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Jiao X, Kabir F, Irum B, Khan AO, Wang Q, Li D, Khan AA, Husnain T, Akram J, Riazuddin S, Hejtmancik JF, Riazuddin SA. A Common Ancestral Mutation in CRYBB3 Identified in Multiple Consanguineous Families with Congenital Cataracts. PLoS One 2016; 11:e0157005. [PMID: 27326458 PMCID: PMC4915718 DOI: 10.1371/journal.pone.0157005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 05/22/2016] [Indexed: 11/19/2022] Open
Abstract
PURPOSE This study was performed to investigate the genetic determinants of autosomal recessive congenital cataracts in large consanguineous families. METHODS Affected individuals underwent a detailed ophthalmological examination and slit-lamp photographs of the cataractous lenses were obtained. An aliquot of blood was collected from all participating family members and genomic DNA was extracted from white blood cells. Initially, a genome-wide scan was performed with genomic DNAs of family PKCC025 followed by exclusion analysis of our familial cohort of congenital cataracts. Protein-coding exons of CRYBB1, CRYBB2, CRYBB3, and CRYBA4 were sequenced bidirectionally. A haplotype was constructed with SNPs flanking the causal mutation for affected individuals in all four families, while the probability that the four familial cases have a common founder was estimated using EM and CHM-based algorithms. The expression of Crybb3 in the developing murine lens was investigated using TaqMan assays. RESULTS The clinical and ophthalmological examinations suggested that all affected individuals had nuclear cataracts. Genome-wide linkage analysis localized the causal phenotype in family PKCC025 to chromosome 22q with statistically significant two-point logarithm of odds (LOD) scores. Subsequently, we localized three additional families, PKCC063, PKCC131, and PKCC168 to chromosome 22q. Bidirectional Sanger sequencing identified a missense variation: c.493G>C (p.Gly165Arg) in CRYBB3 that segregated with the disease phenotype in all four familial cases. This variation was not found in ethnically matched control chromosomes, the NHLBI exome variant server, or the 1000 Genomes or dbSNP databases. Interestingly, all four families harbor a unique disease haplotype that strongly suggests a common founder of the causal mutation (p<1.64E-10). We observed expression of Crybb3 in the mouse lens as early as embryonic day 15 (E15), and expression remained relatively steady throughout development. CONCLUSION Here, we report a common ancestral mutation in CRYBB3 associated with autosomal recessive congenital cataracts identified in four familial cases of Pakistani origin.
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Affiliation(s)
- Xiaodong Jiao
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, MD, 20892, United States of America
| | - Firoz Kabir
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, United States of America
| | - Bushra Irum
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, United States of America
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, 53700, Pakistan
| | - Arif O. Khan
- King Khaled Eye Specialist Hospital, Riyadh, 12329, Saudi Arabia
| | - Qiwei Wang
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, MD, 20892, United States of America
| | - David Li
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, MD, 20892, United States of America
| | - Asma A. Khan
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, 53700, Pakistan
| | - Tayyab Husnain
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, 53700, Pakistan
| | - Javed Akram
- Allama Iqbal Medical College, University of Health Sciences, Lahore, 54550, Pakistan
- National Centre for Genetic Diseases, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad, Pakistan
| | - Sheikh Riazuddin
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, 53700, Pakistan
- Allama Iqbal Medical College, University of Health Sciences, Lahore, 54550, Pakistan
- National Centre for Genetic Diseases, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad, Pakistan
| | - J. Fielding Hejtmancik
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, MD, 20892, United States of America
| | - S. Amer Riazuddin
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, United States of America
- * E-mail:
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Pinto SM, Manda SS, Kim MS, Taylor K, Selvan LDN, Balakrishnan L, Subbannayya T, Yan F, Prasad TSK, Gowda H, Lee C, Hancock WS, Pandey A. Functional annotation of proteome encoded by human chromosome 22. J Proteome Res 2014; 13:2749-60. [PMID: 24669763 PMCID: PMC4059257 DOI: 10.1021/pr401169d] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
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As
part of the chromosome-centric human proteome project (C-HPP)
initiative, we report our progress on the annotation of chromosome 22.
