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Huang Y, Zhang L, Sun Y, Liu Q, Chen J, Qian X, Gao X, Zhu GJ, Wan G. A human-specific cytotoxic neopeptide generated by the deafness gene Cingulin. J Genet Genomics 2024:S1673-8527(24)00195-4. [PMID: 39098598 DOI: 10.1016/j.jgg.2024.07.017] [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: 05/23/2024] [Revised: 07/22/2024] [Accepted: 07/26/2024] [Indexed: 08/06/2024]
Abstract
Accumulation of mutant proteins in cells can induce proteinopathies and cause functional damage to organs. Recently, the Cingulin (CGN) protein has been shown to maintain the morphology of cuticular plates of inner ear hair cells and a frameshift mutation in CGN causes autosomal dominant non-syndromic hearing loss. Here, we find that the mutant CGN proteins form insoluble aggregates which accumulate intracellularly and lead to cell death. Expression of the mutant CGN in the inner ear results in severe hair cell death and hearing loss in mice, resembling the auditory phenotype in human patients. Interestingly, a human-specific residue (V1112) in the neopeptide generated by the frameshift mutation is critical for the aggregation and cytotoxicity of the mutant human CGN. Moreover, the expression of heat shock factor 1 (HSF1) decreases the accumulation of insoluble mutant CGN aggregates and rescues cell death. In summary, these findings identify mutant-specific toxic polypeptides as a disease-causing mechanism of the deafness mutation in CGN, which can be targeted by the expression of the cell chaperone response regulator HSF1.
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Affiliation(s)
- Yuhang Huang
- MOE Key Laboratory of Model Animal for Disease Study, Department of Otolaryngology Head and Neck Surgery, Jiangsu Provincial Key Medical Discipline (Laboratory), The Affiliated Drum Tower Hospital of Medical School, Model Animal Research Center of Medical School, Nanjing University, Nanjing, Jiangsu 210061, China; Jiangsu Key Laboratory of Molecular Medicine and National Resource Center for Mutant Mice of China, Nanjing University, Nanjing, Jiangsu 210061, China
| | - Linqing Zhang
- MOE Key Laboratory of Model Animal for Disease Study, Department of Otolaryngology Head and Neck Surgery, Jiangsu Provincial Key Medical Discipline (Laboratory), The Affiliated Drum Tower Hospital of Medical School, Model Animal Research Center of Medical School, Nanjing University, Nanjing, Jiangsu 210061, China; Jiangsu Key Laboratory of Molecular Medicine and National Resource Center for Mutant Mice of China, Nanjing University, Nanjing, Jiangsu 210061, China
| | - Yuecen Sun
- MOE Key Laboratory of Model Animal for Disease Study, Department of Otolaryngology Head and Neck Surgery, Jiangsu Provincial Key Medical Discipline (Laboratory), The Affiliated Drum Tower Hospital of Medical School, Model Animal Research Center of Medical School, Nanjing University, Nanjing, Jiangsu 210061, China; Jiangsu Key Laboratory of Molecular Medicine and National Resource Center for Mutant Mice of China, Nanjing University, Nanjing, Jiangsu 210061, China
| | - Qing Liu
- MOE Key Laboratory of Model Animal for Disease Study, Department of Otolaryngology Head and Neck Surgery, Jiangsu Provincial Key Medical Discipline (Laboratory), The Affiliated Drum Tower Hospital of Medical School, Model Animal Research Center of Medical School, Nanjing University, Nanjing, Jiangsu 210061, China; Jiangsu Key Laboratory of Molecular Medicine and National Resource Center for Mutant Mice of China, Nanjing University, Nanjing, Jiangsu 210061, China; Research Institute of Otolaryngology, No. 321 Zhongshan Road, Nanjing, Jiangsu 210061, China
| | - Jie Chen
- MOE Key Laboratory of Model Animal for Disease Study, Department of Otolaryngology Head and Neck Surgery, Jiangsu Provincial Key Medical Discipline (Laboratory), The Affiliated Drum Tower Hospital of Medical School, Model Animal Research Center of Medical School, Nanjing University, Nanjing, Jiangsu 210061, China; Research Institute of Otolaryngology, No. 321 Zhongshan Road, Nanjing, Jiangsu 210061, China
| | - Xiaoyun Qian
- MOE Key Laboratory of Model Animal for Disease Study, Department of Otolaryngology Head and Neck Surgery, Jiangsu Provincial Key Medical Discipline (Laboratory), The Affiliated Drum Tower Hospital of Medical School, Model Animal Research Center of Medical School, Nanjing University, Nanjing, Jiangsu 210061, China; Research Institute of Otolaryngology, No. 321 Zhongshan Road, Nanjing, Jiangsu 210061, China
| | - Xia Gao
- MOE Key Laboratory of Model Animal for Disease Study, Department of Otolaryngology Head and Neck Surgery, Jiangsu Provincial Key Medical Discipline (Laboratory), The Affiliated Drum Tower Hospital of Medical School, Model Animal Research Center of Medical School, Nanjing University, Nanjing, Jiangsu 210061, China; Research Institute of Otolaryngology, No. 321 Zhongshan Road, Nanjing, Jiangsu 210061, China.
| | - Guang-Jie Zhu
- MOE Key Laboratory of Model Animal for Disease Study, Department of Otolaryngology Head and Neck Surgery, Jiangsu Provincial Key Medical Discipline (Laboratory), The Affiliated Drum Tower Hospital of Medical School, Model Animal Research Center of Medical School, Nanjing University, Nanjing, Jiangsu 210061, China; Research Institute of Otolaryngology, No. 321 Zhongshan Road, Nanjing, Jiangsu 210061, China.
| | - Guoqiang Wan
- MOE Key Laboratory of Model Animal for Disease Study, Department of Otolaryngology Head and Neck Surgery, Jiangsu Provincial Key Medical Discipline (Laboratory), The Affiliated Drum Tower Hospital of Medical School, Model Animal Research Center of Medical School, Nanjing University, Nanjing, Jiangsu 210061, China; Jiangsu Key Laboratory of Molecular Medicine and National Resource Center for Mutant Mice of China, Nanjing University, Nanjing, Jiangsu 210061, China; Research Institute of Otolaryngology, No. 321 Zhongshan Road, Nanjing, Jiangsu 210061, China.
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Sakkaki E, Jafari B, Gharesouran J, Rezazadeh M. Gene expression patterns of CRYM and SIGLEC10 in Alzheimer's disease: potential early diagnostic indicators. Mol Biol Rep 2024; 51:349. [PMID: 38401023 DOI: 10.1007/s11033-023-09113-w] [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: 09/09/2023] [Accepted: 12/06/2023] [Indexed: 02/26/2024]
Abstract
BACKGROUND Alzheimer's disease (AD) is a neurological condition that may lead to dementia as well as a slow and steady decline in cognitive ability. Finding early signs that may be used in the diagnosis of AD is still a difficult aim to achieve in the field of medical practice. METHODS AND RESULTS The purpose of this research was to investigate to determine any differences in the gene expression patterns of crystallin mu (CRYM) and sialic acid-binding immunoglobulin-like lectin 10 (SIGLEC10) in whole blood samples obtained from fifty individuals who were diagnosed with AD and fifty individuals as a control group. When compared with controls, it was discovered that the expression of the CRYM gene was substantially decreased in AD patients, but the expression of the SIGLEC10 gene was significantly higher. A positive correlation between CRYM and SIGLEC10 was noticed solely in patients with AD. Furthermore, assessing the diagnostic value of these genes, CRYM and SIGLEC10 transcript levels displayed an area under the curve (AUC) of 0.74 and 0.81, respectively. CONCLUSIONS These results suggest that alterations in CRYM and SIGLEC10 expression may be implicated in AD pathology and that these genes expression levels can potentially serve as biomarkers for early detection and diagnosis of AD. Nevertheless, further validation of these findings requires the inclusion of more extensive and heterogeneous cohorts. The findings derived from this study possess the capability to offer a significant contribution towards the progression of innovative diagnostic and therapeutic strategies for AD.
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Affiliation(s)
- Ehsan Sakkaki
- Department of Genetics, Ahar Branch, Islamic Azad University, Ahar, Iran
- Clinical Research Development Unit of Tabriz Valiasr Hospital, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Behboud Jafari
- Department of Microbiology, Ahar Branch, Islamic Azad University, Ahar, Iran.
| | - Jalal Gharesouran
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Maryam Rezazadeh
- Clinical Research Development Unit of Tabriz Valiasr Hospital, Tabriz University of Medical Sciences, Tabriz, Iran.
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
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3
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Tu T, Fang Z, Cheng Z, Spasic S, Palepu A, Stankovic KM, Natarajan V, Peltz G. Genetic Discovery Enabled by A Large Language Model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.09.566468. [PMID: 37986848 PMCID: PMC10659415 DOI: 10.1101/2023.11.09.566468] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Artificial intelligence (AI) has been used in many areas of medicine, and recently large language models (LLMs) have shown potential utility for clinical applications. However, since we do not know if the use of LLMs can accelerate the pace of genetic discovery, we used data generated from mouse genetic models to investigate this possibility. We examined whether a recently developed specialized LLM (Med-PaLM 2) could analyze sets of candidate genes generated from analysis of murine models of biomedical traits. In response to free-text input, Med-PaLM 2 correctly identified the murine genes that contained experimentally verified causative genetic factors for six biomedical traits, which included susceptibility to diabetes and cataracts. Med-PaLM 2 was also able to analyze a list of genes with high impact alleles, which were identified by comparative analysis of murine genomic sequence data, and it identified a causative murine genetic factor for spontaneous hearing loss. Based upon this Med-PaLM 2 finding, a novel bigenic model for susceptibility to spontaneous hearing loss was developed. These results demonstrate Med-PaLM 2 can analyze gene-phenotype relationships and generate novel hypotheses, which can facilitate genetic discovery.
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Affiliation(s)
- Tao Tu
- Google Research, Mountain View, CA, USA
| | - Zhouqing Fang
- Department of Anesthesiology, Pain and Perioperative Medicine
| | - Zhuanfen Cheng
- Department of Anesthesiology, Pain and Perioperative Medicine
| | - Svetolik Spasic
- Department of Otolaryngology - Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | - Konstantina M Stankovic
- Department of Otolaryngology - Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | - Gary Peltz
- Department of Anesthesiology, Pain and Perioperative Medicine
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Aldè M, Cantarella G, Zanetti D, Pignataro L, La Mantia I, Maiolino L, Ferlito S, Di Mauro P, Cocuzza S, Lechien JR, Iannella G, Simon F, Maniaci A. Autosomal Dominant Non-Syndromic Hearing Loss (DFNA): A Comprehensive Narrative Review. Biomedicines 2023; 11:1616. [PMID: 37371710 DOI: 10.3390/biomedicines11061616] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 05/26/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
Autosomal dominant non-syndromic hearing loss (HL) typically occurs when only one dominant allele within the disease gene is sufficient to express the phenotype. Therefore, most patients diagnosed with autosomal dominant non-syndromic HL have a hearing-impaired parent, although de novo mutations should be considered in all cases of negative family history. To date, more than 50 genes and 80 loci have been identified for autosomal dominant non-syndromic HL. DFNA22 (MYO6 gene), DFNA8/12 (TECTA gene), DFNA20/26 (ACTG1 gene), DFNA6/14/38 (WFS1 gene), DFNA15 (POU4F3 gene), DFNA2A (KCNQ4 gene), and DFNA10 (EYA4 gene) are some of the most common forms of autosomal dominant non-syndromic HL. The characteristics of autosomal dominant non-syndromic HL are heterogenous. However, in most cases, HL tends to be bilateral, post-lingual in onset (childhood to early adulthood), high-frequency (sloping audiometric configuration), progressive, and variable in severity (mild to profound degree). DFNA1 (DIAPH1 gene) and DFNA6/14/38 (WFS1 gene) are the most common forms of autosomal dominant non-syndromic HL affecting low frequencies, while DFNA16 (unknown gene) is characterized by fluctuating HL. A long audiological follow-up is of paramount importance to identify hearing threshold deteriorations early and ensure prompt treatment with hearing aids or cochlear implants.
