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Rasool T, Ansar M, Ali I, Ali MI, Jamal A, Badshah M, Huang Z, Urynowicz M. Performance evaluation of gravity-driven bioreactor (GDB) for simultaneous treatment of black liquor and domestic wastewater. Environ Sci Pollut Res Int 2024; 31:7043-7057. [PMID: 38157168 DOI: 10.1007/s11356-023-31576-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 12/11/2023] [Indexed: 01/03/2024]
Abstract
A lab-scale gravity-driven bioreactor (GDB) was designed and constructed to evaluate the simultaneous treatment of black liquor and domestic wastewater. The GDB was operated with a mixture of black liquor and domestic wastewater at a ratio of 1:1 and maintained at an average organic loading rate of 1235 mg-COD/L-Day. The wastewater was fed to the primary sedimentation tank at a flow rate of approximately 12 mL/min and subsequently passed through serially connected anaerobic and aerobic chambers with the same flow rate. Each wastewater sample was allowed to undergo a hydraulic retention time of approximately 72 h, ensuring effective treatment. The GDB was actively operated for nine samples (W1-W9) at a weekly frequency. The entire process was conducted within the workstation's ambient temperature range of 30-35 °C to sustain microbial activity and treatment efficiency in an open environment. The performance of the GDB was evaluated in terms of various pollution indicators, including COD, BOD5, lignin removal, TDS, TSS, EC, PO43-, SO42-, microbial load (CFU/mL and MPN index), total nitrogen, and color reduction. The results showed that the GDB achieved promising treatment efficiencies: 84.5% for COD, 71.80% for BOD5, 82.8% for TDS, 100% for TSS, 74.71% for E.C., 67.25% for PO43-, 81% for SO42-, and 69.36% for TN. Additionally, about 80% reduction in lignin content and 57% color reduction were observed after the treatment. The GDB substantially reduced microbial load in CFU/mL (77.98%) and MPN (90%). This study marks the first to report on wastewater treatment from two different sources (black liquor and domestic wastewater) using a simple GDB design. Furthermore, it highlights the GDB's potential as a cost-effective, environmentally friendly, and efficient solution for wastewater treatment, with no need for supplementary chemical or physical agents and zero operational costs.
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Affiliation(s)
- Tabassum Rasool
- Department of Microbiology, Applied and Environmental Microbiology Research Laboratory, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - Muhammad Ansar
- Department of Microbiology, Applied and Environmental Microbiology Research Laboratory, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - Irfan Ali
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, 38000, Pakistan
| | - Muhammad Ishtiaq Ali
- Department of Microbiology, Applied and Environmental Microbiology Research Laboratory, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - Asif Jamal
- Department of Microbiology, Applied and Environmental Microbiology Research Laboratory, Quaid-I-Azam University, Islamabad, 45320, Pakistan.
| | - Malik Badshah
- Department of Microbiology, Applied and Environmental Microbiology Research Laboratory, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - Zaixing Huang
- Department of Civil and Architectural Engineering, Wyoming University, Laramie, WY, 82071, USA
| | - Michael Urynowicz
- Department of Civil and Architectural Engineering, Wyoming University, Laramie, WY, 82071, USA
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Malik MA, Saqib MAN, Mientjes E, Acharya A, Alam MR, Wallaard I, Schrauwen I, Bamshad MJ, Santos-Cortez RLP, Elgersma Y, Leal SM, Ansar M. A loss of function variant in AGPAT3 underlies intellectual disability and retinitis pigmentosa (IDRP) syndrome. Eur J Hum Genet 2023; 31:1447-1454. [PMID: 37821758 PMCID: PMC10689475 DOI: 10.1038/s41431-023-01475-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 08/17/2023] [Accepted: 09/27/2023] [Indexed: 10/13/2023] Open
Abstract
Intellectual disability (ID) and retinal dystrophy (RD) are the frequently found features of multiple syndromes involving additional systemic manifestations. Here, we studied a family with four members presenting severe ID and retinitis pigmentosa (RP). Using genome wide genotyping and exome sequencing, we identified a nonsense variant c.747 C > A (p.Tyr249Ter) in exon 7 of AGPAT3 which co-segregates with the disease phenotype. Western blot analysis of overexpressed WT and mutant AGPAT3 in HEK293T cells showed the absence of AGPAT3, suggesting instability of the truncated protein. Knockdown of Agpat3 in the embryonic mouse brain caused marked deficits in neuronal migration, strongly suggesting that reduced expression of AGPAT3 affects neuronal function. Altogether, our data indicates that AGPAT3 activity is essential for neuronal functioning and loss of its activity probably causes intellectual disability and retinitis pigmentosa (IDRP) syndrome.
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Affiliation(s)
- Madiha Amin Malik
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
- Department of Neuroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | - Edwin Mientjes
- Department of Neuroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Anushree Acharya
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Muhammad Rizwan Alam
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - Ilse Wallaard
- Department of Neuroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Isabelle Schrauwen
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Michael J Bamshad
- Department of Genome Sciences, University of Washington, William H. Foege Hall, 3720 15th Ave. NE, Seattle, WA, 98195, USA
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Regie Lyn P Santos-Cortez
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus (CU-AMC), 12700 E. 19th Ave, Aurora, CO, 80045, USA
| | - Ype Elgersma
- Department of Neuroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Suzanne M Leal
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Center, New York, NY, USA.
- Taub Institute for Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, USA.
| | - Muhammad Ansar
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan.
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Khan S, Umair M, Abbas S, Ali U, Zaman G, Ansar M, Wang R, Zhang X, Houlden H, Harlalka GV, Gul A. Overlapping neurological phenotypes in two extended consanguineous families with novel variants in the CNTNAP1 and ADGRG1 genes. J Gene Med 2023; 25:e3513. [PMID: 37178061 DOI: 10.1002/jgm.3513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 03/31/2023] [Accepted: 04/03/2023] [Indexed: 05/15/2023] Open
Abstract
BACKGROUND Population diversity is important and rare disease isolates can frequently reveal novel homozygous or biallelic mutations that lead to expanded clinical heterogeneity, with diverse clinical presentations. METHODS The present study describes two consanguineous families with a total of seven affected individuals suffering from a clinically similar severe syndromic neurological disorder, with abnormal development and central nervous system (CNS) and peripheral nervous system (PNS) abnormalities. Whole exome sequencing (WES) and Sanger sequencing followed by 3D protein modeling was performed to identify the disease-causing gene. RNA was extracted from the fresh blood of both families affected and healthy individuals. RESULTS The families were clinically assessed in the field in different regions of Khyber Pakhtunkhwa. Magnetic resonance imagining was obtained in the probands and blood was collected for DNA extraction and WES was performed. Sanger sequencing confirmed a homozygous, likely pathogenic mutation (GRCh38: chr17:42684199G>C; (NM_003632.3): c.333G>C);(NP_003623.1): p.(Trp111Cys) in the CNTNAP1 gene in family A, previously associated with Congenital Hypo myelinating Neuropathy 3 (CHN3; OMIM # 618186) and a novel nonsense variant in family B, (GRCh38: chr16: 57654086C>T; NC_000016.10 (NM_001370440.1): c.721C>T); (NP_001357369.1): p.(Gln241Ter) in the ADGRG1 gene previously associated with bilateral frontoparietal polymicrogyria (OMIM # 606854); both families have extended CNS and PNS clinical manifestations. In addition, 3D protein modeling was performed for the missense variant, p.(Trp111Cys), identified in the CNTNAP1, suggesting extensive secondary structure changes that might lead to improper function or downstream signaling. No RNA expression was observed in both families affected and healthy individuals hence showing that these genes are not expressed in blood. CONCLUSIONS In the present study, two novel biallelic variants in the CNTNAP1 and ADGRG1 genes in two different consanguineous families with a clinical overlap in the phenotype were identified. Thus, the clinical and mutation spectrum is expanded to provide further evidence that CNTNAP1 and ADGRG1 are very important for widespread neurological development.
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Affiliation(s)
- Shazia Khan
- Department of Biological Sciences, International Islamic University, Islamabad, Pakistan
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
- Medical Research, RILD Wellcome Wolfson Centre (Level 4), Royal Devon and Exeter NHS Foundation Trust, Exeter, Devon, UK
- Hafeez Institute of Medical Sciences, Islamabad, Pakistan
| | - Muhammad Umair
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGH), Riyadh, Saudi Arabia
- Department of Life Sciences, School of Science, University of Management and Technology (UMT), Lahore, Pakistan
| | - Safdar Abbas
- Department of Biological Science, Dartmouth College, Hanover, NH, USA
| | - Uroba Ali
- Department of Biological Sciences, International Islamic University, Islamabad, Pakistan
| | - Gohar Zaman
- Department of Computer Science, Abbottabad University of Science and Technology, Havelian, Abbottabad, Pakistan
| | - Muhammad Ansar
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Rongrong Wang
- McKusick-Zhang Center for Genetic Medicine, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Xue Zhang
- McKusick-Zhang Center for Genetic Medicine, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
- The Research Center for Medical Genomics, China Medical University, Shenyang, China
| | - Henry Houlden
- Department of Neuromuscular Disorder, UCL Institute of Neurology, London, UK
| | - Gaurav V Harlalka
- Medical Research, RILD Wellcome Wolfson Centre (Level 4), Royal Devon and Exeter NHS Foundation Trust, Exeter, Devon, UK
- Department of Pharmacology, Samarth College of Pharmacy, Deulgaon Raja, Dist. Buldana, Maharashtra, India
| | - Asma Gul
- Department of Biological Sciences, International Islamic University, Islamabad, Pakistan
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Mattioli F, Worpenberg L, Li CT, Ibrahim N, Naz S, Sharif S, Firouzabadi SG, Vosoogh S, Saraeva-Lamri R, Raymond L, Trujillo C, Guex N, Antonarakis SE, Ansar M, Darvish H, Liu RJ, Roignant JY, Reymond A. Biallelic variants in NSUN6 cause an autosomal recessive neurodevelopmental disorder. Genet Med 2023; 25:100900. [PMID: 37226891 DOI: 10.1016/j.gim.2023.100900] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 05/17/2023] [Accepted: 05/18/2023] [Indexed: 05/26/2023] Open
Abstract
PURPOSE 5-methylcytosine RNA modifications are driven by NSUN methyltransferases. Although variants in NSUN2 and NSUN3 were associated with neurodevelopmental diseases, the physiological role of NSUN6 modifications on transfer RNAs and messenger RNAs remained elusive. METHODS We combined exome sequencing of consanguineous families with functional characterization to identify a new neurodevelopmental disorder gene. RESULTS We identified 3 unrelated consanguineous families with deleterious homozygous variants in NSUN6. Two of these variants are predicted to be loss-of-function. One maps to the first exon and is predicted to lead to the absence of NSUN6 via nonsense-mediated decay, whereas we showed that the other maps to the last exon and encodes a protein that does not fold correctly. Likewise, we demonstrated that the missense variant identified in the third family has lost its enzymatic activity and is unable to bind the methyl donor S-adenosyl-L-methionine. The affected individuals present with developmental delay, intellectual disability, motor delay, and behavioral anomalies. Homozygous ablation of the NSUN6 ortholog in Drosophila led to locomotion and learning impairment. CONCLUSION Our data provide evidence that biallelic pathogenic variants in NSUN6 cause one form of autosomal recessive intellectual disability, establishing another link between RNA modification and cognition.
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Affiliation(s)
- Francesca Mattioli
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Lina Worpenberg
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Cai-Tao Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China; Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Nazia Ibrahim
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland; Department of Zoology, Lahore College for Women University, Jail Road Lahore, Pakistan
| | - Shagufta Naz
- Department of Zoology, Lahore College for Women University, Jail Road Lahore, Pakistan
| | - Saima Sharif
- Department of Zoology, Lahore College for Women University, Jail Road Lahore, Pakistan
| | - Saghar G Firouzabadi
- Neuroscience Research Center, Faculty of Medicine, Golestan University of Medical Sciences, Gorgan, Iran; Nikagene Genetic Diagnostic Laboratory, Gorgan, Golestan, Iran
| | - Shohreh Vosoogh
- Clinical Research Development Unit (CRDU), Sayad Shirazi Hospital, Golestan University of Medical Sciences, Gorgan, Iran
| | | | - Laure Raymond
- Genetics Department, Laboratoire Eurofins Biomnis, Lyon, France
| | - Carlos Trujillo
- Facultad de Medicina, Departmento de Genetica, Universidad CES, Medellin, Colombia; Genome Unit, KFMRC, Jeddah, Saudi Arabia
| | - Nicolas Guex
- Bioinformatics Competence Center, University of Lausanne, Lausanne, Switzerland
| | - Stylianos E Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical Faculty, Geneva, Switzerland; Medigenome, Swiss Institute of Genomic Medicine, Geneva, Switzerland
| | - Muhammad Ansar
- Department of Ophthalmology, University of Lausanne, Jules-Gonin Eye Hospital, Fondation Asile des Aveugles, Lausanne, Switzerland
| | - Hossein Darvish
- Neuroscience Research Center, Faculty of Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - Ru-Juan Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Jean-Yves Roignant
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland; Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Mainz, Germany.
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.
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Siddiqi S, Ain NU, Kauser M, Mukhtar Z, Ansar M, Umair M. Variants in FREM1 and trisomy 18 identified in a neonatal progeria patient. Mol Biol Rep 2023; 50:7935-7939. [PMID: 37470964 DOI: 10.1007/s11033-023-08595-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 06/14/2023] [Indexed: 07/21/2023]
Abstract
BACKGROUND Neonatal progeroid disorders are rare disorders with clinical features including low body mass index, proptosis, aged and dysmorphic facial features at the time of birth, prominent veins, sparse scalp hairs, and severe growth retardation. Very few cases have been identified with an unknown genetic cause. Here, we report clinical and genetic findings of a proband with hallmark features of neonatal progeria. METHODS Microarray comparative genomic hybridization, whole exome sequencing (WES) and Sanger sequencing were performed using standard methods. RESULTS Array combined genome hybridization data revealed trisomy 18 in the proband (II-1), and WES data identified novel compound heterozygous variants (c.247 C > T; p.H83Y and c.14769868InsA) in the FREM1 gene. CONCLUSION We report a novel complex case of neonatal progeria with atrial septal defects, trisomy 18 without typical features of Edward syndrome. The phenotype of the patient was more consistent with neonatal progeria, thus we speculate it to be caused by the FREM1 variants.
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Affiliation(s)
- Saima Siddiqi
- Institute of Biomedical and Genetic Engineering (IBGE), Islamabad, Pakistan.
| | - Noor Ul Ain
- Institute of Biomedical and Genetic Engineering (IBGE), Islamabad, Pakistan
| | - Mehran Kauser
- Institute of Biomedical and Genetic Engineering (IBGE), Islamabad, Pakistan
- Department of Animal Sciences/MLT, Faculty of life sciences, Karakoram International University (KIU), Gilgit, GB, Pakistan
| | - Zahra Mukhtar
- Institute of Biomedical and Genetic Engineering (IBGE), Islamabad, Pakistan
- PMAS arid Agriculture University, Rawalpindi, Pakistan
| | - Muhammad Ansar
- Laboratory of Genetic medicine and Development, University of Geneva, Geneva, Switzerland
| | - Muhammad Umair
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), Ministry of National Guard Health Affairs (MNGH), King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
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Montillot C, Skutunova E, Ayushma, Dubied M, Lahmar A, Nguyen S, Peerally B, Prin F, Duffourd Y, Thauvin-Robinet C, Duplomb L, Wang H, Ansar M, Faivre L, Navarro N, Minocha S, Collins SC, Yalcin B. Characterization of Vps13b-mutant mice reveals neuroanatomical and behavioral phenotypes with females less affected. Neurobiol Dis 2023; 185:106259. [PMID: 37573958 DOI: 10.1016/j.nbd.2023.106259] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/26/2023] [Accepted: 08/11/2023] [Indexed: 08/15/2023] Open
Abstract
The vacuolar protein sorting-associated protein 13B (VPS13B) is a large and highly conserved protein. Disruption of VPS13B causes the autosomal recessive Cohen syndrome, a rare disorder characterized by microcephaly and intellectual disability among other features, including developmental delay, hypotonia, and friendly-personality. However, the underlying mechanisms by which VPS13B disruption leads to brain dysfunction still remain unexplained. To gain insights into the neuropathogenesis of Cohen syndrome, we systematically characterized brain changes in Vps13b-mutant mice and compared murine findings to 235 previously published and 17 new patients diagnosed with VPS13B-related Cohen syndrome. We showed that Vps13b is differentially expressed across brain regions with the highest expression in the cerebellum, the hippocampus and the cortex with postnatal peak. Half of the Vps13b-/- mice die during the first week of life. The remaining mice have a normal lifespan and display the core phenotypes of the human disease, including microcephaly, growth delay, hypotonia, altered memory, and enhanced sociability. Systematic 2D and 3D brain histo-morphological analyses reveal specific structural changes in the brain starting after birth. The dentate gyrus is the brain region with the most prominent reduction in size, while the motor cortex is specifically thinner in layer VI. The fornix, the fasciculus retroflexus, and the cingulate cortex remain unaffected. Interestingly, these neuroanatomical changes implicate an increase of neuronal death during infantile stages with no progression in adulthood suggesting that VPS13B promotes neuronal survival early in life. Importantly, whilst both sexes were affected, some neuroanatomical and behavioral phenotypes were less pronounced or even absent in females. We evaluate sex differences in Cohen patients and conclude that females are less affected both in mice and patients. Our findings provide new insights about the neurobiology of VPS13B and highlight previously unreported brain phenotypes while defining Cohen syndrome as a likely new entity of non-progressive infantile neurodegeneration.
