of Clinical Genetics, Hospital for Rehabilitation of Craniofacial Anomalies, University of São Paulo, Bauru, São Paulo, Brazil
| | - Rodrigo Gonçalves Quiezi
- Medical Research Council (MRC) Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, Edinburgh, United Kingdom
| | - Roseli Maria Zechi-Ceide
- Department of Clinical Genetics, Hospital for Rehabilitation of Craniofacial Anomalies, University of São Paulo, Bauru, São Paulo, Brazil
| | - Nancy Mizue Kokitsu-Nakata
- Department of Clinical Genetics, Hospital for Rehabilitation of Craniofacial Anomalies, University of São Paulo, Bauru, São Paulo, Brazil
| | | | | | - David R FitzPatrick
- Medical Research Council (MRC) Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, Edinburgh, United Kingdom
| | - Maria Leine Guion-Almeida
- Department of Clinical Genetics, Hospital for Rehabilitation of Craniofacial Anomalies, University of São Paulo, Bauru, São Paulo, Brazil
| | - Antonio Richieri-Costa
- Department of Clinical Genetics, Hospital for Rehabilitation of Craniofacial Anomalies, University of São Paulo, Bauru, São Paulo, Brazil
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39
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Satcher KG, Maegawa GHB, Schoch JJ. Microphthalmia and linear skin defects syndrome: Precise diagnosis guides prognosis. Pediatr Dermatol 2020; 37:217-218. [PMID: 31373408 DOI: 10.1111/pde.13946] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Microphthalmia and linear skin defects syndrome (MLS) is a rare X-linked dominant disorder characterized by microphthalmia and linear atrophic plaques of the face and neck. The diagnosis of MLS can be challenging secondary to both its rarity and to clinical overlap with Goltz syndrome. Whereas the skin lesions of MLS are more likely to improve in appearance with age, the lesions of Goltz are typically persistent.
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Affiliation(s)
- Kerrie G Satcher
- Department of Dermatology, University of Florida, Gainesville, Florida
| | - Gustavo H B Maegawa
- Department of Pediatrics/Genetics & Metabolism, University of Florida, Gainesville, Florida
| | - Jennifer J Schoch
- Department of Dermatology, University of Florida, Gainesville, Florida
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40
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Wang Y, Hussein AM, Somasundaram L, Sankar R, Detraux D, Mathieu J, Ruohola-Baker H. microRNAs Regulating Human and Mouse Naïve Pluripotency. Int J Mol Sci 2019; 20:E5864. [PMID: 31766734 PMCID: PMC6929104 DOI: 10.3390/ijms20235864] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 11/07/2019] [Accepted: 11/13/2019] [Indexed: 12/16/2022] Open
Abstract
microRNAs are ~22bp nucleotide non-coding RNAs that play important roles in the post-transcriptional regulation of gene expression. Many studies have established that microRNAs are important for cell fate choices, including the naïve to primed pluripotency state transitions, and their intermediate state, the developmentally suspended diapause state in early development. However, the full extent of microRNAs associated with these stage transitions in human and mouse remain under-explored. By meta-analysis of microRNA-seq, RNA-seq, and metabolomics datasets from human and mouse, we found a set of microRNAs, and importantly, their experimentally validated target genes that show consistent changes in naïve to primed transitions (microRNA up, target genes down, or vice versa). The targets of these microRNAs regulate developmental pathways (e.g., the Hedgehog-pathway), primary cilium, and remodeling of metabolic processes (oxidative phosphorylation, fatty acid metabolism, and amino acid transport) during the transition. Importantly, we identified 115 microRNAs that significantly change in the same direction in naïve to primed transitions in both human and mouse, many of which are novel candidate regulators of pluripotency. Furthermore, we identified 38 microRNAs and 274 target genes that may be involved in diapause, where embryonic development is temporarily suspended prior to implantation to uterus. The upregulated target genes suggest that microRNAs activate stress response in the diapause stage. In conclusion, we provide a comprehensive resource of microRNAs and their target genes involved in naïve to primed transition and in the paused intermediate, the embryonic diapause stage.
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Affiliation(s)
- Yuliang Wang
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA 98195, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA; (A.M.H.); (L.S.); (R.S.); (D.D.)
| | - Abdiasis M. Hussein
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA; (A.M.H.); (L.S.); (R.S.); (D.D.)