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Affiliation(s)
- Mirko Aldè
- Department of Clinical Sciences and Community Health, University of Milan, 20090 Milan, Italy
- Department of Specialist Surgical Sciences, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20090 Milan, Italy
- Otology Study Group of the Young-Otolaryngologists of the International Federations of Oto-Rhino-Laryngological Societies (YO-IFOS), 75000 Paris, France
| | - Giovanna Cantarella
- Department of Clinical Sciences and Community Health, University of Milan, 20090 Milan, Italy
- Department of Specialist Surgical Sciences, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20090 Milan, Italy
| | - Diego Zanetti
- Department of Clinical Sciences and Community Health, University of Milan, 20090 Milan, Italy
- Department of Specialist Surgical Sciences, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20090 Milan, Italy
| | - Lorenzo Pignataro
- Department of Clinical Sciences and Community Health, University of Milan, 20090 Milan, Italy
- Department of Specialist Surgical Sciences, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20090 Milan, Italy
| | - Ignazio La Mantia
- Department of Medical, Surgical Sciences and Advanced Technologies G.F. Ingrassia, University of Catania, 95123 Catania, Italy
| | - Luigi Maiolino
- Department of Medical, Surgical Sciences and Advanced Technologies G.F. Ingrassia, University of Catania, 95123 Catania, Italy
| | - Salvatore Ferlito
- Department of Medical, Surgical Sciences and Advanced Technologies G.F. Ingrassia, University of Catania, 95123 Catania, Italy
| | - Paola Di Mauro
- Department of Medical, Surgical Sciences and Advanced Technologies G.F. Ingrassia, University of Catania, 95123 Catania, Italy
| | - Salvatore Cocuzza
- Department of Medical, Surgical Sciences and Advanced Technologies G.F. Ingrassia, University of Catania, 95123 Catania, Italy
| | - Jérôme René Lechien
- Otology Study Group of the Young-Otolaryngologists of the International Federations of Oto-Rhino-Laryngological Societies (YO-IFOS), 75000 Paris, France
| | - Giannicola Iannella
- Otology Study Group of the Young-Otolaryngologists of the International Federations of Oto-Rhino-Laryngological Societies (YO-IFOS), 75000 Paris, France
| | - Francois Simon
- Otology Study Group of the Young-Otolaryngologists of the International Federations of Oto-Rhino-Laryngological Societies (YO-IFOS), 75000 Paris, France
| | - Antonino Maniaci
- Otology Study Group of the Young-Otolaryngologists of the International Federations of Oto-Rhino-Laryngological Societies (YO-IFOS), 75000 Paris, France
- Department of Medical, Surgical Sciences and Advanced Technologies G.F. Ingrassia, University of Catania, 95123 Catania, Italy
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Dawood M, Akay G, Mitani T, Marafi D, Fatih JM, Gezdirici A, Najmabadi H, Kahrizi K, Punetha J, Grochowski CM, Du H, Jolly A, Li H, Coban-Akdemir Z, Sedlazeck FJ, Hunter JV, Jhangiani SN, Muzny D, Pehlivan D, Posey JE, Carvalho CM, Gibbs RA, Lupski JR. A biallelic frameshift indel in PPP1R35 as a cause of primary microcephaly. Am J Med Genet A 2023; 191:794-804. [PMID: 36598158 PMCID: PMC9928800 DOI: 10.1002/ajmg.a.63080] [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: 06/21/2022] [Revised: 11/05/2022] [Accepted: 12/01/2022] [Indexed: 01/05/2023]
Abstract
Protein phosphatase 1 regulatory subunit 35 (PPP1R35) encodes a centrosomal protein required for recruiting microtubule-binding elongation machinery. Several proteins in this centriole biogenesis pathway correspond to established primary microcephaly (MCPH) genes, and multiple model organism studies hypothesize PPP1R35 as a candidate MCPH gene. Here, using exome sequencing (ES) and family-based rare variant analyses, we report a homozygous, frameshifting indel deleting the canonical stop codon in the last exon of PPP1R35 [Chr7: c.753_*3delGGAAGCGTAGACCinsCG (p.Trp251Cysfs*22)]; the variant allele maps in a 3.7 Mb block of absence of heterozygosity (AOH) in a proband with severe MCPH (-4.3 SD at birth, -6.1 SD by 42 months), pachygyria, and global developmental delay from a consanguineous Turkish kindred. Droplet digital PCR (ddPCR) confirmed mutant mRNA expression in fibroblasts. In silico prediction of the translation of mutant PPP1R35 is expected to be elongated by 18 amino acids before encountering a downstream stop codon. This complex indel allele is absent in public databases (ClinVar, gnomAD, ARIC, 1000 genomes) and our in-house database of 14,000+ exomes including 1800+ Turkish exomes supporting predicted pathogenicity. Comprehensive literature searches for PPP1R35 variants yielded two probands affected with severe microcephaly (-15 SD and -12 SD) with the same homozygous indel from a single, consanguineous, Iranian family from a cohort of 404 predominantly Iranian families. The lack of heterozygous cases in two large cohorts representative of the genetic background of these two families decreased our suspicion of a founder allele and supports the contention of a recurrent mutation. We propose two potential secondary structure mutagenesis models for the origin of this variant allele mediated by hairpin formation between complementary GC rich segments flanking the stop codon via secondary structure mutagenesis.
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Affiliation(s)
- Moez Dawood
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, 77030, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Gulsen Akay
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Tadahiro Mitani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Dana Marafi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Department of Pediatrics, Faculty of Medicine, Kuwait University, P.O. Box 24923, 13110 Safat, Kuwait
| | - Jawid M. Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Alper Gezdirici
- Department of Medical Genetics, Basaksehir Cam and Sakura City Hospital, Istanbul 34480, Turkey
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Jaya Punetha
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | | | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Angad Jolly
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, 77030, USA
| | - He Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Fritz J. Sedlazeck
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Jill V. Hunter
- Department of Radiology, Baylor College of Medicine, Houston, Texas, 77030, USA
- E.B. Singleton Department of Pediatric Radiology, Texas Children’s Hospital, Houston, Texas, 77030, USA
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Shalini N. Jhangiani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Donna Muzny
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Texas Children’s Hospital, Houston, Texas, 77030, USA
| | - Jennifer E. Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Claudia M.B. Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Pacific Northwest Research Institute, Seattle, WA, 98122, USA
| | - Richard A. Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - James R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, 77030, USA
- Texas Children’s Hospital, Houston, Texas, 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030
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FitzHugh ZT, Schiller MR. Systematic Assessment of Protein C-Termini Mutated in Human Disorders. Biomolecules 2023; 13:biom13020355. [PMID: 36830724 PMCID: PMC9953674 DOI: 10.3390/biom13020355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/23/2023] [Accepted: 02/02/2023] [Indexed: 02/16/2023] Open
Abstract
All proteins have a carboxyl terminus, and we previously summarized eight mutations in binding and trafficking sequence determinants in the C-terminus that, when disrupted, cause human diseases. These sequence elements for binding and trafficking sites, as well as post-translational modifications (PTMs), are called minimotifs or short linear motifs. We wanted to determine how frequently mutations in minimotifs in the C-terminus cause disease. We searched specifically for PTMs because mutation of a modified amino acid almost always changes the chemistry of the side chain and can be interpreted as loss-of-function. We analyzed data from ClinVar for disease variants, Minimotif Miner and the C-terminome for PTMs, and RefSeq for protein sequences, yielding 20 such potential disease-causing variants. After additional screening, they include six with a previously reported PTM disruption mechanism and nine with new hypotheses for mutated minimotifs in C-termini that may cause disease. These mutations were generally for different genes, with four different PTM types and several different diseases. Our study helps to identify new molecular mechanisms for nine separate variants that cause disease, and this type of analysis could be extended as databases grow and to binding and trafficking motifs. We conclude that mutated motifs in C-termini are an infrequent cause of disease.
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Affiliation(s)
- Zachary T. FitzHugh
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, 4505 S. Maryland Pkwy, Las Vegas, NV 89154, USA
- School of Life Sciences, University of Nevada, 4505 S. Maryland Parkway, Las Vegas, NV 89154, USA
| | - Martin R. Schiller
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, 4505 S. Maryland Pkwy, Las Vegas, NV 89154, USA
- School of Life Sciences, University of Nevada, 4505 S. Maryland Parkway, Las Vegas, NV 89154, USA
- Heligenics Inc., 833 Las Vegas Blvd. North, Suite B, Las Vegas, NV 89101, USA
- Correspondence: ; Tel.: +1-702-895-5546; Fax: +1-702-895-5728
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Aksoy O, Hantusch B, Kenner L. Emerging role of T3-binding protein μ-crystallin (CRYM) in health and disease. Trends Endocrinol Metab 2022; 33:804-816. [PMID: 36344381 DOI: 10.1016/j.tem.2022.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 09/30/2022] [Accepted: 09/30/2022] [Indexed: 11/06/2022]
Abstract
Thyroid hormones are essential metabolic and developmental regulators that exert a huge variety of effects in different organs. Triiodothyronine (T3) and thyroxine (T4) are synthesized in the thyroid gland and constitute unique iodine-containing hormones that are constantly regulated by a homeostatic feedback mechanism. T3/T4 activity in cells is mainly determined by specific transporters, cytosolic binding proteins, deiodinases (DIOs), and nuclear receptors. Modulation of intracellular T3/T4 level contributes to the maintenance of this regulatory feedback. μ-Crystallin (CRYM) is an important intracellular high-affinity T3-binding protein that buffers the amount of T3 freely available in the cytosol, thereby controlling its action. In this review, we focus on the molecular and pathological properties of CRYM in thyroid hormone signaling, with emphasis on its critical role in malignancies.
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Affiliation(s)
- Osman Aksoy
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Brigitte Hantusch
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Lukas Kenner
- Department of Pathology, Medical University of Vienna, Vienna, Austria; Center for Biomarker Research in Medicine (CBmed), Graz, Austria; Unit for Laboratory Animal Pathology, University of Veterinary Medicine Vienna, Vienna, Austria; Christian Doppler Laboratory for Applied Metabolomics (CDL-AM), Medical University of Vienna, Vienna, Austria.
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8
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Miao X, Wang Y, Miao Z, Pan H. A comprehensive review of the progress of cell migration inducing hyaluronidase 1. Medicine (Baltimore) 2022; 101:e31610. [PMID: 36451490 PMCID: PMC9704909 DOI: 10.1097/md.0000000000031610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
The gene cell migration inducing hyaluronidase 1 (CEMIP) is on chromosome 15q25 and codes for a 150-kDa protein with an N-terminal secretion signal, a G8 domain, 2 GG domains, and several repeats. It was first described as a specific protein in the inner ear relating to nonsyndromic hearing loss. Recently, increasing research detected its association in various cancers, determining the progression, metastasis, and prognosis by influencing the proliferation and invasion of the cells. This relation is accomplished through various interacting pathways, such as the Wnt/β-catenin signaling pathway and the epidermal growth factor receptor signaling pathway. Thus, CEMIP could be a novel and potential focus for tumor diagnosis and treatment, but further studies on the regulatory role of CEMIP in vivo and in vitro are still needed. Herein, we summarize the process in recent studies of CEMIP, especially in cancer research.
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Affiliation(s)
- Xiangguang Miao
- Neurological Institute of Jiangxi Province and Department of Neurology, Jiangxi Provincial People’s Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang, Jiangxi, China
| | - Yukai Wang
- Neurological Institute of Jiangxi Province and Department of Neurology, Jiangxi Provincial People’s Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang, Jiangxi, China
| | - Zhiguo Miao
- Zhengzhou Traditional Chinese Medicine Hospital, Zhengzhou, China
| | - Haili Pan
- Neurological Institute of Jiangxi Province and Department of Neurology, Jiangxi Provincial People’s Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang, Jiangxi, China
- School of Chemistry and Chemical Engineering, Nanchang University, Nanchang, China
- Queen Mary School, Nanchang University, Nanchang, China
- * Correspondence: Haili Pan, Nanchang University and Jiangxi Provincial People’s Hospital, Nanchang 330031, China. (e-mail: )
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Abstract
The clinical availability of tissue-specific biomarkers of thyroid hormone (TH) action constitutes a "holy grail" for the field. Scientists have investigated several TH-dependent markers, including the tissue content of triiodothyronine (T3)-the active form of TH. The study of animal models and humans indicates that the T3 content varies among different tissues, mostly due to the presence of low-affinity, high-capacity cytoplasmic T3 binding proteins. Nonetheless, given that T3 levels in the plasma and tissues are in equilibrium, T3 signaling is defined by the intracellular free T3 levels. The available techniques to assess tissue T3 are invasive and not clinically applicable. However, the tracer kinetic studies revealed that serum T3 levels can accurately predict tissue T3 content and T3 signaling in most tissues, except for the brain and pituitary gland. This is true not only for normal individuals but also for patients with hypo or hyperthyroidism-but not for patients with non-thyroidal illness syndrome. Given this direct relationship between serum and tissue T3 contents and T3 signaling in most tissues, clinicians managing patients with hypothyroidism could refocus attention on monitoring serum T3 levels. Future clinical trials should aim at correlating clinical outcomes with serum T3 levels.
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Affiliation(s)
- Federico Salas-Lucia
- Section of Adult and Pediatric Endocrinology and Metabolism, The University of Chicago, Chicago, IL, United States
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10
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Abstract
µ-Crystallin is a NADPH-regulated thyroid hormone binding protein encoded by the CRYM gene in humans. It is primarily expressed in the brain, muscle, prostate, and kidney, where it binds thyroid hormones, which regulate metabolism and thermogenesis. It also acts as a ketimine reductase in the lysine degradation pathway when it is not bound to thyroid hormone. Mutations in CRYM can result in non-syndromic deafness, while its aberrant expression, predominantly in the brain but also in other tissues, has been associated with psychiatric, neuromuscular, and inflammatory diseases. CRYM expression is highly variable in human skeletal muscle, with 15% of individuals expressing ≥13 fold more CRYM mRNA than the median level. Ablation of the Crym gene in murine models results in the hypertrophy of fast twitch muscle fibers and an increase in fat mass of mice fed a high fat diet. Overexpression of Crym in mice causes a shift in energy utilization away from glycolysis towards an increase in the catabolism of fat via β-oxidation, with commensurate changes of metabolically involved transcripts and proteins. The history, attributes, functions, and diseases associated with CRYM, an important modulator of metabolism, are reviewed.