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Affiliation(s)
- Charlotte Montillot
- Université de Bourgogne, 21000 Dijon, France; Inserm Unit 1231, 21000 Dijon, France
| | - Emilia Skutunova
- Université de Bourgogne, 21000 Dijon, France; Inserm Unit 1231, 21000 Dijon, France
| | - Ayushma
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi (IITD), Hauz Khas, New Delhi 110016, India
| | - Morgane Dubied
- Biogéosciences, UMR 6282 CNRS, EPHE, Université de Bourgogne, 21000 Dijon, France
| | - Adam Lahmar
- Université de Bourgogne, 21000 Dijon, France; Inserm Unit 1231, 21000 Dijon, France
| | - Sylvie Nguyen
- Université de Bourgogne, 21000 Dijon, France; Inserm Unit 1231, 21000 Dijon, France
| | - Benazir Peerally
- Université de Bourgogne, 21000 Dijon, France; Inserm Unit 1231, 21000 Dijon, France
| | - Fabrice Prin
- Crick Advanced Light Microscopy Facility, The Francis Crick Institute, London NW1 1AT, UK
| | - Yannis Duffourd
- Université de Bourgogne, 21000 Dijon, France; Inserm Unit 1231, 21000 Dijon, France; Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, Dijon University Hospital, 21000 Dijon, France
| | - Christel Thauvin-Robinet
- Université de Bourgogne, 21000 Dijon, France; Inserm Unit 1231, 21000 Dijon, France; Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, Dijon University Hospital, 21000 Dijon, France; Reference Center for Rare Diseases "Déficiences intellectuelles de causes rares", Dijon University Hospital, 21000 Dijon, France
| | - Laurence Duplomb
- Université de Bourgogne, 21000 Dijon, France; Inserm Unit 1231, 21000 Dijon, France
| | - Heng Wang
- DDC Clinic for Special Needs Children, Middlefield, OH 44062, USA
| | - Muhammad Ansar
- Jules Gonin Eye Hospital, University of Lausanne, CH-1015 Lausanne, Switzerland; Advanced Molecular Genetics and Genomics Disease Research and Treatment Centre, Dow University of Health Sciences, Karachi, Pakistan
| | - Laurence Faivre
- Université de Bourgogne, 21000 Dijon, France; Inserm Unit 1231, 21000 Dijon, France; Reference Center for Rare Diseases "Anomalies du Développement et syndromes malformatifs", Dijon University Hospital, 21000 Dijon, France
| | - Nicolas Navarro
- Biogéosciences, UMR 6282 CNRS, EPHE, Université de Bourgogne, 21000 Dijon, France; EPHE, PSL University, Paris 75014, France
| | - Shilpi Minocha
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi (IITD), Hauz Khas, New Delhi 110016, India
| | - Stephan C Collins
- Université de Bourgogne, 21000 Dijon, France; Inserm Unit 1231, 21000 Dijon, France
| | - Binnaz Yalcin
- Université de Bourgogne, 21000 Dijon, France; Inserm Unit 1231, 21000 Dijon, France.
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Basharat R, Rodenburg K, Rodríguez-Hidalgo M, Jarral A, Ullah E, Corominas J, Gilissen C, Zehra ST, Hameed U, Ansar M, de Bruijn SE. Combined Single Gene Testing and Genome Sequencing as an Effective Diagnostic Approach for Anophthalmia and Microphthalmia Patients. Genes (Basel) 2023; 14:1573. [PMID: 37628625 PMCID: PMC10454697 DOI: 10.3390/genes14081573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 07/28/2023] [Accepted: 07/29/2023] [Indexed: 08/27/2023] Open
Abstract
Anophthalmia and microphthalmia (A/M) are among the most severe congenital developmental eye disorders. Despite the advancements in genome screening technologies, more than half of A/M patients do not receive a molecular diagnosis. We included seven consanguineous families affected with A/M from Pakistani cohort and an unknown molecular basis. Single gene testing of FOXE3 was performed, followed by genome sequencing for unsolved probands in order to establish a genetic diagnosis for these families. All seven families were provided with a genetic diagnosis. The identified variants were all homozygous, classified as (likely) pathogenic and present in an A/M-associated gene. Targeted FOXE3 sequencing revealed two previously reported pathogenic FOXE3 variants in four families. In the remaining families, genome sequencing revealed a known pathogenic PXDN variant, a novel 13bp deletion in VSX2, and one novel deep intronic splice variant in PXDN. An in vitro splice assay was performed for the PXDN splice variant which revealed a severe splicing defect. Our study confirmed the utility of genome sequencing as a diagnostic tool for A/M-affected individuals. Furthermore, the identification of a novel deep intronic pathogenic variant in PXDN highlights the role of non-coding variants in A/M-disorders and the value of genome sequencing for the identification of this type of variants.
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Affiliation(s)
- Rabia Basharat
- Department of Biochemistry, Quaid-i-Azam University, Islamabad 45320, Pakistan
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
| | - Kim Rodenburg
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
| | - María Rodríguez-Hidalgo
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
- Department of Neuroscience, Biodonostia Health Research Institute, 20014 Donostia-San Sebastián, Spain
| | - Afeefa Jarral
- Department of Biotechnology, Mirpur University of Science and Technology (MUST), Mirpur 10250, AJK, Pakistan
| | - Ehsan Ullah
- Department of Biochemistry, Quaid-i-Azam University, Islamabad 45320, Pakistan
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jordi Corominas
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
| | - Syeda Tatheer Zehra
- Department of Biochemistry, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Usman Hameed
- Department of Biochemistry, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Muhammad Ansar
- Department of Biochemistry, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Suzanne E. de Bruijn
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
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Ullah M, Rehman AU, Folcher M, Ullah A, Usman F, Rashid A, Khan B, Quinodoz M, Ansar M, Rivolta C. A Novel Intronic Deletion in PDE6B Causes Autosomal Recessive Retinitis Pigmentosa by Interfering with RNA Splicing. Ophthalmic Res 2023; 66:878-884. [PMID: 37094557 DOI: 10.1159/000530800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 04/17/2023] [Indexed: 04/26/2023]
Abstract
INTRODUCTION Retinitis pigmentosa (RP) is a rare degenerative retinal disease caused by mutations in approximately seventy genes. Currently, despite the availability of large-scale DNA sequencing technologies, ∼30-40% of patients still cannot be diagnosed at the molecular level. In this study, we investigated a novel intronic deletion of PDE6B, encoding the beta subunit of phosphodiesterase 6 in association with recessive RP. METHODS Three unrelated consanguineous families were recruited from the northwestern part of Pakistan. Whole exome sequencing was performed for the proband of each family, and the data were analyzed according to an in-house computer pipeline. Relevant DNA variants in all available members of these families were assessed through Sanger sequencing. A minigene-based splicing assay was also performed. RESULTS The clinical phenotype for all patients was compatible with rod cone degeneration, with the onset during childhood. Whole exome sequencing revealed a homozygous 18 bp intronic deletion (NM_000283.3:c.1921-20_1921-3del) in PDE6B, which co-segregated with disease in 10 affected individuals. In vitro splicing tests showed that this deletion causes aberrant RNA splicing of the gene, leading to the in-frame deletion of 6 codons and, likely, to disease. CONCLUSION Our findings further expand the mutational spectrum of the PDE6B gene.
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Affiliation(s)
- Mukhtar Ullah
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Atta Ur Rehman
- Department of Zoology, Faculty of Biological and Health Sciences, Hazara University Mansehra, Mansehra, Pakistan
| | - Marc Folcher
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Adnan Ullah
- Department of Zoology, Islamia College Peshawar, Peshawar, Pakistan
| | - Faisal Usman
- Department of Biotechnology and Genetic Engineering, Faculty of Biological and Health Sciences, Hazara University Mansehra, Mansehra, Pakistan
| | - Abdur Rashid
- Department of Higher Education, Archives and Libraries Peshawar, Peshawar, Pakistan
| | - Bilal Khan
- Medical Teaching Institution Khyber Teaching Hospital Peshawar, Peshawar, Pakistan
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Muhammad Ansar
- Department of Ophthalmology, Jules Gonin Eye Hospital, Fondation Asile Des Aveugles, University of Lausanne, Lausanne, Switzerland
- Advanced Molecular Genetics and Genomics Disease Research and Treatment Centre, Dow University of Health Sciences, Karachi, Pakistan
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
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9
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Mao K, Borel C, Ansar M, Jolly A, Makrythanasis P, Froehlich C, Iwaszkiewicz J, Wang B, Xu X, Li Q, Blanc X, Zhu H, Chen Q, Jin F, Ankamreddy H, Singh S, Zhang H, Wang X, Chen P, Ranza E, Paracha SA, Shah SF, Guida V, Piceci-Sparascio F, Melis D, Dallapiccola B, Digilio MC, Novelli A, Magliozzi M, Fadda MT, Streff H, Machol K, Lewis RA, Zoete V, Squeo GM, Prontera P, Mancano G, Gori G, Mariani M, Selicorni A, Psoni S, Fryssira H, Douzgou S, Marlin S, Biskup S, De Luca A, Merla G, Zhao S, Cox TC, Groves AK, Lupski JR, Zhang Q, Zhang YB, Antonarakis SE. FOXI3 pathogenic variants cause one form of craniofacial microsomia. Nat Commun 2023; 14:2026. [PMID: 37041148 PMCID: PMC10090152 DOI: 10.1038/s41467-023-37703-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 03/28/2023] [Indexed: 04/13/2023] Open
Abstract
Craniofacial microsomia (CFM; also known as Goldenhar syndrome), is a craniofacial developmental disorder of variable expressivity and severity with a recognizable set of abnormalities. These birth defects are associated with structures derived from the first and second pharyngeal arches, can occur unilaterally and include ear dysplasia, microtia, preauricular tags and pits, facial asymmetry and other malformations. The inheritance pattern is controversial, and the molecular etiology of this syndrome is largely unknown. A total of 670 patients belonging to unrelated pedigrees with European and Chinese ancestry with CFM, are investigated. We identify 18 likely pathogenic variants in 21 probands (3.1%) in FOXI3. Biochemical experiments on transcriptional activity and subcellular localization of the likely pathogenic FOXI3 variants, and knock-in mouse studies strongly support the involvement of FOXI3 in CFM. Our findings indicate autosomal dominant inheritance with reduced penetrance, and/or autosomal recessive inheritance. The phenotypic expression of the FOXI3 variants is variable. The penetrance of the likely pathogenic variants in the seemingly dominant form is reduced, since a considerable number of such variants in affected individuals were inherited from non-affected parents. Here we provide suggestive evidence that common variation in the FOXI3 allele in trans with the pathogenic variant could modify the phenotypic severity and accounts for the incomplete penetrance.
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Affiliation(s)
- Ke Mao
- School of Engineering Medicine, Beihang University, Beijing, 100191, China
| | - Christelle Borel
- Department of Genetic Medicine and Development, University of Geneva Medical Faculty, Geneva, 1211, Switzerland
| | - Muhammad Ansar
- Department of Genetic Medicine and Development, University of Geneva Medical Faculty, Geneva, 1211, Switzerland
- Jules-Gonin Eye Hospital, Department of Ophthalmology, University of Lausanne, 1004, Lausanne, Switzerland
| | - Angad Jolly
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Periklis Makrythanasis
- Department of Genetic Medicine and Development, University of Geneva Medical Faculty, Geneva, 1211, Switzerland
- Laboratory of Medical Genetics, Medical School, University of Athens, Athens, Greece
- Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | | | - Justyna Iwaszkiewicz
- Molecular Modeling Group, Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland
| | - Bingqing Wang
- Plastic Surgery Hospital, Chinese Academy of Medical Sciences, Beijing, 100144, China
| | - Xiaopeng Xu
- School of Engineering Medicine, Beihang University, Beijing, 100191, China
- Key Laboratory of Big Data-Based Precision Medicine (Beihang University), Ministry of Industry and Information Technology, Beijing, China
| | - Qiang Li
- Department of Plastic Surgery, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221000, China
| | - Xavier Blanc
- Medigenome, Swiss Institute of Genomic Medicine, 1207, Geneva, Switzerland
| | - Hao Zhu
- School of Engineering Medicine, Beihang University, Beijing, 100191, China
| | - Qi Chen
- Plastic Surgery Hospital, Chinese Academy of Medical Sciences, Beijing, 100144, China
| | - Fujun Jin
- School of Engineering Medicine, Beihang University, Beijing, 100191, China
- Key Laboratory of Big Data-Based Precision Medicine (Beihang University), Ministry of Industry and Information Technology, Beijing, China
| | - Harinarayana Ankamreddy
- Department of Biotechnology, School of Bioengineering, SRMIST, Kattankulathur, Tamilnadu, 603203, India
| | - Sunita Singh
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Hongyuan Zhang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Xiaogang Wang
- School of Engineering Medicine, Beihang University, Beijing, 100191, China
- Key Laboratory of Big Data-Based Precision Medicine (Beihang University), Ministry of Industry and Information Technology, Beijing, China
| | - Peiwei Chen
- Department of Otolaryngology-Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Emmanuelle Ranza
- Medigenome, Swiss Institute of Genomic Medicine, 1207, Geneva, Switzerland
| | - Sohail Aziz Paracha
- Anatomy Department, Khyber Medical University Institute of Medical Sciences (KIMS), Kohat, Pakistan
| | - Syed Fahim Shah
- Department of Medicine, KMU Institute of Medical Sciences (KIMS), DHQ Hospital KDA, Kohat, Pakistan
| | - Valentina Guida
- Medical Genetics Division, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | | | - Daniela Melis
- Department of Medicine, Surgery, and Dentistry, Università University degli of Studi di Salerno, Salerno, Italy
| | - Bruno Dallapiccola
- Medical Genetics and Rare Disease Research Division, Pediatric Cardiology, Medical Genetics Laboratory, Neuropsychiatry, Scientific Rectorate, Bambino Gesù Children Hospital, IRCCS, Rome, Italy
| | | | - Antonio Novelli
- Sezione di Genetica Medica, Ospedale 'Bambino Gesù', Rome, Italy
| | - Monia Magliozzi
- Sezione di Genetica Medica, Ospedale 'Bambino Gesù', Rome, Italy
| | - Maria Teresa Fadda
- Department of Maxillo-Facial Surgery, Policlinico Umberto I, Rome, Italy
| | - Haley Streff
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Keren Machol
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Richard A Lewis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Vincent Zoete
- Molecular Modeling Group, Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland
- Department of Fundamental Oncology, Ludwig Institute for Cancer Research, Lausanne University, Epalinges, 1066, Switzerland
| | - Gabriella Maria Squeo
- Laboratory of Regulatory & Functional Genomics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Paolo Prontera
- Medical Genetics Unit, Hospital Santa Maria della Misericordia, Perugia, Italy
| | - Giorgia Mancano
- Medical Genetics Unit, University of Perugia Hospital SM della Misericordia, Perugia, Italy
| | - Giulia Gori
- Medical Genetics Unit, Meyer Children's University Hospital, Florence, Italy
| | - Milena Mariani
- Pediatric Department, ASST Lariana, Santa Anna General Hospital, Como, Italy
| | - Angelo Selicorni
- Pediatric Department, ASST Lariana, Santa Anna General Hospital, Como, Italy
| | - Stavroula Psoni
- Laboratory of Medical Genetics, Medical School, University of Athens, Athens, Greece
| | - Helen Fryssira
- Laboratory of Medical Genetics, Medical School, University of Athens, Athens, Greece
| | - Sofia Douzgou
- Division of Evolution, Infection and Genomics, School of Biological Sciences, University of Manchester, Manchester, UK
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Sandrine Marlin
- Centre de Référence Surdités Génétiques, Hôpital Necker, Institut Imagine, Paris, France
| | - Saskia Biskup
- CeGaT GmbH and Praxis für Humangenetik Tuebingen, Tuebingen, 72076, Germany
| | - Alessandro De Luca
- Medical Genetics Division, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Giuseppe Merla
- Laboratory of Regulatory & Functional Genomics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S. Pansini 5, 80131, Naples, Italy
| | - Shouqin Zhao
- Department of Otolaryngology-Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Timothy C Cox
- Departments of Oral & Craniofacial Sciences and Pediatrics, University of Missouri-Kansas City, Kansas City, MO, 64108, USA
| | - Andrew K Groves
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Qingguo Zhang
- Plastic Surgery Hospital, Chinese Academy of Medical Sciences, Beijing, 100144, China.
| | - Yong-Biao Zhang
- School of Engineering Medicine, Beihang University, Beijing, 100191, China.
- Key Laboratory of Big Data-Based Precision Medicine (Beihang University), Ministry of Industry and Information Technology, Beijing, China.
| | - Stylianos E Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical Faculty, Geneva, 1211, Switzerland.
- Medigenome, Swiss Institute of Genomic Medicine, 1207, Geneva, Switzerland.
- iGE3 Institute of Genetics and Genomes in Geneva, Geneva, Switzerland.
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10
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Tofilo M, Voronova N, Nigmatullina L, Kuznetsova E, Timonina V, Efimenko B, Turgunkhujaev O, Avdeichik S, Ansar M, Popadin K, Kirillova A, Mazunin I. Live Birth of a Healthy Child in a Couple with Identical mtDNA Carrying a Pathogenic c.471_477delTTTAAAAinsG Variant in the MOCS2 Gene. Genes (Basel) 2023; 14:genes14030720. [PMID: 36980992 PMCID: PMC10048300 DOI: 10.3390/genes14030720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 03/04/2023] [Accepted: 03/13/2023] [Indexed: 03/18/2023] Open
Abstract
Molybdenum cofactor deficiency type B (MOCODB; #252160) is an autosomal recessive metabolic disorder that has only been described in 37 affected patients. In this report, we describe the presence of an in-frame homozygous variant (c.471_477delTTTAAAAinsG) in the MOCS2 gene in an affected child, diagnosed with Ohtahara syndrome according to the clinical manifestations. The analysis of the three-dimensional structure of the protein and the amino acid substitutions suggested the pathogenicity of this mutation. To prevent transmitting this mutation to the next generation, we used preimplantation genetic testing for the monogenic disorders (PGT-M) protocol to select MOCS2 gene mutant-free embryos for transfer in an in vitro fertilization (IVF) program. As a result, a healthy child was born. Interestingly, both parents of the proband shared an identical mitochondrial (mt) DNA control region, assuming their close relationship and thus suggesting that both copies of the nuclear rare variant c.471_477delTTTAAAAinsG may have been transmitted from the same female ancestor. Our estimation of the a priori probability of meeting individuals with the same mtDNA haplotype confirms the assumption of a possible distant maternal relationship among the proband’s direct relatives.
