1
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Sadat Kalaki N, Ahmadzadeh M, Najafi M, Mobasheri M, Ajdarkosh H, Karbalaie Niya MH. Systems biology approach to identify biomarkers and therapeutic targets for colorectal cancer. Biochem Biophys Rep 2024; 37:101633. [PMID: 38283191 PMCID: PMC10821538 DOI: 10.1016/j.bbrep.2023.101633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 12/24/2023] [Accepted: 12/27/2023] [Indexed: 01/30/2024] Open
Abstract
Background Colorectal cancer (CRC), is the third most prevalent cancer across the globe, and is often detected at advanced stage. Late diagnosis of CRC, leave the chemotherapy and radiotherapy as the main options for the possible treatment of the disease which are associated with severe side effects. In the present study, we seek to explore CRC gene expression data using a systems biology framework to identify potential biomarkers and therapeutic targets for earlier diagnosis and treatment of the disease. Methods The expression data was retrieved from the gene expression omnibus (GEO). Differential gene expression analysis was conducted using R/Bioconductor package. The PPI network was reconstructed by the STRING. Cystoscope and Gephi software packages were used for visualization and centrality analysis of the PPI network. Clustering analysis of the PPI network was carried out using k-mean algorithm. Gene-set enrichment based on Gene Ontology (GO) and KEGG pathway databases was carried out to identify the biological functions and pathways associated with gene groups. Prognostic value of the selected identified hub genes was examined by survival analysis, using GEPIA. Results A total of 848 differentially expressed genes were identified. Centrality analysis of the PPI network resulted in identification of 99 hubs genes. Clustering analysis dissected the PPI network into seven interactive modules. While several DEGs and the central genes in each module have already reported to contribute to CRC progression, survival analysis confirmed high expression of central genes, CCNA2, CD44, and ACAN contribute to poor prognosis of CRC patients. In addition, high expression of TUBA8, AMPD3, TRPC1, ARHGAP6, JPH3, DYRK1A and ACTA1 was found to associate with decreased survival rate. Conclusion Our results identified several genes with high centrality in PPI network that contribute to progression of CRC. The fact that several of the identified genes have already been reported to be relevant to diagnosis and treatment of CRC, other highlighted genes with limited literature information may hold potential to be explored in the context of CRC biomarker and drug target discovery.
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Affiliation(s)
- Niloufar Sadat Kalaki
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
- International Institute of New Sciences (IINS), Tehran, Iran
| | - Mozhgan Ahmadzadeh
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | - Mohammad Najafi
- Department of Biochemistry, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Meysam Mobasheri
- Department of Biotechnology, Faculty of Advanced Sciences and Technology, Tehran Islamic Azad University of Medical Sciences, Tehran, Iran
- International Institute of New Sciences (IINS), Tehran, Iran
| | - Hossein Ajdarkosh
- Gastrointestinal and Liver Diseases Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Hadi Karbalaie Niya
- Gastrointestinal and Liver Diseases Research Center, Iran University of Medical Sciences, Tehran, Iran
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
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2
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Lipreri da Silva JC, Coelho-Silva JL, Vicari HP, Lima K, Rego EM, Traina F, Machado-Neto JA. ARHGAP6 transcript levels are associated with molecular risk and impact survival outcomes in acute myeloid leukemia. Hematol Transfus Cell Ther 2024; 46:101-105. [PMID: 37541806 PMCID: PMC10935455 DOI: 10.1016/j.htct.2023.06.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 06/07/2023] [Indexed: 08/06/2023] Open
Affiliation(s)
| | - Juan Luiz Coelho-Silva
- Hematology and Clinical Oncology, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo (FMUSP), Ribeirão Preto, SP, Brazil
| | - Hugo Passos Vicari
- Institute of Biomedical Sciences, University de São Paulo (USP), São Paulo, SP, Brazil
| | - Keli Lima
- Laboratory of Medical Investigation in Pathogenesis and Targeted Therapy in Onco-Immuno-Hematology Hospital das Clínicas, Faculdade de Medicina, Universidade de Sao Paulo, (LIM-31 - HCFMUSP) Sao Paulo, SP, Brazil
| | - Eduardo Magalhães Rego
- Laboratory of Medical Investigation in Pathogenesis and Targeted Therapy in Onco-Immuno-Hematology Hospital das Clínicas, Faculdade de Medicina, Universidade de Sao Paulo, (LIM-31 - HCFMUSP) Sao Paulo, SP, Brazil
| | - Fabiola Traina
- Hematology and Clinical Oncology, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo (FMUSP), Ribeirão Preto, SP, Brazil
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3
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Qureshi HM, Mekbib KY, Allington G, Elsamadicy AA, Duy PQ, Kundishora AJ, Jin SC, Kahle KT. Familial and syndromic forms of arachnoid cyst implicate genetic factors in disease pathogenesis. Cereb Cortex 2023; 33:3012-3025. [PMID: 35851401 PMCID: PMC10388392 DOI: 10.1093/cercor/bhac257] [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: 04/29/2022] [Revised: 06/01/2022] [Accepted: 06/04/2022] [Indexed: 11/13/2022] Open
Abstract
Arachnoid cysts (ACs) are the most common space-occupying lesions in the human brain and present significant challenges for clinical management. While most cases of ACs are sporadic, nearly 40 familial forms have been reported. Moreover, ACs are seen with increased frequency in multiple Mendelian syndromes, including Chudley-McCullough syndrome, acrocallosal syndrome, and autosomal recessive primary ciliary dyskinesia. These findings suggest that genetic factors contribute to AC pathogenesis. However, traditional linkage and segregation approaches have been limited in their ability to identify causative genes for ACs because the disease is genetically heterogeneous and often presents asymptomatically and sporadically. Here, we comprehensively review theories of AC pathogenesis, the genetic evidence for AC formation, and discuss a different approach to AC genomics that could help elucidate this perplexing lesion and shed light on the associated neurodevelopmental phenotypes seen in a significant subset of these patients.
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Affiliation(s)
- Hanya M Qureshi
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT 06510, United States
| | - Kedous Y Mekbib
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT 06510, United States
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, United States
| | - Garrett Allington
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, United States
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06510, United States
| | - Aladine A Elsamadicy
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT 06510, United States
| | - Phan Q Duy
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT 06510, United States
| | - Adam J Kundishora
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT 06510, United States
| | - Sheng Chih Jin
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, United States
| | - Kristopher T Kahle
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT 06510, United States
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, United States
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA 02115, United States
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, United States
- Department of Neurology, Harvard Medical School, Boston, MA 02115, United States
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States
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4
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Li P, Lv H, Xu M, Zang B, Ma Y. ARHGAP6 Promotes Apoptosis and Inhibits Glycolysis in Lung Adenocarcinoma Through STAT3 Signaling Pathway. Cancer Manag Res 2020; 12:9665-9678. [PMID: 33116826 PMCID: PMC7547783 DOI: 10.2147/cmar.s257759] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 07/21/2020] [Indexed: 12/26/2022] Open
Abstract
Objective Constitutively activated signal transducer and activator of transcription 3 (STAT3) has been linked to cisplatin (DDP)-resistance in a wide range of cancers. Recent work has indicated that Rho GTPase-activating protein 6 (ARHGAP6) promotes cell cycle arrest and apoptosis in cervical and breast cancers. However, the role of ARHGAP6 in lung adenocarcinoma and DDP-resistance remains unknown. Materials and Methods Bioinformatic analysis, quantitative RT-PCR and IHC staining were used to explore ARHGAP6 expression patterns in The Cancer Genome Atlas (TCGA) dataset and patient samples. Statistical analysis was performed to establish the association of ARHGAP6 expression with the resistance to DDP-based chemotherapy in lung adenocarcinoma patients. Functional assays were then conducted to examine the effect of ARHGAP6 on the apoptosis and glycolysis in DDP-resistant/sensitive A549/DPP cells in vitro. Finally, the effects of ARHGAP6 on the chemosensitivity of DDP were explored in vivo. Results We show that decreased ARHGAP6 levels are a reliable marker of lung adenocarcinoma across published datasets, cell culture lines, and clinical samples. Low ARHGAP6 expression was linked to decreased apoptosis and increased metabolic activity, which highlights ARHGAP6’s role as a tumor suppressor. Furthermore, activated p-STAT3 levels increased dramatically in the absence of ARHGAP6, which suggests that ARHGAP6 can inhibit the STAT3 pathway. In agreement with previous studies that linked p-STAT3 levels to DDP-resistance, our in vitro and in vivo data indicate that tumors became more resistant to DDP-therapy with reduced ARHGAP6 levels and an associated increase in p-STAT3. Conclusion ARHGAP6 presents a novel study target for overcoming p-STAT3-associated DDP-resistance in lung adenocarcinoma and potentially other cancers.
