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Heidary H, Mardi A, Mousavi SM, Khazaie G, Golab F. Hairless Gene Nonsense Mutations in Alopecia Universalis: A Case Report. IRANIAN JOURNAL OF PUBLIC HEALTH 2021; 50:1275-1279. [PMID: 34540749 PMCID: PMC8410955 DOI: 10.18502/ijph.v50i6.6429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 02/14/2021] [Indexed: 11/24/2022]
Abstract
Alopecia universalis (AU) congenital, known as generalized atrichia, is a severe form of autosomal recessive alopecia that results in complete hair loss of scalp and body. Mutations in the human hairless gene (HR) are associated with the phenotype of the disease. A consanguineous couple who had a child with the generalized atrichia sign referred to us for genetic counseling. According to the patient’s symptoms and after thorough examination and history taking, the HR gene was the candidate gene to be assessed and analyzed. For this purpose targeted primers were designed for all exons of the HR gene followed by running PCR for exons amplification. Finally, the PCR products were sequenced. Whole-gene sequence analysis revealed a nonsense homozygous mutation in exon 6 that, according to the ACMG guide, is a pathogenic variant. Sequence analysis of the exon in parents reveals that they are heterozygout for the non-sense mutation, as well.
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Affiliation(s)
- Hamed Heidary
- Department of Medical Genetics, Ali Asghar Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Ali Mardi
- Department of Medical Genetics, Ali Asghar Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Seyyed Mohammad Mousavi
- Department of Medical Genetics, Ali Asghar Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Ghasem Khazaie
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Fereshteh Golab
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran
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Gao WZ, Xue HL, Yang JC. Proteomics analysis of the secondary hair follicle cycle in Liaoning cashmere goat. Small Rumin Res 2021. [DOI: 10.1016/j.smallrumres.2021.106408] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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Brown JG. Ticks, Hair Loss, and Non-Clinging Babies: A Novel Tick-Based Hypothesis for the Evolutionary Divergence of Humans and Chimpanzees. Life (Basel) 2021; 11:435. [PMID: 34066043 PMCID: PMC8150933 DOI: 10.3390/life11050435] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 04/12/2021] [Accepted: 04/30/2021] [Indexed: 02/06/2023] Open
Abstract
Human straight-legged bipedalism represents one of the earliest events in the evolutionary split between humans (Homo spp.) and chimpanzees (Pan spp.), although its selective basis is a mystery. A carrying-related hypothesis has recently been proposed in which hair loss within the hominin lineage resulted in the inability of babies to cling to their mothers, requiring mothers to walk upright to carry their babies. However, a question remains for this model: what drove the hair loss that resulted in upright walking? Observers since Darwin have suggested that hair loss in humans may represent an evolutionary strategy for defence against ticks. The aim of this review is to propose and evaluate a novel tick-based evolutionary hypothesis wherein forest fragmentation in hominin paleoenvironments created conditions that were favourable for tick proliferation, selecting for hair loss in hominins and grooming behaviour in chimpanzees as divergent anti-tick strategies. It is argued that these divergent anti-tick strategies resulted in different methods for carrying babies, driving the locomotor divergence of humans and chimpanzees.
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Nawaz MS, Asghar R, Pervaiz N, Ali S, Hussain I, Xing P, Bao Y, Abbasi AA. Molecular evolutionary and structural analysis of human UCHL1 gene demonstrates the relevant role of intragenic epistasis in Parkinson's disease and other neurological disorders. BMC Evol Biol 2020; 20:130. [PMID: 33028204 PMCID: PMC7542113 DOI: 10.1186/s12862-020-01684-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 09/07/2020] [Indexed: 12/04/2022] Open
Abstract
Background Parkinson’s disease (PD) is the second most common neurodegenerative disorder. PD associated human UCHL1 (Ubiquitin C-terminal hydrolase L1) gene belongs to the family of deubiquitinases and is known to be highly expressed in neurons (1–2% in soluble form). Several functions of UCHL1 have been proposed including ubiquitin hydrolyze activity, ubiquitin ligase activity and stabilization of the mono-ubiquitin. Mutations in human UCHL1 gene have been associated with PD and other neurodegenerative disorders. The present study aims to decipher the sequence evolutionary pattern and structural dynamics of UCHL1. Furthermore, structural and interactional analysis of UCHL1 was performed to help elucidate the pathogenesis of PD. Results The phylogenetic tree topology suggests that the UCHL1 gene had originated in early gnathostome evolutionary history. Evolutionary rate analysis of orthologous sequences reveals strong purifying selection on UCHL1. Comparative structural analysis of UCHL1 pinpoints an important protein segment spanning amino acid residues 32 to 39 within secretion site with crucial implications in evolution and PD pathogenesis through a well known phenomenon called intragenic epistasis. Identified critical protein segment appears to play an indispensable role in protein stability, proper protein conformation as well as harboring critical interaction sites. Conclusions Conclusively, the critical protein segment of UCHL1 identified in the present study not only demonstrates the relevant role of intraprotein conformational epistasis in the pathophysiology of PD but also offers a novel therapeutic target for the disease.