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Affiliation(s)
- Maria Tofilo
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
- Medical Genomics, 170100 Tver, Russia
| | - Natalia Voronova
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
| | - Leila Nigmatullina
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
- Medical Genomics, 170100 Tver, Russia
- Fomin Clinics, 119192 Moscow, Russia
| | | | - Valeria Timonina
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Bogdan Efimenko
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, 236041 Kaliningrad, Russia
| | - Oybek Turgunkhujaev
- Neurology Department, Semeynaya Clinic, 121059 Moscow, Russia
- A.I. Burnazyan Federal Medical and Biophysical Center, 123098 Moscow, Russia
| | - Svetlana Avdeichik
- Medical Genomics, 170100 Tver, Russia
- Fomin Clinics, 119192 Moscow, Russia
| | - Muhammad Ansar
- Department of Ophthalmology, Jules Gonin Eye Hospital, Fondation Asile Des Aveugles, University of Lausanne, 1015 Lausanne, Switzerland
- Advanced Molecular Genetics and Genomics Disease Research and Treatment Centre, Dow University of Health Sciences, Karachi 74200, Pakistan
| | - Konstantin Popadin
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, 236041 Kaliningrad, Russia
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Anastasia Kirillova
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
- Fomin Clinics, 119192 Moscow, Russia
- Correspondence: (A.K.); (I.M.)
| | - Ilya Mazunin
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
- Correspondence: (A.K.); (I.M.)
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11
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Ahmed J, Qadir G, Ansar M, Wattoo FM, Javed T, Ali B, Marc RA, Rahimi M. Shattering and yield expression of sesame (Sesamum indicum L) genotypes influenced by paclobutrazol concentration under rainfed conditions of Pothwar. BMC Plant Biol 2023; 23:137. [PMID: 36907856 PMCID: PMC10009968 DOI: 10.1186/s12870-023-04145-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 02/28/2023] [Indexed: 06/18/2023]
Abstract
Seed shattering is a critical challenge that significantly reduces sesame production by 50%. These shattering losses can be reduced by selecting shattering resistant genotypes or by incorporating modern agronomic management such as paclobutrazol, which can boost productivity and prevent seed shattering in sesame. Two-years of field trials were conducted to examine the effect of sesame genotypes, environment, and paclobutrazol (PBZ) concentrations. Twelve sesame genotypes were used in a four-way factorial RCBD with three replications and five PBZ concentrations (T0 = Control; T1 = 150; T2 = 300; T3 = 450; and T4 = 600 mg L- 1) under rainfed conditions of Pothwar. The findings revealed significant variations in the major effects of all examined variables (genotypes, locations, years, and PBZ levels). Sesame genotypes PI-154304 and PI-175907 had the highest plant height, number of capsule plant- 1, seed capsule- 1, 1000 seed weight, biological yield, and seed yield, while also having the lowest seed losses and shattering percentage. Regarding environments, NARC-Islamabad generated the highest plant height, number of capsule plant- 1, shattering percentage, and biological yield; however, the URF-Koont produced the highest seed yield with the lowest shattering percentage. Additionally, plant height, capsules plant- 1, and biological yield were higher in 2021, while seed capsule- 1, 1000 seed weight, seed losses, shattering percentage, and seed yield were higher in 2020. PBZ concentration affected all measured parameters; plant height and number of seed capsule- 1 decreased with increasing PBZ concentrations. 450 mg L- 1 PBZ concentration generated the highest biomass, number of capsules plant- 1, and seed yield. At the same time, PBZ concentration 600 mg L- 1 generated the smallest plant, the lowest seed capsules- 1, the greatest thousand seed weight, and the lowest shattering percentage. The study concluded that paclobutrazol could dramatically reduce shattering percentage and shattering losses while increasing economic returns through better productivity. Based on the findings, the genotypes PI-154304 and PI-175907 with paclobutrazol level 450 mgL- 1 may be suggested for cultivation in Pothwar farming community under rainfed conditions, as they showed promising shattering resistance as well as enhanced growth and yield.
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Affiliation(s)
- Jahangir Ahmed
- Department of Agronomy, PMAS – Arid Agriculture University Rawalpindi, Rawalpindi, 46300 Pakistan
| | - Ghulam Qadir
- Department of Agronomy, PMAS – Arid Agriculture University Rawalpindi, Rawalpindi, 46300 Pakistan
| | - Muhammad Ansar
- Department of Agronomy, PMAS – Arid Agriculture University Rawalpindi, Rawalpindi, 46300 Pakistan
| | - Fahad Masoud Wattoo
- Department of Plant Breeding & Genetics, PMAS – Arid Agriculture University Rawalpindi, Rawalpindi, 46300 Pakistan
| | - Talha Javed
- Department of Agronomy, University of Agriculture, Faisalabad, 38040 Pakistan
| | - Baber Ali
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320 Pakistan
| | - Romina Alina Marc
- Food Engineering Department, Faculty of Food Science and Technology, University of Agricultural Science and Veterinary Medicine Cluj-Napoca, 3-5 CaleaMănă̧stur Street, 400372 Cluj-Napoca, Romania
| | - Mehdi Rahimi
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran
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12
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Rao AR, Nazir A, Imtiaz S, Paracha SA, Waryah YM, Ujjan ID, Anwar I, Iqbal A, Santoni FA, Shah I, Gul K, Baig HMA, Waryah AM, Antonarakis SE, Ansar M. Delineating the Spectrum of Genetic Variants Associated with Bardet-Biedl Syndrome in Consanguineous Pakistani Pedigrees. Genes (Basel) 2023; 14:404. [PMID: 36833331 PMCID: PMC9956862 DOI: 10.3390/genes14020404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 01/29/2023] [Accepted: 01/30/2023] [Indexed: 02/09/2023] Open
Abstract
This study aimed to find the molecular basis of Bardet-Biedl syndrome (BBS) in Pakistani consanguineous families. A total of 12 affected families were enrolled. Clinical investigations were performed to access the BBS-associated phenotypes. Whole exome sequencing was conducted on one affected individual from each family. The computational functional analysis predicted the variants' pathogenic effects and modeled the mutated proteins. Whole-exome sequencing revealed 9 pathogenic variants in six genes associated with BBS in 12 families. The BBS6/MKS was the most common BBS causative gene identified in five families (5/12, 41.6%), with one novel (c.1226G>A, p.Gly409Glu) and two reported variants. c.774G>A, Thr259LeuTer21 was the most frequent BBS6/MMKS allele in three families 3/5 (60%). Two variants, c.223C>T, p.Arg75Ter and a novel, c. 252delA, p.Lys85STer39 were detected in the BBS9 gene. A novel 8bp deletion c.387_394delAAATAAAA, p. Asn130GlyfsTer3 was found in BBS3 gene. Three known variants were detected in the BBS1, BBS2, and BBS7 genes. Identification of novel likely pathogenic variants in three genes reaffirms the allelic and genetic heterogeneity of BBS in Pakistani patients. The clinical differences among patients carrying the same pathogenic variant may be due to other factors influencing the phenotype, including variants in other modifier genes.
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Affiliation(s)
- Ali Raza Rao
- Molecular Biology and Genetics Department, Medical Research Center, Liaquat University of Medical and Health Sciences, Jamshoro 76090, Pakistan
| | - Aamir Nazir
- Institute of Basic Medical Sciences, Khyber Medical University, Peshawar 25100, Pakistan
| | - Samina Imtiaz
- Department of Genetics, University of Karachi, Karachi 75270, Pakistan
| | - Sohail Aziz Paracha
- Institute of Basic Medical Sciences, Khyber Medical University, Peshawar 25100, Pakistan
| | - Yar Muhammad Waryah
- Scientific and Ophthalmic Research Laboratory, Sindh Institute of Ophthalmology and Visual Sciences, Hyderabad 71000, Pakistan
| | - Ikram Din Ujjan
- Department of Pathology, Liaquat University of Medical and Health Sciences, Jamshoro 76090, Pakistan
| | - Ijaz Anwar
- Department of Ophthalmology, University of Lausanne, Jules Gonin Eye Hospital, Fondation Asile Des Aveugles, 1004 Lausanne, Switzerland
| | - Afia Iqbal
- Department of Zoology, Lahore College for Women University, Lahore 54810, Pakistan
| | - Federico A. Santoni
- Department of Genetic Medicine and Development, University of Geneva, 1211 Geneva, Switzerland
- Department of Endocrinology Diabetes and Metabolism, University Hospital of Lausanne, 1011 Lausanne, Switzerland
| | - Inayat Shah
- Institute of Basic Medical Sciences, Khyber Medical University, Peshawar 25100, Pakistan
| | - Khitab Gul
- Department of Genetics, University of Karachi, Karachi 75270, Pakistan
- Department of BioSciences, Faculty of Life Science, Mohammad Ali Jinnah University, Karachi 75400, Pakistan
| | - Hafiz Muhammad Azhar Baig
- Department of Ophthalmology, University of Lausanne, Jules Gonin Eye Hospital, Fondation Asile Des Aveugles, 1004 Lausanne, Switzerland
- Department of Biotechnology, Institute of Biochemistry, Biotechnology and Bioinformatics, The Islamia University of Bahawalpur, Bahawalpur 63080, Pakistan
| | - Ali Muhammad Waryah
- Molecular Biology and Genetics Department, Medical Research Center, Liaquat University of Medical and Health Sciences, Jamshoro 76090, Pakistan
| | - Stylianos E. Antonarakis
- Department of Genetic Medicine and Development, University of Geneva, 1211 Geneva, Switzerland
- iGE3 Institute of Genetics and Genomics of Geneva, 1211 Geneva, Switzerland
| | - Muhammad Ansar
- Department of Ophthalmology, University of Lausanne, Jules Gonin Eye Hospital, Fondation Asile Des Aveugles, 1004 Lausanne, Switzerland
- Department of Genetic Medicine and Development, University of Geneva, 1211 Geneva, Switzerland
- Advanced Molecular Genetics and Genomics Disease Research and Treatment Centre, Dow University of Health Sciences, Karachi 74200, Pakistan
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13
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Hiatt SM, Trajkova S, Sebastiano MR, Partridge EC, Abidi FE, Anderson A, Ansar M, Antonarakis SE, Azadi A, Bachmann-Gagescu R, Bartuli A, Benech C, Berkowitz JL, Betti MJ, Brusco A, Cannon A, Caron G, Chen Y, Cochran ME, Coleman TF, Crenshaw MM, Cuisset L, Curry CJ, Darvish H, Demirdas S, Descartes M, Douglas J, Dyment DA, Elloumi HZ, Ermondi G, Faoucher M, Farrow EG, Felker SA, Fisher H, Hurst AC, Joset P, Kelly MA, Kmoch S, Leadem BR, Lyons MJ, Macchiaiolo M, Magner M, Mandrile G, Mattioli F, McEown M, Meadows SK, Medne L, Meeks NJ, Montgomery S, Napier MP, Natowicz M, Newberry KM, Niceta M, Noskova L, Nowak CB, Noyes AG, Osmond M, Prijoles EJ, Pugh J, Pullano V, Quélin C, Rahimi-Aliabadi S, Rauch A, Redon S, Reymond A, Schwager CR, Sellars EA, Scheuerle AE, Shukarova-Angelovska E, Skraban C, Stolerman E, Sullivan BR, Tartaglia M, Thiffault I, Uguen K, Umaña LA, van Bever Y, van der Crabben SN, van Slegtenhorst MA, Waisfisz Q, Washington C, Rodan LH, Myers RM, Cooper GM. Deleterious, protein-altering variants in the transcriptional coregulator ZMYM3 in 27 individuals with a neurodevelopmental delay phenotype. Am J Hum Genet 2023; 110:215-227. [PMID: 36586412 PMCID: PMC9943726 DOI: 10.1016/j.ajhg.2022.12.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 12/08/2022] [Indexed: 12/31/2022] Open
Abstract
Neurodevelopmental disorders (NDDs) result from highly penetrant variation in hundreds of different genes, some of which have not yet been identified. Using the MatchMaker Exchange, we assembled a cohort of 27 individuals with rare, protein-altering variation in the transcriptional coregulator ZMYM3, located on the X chromosome. Most (n = 24) individuals were males, 17 of which have a maternally inherited variant; six individuals (4 male, 2 female) harbor de novo variants. Overlapping features included developmental delay, intellectual disability, behavioral abnormalities, and a specific facial gestalt in a subset of males. Variants in almost all individuals (n = 26) are missense, including six that recurrently affect two residues. Four unrelated probands were identified with inherited variation affecting Arg441, a site at which variation has been previously seen in NDD-affected siblings, and two individuals have de novo variation resulting in p.Arg1294Cys (c.3880C>T). All variants affect evolutionarily conserved sites, and most are predicted to damage protein structure or function. ZMYM3 is relatively intolerant to variation in the general population, is widely expressed across human tissues, and encodes a component of the KDM1A-RCOR1 chromatin-modifying complex. ChIP-seq experiments on one variant, p.Arg1274Trp, indicate dramatically reduced genomic occupancy, supporting a hypomorphic effect. While we are unable to perform statistical evaluations to definitively support a causative role for variation in ZMYM3, the totality of the evidence, including 27 affected individuals, recurrent variation at two codons, overlapping phenotypic features, protein-modeling data, evolutionary constraint, and experimentally confirmed functional effects strongly support ZMYM3 as an NDD-associated gene.
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Affiliation(s)
- Susan M. Hiatt
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA,Corresponding author
| | - Slavica Trajkova
- Department of Medical Sciences, University of Torino, 10126 Torino, Italy
| | - Matteo Rossi Sebastiano
- Molecular Biotechnology and Health Sciences Department, Università degli Studi di Torino, via Quarello 15, 10135 Torino, Italy
| | | | | | - Ashlyn Anderson
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Muhammad Ansar
- Department of Ophthalmology, University of Lausanne, Jules Gonin Eye Hospital, Fondation Asile des Aveugles, Lausanne, Switzerland,Advanced Molecular Genetics and Genomics Disease Research and Treatment Centre, Dow University of Health Sciences, Karachi, Pakistan
| | | | - Azadeh Azadi
- Obestetrics and Gynecology Department, Golestan University of Medical Sciences, Gorgan, Iran
| | | | - Andrea Bartuli
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | | | | | | | - Alfredo Brusco
- Department of Medical Sciences, University of Torino, 10126 Torino, Italy
| | - Ashley Cannon
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Giulia Caron
- Molecular Biotechnology and Health Sciences Department, Università degli Studi di Torino, via Quarello 15, 10135 Torino, Italy
| | | | | | | | - Molly M. Crenshaw
- Pediatrics and Medical Genetics, University of Colorado, Aurora CO, USA
| | - Laurence Cuisset
- Service de Médecine Génomique des Maladies de Système et d’Organe, Département Médico-Universitaire BioPhyGen, Hôpital Cochin, APHP, Université Paris Cité, Paris, France
| | | | - Hossein Darvish
- Neuroscience Research Center, Faculty of Medicine, Golestan University of Medical Sciences, Gorgan, Iran,Nikagene Genetic Diagnostic Laboratory, Gorgan, Golestan, Iran
| | - Serwet Demirdas
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Maria Descartes
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - David A. Dyment
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
| | | | - Giuseppe Ermondi
- Molecular Biotechnology and Health Sciences Department, Università degli Studi di Torino, via Quarello 15, 10135 Torino, Italy
| | - Marie Faoucher
- Service de Génétique Moléculaire et Génomique, CHU, Rennes 35033, France,Univ Rennes, CNRS, IGDR, UMR 6290, Rennes 35000, France
| | - Emily G. Farrow
- Children's Mercy Kansas City, Center for Pediatric Genomic Medicine, Kansas City, KS, USA
| | | | | | - Anna C.E. Hurst
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Pascal Joset
- Medical Genetics, Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Melissa A. Kelly
- HudsonAlpha Clinical Services Lab, LLC, Huntsville, AL 35806, USA
| | - Stanislav Kmoch
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, 1st Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | | | | | - Marina Macchiaiolo
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Martin Magner
- Department of Pediatrics and Inherited Metabolic Disorders, General University Hospital and First faculty of Medicine, Charles University, Prague, Czech Republic
| | - Giorgia Mandrile
- Medical Genetics Unit and Thalassemia Center, San Luigi University Hospital, University of Torino, Orbassano, Italy
| | - Francesca Mattioli
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Megan McEown
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Sarah K. Meadows
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Livija Medne
- Childrens Hospital of Philadelphia, Philadelphia, PA, USA
| | - Naomi J.L. Meeks
- Section of Genetics & Metabolism, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Sarah Montgomery
- Division of Genetics and Metabolism, Children’s Health, Dallas, TX, USA
| | | | - Marvin Natowicz
- Pathology & Laboratory Medicine, Genomic Medicine, Neurological and Pediatrics Institutes, Cleveland Clinic, Cleveland, OH, USA
| | | | - Marcello Niceta
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Lenka Noskova
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, 1st Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | | | | | - Matthew Osmond
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
| | | | - Jada Pugh
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Verdiana Pullano
- Department of Medical Sciences, University of Torino, 10126 Torino, Italy
| | - Chloé Quélin
- Service de Génétique Clinique, Centre de Référence Maladies Rares CLAD-Ouest, CHU Hôpital Sud, Rennes, France
| | - Simin Rahimi-Aliabadi
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Utah, Salt Lake City, UT 84112, USA
| | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, Schlieren 8952, Switzerland,University Children’s Hospital Zurich, University of Zurich, Zurich 8032, Switzerland
| | - Sylvia Redon
- Univ Brest, Inserm, EFS, UMR 1078, GGB, 29200 Brest, France,Service de Génétique Médicale et Biologie de la Reproduction, CHU de Brest, Brest, France,Centre de Référence Déficiences Intellectuelles de causes rares, Brest, France
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | | | - Elizabeth A. Sellars
- Genetics and Metabolism, Arkansas Children's Hospital, Little Rock, AR 72202, USA
| | - Angela E. Scheuerle
- Department of Pediatrics, Division of Genetics and Metabolism, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Elena Shukarova-Angelovska
- Department of Endocrinology and Genetics, University Clinic for Children's Diseases, Medical Faculty, University Sv. Kiril i Metodij, Skopje, Republic of Macedonia
| | - Cara Skraban
- Childrens Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Bonnie R. Sullivan
- Division of Genetics, Children’s Mercy Kansas City, Kansas City, MO, USA
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Isabelle Thiffault
- Children's Mercy Kansas City, Center for Pediatric Genomic Medicine, Kansas City, KS, USA
| | - Kevin Uguen
- Univ Brest, Inserm, EFS, UMR 1078, GGB, 29200 Brest, France,Service de Génétique Médicale et Biologie de la Reproduction, CHU de Brest, Brest, France,Centre de Référence Déficiences Intellectuelles de causes rares, Brest, France
| | - Luis A. Umaña
- Department of Pediatrics, Division of Genetics and Metabolism, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yolande van Bever
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | | | | | - Quinten Waisfisz
- Department of Human Genetics, Amsterdam University Medical Centers, VU University Amsterdam, Amsterdam, The Netherlands,Amsterdam Neuroscience, Amsterdam, The Netherlands
| | | | - Lance H. Rodan
- Boston Children's Hospital, Boston, MA, USA,Harvard Medical School, Boston, MA 02115, USA
| | - Richard M. Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Gregory M. Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA,Corresponding author
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Bennani FE, Doudach L, El Rhayam Y, Karrouchi K, Cherrah Y, Tarib A, Ansar M, Faouzi MEA. Identification of the new progress on Pyrazole Derivatives Molecules as Antimicrobial and Antifungal Agents. West Afr J Med 2022; 39:1217-1244. [PMID: 36455285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Microbial infections remain a worldwide leading cause of death, despite the evolution of a large number of new antibiotics every year. Currently, several bacteria have developed resistance against antibiotics drugs which remain a major issue in antibiotics drug discovery. This review provides detailed information about antimicrobial and antifungal agent synthesis belonging to the pyrazoles scaffold. We reassemble the results obtained from several studies to characterize the importance of heteroatom nuclei in many synthetic products. Additionally, several compounds based on pyrazole derivatives such as benzimidazole, benzothiazole, indole, acridine, oxadiazole, imidazole, isoxazole, pyrazole, triazole, quinoline and quinazoline including other pyrazole containing drugs such as pyridazine, pyridine and pyrimidine are highlighted. Furthermore, you will find in this review 134 best promise structures collected from recent studies, relating the pyrazoles structures to the relevant biological activities, in particular, antimicrobial and antifungal one.