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Affiliation(s)
- Pengfei Li
- Department of Thoracic Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang 110042, People's Republic of China
| | - Huina Lv
- Department of Ultrasound, Shengjing Hospital of China Medical University, Shenyang, 110004, People's Republic of China
| | - Min Xu
- Department of Thoracic Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang 110042, People's Republic of China
| | - Bin Zang
- Department of Thoracic Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang 110042, People's Republic of China
| | - Yegang Ma
- Department of Thoracic Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang 110042, People's Republic of China
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5
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Vendramini-Pittoli S, Candido-Souza RM, Quiezi RG, Zechi-Ceide RM, Kokitsu-Nakata NM, Jehee FS, Ribeiro-Bicudo LA, FitzPatrick DR, Guion-Almeida ML, Richieri-Costa A. Microphthalmia, Linear Skin Defects, Callosal Agenesis, and Cleft Palate in a Patient with Deletion at Xp22.3p22.2. J Pediatr Genet 2020; 9:258-262. [PMID: 32765930 DOI: 10.1055/s-0039-3402047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 11/07/2019] [Indexed: 01/23/2023]
Abstract
The authors describe the clinical findings observed in a Brazilian girl that are suggestive of microphthalmia and linear skin defects (MLS) also known as MIDAS syndrome (OMIM #309801). She also presented with short stature, agenesis of corpus callosum, cleft palate, enamel defects, and genitourinary anomalies, which are rarely reported within the clinical spectrum of MLS. The 11,5 Mb deletion in Xp22.3p22.2 observed in the patient includes the entire HCCS gene (responsible for the MLS phenotype) and also encompasses several other genes involved with behavioral phenotypes, craniofacial and central nervous system development such as MID1, NLGN4X, AMELX , ARHGAP6, and TBL1X. The whole clinical features of our proband possibly represents an unusual MLS syndromic phenotype caused by an Xp22.3p22.2 continuous gene deletion.
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Affiliation(s)
- Siulan Vendramini-Pittoli
- Department of Clinical Genetics, Hospital for Rehabilitation of Craniofacial Anomalies, University of São Paulo, Bauru, São Paulo, Brazil
| | - Rosana Maria Candido-Souza
- Department of Clinical Genetics, Hospital for Rehabilitation of Craniofacial Anomalies, University of São Paulo, Bauru, São Paulo, Brazil
| | - Rodrigo Gonçalves Quiezi
- Medical Research Council (MRC) Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, Edinburgh, United Kingdom
| | - Roseli Maria Zechi-Ceide
- Department of Clinical Genetics, Hospital for Rehabilitation of Craniofacial Anomalies, University of São Paulo, Bauru, São Paulo, Brazil
| | - Nancy Mizue Kokitsu-Nakata
- Department of Clinical Genetics, Hospital for Rehabilitation of Craniofacial Anomalies, University of São Paulo, Bauru, São Paulo, Brazil
| | | | | | - David R FitzPatrick
- Medical Research Council (MRC) Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, Edinburgh, United Kingdom
| | - Maria Leine Guion-Almeida
- Department of Clinical Genetics, Hospital for Rehabilitation of Craniofacial Anomalies, University of São Paulo, Bauru, São Paulo, Brazil
| | - Antonio Richieri-Costa
- Department of Clinical Genetics, Hospital for Rehabilitation of Craniofacial Anomalies, University of São Paulo, Bauru, São Paulo, Brazil
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6
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Guo W, Cai Y, Zhang H, Yang Y, Yang G, Wang X, Zhao J, Lin J, Zhu J, Li W, Lv L. Association of ARHGAP18 polymorphisms with schizophrenia in the Chinese-Han population. PLoS One 2017; 12:e0175209. [PMID: 28384650 PMCID: PMC5383423 DOI: 10.1371/journal.pone.0175209] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 03/22/2017] [Indexed: 11/23/2022] Open
Abstract
Numerous developmental genes have been linked to schizophrenia (SZ) by case-control and genome-wide association studies, suggesting that neurodevelopmental disturbances are major pathogenic mechanisms. However, no neurodevelopmental deficit has been definitively linked to SZ occurrence, likely due to disease heterogeneity and the differential effects of various gene variants across ethnicities. Hence, it is critical to examine linkages in specific ethnic populations, such as Han Chinese. The newly identified RhoGAP ARHGAP18 is likely involved in neurodevelopment through regulation of RhoA/C. Here we describe four single nucleotide polymorphisms (SNPs) in ARHGAP18 associated with SZ across a cohort of >2000 cases and controls from the Han population. Two SNPs, rs7758025 and rs9483050, displayed significant differences between case and control groups both in genotype (P = 0.0002 and P = 7.54×10−6) and allelic frequencies (P = 4.36×10−5 and P = 5.98×10−7), respectively. The AG haplotype in rs7758025−rs9385502 was strongly associated with the occurrence of SZ (P = 0.0012, OR = 0.67, 95% CI = 0.48–0.93), an association that still held following a 1000-times random permutation test (P = 0.022). In an independently collected validation cohort, rs9483050 was the SNP most strongly associated with SZ. In addition, the allelic frequencies of rs12197901 remained associated with SZ in the combined cohort (P = 0.021), although not in the validation cohort alone (P = 0.251). Collectively, our data suggest the ARHGAP18 may confer vulnerability to SZ in the Chinese Han population, providing additional evidence for the involvement of neurodevelopmental dysfunction in the pathogenesis of schizophrenia.
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Affiliation(s)
- Weiyun Guo
- College of Life Science and Technology, Xinxiang Medical University, Xinxiang, China.,Henan Key Lab of Biological Psychiatry, Xinxiang Medical University, Xinxiang, China
| | - Yaqi Cai
- Henan Key Lab of Biological Psychiatry, Xinxiang Medical University, Xinxiang, China.,Department of Psychiatry, Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, China
| | - Hongxing Zhang
- Henan Key Lab of Biological Psychiatry, Xinxiang Medical University, Xinxiang, China.,Department of Psychiatry, Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, China.,Department of Psychology, Xinxiang Medical University, Xinxiang, China
| | - Yongfeng Yang
- Henan Key Lab of Biological Psychiatry, Xinxiang Medical University, Xinxiang, China.,Department of Psychiatry, Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, China
| | - Ge Yang
- Henan Key Lab of Biological Psychiatry, Xinxiang Medical University, Xinxiang, China.,Department of Psychiatry, Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, China
| | - Xiujuan Wang
- Henan Key Lab of Biological Psychiatry, Xinxiang Medical University, Xinxiang, China.,Department of Psychiatry, Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, China
| | - Jingyuan Zhao
- Department of Psychiatry, Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, China
| | - Juntang Lin
- College of Life Science and Technology, Xinxiang Medical University, Xinxiang, China.,Henan Key Lab of Biological Psychiatry, Xinxiang Medical University, Xinxiang, China.,Institute of Anatomy I, Friedrich Schiller University Jena, Jena, Germany
| | - Jinfu Zhu
- Institute of Anatomy I, Friedrich Schiller University Jena, Jena, Germany.,Department of Psychology, Xinxiang Medical University, Xinxiang, China
| | - Wenqiang Li
- Henan Key Lab of Biological Psychiatry, Xinxiang Medical University, Xinxiang, China.,Department of Psychiatry, Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, China
| | - Luxian Lv
- Henan Key Lab of Biological Psychiatry, Xinxiang Medical University, Xinxiang, China.,Department of Psychiatry, Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, China
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7
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Hu Y, Smith CE, Cai Z, Donnelly LAJ, Yang J, Hu JCC, Simmer JP. Enamel ribbons, surface nodules, and octacalcium phosphate in C57BL/6 Amelx-/- mice and Amelx+/- lyonization. Mol Genet Genomic Med 2016; 4:641-661. [PMID: 27896287 PMCID: PMC5118209 DOI: 10.1002/mgg3.252] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 09/07/2016] [Accepted: 09/13/2016] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Amelogenin is required for normal enamel formation and is the most abundant protein in developing enamel. METHODS Amelx+/+, Amelx+/- , and Amelx-/- molars and incisors from C57BL/6 mice were characterized using RT-PCR, Western blotting, dissecting and light microscopy, immunohistochemistry (IHC), transmission electron microscopy (TEM), scanning electron microscopy (SEM), backscattered SEM (bSEM), nanohardness testing, and X-ray diffraction. RESULTS No amelogenin protein was detected by Western blot analyses of enamel extracts from Amelx-/- mice. Amelx-/- incisor enamel averaged 20.3 ± 3.3 μm in thickness, or only 1/6th that of the wild type (122.3 ± 7.9 μm). Amelx-/- incisor enamel nanohardness was 1.6 Gpa, less than half that of wild-type enamel (3.6 Gpa). Amelx+/- incisors and molars showed vertical banding patterns unique to each tooth. IHC detected no amelogenin in Amelx-/- enamel and varied levels of amelogenin in Amelx+/- incisors, which correlated positively with enamel thickness, strongly supporting lyonization as the cause of the variations in enamel thickness. TEM analyses showed characteristic mineral ribbons in Amelx+/+ and Amelx-/- enamel extending from mineralized dentin collagen to the ameloblast. The Amelx-/- enamel ribbons were not well separated by matrix and appeared to fuse together, forming plates. X-ray diffraction determined that the predominant mineral in Amelx-/- enamel is octacalcium phosphate (not calcium hydroxyapatite). Amelx-/- ameloblasts were similar to wild-type ameloblasts except no Tomes' processes extended into the thin enamel. Amelx-/- and Amelx+/- molars both showed calcified nodules on their occlusal surfaces. Histology of D5 and D11 developing molars showed nodules forming during the maturation stage. CONCLUSION Amelogenin forms a resorbable matrix that separates and supports, but does not shape early secretory-stage enamel ribbons. Amelogenin may facilitate the conversion of enamel ribbons into hydroxyapatite by inhibiting the formation of octacalcium phosphate. Amelogenin is necessary for thickening the enamel layer, which helps maintain ribbon organization and development and maintenance of the Tomes' process.
