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Qin L, Zhang FZ, Lv JH, Tang LF. Clinical Features in Patients with Xq23 Microdeletion: A Case Report and Literature Review. J Clin Res Pediatr Endocrinol 2022; 14:339-343. [PMID: 33535730 PMCID: PMC9422909 DOI: 10.4274/jcrpe.galenos.2020.2020.0100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Xq22.3-q23 microdeletion is a rare genomic disorder. The purpose of this study was to emphasize the correlation between clinical phenotype and genotype of proximal deletion on chromosome Xq22.3-q23. A 5 years old boy had a 671 KB microdeletion on Xq23 by chromosomal microarray analysis, including AMMECR1 and CHRDL1 genes. He presented with microsomia, midface hypoplasia, right kidney dysplasia and mildly motor retardation, which have not previously been reported in relation to Xq23 deletion. To the best of our knowledge, this is the first case with Xq23 microdeletion. A total of nine cases with microdeletion at Xq22.3-q23 affecting AMMECR1 and two cases with CHRDL1 mutation were reviewed. This review showed that Xq23 microdeletion with microsomia, midface hypoplasia, kidney dysplasia, and mild motor retardation was rare. The previous literature showed two novel point mutations in AMMECR1 and CHRDL1 with some phenotype difference from the presented case. Xq23 microdeletion should be considered for patients with microsomia, midface hypoplasia, kidney dysplasia and growth retardation.
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Affiliation(s)
- Lu Qin
- Children’s Hospital of Zhejiang University School of Medicine, Department of Pulmonology, Zhejiang, China
| | - Fei-Zhou Zhang
- Children’s Hospital of Zhejiang University School of Medicine, Department of Pulmonology, Zhejiang, China
| | - Jian-Hai Lv
- Shangyu People’s Hospital, Clinic of Pediatrics, Zhejiang, China
| | - Lan-Fang Tang
- Shangyu People’s Hospital, Clinic of Pediatrics, Zhejiang, China,* Address for Correspondence: Shangyu People’s Hospital, Clinic of Pediatrics, Zhejiang, China Phone: +86-13868138022 E-mail:
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2
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Koene S, Knijnenburg J, Hoffer MJV, Zwanenburg F, Haak MC, Locher H, Beelen ESA, Santen GWE, Rotteveel LJC. Hearing loss, cleft palate, and congenital hip dysplasia in female carriers of an intragenic deletion of
AMMECR1. Am J Med Genet A 2022; 188:1578-1582. [PMID: 35084080 PMCID: PMC9305766 DOI: 10.1002/ajmg.a.62669] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 10/25/2021] [Accepted: 01/06/2022] [Indexed: 01/18/2023]
Abstract
Previously, mutations in the AMMECR1 gene have been described in six males with developmental delay, sensorineural hearing loss (SNHL) and/or congenital abnormalities, including fetal nuchal edema, fetal pericardial effusion, talipes, congenital hip dysplasia, elliptocytosis and cleft palate. In this report, we present three female relatives of a male fetus with an intragenic deletion in this X‐linked gene. All three women reported hearing loss and one was born with a soft cleft palate and hip dysplasia. The audiograms showed mild to moderate SNHL with a variable pattern of the affected frequencies. Immunohistochemical analysis of fetal cochlea was performed confirming the expression of AMMECR1 in the human inner ear. Since hearing loss, cleft palate and congenital hip dysplasia were reported before in male AMMECR1 point mutation carriers and AMMECR1 is expressed in fetal inner ear, we suggest that female carriers may display a partial phenotype in this X‐linked condition.