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Affiliation(s)
- F E Bennani
- Laboratory of Pharmacology and Toxicology, Bio Pharmaceutical and Toxicological Analysis Research Team, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, BP 6203, Rabat, Morocco
- Laboratory of Therapeutic Chemistry, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, BP 6203, Rabat, Morocco
| | - L Doudach
- Department of Biomedical Engineering Medical Physiology, Higher School of Technical Education of Rabat, Mohammed V University in Rabat, BP 6203, Rabat, Morocco
| | - Y El Rhayam
- Agro-Resources Laboratory, Organic Polymers and Process Engineering (LRGP)/Organic and Polymer Chemistry Team (ECOP). Faculty of Sciences, Ibn Tofail University, Kenitra, Morocco. #Pr Faouzi and Pr Ansar are contributing equality in this work
| | - K Karrouchi
- Laboratory of Therapeutic Chemistry, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, BP 6203, Rabat, Morocco
| | - Y Cherrah
- Laboratory of Pharmacology and Toxicology, Bio Pharmaceutical and Toxicological Analysis Research Team, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, BP 6203, Rabat, Morocco
| | - A Tarib
- Laboratory of Pharmacology and Toxicology, Bio Pharmaceutical and Toxicological Analysis Research Team, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, BP 6203, Rabat, Morocco
| | - M Ansar
- Laboratory of Therapeutic Chemistry, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, BP 6203, Rabat, Morocco
| | - M E A Faouzi
- Laboratory of Pharmacology and Toxicology, Bio Pharmaceutical and Toxicological Analysis Research Team, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, BP 6203, Rabat, Morocco
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15
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Ghafoor S, Rafiq MA, Shah STA, Ansar M, Paton T, Ajmal M, Agha Z, Qamar R, Azam M. KIF1A novel frameshift variant p.(Ser887Profs*64) exhibits clinical heterogeneity in a Pakistani family with Hereditary Sensory and Autonomic Neuropathy Type IIC. Int J Neurosci 2022:1-11. [DOI: 10.1080/00207454.2022.2140428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Affiliation(s)
- Saima Ghafoor
- Translational Genomics Laboratory, COMSATS University Islamabad, Pakistan
| | - Muhammad Arshad Rafiq
- Translational Genomics Laboratory, COMSATS University Islamabad, Pakistan
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | | | - Muhammad Ansar
- Jules-Gonin Eye Hospital, Ophthalmology Department of the University of Lausanne
| | - Tara Paton
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Centre for Applied Genomics (TCAG), The Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada
| | - Muhmmad Ajmal
- Translational Genomics Laboratory, COMSATS University Islamabad, Pakistan
| | - Zehra Agha
- Translational Genomics Laboratory, COMSATS University Islamabad, Pakistan
| | - Raheel Qamar
- Pakistan Academy of Sciences, Islamabad, Pakistan
- Science and Technology Sector, ICESCO, Rabat, Morocco
| | - Maleeha Azam
- Translational Genomics Laboratory, COMSATS University Islamabad, Pakistan
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16
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Ansar M, Sikandar MA, Althoey F, Tariq MAUR, Alyami SH, Elsayed Elkhatib S. Rheological, Aging, and Microstructural Properties of Polycarbonate and Polytetrafluoroethylene Modified Bitumen. Polymers (Basel) 2022; 14:polym14163283. [PMID: 36015539 PMCID: PMC9414428 DOI: 10.3390/polym14163283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 11/17/2022] Open
Abstract
Deterioration of asphalt pavements due to massive load of vehicles and climatic variation has demanded the use of pavements construction material with an excellent resilience characteristic, resistance to permanent deformation, and most importantly, a much longer service lifespan. The main structural distresses in pavement construction are permanent deformation at high temperatures and fatigue cracking under repetitive traffic loadings. To comprehensively investigate the performance of bitumen penetration grade (PG) 70 against rutting, fatigue, and high temperature cracking in hot mix asphalt (HMA) pavements, polycarbonate (PC) and polytetrafluoroethylene (PTFE) were used. The investigation of the internal structure, rheological, and physical properties of base and modified bitumen (MB) mixes with different percentages of modifiers (0%, 2.5%, and 5%) by weight were performed via scanning electron microscope (SEM), Fourier transform infrared spectroscopy (FTIR) analysis, X-ray diffraction (XRD) pattern analysis, rolling thin-film oven test (RTFOT), pressurized aging vessel (PAV), dynamic shear rheometer (DSR), rotational viscosity (RV), and bending beam rheometer (BBR). The results of the RV test indicate that modification of neat bitumen with polycarbonate and polytetrafluoroethylene increased the viscosity for polycarbonate-modified bitumen (PCMB), polytetrafluoroethylene-modified bitumen (PTFEMB), and for a blend of PCMB-PTFEMB by 44%, 50%, and 55.75% at 135 °C and 111.10%, 127.80%, and 138.88% at 165 °C, accordingly. BBR test results revealed that modifiers increased the rigidity of neat bitumen by 74.8%, 75.8%, and 74.5% at −16 °C, −22 °C, and −28 °C, respectively.
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Affiliation(s)
- Muhammad Ansar
- Department of Civil Engineering, CECOS University of IT and Emerging Sciences, Peshawar 25000, Pakistan
| | - Muhammad Ali Sikandar
- Department of Civil Engineering, CECOS University of IT and Emerging Sciences, Peshawar 25000, Pakistan
- Correspondence:
| | - Fadi Althoey
- Department of Civil Engineering, Najran University, Najran 66454, Saudi Arabia
| | - Muhammad Atiq Ur Rehman Tariq
- College of Engineering and Science, Victoria University, Melbourne, VIC 8001, Australia
- Institute for Sustainable Industries & Liveable Cities, Victoria University, Melbourne, VIC 8001, Australia
| | - Saleh H. Alyami
- Department of Civil Engineering, Najran University, Najran 66454, Saudi Arabia
| | - Samah Elsayed Elkhatib
- Mechanical Engineering Department, Faculty of Engineering and Technology, Future University in Egypt, New Cairo 11835, Egypt
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17
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Ansar M, Javed S, Baig HMA, Quinodoz M, Ullah M, Han JH, Rahim MU, Kausar H, Calzetti G, Rivolta C. A new nonsense mutation in HMX1 in two siblings with oculoauricular syndrome. Ophthalmic Genet 2022; 43:720-723. [PMID: 35946463 DOI: 10.1080/13816810.2022.2096242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Affiliation(s)
- Muhammad Ansar
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland.,Advanced Molecular Genetics and Genomics Disease Research and Treatment Centre, Dow University of Health Sciences, Karachi, Pakistan
| | - Samra Javed
- Department of Biotechnology, Kinnaird College for Women, Lahore, Pakistan
| | - Hafiz Muhammad Azhar Baig
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland.,Department of Biotechnology, Institute of Biochemistry, Biotechnology and Bioinformatics, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Mukhtar Ullah
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Ji Hoon Han
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland
| | | | - Humera Kausar
- Department of Biotechnology, Kinnaird College for Women, Lahore, Pakistan
| | - Giacomo Calzetti
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
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Urooj M, Shoukat M, Imran M, Ansar M, Faryal R. Emergence of hypermucoviscous colistin-resistant high-risk convergent Klebsiella pneumoniae ST-2096 clone from Pakistan. Future Microbiol 2022; 17:989-1000. [PMID: 35860964 DOI: 10.2217/fmb-2021-0292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Klebsiella pneumoniae convergent clones are considered a threat to healthcare settings. Here we report a comprehensive genomic profiling of an emerging colistin-resistant K. pneumoniae ST-2096 convergent clone from Pakistan. Methods: Whole-genome sequencing was performed and raw reads were assembled antimicrobial resistance and virulence genes were predicted using various online tools. Results & conclusion: The phenotypically multidrug-resistant (MDR) and hypermucoviscous (hv) colistin-resistant K. pneumoniae (hvCRKP-10718), which, intriguingly, possessed a wide range of antimicrobial resistance (blaTEM-1A, blaOXA-1, blaOXA-232, blaCTX-M-15, blaSHV-106, oqxA, oqxB, aac(6')-Ib-cr, aadA2, aac(6')-Ib-cr, armA, tetD, mphE, msrE, fosA, dfrA1, dfrA12, dfrA14, catB3, sul1) and virulence determinants (RmpA/RmpA2, yersiniabactin [ybt], aerobactin [iuc/iut], enterobactin). Furthermore, the acquisition of various mobile genetic elements (MDR/virulent plasmids, type II integron gene cassette, insertional sequences, transposases) and associated hv capsular type made this MDR/hv isolate a convergent clone belonging to a high-risk lineage (ST-2096). Based on core-genome multilocus sequence typing and single-nucleotide polymorphism analysis, this isolate showed ≥99% nucleotide identity with MDR K. pneumoniae isolates from India, depicting its evolutionary background. This study provides a comprehensive genomic profiling of this high-risk convergent K. pneumoniae ST-2096 clone from Pakistan. Comparative genomics of MDR/hv colistin-resistant K. pneumoniae isolates with other MDR convergent strains from the Indian subcontinent indicated the emergence of this evolving superbug.
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Affiliation(s)
- Maleeha Urooj
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University Islamabad, 45320, Pakistan
| | - Mehreen Shoukat
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University Islamabad, 45320, Pakistan
| | - Muhammad Imran
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University Islamabad, 45320, Pakistan
| | - Muhammad Ansar
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University Islamabad, 45320, Pakistan
| | - Rani Faryal
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University Islamabad, 45320, Pakistan
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19
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Azhar Baig HM, Ansar M, Iqbal A, Naeem MA, Quinodoz M, Calzetti G, Iqbal M, Rivolta C. Genetic analysis of consanguineous Pakistani families with congenital stationary night blindness. Ophthalmic Res 2021; 65:104-110. [PMID: 34781300 DOI: 10.1159/000520895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 10/28/2021] [Indexed: 11/19/2022]
Abstract
AIM Congenital stationary night blindness (CSNB) is a rare, largely non progressive, inherited retinal disorder that can be clinically classified on the basis of fundus and electroretinogram (ERG) abnormalities. METHODS We analyzed four large consanguineous families from the Southern Punjab region of Pakistan including multiple individuals affected with CSNB. Exome sequencing (ES) was performed in probands of all four families; Sanger sequencing was performed in additional members to test co-segregation of the variants identified. RESULTS We identified two novel and likely pathogenic variants in two pedigrees, namely NM_002905.4:c.668A>C (p.Gln223Pro) in RDH5, and NM_022567.2:c.908del (p.Gly303ValfsTer45) in NYX. In the two other families, the variants NM_002905.4:c.319G>C (p.Gly107Arg) in RDH5 and NM_000541.5:c.874C>T (p.Arg292Ter) in SAG were identified. These variants have been reported previously, but not in the Pakistani population. CONCLUSIONS Our findings expand the mutational spectrum of CSNB, in particular within the population of Southern Punjab.
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Affiliation(s)
- Hafiz Muhammad Azhar Baig
- Department of Biotechnology, Institute of Biochemistry, Biotechnology and Bioinformatics, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Muhammad Ansar
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Afia Iqbal
- Department of Zoology, Lahore College for Women University, Lahore, Pakistan
| | - Muhammad Asif Naeem
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Giacomo Calzetti
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Muhammad Iqbal
- Department of Biotechnology, Institute of Biochemistry, Biotechnology and Bioinformatics, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
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20
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Levy MA, Beck DB, Metcalfe K, Douzgou S, Sithambaram S, Cottrell T, Ansar M, Kerkhof J, Mignot C, Nougues MC, Keren B, Moore HW, Oegema R, Giltay JC, Simon M, van Jaarsveld RH, Bos J, van Haelst M, Motazacker MM, Boon EMJ, Santen GWE, Ruivenkamp CAL, Alders M, Luperchio TR, Boukas L, Ramsey K, Narayanan V, Schaefer GB, Bonasio R, Doheny KF, Stevenson RE, Banka S, Sadikovic B, Fahrner JA. Deficiency of TET3 leads to a genome-wide DNA hypermethylation episignature in human whole blood. NPJ Genom Med 2021; 6:92. [PMID: 34750377 PMCID: PMC8576018 DOI: 10.1038/s41525-021-00256-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 09/23/2021] [Indexed: 11/08/2022] Open
Abstract
TET3 encodes an essential dioxygenase involved in epigenetic regulation through DNA demethylation. TET3 deficiency, or Beck-Fahrner syndrome (BEFAHRS; MIM: 618798), is a recently described neurodevelopmental disorder of the DNA demethylation machinery with a nonspecific phenotype resembling other chromatin-modifying disorders, but inconsistent variant types and inheritance patterns pose diagnostic challenges. Given TET3's direct role in regulating 5-methylcytosine and recent identification of syndrome-specific DNA methylation profiles, we analyzed genome-wide DNA methylation in whole blood of TET3-deficient individuals and identified an episignature that distinguishes affected and unaffected individuals and those with mono-allelic and bi-allelic pathogenic variants. Validation and testing of the episignature correctly categorized known TET3 variants and determined pathogenicity of variants of uncertain significance. Clinical utility was demonstrated when the episignature alone identified an affected individual from over 1000 undiagnosed cases and was confirmed upon distinguishing TET3-deficient individuals from those with 46 other disorders. The TET3-deficient signature - and the signature resulting from activating mutations in DNMT1 which normally opposes TET3 - are characterized by hypermethylation, which for BEFAHRS involves CpG sites that may be biologically relevant. This work expands the role of epi-phenotyping in molecular diagnosis and reveals genome-wide DNA methylation profiling as a quantitative, functional readout for characterization of this new biochemical category of disease.