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Affiliation(s)
- Christian J Kinney
- Department of Physiology School of Medicine, University of Maryland, Baltimore, Baltimore, MD 21201
| | - Robert J Bloch
- Department of Physiology School of Medicine, University of Maryland, Baltimore, Baltimore, MD 21201
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11
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Kinney CJ, O'Neill A, Noland K, Huang W, Muriel J, Lukyanenko V, Kane MA, Ward CW, Collier AF, Roche JA, McLenithan JC, Reed PW, Bloch RJ. μ-Crystallin in Mouse Skeletal Muscle Promotes a Shift from Glycolytic toward Oxidative Metabolism. Curr Res Physiol 2021; 4:47-59. [PMID: 34746826 PMCID: PMC8562245 DOI: 10.1016/j.crphys.2021.02.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 01/31/2021] [Accepted: 02/04/2021] [Indexed: 01/24/2023] Open
Abstract
μ-Crystallin, encoded by the CRYM gene, binds the thyroid hormones, T3 and T4. Because T3 and T4 are potent regulators of metabolism and gene expression, and CRYM levels in human skeletal muscle can vary widely, we investigated the effects of overexpression of Crym. We generated transgenic mice, Crym tg, that expressed Crym protein specifically in skeletal muscle at levels 2.6-147.5 fold higher than in controls. Muscular functions, Ca2+ transients, contractile force, fatigue, running on treadmills or wheels, were not significantly altered, although T3 levels in tibialis anterior (TA) muscle were elevated ~190-fold and serum T4 was decreased 1.2-fold. Serum T3 and thyroid stimulating hormone (TSH) levels were unaffected. Crym transgenic mice studied in metabolic chambers showed a significant decrease in the respiratory exchange ratio (RER) corresponding to a 13.7% increase in fat utilization as an energy source compared to controls. Female but not male Crym tg mice gained weight more rapidly than controls when fed high fat or high simple carbohydrate diets. Although labeling for myosin heavy chains showed no fiber type differences in TA or soleus muscles, application of machine learning algorithms revealed small but significant morphological differences between Crym tg and control soleus fibers. RNA-seq and gene ontology enrichment analysis showed a significant shift towards genes associated with slower muscle function and its metabolic correlate, β-oxidation. Protein expression showed a similar shift, though with little overlap. Our study shows that μ-crystallin plays an important role in determining substrate utilization in mammalian muscle and that high levels of μ-crystallin are associated with a shift toward greater fat metabolism.
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Affiliation(s)
- Christian J. Kinney
- Department of Physiology School of Medicine, University of Maryland Baltimore, Baltimore, MD, 21201, USA
| | - Andrea O'Neill
- Department of Physiology School of Medicine, University of Maryland Baltimore, Baltimore, MD, 21201, USA
| | - Kaila Noland
- Department of Physiology School of Medicine, University of Maryland Baltimore, Baltimore, MD, 21201, USA
| | - Weiliang Huang
- Department of Pharmaceutical Sciences School of Pharmacy, University of Maryland Baltimore, Baltimore, MD, 21201, USA
| | - Joaquin Muriel
- Department of Physiology School of Medicine, University of Maryland Baltimore, Baltimore, MD, 21201, USA
| | - Valeriy Lukyanenko
- Department of Physiology School of Medicine, University of Maryland Baltimore, Baltimore, MD, 21201, USA
| | - Maureen A. Kane
- Department of Pharmaceutical Sciences School of Pharmacy, University of Maryland Baltimore, Baltimore, MD, 21201, USA
| | - Christopher W. Ward
- Department of Orthopedics School of Medicine, University of Maryland Baltimore, Baltimore, MD, 21201, USA
| | - Alyssa F. Collier
- Department of Physiology School of Medicine, University of Maryland Baltimore, Baltimore, MD, 21201, USA
| | - Joseph A. Roche
- Department of Physiology School of Medicine, University of Maryland Baltimore, Baltimore, MD, 21201, USA
| | - John C. McLenithan
- Department of Medicine School of Medicine, University of Maryland Baltimore, Baltimore, MD, 21201, USA
| | - Patrick W. Reed
- Department of Physiology School of Medicine, University of Maryland Baltimore, Baltimore, MD, 21201, USA
| | - Robert J. Bloch
- Department of Physiology School of Medicine, University of Maryland Baltimore, Baltimore, MD, 21201, USA
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12
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Vona B, Doll J, Hofrichter MAH, Haaf T, Varshney GK. Small fish, big prospects: using zebrafish to unravel the mechanisms of hereditary hearing loss. Hear Res 2020; 397:107906. [PMID: 32063424 PMCID: PMC7415493 DOI: 10.1016/j.heares.2020.107906] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 01/13/2020] [Accepted: 01/29/2020] [Indexed: 12/16/2022]
Abstract
Over the past decade, advancements in high-throughput sequencing have greatly enhanced our knowledge of the mutational signatures responsible for hereditary hearing loss. In its present state, the field has a largely uncensored view of protein coding changes in a growing number of genes that have been associated with hereditary hearing loss, and many more that have been proposed as candidate genes. Sequencing data can now be generated using methods that have become widespread and affordable. The greatest hurdles facing the field concern functional validation of uncharacterized genes and rapid application to human diseases, including hearing and balance disorders. To date, over 30 hearing-related disease models exist in zebrafish. New genome editing technologies, including CRISPR/Cas9 will accelerate the functional validation of hearing loss genes and variants in zebrafish. Here, we discuss current progress in the field and recent advances in genome editing approaches.
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Affiliation(s)
- Barbara Vona
- Department of Otolaryngology--Head & Neck Surgery, Tübingen Hearing Research Centre, Eberhard Karls University Tübingen, Tübingen, Germany.
| | - Julia Doll
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
| | | | - Thomas Haaf
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
| | - Gaurav K Varshney
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States.
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13
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Saad AK, Marafi D, Mitani T, Jolly A, Du H, Elbendary HM, Jhangiani SN, Akdemir ZC, Gibbs RA, Hunter JV, Carvalho CMBC, Pehlivan D, Posey JE, Zaki MS, Lupski JR. Biallelic in-frame deletion in TRAPPC4 in a family with developmental delay and cerebellar atrophy. Brain 2020; 143:e83. [PMID: 33011761 PMCID: PMC7586085 DOI: 10.1093/brain/awaa256] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Ahmed K Saad
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Department of Medical Molecular Genetics, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Dana Marafi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Department of Pediatrics, Faculty of Medicine, Kuwait University, P.O. Box 24923, 13110 Safat, Kuwait
| | - Tadahiro Mitani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Angad Jolly
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- MD/PhD Medical Scientist Training Program, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Hasnaa M Elbendary
- Department of Clinical Genetics, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Zeynep C Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | | | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Jill V Hunter
- Department of Radiology, Baylor College of Medicine, Houston, Texas, 77030, USA
- E.B. Singleton Department of Pediatric Radiology, Texas Children's Hospital, Houston, Texas, 77030, USA
| | - Claudia M B C Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Texas Children's Hospital, Houston, Texas, 77030, USA
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Maha S Zaki
- Department of Clinical Genetics, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, 77030, USA
- Texas Children's Hospital, Houston, Texas, 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, 77030, USA
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14
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Wang M, Li Q, Deng A, Zhu X, Yang J. Identification of a novel mutation in CRYM in a Chinese family with hearing loss using whole-exome sequencing. Exp Ther Med 2020; 20:1447-1454. [PMID: 32742378 PMCID: PMC7388290 DOI: 10.3892/etm.2020.8890] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Accepted: 05/07/2020] [Indexed: 12/26/2022] Open
Abstract
Previous studies have identified ~50 genes that contribute to non-syndromic autosomal dominant sensorineural deafness (DFNA). However, in numerous families with hearing loss, the specific gene mutation remains to be identified. In the present study, the clinical characteristics and gene mutations were analyzed in a Chinese pedigree with hereditary hearing loss. The clinical characteristics of the family members were assessed and a detailed audiology function examination was performed. Whole-exome sequencing (WES) was performed to identify the gene mutation responsible for the hearing loss. Sanger sequencing was used to verify the candidate mutation detected in the family. The family consisted of 31 members, seven of whom were diagnosed with sensorineural deafness of varying degrees. No mutation was identified by the general deafness gene chip. However, a novel heterozygous mutation in exon 3 (c.152C>T; Pro51Leu) of the gene crystallin µ (CRYM) was identified by WES. This result was further verified by Sanger sequencing. Co-segregation of genotypes and phenotypes suggested that this novel mutation was instrumental for the hearing loss/DFNA. In conclusion, the present study identified a novel pathogenic mutation, NM_001888.5(CRYM): c.152C>T(Pro51Leu), associated with DFNA. This mutation has not been reported previously and further functional studies are warranted.
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Affiliation(s)
- Min Wang
- Department of Otorhinolaryngology and Head and Neck Surgery, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing 400037, P.R. China
| | - Qian Li
- Department of Otorhinolaryngology and Head and Neck Surgery, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing 400037, P.R. China
| | - Anchun Deng
- Department of Otorhinolaryngology and Head and Neck Surgery, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing 400037, P.R. China
| | - Xianbai Zhu
- Department of Otorhinolaryngology and Head and Neck Surgery, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing 400037, P.R. China
| | - Junjie Yang
- Department of Otorhinolaryngology and Head and Neck Surgery, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing 400037, P.R. China
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15
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New markers of human cumulus oophorus cells cultured in vitro – transcriptomic profile. ACTA ACUST UNITED AC 2020. [DOI: 10.2478/acb-2020-0007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Abstract
The presence of CCs around the oocyte after ovulation is one of the key elements contributing to oocyte developmental competence. In the presented study, we used CCs from 12 patients aged 18-40 diagnosed with infertility. After harvesting cells on day 1, 7, 15 and 30 of culture, total RNA was isolated and transcriptomic analysis was performed. The DAVID software indicated the following GO BP terms: “cell junction organization”, “cell migration”, “cell morphogenesis involved in differentiation”, “cell morphogenesis” and “cell motility”. Of the genes belonging to all ontological groups, the most downregulated were: SLC7A8, DFNB31, COL1A1, CDC42SE1, TGFBR3, HMGB1, with the most upregulated genes being: ANXA3, KIAA1199, HTR2B, VCAM1, DKK1.
While many studies focus on attempts to obtain fully competent oocytes, scientists still have difficulty attaining adequate results in vitro. Lack of adequate knowledge often results in low in vitro fertilization efficiency. Therefore, our research focuses on CCs cells, thanks to which the oocyte most likely acquires developmental competence. The main purpose of the study was to identify the potential molecular markers responsible for cell junction organization, migration, differentiation, morphogenesis and motility.
Running title: New markers of human cumulus oophorus cells cultured in vitro
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16
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Yarman S, Tuncer FN, Serbest E. Three Novel MEN1 Variants in AIP-Negative Familial Isolated Pituitary Adenoma Patients. Pathobiology 2019; 86:128-134. [PMID: 30630164 DOI: 10.1159/000495252] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 11/01/2018] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVES Pituitary adenomas (PAs) may rarely occur in well-defined hereditary conditions, like multiple endocrine neoplasia type 1 (MEN1) syndrome and familial isolated pituitary adenoma (FIPA) associated with germline mutations in MEN1 and AIP, respectively. This study aimed to assess MEN1 genetic abnormalities in AIP mutation-negative FIPA patients, not associated with MEN1 components. METHODS Among 20 patients evaluated in 13 FIPA families, 12 were previously reported as AIP mutation-negative. In this study, 6 new families with 8 patients were recruited. All patients were subjected to multiplex ligation-dependent probe amplification to detect copy number variations in AIP and MEN1, and AIP sequencing was performed in additional patients. AIP mutation-negative patients were subjected to MEN1 sequencing. RESULTS Our cohort revealed only 3 novel heterozygous MEN1 variants including c.1846T>A p.(*616Argext*21), rs778272737:T>C, and rs972128957:C>T in 2 families, with patients diagnosed with Cushing disease, nonfunction al adenoma, and acromegaly, respectively. Among them, c.1846T>A p. (*616Argext*21) is a stop codon read-through, whereas the others are 3'UTR variations. MEN1 variation frequency was detected as 15%. CONCLUSIONS MEN1 alterations can be of significance in FIPA patients and screening could be offered to AIP mutation-negative patients without MEN1 features. Further studies are needed to clarify the role of MEN1 in FIPA patients.
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Affiliation(s)
- Sema Yarman
- Division of Endocrinology and Metabolic Diseases, Department of Internal Medicine, Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Feyza Nur Tuncer
- Department of Genetics, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey,
| | - Esin Serbest
- Department of Genetics, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
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17
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Carpena NT, Lee MY. Genetic Hearing Loss and Gene Therapy. Genomics Inform 2018; 16:e20. [PMID: 30602081 PMCID: PMC6440668 DOI: 10.5808/gi.2018.16.4.e20] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 12/04/2018] [Indexed: 12/15/2022] Open
Abstract
Genetic hearing loss crosses almost all the categories of hearing loss which includes the following: conductive, sensory, and neural; syndromic and nonsyndromic; congenital, progressive, and adult onset; high-frequency, low-frequency, or mixed frequency; mild or profound; and recessive, dominant, or sex-linked. Genes play a role in almost half of all cases of hearing loss but effective treatment options are very limited. Genetic hearing loss is considered to be extremely genetically heterogeneous. The advancements in genomics have been instrumental to the identification of more than 6,000 causative variants in more than 150 genes causing hearing loss. Identification of genes for hearing impairment provides an increased insight into the normal development and function of cells in the auditory system. These defective genes will ultimately be important therapeutic targets. However, the auditory system is extremely complex which requires tremendous advances in gene therapy including gene vectors, routes of administration, and therapeutic approaches. This review summarizes and discusses recent advances in elucidating the genomics of genetic hearing loss and technologies aimed at developing a gene therapy that may become a treatment option for in the near future.