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Affiliation(s)
- Muhammad Saqib Nawaz
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Razia Asghar
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Nashaiman Pervaiz
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Shahid Ali
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Irfan Hussain
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Peiqi Xing
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yiming Bao
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Amir Ali Abbasi
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan.
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Seemab S, Pervaiz N, Zehra R, Anwar S, Bao Y, Abbasi AA. Molecular evolutionary and structural analysis of familial exudative vitreoretinopathy associated FZD4 gene. BMC Evol Biol 2019; 19:72. [PMID: 30849938 PMCID: PMC6408821 DOI: 10.1186/s12862-019-1400-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 02/22/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Frizzled family members belong to G-protein coupled receptors and encode proteins accountable for cell signal transduction, cell proliferation and cell death. Members of Frizzled receptor family are considered to have critical roles in causing various forms of cancer, cardiac hypertrophy, familial exudative vitreoretinopathy (FEVR) and schizophrenia. RESULTS This study investigates the evolutionary and structural aspects of Frizzled receptors, with particular focus on FEVR associated FZD4 gene. The phylogenetic tree topology suggests the diversification of Frizzled receptors at the root of metazoans history. Moreover, comparative structural data reveals that FEVR associated missense mutations in FZD4 effect the common protein region (amino acids 495-537) through a well-known phenomenon called epistasis. This critical protein region is present at the carboxyl-terminal domain and encompasses the K-T/S-XXX-W, a PDZ binding motif and S/T-X-V PDZ recognition motif. CONCLUSION Taken together these results demonstrate that during the course of evolution, FZD4 has acquired new functions or epistasis via complex patter of gene duplications, sequence divergence and conformational remodeling. In particular, amino acids 495-537 at the C-terminus region of FZD4 protein might be crucial in its normal function and/or pathophysiology. This critical region of FZD4 protein may offer opportunities for the development of novel therapeutics approaches for human retinal vascular disease.
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Affiliation(s)
- Suman Seemab
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320 Pakistan
| | - Nashaiman Pervaiz
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320 Pakistan
| | - Rabail Zehra
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320 Pakistan
| | - Saneela Anwar
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320 Pakistan
| | - Yiming Bao
- BIG Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Amir Ali Abbasi
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320 Pakistan
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Jin M, Cao M, Chu M, Piao J, Guo X, Zhao F, Piao J. Gene Expression and Localization of LAMTOR3 in the Skin Cells of Liaoning Cashmere Goats. Anim Biotechnol 2018; 30:36-42. [PMID: 29564941 DOI: 10.1080/10495398.2018.1428198] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Liaoning cashmere goats are the most precious genetic resources in China. The function of LAMTOR3 [late endosomal/lysosomal adaptor, mitogen-activated protein kinase (MAPK), and mammalian target of rapamycin activator 3/MAPK scaffold protein 1] gene is expressed in the skin of Liaoning cashmere goats. In situ hybridization (ISH) found that LAMTOR3 is expressed in the inner root sheath (IRS) of hair follicles. During the anagen or catagen phase, the expression of LAMTOR3 is higher in secondary hair follicles than in primary hair follicles. Expression of LAMTOR3 in skin cells treated with melatonin or insulin-like growth factor-1 (IGF-1) is lower than in untreated cells. In addition, the simultaneous treatment of fibroblast growth factor 5 and melatonin decrease the expression of LAMTOR3 in skin cells. The simultaneous treatment with melatonin and 10-5 g/L IGF-1 or 10-4 g/L IGF-1 increases the expression of LAMTOR3 gene in skin cells. If Noggin expression is decreased, then LAMTOR3 expression is increased. This hypothesis suggested that LAMTOR3 influences the character of cashmere fiber, and it may regulate the development of hair follicle and cashmere growth by inducing the MAPK signaling pathway.