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Affiliation(s)
- Michael A Levy
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, N6A5W9, Canada
| | - David B Beck
- National Human Genome Research Institute, Bethesda, MD, 20892, USA
| | - Kay Metcalfe
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PL, UK
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Health Innovation Manchester, Manchester University NHS Foundation Trust, Manchester, M13 9WL, UK
| | - Sofia Douzgou
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PL, UK
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Health Innovation Manchester, Manchester University NHS Foundation Trust, Manchester, M13 9WL, UK
| | - Sivagamy Sithambaram
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Health Innovation Manchester, Manchester University NHS Foundation Trust, Manchester, M13 9WL, UK
| | - Trudie Cottrell
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Health Innovation Manchester, Manchester University NHS Foundation Trust, Manchester, M13 9WL, UK
| | - Muhammad Ansar
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-I-Azam University, 45320, Islamabad, Pakistan
| | - Jennifer Kerkhof
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, N6A5W9, Canada
| | - Cyril Mignot
- Assistance Publique-Hopitaux de Paris, Sorbonne Université, Departement de Génétique, Groupe Hospitalier Pitie-Salpetriere et Hopital Trousseau, Paris, 75651, France
| | - Marie-Christine Nougues
- Department of Neuropediatrics, Armand Trousseau Hospital, Assistance Publique-Hopitaux de Paris, Paris, 75012, France
| | - Boris Keren
- Laboratoire de génétique, Hôpital Pïtié-Salpêtrière, Assistance Publique-Hopitaux de Paris, Paris, 75013, France
| | | | - Renske Oegema
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Jacques C Giltay
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Marleen Simon
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Richard H van Jaarsveld
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Jessica Bos
- Section Clinical Genetics, Department Human Genetics, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Mieke van Haelst
- Section Clinical Genetics, Department Human Genetics, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - M Mahdi Motazacker
- Department of Human Genetics, Laboratory of Genome Diagnostics, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam, Netherlands
| | - Elles M J Boon
- Department of Human Genetics, VU University Medical Center Amsterdam, Amsterdam UMC, van der Boechorststraat 7, 1081 BT, Amsterdam, The Netherlands
| | - Gijs W E Santen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Claudia A L Ruivenkamp
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Marielle Alders
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - Teresa Romeo Luperchio
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Leandros Boukas
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Biostatistics, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Keri Ramsey
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Vinodh Narayanan
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ, USA
| | | | - Roberto Bonasio
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Kimberly F Doheny
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Center for Inherited Disease Research, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Siddharth Banka
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PL, UK
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Health Innovation Manchester, Manchester University NHS Foundation Trust, Manchester, M13 9WL, UK
| | - Bekim Sadikovic
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, N6A5W9, Canada.
- Department of Pathology and Laboratory Medicine, Western University, London, ON, N6A5W9, Canada.
| | - Jill A Fahrner
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
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21
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Nawal W, Ullah A, Ullah U, Farrakh K, Ahmad F, Khan H, Ahmad GS, Khan B, Ansar M, Kalsoom UE, Ahmad W. Loss of Function Variants in the XPC Causes Severe Xeroderma Pigmentosum in Three Large Consanguineous Families. Klin Padiatr 2021; 234:123-129. [PMID: 34544175 DOI: 10.1055/a-1552-3788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
BACKGROUND Xeroderma pigmentosum (XP) is a rare recessively inherited disorder that presents clinical and genetic heterogeneity. Mutations in eight genes, of which seven are involved in nucleotide excision repair (NER) pathway have been reported to cause the XP. METHODS AND RESULTS Three large consanguineous families of Pakistani origin displaying typical clinical hallmarks of XP were evaluated at clinical and molecular level. Homozygosity mapping using microsatellite markers established linkage of the families to XPC gene on chromosome 3p25.1. Sanger sequencing of the XPC gene identified a novel homozygous single bp deletion [NM_004628.5; c.1934del; p.(Pro645Leufs*5)] and two previously reported mutations that included a nonsense [c.1243 C>T; p.(Arg415*)] and a splice acceptor site (c.2251-1 G>C), all segregating with the disease phenotypes in the families. CONCLUSION This report has extended the spectrum of mutations in the XPC gene and will also facilitate in diagnosis of XP and counselling of families inheriting it, which is the only inevitable tool for preventing the disease occurrence in future generations.
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Affiliation(s)
- Warda Nawal
- Department of Biochemistry, Quaid-i-Azam University, Islamabad, Pakistan
| | - Asmat Ullah
- Department of Biochemistry, Quaid-i-Azam University, Islamabad, Pakistan.,Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, University of Copenhagen Faculty of Health and Medical Sciences, Kobenhavn, Denmark.,Department of Molecular Biology, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad, Pakistan
| | - Ubaid Ullah
- Department of Biochemistry, Hazara University, Mansehra, Pakistan
| | - Kanza Farrakh
- Department of Biochemistry, Quaid-i-Azam University, Islamabad, Pakistan
| | - Farooq Ahmad
- Department of Chemistry, Women University Swabi Swabi, Pakistan
| | - Hammal Khan
- Department of Biochemistry, Quaid-i-Azam University, Islamabad, Pakistan
| | - Gul Saeed Ahmad
- Department of Biochemistry, Quaid-i-Azam University, Islamabad, Pakistan
| | - Bushra Khan
- Department of Biochemistry, Abdul Wali Khan University, Mardan, Pakistan
| | - Muhammad Ansar
- Department of Biochemistry, Quaid-i-Azam University, Islamabad, Pakistan
| | - Umm-E- Kalsoom
- Department of Biochemistry, Hazara University, Mansehra, Pakistan
| | - Wasim Ahmad
- Department of Biochemistry, Quaid-i-Azam University, Islamabad, Pakistan
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22
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Rasheed M, Khan V, Harripaul R, Siddiqui M, Malik MA, Ullah Z, Zahid M, Vincent JB, Ansar M. Exome sequencing identifies novel and known mutations in families with intellectual disability. BMC Med Genomics 2021; 14:211. [PMID: 34452636 PMCID: PMC8399827 DOI: 10.1186/s12920-021-01066-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 08/25/2021] [Indexed: 12/29/2022] Open
Abstract
Background Intellectual disability (ID) is a phenotypically and genetically heterogeneous disorder. Methods In this study, genome wide SNP microarray and whole exome sequencing are used for the variant identification in eight Pakistani families with ID. Beside ID, most of the affected individuals had speech delay, facial dysmorphism and impaired cognitive abilities. Repetitive behavior was observed in MRID143, while seizures were reported in affected individuals belonging to MRID137 and MRID175. Results In two families (MRID137b and MRID175), we identified variants in the genes CCS and ELFN1, which have not previously been reported to cause ID. In four families, variants were identified in ARX, C5orf42, GNE and METTL4. A copy number variation (CNV) was identified in IL1RAPL1 gene in MRID165. Conclusion These findings expand the existing knowledge of variants and genes implicated in autosomal recessive and X linked ID. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-021-01066-y.
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Affiliation(s)
- Memoona Rasheed
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - Valeed Khan
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - Ricardo Harripaul
- Molecular Neuropsychiatry and Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, M5T 1R8, Canada.,Institute of Medical Science, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Maimoona Siddiqui
- Division of Neurology, Shifa College of Medicine, H-8/1, Islamabad, Pakistan
| | - Madiha Amin Malik
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - Zahid Ullah
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - Muhammad Zahid
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - John B Vincent
- Molecular Neuropsychiatry and Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, M5T 1R8, Canada.,Institute of Medical Science, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Department of Psychiatry, University of Toronto, Toronto, ON, M5T 1R8, Canada
| | - Muhammad Ansar
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan.
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23
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Gabrielle PH, Faivre L, Audo I, Zanlonghi X, Dollfus H, Thiadens AAHJ, Zeitz C, Mancini GMS, Perdomo Y, Mohand-Saïd S, Lizé E, Lhussiez V, Nandrot EF, Acar N, Creuzot-Garcher C, Sahel JA, Ansar M, Thauvin-Robinet C, Duplomb L, Da Costa R. Cystoid maculopathy is a frequent feature of Cohen syndrome-associated retinopathy. Sci Rep 2021; 11:16412. [PMID: 34385517 PMCID: PMC8361024 DOI: 10.1038/s41598-021-95743-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 07/30/2021] [Indexed: 01/14/2023] Open
Abstract
Cohen syndrome (CS) is a rare syndromic form of rod-cone dystrophy. Recent case reports have suggested that cystoid maculopathy (CM) could affect CS patients with an early onset and high prevalence. Our study aims at improving our understanding and management of CM in CS patients through a retrospective case series of ten CS patients with identified pathogenic variants in VPS13B. Longitudinal optical coherence tomography (OCT) imaging was performed and treatment with carbonic anhydrase inhibitors (CAI) was provided to reduce the volume of cystoid spaces. CM affected eight out of ten patients in our cohort. The youngest patient showed a strong progression of macular cysts from the age of 4.5 to 5 years despite oral CAI medication. Other teenage and young adult patients showed stable macular cysts with and without treatment. One patient showed a moderate decrease of cystoid spaces in the absence of treatment at 22 years of age. Through a correlative analysis we found that the volume of cystoid spaces was positively correlated to the thickness of peripheral and macular photoreceptor-related layers. This study suggests that CAI treatments may not suffice to improve CM in CS patients, and that CM may resolve spontaneously during adulthood as photoreceptor dystrophy progresses.
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Affiliation(s)
- Pierre-Henry Gabrielle
- Department of Ophthalmology, University Hospital, 14 rue Paul Gaffarel, 21079, Dijon, France
| | - Laurence Faivre
- Inserm, UMR1231, Equipe GAD, Université de Bourgogne Franche Comté, Bâtiment B3, 15 Boulevard du Maréchal de Lattre de Tassigny, 21079, Dijon Cedex, France.,FHU TRANSLAD, CHU Dijon, 21000, Dijon, France.,Centre de Référence Anomalies du Développement et Syndromes Malformatifs, CHU Dijon, 21000, Dijon, France
| | - Isabelle Audo
- Sorbonne Université, INSERM, CNRS, Institut de La Vision, 17 rue Moreau, 75012, Paris, France.,CHNO Des Quinze-Vingts, DHU Sight Restore, INSERM-DGOS CIC 1423, 75012, Paris, France
| | - Xavier Zanlonghi
- Maladies Rares, Service d'Ophtalmologie, CHU Rennes, 2 rue Henri Le Guilloux, 35033, Rennes, France
| | - Hélène Dollfus
- Centre de Référence Pour Les Affections Rares en Génétique Ophtalmologique (CARGO), FSMR SENSGENE, ERN-EYE, Hôpitaux Universitaires de Strasbourg, 67000, Strasbourg, France.,Laboratoire de Génétique Médicale, Inserm, UMR1112, Institut de Génétique Médicale D'Alsace, Université de Strasbourg, 67000, Strasbourg, France
| | | | - Christina Zeitz
- Sorbonne Université, INSERM, CNRS, Institut de La Vision, 17 rue Moreau, 75012, Paris, France
| | - Grazia M S Mancini
- Department of Clinical Genetics, Erasmus MC, 3015, Rotterdam, The Netherlands
| | - Yaumara Perdomo
- Centre de Référence Pour Les Affections Rares en Génétique Ophtalmologique (CARGO), FSMR SENSGENE, ERN-EYE, Hôpitaux Universitaires de Strasbourg, 67000, Strasbourg, France.,Laboratoire de Génétique Médicale, Inserm, UMR1112, Institut de Génétique Médicale D'Alsace, Université de Strasbourg, 67000, Strasbourg, France
| | - Saddek Mohand-Saïd
- Sorbonne Université, INSERM, CNRS, Institut de La Vision, 17 rue Moreau, 75012, Paris, France.,CHNO Des Quinze-Vingts, DHU Sight Restore, INSERM-DGOS CIC 1423, 75012, Paris, France
| | - Eléonore Lizé
- Inserm, UMR1231, Equipe GAD, Université de Bourgogne Franche Comté, Bâtiment B3, 15 Boulevard du Maréchal de Lattre de Tassigny, 21079, Dijon Cedex, France
| | - Vincent Lhussiez
- Inserm, UMR1231, Equipe GAD, Université de Bourgogne Franche Comté, Bâtiment B3, 15 Boulevard du Maréchal de Lattre de Tassigny, 21079, Dijon Cedex, France
| | - Emeline F Nandrot
- Sorbonne Université, INSERM, CNRS, Institut de La Vision, 17 rue Moreau, 75012, Paris, France
| | - Niyazi Acar
- Centre Des Sciences du Goût Et de L'Alimentation, AgroSup Dijon, CNRS, INRA, Université Bourgogne Franche-Comté, 9E Boulevard Jeanne d'Arc, 21000, Dijon, France
| | - Catherine Creuzot-Garcher
- Department of Ophthalmology, University Hospital, 14 rue Paul Gaffarel, 21079, Dijon, France.,Centre Des Sciences du Goût Et de L'Alimentation, AgroSup Dijon, CNRS, INRA, Université Bourgogne Franche-Comté, 9E Boulevard Jeanne d'Arc, 21000, Dijon, France
| | - José-Alain Sahel
- Sorbonne Université, INSERM, CNRS, Institut de La Vision, 17 rue Moreau, 75012, Paris, France.,CHNO Des Quinze-Vingts, DHU Sight Restore, INSERM-DGOS CIC 1423, 75012, Paris, France.,Department of Ophthalmology, The University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
| | - Muhammad Ansar
- Institute of Molecular and Clinical Ophthalmology Basel, 4031, Basel, Switzerland.,Department of Ophthalmology, Jules-Gonin Eye Hospital, University of Lausanne, 1004, Lausanne, Switzerland
| | - Christel Thauvin-Robinet
- Inserm, UMR1231, Equipe GAD, Université de Bourgogne Franche Comté, Bâtiment B3, 15 Boulevard du Maréchal de Lattre de Tassigny, 21079, Dijon Cedex, France.,FHU TRANSLAD, CHU Dijon, 21000, Dijon, France.,Centre de Référence Déficiences Intellectuelles de Causes Rares, CHU Dijon, 21000, Dijon, France
| | - Laurence Duplomb
- Inserm, UMR1231, Equipe GAD, Université de Bourgogne Franche Comté, Bâtiment B3, 15 Boulevard du Maréchal de Lattre de Tassigny, 21079, Dijon Cedex, France.,FHU TRANSLAD, CHU Dijon, 21000, Dijon, France
| | - Romain Da Costa
- Inserm, UMR1231, Equipe GAD, Université de Bourgogne Franche Comté, Bâtiment B3, 15 Boulevard du Maréchal de Lattre de Tassigny, 21079, Dijon Cedex, France. .,FHU TRANSLAD, CHU Dijon, 21000, Dijon, France.
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24
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Ansar M, Ebstein F, Özkoç H, Paracha SA, Iwaszkiewicz J, Gesemann M, Zoete V, Ranza E, Santoni FA, Sarwar MT, Ahmed J, Krüger E, Bachmann-Gagescu R, Antonarakis SE. Biallelic variants in PSMB1 encoding the proteasome subunit β6 cause impairment of proteasome function, microcephaly, intellectual disability, developmental delay and short stature. Hum Mol Genet 2021; 29:1132-1143. [PMID: 32129449 DOI: 10.1093/hmg/ddaa032] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 02/17/2020] [Accepted: 02/17/2020] [Indexed: 12/30/2022] Open
Abstract
The molecular cause of the majority of rare autosomal recessive disorders remains unknown. Consanguinity due to extensive homozygosity unravels many recessive phenotypes and facilitates the detection of novel gene-disease links. Here, we report two siblings with phenotypic signs, including intellectual disability (ID), developmental delay and microcephaly from a Pakistani consanguineous family in which we have identified homozygosity for p(Tyr103His) in the PSMB1 gene (Genbank NM_002793) that segregated with the disease phenotype. PSMB1 encodes a β-type proteasome subunit (i.e. β6). Modeling of the p(Tyr103His) variant indicates that this variant weakens the interactions between PSMB1/β6 and PSMA5/α5 proteasome subunits and thus destabilizes the 20S proteasome complex. Biochemical experiments in human SHSY5Y cells revealed that the p(Tyr103His) variant affects both the processing of PSMB1/β6 and its incorporation into proteasome, thus impairing proteasome activity. CRISPR/Cas9 mutagenesis or morpholino knock-down of the single psmb1 zebrafish orthologue resulted in microcephaly, microphthalmia and reduced brain size. Genetic evidence in the family and functional experiments in human cells and zebrafish indicates that PSMB1/β6 pathogenic variants are the cause of a recessive disease with ID, microcephaly and developmental delay due to abnormal proteasome assembly.