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Affiliation(s)
- Yuanyuan Hu
- Department of Biologic and Materials Sciences University of Michigan School of Dentistry 1210 Eisenhower Place Ann Arbor Michigan 48108
| | - Charles E Smith
- Department of Biologic and Materials SciencesUniversity of Michigan School of Dentistry1210Eisenhower PlaceAnn ArborMichigan48108; Facility for Electron Microscopy ResearchDepartment of Anatomy and Cell BiologyFaculty of DentistryMcGill UniversityMontrealQuebecH3A 2B2Canada
| | - Zhonghou Cai
- Advanced Photon Source Argonne National Laboratory 9700 S. Cass Ave Building 431-B005 Argonne Illinois 60439
| | - Lorenza A-J Donnelly
- Department of Biologic and Materials Sciences University of Michigan School of Dentistry 1210 Eisenhower Place Ann Arbor Michigan 48108
| | - Jie Yang
- Department of Biologic and Materials SciencesUniversity of Michigan School of Dentistry1210Eisenhower PlaceAnn ArborMichigan48108; Department of Pediatric DentistrySchool and Hospital of StomatologyPeking University22 South AvenueZhongguancun Haidian DistrictBeijing100081China
| | - Jan C-C Hu
- Department of Biologic and Materials Sciences University of Michigan School of Dentistry 1210 Eisenhower Place Ann Arbor Michigan 48108
| | - James P Simmer
- Department of Biologic and Materials Sciences University of Michigan School of Dentistry 1210 Eisenhower Place Ann Arbor Michigan 48108
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8
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Ansari M, Rainger J, Hanson IM, Williamson KA, Sharkey F, Harewood L, Sandilands A, Clayton-Smith J, Dollfus H, Bitoun P, Meire F, Fantes J, Franco B, Lorenz B, Taylor DS, Stewart F, Willoughby CE, McEntagart M, Khaw PT, Clericuzio C, Van Maldergem L, Williams D, Newbury-Ecob R, Traboulsi EI, Silva ED, Madlom MM, Goudie DR, Fleck BW, Wieczorek D, Kohlhase J, McTrusty AD, Gardiner C, Yale C, Moore AT, Russell-Eggitt I, Islam L, Lees M, Beales PL, Tuft SJ, Solano JB, Splitt M, Hertz JM, Prescott TE, Shears DJ, Nischal KK, Doco-Fenzy M, Prieur F, Temple IK, Lachlan KL, Damante G, Morrison DA, van Heyningen V, FitzPatrick DR. Genetic Analysis of 'PAX6-Negative' Individuals with Aniridia or Gillespie Syndrome. PLoS One 2016; 11:e0153757. [PMID: 27124303 PMCID: PMC4849793 DOI: 10.1371/journal.pone.0153757] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 04/04/2016] [Indexed: 12/26/2022] Open
Abstract
We report molecular genetic analysis of 42 affected individuals referred with a diagnosis of aniridia who previously screened as negative for intragenic PAX6 mutations. Of these 42, the diagnoses were 31 individuals with aniridia and 11 individuals referred with a diagnosis of Gillespie syndrome (iris hypoplasia, ataxia and mild to moderate developmental delay). Array-based comparative genomic hybridization identified six whole gene deletions: four encompassing PAX6 and two encompassing FOXC1. Six deletions with plausible cis-regulatory effects were identified: five that were 3' (telomeric) to PAX6 and one within a gene desert 5' (telomeric) to PITX2. Sequence analysis of the FOXC1 and PITX2 coding regions identified two plausibly pathogenic de novo FOXC1 missense mutations (p.Pro79Thr and p.Leu101Pro). No intragenic mutations were detected in PITX2. FISH mapping in an individual with Gillespie-like syndrome with an apparently balanced X;11 reciprocal translocation revealed disruption of a gene at each breakpoint: ARHGAP6 on the X chromosome and PHF21A on chromosome 11. In the other individuals with Gillespie syndrome no mutations were identified in either of these genes, or in HCCS which lies close to the Xp breakpoint. Disruption of PHF21A has previously been implicated in the causation of intellectual disability (but not aniridia). Plausibly causative mutations were identified in 15 out of 42 individuals (12/32 aniridia; 3/11 Gillespie syndrome). Fourteen of these mutations presented in the known aniridia genes; PAX6, FOXC1 and PITX2. The large number of individuals in the cohort with no mutation identified suggests greater locus heterogeneity may exist in both isolated and syndromic aniridia than was previously appreciated.
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Affiliation(s)
- Morad Ansari
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Jacqueline Rainger
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Isabel M. Hanson
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Kathleen A. Williamson
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Freddie Sharkey
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Louise Harewood
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Angela Sandilands
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Jill Clayton-Smith
- Faculty of Medical and Human Sciences, Manchester Centre for Genomic Medicine, Institute of Human Development, University of Manchester, Manchester Academic Health Science Centre (MAHSC), Manchester, United Kingdom
| | - Helene Dollfus
- Service de Génétique Médicale, Hôpital de Haute-Pierre, Strasbourg, France
| | - Pierre Bitoun
- Medical Genetics Departments, University Hospital Jean Verdier, Bondy, France
| | - Francoise Meire
- Department of ophthalmopediatrics, Hôpital Universitaire des Enfants Reine Fabiola, Bruxelles, Belgium
| | - Judy Fantes
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Brunella Franco
- Medical Genetics, Department of Medical Translational Sciences, Federico II University, Naples, Italy
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | - Birgit Lorenz
- Department of Ophthalmology, Justus-Liebig-University Giessen, Universitaetsklinikum Giessen and Marburg UKGM, Giessen, Germany
| | - David S. Taylor
- Institute of Child Health, University College London, UK and Great Ormond Street Hospital for Children, London, United Kingdom
| | - Fiona Stewart
- Northern Ireland Regional Genetics Service (NIRGS), Belfast City Hospital, Belfast, United Kingdom
| | - Colin E. Willoughby
- Department of Eye and Vision Science, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, United Kingdom
| | - Meriel McEntagart
- Medical Genetics Unit, St George's University of London, London, United Kingdom
| | - Peng Tee Khaw
- Moorfields Eye Hospital, London, UK and University College London, Institute of Ophthalmology, London, United Kingdom
| | - Carol Clericuzio
- Department of Pediatric Genetics, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States of America
| | | | - Denise Williams
- Clinical Genetics Unit, Birmingham Women's Hospital, Birmingham, United Kingdom
| | - Ruth Newbury-Ecob
- Department of Clinical Genetics, University Hospitals, Bristol, United Kingdom
| | - Elias I. Traboulsi
- Center for Genetic Eye Diseases, Cole Eye Institute, Cleveland Clinic Foundation, Cleveland, OH, United States of America
| | - Eduardo D. Silva
- Department Ophthalmology, University Hospital of Coimbra, Coimbra, Portugal
| | - Mukhlis M. Madlom
- Children's Hospital, Doncaster Royal Infirmary, Doncaster, United Kingdom
| | - David R. Goudie
- Human Genetics Unit, University of Dundee College of Medicine, Dentistry and Nursing, Ninewells Hospital, Dundee, United Kingdom
| | - Brian W. Fleck
- Department of Ophthalmology, Princess Alexandra Eye Pavilion, Chalmers Street, Edinburgh, United Kingdom
| | - Dagmar Wieczorek
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
- Institut für Humangenetik, Universitätsklinikum Düsseldorf, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | | | - Alice D. McTrusty
- Department of Life Sciences, Glasgow Caledonian University, Glasgow, United Kingdom
| | - Carol Gardiner
- Clinical Genetics, Southern General Hospital, Glasgow, United Kingdom
| | - Christopher Yale
- Department of Paediatrics and Child Health, Ipswich Hospital, Ipswich, United Kingdom
| | - Anthony T. Moore
- Moorfields Eye Hospital, London, UK and University College London, Institute of Ophthalmology, London, United Kingdom
| | - Isabelle Russell-Eggitt
- Institute of Child Health, University College London, UK and Great Ormond Street Hospital for Children, London, United Kingdom
| | - Lily Islam
- Institute of Child Health, University College London, UK and Great Ormond Street Hospital for Children, London, United Kingdom
| | - Melissa Lees
- North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, Great Ormond Street Hospital, London, United Kingdom
| | - Philip L. Beales
- Institute of Child Health, University College London, UK and Great Ormond Street Hospital for Children, London, United Kingdom
| | - Stephen J. Tuft
- Moorfields Eye Hospital, London, UK and University College London, Institute of Ophthalmology, London, United Kingdom
| | - Juan B. Solano
- Ruber International Hospital, Medical Genetics Unit, Mirasierra, Madrid, Spain
| | - Miranda Splitt
- Northern Genetics Service, Institute of Genetic Medicine, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, United Kingdom
| | - Jens Michael Hertz