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Affiliation(s)
- Saskia Koene
- Department of Clinical Genetics Leiden University Medical Centre Leiden Netherlands
| | - Jeroen Knijnenburg
- Department of Clinical Genetics Leiden University Medical Centre Leiden Netherlands
| | | | - Fleur Zwanenburg
- Department of Obstetrics and Gynaecology Leiden University Medical Centre Leiden Netherlands
| | - Monique C. Haak
- Department of Obstetrics and Gynaecology Leiden University Medical Centre Leiden Netherlands
| | - Heiko Locher
- Department of Otorhinolaryngology, Head&Neck surgery Leiden University Medical Centre Leiden Netherlands
| | - Edward S. A. Beelen
- Department of Otorhinolaryngology, Head&Neck surgery Leiden University Medical Centre Leiden Netherlands
| | - Gijs W. E. Santen
- Department of Clinical Genetics Leiden University Medical Centre Leiden Netherlands
| | - Liselotte J. C. Rotteveel
- Department of Otorhinolaryngology, Head&Neck surgery Leiden University Medical Centre Leiden Netherlands
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3
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Burroughs AM, Glasner ME, Barry KP, Taylor EA, Aravind L. Oxidative opening of the aromatic ring: Tracing the natural history of a large superfamily of dioxygenase domains and their relatives. J Biol Chem 2019; 294:10211-10235. [PMID: 31092555 PMCID: PMC6664185 DOI: 10.1074/jbc.ra119.007595] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 05/09/2019] [Indexed: 12/20/2022] Open
Abstract
A diverse collection of enzymes comprising the protocatechuate dioxygenases (PCADs) has been characterized in several extradiol aromatic compound degradation pathways. Structural studies have shown a relationship between PCADs and the more broadly-distributed, functionally enigmatic Memo domain linked to several human diseases. To better understand the evolution of this PCAD-Memo protein superfamily, we explored their structural and functional determinants to establish a unified evolutionary framework, identifying 15 clearly-delineable families, including a previously-underappreciated diversity in five Memo clade families. We place the superfamily's origin within the greater radiation of the nucleoside phosphorylase/hydrolase-peptide/amidohydrolase fold prior to the last universal common ancestor of all extant organisms. In addition to identifying active-site residues across the superfamily, we describe three distinct, structurally-variable regions emanating from the core scaffold often housing conserved residues specific to individual families. These were predicted to contribute to the active-site pocket, potentially in substrate specificity and allosteric regulation. We also identified several previously-undescribed conserved genome contexts, providing insight into potentially novel substrates in PCAD clade families. We extend known conserved contextual associations for the Memo clade beyond previously-described associations with the AMMECR1 domain and a radical S-adenosylmethionine family domain. These observations point to two distinct yet potentially overlapping contexts wherein the elusive molecular function of the Memo domain could be finally resolved, thereby linking it to nucleotide base and aliphatic isoprenoid modification. In total, this report throws light on the functions of large swaths of the experimentally-uncharacterized PCAD-Memo families.
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Affiliation(s)
- A Maxwell Burroughs
- From the Computational Biology Branch, NCBI, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894
| | - Margaret E Glasner
- the Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, and
| | - Kevin P Barry
- the Department of Chemistry, Wesleyan University, Middletown, Connecticut 06459
| | - Erika A Taylor
- the Department of Chemistry, Wesleyan University, Middletown, Connecticut 06459
| | - L Aravind
- From the Computational Biology Branch, NCBI, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894,
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4
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Poreau B, Ramond F, Harbuz R, Satre V, Barro C, Vettier C, Adouard V, Thevenon J, Jouk PS, Coutton C, Touraine R, Dieterich K. Xq22.3q23 microdeletion harboring TMEM164 and AMMECR1 genes: Two case reports confirming a recognizable phenotype with short stature, midface hypoplasia, intellectual delay, and elliptocytosis. Am J Med Genet A 2019; 179:650-654. [PMID: 30737907 DOI: 10.1002/ajmg.a.61057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 12/06/2018] [Accepted: 01/10/2019] [Indexed: 11/09/2022]
Abstract
The AMME syndrome defined as the combination of Alport syndrome, intellectual disability, midface hypoplasia, and elliptocytosis (AMME) is known to be a contiguous gene syndrome associated with microdeletions in the region Xq22.3q23. Recently, using exome sequencing, missense pathogenic variants in AMMECR1 have been associated with intellectual disability, midface hypoplasia, and elliptocytosis. In these cases, AMMECR1 gene appears to be responsible for most of the clinical features of the AMME syndrome except for Alport syndrome. In this article, we present two unrelated male patients with short stature, mild intellectual disability or neurodevelopmental delay, sensorineural hearing loss, and elliptocytosis harboring small microdeletions identified by array-CGH involving TMEM164 and AMMECR1 genes and SNORD96B small nucleolar RNA for one patient, inherited from their mothers. These original cases further confirm that most specific AMME features are ascribed to AMMECR1 haploinsufficiency. These cases reporting the smallest microdeletions encompassing AMMECR1 gene provide new evidence for involvement of AMMECR1 in the AMME phenotype and permit to discuss a phenotype related to AMMECR1 haploinsufficiency: developmental delay/intellectual deficiency, midface hypoplasia, midline defect, deafness, and short stature.