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Affiliation(s)
- Muhammad Ansar
- Department of Genetic Medicine and Development, University of Geneva, Geneva 1211, Switzerland
| | - Frédéric Ebstein
- Institut für Medizinische Biochemie und Molekularbiologie, Universitätsmedizin Greifswald, Greifswald 17475, Germany
| | - Hayriye Özkoç
- Institute of Medical Genetics, University of Zurich, Schlieren 8952, Switzerland
| | - Sohail A Paracha
- Institute of Basic Medical Sciences, Khyber Medical University, Peshawar 25100, Pakistan
| | - Justyna Iwaszkiewicz
- Molecular Modeling Group, Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Matthias Gesemann
- Department of Molecular Life Sciences, University of Zurich, Zurich 8057, Switzerland
| | - Vincent Zoete
- Molecular Modeling Group, Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland.,Department of Fundamental Oncology, Ludwig Institute for Cancer Research, Lausanne University, Epalinges 1066, Switzerland
| | - Emmanuelle Ranza
- Department of Genetic Medicine and Development, University of Geneva, Geneva 1211, Switzerland.,Service of Genetic Medicine, University Hospitals of Geneva, Geneva 1205, Switzerland
| | - Federico A Santoni
- Department of Genetic Medicine and Development, University of Geneva, Geneva 1211, Switzerland.,Department of Endocrinology Diabetes and Metabolism, Lausanne University Hospital, Lausanne 1011, Switzerland
| | - Muhammad T Sarwar
- Institute of Basic Medical Sciences, Khyber Medical University, Peshawar 25100, Pakistan
| | - Jawad Ahmed
- Institute of Basic Medical Sciences, Khyber Medical University, Peshawar 25100, Pakistan
| | - Elke Krüger
- Institut für Medizinische Biochemie und Molekularbiologie, Universitätsmedizin Greifswald, Greifswald 17475, Germany
| | - Ruxandra Bachmann-Gagescu
- Institute of Medical Genetics, University of Zurich, Schlieren 8952, Switzerland.,Department of Molecular Life Sciences, University of Zurich, Zurich 8057, Switzerland
| | - Stylianos E Antonarakis
- Department of Genetic Medicine and Development, University of Geneva, Geneva 1211, Switzerland.,Service of Genetic Medicine, University Hospitals of Geneva, Geneva 1205, Switzerland.,iGE3 Institute of Genetics and Genomics of Geneva, Geneva 1211, Switzerland
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25
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Raza MA, Cui L, Khan I, Din AMU, Chen G, Ansar M, Ahmed M, Ahmad S, Manaf A, Titriku JK, Shah GA, Yang F, Yang W. Compact maize canopy improves radiation use efficiency and grain yield of maize/soybean relay intercropping system. Environ Sci Pollut Res Int 2021; 28:41135-41148. [PMID: 33779899 DOI: 10.1007/s11356-021-13541-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 03/16/2021] [Indexed: 06/12/2023]
Abstract
Maize/soybean relay intercropping system is a popular cultivation system to obtain high yields of both crops with reduced inputs. However, shading by maize decreases the photosynthetically active radiation, reaching the soybean canopy in maize/soybean relay intercropping system, which reduces soybean radiation use efficiency and competitiveness. Here, we reveal that compact maize in maize/soybean relay intercropping system enhances the photosynthetically active radiation transmittance, leaf area index, dry matter production, radiation use efficiency, and competitiveness of soybean and compensates the slight maize yield loss by substantially increasing soybean yield. In this experiment, soybean was relay intercropped with different maize types (SI, spreading maize; SII, semi-compact maize; and SIII, compact maize) in maize/soybean relay intercropping system, and all the relay intercropping treatments were compared with sole cropping systems of soybean and maize. Results revealed that SIII significantly enhanced the soybean radiation use efficiency (by 77%, from 0.35 g MJ-1 in SI to 0.61 g MJ-1 in SIII) and total radiation use efficiency (soybean radiation use efficiency + maize radiation use efficiency) of maize/soybean relay intercropping system (by 5%, from 3.53 g MJ-1 in SI to 3.73 g MJ-1 in SIII). Similarly, SIII improved the competitiveness (by 62%, from 0.58% in SI to 0.94% in SIII) of soybean but reduced the competitiveness (by 38%, from 1.73% in SI to 1.07% in SIII) of maize, which, in turn, considerably increased soybean yield by maintaining maize yield. On average, over the 2 years, in SIII, relay-intercropped soybean produced 89% of the sole soybean yield, and relay-intercropped maize produced 95% of the sole maize yield. Besides, treatment SIII achieved the mean highest land equivalent ratio value of 1.84 in both years. Thus, enhanced radiation use efficiency of soybean, especially during the co-growth period, was the primary factor responsible for the high productivity of the maize/soybean relay intercropping system.
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Affiliation(s)
- Muhammad Ali Raza
- College of Agronomy, Sichuan Agricultural University, No. 211, Huimin Road, Wenjiang District, Chengdu, 611130, Sichuan, China
- Sichuan Engineering Research Center for Crop Strip Intercropping System, Southwest China, Key Laboratory of Crop Ecophysiology and Farming System in Southwest China, Sichuan Agricultural University, Chengdu, China
- Cholistan Institute of Desert Studies, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Liang Cui
- College of Agronomy, Sichuan Agricultural University, No. 211, Huimin Road, Wenjiang District, Chengdu, 611130, Sichuan, China
- Sichuan Engineering Research Center for Crop Strip Intercropping System, Southwest China, Key Laboratory of Crop Ecophysiology and Farming System in Southwest China, Sichuan Agricultural University, Chengdu, China
- Crop Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang, 110161, Liaoning, China
| | - Imran Khan
- College of Agronomy, Sichuan Agricultural University, No. 211, Huimin Road, Wenjiang District, Chengdu, 611130, Sichuan, China
| | - Atta Mohi Ud Din
- College of Agronomy, Sichuan Agricultural University, No. 211, Huimin Road, Wenjiang District, Chengdu, 611130, Sichuan, China
| | - Guopeng Chen
- College of Agronomy, Sichuan Agricultural University, No. 211, Huimin Road, Wenjiang District, Chengdu, 611130, Sichuan, China
- Sichuan Engineering Research Center for Crop Strip Intercropping System, Southwest China, Key Laboratory of Crop Ecophysiology and Farming System in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Muhammad Ansar
- Department of Agronomy, Pir Mehr Ali Shah Arid Agriculture University, Rawalpindi, Pakistan
| | - Mukhtar Ahmed
- Department of Agronomy, Pir Mehr Ali Shah Arid Agriculture University, Rawalpindi, Pakistan
- Department of Agricultural Research for Northern Sweden, Swedish University of Agricultural Sciences, 90183, Umeå, Sweden
| | - Shakeel Ahmad
- Bahauddin Zakariya University, Multan, 60800, Pakistan
| | - Abdul Manaf
- Department of Agronomy, Pir Mehr Ali Shah Arid Agriculture University, Rawalpindi, Pakistan
| | - John Kwame Titriku
- College of Agronomy, Sichuan Agricultural University, No. 211, Huimin Road, Wenjiang District, Chengdu, 611130, Sichuan, China
- Sichuan Engineering Research Center for Crop Strip Intercropping System, Southwest China, Key Laboratory of Crop Ecophysiology and Farming System in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Ghulam Abbas Shah
- Department of Agronomy, Pir Mehr Ali Shah Arid Agriculture University, Rawalpindi, Pakistan.
| | - Feng Yang
- College of Agronomy, Sichuan Agricultural University, No. 211, Huimin Road, Wenjiang District, Chengdu, 611130, Sichuan, China.
- Sichuan Engineering Research Center for Crop Strip Intercropping System, Southwest China, Key Laboratory of Crop Ecophysiology and Farming System in Southwest China, Sichuan Agricultural University, Chengdu, China.
| | - Wenyu Yang
- College of Agronomy, Sichuan Agricultural University, No. 211, Huimin Road, Wenjiang District, Chengdu, 611130, Sichuan, China.
- Sichuan Engineering Research Center for Crop Strip Intercropping System, Southwest China, Key Laboratory of Crop Ecophysiology and Farming System in Southwest China, Sichuan Agricultural University, Chengdu, China.
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26
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Polla DL, Fard MAF, Tabatabaei Z, Habibzadeh P, Levchenko OA, Nikuei P, Makrythanasis P, Hussain M, von Hardenberg S, Zeinali S, Fallah MS, Schuurs-Hoeijmakers JHM, Shahzad M, Fatima F, Fatima N, Kaat LD, Bruggenwirth HT, Fleming LR, Condie J, Ploski R, Pollak A, Pilch J, Demina NA, Chukhrova AL, Sergeeva VS, Venselaar H, Masri AT, Hamamy H, Santoni FA, Linda K, Ahmed ZM, Kasri NN, de Brouwer APM, Bergmann AK, Hethey S, Yavarian M, Ansar M, Riazuddin S, Riazuddin S, Silawi M, Ruggeri G, Pirozzi F, Eftekhar E, Sheshdeh AT, Bahramjahan S, Mirzaa GM, Lavrov AV, Antonarakis SE, Faghihi MA, van Bokhoven H. Biallelic variants in TMEM222 cause a new autosomal recessive neurodevelopmental disorder. Genet Med 2021; 23:1246-1254. [PMID: 33824500 PMCID: PMC8725574 DOI: 10.1038/s41436-021-01133-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 02/12/2021] [Accepted: 02/16/2021] [Indexed: 01/25/2023] Open
Abstract
PURPOSE To elucidate the novel molecular cause in families with a new autosomal recessive neurodevelopmental disorder. METHODS A combination of exome sequencing and gene matching tools was used to identify pathogenic variants in 17 individuals. Quantitative reverse transcription polymerase chain reaction (RT-qPCR) and subcellular localization studies were used to characterize gene expression profile and localization. RESULTS Biallelic variants in the TMEM222 gene were identified in 17 individuals from nine unrelated families, presenting with intellectual disability and variable other features, such as aggressive behavior, shy character, body tremors, decreased muscle mass in the lower extremities, and mild hypotonia. We found relatively high TMEM222 expression levels in the human brain, especially in the parietal and occipital cortex. Additionally, subcellular localization analysis in human neurons derived from induced pluripotent stem cells (iPSCs) revealed that TMEM222 localizes to early endosomes in the synapses of mature iPSC-derived neurons. CONCLUSION Our findings support a role for TMEM222 in brain development and function and adds variants in the gene TMEM222 as a novel underlying cause of an autosomal recessive neurodevelopmental disorder.
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Affiliation(s)
- Daniel L. Polla
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands.,CAPES Foundation, Ministry of Education of Brazil, Brasília, Brazil.,These authors contributed equally: Daniel L. Polla, Mohammad Ali Farazi Fard
| | - Mohammad Ali Farazi Fard
- Persian BayanGene Research and Training Center, Shiraz University of Medical Sciences, Shiraz, Fars, Iran.,These authors contributed equally: Daniel L. Polla, Mohammad Ali Farazi Fard
| | - Zahra Tabatabaei
- Persian BayanGene Research and Training Center, Shiraz University of Medical Sciences, Shiraz, Fars, Iran
| | - Parham Habibzadeh
- Persian BayanGene Research and Training Center, Shiraz University of Medical Sciences, Shiraz, Fars, Iran
| | | | - Pooneh Nikuei
- Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Periklis Makrythanasis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.,Present address: Biomedical Research Foundation Academy of Athens, Athens, Greece
| | - Mureed Hussain
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Sirous Zeinali
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | | | - Janneke H. M. Schuurs-Hoeijmakers
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Mohsin Shahzad
- Department of Otorhinolaryngology Head & Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD, USA.,Department of Molecular Biology, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad, Pakistan.,Jinnah Burn and Reconstructive Surgery Center, Allama Iqbal Medical Research Center, University of Health Sciences, Lahore, Pakistan
| | - Fareeha Fatima
- Center for Excellence in Molecular Biology, University of Punjab, Lahore, Pakistan
| | - Neelam Fatima
- Center for Excellence in Molecular Biology, University of Punjab, Lahore, Pakistan
| | - Laura Donker Kaat
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Hennie T. Bruggenwirth
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Leah R. Fleming
- St. Luke’s Children’s Genetics and Metabolic Clinic, Boise, ID, USA
| | - John Condie
- St Luke’s Pediatric Neurology Clinic, Boise, ID, USA
| | - Rafal Ploski
- Department of Medical Genetics, Warsaw Medical University, Warsaw, Poland
| | - Agnieszka Pollak
- Department of Medical Genetics, Warsaw Medical University, Warsaw, Poland
| | - Jacek Pilch
- Department of Pediatric Neurology, Medical University of Silesia, Katowice, Poland
| | | | | | | | - Hanka Venselaar
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Amira T. Masri
- Faculty of Medicine, Pediatric Department Division of Child Neurology, The University of Jordan, Amman, Jordan
| | - Hanan Hamamy
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Federico A. Santoni
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.,Department of Endocrinology Diabetes and Metabolism, Lausanne University Hospital, Lausanne, Switzerland
| | - Katrin Linda
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Zubair M. Ahmed
- Department of Otorhinolaryngology Head & Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD, USA
| | - Nael Nadif Kasri
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Arjan P. M. de Brouwer
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Anke K. Bergmann
- Department of Human Genetics, Hannover Medical School, Hanover, Germany
| | - Sven Hethey
- Department of Neuropediatrics, Children’s and Youth Hospital Auf der Bult, Hanover, Germany
| | - Majid Yavarian
- Persian BayanGene Research and Training Center, Shiraz University of Medical Sciences, Shiraz, Fars, Iran
| | - Muhammad Ansar
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.,Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
| | - Saima Riazuddin
- Department of Otorhinolaryngology Head & Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD, USA
| | - Sheikh Riazuddin
- Department of Molecular Biology, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad, Pakistan.,Jinnah Burn and Reconstructive Surgery Center, Allama Iqbal Medical Research Center, University of Health Sciences, Lahore, Pakistan
| | - Mohammad Silawi
- Persian BayanGene Research and Training Center, Shiraz University of Medical Sciences, Shiraz, Fars, Iran
| | - Gaia Ruggeri
- Center for Integrative Brain Research, Seattle Children’s Research Institute, Seattle, WA, USA
| | - Filomena Pirozzi
- Center for Integrative Brain Research, Seattle Children’s Research Institute, Seattle, WA, USA
| | - Ebrahim Eftekhar
- Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Afsaneh Taghipour Sheshdeh
- Persian BayanGene Research and Training Center, Shiraz University of Medical Sciences, Shiraz, Fars, Iran
| | - Shima Bahramjahan
- Persian BayanGene Research and Training Center, Shiraz University of Medical Sciences, Shiraz, Fars, Iran
| | - Ghayda M. Mirzaa
- Center for Integrative Brain Research, Seattle Children’s Research Institute, Seattle, WA, USA.,Department of Pediatrics, University of Washington, Seattle, WA, USA.,Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | | | - Stylianos E. Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.,Medigenome, Swiss Institute of Genomic Medicine, Geneva, Switzerland
| | - Mohammad Ali Faghihi
- Persian BayanGene Research and Training Center, Shiraz University of Medical Sciences, Shiraz, Fars, Iran.,Department of Psychiatry & Behavioral Sciences, Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA
| | - Hans van Bokhoven
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands.
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27
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Acharya A, Raza SI, Anwar MZ, Bharadwaj T, Liaqat K, Khokhar MAS, Everard JL, Nasir A, Nickerson DA, Bamshad MJ, Ansar M, Schrauwen I, Ahmad W, Leal SM. Correction: Wolfram-like syndrome with bicuspid aortic valve due to a homozygous missense variant in CDK13. J Hum Genet 2021; 66:1019. [PMID: 34135457 PMCID: PMC8472884 DOI: 10.1038/s10038-021-00949-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Anushree Acharya
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Syed Irfan Raza
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan.,Department of Biochemistry, HBS Medical and Dental College, Islamabad, Pakistan
| | | | - Thashi Bharadwaj
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Khurram Liaqat
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | | | - Jenna L Everard
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Abdul Nasir
- Synthetic Protein Engineering Lab (SPEL), Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
| | | | | | - Michael J Bamshad
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.,Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Muhammad Ansar
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Isabelle Schrauwen
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Wasim Ahmad
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Suzanne M Leal
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Center, New York, NY, USA. .,Taub Institute for Alzheimer's Disease and The Aging Brain, Columbia University Medical Center, New York, NY, USA.
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28
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Ansar M, Ranza E, Shetty M, Paracha SA, Azam M, Kern I, Iwaszkiewicz J, Farooq O, Pournaras CJ, Malcles A, Kecik M, Rivolta C, Muzaffar W, Qurban A, Ali L, Aggoun Y, Santoni FA, Makrythanasis P, Ahmed J, Qamar R, Sarwar MT, Henry LK, Antonarakis SE. Taurine treatment of retinal degeneration and cardiomyopathy in a consanguineous family with SLC6A6 taurine transporter deficiency. Hum Mol Genet 2021; 29:618-623. [PMID: 31903486 DOI: 10.1093/hmg/ddz303] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 12/03/2019] [Accepted: 12/05/2019] [Indexed: 01/05/2023] Open
Abstract
In a consanguineous Pakistani family with two affected individuals, a homozygous variant Gly399Val in the eighth transmembrane domain of the taurine transporter SLC6A6 was identified resulting in a hypomorph transporting capacity of ~15% compared with normal. Three-dimensional modeling of this variant has indicated that it likely causes displacement of the Tyr138 (TM3) side chain, important for transport of taurine. The affected individuals presented with rapidly progressive childhood retinal degeneration, cardiomyopathy and almost undetectable plasma taurine levels. Oral taurine supplementation of 100 mg/kg/day resulted in maintenance of normal blood taurine levels. Following approval by the ethics committee, a long-term supplementation treatment was introduced. Remarkably, after 24-months, the cardiomyopathy was corrected in both affected siblings, and in the 6-years-old, the retinal degeneration was arrested, and the vision was clinically improved. Similar therapeutic approaches could be employed in Mendelian phenotypes caused by the dysfunction of the hundreds of other molecular transporters.