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Logeshwaran Somasundaram
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA; (A.M.H.); (L.S.); (R.S.); (D.D.)
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Rithika Sankar
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA; (A.M.H.); (L.S.); (R.S.); (D.D.)
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Damien Detraux
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA; (A.M.H.); (L.S.); (R.S.); (D.D.)
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Department of Comparative Medicine, University of Washington, Seattle, WA 98195, USA
| | - Julie Mathieu
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA; (A.M.H.); (L.S.); (R.S.); (D.D.)
- Department of Comparative Medicine, University of Washington, Seattle, WA 98195, USA
| | - Hannele Ruohola-Baker
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA; (A.M.H.); (L.S.); (R.S.); (D.D.)
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
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41
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Sprenger HG, Wani G, Hesseling A, König T, Patron M, MacVicar T, Ahola S, Wai T, Barth E, Rugarli EI, Bergami M, Langer T. Loss of the mitochondrial i-AAA protease YME1L leads to ocular dysfunction and spinal axonopathy. EMBO Mol Med 2019; 11:emmm.201809288. [PMID: 30389680 PMCID: PMC6328943 DOI: 10.15252/emmm.201809288] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Disturbances in the morphology and function of mitochondria cause neurological diseases, which can affect the central and peripheral nervous system. The i‐AAA protease YME1L ensures mitochondrial proteostasis and regulates mitochondrial dynamics by processing of the dynamin‐like GTPase OPA1. Mutations in YME1L cause a multi‐systemic mitochondriopathy associated with neurological dysfunction and mitochondrial fragmentation but pathogenic mechanisms remained enigmatic. Here, we report on striking cell‐type‐specific defects in mice lacking YME1L in the nervous system. YME1L‐deficient mice manifest ocular dysfunction with microphthalmia and cataracts and develop deficiencies in locomotor activity due to specific degeneration of spinal cord axons, which relay proprioceptive signals from the hind limbs to the cerebellum. Mitochondrial fragmentation occurs throughout the nervous system and does not correlate with the degenerative phenotype. Deletion of Oma1 restores tubular mitochondria but deteriorates axonal degeneration in the absence of YME1L, demonstrating that impaired mitochondrial proteostasis rather than mitochondrial fragmentation causes the observed neurological defects.
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Affiliation(s)
- Hans-Georg Sprenger
- Max-Planck-Institute for Biology of Ageing, Cologne, Germany.,Institute of Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Gulzar Wani
- Institute of Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Annika Hesseling
- Institute of Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Tim König
- Institute of Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Maria Patron
- Max-Planck-Institute for Biology of Ageing, Cologne, Germany.,Institute of Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Thomas MacVicar
- Max-Planck-Institute for Biology of Ageing, Cologne, Germany.,Institute of Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Sofia Ahola
- Max-Planck-Institute for Biology of Ageing, Cologne, Germany.,Institute of Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Timothy Wai
- Institute of Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Esther Barth
- Institute of Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Elena I Rugarli
- Institute of Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Matteo Bergami
- Institute of Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Center for Molecular Medicine, University of Cologne, Cologne, Germany
| | - Thomas Langer
- Max-Planck-Institute for Biology of Ageing, Cologne, Germany .,Institute of Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Center for Molecular Medicine, University of Cologne, Cologne, Germany
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42
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Inoue M, Uchino S, Iida A, Noguchi S, Hayashi S, Takahashi T, Fujii K, Komaki H, Takeshita E, Nonaka I, Okada Y, Yoshizawa T, Van Lommel L, Schuit F, Goto YI, Mimaki M, Nishino I. COX6A2 variants cause a muscle-specific cytochrome c oxidase deficiency. Ann Neurol 2019; 86:193-202. [PMID: 31155743 DOI: 10.1002/ana.25517] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 05/28/2019] [Accepted: 05/31/2019] [Indexed: 12/11/2022]
Abstract
OBJECTIVE Cytochrome c oxidase (COX) deficiency is a major mitochondrial respiratory chain defect that has vast genetic and phenotypic heterogeneity. This study aims to identify novel causative genes of COX deficiency with only striated muscle-specific symptoms. METHODS Whole exome sequencing was performed in 2 unrelated individuals who were diagnosed with congenital myopathy and presented COX deficiency in muscle pathology. We assessed the COX6A2 variants using measurements of enzymatic activities and assembly of mitochondrial respiratory chain complexes in the samples from the patients and knockout mice. RESULTS Both patients presented muscle weakness and hypotonia in 4 limbs along with facial muscle weakness. One patient had cardiomyopathy. Neither patient exhibited involvement from other organs. Whole exome sequencing identified biallelic missense variants in COX6A2, which is expressed only in the skeletal muscle and heart. The variants detected were homozygous c.117C > A (p.Ser39Arg) and compound heterozygous c.117C > A (p.Ser39Arg) and c.127T > C (p.Cys43Arg). We found specific reductions in complex IV activities in the skeletal muscle of both individuals. Assembly of complex IV and its supercomplex formation were impaired in the muscle. INTERPRETATION This study indicates that biallelic variants in COX6A2 cause a striated muscle-specific form of COX deficiency. ANN NEUROL 2019;86:193-202.