Chromosome 22, spanning 51 million base pairs, was the first chromosome
to be sequenced. Gene dosage alterations on this chromosome have been
shown to be associated with a number of congenital anomalies. In addition,
several rare but aggressive tumors have been associated with this
chromosome. A number of important gene families including immunoglobulin
lambda locus, Crystallin beta family, and APOBEC gene family are located
on this chromosome. On the basis of proteomic profiling of 30 histologically
normal tissues and cells using high-resolution mass spectrometry,
we show protein evidence of 367 genes on chromosome 22. Importantly,
this includes 47 proteins, which are currently annotated as “missing”
proteins. We also confirmed the translation start sites of 120 chromosome 22-encoded
proteins. Employing a comprehensive proteogenomics analysis pipeline,
we provide evidence of novel coding regions on this chromosome which
include upstream ORFs and novel exons in addition to correcting existing
gene structures. We describe tissue-wise expression of the proteins
and the distribution of gene families on this chromosome. These data
have been deposited to ProteomeXchange with the identifier PXD000561.
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Affiliation(s)
- Sneha M Pinto
- Institute of Bioinformatics, International Tech Park , Bangalore, Karnataka 560066, India
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Gao L, Qin W, Cui H, Feng G, Liu P, Gao W, Ma L, Li P, He L, Fu S. A novel locus of coralliform cataract mapped to chromosome 2p24-pter. J Hum Genet 2005; 50:305-310. [PMID: 15933805 DOI: 10.1007/s10038-005-0251-y] [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] [Received: 01/14/2005] [Accepted: 03/23/2005] [Indexed: 11/28/2022]
Abstract
Congenital cataract is a common major abnormality of the eye, which can result in significant visual impairment or blindness in childhood. In this work, we studied four generations of a Chinese family that exhibited autosomal dominant coralliform cataract but no other ocular or systemic abnormalities. Members of the family were firstly genotyped with microsatellite markers at loci associated with congenital cataract on the reported regions of chromosomes 1, 2, 3, 10, 11, 12, 13, 15, 16, 17, 20, 21, and 22, but negative LOD scores were obtained. Following exclusion of these loci, a genome-wide scan was performed, and significant evidence of linkage was obtained for marker D2S2211 (Z = 2.69, theta = 0.00). In multipoint analysis, a maximum LOD score 4.87 (theta = 0.00) was reached between markers D2S2211 and D2S2164. Haplotype data indicated a coralliform cataract disease gene in a 26-cM interval at a novel disease locus 2p24-pter between D2S297 and D2S2268. No genes related to cataract in this region have been reported so far.
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Affiliation(s)
- Linghan Gao
- Laboratory of Medical Genetics, Harbin Medical University, 194 Xuefu Road, Harbin, 150086, P.R. China
| | - Wei Qin
- Bio-X Life Science Research Center, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai, 200030, P.R. China
- Institute for Nutritional Sciences, Shanghai Institute of Biological Sciences, Chinese Academy of Sciences, 319 Yueyang Road, Shanghai, 200031, P.R. China
| | - Hao Cui
- Eye Hospital of the First affiliated Hospital, Harbin medical University, 23 Youzheng Street, Harbin, 150001, P.R. China
| | - Guoyin Feng
- Bio-X Life Science Research Center, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai, 200030, P.R. China
- Institute for Nutritional Sciences, Shanghai Institute of Biological Sciences, Chinese Academy of Sciences, 319 Yueyang Road, Shanghai, 200031, P.R. China
| | - Ping Liu
- Eye Hospital of the First affiliated Hospital, Harbin medical University, 23 Youzheng Street, Harbin, 150001, P.R. China
| | - Weiqi Gao
- Eye Hospital of the First affiliated Hospital, Harbin medical University, 23 Youzheng Street, Harbin, 150001, P.R. China
| | - Lin Ma
- Eye Hospital of the First affiliated Hospital, Harbin medical University, 23 Youzheng Street, Harbin, 150001, P.R. China
| | - Pu Li
- Laboratory of Medical Genetics, Harbin Medical University, 194 Xuefu Road, Harbin, 150086, P.R. China
| | - Lin He
- Bio-X Life Science Research Center, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai, 200030, P.R. China
- Institute for Nutritional Sciences, Shanghai Institute of Biological Sciences, Chinese Academy of Sciences, 319 Yueyang Road, Shanghai, 200031, P.R. China
| | - Songbin Fu
- Laboratory of Medical Genetics, Harbin Medical University, 194 Xuefu Road, Harbin, 150086, P.R. China.