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Affiliation(s)
- Mei Jin
- a Faculty of Life Science, Liaoning Provincial Key Laboratory of Biotechnology and Drug Discovery , Liaoning Normal University , Dalian , China
| | - Ming Cao
- a Faculty of Life Science, Liaoning Provincial Key Laboratory of Biotechnology and Drug Discovery , Liaoning Normal University , Dalian , China
| | - Mingxing Chu
- b Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture , Institute of Animal Science, Chinese Academy of Agricultural Sciences , Beijing , China
| | - Jing'ai Piao
- a Faculty of Life Science, Liaoning Provincial Key Laboratory of Biotechnology and Drug Discovery , Liaoning Normal University , Dalian , China
| | - Xu Guo
- a Faculty of Life Science, Liaoning Provincial Key Laboratory of Biotechnology and Drug Discovery , Liaoning Normal University , Dalian , China
| | - Fengqin Zhao
- a Faculty of Life Science, Liaoning Provincial Key Laboratory of Biotechnology and Drug Discovery , Liaoning Normal University , Dalian , China
| | - Jun Piao
- a Faculty of Life Science, Liaoning Provincial Key Laboratory of Biotechnology and Drug Discovery , Liaoning Normal University , Dalian , China
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Siddiqui IJ, Pervaiz N, Abbasi AA. The Parkinson Disease gene SNCA: Evolutionary and structural insights with pathological implication. Sci Rep 2016; 6:24475. [PMID: 27080380 PMCID: PMC4832246 DOI: 10.1038/srep24475] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Accepted: 03/30/2016] [Indexed: 01/01/2023] Open
Abstract
After Alzheimer, Parkinson's disease (PD) is the second most common neurodegenerative disorder. Alpha synuclein (SNCA) is deemed as a major component of Lewy bodies, a neuropathological feature of PD. Five point mutations in SNCA have been reported so far, responsible for autosomal dominant PD. This study aims to decipher evolutionary and structural insights of SNCA by revealing its sequence and structural evolutionary patterns among sarcopterygians and its paralogous counterparts (SNCB and SNCG). Rate analysis detected strong purifying selection on entire synuclein family. Structural dynamics divulges that during the course of sarcopterygian evolutionary history, the region encompassed 32 to 58 of N-terminal domain of SNCA has acquired its critical functional significance through the epistatic influence of the lineage specific substitutions. In sum, these findings provide an evidence that the region from 32 to 58 of N-terminal lipid binding alpha helix domain of SNCA is the most critical region, not only from the evolutionary perspective but also for the stability and the proper conformation of the protein as well as crucial for the disease pathogenesis, harboring critical interaction sites.
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Affiliation(s)
- Irum Javaid Siddiqui
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Nashaiman Pervaiz
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Amir Ali Abbasi
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
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Parveen N, Masood A, Iftikhar N, Minhas BF, Minhas R, Nawaz U, Abbasi AA. Comparative genomics using teleost fish helps to systematically identify target gene bodies of functionally defined human enhancers. BMC Genomics 2013; 14:122. [PMID: 23432897 PMCID: PMC3599049 DOI: 10.1186/1471-2164-14-122] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Accepted: 02/19/2013] [Indexed: 12/03/2022] Open
Abstract
Background Human genome is enriched with thousands of conserved non-coding elements (CNEs). Recently, a medium throughput strategy was employed to analyze the ability of human CNEs to drive tissue specific expression during mouse embryogenesis. These data led to the establishment of publicly available genome wide catalog of functionally defined human enhancers. Scattering of enhancers over larger regions in vertebrate genomes seriously impede attempts to pinpoint their precise target genes. Such associations are prerequisite to explore the significance of this in vivo characterized catalog of human enhancers in development, disease and evolution. Results This study is an attempt to systematically identify the target gene-bodies for functionally defined human CNE-enhancers. For the purpose we adopted the orthology/paralogy mapping approach and compared the CNE induced reporter expression with reported endogenous expression pattern of neighboring genes. This procedure pinpointed specific target gene-bodies for the total of 192 human CNE-enhancers. This enables us to gauge the maximum genomic search space for enhancer hunting: 4 Mb of genomic sequence around the gene of interest (2 Mb on either side). Furthermore, we used human-rodent comparison for a set of 159 orthologous enhancer pairs to infer that the central nervous system (CNS) specific gene expression is closely associated with the cooperative interaction among at least eight distinct transcription factors: SOX5, HFH, SOX17, HNF3β, c-FOS, Tal1beta-E47S, MEF and FREAC. Conclusions In conclusion, the systematic wiring of cis-acting sites and their target gene bodies is an important step to unravel the role of in vivo characterized catalog of human enhancers in development, physiology and medicine.
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Affiliation(s)
- Nazia Parveen
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
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Wang J, Wang G, Zhang J. Mutations with Hair Shape Phenotypes Abnormalities—The Morphogenetic Waves and Related Diseases. ACTA ACUST UNITED AC 2013. [DOI: 10.4236/jcdsa.2013.33a1004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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