- Department of Clinical Genetics, Odense University Hospital, Odense C, Denmark
| | - Trine E. Prescott
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Deborah J. Shears
- Department of Clinical Genetics, Churchill Hospital, Oxford University Hospitals NHS Trust, Oxford, United Kingdom
| | - Ken K. Nischal
- UPMC Eye Center, Children's Hospital of Pittsburgh of UPMC, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | | | - Fabienne Prieur
- CHU de Saint Etienne, Service de génétique médicale, Saint-Etienne, France
| | - I. Karen Temple
- Academic Unit of Genetic Medicine, Division of Human Genetics, University of Southampton, Southampton, United Kingdom
| | - Katherine L. Lachlan
- Wessex Clinical Genetics Service, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Giuseppe Damante
- Department of Medical and Biological Sciences, University of Udine, Udine, Italy
| | - Danny A. Morrison
- St. Thomas’ Hospital, Westminster Bridge Road, London, United Kingdom
| | - Veronica van Heyningen
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - David R. FitzPatrick
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
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9
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Inhibitory effects of Arhgap6 on cervical carcinoma cells. Tumour Biol 2015; 37:1411-25. [DOI: 10.1007/s13277-015-4502-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 11/24/2015] [Indexed: 12/12/2022] Open
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10
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Identification of Rho GTPase Activating Protein 6 Isoform 1 Variant as a New Molecular Marker in Human Colorectal Tumors. Pathol Oncol Res 2009; 16:319-26. [DOI: 10.1007/s12253-009-9226-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2009] [Accepted: 11/09/2009] [Indexed: 01/16/2023]
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11
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Wang X, Sutton VR, Eble T, Lewis RA, Gunaratne P, Patel A, Van den Veyver IB. A genome-wide screen for copy number alterations in Aicardi syndrome. Am J Med Genet A 2009; 149A:2113-21. [PMID: 19760649 PMCID: PMC3640635 DOI: 10.1002/ajmg.a.32976] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Aicardi syndrome is a severe neurodevelopmental disorder that affects females or rarely males with a 47,XXY karyotype. Therefore, it is thought to be caused by heterozygous defects in an essential X-linked gene or by defects in an autosomal gene with sex-limited expression. Because all reported cases are sporadic with one exception, traditional linkage analysis to identify the mutant gene is not possible, and the de novo mutation rate must be high. As an alternative approach to localize the mutant gene, we screened the DNA of 38 girls with Aicardi syndrome by high-resolution, genome-wide array comparative genomic hybridization for copy number gains and losses. We found 110 copy number variants (CNVs), 97 of which are known, presumably polymorphic, CNVs; 8 have been seen before in unrelated studies in unaffected individuals. Four previously unseen CNVs on autosomes were each inherited from a healthy parent. One subject with Aicardi syndrome had a de novo loss of X-linked copy number in a region without known genes. Detailed analysis of this and flanking regions did not reveal CNVs or mutations in annotated genes in other affected subjects. We conclude that, in this study population of 38 subjects, Aicardi syndrome is not caused by CNVs detectable with the high-resolution array platform that was used.
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Affiliation(s)
- Xiaoling Wang
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX
| | - V. Reid Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Tanya Eble
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Richard Alan Lewis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
- Department of Ophthalmology, Baylor College of Medicine, Houston, TX
- Department of Medicine, Baylor College of Medicine, Houston, TX
- Department of Pediatrics, Baylor College of Medicine, Houston, TX
| | - Preethi Gunaratne
- Department of Pathology, Baylor College of Medicine, Houston, TX
- Department of Biology and Biochemistry, University of Houston, Houston, TX
| | - Ankita Patel
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Ignatia B. Van den Veyver
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
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12
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Hobson GM, Gibson CW, Aragon M, Yuan ZA, Davis-Williams A, Banser L, Kirkham J, Brook AH. A large X-chromosomal deletion is associated with microphthalmia with linear skin defects (MLS) and amelogenesis imperfecta (XAI). Am J Med Genet A 2009; 149A:1698-705. [PMID: 19610109 PMCID: PMC2760392 DOI: 10.1002/ajmg.a.32968] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
A female patient is described with clinical symptoms of both microphthalmia with linear skin defects (MLS or MIDAS) and dental enamel defects, having an appearance compatible with X-linked amelogenesis imperfecta (XAI). Genomic DNA was purified from the patient's blood and semiquantitative multiplex PCR revealed a deletion encompassing the amelogenin gene (AMELX). Because MLS is also localized to Xp22, genomic DNA was subjected to array comparative genomic hybridization, and a large heterozygous deletion was identified. Histopathology of one primary and one permanent molar tooth showed abnormalities in the dental enamel layer, and a third tooth had unusually high microhardness measurements, possibly due to its ultrastructural anomalies as seen by scanning electron microscopy. This is the first report of a patient with both of these rare conditions, and the first description of the phenotype resulting from a deletion encompassing the entire AMELX gene. More than 50 additional genes were monosomic in this patient.
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Affiliation(s)
- Grace M. Hobson
- Nemours Biomedical Research, Alfred I. duPont Hospital for Children, Wilmington, DE, USA
| | - Carolyn W. Gibson
- Department of Anatomy and Cell Biology, University of Pennsylvania School of Dental Medicine, Philadelphia, PA, USA
| | - Melissa Aragon
- Department of Anatomy and Cell Biology, University of Pennsylvania School of Dental Medicine, Philadelphia, PA, USA
| | - Zhi-an Yuan
- Department of Anatomy and Cell Biology, University of Pennsylvania School of Dental Medicine, Philadelphia, PA, USA
| | | | - Linda Banser
- Nemours Biomedical Research, Alfred I. duPont Hospital for Children, Wilmington, DE, USA
| | | | - Alan H. Brook
- International Collaborating Centre in Oro-facial Genetics and Development, University of Liverpool, Liverpool, UK
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13
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Hopkins B, Sutton VR, Lewis RA, Van den Veyver I, Clark G. Neuroimaging aspects of Aicardi syndrome. Am J Med Genet A 2008; 146A:2871-8. [PMID: 18925666 PMCID: PMC2597151 DOI: 10.1002/ajmg.a.32537] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Aicardi syndrome is a rare neurodevelopmental disorder characterized by congenital chorioretinal lacunae, corpus callosum dysgenesis, seizures, polymicrogyria, cerebral heterotopias, intracranial cysts, and costovertebral defects. Cerebellar abnormalities have been described occasionally. Aicardi syndrome is sporadic and has been observed only in females and 47,XXY males. Therefore, it is thought to result from a mutation in an X-linked gene. Improved definition of the clinical phenotype should focus the selection of functional candidate genes for mutation analysis. Because central nervous system abnormalities are the most prominent component of the phenotype, we performed a detailed characterization of abnormalities identified on magnetic resonance neuroimaging studies from 23 girls with Aicardi syndrome, the largest cohort to undergo such review by a single group of investigators. All patients had polymicrogyria that was predominantly frontal and perisylvian and often associated with underopercularization. Periventricular nodular heterotopias, present in all patients, were more frequent than previously reported; 10 had single and 11 had multiple intracranial cysts. Posterior fossa abnormalities were also more frequent than previously described. Cerebellar abnormalities were noted in 95% of studies where they could be evaluated. As a novel finding, we noted tectal enlargement in 10 patients. Since mildly affected girls with variable callosal dysgenesis have now been reported, the constellation of frontal-dominant and perisylvian polymicrogyria, periventricular nodular heterotopias, intracranial cysts, and posterior fossa abnormalities, including tectal enlargement, should prompt consideration of the diagnosis of Aicardi syndrome. We further propose that improved characterization of the neurological phenotype will benefit the selection of candidate genes for mutation analysis.