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Affiliation(s)
- Michio Inoue
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan.,Integrated Graduate School of Medicine, Engineering, and Agricultural Science, University of Yamanashi, Yamanashi, Japan.,Medical Genome Center, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Shumpei Uchino
- Department of Mental Retardation and Birth Defect Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan.,Department of Pediatrics, Teikyo University School of Medicine, Tokyo, Japan
| | - Aritoshi Iida
- Medical Genome Center, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Satoru Noguchi
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan.,Medical Genome Center, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Shinichiro Hayashi
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan.,Medical Genome Center, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Tsutomu Takahashi
- Department of Pediatrics, Saiseikai Utsunomiya Hospital, Tochigi, Japan
| | - Katsunori Fujii
- Department of Pediatrics, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Hirofumi Komaki
- Department of Mental Retardation and Birth Defect Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan.,Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Eri Takeshita
- Department of Mental Retardation and Birth Defect Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan.,Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Ikuya Nonaka
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Takuya Yoshizawa
- College of Life Sciences, Ritsumeikan University, Kusatsu, Japan
| | - Leentje Van Lommel
- Department of Cellular and Molecular Medicine, Faculty of Medicine, KU Leuven, Leuven, Belgium
| | - Frans Schuit
- Department of Cellular and Molecular Medicine, Faculty of Medicine, KU Leuven, Leuven, Belgium
| | - Yu-Ichi Goto
- Medical Genome Center, National Center of Neurology and Psychiatry, Tokyo, Japan.,Department of Mental Retardation and Birth Defect Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan.,Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Masakazu Mimaki
- Department of Mental Retardation and Birth Defect Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan.,Department of Pediatrics, Teikyo University School of Medicine, Tokyo, Japan
| | - Ichizo Nishino
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan.,Medical Genome Center, National Center of Neurology and Psychiatry, Tokyo, Japan
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43
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Indrieri A, Carrella S, Romano A, Spaziano A, Marrocco E, Fernandez‐Vizarra E, Barbato S, Pizzo M, Ezhova Y, Golia FM, Ciampi L, Tammaro R, Henao‐Mejia J, Williams A, Flavell RA, De Leonibus E, Zeviani M, Surace EM, Banfi S, Franco B. miR-181a/b downregulation exerts a protective action on mitochondrial disease models. EMBO Mol Med 2019; 11:emmm.201708734. [PMID: 30979712 PMCID: PMC6505685 DOI: 10.15252/emmm.201708734] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Mitochondrial diseases (MDs) are a heterogeneous group of devastating and often fatal disorders due to defective oxidative phosphorylation. Despite the recent advances in mitochondrial medicine, effective therapies are still not available for these conditions. Here, we demonstrate that the microRNAs miR-181a and miR-181b (miR-181a/b) regulate key genes involved in mitochondrial biogenesis and function and that downregulation of these miRNAs enhances mitochondrial turnover in the retina through the coordinated activation of mitochondrial biogenesis and mitophagy. We thus tested the effect of miR-181a/b inactivation in different animal models of MDs, such as microphthalmia with linear skin lesions and Leber's hereditary optic neuropathy. We found that miR-181a/b downregulation strongly protects retinal neurons from cell death and significantly ameliorates the disease phenotype in all tested models. Altogether, our results demonstrate that miR-181a/b regulate mitochondrial homeostasis and that these miRNAs may be effective gene-independent therapeutic targets for MDs characterized by neuronal degeneration.