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Affiliation(s)
- Nathanial T Carpena
- Department of Otolaryngology-Head and Neck Surgery, Dankook University College of Medicine, Cheonan 31116, Korea
| | - Min Young Lee
- Department of Otolaryngology-Head and Neck Surgery, Dankook University College of Medicine, Cheonan 31116, Korea.,Beckman Laser Institute Korea, Dankook University, Cheonan 31116, Korea
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18
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Hommyo R, Suzuki SO, Abolhassani N, Hamasaki H, Shijo M, Maeda N, Honda H, Nakabeppu Y, Iwaki T. Expression of CRYM in different rat organs during development and its decreased expression in degenerating pyramidal tracts in amyotrophic lateral sclerosis. Neuropathology 2018; 38:247-259. [PMID: 29603402 DOI: 10.1111/neup.12466] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 02/20/2018] [Accepted: 02/27/2018] [Indexed: 11/30/2022]
Abstract
The protein μ-crystallin (CRYM) is a novel component of the marsupial lens that has two functions: it is a key regulator of thyroid hormone transportation and a reductase of sulfur-containing cyclic ketimines. In this study, we examined changes of the expression pattern of CRYM in different rat organs during development using immunohistochemistry and immunoblotting. As CRYM is reportedly expressed in the corticospinal tract, we also investigated CRYM expression in human cases of amyotrophic lateral sclerosis (ALS) using immunohistochemistry. In the rat brain, CRYM was expressed in the cerebral cortex, basal ganglia, hippocampus and corticospinal tract in the early postnatal period. As postnatal development progressed, CRYM expression was restricted to large pyramidal neurons in layers V and VI of the cerebral cortex and pyramidal cells in the deep layer of CA1 in the hippocampus. Even within the same regions, CRYM-positive and negative neurons were distributed in a mosaic pattern. In the kidney, CRYM was expressed in epithelial cells of the proximal tubule and mesenchymal cells of the medulla in the early postnatal period; however, CRYM expression in the medulla was lost as mesenchymal cell numbers decreased with the rapid growth of the medulla. In human ALS brains, we observed marked loss of CRYM in the corticospinal tract, especially distally. Our results suggest that CRYM may play roles in development of cortical and hippocampal pyramidal cells in the early postnatal period, and in the later period, performs cell-specific functions in selected neuronal populations. In the kidney, CRYM may play roles in maturation of renal function. The expression patterns of CRYM may reflect significance of its interactions with T3 or ketimines in these cells and organs. The results also indicate that CRYM may be used as a marker of axonal degeneration in the corticospinal tract.
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Affiliation(s)
- Reiji Hommyo
- Department of Neuropathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Satoshi O Suzuki
- Department of Neuropathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Nona Abolhassani
- Division of Neurofunctional Genomics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Hideomi Hamasaki
- Department of Neuropathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Masahiro Shijo
- Department of Neuropathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Norihisa Maeda
- Department of Neuropathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hiroyuki Honda
- Department of Neuropathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yusaku Nakabeppu
- Division of Neurofunctional Genomics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Toru Iwaki
- Department of Neuropathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
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19
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Frejo L, Requena T, Okawa S, Gallego-Martinez A, Martinez-Bueno M, Aran I, Batuecas-Caletrio A, Benitez-Rosario J, Espinosa-Sanchez JM, Fraile-Rodrigo JJ, García-Arumi AM, González-Aguado R, Marques P, Martin-Sanz E, Perez-Fernandez N, Pérez-Vázquez P, Perez-Garrigues H, Santos-Perez S, Soto-Varela A, Tapia MC, Trinidad-Ruiz G, Del Sol A, Alarcon Riquelme ME, Lopez-Escamez JA. Regulation of Fn14 Receptor and NF-κB Underlies Inflammation in Meniere's Disease. Front Immunol 2017; 8:1739. [PMID: 29326686 PMCID: PMC5733484 DOI: 10.3389/fimmu.2017.01739] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 11/23/2017] [Indexed: 12/17/2022] Open
Abstract
Meniere’s disease (MD) is a rare disorder characterized by episodic vertigo, sensorineural hearing loss, tinnitus, and aural fullness. It is associated with a fluid imbalance between the secretion of endolymph in the cochlear duct and its reabsorption into the subarachnoid space, leading to an accumulation of endolymph in the inner ear. Epidemiological evidence, including familial aggregation, indicates a genetic contribution and a consistent association with autoimmune diseases (AD). We conducted a case–control study in two phases using an immune genotyping array in a total of 420 patients with bilateral MD and 1,630 controls. We have identified the first locus, at 6p21.33, suggesting an association with bilateral MD [meta-analysis leading signal rs4947296, OR = 2.089 (1.661–2.627); p = 1.39 × 10−09]. Gene expression profiles of homozygous genotype-selected peripheral blood mononuclear cells (PBMCs) demonstrated that this region is a trans-expression quantitative trait locus (eQTL) in PBMCs. Signaling analysis predicted several tumor necrosis factor-related pathways, the TWEAK/Fn14 pathway being the top candidate (p = 2.42 × 10−11). This pathway is involved in the modulation of inflammation in several human AD, including multiple sclerosis, systemic lupus erythematosus, or rheumatoid arthritis. In vitro studies with genotype-selected lymphoblastoid cells from patients with MD suggest that this trans-eQTL may regulate cellular proliferation in lymphoid cells through the TWEAK/Fn14 pathway by increasing the translation of NF-κB. Taken together; these findings suggest that the carriers of the risk genotype may develop an NF-κB-mediated inflammatory response in MD.
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Affiliation(s)
- Lidia Frejo
- Otology and Neurotology Group CTS495, Department of Genomic Medicine - Centre for Genomics and Oncological Research - Pfizer/Universidad de Granada/Junta de Andalucía (GENYO), Granada, Spain
| | - Teresa Requena
- Otology and Neurotology Group CTS495, Department of Genomic Medicine - Centre for Genomics and Oncological Research - Pfizer/Universidad de Granada/Junta de Andalucía (GENYO), Granada, Spain
| | - Satoshi Okawa
- Computational Biology Group, Luxembourg Centre for Systems Biomedicine (LCSB), Universite du Luxembourg, Belval, Luxembourg
| | - Alvaro Gallego-Martinez
- Otology and Neurotology Group CTS495, Department of Genomic Medicine - Centre for Genomics and Oncological Research - Pfizer/Universidad de Granada/Junta de Andalucía (GENYO), Granada, Spain
| | - Manuel Martinez-Bueno
- Group of Genetics of Complex Diseases, Department of Genomic Medicine - Centre for Genomics and Oncological Research - Pfizer/Universidad de Granada/Junta de Andalucía (GENYO), Granada, Spain
| | - Ismael Aran
- Department of Otolaryngology, Complexo Hospitalario de Pontevedra, Pontevedra, Spain
| | | | - Jesus Benitez-Rosario
- Department of Otolaryngology, Hospital Universitario de Gran Canaria Dr Negrin, Las Palmas de Gran Canaria, Las Palmas, Spain
| | - Juan M Espinosa-Sanchez
- Otology and Neurotology Group CTS495, Department of Genomic Medicine - Centre for Genomics and Oncological Research - Pfizer/Universidad de Granada/Junta de Andalucía (GENYO), Granada, Spain.,Department of Otolaryngology, Instituto de Investigación Biosanitaria ibs.GRANADA, Hospital Universitario Virgen de las Nieves, Granada, Spain
| | | | - Ana María García-Arumi
- Department of Otorhinolaryngology, Hospital Universitario Vall d'Hebron, Barcelona, Spain
| | - Rocío González-Aguado
- Department of Otorhinolaryngology, Hospital Universitario Marqués de Valdecilla, Santander, Cantabria, Spain
| | - Pedro Marques
- Department of Otorhinolaryngology, Centro Hospitalar de S.João, EPE, University of Porto Medical School, Porto, Portugal
| | - Eduardo Martin-Sanz
- Department of Otolaryngology, Hospital Universitario de Getafe, Getafe, Madrid, Spain
| | | | - Paz Pérez-Vázquez
- Department of Otorhinolaryngology, Hospital Universitario de Cabueñes, Gijón, Asturias, Spain
| | | | - Sofía Santos-Perez
- Division of Otoneurology, Department of Otorhinolaryngology, Complexo Hospitalario Universitario, Santiago de Compostela, Spain
| | - Andres Soto-Varela
- Division of Otoneurology, Department of Otorhinolaryngology, Complexo Hospitalario Universitario, Santiago de Compostela, Spain
| | - Maria C Tapia
- Department of Otorhinolaryngology, Instituto Antolí Candela, Madrid, Spain
| | - Gabriel Trinidad-Ruiz
- Division of Otoneurology, Department of Otorhinolaryngology, Complejo Hospitalario Badajoz, Badajoz, Spain
| | - Antonio Del Sol
- Computational Biology Group, Luxembourg Centre for Systems Biomedicine (LCSB), Universite du Luxembourg, Belval, Luxembourg
| | - Marta E Alarcon Riquelme
- Group of Genetics of Complex Diseases, Department of Genomic Medicine - Centre for Genomics and Oncological Research - Pfizer/Universidad de Granada/Junta de Andalucía (GENYO), Granada, Spain.,Unit of Chronic Inflammatory Diseases, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Jose A Lopez-Escamez
- Otology and Neurotology Group CTS495, Department of Genomic Medicine - Centre for Genomics and Oncological Research - Pfizer/Universidad de Granada/Junta de Andalucía (GENYO), Granada, Spain.,Department of Otolaryngology, Instituto de Investigación Biosanitaria ibs.GRANADA, Hospital Universitario Virgen de las Nieves, Granada, Spain.,Luxembourg Centre for System Biomedicine (LCSB), Universite du Luxembourg, Belval, Luxembourg
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20
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Duan H, Zhang D, Cheng J, Lu Y, Yuan H. Gene screening facilitates diagnosis of complicated symptoms: A case report. Mol Med Rep 2017; 16:7915-7922. [PMID: 28944914 PMCID: PMC5779872 DOI: 10.3892/mmr.2017.7590] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 05/02/2017] [Indexed: 01/22/2023] Open
Abstract
Gene mutation has an important role in disease pathogenesis; therefore, genetic screening is a useful tool for diagnosis. The present study screened pathogenic genes, ectodysplasin A (EDA) and lamin A/C (LMNA), in a patient with suspected syndromic hearing impairment and various other symptoms including tooth and skin abnormalities. Large-scale sequencing of 438 deafness-associated genes and whole-genome sequencing was also performed. The present findings did not identify copy number variation and mutations in EDA; therefore, excluding the possibility of EDA-initiated ectodermal dysplasia syndrome. A synonymous mutation in LMNA, possibly due to a splicing abnormality, did not elucidate the pathogenesis of Hutchinson-Gilford progeria syndrome. Whole-genome sequencing revealed copy number variations or mutations in various candidate genes which may elucidate part of the symptoms observed. The copy number variations and mutations were also used to identify single nucleotide variations (SNVs) in crystallin mu (CRYM), RAB3 GTPase activating protein catalytic subunit 1 (RAB3GAP1) and Wnt family member 10A (WNT10A), implicated in deafness, hypogonadism and tooth/skin abnormalities, respectively. The importance of an existing SNV in CRYM and a novel SNV in RAB3GAP1 in pathogenesis remains to be further elucidated. The WNT10A p.G213S mutation was confirmed to be the etiological cause of tooth agenesis and ectodermal dysplasia as previously described. It was concluded that a mutation in WNT10A may be the reason for some of the symptoms observed in the patient; however, other genes may also be involved for other symptoms. The findings of the present study provide putative gene mutations that require further investigation in order to determine their roles in pathogenesis.
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Affiliation(s)
- Hong Duan
- Department of Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing 100853, P.R. China
| | - Di Zhang
- Department of Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing 100853, P.R. China
| | - Jing Cheng
- Department of Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing 100853, P.R. China
| | - Yu Lu
- Department of Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing 100853, P.R. China
| | - Huijun Yuan
- Department of Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing 100853, P.R. China
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21
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Sachs LM, Buchholz DR. Frogs model man: In vivo thyroid hormone signaling during development. Genesis 2017; 55. [PMID: 28109053 DOI: 10.1002/dvg.23000] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 11/14/2016] [Accepted: 11/16/2016] [Indexed: 12/25/2022]
Abstract
Thyroid hormone (TH) signaling comprises TH transport across cell membranes, metabolism by deiodinases, and molecular mechanisms of gene regulation. Proper TH signaling is essential for normal perinatal development, most notably for neurogenesis and fetal growth. Knowledge of perinatal TH endocrinology needs improvement to provide better treatments for premature infants and endocrine diseases during gestation and to counteract effects of endocrine disrupting chemicals. Studies in amphibians have provided major insights to understand in vivo mechanisms of TH signaling. The frog model boasts dramatic TH-dependent changes directly observable in free-living tadpoles with precise and easy experimental control of the TH response at developmental stages comparable to fetal stages in mammals. The hormones, their receptors, molecular mechanisms, and developmental roles of TH signaling are conserved to a high degree in humans and amphibians, such that with respect to developmental TH signaling "frogs are just little people that hop." The frog model is exceptionally illustrative of fundamental molecular mechanisms of in vivo TH action involving TH receptors, transcriptional cofactors, and chromatin remodeling. This review highlights the current need, recent successes, and future prospects using amphibians as a model to elucidate molecular mechanisms and functional roles of TH signaling during post-embryonic development.