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Affiliation(s)
- Muhammad Ansar
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
| | - Emmanuelle Ranza
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland.,Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland
| | - Madhur Shetty
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND, USA
| | - Sohail A Paracha
- Institute of Basic Medical Sciences, Khyber Medical University, Peshawar, Pakistan
| | - Maleeha Azam
- Department of Biosciences, Faculty of Science, COMSATS University, Islamabad, Pakistan
| | - Ilse Kern
- Pediatric Nephrology and Metabolism Unit, Pediatric Subspecialties Service, Children's Hospital, Geneva University Hospitals, Geneva, Switzerland
| | - Justyna Iwaszkiewicz
- Swiss Institute of Bioinformatics, Molecular Modeling Group, University of Lausanne, Lausanne, Switzerland
| | - Omer Farooq
- Bahria University Medical and Dental College, Karachi, Pakistan
| | | | - Ariane Malcles
- Department of Ophthalmology, University Hospitals of Geneva, Geneva, Switzerland
| | - Mateusz Kecik
- Department of Ophthalmology, University Hospitals of Geneva, Geneva, Switzerland
| | - Carlo Rivolta
- Clinical Research Center, Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University Hospital Basel, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Waqar Muzaffar
- Armed Forces Institute of Ophthalmology, Rawalpindi, Pakistan
| | - Aziz Qurban
- Armed Forces Institute of Ophthalmology, Rawalpindi, Pakistan
| | - Liaqat Ali
- Department of Biosciences, Faculty of Science, COMSATS University, Islamabad, Pakistan
| | - Yacine Aggoun
- Pediatric Cardiology, Geneva University Hospitals, Geneva, Switzerland
| | - Federico A Santoni
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
| | - Periklis Makrythanasis
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
| | - Jawad Ahmed
- Institute of Basic Medical Sciences, Khyber Medical University, Peshawar, Pakistan
| | - Raheel Qamar
- Department of Biosciences, Faculty of Science, COMSATS University, Islamabad, Pakistan
| | - Muhammad T Sarwar
- Institute of Basic Medical Sciences, Khyber Medical University, Peshawar, Pakistan
| | - L Keith Henry
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND, USA
| | - Stylianos E Antonarakis
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland.,Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland.,iGE3 Institute of Genetics and Genomics of Geneva, Geneva, Switzerland
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29
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Acharya A, Raza SI, Anwar MZ, Bharadwaj T, Liaqat K, Khokhar MAS, Everard JL, Nasir A, Nickerson DA, Bamshad MJ, Ansar M, Schrauwen I, Ahmad W, Leal SM. Wolfram-like syndrome with bicuspid aortic valve due to a homozygous missense variant in CDK13. J Hum Genet 2021; 66:1009-1018. [PMID: 33879837 PMCID: PMC8472924 DOI: 10.1038/s10038-021-00922-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 03/17/2021] [Accepted: 03/18/2021] [Indexed: 12/03/2022]
Abstract
Background Wolfram syndrome (WFS) is characterized by deafness, diabetes mellitus, and diabetes insipidus along with optic atrophy. WFS has an autosomal recessive mode of inheritance and is due to variants in WFS1 and CISD2. Methods We evaluated the underlying molecular etiology of three affected members of a consanguineous family with hearing impairment, bicuspid aortic valve, diabetes mellitus and insipidus, clinodactyly, and gastrointestinal tract abnormalities via exome sequencing approach. We correlated clinical and imaging data with the genetic findings and their associated phenotypes. Results We identified a homozygous missense variant p.(Asn1097Lys) in CDK13, a gene previously associated with autosomal dominant congenital heart defects, dysmorphic facial features, clinodactyly, gastrointestinal tract abnormalities, intellectual developmental disorder, and seizures with variable phenotypic features. Conclusion We report a homozygous variant in CDK13 and suggest that this gene causes an autosomal recessive disorder with hearing impairment, bicuspid aortic valve, diabetes mellitus and insipidus, clinodactyly, and gastrointestinal tract abnormalities.
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Affiliation(s)
- Anushree Acharya
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Syed Irfan Raza
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan.,Department of Biochemistry, HBS Medical and Dental College, Islamabad, Pakistan
| | | | - Thashi Bharadwaj
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Khurram Liaqat
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | | | - Jenna L Everard
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Abdul Nasir
- Synthetic Protein Engineering Lab (SPEL), Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
| | | | | | - Michael J Bamshad
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.,Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Muhammad Ansar
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Isabelle Schrauwen
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Wasim Ahmad
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Suzanne M Leal
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Center, New York, NY, USA. .,Taub Institute for Alzheimer's Disease and The Aging Brain, Columbia University Medical Center, New York, NY, USA.
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30
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Lhussiez V, Dubus E, Cesar Q, Acar N, Nandrot EF, Simonutti M, Audo I, Lizé E, Nguyen S, Geissler A, Bouchot A, Ansar M, Picaud S, Thauvin-Robinet C, Olivier-Faivre L, Duplomb L, Da Costa R. Cohen Syndrome-Associated Cataract Is Explained by VPS13B Functions in Lens Homeostasis and Is Modified by Additional Genetic Factors. Invest Ophthalmol Vis Sci 2021; 61:18. [PMID: 32915983 PMCID: PMC7488618 DOI: 10.1167/iovs.61.11.18] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Purpose Cohen syndrome (CS) is a rare genetic disorder caused by variants of the VPS13B gene. CS patients are affected with a severe form of retinal dystrophy, and in several cases cataracts also develop. The purpose of this study was to investigate the mechanisms and risk factors for cataract in CS, as well as to report on cataract surgeries in CS patients. Methods To understand how VPS13B is associated with visual impairments in CS, we generated the Vps13b∆Ex3/∆Ex3 mouse model. Mice from 1 to 3 months of age were followed by ophthalmoscopy and slit-lamp examinations. Phenotypes were investigated by histology, immunohistochemistry, and western blot. Literature analysis was performed to determine specific characteristic features of cataract in CS and to identify potential genotype–phenotype correlations. Results Cataracts rapidly developed in 2-month-old knockout mice and were present in almost all lenses at 3 months. Eye fundi appeared normal until cataract development. Lens immunostaining revealed that cataract formation was associated with the appearance of large vacuoles in the cortical area, epithelial–mesenchymal transition, and fibrosis. In later stages, cataracts became hypermature, leading to profound retinal remodeling due to inflammatory events. Literature analysis showed that CS-related cataracts display specific features compared to other forms of retinitis pigmentosa-related cataracts, and their onset is modified by additional genetic factors. Corroboratively, we were able to isolate a subline of the Vps13b∆Ex3/∆Ex3 model with delayed cataract onset. Conclusions VPS13B participates in lens homeostasis, and the CS-related cataract development dynamic is linked to additional genetic factors.
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Affiliation(s)
- Vincent Lhussiez
- INSERM UMR1231, Equipe GAD, Université de Bourgogne Franche Comté, Dijon, France
| | - Elisabeth Dubus
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France.,Centre des Sciences du Goût et de l'Alimentation, AgroSup Dijon, CNRS, INRAE, Université Bourgogne Franche-Comté, Dijon, France
| | - Quénol Cesar
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Niyazi Acar
- Centre des Sciences du Goût et de l'Alimentation, AgroSup Dijon, CNRS, INRAE, Université Bourgogne Franche-Comté, Dijon, France
| | - Emeline F Nandrot
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Manuel Simonutti
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Isabelle Audo
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Eléonore Lizé
- INSERM UMR1231, Equipe GAD, Université de Bourgogne Franche Comté, Dijon, France
| | - Sylvie Nguyen
- INSERM UMR1231, Equipe GAD, Université de Bourgogne Franche Comté, Dijon, France
| | - Audrey Geissler
- Plateforme d'Imagerie Cellulaire DImaCell (site CellImaP), INSERM LNC UMR1231, Dijon, France
| | - André Bouchot
- Plateforme d'Imagerie Cellulaire DImaCell (site CellImaP), INSERM LNC UMR1231, Dijon, France
| | - Muhammad Ansar
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland.,Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Serge Picaud
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Christel Thauvin-Robinet
- INSERM UMR1231, Equipe GAD, Université de Bourgogne Franche Comté, Dijon, France.,FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France.,Centre de Référence Déficiences Intellectuelles de Causes Rares, CHU Dijon Bourgogne, Dijon, France
| | - Laurence Olivier-Faivre
- INSERM UMR1231, Equipe GAD, Université de Bourgogne Franche Comté, Dijon, France.,FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France.,Centre de Référence Anomalies du Développement et Syndromes Malformatifs, CHU Dijon Bourgogne, Dijon, France
| | - Laurence Duplomb
- INSERM UMR1231, Equipe GAD, Université de Bourgogne Franche Comté, Dijon, France.,FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Romain Da Costa
- INSERM UMR1231, Equipe GAD, Université de Bourgogne Franche Comté, Dijon, France.,FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
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31
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Antonarakis SE, Holoubek A, Rapti M, Rademaker J, Meylan J, Iwaszkiewicz J, Zoete V, Wilson C, Taylor J, Ansar M, Borel C, Menzel O, Kuželová K, Santoni FA. Dominant monoallelic variant in the PAK2 gene causes Knobloch syndrome type 2. Hum Mol Genet 2021; 31:1-9. [PMID: 33693784 DOI: 10.1093/hmg/ddab026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 01/11/2021] [Accepted: 01/31/2021] [Indexed: 11/12/2022] Open
Abstract
Knobloch syndrome is an autosomal recessive phenotype mainly characterized by retinal detachment and encephalocele caused by biallelic pathogenic variants in the COL18A1 gene. However, there are patients clinically diagnosed as Knobloch syndrome with unknown molecular etiology not linked to COL18A1. We studied an historical pedigree (published in 1998) designated as KNO2 (Knobloch type 2 syndrome with intellectual disability, autistic behavior, retinal degeneration, encephalocele). Whole exome sequencing of the two affected siblings and the normal parents resulted in the identification of a PAK2 non-synonymous substitution p.(Glu435Lys) as a causative variant. The variant was monoallelic and apparently de novo in both siblings indicating a likely germline mosaicism in one of the parents; the mosaicism however could not be observed after deep sequencing of blood parental DNA. PAK2 encodes a member of a small group of serine/threonine kinases; these P21-activating kinases (PAKs) are essential in signal transduction and cellular regulation (cytoskeletal dynamics, cell motility, death and survival signaling, and cell cycle progression). Structural analysis of the PAK2 p.(Glu435Lys) variant which is located in the kinase domain of the protein predicts a possible compromise in the kinase activity. Functional analysis of the p.(Glu435Lys) PAK2 variant in transfected HEK293T cells results in a partial loss of the kinase activity. PAK2 has been previously suggested as an autism related gene. Our results show that PAK2 induced phenotypic spectrum is broad and not fully understood. We conclude that the KNO2 syndrome in the studied family is dominant and caused by a deleterious variant in the PAK2 gene.
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Affiliation(s)
- Stylianos E Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical Faculty, Geneva 1211, Switzerland.,iGE3 Institute of Genetics and Genomics of Geneva, Geneva 1211, Switzerland
| | - Ales Holoubek
- Department of Proteomics, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Melivoia Rapti
- Department of Endocrinology Diabetes and Metabolism, Lausanne University Hospital, Lausanne 1011, Switzerland
| | - Jesse Rademaker
- Department of Endocrinology Diabetes and Metabolism, Lausanne University Hospital, Lausanne 1011, Switzerland
| | - Jenny Meylan
- Department of Endocrinology Diabetes and Metabolism, Lausanne University Hospital, Lausanne 1011, Switzerland
| | - Justyna Iwaszkiewicz
- Molecular Modeling Group, Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Vincent Zoete
- Molecular Modeling Group, Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland.,Department of Fundamental Oncology, Ludwig Institute for Cancer Research, Lausanne University, Epalinges 1066, Switzerland
| | - Callum Wilson
- National Metabolic Service, Starship Children's Hospital, Auckland 1142, New Zealand
| | - Juliet Taylor
- National Metabolic Service, Starship Children's Hospital, Auckland 1142, New Zealand
| | - Muhammad Ansar
- Institute of Molecular and Clinical Ophthalmology, Basel 4031, Switzerland
| | - Christelle Borel
- Department of Genetic Medicine and Development, University of Geneva Medical Faculty, Geneva 1211, Switzerland
| | - Olivier Menzel
- Health 2030 Genome Center, Foundation Campus Biotech Geneva Foundation, Geneva 1202, Switzerland
| | - Kateřina Kuželová
- Department of Proteomics, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Federico A Santoni
- Department of Endocrinology Diabetes and Metabolism, Lausanne University Hospital, Lausanne 1011, Switzerland.,Faculty of Biology and Medicine, University of Lausanne, Lausanne 1011, Switzerland
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Poulter JA, Gravett MSC, Taylor RL, Fujinami K, De Zaeytijd J, Bellingham J, Rehman AU, Hayashi T, Kondo M, Rehman A, Ansar M, Donnelly D, Toomes C, Ali M, De Baere E, Leroy BP, Davies NP, Henderson RH, Webster AR, Rivolta C, Zeitz C, Mahroo OA, Arno G, Black GCM, McKibbin M, Harris SA, Khan KN, Inglehearn CF. New variants and in silico analyses in GRK1 associated Oguchi disease. Hum Mutat 2021; 42:164-176. [PMID: 33252155 PMCID: PMC7898643 DOI: 10.1002/humu.24140] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 09/15/2020] [Accepted: 11/05/2020] [Indexed: 12/16/2022]
Abstract
Biallelic mutations in G-Protein coupled receptor kinase 1 (GRK1) cause Oguchi disease, a rare subtype of congenital stationary night blindness (CSNB). The purpose of this study was to identify disease causing GRK1 variants and use in-depth bioinformatic analyses to evaluate how their impact on protein structure could lead to pathogenicity. Patients' genomic DNA was sequenced by whole genome, whole exome or focused exome sequencing. Disease associated variants, published and novel, were compared to nondisease associated missense variants. The impact of GRK1 missense variants at the protein level were then predicted using a series of computational tools. We identified twelve previously unpublished cases with biallelic disease associated GRK1 variants, including eight novel variants, and reviewed all GRK1 disease associated variants. Further structure-based scoring revealed a hotspot for missense variants in the kinase domain. In addition, to aid future clinical interpretation, we identified the bioinformatics tools best able to differentiate disease associated from nondisease associated variants. We identified GRK1 variants in Oguchi disease patients and investigated how disease-causing variants may impede protein function in-silico.
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Affiliation(s)
- James A. Poulter
- Division of Molecular Medicine, Leeds Institute of Medical ResearchUniversity of LeedsLeedsUK
| | | | - Rachel L. Taylor
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicines and HealthUniversity of ManchesterManchesterUK
| | - Kaoru Fujinami
- National Institute of Sensory Organs, National Hospital Organization Tokyo Medical CentreTokyoJapan
- Moorfields Eye HospitalLondonUK
- UCL Institute of OphthalmologyLondonUK
- Keio University School of MedicineTokyoJapan
| | | | | | - Atta Ur Rehman
- Division of Genetic Medicine, Centre Hospitalier Universitaire Vaudois (CHUV)University of LausanneLausanneSwitzerland
| | | | - Mineo Kondo
- Mie University Graduate School of MedicineMieJapan
| | - Abdur Rehman
- Department of Genetics, Faculty of ScienceHazara University MansehraDhodialPakistan
| | - Muhammad Ansar
- Clinical Research Center, Institute of Molecular and Clinical Ophthalmology Basel (IOB)BaselSwitzerland
| | - Dan Donnelly
- School of Biomedical Sciences, University of LeedsLeedsUK
| | - Carmel Toomes
- Division of Molecular Medicine, Leeds Institute of Medical ResearchUniversity of LeedsLeedsUK
| | - Manir Ali
- Division of Molecular Medicine, Leeds Institute of Medical ResearchUniversity of LeedsLeedsUK
| | | | | | - Bart P. Leroy
- Ghent UniversityGhentBelgium
- Children's Hospital of PhiladelphiaPhiladelphiaPennsylvaniaUSA
| | | | | | - Andrew R. Webster
- Moorfields Eye HospitalLondonUK
- UCL Institute of OphthalmologyLondonUK
| | - Carlo Rivolta
- Department of Genetics and Genome BiologyUniversity of LeicesterLeicesterUK
- Clinical Research Center, Institute of Molecular and Clinical Ophthalmology Basel (IOB)BaselSwitzerland
- Department of OphthalmologyUniversity Hospital BaselBaselSwitzerland
| | - Christina Zeitz
- Sorbonne UniversitéINSERM, CNRS, Institut de la VisionParisFrance
| | - Omar A. Mahroo
- Moorfields Eye HospitalLondonUK
- UCL Institute of OphthalmologyLondonUK
| | - Gavin Arno
- National Institute of Sensory Organs, National Hospital Organization Tokyo Medical CentreTokyoJapan
- Moorfields Eye HospitalLondonUK
- UCL Institute of OphthalmologyLondonUK
| | - Graeme C. M. Black
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicines and HealthUniversity of ManchesterManchesterUK
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Manchester University NHS Foundation TrustManchesterUK
| | - Martin McKibbin
- Division of Molecular Medicine, Leeds Institute of Medical ResearchUniversity of LeedsLeedsUK
- Leeds Teaching Hospitals NHS Trust, St James’ University HospitalLeedsUK
| | | | - Kamron N. Khan
- Division of Molecular Medicine, Leeds Institute of Medical ResearchUniversity of LeedsLeedsUK
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Manchester University NHS Foundation TrustManchesterUK
| | - Chris F. Inglehearn
- Division of Molecular Medicine, Leeds Institute of Medical ResearchUniversity of LeedsLeedsUK
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Poulter JA, Gravett MSC, Taylor RL, Fujinami K, De Zaeytijd J, Bellingham J, Rehman AU, Hayashi T, Kondo M, Rehman A, Ansar M, Donnelly D, Toomes C, Ali M, De Baere E, Leroy BP, Davies NP, Henderson RH, Webster AR, Rivolta C, Zeitz C, Mahroo OA, Arno G, Black GCM, McKibbin M, Harris SA, Khan KN, Inglehearn CF. Cover, Volume 42, Issue 2. Hum Mutat 2021. [DOI: 10.1002/humu.24169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- James A. Poulter
- Division of Molecular Medicine, Leeds Institute of Medical Research University of Leeds Leeds UK
| | | | - Rachel L. Taylor
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicines and Health University of Manchester Manchester UK
| | - Kaoru Fujinami
- National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Centre Tokyo Japan
- Moorfields Eye Hospital London UK
- UCL Institute of Ophthalmology London UK
- Keio University School of Medicine Tokyo Japan
| | | | | | - Atta Ur Rehman
- Division of Genetic Medicine, Centre Hospitalier Universitaire Vaudois (CHUV) University of Lausanne Lausanne Switzerland
| | | | - Mineo Kondo
- Mie University Graduate School of Medicine Mie Japan
| | - Abdur Rehman
- Department of Genetics, Faculty of Science Hazara University Mansehra Dhodial Pakistan
| | - Muhammad Ansar
- Clinical Research Center, Institute of Molecular and Clinical Ophthalmology Basel (IOB) Basel Switzerland
| | - Dan Donnelly
- School of Biomedical Sciences, University of Leeds Leeds UK
| | - Carmel Toomes
- Division of Molecular Medicine, Leeds Institute of Medical Research University of Leeds Leeds UK
| | - Manir Ali
- Division of Molecular Medicine, Leeds Institute of Medical Research University of Leeds Leeds UK
| | | | - Bart P. Leroy
- Ghent University Ghent Belgium
- Children's Hospital of Philadelphia Philadelphia Pennsylvania USA
| | | | | | - Andrew R. Webster
- Moorfields Eye Hospital London UK
- UCL Institute of Ophthalmology London UK
| | - Carlo Rivolta
- Department of Genetics and Genome Biology University of Leicester Leicester UK
- Clinical Research Center, Institute of Molecular and Clinical Ophthalmology Basel (IOB) Basel Switzerland
- Department of Ophthalmology University Hospital Basel Basel Switzerland
| | - Christina Zeitz
- Sorbonne Université INSERM, CNRS, Institut de la Vision Paris France
| | - Omar A. Mahroo
- Moorfields Eye Hospital London UK
- UCL Institute of Ophthalmology London UK
| | - Gavin Arno
- National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Centre Tokyo Japan
- Moorfields Eye Hospital London UK
- UCL Institute of Ophthalmology London UK
| | - Graeme C. M. Black
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicines and Health University of Manchester Manchester UK
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Manchester University NHS Foundation Trust Manchester UK
| | - Martin McKibbin
- Division of Molecular Medicine, Leeds Institute of Medical Research University of Leeds Leeds UK
- Leeds Teaching Hospitals NHS Trust, St James’ University Hospital Leeds UK
| | - Sarah A. Harris
- School of Physics and Astronomy, University of Leeds Leeds UK
| | - Kamron N. Khan
- Division of Molecular Medicine, Leeds Institute of Medical Research University of Leeds Leeds UK
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Manchester University NHS Foundation Trust Manchester UK
| | - Chris F. Inglehearn
- Division of Molecular Medicine, Leeds Institute of Medical Research University of Leeds Leeds UK
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Bibi S, Ahmad F, Alam MR, Ansar M, Yeou KS, Wahedi HM. Lapachol-Induced Upregulation of Sirt1/Sirt3 is linked with Improved Skin Wound Healing in Alloxan-induced Diabetic Mice. Iran J Pharm Res 2021; 20:419-430. [PMID: 34903998 PMCID: PMC8653681 DOI: 10.22037/ijpr.2021.112722.13914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Timely repair of damaged skin is very important to maintain the integrity and homeostasis of skin, but the wound healing process is compromised in diabetic patients due to several extrinsic and intrinsic factors thus lead to leg amputation and death eventually. Sirtuins, a family of seven conserved proteins are known to be associated with pathophysiological processes of the skin. The most important among them are sirt1and sirt3 involved in cell regeneration and cell survival. Naphthoquinone derivatives have a wide range of therapeutic properties, but the potential diabetic wound healing activity of lapachol has not been identified yet. The present study thus aimed to investigate the wound healing effects of lapachol in a diabetic mouse model. Diabetic wounded mice were divided into 3 groups; vehicle, lapachol 0.05%, and lapachol 0.1%. Skin samples collected from diabetic wounded mice on different time points after treatment for 10 consecutive days were subjected to downstream analysis by western blot, ELISA and histology. Lapachol treatment was found to enhance the expression of sirt1/sirt3 and other proteins involved in cell migration and blood vessel formation. The tissue development rate was increased by lapachol treatment with better collagen deposition. Interestingly, lapachol treatment also gave rise to a high concentration of growth factors resulting in speedy and timely recovery of injured skin. In summary, our findings suggest that lapachol promotes efficient wound healing in a diabetic mouse model by increasing the expression of sirt1 and sirt3 and other proteins related to wound repair and skin regeneration including α-PAK, RAC1/CDC42, VEGF and growth factors viz PDGF and VEGF. This research work finds a novel potential activator of sirtuins in the form of lapachol and depicts the role of activated sirtuins in diabetic wound healing.