- Bio-pharmaceutical Key Laboratory of Heilongjiang Province, 194 Xuefu Road, Harbin, 150086, P.R. China.
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Jennen DGJ, Crooijmans RPMA, Kamps B, Açar R, van der Poel JJ, Groenen MAM. Comparative map between chicken chromosome 15 and human chromosomal region 12q24 and 22q11-q12. Mamm Genome 2004; 14:629-39. [PMID: 14629113 DOI: 10.1007/s00335-003-3007-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The physical and comparative map of GGA15 was improved by the construction of 9 BAC contigs around loci previously mapped on GGA15 by linkage analysis. In total, 240 BAC clones were isolated, covering 30-35% of GGA15, and 120 STS were developed (104 STS derived from BAC end sequences and 18 STS derived within genes). Seventeen chicken orthologues of human genes located on human Chr 22q11-q12 were directly mapped within BAC contigs of GGA15. Furthermore, the partial sequences of the chicken BAC clones were compared with sequences present in the EMBL/GenBank databases and revealed matches to 26 genes, ESTs, and genomic clones located on HSA22q11-q12 and HSA12q24. These results provide a better alignment of GGA15 with the corresponding regions in human and mouse, and improve our knowledge of the evolution and dynamics of the vertebrate genome.
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Affiliation(s)
- Danyel G J Jennen
- Wageningen Institute of Animal Sciences, Animal Breeding and Genetics Group, Wageningen University, Marijkeweg 40, 6709 PG Wageningen, The Netherlands.
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Liao X, Buchberg AM, Jenkins NA, Copeland NG. Evi-5, a common site of retroviral integration in AKXD T-cell lymphomas, maps near Gfi-1 on mouse chromosome 5. J Virol 1995; 69:7132-7. [PMID: 7474133 PMCID: PMC189633 DOI: 10.1128/jvi.69.11.7132-7137.1995] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
We have identified a novel common site of retroviral integration, Evi-5, in AKXD T-cell lymphomas. All proviruses located at Evi-5 are clustered within a 7-kb genomic region and, where determined, are oriented in the same transcriptional direction. Interspecific backcross analysis localized Evi-5 to mouse chromosome 5, where it cosegregated with another common viral integration site, Gfi-1. Gfi-1 encodes a novel zinc finger transcription factor whose expression is thought to be important for interleukin-2 signaling. Physical mapping studies showed that Evi-5 is located approximately 18 kb upstream of Gfi-1, and Southern analysis showed that Gfi-1, like Evi-5, is a common integration site in AKXD T-cell tumors. With one exception, Evi-5 and Gfi-1 integrations were mutually exclusive. Ten of the tumors with Evi-5 or Gfi-1 integrations also harbored viral integrations at other common integration sites causally associated with T-cell disease. These results are consistent with the hypothesis that T-cell lymphomagenesis is a multistep disease and that viral integration at Evi-5 or Gfi-1 is causally associated with this disease process.
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Affiliation(s)
- X Liao
- Mammalian Genetics Laboratory, ABL-Basic Research Program, NCI-Frederick Cancer Research and Development Center, Maryland 21702, USA
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