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Affiliation(s)
- Brice Poreau
- Département de Génétique et Procréation, Centre Hospitalo-Universitaire Grenoble Alpes, Grenoble Cedex, France.,Univ. Grenoble Alpes, Inserm, U1216, CHU Grenoble Alpes, GIN, 38000 Grenoble, France
| | - Francis Ramond
- Département de Génétique Clinique, Chromosomique et Moléculaire, CHU-Hôpital Nord, Saint Etienne, France
| | - Radu Harbuz
- Département de Génétique et Procréation, Centre Hospitalo-Universitaire Grenoble Alpes, Grenoble Cedex, France
| | - Véronique Satre
- Département de Génétique et Procréation, Centre Hospitalo-Universitaire Grenoble Alpes, Grenoble Cedex, France.,Equipe "Genetics Epigenetics and Therapies of Infertility" Institut Albert Bonniot, INSERM U823, La Tronche, France
| | - Claire Barro
- Département d'Hématologie, Oncogénétique, Immunologie, Centre Hospitalo-Universitaire Grenoble Alpes, Grenoble Cedex, France
| | - Claire Vettier
- Département d'Hématologie, Oncogénétique, Immunologie, Centre Hospitalo-Universitaire Grenoble Alpes, Grenoble Cedex, France
| | - Véronique Adouard
- Département de Génétique Clinique, Chromosomique et Moléculaire, CHU-Hôpital Nord, Saint Etienne, France
| | - Julien Thevenon
- Département de Génétique et Procréation, Centre Hospitalo-Universitaire Grenoble Alpes, Grenoble Cedex, France
| | - Pierre-Simon Jouk
- Département de Génétique et Procréation, Centre Hospitalo-Universitaire Grenoble Alpes, Grenoble Cedex, France
| | - Charles Coutton
- Département de Génétique et Procréation, Centre Hospitalo-Universitaire Grenoble Alpes, Grenoble Cedex, France.,Equipe "Genetics Epigenetics and Therapies of Infertility" Institut Albert Bonniot, INSERM U823, La Tronche, France
| | - Renaud Touraine
- Département de Génétique Clinique, Chromosomique et Moléculaire, CHU-Hôpital Nord, Saint Etienne, France
| | - Klaus Dieterich
- Département de Génétique et Procréation, Centre Hospitalo-Universitaire Grenoble Alpes, Grenoble Cedex, France.,Univ. Grenoble Alpes, Inserm, U1216, CHU Grenoble Alpes, GIN, 38000 Grenoble, France
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5
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Towards functional characterization of archaeal genomic dark matter. Biochem Soc Trans 2019; 47:389-398. [PMID: 30710061 PMCID: PMC6393860 DOI: 10.1042/bst20180560] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 01/08/2019] [Accepted: 01/09/2019] [Indexed: 01/07/2023]
Abstract
A substantial fraction of archaeal genes, from ∼30% to as much as 80%, encode ‘hypothetical' proteins or genomic ‘dark matter'. Archaeal genomes typically contain a higher fraction of dark matter compared with bacterial genomes, primarily, because isolation and cultivation of most archaea in the laboratory, and accordingly, experimental characterization of archaeal genes, are difficult. In the present study, we present quantitative characteristics of the archaeal genomic dark matter and discuss comparative genomic approaches for functional prediction for ‘hypothetical' proteins. We propose a list of top priority candidates for experimental characterization with a broad distribution among archaea and those that are characteristic of poorly studied major archaeal groups such as Thaumarchaea, DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota and Nanohaloarchaeota) and Asgard.
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Abstract
PURPOSE OF REVIEW Genome-wide approaches including genome-wide association studies as well as exome and genome sequencing represent powerful new approaches that have improved our ability to identify genetic causes of human disorders. The purpose of this review is to describe recent advances in the genetic causes of short stature. RECENT FINDINGS In addition to SHOX deficiency which is one of the most common causes of isolated short stature, PAPPA2, ACAN, NPPC, NPR2, PTPN11 (and other rasopathies), FBN1, IHH and BMP2 have been identified in isolated growth disorders with or without other mild skeletal findings. In addition, novel genetic causes of syndromic short stature have been discovered, including pathogenic variants in BRCA1, DONSON, AMMECR1, NFIX, SLC25A24, and FN1. SUMMARY Isolated growth disorders are often monogenic. Specific genetic causes typically have specific biochemical and/or phenotype characteristics which are diagnostically helpful. Identification of additional subjects with a specific genetic cause of short stature often leads to a broadening of the known clinical spectrum for that condition. The identification of novel genetic causes of short stature has provided important insights into the underlying molecular mechanisms of growth failure.
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7
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Genetic interactions between the chromosome axis-associated protein Hop1 and homologous recombination determinants in Schizosaccharomyces pombe. Curr Genet 2018; 64:1089-1104. [PMID: 29550859 PMCID: PMC6153652 DOI: 10.1007/s00294-018-0827-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 03/14/2018] [Indexed: 11/28/2022]
Abstract
Hop1 is a component of the meiosis-specific chromosome axis and belongs to the evolutionarily conserved family of HORMA domain proteins. Hop1 and its orthologs in higher eukaryotes are a major factor in promoting double-strand DNA break formation and inter-homolog recombination. In budding yeast and mammals, they are also involved in a meiotic checkpoint kinase cascade monitoring the completion of double-strand DNA break repair. We used the fission yeast, Schizosaccharomyces pombe, which lacks a canonical synaptonemal complex to test whether Hop1 has a role beyond supporting the generation of double-strand DNA breaks and facilitating inter-homolog recombination events. We determined how mutants of homologous recombination factors genetically interact with hop1, studied the role(s) of the HORMA domain of Hop1, and characterized a bio-informatically predicted interactor of Hop1, Aho1 (SPAC688.03c). Our observations indicate that in fission yeast, Hop1 does require its HORMA domain to support wild-type levels of meiotic recombination and localization to meiotic chromatin. Furthermore, we show that hop1∆ only weakly interacts genetically with mutants of homologous recombination factors, and in fission yeast likely has no major role beyond break formation and promoting inter-homolog events. We speculate that after the evolutionary loss of the synaptonemal complex, Hop1 likely has become less important for modulating recombination outcome during meiosis in fission yeast, and that this led to a concurrent rewiring of genetic pathways controlling meiotic recombination.