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Affiliation(s)
- Bobbi Hopkins
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
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14
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Potet F, Petersen CI, Boutaud O, Shuai W, Stepanovic SZ, Balser JR, Kupershmidt S. Genetic screening in C. elegans identifies rho-GTPase activating protein 6 as novel HERG regulator. J Mol Cell Cardiol 2008; 46:257-67. [PMID: 19038263 DOI: 10.1016/j.yjmcc.2008.10.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2008] [Revised: 09/17/2008] [Accepted: 10/10/2008] [Indexed: 10/21/2022]
Abstract
The human ether-a-go-go related gene (HERG) constitutes the pore forming subunit of I(Kr), a K(+) current involved in repolarization of the cardiac action potential. While mutations in HERG predispose patients to cardiac arrhythmias (Long QT syndrome; LQTS), altered function of HERG regulators are undoubtedly LQTS risk factors. We have combined RNA interference with behavioral screening in Caenorhabditis elegans to detect genes that influence function of the HERG homolog, UNC-103. One such gene encodes the worm ortholog of the rho-GTPase activating protein 6 (ARHGAP6). In addition to its GAP function, ARHGAP6 induces cytoskeletal rearrangements and activates phospholipase C (PLC). Here we show that I(Kr) recorded in cells co-expressing HERG and ARHGAP6 was decreased by 43% compared to HERG alone. Biochemical measurements of cell-surface associated HERG revealed that ARHGAP6 reduced membrane expression of HERG by 35%, which correlates well with the reduction in current. In an atrial myocyte cell line, suppression of endogenous ARHGAP6 by virally transduced shRNA led to a 53% enhancement of I(Kr). ARHGAP6 effects were maintained when we introduced a dominant negative rho-GTPase, or ARHGAP6 devoid of rhoGAP function, indicating ARHGAP6 regulation of HERG is independent of rho activation. However, ARHGAP6 lost effectiveness when PLC was inhibited. We further determined that ARHGAP6 effects are mediated by a consensus SH3 binding domain within the C-terminus of HERG, although stable ARHGAP6-HERG complexes were not observed. These data link a rhoGAP-activated PLC pathway to HERG membrane expression and implicate this family of proteins as candidate genes in disorders involving HERG.
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Affiliation(s)
- Franck Potet
- Department of Anesthesiology, Vanderbilt University, Nashville, TN 37232, USA
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15
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Abstract
The Rho GTPases are implicated in almost every fundamental cellular process. They act as molecular switches that cycle between an active GTP-bound and an inactive GDP-bound state. Their slow intrinsic GTPase activity is greatly enhanced by RhoGAPs (Rho GTPase-activating proteins), thus causing their inactivation. To date, more than 70 RhoGAPs have been identified in eukaryotes, ranging from yeast to human, and based on sequence homology of their RhoGAP domain, we have grouped them into subfamilies. In the present Review, we discuss their regulation, biological functions and implication in human diseases.
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Affiliation(s)
- Joseph Tcherkezian
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada H3A 2B2
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Tcherkezian J, Triki I, Stenne R, Danek EI, Lamarche-Vane N. The human orthologue of CdGAP is a phosphoprotein and a GTPase-activating protein for Cdc42 and Rac1 but not RhoA. Biol Cell 2006; 98:445-56. [PMID: 16519628 DOI: 10.1042/bc20050101] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
BACKGROUND INFORMATION Rho GTPases regulate a wide range of cellular functions affecting both cell proliferation and cytoskeletal dynamics. They cycle between inactive GDP- and active GTP-bound states. This cycle is tightly regulated by GEFs (guanine nucleotide-exchange factors) and GAPs (GTPase-activating proteins). Mouse CdGAP (mCdc42 GTPase-activating protein) has been previously identified and characterized as a specific GAP for Rac1 and Cdc42, but not for RhoA. It consists of an N-terminal RhoGAP domain and a C-terminal proline-rich region. In addition, CdGAP-related genes are present in both vertebrates and invertebrates. We have recently reported that two predominant isoforms of CdGAP (250 and 90 kDa) exist in specific mouse tissues. RESULTS In the present study, we have identified and characterized human CdGAP (KIAA1204) which shares 76% sequence identity to the long isoform of mCdGAP (mCdGAP-l). Similar to mCdGAP, it is active in vitro and in vivo on both Cdc42 and Rac1, but not RhoA, and is phosphorylated in vivo on serine and threonine residues. In contrast with mCdGAP-l, human CdGAP interacts with ERK1/2 (extracellular-signal-regulated kinase 1/2) through a region that does not involve a DEF (docking site for ERK Phe-Xaa-Phe-Pro) domain. Also, the tissue distribution of CdGAP proteins appears to be different between human and mouse species. Interestingly, we found that CdGAP proteins cause membrane blebbing in COS-7 cells. CONCLUSIONS Our results suggest that CdGAP properties are well conserved between human and mouse species, and that CdGAP may play an unexpected role in apoptosis.
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Affiliation(s)
- Joseph Tcherkezian
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada H3A 2B2
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17
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Wimplinger I, Morleo M, Rosenberger G, Iaconis D, Orth U, Meinecke P, Lerer I, Ballabio A, Gal A, Franco B, Kutsche K. Mutations of the mitochondrial holocytochrome c-type synthase in X-linked dominant microphthalmia with linear skin defects syndrome. Am J Hum Genet 2006; 79:878-89. [PMID: 17033964 PMCID: PMC1698567 DOI: 10.1086/508474] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2006] [Accepted: 08/15/2006] [Indexed: 12/23/2022] Open
Abstract
The microphthalmia with linear skin defects syndrome (MLS, or MIDAS) is an X-linked dominant male-lethal disorder almost invariably associated with segmental monosomy of the Xp22 region. In two female patients, from two families, with MLS and a normal karyotype, we identified heterozygous de novo point mutations--a missense mutation (p.R217C) and a nonsense mutation (p.R197X)--in the HCCS gene. HCCS encodes the mitochondrial holocytochrome c-type synthase that functions as heme lyase by covalently adding the prosthetic heme group to both apocytochrome c and c(1). We investigated a third family, displaying phenotypic variability, in which the mother and two of her daughters carry an 8.6-kb submicroscopic deletion encompassing part of the HCCS gene. Functional analysis demonstrates that both mutant proteins (R217C and Delta 197-268) were unable to complement a Saccharomyces cerevisiae mutant deficient for the HCCS orthologue Cyc3p, in contrast to wild-type HCCS. Moreover, ectopically expressed HCCS wild-type and the R217C mutant protein are targeted to mitochondria in CHO-K1 cells, whereas the C-terminal-truncated Delta 197-268 mutant failed to be sorted to mitochondria. Cytochrome c, the final product of holocytochrome c-type synthase activity, is implicated in both oxidative phosphorylation (OXPHOS) and apoptosis. We hypothesize that the inability of HCCS-deficient cells to undergo cytochrome c-mediated apoptosis may push cell death toward necrosis that gives rise to severe deterioration of the affected tissues. In summary, we suggest that disturbance of both OXPHOS and the balance between apoptosis and necrosis, as well as the X-inactivation pattern, may contribute to the variable phenotype observed in patients with MLS.
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Affiliation(s)
- Isabella Wimplinger
- Institut fur Humangenetik, Universitatsklinikum Hamburg-Eppendorf, Butenfeld 42, Hamburg, Germany
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18
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Li Y, Yuan ZA, Aragon MA, Kulkarni AB, Gibson CW. Comparison of body weight and gene expression in amelogenin null and wild-type mice. Eur J Oral Sci 2006; 114 Suppl 1:190-3; discussion 201-2, 381. [PMID: 16674684 DOI: 10.1111/j.1600-0722.2006.00286.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Amelogenin (AmelX) null mice develop hypomineralized enamel lacking normal prism structure, but are healthy and fertile. Because these mice are smaller than wild-type mice prior to weaning, we undertook a detailed analysis of the weight of mice and analyzed AmelX expression in non-dental tissues. Wild-type mice had a greater average weight each day within the 3-wk period. Using reverse transcription-polymerase chain reaction (RT-PCR), products of approximately 200 bp in size were generated from wild-type teeth, brain, eye, and calvariae. DNA sequence analysis of RT-PCR products from calvariae indicated that the small amelogenin leucine-rich amelogenin peptide (LRAP), both with and without exon 4, was expressed. No products were obtained from any of the samples from the AmelX null mice. We also isolated mRNAs that included AmelX exons 8 and 9, and identified a duplication within the murine AmelX gene with 91% homology. Our results add additional support to the hypothesis that amelogenins are multifunctional proteins, with potential roles in non-ameloblasts and in non-mineralizing tissues during development. The smaller size of AmelX null mice could potentially be explained by the lack of LRAP expression in some of these tissues, leading to a delay in development.
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Affiliation(s)
- Yong Li
- Department of Anatomy and Cell Biology, University of Pennsylvania School of Dental Medicine, Philadelphia, PA 19104, USA
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19
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Crampton N, Thomson NH, Kirkham J, Gibson CW, Bonass WA. Imaging RNA polymerase-amelogenin gene complexes with single molecule resolution using atomic force microscopy. Eur J Oral Sci 2006; 114 Suppl 1:133-8; discussion 164-5, 380-1. [PMID: 16674675 DOI: 10.1111/j.1600-0722.2006.00274.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The AMELX gene encoding the enamel matrix protein, amelogenin, is located within (and in the opposite orientation to) the first intron of the ARHGAP6 gene, which encodes a GTPase-activating protein. The orientation of these two genes with respect to each other raises the possibility that they may undergo simultaneous convergent transcription during amelogenesis. The aim of this study was to use atomic force microscopy (AFM) to study a transcriptionally active amelogenin DNA template and to investigate the binding of RNA polymerase to convergently aligned promoters. Images of RNA polymerases stalled on DNA templates were obtained following incubation of the template with RNA polymerases and ribonucleotide triphosphates. A linear DNA template incorporating an intact rat amelogenin cDNA flanked by convergently aligned coliphage T7 and T3 promoters was constructed and shown to be transcriptionally active in vitro. Atomic force microscopy images of transcription complexes revealed globular structures, corresponding to single RNA polymerase molecules bound at specific locations on the DNA templates. These results indicate that AFM allows the visualization of individual RNA polymerases on DNA templates, offering a realistic approach to investigating the concept of convergent transcription of nested genes, which may lead to an understanding of whether the simultaneous expression of AMELX and ARHGAP6 is possible during the formation of tooth enamel.