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Affiliation(s)
- Laurent M Sachs
- UMR 7221 CNRS, Muséum National d'histoire Naturelle, Dépt. Régulation, Développement et Diversité Moléculaire, Sorbonne Universités, Paris, 75005, France
| | - Daniel R Buchholz
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio, 45221
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22
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Hosoya M, Fujioka M, Sone T, Okamoto S, Akamatsu W, Ukai H, Ueda HR, Ogawa K, Matsunaga T, Okano H. Cochlear Cell Modeling Using Disease-Specific iPSCs Unveils a Degenerative Phenotype and Suggests Treatments for Congenital Progressive Hearing Loss. Cell Rep 2017; 18:68-81. [DOI: 10.1016/j.celrep.2016.12.020] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 09/20/2016] [Accepted: 12/06/2016] [Indexed: 12/29/2022] Open
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23
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van Mullem AA, van Gucht ALM, Visser WE, Meima ME, Peeters RP, Visser TJ. Effects of thyroid hormone transporters MCT8 and MCT10 on nuclear activity of T3. Mol Cell Endocrinol 2016; 437:252-260. [PMID: 27492966 DOI: 10.1016/j.mce.2016.07.037] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 07/10/2016] [Accepted: 07/27/2016] [Indexed: 11/22/2022]
Abstract
Transport of thyroid hormone (TH) across the plasma membrane is necessary for the genomic action of T3 mediated by its nuclear T3 receptor. MCT8 and MCT10 have been identified as important TH transporters. Mutations in MCT8 result in severe psychomotor retardation. In addition to TH transport into the cell, MCT8 and MCT10 also facilitate TH efflux from cells. Therefore, the aim of this study was to examine if MCT8 and MCT10 increase the availability of T3 for its nuclear receptor rather than generate a rapid equilibrium between cellular and serum T3. T3 action was investigated in JEG3 cells co-transfected with TRβ1 and a T3 response element-driven luciferase construct, and T3 metabolism was analyzed in cells transfected with type 3 deiodinase (D3). In addition, cells were transfected with MCT8 or MCT10 and/or the cytoplasmic T3-binding protein mu-crystallin (CRYM). Luciferase signal was markedly stimulated by incubating cells for 24 h with 1 nM T3, but this response was not augmented by MCT8 or MCT10 expression. Limiting the time of T3 exposure to 1-6 h and co-transfection with CRYM allowed for a modest increase in luciferase response to T3. In contrast, T3 metabolism by D3 was potently stimulated by MCT8 or MCT10 expression, but it was not affected by expression of CRYM. These results suggest that MCT8 and MCT10 by virtue of their bidirectional T3 transport have less effect on steady-state nuclear T3 levels than on T3 levels at the cell periphery where D3 is located. CRYM alters the dynamics of cellular TH transport but its exact function in the cellular distribution of TH remains to be determined.
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Affiliation(s)
- Alies A van Mullem
- Department of Internal Medicine and Rotterdam Thyroid Center, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Anja L M van Gucht
- Department of Internal Medicine and Rotterdam Thyroid Center, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - W Edward Visser
- Department of Internal Medicine and Rotterdam Thyroid Center, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Marcel E Meima
- Department of Internal Medicine and Rotterdam Thyroid Center, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Robin P Peeters
- Department of Internal Medicine and Rotterdam Thyroid Center, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Theo J Visser
- Department of Internal Medicine and Rotterdam Thyroid Center, Erasmus University Medical Center, Rotterdam, The Netherlands.
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24
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Ueyama T, Ninoyu Y, Nishio SY, Miyoshi T, Torii H, Nishimura K, Sugahara K, Sakata H, Thumkeo D, Sakaguchi H, Watanabe N, Usami SI, Saito N, Kitajiri SI. Constitutive activation of DIA1 (DIAPH1) via C-terminal truncation causes human sensorineural hearing loss. EMBO Mol Med 2016; 8:1310-1324. [PMID: 27707755 PMCID: PMC5090661 DOI: 10.15252/emmm.201606609] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
DIAPH1 encodes human DIA1, a formin protein that elongates unbranched actin. The c.3634+1G>T DIAPH1 mutation causes autosomal dominant nonsyndromic sensorineural hearing loss, DFNA1, characterized by progressive deafness starting in childhood. The mutation occurs near the C‐terminus of the diaphanous autoregulatory domain (DAD) of DIA1, which interacts with its N‐terminal diaphanous inhibitory domain (DID), and may engender constitutive activation of DIA1. However, the underlying pathogenesis that causes DFNA1 is unclear. We describe a novel patient‐derived DIAPH1 mutation (c.3610C>T) in two unrelated families, which results in early termination prior to a basic amino acid motif (RRKR1204–1207) at the DAD C‐terminus. The mutant DIA1(R1204X) disrupted the autoinhibitory DID‐DAD interaction and was constitutively active. This unscheduled activity caused increased rates of directional actin polymerization movement and induced formation of elongated microvilli. Mice expressing FLAG‐tagged DIA1(R1204X) experienced progressive deafness and hair cell loss at the basal turn and had various morphological abnormalities in stereocilia (short, fused, elongated, sparse). Thus, the basic region of the DAD mediates DIA1 autoinhibition; disruption of the DID‐DAD interaction and consequent activation of DIA1(R1204X) causes DFNA1.
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Affiliation(s)
- Takehiko Ueyama
- Laboratory of Molecular Pharmacology, Biosignal Research Center, Kobe University, Kobe, Japan
| | - Yuzuru Ninoyu
- Laboratory of Molecular Pharmacology, Biosignal Research Center, Kobe University, Kobe, Japan
| | - Shin-Ya Nishio
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Takushi Miyoshi
- Department of Otolaryngology, Head and Neck Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiroko Torii
- Department of Otolaryngology, Head and Neck Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Koji Nishimura
- Department of Otolaryngology, Head and Neck Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kazuma Sugahara
- Department of Otolaryngology, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | | | - Dean Thumkeo
- Medical Innovation Center, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Hirofumi Sakaguchi
- Department of Otolaryngology-Head and Neck Surgery, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Naoki Watanabe
- Department of Pharmacology, Kyoto University Graduate School of Medicine, Kyoto, Japan.,Laboratory of Single-Molecule Cell Biology, Kyoto University Graduate School of Biostudies, Kyoto, Japan
| | - Shin-Ichi Usami
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Naoaki Saito
- Laboratory of Molecular Pharmacology, Biosignal Research Center, Kobe University, Kobe, Japan
| | - Shin-Ichiro Kitajiri
- Department of Otolaryngology, Head and Neck Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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25
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Reciprocal Control of Thyroid Binding and the Pipecolate Pathway in the Brain. Neurochem Res 2016; 42:217-243. [DOI: 10.1007/s11064-016-2015-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 07/15/2016] [Accepted: 07/22/2016] [Indexed: 12/21/2022]
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26
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Distinct Expression Pattern of a Deafness Gene, KIAA1199, in a Primate Cochlea. BIOMED RESEARCH INTERNATIONAL 2016; 2016:1781894. [PMID: 27403418 PMCID: PMC4923552 DOI: 10.1155/2016/1781894] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 05/12/2016] [Accepted: 05/23/2016] [Indexed: 11/17/2022]
Abstract
Deafness is one of the most common types of congenital impairments, and at least half of the cases are caused by hereditary mutations. Mutations of the gene KIAA1199 are associated with progressive hearing loss. Its expression is abundant in human cochlea, but interestingly the spatial expression patterns are different between mouse and rat cochleae; the pattern in humans has not been fully investigated. We performed immunohistochemical analysis of a nonhuman primate, common marmoset (Callithrix jacchus), cochlea with a KIAA1199-specific antibody. In the common marmoset cochlea, KIAA1199 protein expression was more widespread than in rodents, with all epithelial cells, including hair cells, expressing KIAA1199. Our results suggest that the primate pattern of KIAA1199 expression is wider in comparison with rodents and may play an essential role in the maintenance of cochlear epithelial cells.
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27
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Hosoya M, Fujioka M, Ogawa K, Okano H. Distinct Expression Patterns Of Causative Genes Responsible For Hereditary Progressive Hearing Loss In Non-Human Primate Cochlea. Sci Rep 2016; 6:22250. [PMID: 26915689 PMCID: PMC4768099 DOI: 10.1038/srep22250] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 02/10/2016] [Indexed: 12/18/2022] Open
Abstract
Hearing impairment is the most frequent sensory deficit in humans. Deafness genes, which harbor pathogenic mutations that have been identified in families with hereditary hearing loss, are commonly expressed in the auditory end organ or the cochlea and may contribute to normal hearing function, yet some of the mouse models carrying these mutations fail to recapitulate the hearing loss phenotype. In this study, we find that distinct expression patterns of those deafness genes in the cochlea of a non-human primate, the common marmoset (Callithrix jacchus). We examined 20 genes whose expression in the cochlea has already been reported. The deafness genes GJB3, CRYM, GRHL2, DFNA5, and ATP6B1 were expressed in marmoset cochleae in patterns different from those in mouse cochleae. Of note, all those genes are causative for progressive hearing loss in humans, but not in mice. The other tested genes, including the deafness gene COCH, in which mutation recapitulates deafness in mice, were expressed in a similar manner in both species. The result suggests that the discrepancy in the expression between rodents and primates may account for the phenotypic difference. This limitation of the rodent models can be bypassed by using non-human primate models such as the marmoset.
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Affiliation(s)
- Makoto Hosoya
- Keio University School of Medicine, Department of Otorhinolaryngology, Head and Neck Surgery, 35 Shinanomachi Shinjyuku-ku Tokyo, 160-8582, Japan
| | - Masato Fujioka
- Keio University School of Medicine, Department of Otorhinolaryngology, Head and Neck Surgery, 35 Shinanomachi Shinjyuku-ku Tokyo, 160-8582, Japan
| | - Kaoru Ogawa
- Keio University School of Medicine, Department of Otorhinolaryngology, Head and Neck Surgery, 35 Shinanomachi Shinjyuku-ku Tokyo, 160-8582, Japan
| | - Hideyuki Okano
- Keio University School of Medicine, Department of Physiology, 35 Shinanomachi Shinjyuku-ku Tokyo, 160-8582, Japan
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28
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Abstract
The identification of transcriptional differences has served as an important starting point in understanding the molecular mechanisms behind biological processes and systems. The developmental biology of the inner ear, the biology of hearing and of course the pathology of deafness are all processes that warrant a molecular description if we are to improve human health. To this end, technological innovation has meant that larger scale analysis of gene transcription has been possible for a number of years now, extending our molecular analysis of genes to beyond those that are currently in vogue for a given system. In this review, some of the contributions gene profiling has made to understanding developmental, pathological and physiological processes in the inner ear are highlighted.
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Affiliation(s)
- Thomas Schimmang
- Instituto de Biología y Genética MolecularUniversidad de Valladolid y Consejo Superior de Investigaciones CientíficasValladolidSpain
| | - Mark Maconochie
- School of Biological and Chemical SciencesQueen Mary University of LondonLondonUK
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29
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More similar than you think: Frog metamorphosis as a model of human perinatal endocrinology. Dev Biol 2015; 408:188-95. [DOI: 10.1016/j.ydbio.2015.02.018] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 02/05/2015] [Accepted: 02/20/2015] [Indexed: 11/21/2022]
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30
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Abou Tayoun AN, Al Turki SH, Oza AM, Bowser MJ, Hernandez AL, Funke BH, Rehm HL, Amr SS. Improving hearing loss gene testing: a systematic review of gene evidence toward more efficient next-generation sequencing-based diagnostic testing and interpretation. Genet Med 2015; 18:545-53. [PMID: 26562227 DOI: 10.1038/gim.2015.141] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 08/27/2015] [Indexed: 12/11/2022] Open
Abstract
PURPOSE With next generation sequencing technology improvement and cost reductions, it has become technically feasible to sequence a large number of genes in one diagnostic test. This is especially relevant for diseases with large genetic and/or phenotypic heterogeneity, such as hearing loss. However, variant interpretation remains the major bottleneck. This is further exacerbated by the lack in the clinical genetics community of consensus criteria for defining the evidence necessary to include genes on targeted disease panels or in genomic reports, and the consequent risk of reporting variants in genes with no relevance to disease. METHODS We describe a systematic evidence-based approach for assessing gene-disease associations and for curating relevant genes for different disease aspects, including mode of inheritance, phenotypic severity, and mutation spectrum. RESULTS By applying this approach to clinically available hearing loss gene panels with a total of 163 genes, we show that a significant number (45%) of genes lack sufficient evidence of association with disease and thus are expected to increase uncertainty and patient anxiety, in addition to intensifying the interpretation burden. Information about all curated genes is summarized. Our retrospective analysis of 539 hearing loss cases tested by our previous OtoGenomeV2 panel demonstrates the impact of including genes with weak disease association in laboratory wet-bench and interpretation processes. CONCLUSION Our study is, to our knowledge, the first to highlight the urgent need for defining the clinical validity of gene-disease relationships for more efficient and accurate clinical testing and reporting.Genet Med 18 6, 545-553.
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Affiliation(s)
- Ahmad N Abou Tayoun
- Genetics Training Program, Harvard Medical School, Cambridge, Massachusetts, USA.,Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts, USA.,Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, The University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Saeed H Al Turki
- Genetics Training Program, Harvard Medical School, Cambridge, Massachusetts, USA
| | - Andrea M Oza
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts, USA
| | - Mark J Bowser
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts, USA
| | - Amy L Hernandez
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts, USA
| | - Birgit H Funke
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts, USA.,Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Heidi L Rehm
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts, USA.,Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Sami S Amr
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts, USA.,Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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31
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Shibata N, Ohoka N, Sugaki Y, Onodera C, Inoue M, Sakuraba Y, Takakura D, Hashii N, Kawasaki N, Gondo Y, Naito M. Degradation of Stop Codon Read-through Mutant Proteins via the Ubiquitin-Proteasome System Causes Hereditary Disorders. J Biol Chem 2015; 290:28428-28437. [PMID: 26442586 DOI: 10.1074/jbc.m115.670901] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Indexed: 12/26/2022] Open
Abstract
During translation, stop codon read-through occasionally happens when the stop codon is misread, skipped, or mutated, resulting in the production of aberrant proteins with C-terminal extension. These extended proteins are potentially deleterious, but their regulation is poorly understood. Here we show in vitro and in vivo evidence that mouse cFLIP-L with a 46-amino acid extension encoded by a read-through mutant gene is rapidly degraded by the ubiquitin-proteasome system, causing hepatocyte apoptosis during embryogenesis. The extended peptide interacts with an E3 ubiquitin ligase, TRIM21, to induce ubiquitylation of the mutant protein. In humans, 20 read-through mutations are related to hereditary disorders, and extended peptides found in human PNPO and HSD3B2 similarly destabilize these proteins, involving TRIM21 for PNPO degradation. Our findings indicate that degradation of aberrant proteins with C-terminal extension encoded by read-through mutant genes is a mechanism for loss of function resulting in hereditary disorders.