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8
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Moysés-Oliveira M, Giannuzzi G, Fish RJ, Rosenfeld JA, Petit F, Soares MDF, Kulikowski LD, Di-Battista A, Zamariolli M, Xia F, Liehr T, Kosyakova N, Carvalheira G, Parker M, Seaby EG, Ennis S, Gilbert RD, Hagelstrom RT, Cremona ML, Li WL, Malhotra A, Chandrasekhar A, Perry DL, Taft RJ, McCarrier J, Basel DG, Andrieux J, Stumpp T, Antunes F, Pereira GJ, Neerman-Arbez M, Meloni VA, Drummond-Borg M, Melaragno MI, Reymond A. Inactivation of AMMECR1 is associated with growth, bone, and heart alterations. Hum Mutat 2017; 39:281-291. [PMID: 29193635 DOI: 10.1002/humu.23373] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 11/18/2017] [Accepted: 11/18/2017] [Indexed: 01/26/2023]
Abstract
We report five individuals with loss-of-function of the X-linked AMMECR1: a girl with a balanced X-autosome translocation and inactivation of the normal X-chromosome; two boys with maternally inherited and de novo nonsense variants; and two half-brothers with maternally inherited microdeletion variants. They present with short stature, cardiac and skeletal abnormalities, and hearing loss. Variants of unknown significance in AMMECR1 in four male patients from two families with partially overlapping phenotypes were previously reported. AMMECR1 is coexpressed with genes implicated in cell cycle regulation, five of which were previously associated with growth and bone alterations. Our knockdown of the zebrafish orthologous gene resulted in phenotypes reminiscent of patients' features. The increased transcript and encoded protein levels of AMMECR1L, an AMMECR1 paralog, in the t(X;9) patient's cells indicate a possible partial compensatory mechanism. AMMECR1 and AMMECR1L proteins dimerize and localize to the nucleus as suggested by their nucleic acid-binding RAGNYA folds. Our results suggest that AMMECR1 is potentially involved in cell cycle control and linked to a new syndrome with growth, bone, heart, and kidney alterations with or without elliptocytosis.
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Affiliation(s)
- Mariana Moysés-Oliveira
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil.,Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Giuliana Giannuzzi
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Richard J Fish
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Florence Petit
- Clinique de Génétique, CHU Lille - Hôpital Jeanne de Flandre, Lille, France
| | | | - Leslie Domenici Kulikowski
- Department of Pathology, Laboratório de Citogenômica, LIM 03, Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Adriana Di-Battista
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Malú Zamariolli
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Thomas Liehr
- Universitätsklinikum Jena, Institut für Humangenetik, Jena, Germany
| | | | - Gianna Carvalheira
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Michael Parker
- Sheffield Clinical Genetics Service, Sheffield Children's Hospital, Sheffield, United Kingdom
| | - Eleanor G Seaby
- Genomic Informatics Group, University Hospital Southampton, Southampton, United Kingdom
| | - Sarah Ennis
- Genomic Informatics Group, University Hospital Southampton, Southampton, United Kingdom
| | - Rodney D Gilbert
- Southampton Children's Hospital, University Hospital Southampton, Southampton, United Kingdom
| | | | - Maria L Cremona
- Illumina Clinical Services Laboratory, San Diego, California
| | - Wenhui L Li
- Illumina Clinical Services Laboratory, San Diego, California
| | - Alka Malhotra
- Illumina Clinical Services Laboratory, San Diego, California
| | | | - Denise L Perry
- Illumina Clinical Services Laboratory, San Diego, California
| | - Ryan J Taft
- Illumina Clinical Services Laboratory, San Diego, California
| | - Julie McCarrier
- Department of Pediatrics, Section of Genetics, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Donald G Basel
- Department of Pediatrics, Section of Genetics, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Joris Andrieux
- Institut de Génétique Médicale, CHU Lille - Hôpital Jeanne de Flandre, Lille, France
| | - Taiza Stumpp
- Developmental Biology Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Fernanda Antunes
- Department of Pharmacology, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Gustavo José Pereira
- Department of Pharmacology, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Marguerite Neerman-Arbez
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Vera Ayres Meloni
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | | | - Maria Isabel Melaragno
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
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Basel-Vanagaite L, Pillar N, Isakov O, Smirin-Yosef P, Lagovsky I, Orenstein N, Salmon-Divon M, Tamary H, Zaft T, Bazak L, Meyerovitch J, Pelli T, Botchan S, Farberov L, Weissglas-Volkov D, Shomron N. X-linked elliptocytosis with impaired growth is related to mutated AMMECR1. Gene 2017; 606:47-52. [PMID: 28089922 DOI: 10.1016/j.gene.2017.01.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 12/17/2016] [Accepted: 01/05/2017] [Indexed: 12/15/2022]