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Affiliation(s)
- Neal Crampton
- School of Physics and Astronomy, University of Leeds, and Department of Oral Biology, Leeds Dental Institute, UK
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20
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Hao J, He G, Narayanan K, Zou B, Lin L, Muni T, Ramachandran A, George A. Identification of differentially expressed cDNA transcripts from a rat odontoblast cell line. Bone 2005; 37:578-88. [PMID: 16054450 DOI: 10.1016/j.bone.2005.05.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2004] [Revised: 04/08/2005] [Accepted: 05/13/2005] [Indexed: 10/25/2022]
Abstract
Odontoblasts and osteoblasts are two among the myriads of cell types present in the craniofacial complex. Both have a common ectomesenchymal origin and secrete macromolecules that are necessary for the formation of dentin and alveolar bone via matrix-mediated mechanisms. The mineralized matrices of bone and dentin differ in morphology and function but several mineral associated proteins, formerly thought to be tissue specific, have been found to be common in both tissues. To decipher the complex molecular mechanisms involved in mineralized dentin formation, the suppressive subtraction hybridization (SSH) approach has been used to identify the genes expressed by polarized odontoblasts. Employing SSH, 187 cDNA clones were identified from the subtracted cDNA library. Many of these genes have not been previously reported to be expressed by terminally differentiated odontoblasts. Genes were classified into seven groups based on the predicted function of the encoded proteins: extracellular matrix; cytoskeletal components, molecules involved in adhesion and cell-cell interaction; metabolic enzymes, transporters, ion channels; protein processing, protein transport and protein folding molecules; nuclear proteins (transcription factors, DNA processing enzymes); signaling molecules and genes of yet unknown function. Northern blot and in situ hybridization analysis performed for five putative novel genes and one new isoform of amelogenin revealed differential expression levels in the osteoblasts, ameloblasts and the odontoblasts of the developing rat molars. Some of the known genes isolated from this enriched pool were the cleavage products of dentin sialophosphoprotein (DSPP) namely, phosphophoryn (PP) and dentin sialoprotein (DSP). Interestingly amelogenin, ameloblastin and enamelin were also expressed in the odontoblasts during dentin formation.
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Affiliation(s)
- Jianjun Hao
- Department of Oral Biology (M/C 690), University of Illinois at Chicago, Chicago, IL 60612, USA
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21
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Morleo M, Pramparo T, Perone L, Gregato G, Le Caignec C, Mueller RF, Ogata T, Raas-Rothschild A, de Blois MC, Wilson LC, Zaidman G, Zuffardi O, Ballabio A, Franco B. Microphthalmia with linear skin defects (MLS) syndrome: Clinical, cytogenetic, and molecular characterization of 11 cases. Am J Med Genet A 2005; 137:190-8. [PMID: 16059943 DOI: 10.1002/ajmg.a.30864] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The microphthalmia with linear skin defects (MLS) syndrome (MIM 309801) is a severe and rare developmental disorder, which is inherited as an X-linked dominant trait with male lethality. In the vast majority of patients, this syndrome is associated with terminal deletion of the Xp22.3 region. Thirty-five cases have been described to date in the literature since the first description of the syndrome in the early 1990s. We now report on the clinical, cytogenetic, and molecular characterization of 11 patients, 7 of whom have not been described previously. Seven of these patients have chromosomal abnormalities of the short arm of the X-chromosome, which were characterized and defined by fluorescence in situ hybridization (FISH) analysis. Intriguingly, one of the patients displays an interstitial Xp22.3 deletion, which to the best of our knowledge is the first reported for this condition. Finally we report on the identification and molecular characterization of four cases with clinical features of MLS but apparently normal karyotypes, verified by FISH analysis using genomic clones spanning the MLS minimal critical region, and with genome-wide analysis using a 1 Mb resolution BAC microarray. These patients made it possible to undertake mutation screening of candidate genes and may prove critical for the identification of the gene responsible for this challenging and intriguing genetic disease.
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Affiliation(s)
- Manuela Morleo
- Telethon Institute of Genetics and Medicine (TIGEM), Via Pietro Castellino 111, 80131 Naples, Italy
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22
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Prakash SK, Gibson CW, Wright JT, Boyd C, Cormier T, Sierra R, Li Y, Abrams WR, Aragon MA, Yuan ZA, van den Veyver IB. Tooth enamel defects in mice with a deletion at the Arhgap 6/Amel X locus. Calcif Tissue Int 2005; 77:23-9. [PMID: 16007484 DOI: 10.1007/s00223-004-1213-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2004] [Accepted: 02/01/2005] [Indexed: 11/27/2022]
Abstract
The amelogenin proteins regulate enamel mineral formation in the developing tooth. The human AMELX gene, which encodes the amelogenin proteins, is located within an intron of the Arhgap 6 gene. ARHGAP 6 encodes a Rho GAP, which regulates activity of Rho A, a small G protein involved in intracellular signal transduction. Mice were generated in which the entire ARHGAP 6 gene was deleted by Cre-mediated recombination, which also removed the nested Amel X gene. Enamel from these mice appeared chalky white, and the molars showed excessive wear. The enamel layer was hypoplastic and non-prismatic, whereas other dental tissues had normal morphology. This phenotype is similar to that reported for Amel X null mice, which have a short deletion that removed the region surrounding the translation initiation site, and resembles some forms of X-linked amelogenesis imperfecta in humans. Analysis of the enamel from the Arhgap 6/Amel X-deleted mice verifies that the Amel X gene is nested within the murine Arhgap 6 gene and shows that removal of the entire Amel X gene leads to a phenotype similar to the earlier Amel X null mouse results, in which no amelogenin protein was detected. However, an unusual layer of aprismatic enamel covers the enamel surface, which may be related to the 1.1-Mb deletion, which included Arhgap 6 in these mice.
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Affiliation(s)
- S K Prakash
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
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23
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Gibson CW, Thomson NH, Abrams WR, Kirkham J. Nested genes: Biological implications and use of AFM for analysis. Gene 2005; 350:15-23. [PMID: 15780979 DOI: 10.1016/j.gene.2004.12.045] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2004] [Revised: 12/10/2004] [Accepted: 12/27/2004] [Indexed: 11/15/2022]
Abstract
A "nested" gene is located within the boundaries of a larger gene, often within an intron and in the opposite orientation. Such structures are common in bacteria and viruses, but have also been described in higher species as diverse as Drosophila and humans. Expression of nested and host genes may be simultaneously up-regulated due to use of common enhancers, or down-regulated through steric hindrance or interference caused by annealing of the complementary RNAs, leading to degradation. Methods for RNA analysis such as RT-PCR and in situ hybridization reveal the presence of specific mRNAs, but do not address regulation of expression within a single cell at a single genetic locus. Atomic force microscopy is a relatively new technology, which allows visualization of the movement of an RNA polymerase along a DNA template. The potential of this technology includes a greater molecular understanding of cellular decision making processes, leading to enhanced opportunities to intervene in disease progression through use of novel treatment modalities.
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Affiliation(s)
- Carolyn W Gibson
- University of Pennsylvania School of Dental Medicine, Department of Anatomy and Cell Biology, 240 S. 40th Street, Philadelphia, PA 19104, USA.
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24
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Abstract
The small GTPases of the Ras superfamily mediate numerous biological processes through their ability to cycle between an inactive GDP-bound and an active GTP-bound form. Among the key regulators of GTPase cycling are the GTPase-activating proteins (GAPs), which stimulate the weak intrinsic GTP-hydrolysis activity of the GTPases, thereby inactivating them. Despite the abundance of GAPs and the fact that mutations in GAP-encoding genes underlie several human diseases, these proteins have received relatively little attention. Recent studies have addressed the regulatory mechanisms that influence GAP activity. So far, findings suggest that GAP activity is regulated by several mechanisms, including protein-protein interactions, phospholipid interactions, phosphorylation, subcellular translocation and proteolytic degradation.