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Affiliation(s)
- Norihito Shibata
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, Setagaya-ku, Tokyo 158-8501, Japan
| | - Nobumichi Ohoka
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, Setagaya-ku, Tokyo 158-8501, Japan
| | - Yusuke Sugaki
- Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba 277-8561, Japan
| | - Chiaki Onodera
- Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba 277-8561, Japan
| | - Mizuho Inoue
- Faculty of Pharmaceutical Sciences, University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yoshiyuki Sakuraba
- Mutagenesis and Genomics Team, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Daisuke Takakura
- Division of Biological Chemistry and Biologicals, National Institute of Health Sciences, Setagaya-ku, Tokyo 158-8501, Japan
| | - Noritaka Hashii
- Division of Biological Chemistry and Biologicals, National Institute of Health Sciences, Setagaya-ku, Tokyo 158-8501, Japan
| | - Nana Kawasaki
- Division of Biological Chemistry and Biologicals, National Institute of Health Sciences, Setagaya-ku, Tokyo 158-8501, Japan
| | - Yoichi Gondo
- Mutagenesis and Genomics Team, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Mikihiko Naito
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, Setagaya-ku, Tokyo 158-8501, Japan.
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32
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Hofrichter MAH, Nanda I, Gräf J, Schröder J, Shehata-Dieler W, Vona B, Haaf T. A Novel de novo Mutation in CEACAM16 Associated with Postlingual Hearing Impairment. Mol Syndromol 2015; 6:156-63. [PMID: 26648831 DOI: 10.1159/000439576] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/13/2015] [Indexed: 12/20/2022] Open
Abstract
Mutations in CEACAM16 cause autosomal dominant nonsyndromic hearing loss (DFNA4B). So far, 2 families have been reported with segregating missense mutations, both in the immunoglobulin constant domain A of the CEACAM16 protein. In this study, we used the TruSight One panel to investigate a parent-child trio without familial history of hearing loss and one affected child. When filtering for recessive inheritance and de novo events, we discovered a de novo CEACAM16 mutation (c.1094T>G, p.Leu365Arg) as the sole likely pathogenic variant. The de novo mutation was confirmed by Sanger sequencing and STR analysis. The proband's hearing loss closely matches the described onset and severity for DFNA4B. We present the third CEACAM16 variant and the first de novo mutation in CEACAM16. This de novo mutation is robustly described as a pathogenic mutation according to in silico mutation prediction tools and affects a highly conserved amino acid in the most strongly conserved CEACAM16 N2 domain. Our strategy of screening family trios enhances de novo mutation discovery and the exclusion of other variants of potential interest through pedigree filtering.
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Affiliation(s)
| | - Indrajit Nanda
- Department of Human Genetics, Julius Maximilian University, Würzburg, Germany
| | - Jens Gräf
- Department of Human Genetics, Julius Maximilian University, Würzburg, Germany
| | - Jörg Schröder
- Department of Human Genetics, Julius Maximilian University, Würzburg, Germany
| | - Wafaa Shehata-Dieler
- Department of Otorhinolaryngology, Comprehensive Hearing Center, University Hospitals, Würzburg, Germany
| | - Barbara Vona
- Department of Human Genetics, Julius Maximilian University, Würzburg, Germany
| | - Thomas Haaf
- Department of Human Genetics, Julius Maximilian University, Würzburg, Germany
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33
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Rodríguez-de la Rosa L, Sánchez-Calderón H, Contreras J, Murillo-Cuesta S, Falagan S, Avendaño C, Dopazo J, Varela-Nieto I, Milo M. Comparative gene expression study of the vestibular organ of the Igf1 deficient mouse using whole-transcript arrays. Hear Res 2015; 330:62-77. [PMID: 26341476 DOI: 10.1016/j.heares.2015.08.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 08/27/2015] [Accepted: 08/28/2015] [Indexed: 10/23/2022]
Abstract
The auditory and vestibular organs form the inner ear and have a common developmental origin. Insulin like growth factor 1 (IGF-1) has a central role in the development of the cochlea and maintenance of hearing. Its deficiency causes sensorineural hearing loss in man and mice. During chicken early development, IGF-1 modulates neurogenesis of the cochleovestibular ganglion but no further studies have been conducted to explore the potential role of IGF-1 in the vestibular system. In this study we have compared the whole transcriptome of the vestibular organ from wild type and Igf1(-/-) mice at different developmental and postnatal times. RNA was prepared from E18.5, P15 and P90 vestibular organs of Igf1(-/-) and Igf1(+/+) mice and the transcriptome analysed in triplicates using Affymetrix(®) Mouse Gene 1.1 ST Array Plates. These plates are whole-transcript arrays that include probes to measure both messenger (mRNA) and long intergenic non-coding RNA transcripts (lincRNA), with a coverage of over 28 thousand coding transcripts and over 7 thousands non-coding transcripts. Given the complexity of the data we used two different methods VSN-RMA and mmBGX to analyse and compare the data. This is to better evaluate the number of false positives and to quantify uncertainty of low signals. We identified a number of differentially expressed genes that we described using functional analysis and validated using RT-qPCR. The morphology of the vestibular organ did not show differences between genotypes and no evident alterations were observed in the vestibular sensory areas of the null mice. However, well-defined cellular alterations were found in the vestibular neurons with respect their number and size. Although these mice did not show a dramatic vestibular phenotype, we conducted a functional analysis on differentially expressed genes between genotypes and across time. This was with the aim to identify new pathways that are involved in the development of the vestibular organ as well as pathways that maybe affected by the lack of IGF-1 and be associated to the morphological changes of the vestibular neurons that we observed in the Igf1(-/-) mice.
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Affiliation(s)
- Lourdes Rodríguez-de la Rosa
- Neurobiology of Hearing, Department of Endocrine and Nervous System Pathophysiology, Alberto Sols Biomedical Research Institute (IIBM), CSIC-UAM, Madrid, Spain; Biomedical Research Networking Center on Rare Diseases (CIBERER), Institute of Health Carlos III (ISCIII), Madrid, Spain; IdiPAZ Institute for Health Research, Madrid, Spain
| | - Hortensia Sánchez-Calderón
- Neurobiology of Hearing, Department of Endocrine and Nervous System Pathophysiology, Alberto Sols Biomedical Research Institute (IIBM), CSIC-UAM, Madrid, Spain
| | - Julio Contreras
- Neurobiology of Hearing, Department of Endocrine and Nervous System Pathophysiology, Alberto Sols Biomedical Research Institute (IIBM), CSIC-UAM, Madrid, Spain; Biomedical Research Networking Center on Rare Diseases (CIBERER), Institute of Health Carlos III (ISCIII), Madrid, Spain; Department of Anatomy, Faculty of Veterinary, Complutense University, Madrid, Spain
| | - Silvia Murillo-Cuesta
- Neurobiology of Hearing, Department of Endocrine and Nervous System Pathophysiology, Alberto Sols Biomedical Research Institute (IIBM), CSIC-UAM, Madrid, Spain; Biomedical Research Networking Center on Rare Diseases (CIBERER), Institute of Health Carlos III (ISCIII), Madrid, Spain; IdiPAZ Institute for Health Research, Madrid, Spain
| | - Sandra Falagan
- Department of Anatomy, Faculty of Medicine, Autonomous University, Madrid, Spain
| | - Carlos Avendaño
- IdiPAZ Institute for Health Research, Madrid, Spain; Department of Anatomy, Faculty of Medicine, Autonomous University, Madrid, Spain
| | - Joaquín Dopazo
- Biomedical Research Networking Center on Rare Diseases (CIBERER), Institute of Health Carlos III (ISCIII), Madrid, Spain; Department of Computational Genomics, Centro de Investigación Príncipe Felipe, Valencia, Spain
| | - Isabel Varela-Nieto
- Neurobiology of Hearing, Department of Endocrine and Nervous System Pathophysiology, Alberto Sols Biomedical Research Institute (IIBM), CSIC-UAM, Madrid, Spain; Biomedical Research Networking Center on Rare Diseases (CIBERER), Institute of Health Carlos III (ISCIII), Madrid, Spain; IdiPAZ Institute for Health Research, Madrid, Spain
| | - Marta Milo
- Department of Biomedical Science, University of Sheffield, Sheffield, UK.
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Schrauwen I, Hasin-Brumshtein Y, Corneveaux JJ, Ohmen J, White C, Allen AN, Lusis AJ, Van Camp G, Huentelman MJ, Friedman RA. A comprehensive catalogue of the coding and non-coding transcripts of the human inner ear. Hear Res 2015; 333:266-274. [PMID: 26341477 DOI: 10.1016/j.heares.2015.08.013] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Revised: 08/12/2015] [Accepted: 08/27/2015] [Indexed: 10/23/2022]
Abstract
The mammalian inner ear consists of the cochlea and the vestibular labyrinth (utricle, saccule, and semicircular canals), which participate in both hearing and balance. Proper development and life-long function of these structures involves a highly complex coordinated system of spatial and temporal gene expression. The characterization of the inner ear transcriptome is likely important for the functional study of auditory and vestibular components, yet, primarily due to tissue unavailability, detailed expression catalogues of the human inner ear remain largely incomplete. We report here, for the first time, comprehensive transcriptome characterization of the adult human cochlea, ampulla, saccule and utricle of the vestibule obtained from patients without hearing abnormalities. Using RNA-Seq, we measured the expression of >50,000 predicted genes corresponding to approximately 200,000 transcripts, in the adult inner ear and compared it to 32 other human tissues. First, we identified genes preferentially expressed in the inner ear, and unique either to the vestibule or cochlea. Next, we examined expression levels of specific groups of potentially interesting RNAs, such as genes implicated in hearing loss, long non-coding RNAs, pseudogenes and transcripts subject to nonsense mediated decay (NMD). We uncover the spatial specificity of expression of these RNAs in the hearing/balance system, and reveal evidence of tissue specific NMD. Lastly, we investigated the non-syndromic deafness loci to which no gene has been mapped, and narrow the list of potential candidates for each locus. These data represent the first high-resolution transcriptome catalogue of the adult human inner ear. A comprehensive identification of coding and non-coding RNAs in the inner ear will enable pathways of auditory and vestibular function to be further defined in the study of hearing and balance. Expression data are freely accessible at https://www.tgen.org/home/research/research-divisions/neurogenomics/supplementary-data/inner-ear-transcriptome.aspx.
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Affiliation(s)
- Isabelle Schrauwen
- Department of Medical Genetics, University of Antwerp, 2610 Antwerp, Belgium.,Neurogenomics Division and The Dorrance Center for Rare Childhood Disorders, Translational Genomics Research Institute, 85004 Phoenix, AZ
| | - Yehudit Hasin-Brumshtein
- Department of Medicine/Division of Cardiology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Jason J Corneveaux
- Neurogenomics Division and The Dorrance Center for Rare Childhood Disorders, Translational Genomics Research Institute, 85004 Phoenix, AZ
| | - Jeffrey Ohmen
- House Ear Institute, Los Angeles 90057, CA, United States
| | - Cory White
- House Ear Institute, Los Angeles 90057, CA, United States.,Keck School of Medicine, USC, Los Angeles, CA, United States
| | - April N Allen
- Neurogenomics Division and The Dorrance Center for Rare Childhood Disorders, Translational Genomics Research Institute, 85004 Phoenix, AZ
| | - Aldons J Lusis
- Department of Medicine/Division of Cardiology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Guy Van Camp
- Department of Medical Genetics, University of Antwerp, 2610 Antwerp, Belgium
| | - Matthew J Huentelman
- Neurogenomics Division and The Dorrance Center for Rare Childhood Disorders, Translational Genomics Research Institute, 85004 Phoenix, AZ
| | - Rick A Friedman
- Keck School of Medicine, USC, Los Angeles, CA, United States
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Nishio SY, Usami SI. Deafness gene variations in a 1120 nonsyndromic hearing loss cohort: molecular epidemiology and deafness mutation spectrum of patients in Japan. Ann Otol Rhinol Laryngol 2015; 124 Suppl 1:49S-60S. [PMID: 25788563 DOI: 10.1177/0003489415575059] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
OBJECTIVES To elucidate the molecular epidemiology of hearing loss in a large number of Japanese patients analyzed using massively parallel DNA sequencing (MPS) of target genes. METHODS We performed MPS of target genes using the Ion PGM system with the Ion AmpliSeq and HiSeq 2000 systems using SureSelect in 1389 samples (1120 nonsyndromic hearing loss cases and 269 normal hearing controls). We filtered the variants identified using allele frequencies in a large number of controls and 12 predication program scores. RESULTS We identified 8376 kinds of variants in the 1389 samples, and 409 835 total variants were detected. After filtering the variants, we selected 2631 kinds of candidate variants. The number of GJB2 mutations was exceptionally high among these variants, followed by those in CDH23, SLC26A4, MYO15A, COL11A2, MYO7A, and OTOF. CONCLUSIONS We performed a large number of MPS analyses and clarified the genetic background of Japanese patients with hearing loss. This data set will be a powerful tool to discover rare causative gene mutations in highly heterogeneous monogenic diseases and reveal the genetic epidemiology of deafness.