Abstract
In this study, we report a family with X-linked recessive syndrome caused by mutated AMMECR1 and characterized by elliptocytosis with or without anemia, midface hypoplasia, proportionate short stature and hearing loss. Recently, mutations in AMMECR1 were reported in two maternal half-brothers, presenting with nephrocalcinosis, midface hypoplasia and, in one of the siblings, deafness and elliptocytosis. AMMECR1 gene is localized in the critical region of contiguous deletion syndrome on Xq22.3 implicated in Alport syndrome, mental retardation, midface hypoplasia, and elliptocytosis (AMME complex). Interestingly, alternative splicing of exon 2, the same exon harboring the truncating mutation, was observed in the proband and in his unaffected mother. Alternative splicing of this exon is predicted to lead to an in-frame deletion. We provide further evidence that mutated AMMECR1 gene is responsible for this clinically recognizable X-linked condition with variable expressivity.
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Affiliation(s)
- Lina Basel-Vanagaite
- Raphael Recanati Genetics Institute, Rabin Medical Center, Beilinson Campus, Petah Tikva, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Pediatric Genetics Unit, Schneider Children's Medical Center of Israel, Petah Tikva, Israel; Felsenstein Medical Research Center, Rabin Medical Center, Petah Tikva, Israel.
| | - Nir Pillar
- Department of Cell and Developmental Biology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ofer Isakov
- Department of Cell and Developmental Biology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Pola Smirin-Yosef
- Genomic Bioinformatics Laboratory, Department of Molecular Biology, Ariel University, Israel
| | - Irina Lagovsky
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Felsenstein Medical Research Center, Rabin Medical Center, Petah Tikva, Israel
| | - Naama Orenstein
- Raphael Recanati Genetics Institute, Rabin Medical Center, Beilinson Campus, Petah Tikva, Israel; Pediatric Genetics Unit, Schneider Children's Medical Center of Israel, Petah Tikva, Israel
| | - Mali Salmon-Divon
- Genomic Bioinformatics Laboratory, Department of Molecular Biology, Ariel University, Israel
| | - Hannah Tamary
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Hematology Unit, Schneider Children's Medical Center of Israel, Petah Tikva, Israel
| | - Tami Zaft
- Raphael Recanati Genetics Institute, Rabin Medical Center, Beilinson Campus, Petah Tikva, Israel
| | - Lily Bazak
- Raphael Recanati Genetics Institute, Rabin Medical Center, Beilinson Campus, Petah Tikva, Israel
| | - Joseph Meyerovitch
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; The Jesse Z and Sara Lea Shafer Institute for Endocrinology and Diabetes, National Center for Childhood Diabetes, Schneider Children's Medical Center of Israel, Petah Tikva, Israel
| | - Tal Pelli
- Department of Cell and Developmental Biology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Shay Botchan
- Department of Cell and Developmental Biology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Luba Farberov
- Department of Cell and Developmental Biology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Daphna Weissglas-Volkov
- Department of Cell and Developmental Biology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Noam Shomron
- Department of Cell and Developmental Biology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.
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Similarities in Gene Expression Profiles during In Vitro Aging of Primary Human Embryonic Lung and Foreskin Fibroblasts. BIOMED RESEARCH INTERNATIONAL 2015; 2015:731938. [PMID: 26339636 PMCID: PMC4538583 DOI: 10.1155/2015/731938] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 06/14/2015] [Accepted: 06/22/2015] [Indexed: 01/18/2023]
Abstract
Replicative senescence is of fundamental importance for the process of cellular aging, since it is a property of most of our somatic cells. Here, we elucidated this process by comparing gene expression changes, measured by RNA-seq, in fibroblasts originating from two different tissues, embryonic lung (MRC-5) and foreskin (HFF), at five different time points during their transition into senescence. Although the expression patterns of both fibroblast cell lines can be clearly distinguished, the similar differential expression of an ensemble of genes was found to correlate well with their transition into senescence, with only a minority of genes being cell line specific. Clustering-based approaches further revealed common signatures between the cell lines. Investigation of the mRNA expression levels at various time points during the lifespan of either of the fibroblasts resulted in a number of monotonically up- and downregulated genes which clearly showed a novel strong link to aging and senescence related processes which might be functional. In terms of expression profiles of differentially expressed genes with age, common genes identified here have the potential to rule the transition into senescence of embryonic lung and foreskin fibroblasts irrespective of their different cellular origin.