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Affiliation(s)
- Andre Bernards
- MGH Cancer Center and Harvard Medical School, 149 13th Street, Charlestown, MA 02129, USA
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25
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Lavelin I, Geiger B. Characterization of a novel GTPase-activating protein associated with focal adhesions and the actin cytoskeleton. J Biol Chem 2004; 280:7178-85. [PMID: 15611138 DOI: 10.1074/jbc.m411990200] [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] [Indexed: 11/06/2022] Open
Abstract
In the present study we characterize a novel RhoGAP protein (RC-GAP72) that interacts with actin stress fibers, focal adhesions, and cell-cell adherens junctions via its 185-amino acid C-terminal region. Overexpression of RC-GAP72 in fibroblasts induces cell rounding with partial or complete disruption of actin stress fibers and formation of membrane ruffles, lamellipodia, and filopodia. RC-GAP72 mutant truncated downstream of the GTPase-activating protein (GAP) domain retains the ability to stimulate membrane protrusions but fails to affect stress fiber integrity or induce cell retraction. A mutant protein consisting of the C terminus of RC-GAP72 and lacking the GAP domain does not exert any visible effect on cellular morphology. Inactivation of the GAP domain by a point mutation does not abolish the effect of RC-GAP72 on actin stress fibers but moderates its capability to induce membrane protrusions. Our data imply that the cytoskeletal localization of RC-GAP72 and its interaction with GTPases are essential for its effect on the integrity of actin stress fibers, whereas the induction of lamellipodia and filopodia depends on the activity of the GAP domain irrespective of binding to the actin cytoskeleton. We propose that RC-GAP72 affects cellular morphology by targeting activated Cdc42 and Rac1 GTPases to specific subcellular sites, triggering local morphological changes. The overall physiological functions of RC-GAP72 are presently unknown, yet our data suggest that RC-GAP72 plays a role in regulating cell morphology and cytoskeletal organization.
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Affiliation(s)
- Irena Lavelin
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
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26
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Kutsche K, Werner W, Bartsch O, von der Wense A, Meinecke P, Gal A. Microphthalmia with linear skin defects syndrome (MLS): a male with a mosaic paracentric inversion of Xp. Cytogenet Genome Res 2004; 99:297-302. [PMID: 12900578 DOI: 10.1159/000071607] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2002] [Accepted: 12/20/2002] [Indexed: 11/19/2022] Open
Abstract
The microphthalmia with linear skin defects syndrome (MLS) is an X-linked dominant disorder with male lethality. In the majority of the patients reported, the MLS syndrome is caused by segmental monosomy of the Xp22.3 region. To date, five male patients with MLS and 46,XX karyotype ("XX males") have been described. Here we report on the first male case with MLS and an XY complement. The patient showed agenesis of the corpus callosum, histiocytoid cardiomyopathy, and lactic acidosis but no microphthalmia, and carried a mosaic subtle inversion of the short arm of the X chromosome in 15% of his peripheral blood lymphocytes, 46,Y,inv(X)(p22.13 approximately 22.2p22.32 approximately 22.33)[49]/46,XY[271]. By fluorescence IN SITU hybridization (FISH), we showed that YAC 225H10 spans the breakpoint in Xp22.3. End-sequencing and database analysis revealed a YAC insert of at least 416 kb containing the genes HCCS and AMELX, and exons 2-16 of ARHGAP6. Molecular cytogenetic data suggest that the Xp22.3 inversion breakpoint is located in intron 1 of ARHGAP6, the gene encoding the Rho GTPase activating protein 6. Future molecular studies in karyotypically normal female MLS patients to detect submicroscopic rearrangements including the ARHGAP6 gene as well as mutation screening of ARHGAP6 in patients with no obvious chromosomal rearrangements will clarify the role of this gene in MLS syndrome.
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Affiliation(s)
- K Kutsche
- Institut für Humangenetik, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany.
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27
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Van den Veyver IB. Microphthalmia with linear skin defects (MLS), Aicardi, and Goltz syndromes: are they related X-linked dominant male-lethal disorders? Cytogenet Genome Res 2004; 99:289-96. [PMID: 12900577 DOI: 10.1159/000071606] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2003] [Accepted: 02/13/2003] [Indexed: 11/19/2022] Open
Abstract
Gene identification for X-linked dominant sporadic disorders is challenging because no extended families exist that can be studied by linkage analysis. Therefore, classic positional cloning approaches are not possible, and other methods have to be used to search for candidate genes. These conditions present the next challenge for disease-gene identification of Mendelian disorders. The various issues and difficulties involved, such as male lethality, X chromosome inactivation, and analysis of phenotypic similarities among different conditions are illustrated through discussion of three X-linked developmental disorders: microphthalmia with linear skin defects (MLS) syndrome, Aicardi syndrome, and Goltz syndrome (focal dermal hypoplasia).
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Affiliation(s)
- I B Van den Veyver
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX 77030, USA.
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28
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Van den Veyver IB, Panichkul PP, Antalffy BA, Sun Y, Hunter JV, Armstrong DD. Presence of filamin in the astrocytic inclusions of Aicardi syndrome. Pediatr Neurol 2004; 30:7-15. [PMID: 14738943 DOI: 10.1016/s0887-8994(03)00311-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Aicardi syndrome affects only females and has been hypothesized to be an X-linked dominant male-lethal disorder. Because no familial cases can be studied for genetic linkage analysis, the mutated gene has remained elusive. With the goal of selecting genes for mutation analysis by a functional candidate approach, a detailed pathologic analysis of two brains from deceased Aicardi syndrome patients was performed. The presence of micrencephaly, absent or hypoplastic corpus callosum, polymicrogyria, heterotopia, ventriculomegaly, intracerebral cyst, and intracytoplasmic eosinophilic inclusions was confirmed in glial fibrillary acidic protein-positive astrocytes in the cortex and heterotopias, but not in white matter. The inclusions demonstrated strong immunolabeling with antibodies to filamin and vimentin but weak labeling with antibodies to proteins S100 and microtubule-associated protein 1. These findings suggested that an underlying defect in the cytoskeleton, which involves filamin, may cause this condition. Because the filamin A gene in Xq28 is mutated in another disorder with heterotopia, familial bilateral periventricular heterotopia, mutation analysis of filamin A in Aicardi syndrome patients was pursued. No mutations were found, and the full-length protein was expressed in both brain samples. Future studies will focus on investigation of X-linked genes that may affect function of filamin or other cytoskeletal proteins.
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Affiliation(s)
- Ignatia B Van den Veyver
- Department of Obstetrics and Gynecology, Baylor College of Medicine and Texas Children's Hospital, Houston, Texas 77030, USA
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29
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Anguiano A, Yang X, Felix JK, Hoo JJ. Twin brothers with MIDAS syndrome and XX karyotype. Am J Med Genet A 2003; 119A:47-9. [PMID: 12707958 DOI: 10.1002/ajmg.a.10172] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Twin brothers with microphthalmia, facial dermal hypoplasia, sclerocornea, and supraventricular tachycardia, are reported. Their clinical features are compatible with MIDAS syndrome, a known X-linked and hemizygous male lethal condition. Their karyotypes showed an XX sex chromosome modality with a subtle Xp/Yp translocation proven by the presence of SRY gene. The pregnancy was complicated with fetal supraventricular tachycardia, which was treated with digoxin prenatally. Postnatally, both twins required treatment with adenosine, digoxin, and propanolol to remain in normal sinus rhythm. The possible involvement of the heart, only in the form of cardiomyopathy with arrhythmia is emphasized. Both twins had a selective X-inactivation of the derivative chromosome X with Xp/Yp translocation.
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Affiliation(s)
- A Anguiano
- Cytogenetics Department, Quest Diagnostics, Nichols Institute, San Juan Capistrano, California, USA
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30
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Bernards A. GAPs galore! A survey of putative Ras superfamily GTPase activating proteins in man and Drosophila. BIOCHIMICA ET BIOPHYSICA ACTA 2003; 1603:47-82. [PMID: 12618308 DOI: 10.1016/s0304-419x(02)00082-3] [Citation(s) in RCA: 154] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Typical members of the Ras superfamily of small monomeric GTP-binding proteins function as regulators of diverse processes by cycling between biologically active GTP- and inactive GDP-bound conformations. Proteins that control this cycling include guanine nucleotide exchange factors or GEFs, which activate Ras superfamily members by catalyzing GTP for GDP exchange, and GTPase activating proteins or GAPs, which accelerate the low intrinsic GTP hydrolysis rate of typical Ras superfamily members, thus causing their inactivation. Two among the latter class of proteins have been implicated in common genetic disorders associated with an increased cancer risk, neurofibromatosis-1, and tuberous sclerosis. To facilitate genetic analysis, I surveyed Drosophila and human sequence databases for genes predicting proteins related to GAPs for Ras superfamily members. Remarkably, close to 0.5% of genes in both species (173 human and 64 Drosophila genes) predict proteins related to GAPs for Arf, Rab, Ran, Rap, Ras, Rho, and Sar family GTPases. Information on these genes has been entered into a pair of relational databases, which can be used to identify evolutionary conserved proteins that are likely to serve basic biological functions, and which can be updated when definitive information on the coding potential of both genomes becomes available.