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Affiliation(s)
- Shin-Ya Nishio
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan Department of Hearing Implant Sciences, Shinshu University School of Medicine, Matsumoto, Japan
| | - Shin-Ichi Usami
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan Department of Hearing Implant Sciences, Shinshu University School of Medicine, Matsumoto, Japan
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Francelle L, Galvan L, Gaillard MC, Guillermier M, Houitte D, Bonvento G, Petit F, Jan C, Dufour N, Hantraye P, Elalouf JM, De Chaldée M, Déglon N, Brouillet E. Loss of the thyroid hormone-binding protein Crym renders striatal neurons more vulnerable to mutant huntingtin in Huntington's disease. Hum Mol Genet 2014; 24:1563-73. [PMID: 25398949 PMCID: PMC4381754 DOI: 10.1093/hmg/ddu571] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The mechanisms underlying preferential atrophy of the striatum in Huntington's disease (HD) are unknown. One hypothesis is that a set of gene products preferentially expressed in the striatum could determine the particular vulnerability of this brain region to mutant huntingtin (mHtt). Here, we studied the striatal protein µ-crystallin (Crym). Crym is the NADPH-dependent p38 cytosolic T3-binding protein (p38CTBP), a key regulator of thyroid hormone (TH) T3 (3,5,3'-triiodo-l-thyronine) transportation. It has been also recently identified as the enzyme that reduces the sulfur-containing cyclic ketimines, which are potential neurotransmitters. Here, we confirm the preferential expression of the Crym protein in the rodent and macaque striatum. Crym expression was found to be higher in the macaque caudate than in the putamen. Expression of Crym was reduced in the BACHD and Knock-in 140CAG mouse models of HD before onset of striatal atrophy. We show that overexpression of Crym in striatal medium-size spiny neurons using a lentiviral-based strategy in mice is neuroprotective against the neurotoxicity of an N-terminal fragment of mHtt in vivo. Thus, reduction of Crym expression in HD could render striatal neurons more susceptible to mHtt suggesting that Crym may be a key determinant of the vulnerability of the striatum. In addition our work points to Crym as a potential molecular link between striatal degeneration and the THs deregulation reported in HD patients.
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Affiliation(s)
- Laetitia Francelle
- CEA, DSV, I²BM, Molecular Imaging Research Center (MIRCen), F-92265 Fontenay-aux-Roses, France, Neurodegenerative Diseases Laboratory, CNRS CEA URA 2210, F-92265 Fontenay-aux-Roses, France
| | - Laurie Galvan
- CEA, DSV, I²BM, Molecular Imaging Research Center (MIRCen), F-92265 Fontenay-aux-Roses, France, Neurodegenerative Diseases Laboratory, CNRS CEA URA 2210, F-92265 Fontenay-aux-Roses, France
| | - Marie-Claude Gaillard
- CEA, DSV, I²BM, Molecular Imaging Research Center (MIRCen), F-92265 Fontenay-aux-Roses, France, Neurodegenerative Diseases Laboratory, CNRS CEA URA 2210, F-92265 Fontenay-aux-Roses, France
| | - Martine Guillermier
- CEA, DSV, I²BM, Molecular Imaging Research Center (MIRCen), F-92265 Fontenay-aux-Roses, France, Neurodegenerative Diseases Laboratory, CNRS CEA URA 2210, F-92265 Fontenay-aux-Roses, France
| | - Diane Houitte
- CEA, DSV, I²BM, Molecular Imaging Research Center (MIRCen), F-92265 Fontenay-aux-Roses, France, Neurodegenerative Diseases Laboratory, CNRS CEA URA 2210, F-92265 Fontenay-aux-Roses, France
| | - Gilles Bonvento
- CEA, DSV, I²BM, Molecular Imaging Research Center (MIRCen), F-92265 Fontenay-aux-Roses, France, Neurodegenerative Diseases Laboratory, CNRS CEA URA 2210, F-92265 Fontenay-aux-Roses, France
| | - Fanny Petit
- CEA, DSV, I²BM, Molecular Imaging Research Center (MIRCen), F-92265 Fontenay-aux-Roses, France, Neurodegenerative Diseases Laboratory, CNRS CEA URA 2210, F-92265 Fontenay-aux-Roses, France
| | - Caroline Jan
- CEA, DSV, I²BM, Molecular Imaging Research Center (MIRCen), F-92265 Fontenay-aux-Roses, France, Neurodegenerative Diseases Laboratory, CNRS CEA URA 2210, F-92265 Fontenay-aux-Roses, France
| | - Noëlle Dufour
- CEA, DSV, I²BM, Molecular Imaging Research Center (MIRCen), F-92265 Fontenay-aux-Roses, France, Neurodegenerative Diseases Laboratory, CNRS CEA URA 2210, F-92265 Fontenay-aux-Roses, France
| | - Philippe Hantraye
- CEA, DSV, I²BM, Molecular Imaging Research Center (MIRCen), F-92265 Fontenay-aux-Roses, France, Neurodegenerative Diseases Laboratory, CNRS CEA URA 2210, F-92265 Fontenay-aux-Roses, France
| | - Jean-Marc Elalouf
- CEA, iBiTecS, F-91191 Gif-sur-Yvette Cedex, France, CNRS, FRE 3377, F-91191 Gif-sur-Yvette Cedex, France, Université Paris-Sud, FRE 3377, F-91191 Gif-sur-Yvette Cedex, France
| | - Michel De Chaldée
- CEA, iBiTecS, F-91191 Gif-sur-Yvette Cedex, France, CNRS, FRE 3377, F-91191 Gif-sur-Yvette Cedex, France, Université Paris-Sud, FRE 3377, F-91191 Gif-sur-Yvette Cedex, France
| | - Nicole Déglon
- CEA, DSV, I²BM, Molecular Imaging Research Center (MIRCen), F-92265 Fontenay-aux-Roses, France, Neurodegenerative Diseases Laboratory, CNRS CEA URA 2210, F-92265 Fontenay-aux-Roses, France, Laboratory of Cellular and Molecular Neurotherapies, Department of Clinical Neurociences, Lausanne University Hospital, Lausanne, Switzerland
| | - Emmanuel Brouillet
- CEA, DSV, I²BM, Molecular Imaging Research Center (MIRCen), F-92265 Fontenay-aux-Roses, France, Neurodegenerative Diseases Laboratory, CNRS CEA URA 2210, F-92265 Fontenay-aux-Roses, France,
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Andrews CD, Payne JF, Rise ML. Identification of a gene set to evaluate the potential effects of loud sounds from seismic surveys on the ears of fishes: a study with Salmo salar. JOURNAL OF FISH BIOLOGY 2014; 84:1793-1819. [PMID: 24814183 PMCID: PMC4277336 DOI: 10.1111/jfb.12398] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Accepted: 03/05/2014] [Indexed: 06/03/2023]
Abstract
Functional genomic studies were carried out on the inner ear of Atlantic salmon Salmo salar following exposure to a seismic airgun. Microarray analyses revealed 79 unique transcripts (passing background threshold), with 42 reproducibly up-regulated and 37 reproducibly down-regulated in exposed v. control fish. Regarding the potential effects on cellular energetics and cellular respiration, altered transcripts included those with roles in oxygen transport, the glycolytic pathway, the Krebs cycle and the electron transport chain. Of these, a number of transcripts encoding haemoglobins that are important in oxygen transport were up-regulated and among the most highly expressed. Up-regulation of transcripts encoding nicotinamide riboside kinase 2, which is also important in energy production and linked to nerve cell damage, points to evidence of neuronal damage in the ear following noise exposure. Transcripts related to protein modification or degradation also indicated potential damaging effects of sound on ear tissues. Notable in this regard were transcripts associated with the proteasome-ubiquitin pathway, which is involved in protein degradation, with the transcript encoding ubiquitin family domain-containing protein 1 displaying the highest response to exposure. The differential expression of transcripts observed for some immune responses could potentially be linked to the rupture of cell membranes. Meanwhile, the altered expression of transcripts for cytoskeletal proteins that contribute to the structural integrity of the inner ear could point to repair or regeneration of ear tissues including auditory hair cells. Regarding potential effects on hormones and vitamins, the protein carrier for thyroxine and retinol (vitamin A), namely transthyretin, was altered at the transcript expression level and it has been suggested from studies in mammalian systems that retinoic acid may play a role in the regeneration of damaged hair cells. The microarray experiment identified the transcript encoding growth hormone I as up-regulated by loud sound, supporting previous evidence linking growth hormone to hair cell regeneration in fishes. Quantitative (q) reverse transcription (RT) polymerase chain reaction (qRT-PCR) analyses confirmed dysregulation of some microarray-identified transcripts and in some cases revealed a high level of biological variability in the exposed group. These results support the potential utility of molecular biomarkers to evaluate the effect of seismic surveys on fishes with studies on the ears being placed in a priority category for development of exposure-response relationships. Knowledge of such relationships is necessary for addressing the question of potential size of injury zones.
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Affiliation(s)
- C D Andrews
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, 80 East White Hills Rd, St John's, NL, A1C 5X1, Canada
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Yoshimura H, Takumi Y, Nishio SY, Suzuki N, Iwasa YI, Usami SI. Deafness gene expression patterns in the mouse cochlea found by microarray analysis. PLoS One 2014; 9:e92547. [PMID: 24676347 PMCID: PMC3967995 DOI: 10.1371/journal.pone.0092547] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2013] [Accepted: 02/24/2014] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Tonotopy is one of the most fundamental principles of auditory function. While gradients in various morphological and physiological characteristics of the cochlea have been reported, little information is available on gradient patterns of gene expression. In addition, the audiograms in autosomal dominant non syndromic hearing loss can be distinctive, however, the mechanism that accounts for that has not been clarified. We thought that it is possible that tonotopic gradients of gene expression within the cochlea account for the distinct audiograms. METHODOLOGY/PRINCIPAL FINDINGS We compared expression profiles of genes in the cochlea between the apical, middle, and basal turns of the mouse cochlea by microarray technology and quantitative RT-PCR. Of 24,547 genes, 783 annotated genes expressed more than 2-fold. The most remarkable finding was a gradient of gene expression changes in four genes (Pou4f3, Slc17a8, Tmc1, and Crym) whose mutations cause autosomal dominant deafness. Expression of these genes was greater in the apex than in the base. Interestingly, expression of the Emilin-2 and Tectb genes, which may have crucial roles in the cochlea, was also greater in the apex than in the base. CONCLUSIONS/SIGNIFICANCE This study provides baseline data of gradient gene expression in the cochlea. Especially for genes whose mutations cause autosomal dominant non syndromic hearing loss (Pou4f3, Slc17a8, Tmc1, and Crym) as well as genes important for cochlear function (Emilin-2 and Tectb), gradual expression changes may help to explain the various pathological conditions.
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Affiliation(s)
- Hidekane Yoshimura
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Nagano, Japan
| | - Yutaka Takumi
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Nagano, Japan
| | - Shin-ya Nishio
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Nagano, Japan
| | - Nobuyoshi Suzuki
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Nagano, Japan
| | - Yoh-ichiro Iwasa
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Nagano, Japan
| | - Shin-ichi Usami
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Nagano, Japan
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ZHANG YONGSHENG, JIA SHUQIN, JIANG WENG. KIAA1199 and its biological role in human cancer and cancer cells (Review). Oncol Rep 2014; 31:1503-8. [DOI: 10.3892/or.2014.3038] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Accepted: 01/24/2014] [Indexed: 11/05/2022] Open
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Borel F, Hachi I, Palencia A, Gaillard MC, Ferrer JL. Crystal structure of mouse mu-crystallin complexed with NADPH and the T3 thyroid hormone. FEBS J 2014; 281:1598-612. [PMID: 24467707 DOI: 10.1111/febs.12726] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Revised: 01/17/2014] [Accepted: 01/20/2014] [Indexed: 01/17/2023]
Abstract
UNLABELLED Mu-crystallin (CRYM), first described as a structural component of the eye lens in marsupials, has been characterized as an NADPH-dependent cytosolic T3 thyroid hormone (triiodothyronine) binding protein. More recently, CRYM has also been associated with ketimine reductase activity. Here, we report three crystal structures: mouse CRYM (mCRYM) in its apo form, in a form complexed with NADPH, and in a form with both NADPH and triiodothyronine bound. Comparison of the apo and NADPH forms reveals a rearrangement of the protein upon NADPH binding that reduces the degrees of freedom of several residues and traps the conformation of the binding pocket in a more T3 competent state. These findings are in agreement with the cooperative mechanism identified using isothermal titration calorimetry. Our structure with T3 reveals for the first time the location of the hormone binding site and shows its detailed interactions. T3 binding involves mainly hydrophobic interactions. Only five residues, either directly or through bridging water molecules, are hydrogen bonded to the hormone. Using in silico docking analysis, a series of ring-containing hydrophobic molecules were identified as potential mCRYM ligands, suggesting that the specificity for the recognition of the hydrophobic part of the hormone might be low. This is in agreement with the ketimine reductase activity that has been identified for ovine CRYM, as it demonstrates how a protein known as a thyroid hormone transporter can accommodate the ringed molecules required for its ketimine reductase activity. In the light of our results, a putative role of CRYM in thyroid hormone metabolism is also discussed. STRUCTURED DIGITAL ABSTRACT CRYM and CRYM bind by x-ray crystallography (View interaction).
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Affiliation(s)
- Franck Borel
- Institut de Biologie Structurale, Université de Grenoble Alpes, CEA, CNRS, France
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Chiang DY, Cuthbertson DW, Ruiz FR, Li N, Pereira FA. A coregulatory network of NR2F1 and microRNA-140. PLoS One 2013; 8:e83358. [PMID: 24349493 PMCID: PMC3857795 DOI: 10.1371/journal.pone.0083358] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Accepted: 11/11/2013] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Both nuclear receptor subfamily 2 group F member 1 (NR2F1) and microRNAs (miRNAs) have been shown to play critical roles in the developing and functional inner ear. Based on previous studies suggesting interplay between NR2F1 and miRNAs, we investigated the coregulation between NR2F1 and miRNAs to better understand the regulatory mechanisms of inner ear development and functional maturation. RESULTS Using a bioinformatic approach, we identified 11 potential miRNAs that might coregulate target genes with NR2F1 and analyzed their targets and potential roles in physiology and disease. We selected 6 miRNAs to analyze using quantitative real-time (qRT) -PCR and found that miR-140 is significantly down-regulated by 4.5-fold (P=0.004) in the inner ear of NR2F1 knockout (Nr2f1(-/-)) mice compared to wild-type littermates but is unchanged in the brain. Based on this, we performed chromatin-immunoprecipitation followed by qRT-PCR and confirmed that NR2F1 directly binds and regulates both miR-140 and Klf9 in vivo. Furthermore, we performed luciferase reporter assay and showed that miR-140 mimic directly regulates KLF9-3'UTR, thereby establishing and validating an example coregulatory network involving NR2F1, miR-140, and Klf9. CONCLUSIONS We have described and experimentally validated a novel tissue-dependent coregulatory network for NR2F1, miR-140, and Klf9 in the inner ear and we propose the existence of many such coregulatory networks important for both inner ear development and function.