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12
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周 化. Research Advances of AMMECR1. Biophysics (Nagoya-shi) 2015. [DOI: 10.12677/biphy.2015.31001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Cole J, Waurich B, Wensch-Dorendorf M, Bickhart D, Swalve H. A genome-wide association study of calf birth weight in Holstein cattle using single nucleotide polymorphisms and phenotypes predicted from auxiliary traits. J Dairy Sci 2014; 97:3156-72. [DOI: 10.3168/jds.2013-7409] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 01/28/2014] [Indexed: 02/04/2023]
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Sun T, Wang X, He HH, Sweeney CJ, Liu SX, Brown M, Balk S, Lee GS, Kantoff PW. MiR-221 promotes the development of androgen independence in prostate cancer cells via downregulation of HECTD2 and RAB1A. Oncogene 2013; 33:2790-800. [PMID: 23770851 DOI: 10.1038/onc.2013.230] [Citation(s) in RCA: 113] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Revised: 04/15/2013] [Accepted: 04/25/2013] [Indexed: 12/18/2022]
Abstract
Hormone-sensitive prostate cancer typically progresses to castration resistant prostate cancer (CRPC) after the androgen deprivation therapy. We investigated the impact of microRNAs (miRs) in the transition of prostate cancer to CRPC. MiR-221/-222 was highly expressed in bone metastatic CRPC tumor specimens. We previously demonstrated that transient overexpression of miR-221/-222 in LNCaP promoted the development of the CRPC phenotype. In current study, we show that stably overexpressing miR-221 confers androgen independent (AI) cell growth in LNCaP by rescuing LNCaP cells from growth arrest at G1 phase due to the lack of androgen. Overexpressing of miR-221 in LNCaP reduced the transcription of a subgroup of androgen-responsive genes without affecting the androgen receptor (AR) or AR-androgen integrity. By performing systematic biochemical and bioinformatical analyses, we identified two miR-221 targets, HECTD2 and RAB1A, which could mediate the development of CRPC phenotype in multiple prostate cancer cell lines. Downregulation of HECTD2 significantly affected the androgen-induced and AR-mediated transcription, and downregulation of HECTD2 or RAB1A enhances AI cell growth. As a result of the elevated expression of miR-221, expression of many cell cycle genes was altered and pathways promoting epithelial to mesenchymal transition/tumor metastasis were activated. We hypothesize that a major biological consequence of upregulation of miR-221 is reprogramming of AR signaling, which in turn may mediate the transition to the CRPC phenotype.
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Affiliation(s)
- T Sun
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - X Wang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - H H He
- 1] Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA [2] Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - C J Sweeney
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - S X Liu
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - M Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - S Balk
- Cancer Biology Program, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - G-Sm Lee
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - P W Kantoff
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
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15
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Gazou A, Riess A, Grasshoff U, Schäferhoff K, Bonin M, Jauch A, Riess O, Tzschach A. Xq22.3-q23 deletion includingACSL4in a patient with intellectual disability. Am J Med Genet A 2013; 161A:860-4. [DOI: 10.1002/ajmg.a.35778] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Accepted: 10/28/2012] [Indexed: 11/11/2022]
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16
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Hoischen A, Landwehr C, Kabisch S, Ding XQ, Trost D, Stropahl G, Wigger M, Radlwimmer B, Weber RG, Haffner D. Array-CGH in unclear syndromic nephropathies identifies a microdeletion in Xq22.3-q23. Pediatr Nephrol 2009; 24:1673-81. [PMID: 19444485 DOI: 10.1007/s00467-009-1184-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2009] [Revised: 03/08/2009] [Accepted: 03/13/2009] [Indexed: 12/14/2022]
Abstract
To investigate whether submicroscopic chromosomal deletions or duplications can be causative of unclear syndromic nephropathies, we analyzed ten patients with congenital abnormalities of the kidney and urinary tract or glomerulopathies combined with important extrarenal anomalies by whole-genome array-based comparative genomic hybridization. In a 14-year-old girl presenting with hematuria, proteinuria, mental retardation (MR), sensorineural hearing loss, dysmorphisms, and epilepsy, we detected a microdeletion in chromosome Xq22.3-q23. This deletion was verified and characterized by fluorescence in situ hybridization and multiplex ligation-dependent probe amplification analyses, found to be de novo, uniallelic and 3.3 Mb in size. Electron microscopy of a kidney biopsy showed glomerular basement membrane thinning and segmental splitting of the lamina densa compatible with Alport syndrome. Cranial magnetic resonance and diffusion tensor imaging detected a severe neuronal migration disorder with double cortex formation and pronounced reduction of the fronto-occipital tract system. Thus, in one of ten patients with unclear syndromic nephropathies we identified a previously undescribed contiguous gene syndrome at Xq22.3-q23. The microdeletion contains the X-linked Alport syndrome gene COL4A5, the MR genes FACL4 and PAK3, and parts of the X-chromosomal lissencephaly gene DCX associated with double cortex formation in girls, MR, and epilepsy. The phenotype in our patient combines features of the Alport-MR contiguous gene syndrome with lissencephaly.