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Affiliation(s)
- Alessia Indrieri
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly,Medical GeneticsDepartment of Translational Medical ScienceUniversity of Naples “Federico II”NaplesItaly
| | - Sabrina Carrella
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly,Medical GeneticsDepartment of Precision MedicineUniversity of Campania “L. Vanvitelli”Caserta CEItaly
| | - Alessia Romano
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
| | | | - Elena Marrocco
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
| | | | - Sara Barbato
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
| | | | - Yulia Ezhova
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
| | | | - Ludovica Ciampi
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
| | - Roberta Tammaro
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
| | - Jorge Henao‐Mejia
- Department of Pathology and Laboratory MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA,Institute for ImmunologyPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Adam Williams
- The Jackson Laboratory for Genomic MedicineFarmingtonCTUSA,Department of Genetics and Genomic SciencesUniversity of Connecticut Health CenterFarmingtonCTUSA
| | - Richard A Flavell
- Department of ImmunobiologyYale University School of MedicineNew HavenCTUSA,Howard Hughes Medical InstituteChevy ChaseMDUSA
| | - Elvira De Leonibus
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly,Institute of Cellular Biology and Neurobiology “ABT”CNRRomaItaly
| | - Massimo Zeviani
- MRC Mitochondrial Biology UnitUniversity of CambridgeCambridgeUK
| | - Enrico M Surace
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly,Medical GeneticsDepartment of Translational Medical ScienceUniversity of Naples “Federico II”NaplesItaly,Present address:
Medical GeneticsDepartment of Translational Medical ScienceUniversity of Naples “Federico II”NaplesItaly
| | - Sandro Banfi
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy .,Medical Genetics, Department of Precision Medicine, University of Campania "L. Vanvitelli", Caserta CE, Italy
| | - Brunella Franco
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy .,Medical Genetics, Department of Translational Medical Science, University of Naples "Federico II", Naples, Italy
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44
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Winter C, Kosch R, Ludlow M, Osterhaus ADME, Jung K. Network meta-analysis correlates with analysis of merged independent transcriptome expression data. BMC Bioinformatics 2019; 20:144. [PMID: 30876387 PMCID: PMC6420731 DOI: 10.1186/s12859-019-2705-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 02/27/2019] [Indexed: 12/15/2022] Open
Abstract
Background Using meta-analysis, high-dimensional transcriptome expression data from public repositories can be merged to make group comparisons that have not been considered in the original studies. Merging of high-dimensional expression data can, however, implicate batch effects that are sometimes difficult to be removed. Removing batch effects becomes even more difficult when expression data was taken using different technologies in the individual studies (e.g. merging of microarray and RNA-seq data). Network meta-analysis has so far not been considered to make indirect comparisons in transcriptome expression data, when data merging appears to yield biased results. Results We demonstrate in a simulation study that the results from analyzing merged data sets and the results from network meta-analysis are highly correlated in simple study networks. In the case that an edge in the network is supported by multiple independent studies, network meta-analysis produces fold changes that are closer to the simulated ones than those obtained from analyzing merged data sets. Finally, we also demonstrate the practicability of network meta-analysis on a real-world data example from neuroinfection research. Conclusions Network meta-analysis is a useful means to make new inferences when combining multiple independent studies of molecular, high-throughput expression data. This method is especially advantageous when batch effects between studies are hard to get removed. Electronic supplementary material The online version of this article (10.1186/s12859-019-2705-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Christine Winter
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Bünteweg 17p, Hannover, 30559, Germany
| | - Robin Kosch
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Bünteweg 17p, Hannover, 30559, Germany
| | - Martin Ludlow
- Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, Bünteweg 17p, Hannover, 30559, Germany
| | - Albert D M E Osterhaus
- Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, Bünteweg 17p, Hannover, 30559, Germany
| | - Klaus Jung
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Bünteweg 17p, Hannover, 30559, Germany.