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Affiliation(s)
- David Y. Chiang
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas, United States of America
- Interdepartmental Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, Texas, United States of America
| | - David W. Cuthbertson
- Bobby R. Alford Department of Otolaryngology- Head and Neck Surgery, Baylor College of Medicine, Houston, Texas, United States of America
| | - Fernanda R. Ruiz
- Huffington Center on Aging and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Na Li
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Fred A. Pereira
- Bobby R. Alford Department of Otolaryngology- Head and Neck Surgery, Baylor College of Medicine, Houston, Texas, United States of America
- Huffington Center on Aging and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, United States of America
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Hallen A, Jamie JF, Cooper AJL. Lysine metabolism in mammalian brain: an update on the importance of recent discoveries. Amino Acids 2013. [PMID: 24043460 DOI: 10.1007/s00726-013-1590-1591] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
The lysine catabolism pathway differs in adult mammalian brain from that in extracerebral tissues. The saccharopine pathway is the predominant lysine degradative pathway in extracerebral tissues, whereas the pipecolate pathway predominates in adult brain. The two pathways converge at the level of ∆(1)-piperideine-6-carboxylate (P6C), which is in equilibrium with its open-chain aldehyde form, namely, α-aminoadipate δ-semialdehyde (AAS). A unique feature of the pipecolate pathway is the formation of the cyclic ketimine intermediate ∆(1)-piperideine-2-carboxylate (P2C) and its reduced metabolite L-pipecolate. A cerebral ketimine reductase (KR) has recently been identified that catalyzes the reduction of P2C to L-pipecolate. The discovery that this KR, which is capable of reducing not only P2C but also other cyclic imines, is identical to a previously well-described thyroid hormone-binding protein [μ-crystallin (CRYM)], may hold the key to understanding the biological relevance of the pipecolate pathway and its importance in the brain. The finding that the KR activity of CRYM is strongly inhibited by the thyroid hormone 3,5,3'-triiodothyronine (T3) has far-reaching biomedical and clinical implications. The inter-relationship between tryptophan and lysine catabolic pathways is discussed in the context of shared degradative enzymes and also potential regulation by thyroid hormones. This review traces the discoveries of enzymes involved in lysine metabolism in mammalian brain. However, there still remain unanswered questions as regards the importance of the pipecolate pathway in normal or diseased brain, including the nature of the first step in the pathway and the relationship of the pipecolate pathway to the tryptophan degradation pathway.
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Affiliation(s)
- André Hallen
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Balaclava Road, North Ryde, NSW, 2109, Australia,
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Hallen A, Jamie JF, Cooper AJL. Lysine metabolism in mammalian brain: an update on the importance of recent discoveries. Amino Acids 2013; 45:1249-72. [PMID: 24043460 DOI: 10.1007/s00726-013-1590-1] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Accepted: 08/29/2013] [Indexed: 12/23/2022]
Abstract
The lysine catabolism pathway differs in adult mammalian brain from that in extracerebral tissues. The saccharopine pathway is the predominant lysine degradative pathway in extracerebral tissues, whereas the pipecolate pathway predominates in adult brain. The two pathways converge at the level of ∆(1)-piperideine-6-carboxylate (P6C), which is in equilibrium with its open-chain aldehyde form, namely, α-aminoadipate δ-semialdehyde (AAS). A unique feature of the pipecolate pathway is the formation of the cyclic ketimine intermediate ∆(1)-piperideine-2-carboxylate (P2C) and its reduced metabolite L-pipecolate. A cerebral ketimine reductase (KR) has recently been identified that catalyzes the reduction of P2C to L-pipecolate. The discovery that this KR, which is capable of reducing not only P2C but also other cyclic imines, is identical to a previously well-described thyroid hormone-binding protein [μ-crystallin (CRYM)], may hold the key to understanding the biological relevance of the pipecolate pathway and its importance in the brain. The finding that the KR activity of CRYM is strongly inhibited by the thyroid hormone 3,5,3'-triiodothyronine (T3) has far-reaching biomedical and clinical implications. The inter-relationship between tryptophan and lysine catabolic pathways is discussed in the context of shared degradative enzymes and also potential regulation by thyroid hormones. This review traces the discoveries of enzymes involved in lysine metabolism in mammalian brain. However, there still remain unanswered questions as regards the importance of the pipecolate pathway in normal or diseased brain, including the nature of the first step in the pathway and the relationship of the pipecolate pathway to the tryptophan degradation pathway.
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Affiliation(s)
- André Hallen
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Balaclava Road, North Ryde, NSW, 2109, Australia,
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Miyagawa M, Naito T, Nishio SY, Kamatani N, Usami SI. Targeted exon sequencing successfully discovers rare causative genes and clarifies the molecular epidemiology of Japanese deafness patients. PLoS One 2013; 8:e71381. [PMID: 23967202 PMCID: PMC3742761 DOI: 10.1371/journal.pone.0071381] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Accepted: 06/30/2013] [Indexed: 11/19/2022] Open
Abstract
Target exon resequencing using Massively Parallel DNA Sequencing (MPS) is a new powerful strategy to discover causative genes in rare Mendelian disorders such as deafness. We attempted to identify genomic variations responsible for deafness by massive sequencing of the exons of 112 target candidate genes. By the analysis of 216randomly selected Japanese deafness patients (120 early-onset and 96 late-detected), who had already been evaluated for common genes/mutations by Invader assay and of which 48 had already been diagnosed, we efficiently identified causative mutations and/or mutation candidates in 57 genes. Approximately 86.6% (187/216) of the patients had at least one mutation. Of the 187 patients, in 69 the etiology of the hearing loss was completely explained. To determine which genes have the greatest impact on deafness etiology, the number of mutations was counted, showing that those in GJB2 were exceptionally higher, followed by mutations in SLC26A4, USH2A, GPR98, MYO15A, COL4A5 and CDH23. The present data suggested that targeted exon sequencing of selected genes using the MPS technology followed by the appropriate filtering algorithm will be able to identify rare responsible genes including new candidate genes for individual patients with deafness, and improve molecular diagnosis. In addition, using a large number of patients, the present study clarified the molecular epidemiology of deafness in Japanese. GJB2 is the most prevalent causative gene, and the major (commonly found) gene mutations cause 30–40% of deafness while the remainder of hearing loss is the result of various rare genes/mutations that have been difficult to diagnose by the conventional one-by-one approach. In conclusion, target exon resequencing using MPS technology is a suitable method to discover common and rare causative genes for a highly heterogeneous monogenic disease like hearing loss.
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Affiliation(s)
- Maiko Miyagawa
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Asahi, Matsumoto, Japan
| | - Takehiko Naito
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Asahi, Matsumoto, Japan
| | - Shin-ya Nishio
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Asahi, Matsumoto, Japan
| | | | - Shin-ichi Usami
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Asahi, Matsumoto, Japan
- * E-mail:
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Hallen A, Jamie JF, Cooper AJL. Imine reductases: a comparison of glutamate dehydrogenase to ketimine reductases in the brain. Neurochem Res 2013; 39:527-41. [PMID: 23314864 DOI: 10.1007/s11064-012-0964-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Revised: 12/12/2012] [Accepted: 12/22/2012] [Indexed: 02/06/2023]
Abstract
A key intermediate in the glutamate dehydrogenase (GDH)-catalyzed reaction is an imine. Mechanistically, therefore, GDH exhibits similarities to the ketimine reductases. In the current review, we briefly discuss (a) the metabolic importance of the GDH reaction in liver and brain, (b) the mechanistic similarities between GDH and the ketimine reductases, (c) the metabolic importance of the brain ketimine reductases, and (d) the neurochemical consequences of defective ketimine reductases. Our review contains many historical references to the early work on amino acid metabolism. This work tends to be overlooked nowadays, but is crucial for a contemporary understanding of the central importance of ketimines in nitrogen and intermediary metabolism. The ketimine reductases are important enzymes linking nitrogen flow among several key amino acids, yet have been little studied. The cerebral importance of the ketimine reductases is an area of biomedical research that deserves far more attention.
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Affiliation(s)
- André Hallen
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Balaclava Road, North Ryde, NSW, 2109, Australia,
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Abstract
Crystallins are the abundant, long-lived proteins of the eye lens. The major human crystallins belong to two different superfamilies: the small heat-shock proteins (α-crystallins) and the βγ-crystallins. During evolution, other proteins have sometimes been recruited as crystallins to modify the properties of the lens. In the developing human lens, the enzyme betaine-homocysteine methyltransferase serves such a role. Evolutionary modification has also resulted in loss of expression of some human crystallin genes or of specific splice forms. Crystallin organization is essential for lens transparency and mutations; even minor changes to surface residues can cause cataract and loss of vision.
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Affiliation(s)
- Graeme Wistow
- Section on Molecular Structure and Functional Genomics, National Eye Institute, National Institutes of Health, Bethesda, MD 20892-0608, USA.
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Hertzano R, Elkon R. High throughput gene expression analysis of the inner ear. Hear Res 2012; 288:77-88. [PMID: 22710153 DOI: 10.1016/j.heares.2012.01.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Revised: 12/30/2011] [Accepted: 01/02/2012] [Indexed: 12/25/2022]
Abstract
The mouse auditory and vestibular epithelia consist of a complex array of many different cell types. Over the last decade microarrays were used to characterize gene expression in the inner ear. Studies were performed on wild type mice to identify deafness genes, transcriptional networks activated during development, or identify miRNA with a functional role in the ear. Other studies focused on the molecular response of the inner ear to stimuli ranging from ototoxic medications to hypergravity and caloric restriction. Finally, microarrays were used to identify transcriptional networks activated downstream of deafness genes. As template-free high throughput gene expression profiling methods such as RNA-seq are increasingly popular, we offer a critical review of the data generated over the last decade relating to microarrays for gene expression profiling of the inner ear. Moreover, as most of the published data is available through the gene expression omnibus (GEO), we demonstrate the feasibility of integrating data from independent experiments to reach novel insights.
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Affiliation(s)
- Ronna Hertzano
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Maryland, 16 S Eutaw St. Suite 500, Baltimore, MD 21201, USA.
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Lysaght AC, Kao SY, Paulo JA, Merchant SN, Steen H, Stankovic KM. Proteome of human perilymph. J Proteome Res 2011; 10:3845-51. [PMID: 21740021 DOI: 10.1021/pr200346q] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Current diagnostic tools limit a clinician's ability to discriminate between many possible causes of sensorineural hearing loss. This constraint leads to the frequent diagnosis of the idiopathic condition, leaving patients without a clear prognosis and only general treatment options. As a first step toward developing new diagnostic tools and improving patient care, we report the first use of liquid chromatography-tandem mass-spectrometry (LC-MS/MS) to map the proteome of human perilymph. Using LC-MS/MS, we analyzed four samples, two collected from patients with vestibular schwannoma (VS) and two from patients undergoing cochlear implantation (CI). For each cohort, one sample contained pooled specimens collected from five patients and the second contained a specimen obtained from a single patient. Of the 271 proteins identified with high confidence among the samples, 71 proteins were common in every sample and used to conservatively define the proteome of human perilymph. Comparison to human cerebrospinal fluid and blood plasma, as well as murine perilymph, showed significant similarity in protein content across fluids; however, a quantitative comparison was not possible. Fifteen candidate biomarkers of VS were identified by comparing VS and CI samples. This list will be used in future investigations targeted at discriminating between VS tumors associated with good versus poor hearing.
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Affiliation(s)
- Andrew C Lysaght
- Program in Speech and Hearing Bioscience and Technology, Harvard & MIT, Cambridge, Massachusetts 02139, United States
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Hallen A, Cooper AJL, Jamie JF, Haynes PA, Willows RD. Mammalian forebrain ketimine reductase identified as μ-crystallin; potential regulation by thyroid hormones. J Neurochem 2011; 118:379-87. [PMID: 21332720 DOI: 10.1111/j.1471-4159.2011.07220.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ketimine reductase (E.C. 1.5.1.25) was purified to apparent homogeneity from lamb forebrain by means of a rapid multi-step chromatography protocol. The purified enzyme was identified by MS/MS (mass spectrometry) as μ-crystallin. The identity was confirmed by heterologously expressing human μ-crystallin in Escherichia coli and subsequent chromatographic purification of the protein. The purified human μ-crystallin was confirmed to have ketimine reductase activity with a maximum specific activity similar to that of native ovine ketimine reductase, and was found to catalyse a sequential reaction. The enzyme substrates are putative neuromodulator/transmitters. The thyroid hormone 3,5,3'-l-triiodothyronine (T3) was found to be a strong reversible competitive inhibitor, and may have a novel role in regulating their concentrations. μ-Crystallin is also involved in intracellular T3 storage and transport. This research is the first to demonstrate an enzyme function for μ-crystallin. This newly demonstrated enzymatic activity identifies a new role for thyroid hormones in regulating mammalian amino acid metabolism, and a possible reciprocal role of enzyme activity regulating bioavailability of intracellular T3.
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Affiliation(s)
- André Hallen
- Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, New South Wales, Australia
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