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Affiliation(s)
- Alexander Hoischen
- Institute of Human Genetics, Rheinische Friedrich-Wilhelms-University, Bonn, Germany
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17
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Gubler MC. Inherited diseases of the glomerular basement membrane. ACTA ACUST UNITED AC 2008; 4:24-37. [DOI: 10.1038/ncpneph0671] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2007] [Accepted: 09/13/2007] [Indexed: 01/15/2023]
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18
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Tajika Y, Sakai N, Tamura T, Yao M, Watanabe N, Tanaka I. Crystal structure of PH0010 from Pyrococcus horikoshii, which is highly homologous to human AMMECR 1C-terminal region. Proteins 2006; 58:501-3. [PMID: 15558565 DOI: 10.1002/prot.20315] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Yosuke Tajika
- Division of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo, Japan
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19
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Makarova KS, Koonin EV. Evolutionary and functional genomics of the Archaea. Curr Opin Microbiol 2005; 8:586-94. [PMID: 16111915 DOI: 10.1016/j.mib.2005.08.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2005] [Accepted: 08/05/2005] [Indexed: 11/20/2022]
Abstract
In the past two years, archaeal genomics has achieved several breakthroughs. On the evolutionary front the most exciting development was the sequencing and analysis of the genome of Nanoarchaeum equitans, a tiny parasitic organism that has only approximately 540 genes. The genome of Nanoarchaeum shows signs of extreme rearrangement including the virtual absence of conserved operons and the presence of several split genes. Nanoarchaeum is distantly related to other archaea, and it has been proposed to represent a deep archaeal branch that is distinct from Euryarchaeota and Crenarchaeota. This would imply that many features of its gene repertoire and genome organization might be ancestral. However, additional genome analysis has provided a more conservative suggestion - that Nanoarchaeum is a highly derived euryarchaeon. Also there have been substantial developments in functional genomics, including the discovery of the elusive aminoacyl-tRNA synthetase that is involved in both the biosynthesis of cysteine and its incorporation into proteins in methanogens, and the first experimental validation of the predicted archaeal exosome.
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Affiliation(s)
- Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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20
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Galperin MY, Koonin EV. 'Conserved hypothetical' proteins: prioritization of targets for experimental study. Nucleic Acids Res 2004; 32:5452-63. [PMID: 15479782 PMCID: PMC524295 DOI: 10.1093/nar/gkh885] [Citation(s) in RCA: 289] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Comparative genomics shows that a substantial fraction of the genes in sequenced genomes encodes 'conserved hypothetical' proteins, i.e. those that are found in organisms from several phylogenetic lineages but have not been functionally characterized. Here, we briefly discuss recent progress in functional characterization of prokaryotic 'conserved hypothetical' proteins and the possible criteria for prioritizing targets for experimental study. Based on these criteria, the chief one being wide phyletic spread, we offer two 'top 10' lists of highly attractive targets. The first list consists of proteins for which biochemical activity could be predicted with reasonable confidence but the biological function was predicted only in general terms, if at all ('known unknowns'). The second list includes proteins for which there is no prediction of biochemical activity, even if, for some, general biological clues exist ('unknown unknowns'). The experimental characterization of these and other 'conserved hypothetical' proteins is expected to reveal new, crucial aspects of microbial biology and could also lead to better functional prediction for medically relevant human homologs.
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Affiliation(s)
- Michael Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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21
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Meloni I, Muscettola M, Raynaud M, Longo I, Bruttini M, Moizard MP, Gomot M, Chelly J, des Portes V, Fryns JP, Ropers HH, Magi B, Bellan C, Volpi N, Yntema HG, Lewis SE, Schaffer JE, Renieri A. FACL4, encoding fatty acid-CoA ligase 4, is mutated in nonspecific X-linked mental retardation. Nat Genet 2002; 30:436-40. [PMID: 11889465 DOI: 10.1038/ng857] [Citation(s) in RCA: 118] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
X-linked mental retardation (XLMR) is an inherited condition that causes failure to develop cognitive abilities, owing to mutations in a gene on the X chromosome. The latest XLMR update lists up to 136 conditions leading to 'syndromic', or 'specific', mental retardation (MRXS) and 66 entries leading to 'nonspecific' mental retardation (MRX). For 9 of the 66 MRX entries, the causative gene has been identified. Our recent discovery of the contiguous gene deletion syndrome ATS-MR (previously known as Alport syndrome, mental retardation, midface hypoplasia, elliptocytosis, OMIM #300194), characterized by Alport syndrome (ATS) and mental retardation (MR), indicated Xq22.3 as a region containing one mental retardation gene. Comparing the extent of deletion between individuals with ATS-MR and individuals with ATS alone allowed us to define a critical region for mental retardation of approximately 380 kb, containing four genes. Here we report the identification of two point mutations, one missense and one splice-site change, in the gene FACL4 in two families with nonspecific mental retardation. Analysis of enzymatic activity in lymphoblastoid cell lines from affected individuals of both families revealed low levels compared with normal cells, indicating that both mutations are null mutations. All carrier females with either point mutations or genomic deletions in FACL4 showed a completely skewed X-inactivation, suggesting that the gene influences survival advantage. FACL4 is the first gene shown to be involved in nonspecific mental retardation and fatty-acid metabolism.