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45
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Signes A, Cerutti R, Dickson AS, Benincá C, Hinchy EC, Ghezzi D, Carrozzo R, Bertini E, Murphy MP, Nathan JA, Viscomi C, Fernandez-Vizarra E, Zeviani M. APOPT1/COA8 assists COX assembly and is oppositely regulated by UPS and ROS. EMBO Mol Med 2019; 11:e9582. [PMID: 30552096 PMCID: PMC6328941 DOI: 10.15252/emmm.201809582] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 11/20/2018] [Accepted: 11/21/2018] [Indexed: 02/02/2023] Open
Abstract
Loss-of-function mutations in APOPT1, a gene exclusively found in higher eukaryotes, cause a characteristic type of cavitating leukoencephalopathy associated with mitochondrial cytochrome c oxidase (COX) deficiency. Although the genetic association of APOPT1 pathogenic variants with isolated COX defects is now clear, the biochemical link between APOPT1 function and COX has remained elusive. We investigated the molecular role of APOPT1 using different approaches. First, we generated an Apopt1 knockout mouse model which shows impaired motor skills, e.g., decreased motor coordination and endurance, associated with reduced COX activity and levels in multiple tissues. In addition, by achieving stable expression of wild-type APOPT1 in control and patient-derived cultured cells we ruled out a role of this protein in apoptosis and established instead that this protein is necessary for proper COX assembly and function. On the other hand, APOPT1 steady-state levels were shown to be controlled by the ubiquitination-proteasome system (UPS). Conversely, in conditions of increased oxidative stress, APOPT1 is stabilized, increasing its mature intramitochondrial form and thereby protecting COX from oxidatively induced degradation.
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Affiliation(s)
- Alba Signes
- MRC-Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Raffaele Cerutti
- MRC-Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Anna S Dickson
- Department of Medicine, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Cristiane Benincá
- MRC-Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | | | - Daniele Ghezzi
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico "Carlo Besta", Milan, Italy
- Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Rosalba Carrozzo
- Unit of Neuromuscular and Neurodegenerative Disorders, Bambino Gesù Children's Research Hospital, IRCCS, Rome, Italy
| | - Enrico Bertini
- Unit of Neuromuscular and Neurodegenerative Disorders, Bambino Gesù Children's Research Hospital, IRCCS, Rome, Italy
| | - Michael P Murphy
- MRC-Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - James A Nathan
- Department of Medicine, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Carlo Viscomi
- MRC-Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | | | - Massimo Zeviani
- MRC-Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
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46
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Slavotinek A. Genetics of anophthalmia and microphthalmia. Part 2: Syndromes associated with anophthalmia-microphthalmia. Hum Genet 2018; 138:831-846. [PMID: 30374660 DOI: 10.1007/s00439-018-1949-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Accepted: 10/20/2018] [Indexed: 12/12/2022]
Abstract
As new genes for A/M are identified in the genomic era, the number of syndromes associated with A/M has greatly expanded. In this review, we provide a brief synopsis of the clinical presentation and molecular genetic etiology of previously characterized pathways involved in A/M, including the Sex-determining region Y-box 2 (SOX2), Orthodenticle Homeobox 2 (OTX2) and Paired box protein-6 (PAX6) genes, and the Stimulated by retinoic acid gene 6 homolog (STRA6), Aldehyde Dehydrogenase 1 Family Member A3 (ALDH1A3), and RA Receptor Beta (RARβ) genes that are involved in retinoic acid synthesis. Less common genetic causes of A/M, including genes involved in BMP signaling [Bone Morphogenetic Protein 4 (BMP4), Bone Morphogenetic Protein 7 (BMP7) and SPARC-related modular calcium-binding protein 1 (SMOC1)], genes involved in the mitochondrial respiratory chain complex [Holocytochrome c-type synthase (HCCS), Cytochrome C Oxidase Subunit 7B (COX7B), and NADH:Ubiquinone Oxidoreductase subunit B11 (NDUFB11)], the BCL-6 corepressor gene (BCOR), Yes-Associated Protein 1 (YAP1) and Transcription Factor AP-2 Alpha (TFAP2α), are more briefly discussed. We also review several recently described genes and pathways associated with A/M, including Smoothened (SMO) that is involved in Sonic hedgehog (SHH) signaling, Structural maintenance of chromosomes flexible hinge domain containing 1 (SMCHD1) and Solute carrier family 25 member 24 (SLC25A24), emphasizing phenotype-genotype correlations and shared pathways where relevant.
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Affiliation(s)
- Anne Slavotinek
- Division of Genetics, Department of Pediatrics, University of California, San Francisco Room RH384C, 1550 4th St, San Francisco, CA, 94143-2711, USA.