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Affiliation(s)
- André Bernards
- Massachusetts General Hospital Cancer Center, Building 149, 13th Street, Charlestown, MA 02129-2000, USA.
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31
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Rao V, Wawrousek E, Tamm ER, Zigler S. Rho GTPase inactivation impairs lens growth and integrity. J Transl Med 2002; 82:231-9. [PMID: 11850536 DOI: 10.1038/labinvest.3780415] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
To elucidate the significance of Rho GTPase signaling on lens growth and structural integrity, we have selectively inactivated Rho GTPase in the ocular lens. To achieve this tissue-specific inactivation, a transgene encoding the C3-exoenzyme from Clostridium botulinum has been expressed in mice under transcriptional control of the lens-specific alphaA-crystallin promoter. C3-exoenzyme is known to selectively inactivate all Rho GTPase isoforms by ADP-ribosylating an asparagine residue at position 41. Mice expressing the C3-exoenzyme transgene exhibited selective ocular defects, including cataract and microphthalmia. Extralenticular effects included ocular hemorrhage (blood accumulation in the anterior and posterior chambers of the eye) and abnormalities of the iris including focal attachments to lens and cornea (synechiae). C3-transgene expression was found only in the lens and not in the other ocular tissues as determined by RT-PCR analysis. Histologic examination of the eyes of C3 transgenic mice from two independent lines revealed extensive abnormalities of the lens, including defective fiber cell differentiation and elongation, ruptured posterior lens capsule, and thickened anterior lens capsule. Electron microscopic analysis of hemorrhaged C3 eyes showed abnormalities in the posterior hyaloid vessels. Collectively these data reveal the importance of Rho GTPase signaling in regulating lens growth and maintenance of lens transparency.
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Affiliation(s)
- Vasantha Rao
- Department of Ophthalmology, Duke University Medical School, Durham, North Carolina 27710-3802, USA.
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32
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Schwarz QP, Cox TC. Complementation of a yeast CYC3 deficiency identifies an X-linked mammalian activator of apocytochrome c. Genomics 2002; 79:51-7. [PMID: 11827457 DOI: 10.1006/geno.2001.6677] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We have shown by indirect immunofluorescence and enhanced green fluorescent protein fusions that a mammalian sequence exhibiting similar levels of homology to the two yeast heme lyases Cyc3p (holocytochrome c synthase; HCCS) and Cyt2p (holocytochrome c1 synthase; HCC1S) is also targeted to mitochondria. The human protein was able to complement the yeast Cyc3p (but not Cyt2p) deficiency, which indicates that it specifically activates apocytochrome c. Consistent with a respiratory role, expression of the mammalian gene was detected in all tissues, with the highest levels found in heart. Notably, the human gene HCCS is the only known gene located within the critical region for the deletion-defined disorder microphthalmia with linear skin defects (MLS). We believe the spectrum of clinical features seen in females with MLS and the paucity of male patients are consistent with significant involvement of HCCS. Toward clarification of a role for HCCS in disease, we have extensively characterized the X-linked mouse Hccs genomic locus, showing conservation in gene size and arrangement despite its location in a region that has undergone significant evolutionary rearrangement.
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Affiliation(s)
- Quenten P Schwarz
- Department of Molecular Biosciences and Centre for the Molecular Genetics of Development, University of Adelaide, North Terrace, Adelaide, South Australia, Australia 5005
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33
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Kayserili H, Cox TC, Cox LL, Basaran S, Kiliç G, Ballabio A, Yüksel-Apak M. Molecular characterisation of a new case of microphthalmia with linear skin defects (MLS). J Med Genet 2001; 38:411-7. [PMID: 11424926 PMCID: PMC1734893 DOI: 10.1136/jmg.38.6.411] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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34
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Schöneberg T, Pasel K, von Baehr V, Schulz A, Volk HD, Gudermann T, Filler G. Compound deletion of the rhoGAP C1 and V2 vasopressin receptor genes in a patient with nephrogenic diabetes insipidus. Hum Mutat 1999; 14:163-74. [PMID: 10425039 DOI: 10.1002/(sici)1098-1004(1999)14:2<163::aid-humu8>3.0.co;2-b] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The function of small GTPases is fine-tuned by a complex network of regulatory proteins such as GTPase-activating proteins. The C1 gene at Xq28 encodes a protein assumed to function as a Rho GTPase-activating protein (rhoGAP). Characterization of the molecular defect causing X-linked nephrogenic diabetes insipidus (NDI) in a patient revealed a submicroscopic deletion of a 21.5-kb genomic fragment encompassing the entire arginine-vasopressin V2 receptor gene (AVPR2) and most of the C1 gene locus. In the absence of detailed information about the physiological relevance and specific functions of rhoGAP C1, a thorough clinical and laboratory investigation of the patient was performed. Besides clearly defined NDI symptoms caused by deletion of the AVPR2 gene, no major morphological abnormalities as determined by physical examination, radiography, ultrasound, and computed tomographic scan were detected. Extensive analysis of blood chemical, enzyme, and hormone values over a period of 16 years showed no deviations from normal ranges. On the basis of our observations, the rhoGAP C1 protein is not essential for normal development in the human. Because of a predominant expression pattern of the C1 gene in hematopoietic cells, we focused on immunologic and hematologic laboratory parameters of the affected boy and the mother who was found to be heterozygous. Differential white cell counts, including lymphocyte typing, determination of lymphokines, cytokines, and immunoglobulins, as well as numerous leukocyte function tests, showed no pathological findings. Therefore, we postulate that the loss of rhoGAP C1 function is most likely compensated by other members of the GAP family.
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Affiliation(s)
- T Schöneberg
- Institut für Pharmakologie, Freie Universität Berlin, Berlin, Germany.
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35
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Prakash SK, Van den Veyver IB, Franco B, Volta M, Ballabio A, Zoghbi HY. Characterization of a novel chromo domain gene in xp22.3 with homology to Drosophila msl-3. Genomics 1999; 59:77-84. [PMID: 10395802 DOI: 10.1006/geno.1999.5844] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The Drosophila male-specific lethal (MSL) genes regulate transcription from the male X chromosome in a dosage compensation pathway that equalizes X-linked gene expression in males and females. The members of this gene family, including msl-1, msl-2, msl-3, mle, and mof, encode proteins with no sequence homology. However, mutations in each of these genes produce a similar phenotype: sex-specific lethality of male embryos caused by the failure of mutants to increase transcription from the single male X chromosome. The MSL gene products assemble into a multiprotein transcriptional activation complex at hundreds of sites along the chromatin of the X chromosome. Here we report the isolation and characterization of a human gene, named MSL3L1, that encodes a protein with significant homology to Drosophila MSL-3 in three distinct regions, including two putative chromo domains. MSL3L1 was identified by database queries with genomic sequence from BAC GS-590J6 (GenBank AC0004554) in Xp22.3 and was evaluated as a candidate gene for several developmental disorders mapping to this region, including OFD1 and SED tarda, as well as Aicardi syndrome and Goltz syndrome.
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MESH Headings
- Amino Acid Sequence
- Animals
- Base Sequence
- Binding Sites
- Chromatin/metabolism
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- Chromosome Mapping
- DNA/chemistry
- DNA/genetics
- DNA Mutational Analysis
- DNA, Complementary/chemistry
- DNA, Complementary/genetics
- DNA-Binding Proteins
- Dosage Compensation, Genetic
- Drosophila/genetics
- Drosophila Proteins
- Exons
- Female
- Gene Expression Regulation, Developmental
- Genes/genetics
- Humans
- Introns
- Male
- Molecular Sequence Data
- Nuclear Proteins/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
- Tissue Distribution
- Transcription Factors/genetics
- X Chromosome/genetics
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Affiliation(s)
- S K Prakash
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
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36
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Van den Veyver IB, Cormier TA, Jurecic V, Baldini A, Zoghbi HY. Characterization and physical mapping in human and mouse of a novel RING finger gene in Xp22. Genomics 1998; 51:251-61. [PMID: 9722948 DOI: 10.1006/geno.1998.5350] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Microphthalmia with linear skin defects (MLS) is an X-linked dominant male-lethal syndrome caused by different deletions of chromosome Xp22. Through the screening of cDNA libraries with the cross-species conserved marker 61B3-R (DXS1141), we identified a new gene at the telomeric breakpoint of the MLS critical region, which encodes a transcript containing a RING finger domain. This novel gene was independently cloned by another group and found to be mutated in Opitz syndrome. In this study we characterized the expression pattern of this gene, identified various splice variants, delineated its exon-intron boundaries, and determined that it is not mutated in either Aicardi or Goltz syndrome, two X-linked dominant conditions with phenotypes that overlap with that of MLS syndrome. This novel RING finger gene is expressed throughout mouse embryonic development, with the highest levels of expression in E7-E11. FISH and hybridization to mouse YACs confirmed human and mouse synteny in the order of this gene and other genes in the MLS critical region; however, this gene spans the boundary of the pseudoautosomal region in mouse but not in humans.
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Affiliation(s)
- I B Van den Veyver
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
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