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Affiliation(s)
- Ilaria Meloni
- Medical Genetics, Department of Molecular Biology, University of Siena, Italy
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22
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Piccini M, Vitelli F, Seri M, Galietta LJ, Moran O, Bulfone A, Banfi S, Pober B, Renieri A. KCNE1-like gene is deleted in AMME contiguous gene syndrome: identification and characterization of the human and mouse homologs. Genomics 1999; 60:251-7. [PMID: 10493825 DOI: 10.1006/geno.1999.5904] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We describe the identification and characterization of a new gene deleted in the AMME contiguous gene syndrome. This gene is predominantly expressed in heart, skeletal muscle, spinal cord, and brain. Screening of placenta and NT2 cDNA libraries enabled us to obtain the 1.5-kb full-length transcript, which shows a 426-bp open reading frame. Since the resulting 142-amino-acid peptide has a single putative transmembrane domain and a weak but suggestive homology with KCNE1 (minK), a protein associated with the KCNQ1 potassium channel (KVLQT1), we named this new gene KCNE1-like (KCNE1L). To obtain greater insight into this new member of an apparently distinct protein family, we have identified and characterized the homologous mouse gene (Kcne1l), which encodes a peptide of 143 amino acids with 91% homology and 80% identity. The expression pattern of mouse Kcne1l in the developing embryo revealed strong signal in ganglia, in the migrating neural crest cells of cranial nerves, in the somites, and in the myoepicardial layer of the heart. The specific distribution in adult tissues, the putative channel function, and the expression pp6tern in the developing mouse embryo suggest that KCNE1L could be involved in the development of the cardiac abnormalities as well as of some neurological signs observed in patients with AMME contiguous gene syndrome.
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Affiliation(s)
- M Piccini
- Genetica Medica, Policlinico Le Scotte, Siena, 53100, Italy
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23
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Abstract
Alport syndrome (AS) is a genetically heterogeneous disease arising from mutations in genes coding for basement membrane type IV collagen. About 80% of AS is X-linked, due to mutations in COL4A5, the gene encoding the alpha 5 chain of type IV collagen (alpha 5[IV]). A subtype of X-linked Alport syndrome (XLAS) in which diffuse leiomyomatosis is an associated feature reflects deletion mutations involving the adjacent COL4A5 and COL4A6 genes. Most other patients have autosomal recessive Alport syndrome (ARAS) due to mutations in COL4A3 or COL4A4, which encode the alpha 3(IV) and alpha 4(IV) chains, respectively. Autosomal dominant AS has been mapped to chromosome 2 in the region of COL4A3 and COL4A4. The features of AS reflect derangements of basement membrane structure and function resulting from changes in type IV collagen expression. The primary pathologic event appears to be the loss from basement membranes of a type IV collagen network composed of alpha 3, alpha 4, and alpha 5(IV) chains. While this network is not critical for normal glomerulogenesis, its absence appears to provoke the overexpression of other extracellular matrix proteins, such as the alpha 1 and alpha 2(IV) chains, in glomerular basement membranes, leading to glomerulosclerosis. The diagnosis of AS still relies heavily on histologic studies, although routine application of molecular genetic diagnosis will probably be available in the future. Absence of epidermal basement membrane expression of alpha 5(IV) is diagnostic of XLAS, so in some cases kidney biopsy may not be necessary for diagnosis. Analysis of renal expression of alpha 3(IV)-alpha 5(IV) chains may be a useful adjunct to routine renal biopsy studies, especially when ultrastructural changes in the GBM are ambiguous. There are no specific therapies for AS. Spontaneous and engineered animal models are being used to study genetic and pharmacologic therapies. Renal transplantation for AS is usually very successful. Occasional patients develop anti-GBM nephritis of the allograft, almost always resulting in graft loss.
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Affiliation(s)
- C E Kashtan
- Department of Pediatrics, University of Minnesota Medical School, Minneapolis 55455, USA.
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