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Prepeluh N, Korpar B, Zagorac A, Zagradišnik B, Golub A, Kokalj Vokač N. A mosaic form of microphthalmia with linear skin defects. BMC Pediatr 2018; 18:254. [PMID: 30068298 PMCID: PMC6090767 DOI: 10.1186/s12887-018-1234-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 07/20/2018] [Indexed: 11/29/2022] Open
Abstract
Background Microphthalmia with linear skin defects (MLS) syndrome is a rare neurodevelopmental X-dominant disorder. It presents in females as it is normally lethal in males. Three causative genes for MLS syndrome (OMIM 309801) have been identified all taking part in mitochondrial respiratory chain and oxidative phosphorylation. In our case, we describe a newborn with mosaic deletion encompassing HCCS gene resulting in unilateral microphthalmia and facial skin lesions. Case presentation A girl was born with caesarean section at 40 weeks of gestation. Clinical findings revealed anophthalmia of the left eye. The left eyelids were intact, the orbit was empty and the right eye was normal, without any abnormalities. She had typical linear skin defects on the left cheek, one on the left side of the neck, and two on the 3th and 4th fingers of the left hand. The other clinical findings and the neurological exam were normal. US of the brain and EEG were normal. Molecular karyotyping using BlueGnome CytoChip Oligo 4× 180K array was performed detecting an approximately 18% mosaic 3.3 Mb deletion (arr[GRCh37] Xp22.31p22.2(8,622,553_11,887,361)× 1[0.18]). FISH using RPCI11-768H20 BAC clone on cultivated interphase and metaphase lymphocytes was used to confirm the array results. The observed deletion was present in 29% of cells (46,XX,ish del(p22.2p22.31)(RPCI11-768H20)[60/205]). Conclusions In this report we present a female proband with MLS syndrome. To our knowledge, there have been only few other cases of mosaic MLS syndrome described in the literature. Our case shows that low grade mosaicism does not preclude full clinical presentation and further supports the critical role of the X inactivation pattern in the development of the clinical findings.
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Affiliation(s)
- Nina Prepeluh
- Laboratory of Medical Genetics, University Medical Centre Maribor, Ljubljanska 5, 2000, Maribor, Slovenia
| | - Bojan Korpar
- Department of Perinatology, Division of Gynaecology and Perinatology, University Medical Centre Maribor, Maribor, Slovenia
| | - Andreja Zagorac
- Laboratory of Medical Genetics, University Medical Centre Maribor, Ljubljanska 5, 2000, Maribor, Slovenia
| | - Boris Zagradišnik
- Laboratory of Medical Genetics, University Medical Centre Maribor, Ljubljanska 5, 2000, Maribor, Slovenia
| | - Andreja Golub
- Laboratory of Medical Genetics, University Medical Centre Maribor, Ljubljanska 5, 2000, Maribor, Slovenia
| | - Nadja Kokalj Vokač
- Laboratory of Medical Genetics, University Medical Centre Maribor, Ljubljanska 5, 2000, Maribor, Slovenia. .,Medical Faculty, University of Maribor, Maribor, Slovenia.
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Regulation of mitochondrial respiration and ATP synthesis via cytochrome c oxidase. RENDICONTI LINCEI-SCIENZE FISICHE E NATURALI 2018. [DOI: 10.1007/s12210-018-0710-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Porpora M, Sauchella S, Rinaldi L, Delle Donne R, Sepe M, Torres-Quesada O, Intartaglia D, Garbi C, Insabato L, Santoriello M, Bachmann VA, Synofzik M, Lindner HH, Conte I, Stefan E, Feliciello A. Counterregulation of cAMP-directed kinase activities controls ciliogenesis. Nat Commun 2018; 9:1224. [PMID: 29581457 PMCID: PMC5964327 DOI: 10.1038/s41467-018-03643-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 02/28/2018] [Indexed: 01/13/2023] Open
Abstract
The primary cilium emanates from the cell surface of growth-arrested cells and plays a central role in vertebrate development and tissue homeostasis. The mechanisms that control ciliogenesis have been extensively explored. However, the intersection between GPCR signaling and the ubiquitin pathway in the control of cilium stability are unknown. Here we observe that cAMP elevation promotes cilia resorption. At centriolar satellites, we identify a multimeric complex nucleated by PCM1 that includes two kinases, NEK10 and PKA, and the E3 ubiquitin ligase CHIP. We show that NEK10 is essential for ciliogenesis in mammals and for the development of medaka fish. PKA phosphorylation primes NEK10 for CHIP-mediated ubiquitination and proteolysis resulting in cilia resorption. Disarrangement of this control mechanism occurs in proliferative and genetic disorders. These findings unveil a pericentriolar kinase signalosome that efficiently links the cAMP cascade with the ubiquitin-proteasome system, thereby controlling essential aspects of ciliogenesis.
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Affiliation(s)
- Monia Porpora
- Department of Molecular Medicine and Medical Biotechnologies, University 'Federico II', Naples, 80131, Italy
| | - Simona Sauchella
- Department of Molecular Medicine and Medical Biotechnologies, University 'Federico II', Naples, 80131, Italy
| | - Laura Rinaldi
- Department of Molecular Medicine and Medical Biotechnologies, University 'Federico II', Naples, 80131, Italy
| | - Rossella Delle Donne
- Department of Molecular Medicine and Medical Biotechnologies, University 'Federico II', Naples, 80131, Italy
| | - Maria Sepe
- Department of Molecular Medicine and Medical Biotechnologies, University 'Federico II', Naples, 80131, Italy
| | - Omar Torres-Quesada
- Institute of Biochemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, A-6020 Innsbruck, Austria
| | - Daniela Intartaglia
- Telethon Institute of Genetics and Medicine, Pozzuoli (Naples), 80078, Italy
| | - Corrado Garbi
- Department of Molecular Medicine and Medical Biotechnologies, University 'Federico II', Naples, 80131, Italy
| | - Luigi Insabato
- Department of Advanced Biomedical Sciences, University Federico II, Naples, 80131, Italy
| | - Margherita Santoriello
- Department of Molecular Medicine and Medical Biotechnologies, University 'Federico II', Naples, 80131, Italy
| | - Verena A Bachmann
- Institute of Biochemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, A-6020 Innsbruck, Austria
| | - Matthis Synofzik
- Department of Neurodegeneration, Hertie Institute for Clinical Brain Research (HIH), University of Tübingen and German Center for Neurodegenerative Diseases (DZNE), 72076, Tübingen, Germany
| | - Herbert H Lindner
- Division of Clinical Biochemistry, Biocenter Medical University of Innsbruck, Innrain 80-82, A-6020, Innsbruck, Austria
| | - Ivan Conte
- Telethon Institute of Genetics and Medicine, Pozzuoli (Naples), 80078, Italy
| | - Eduard Stefan
- Institute of Biochemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, A-6020 Innsbruck, Austria
| | - Antonio Feliciello
- Department of Molecular Medicine and Medical Biotechnologies, University 'Federico II', Naples, 80131, Italy.
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Abstract
Mitochondria are the power stations of the eukaryotic cell, using the energy released by the oxidation of glucose and other sugars to produce ATP. Electrons are transferred from NADH, produced in the citric acid cycle in the mitochondrial matrix, to oxygen by a series of large protein complexes in the inner mitochondrial membrane, which create a transmembrane electrochemical gradient by pumping protons across the membrane. The flow of protons back into the matrix via a proton channel in the ATP synthase leads to conformational changes in the nucleotide binding pockets and the formation of ATP. The three proton pumping complexes of the electron transfer chain are NADH-ubiquinone oxidoreductase or complex I, ubiquinone-cytochrome c oxidoreductase or complex III, and cytochrome c oxidase or complex IV. Succinate dehydrogenase or complex II does not pump protons, but contributes reduced ubiquinone. The structures of complex II, III and IV were determined by x-ray crystallography several decades ago, but complex I and ATP synthase have only recently started to reveal their secrets by advances in x-ray crystallography and cryo-electron microscopy. The complexes I, III and IV occur to a certain extent as supercomplexes in the membrane, the so-called respirasomes. Several hypotheses exist about their function. Recent cryo-electron microscopy structures show the architecture of the respirasome with near-atomic detail. ATP synthase occurs as dimers in the inner mitochondrial membrane, which by their curvature are responsible for the folding of the membrane into cristae and thus for the huge increase in available surface that makes mitochondria the efficient energy plants of the eukaryotic cell.
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Affiliation(s)
- Joana S Sousa
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Edoardo D'Imprima
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Janet Vonck
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.
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