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Affiliation(s)
- Shaheen Bibi
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam, University, Islamabad, 45320, Pakistan.
| | - Fayyaz Ahmad
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam, University, Islamabad, 45320, Pakistan.
| | - Muhammad Rizwan Alam
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam, University, Islamabad, 45320, Pakistan.
| | - Muhammad Ansar
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam, University, Islamabad, 45320, Pakistan.
| | - Kim Sun Yeou
- College of Pharmacy, Gachon University, #191, Hambakmoero, Yeonsu-gu, Incheon 21936, Republic of Korea.
| | - Hussain Mustatab Wahedi
- Department of Biological Sciences, National University of Medical Sciences, C/O Military Hospital, The Mall Road, 46000 Rawalpindi, Pakistan.
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Abstract
Hashimoto encephalopathy (HE) is a heterogenous neurological syndrome that can manifest with encephalopathy, seizures, headaches, and variable neuropsychiatric disturbances. The underlying mechanism remains unclear; however, autoimmune pathogenesis is suspected due to its association with autoimmune thyroid disease, high titers of anti-thyroid antibodies, and quick response to steroid therapy. We report a 59-year-old female patient with a remote history of hypothyroidism who presented with status epilepticus and complaints of chronic headaches and cognitive impairment. The presence of sharp frontal waves was identified on her EEG. The patient was initially started on anti-epileptics only; however, her headaches and memory loss escalated, further diagnostic workup was pursued, which revealed high anti-thyroid peroxidase antibodies with normal thyroid function tests. The only cerebrospinal fluid (CSF) abnormality noticed was an elevated protein concentration. MRI showed non-specific right frontal lobe pial enhancement. Remaining infectious, rheumatologic, and neurologic testing was unremarkable. The patient was started on a steroid regimen with successful resolution of symptoms and return of cognitive baseline. Hashimoto’s encephalopathy is a diagnosis of exclusion; however, it should be considered in patients with high titers of anti-thyroid antibodies and neurological symptoms that cannot be explained by thorough infectious, metabolic, and autoimmune testing. It is essential to recognize this neurological entity as fast clinical improvement may be achieved with steroids and other immunotherapies.
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Affiliation(s)
- Aleksandra Sliwinska
- Department of Medicine, University of Connecticut School of Medicine, Farmington, USA
| | - Perry Fumuso
- Department of Medicine, University of Connecticut School of Medicine, Farmington, USA
| | - Bryan Stringer
- Department of Medicine, University of Connecticut School of Medicine, Farmington, USA
| | - Muhammad Ansar
- Department of Endocrinology and Metabolism, University of Connecticut School of Medicine, Farmington, USA
| | - Jennifer Baldwin
- Department of Medicine, University of Connecticut School of Medicine, Farmington, USA
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Ahmad F, Bibi S, Kang M, Anees M, Ansar M, Alam MR, Kim SY, Wahedi HM. Naphthoquinones from Handroanthus impetiginosus promote skin wound healing through Sirt3 regulation. Iran J Basic Med Sci 2020; 23:1139-1145. [PMID: 32963735 PMCID: PMC7491501 DOI: 10.22038/ijbms.2020.43706.10275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Objective(s): Lapachone is a natural naphthoquinone-derived compound found in Tabebuia avellanedae. It is well-known for its analgesic, anti-inflammatory, anti-microbial, diuretic, and anti-cancerous effects. However, the wound-healing effects of this compound are not known yet. The aim of this study was to investigate the wound healing activity of naphthoquinones (α-lapachone and β-lapachone) from Handroanthus impetiginosus. Materials and Methods: Expression of Sirt3, migration-related proteins (Rac1, Cdc42, α-Pak) and angiogenesis-related protein of vascular endothelial growth factor (VEGF) was monitored using western blot analysis. Blood vessel formation and tissue development were monitored by angiogenesis assay and hematoxylin & eosin (H & E) staining, respectively on mouse skin tissue samples. Both α-lapachone and β-lapachone increased Sirt3 expression in vivo, but only β-lapachone increased Sirt3 expression in vitro. Results: Both the compounds accelerated wound healing in cultured skin cells as well as mouse skin; however, β-lapachone was more effective at lower concentrations. Both of the compounds increased the expression of migration-related proteins both in vitro and in vivo. Similarly, α-lapachone and β-lapachone increased VEGF expression, tissue development and blood vessel formation in mouse skin. Conclusion: These findings indicated that α-lapachone and β-lapachone are novel Sirt3 activators, and Sirt3 has a role in wound healing. Thus, Sirt3 and its regulators come out as a novel target and potential drug candidates, respectively in the important field of cutaneous wound healing.
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Affiliation(s)
- Fayyaz Ahmad
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, 45320 Islamabad, Pakistan
| | - Shaheen Bibi
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, 45320 Islamabad, Pakistan
| | - Mincheol Kang
- College of Pharmacy, Gachon University, 191 Hambakmaero, Incheon, South Korea
| | - Mariam Anees
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, 45320 Islamabad, Pakistan
| | - Muhammad Ansar
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, 45320 Islamabad, Pakistan
| | - Muhammad Rizwan Alam
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, 45320 Islamabad, Pakistan
| | - Sun Yeou Kim
- College of Pharmacy, Gachon University, 191 Hambakmaero, Incheon, South Korea
| | - Hussain Mustatab Wahedi
- Department of Biological Sciences, National University of Medical Sciences, C/O Military Hospital, Mall Road Rawalpindi, Pakistan
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Khan A, Miao Z, Umair M, Ullah A, Alshabeeb MA, Bilal M, Ahmad F, Rappold GA, Ansar M, Carapito R. Two Cases of Recessive Intellectual Disability Caused by NDST1 and METTL23 Variants. Genes (Basel) 2020; 11:E1021. [PMID: 32878022 PMCID: PMC7563614 DOI: 10.3390/genes11091021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 08/24/2020] [Accepted: 08/26/2020] [Indexed: 12/03/2022] Open
Abstract
Intellectual disability (ID) is a highly heterogeneous genetic condition with more than a thousand genes described so far. By exome sequencing of two consanguineous families presenting hallmark features of ID, we identified two homozygous variants in two genes previously associated with autosomal recessive ID: NDST1 (c.1966G>A; p.Asp656Asn) and METTL23 (c.310T>C; p.Phe104Leu). The segregation of the variants was validated by Sanger sequencing in all family members. In silico homology modeling of wild-type and mutated proteins revealed substantial changes in the secondary structure of both proteins, indicating a possible effect on function. The identification and validation of new pathogenic NDST1 and METTL23 variants in two cases of autosomal recessive ID further highlight the importance of these genes in proper brain function and development.
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Affiliation(s)
- Amjad Khan
- Laboratoire d’ImmunoRhumatologie Moléculaire, Plateforme GENOMAX, INSERM UMR_S 1109, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), LabEx TRANSPLANTEX, Université de Strasbourg, 67085 Strasbourg, France;
| | - Zhichao Miao
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, UK;
- Shanghai Fourth People’s Hospital Affiliated to Tongji University School of Medicine, No.1878 North Sichuan Road, Hongkou District, Shanghai 200081, China
| | - Muhammad Umair
- Medical Genomics Research Department, King Abdullah International Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh 11481, Saudi Arabia;
| | - Amir Ullah
- Nephrology and Dialysis Unit, District Head Quarter Teaching Hospital, Bannu 28100, Pakistan;
| | - Mohammad A. Alshabeeb
- Developmental Medicine Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard-Health Affairs (MNGHA), Riyadh 11481, Saudi Arabia;
| | - Muhammad Bilal
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan; (M.B.); (M.A.)
| | - Farooq Ahmad
- Department of Chemistry, Women University Swabi, Khyber Pakhtunkhwa 23430, Pakistan;
| | - Gudrun A. Rappold
- Department of Human Molecular Genetics, Institute of Human Genetics, Ruprecht-Karls-University, 69118 Heidelberg, Germany;
| | - Muhammad Ansar
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan; (M.B.); (M.A.)
| | - Raphael Carapito
- Laboratoire d’ImmunoRhumatologie Moléculaire, Plateforme GENOMAX, INSERM UMR_S 1109, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), LabEx TRANSPLANTEX, Université de Strasbourg, 67085 Strasbourg, France;
- Service d’Immunologie Biologique, Plateau Technique de Biologie, Pôle de Biologie, Nouvel Hôpital Civil, Hôpitaux Universitaires de Strasbourg, 1 Place de l’Hôpital, 67091 Strasbourg, France
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38
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Manole A, Efthymiou S, O'Connor E, Mendes MI, Jennings M, Maroofian R, Davagnanam I, Mankad K, Lopez MR, Salpietro V, Harripaul R, Badalato L, Walia J, Francklyn CS, Athanasiou-Fragkouli A, Sullivan R, Desai S, Baranano K, Zafar F, Rana N, Ilyas M, Horga A, Kara M, Mattioli F, Goldenberg A, Griffin H, Piton A, Henderson LB, Kara B, Aslanger AD, Raaphorst J, Pfundt R, Portier R, Shinawi M, Kirby A, Christensen KM, Wang L, Rosti RO, Paracha SA, Sarwar MT, Jenkins D, Ahmed J, Santoni FA, Ranza E, Iwaszkiewicz J, Cytrynbaum C, Weksberg R, Wentzensen IM, Guillen Sacoto MJ, Si Y, Telegrafi A, Andrews MV, Baldridge D, Gabriel H, Mohr J, Oehl-Jaschkowitz B, Debard S, Senger B, Fischer F, van Ravenwaaij C, Fock AJM, Stevens SJC, Bähler J, Nasar A, Mantovani JF, Manzur A, Sarkozy A, Smith DEC, Salomons GS, Ahmed ZM, Riazuddin S, Riazuddin S, Usmani MA, Seibt A, Ansar M, Antonarakis SE, Vincent JB, Ayub M, Grimmel M, Jelsig AM, Hjortshøj TD, Karstensen HG, Hummel M, Haack TB, Jamshidi Y, Distelmaier F, Horvath R, Gleeson JG, Becker H, Mandel JL, Koolen DA, Houlden H. De Novo and Bi-allelic Pathogenic Variants in NARS1 Cause Neurodevelopmental Delay Due to Toxic Gain-of-Function and Partial Loss-of-Function Effects. Am J Hum Genet 2020; 107:311-324. [PMID: 32738225 PMCID: PMC7413890 DOI: 10.1016/j.ajhg.2020.06.016] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 06/23/2020] [Indexed: 12/19/2022] Open
Abstract
Aminoacyl-tRNA synthetases (ARSs) are ubiquitous, ancient enzymes that charge amino acids to cognate tRNA molecules, the essential first step of protein translation. Here, we describe 32 individuals from 21 families, presenting with microcephaly, neurodevelopmental delay, seizures, peripheral neuropathy, and ataxia, with de novo heterozygous and bi-allelic mutations in asparaginyl-tRNA synthetase (NARS1). We demonstrate a reduction in NARS1 mRNA expression as well as in NARS1 enzyme levels and activity in both individual fibroblasts and induced neural progenitor cells (iNPCs). Molecular modeling of the recessive c.1633C>T (p.Arg545Cys) variant shows weaker spatial positioning and tRNA selectivity. We conclude that de novo and bi-allelic mutations in NARS1 are a significant cause of neurodevelopmental disease, where the mechanism for de novo variants could be toxic gain-of-function and for recessive variants, partial loss-of-function.
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Affiliation(s)
- Andreea Manole
- Department of Neuromuscular Disorders, University College London (UCL) Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Stephanie Efthymiou
- Department of Neuromuscular Disorders, University College London (UCL) Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Emer O'Connor
- Department of Neuromuscular Disorders, University College London (UCL) Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Marisa I Mendes
- Metabolic Unit, Department of Clinical Chemistry, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam, Amsterdam Neuroscience, Amsterdam Gastroenterology and Metabolism, Amsterdam, 1081 the Netherlands
| | - Matthew Jennings
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, CB2 0QQ UK
| | - Reza Maroofian
- Department of Neuromuscular Disorders, University College London (UCL) Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Indran Davagnanam
- Department of Brain Repair and Rehabilitation, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Kshitij Mankad
- Department of Neuroradiology, Great Ormond Street Hospital for Children, London, WC1N 3JH, UK
| | - Maria Rodriguez Lopez
- Institute of Healthy Ageing, Department of Genetics, Evolution and Environment, University College London (UCL), London, WC1E 6BT, UK
| | - Vincenzo Salpietro
- Department of Neuromuscular Disorders, University College London (UCL) Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Ricardo Harripaul
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, ON, M5T 1R8, Canada; Institute of Medical Science and Department of Psychiatry, University of Toronto, Toronto, ON, M5T 1R8, Canada
| | - Lauren Badalato
- Department of Pediatrics, Queen's University, Kingston, ON, K7L 2V7, Canada
| | - Jagdeep Walia
- Department of Pediatrics, Queen's University, Kingston, ON, K7L 2V7, Canada
| | - Christopher S Francklyn
- Department of Biochemistry, University of Vermont College of Medicine, Burlington, VT 05405, USA
| | - Alkyoni Athanasiou-Fragkouli
- Department of Neuromuscular Disorders, University College London (UCL) Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Roisin Sullivan
- Department of Neuromuscular Disorders, University College London (UCL) Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Sonal Desai
- Department of Neurology and Pediatrics, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Kristin Baranano
- Department of Neurology and Pediatrics, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Faisal Zafar
- Department of Pediatrics, Multan Hospital, Multan, 60000, Pakistan
| | - Nuzhat Rana
- Department of Pediatrics, Multan Hospital, Multan, 60000, Pakistan
| | | | - Alejandro Horga
- Department of Neuromuscular Disorders, University College London (UCL) Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Majdi Kara
- Department of Pediatrics, Tripoli Children's Hospital, Tripoli, Libya
| | - Francesca Mattioli
- Institute for Genetics and Molecular and Cellular Biology (IGBMC), University of Strasbourg, CNRS UMR7104, INSERM U1258, Illkirch, 67404, France
| | - Alice Goldenberg
- Département de Génétique, centre de référence anomalies du développement et syndromes malformatifs, CHU de Rouen, Inserm U1245, UNIROUEN, Normandie Université, Centre Normand de Génomique et de Médecine Personnalisée, Rouen, 76031, France
| | - Helen Griffin
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, CB2 0QQ UK
| | - Amelie Piton
- Institute for Genetics and Molecular and Cellular Biology (IGBMC), University of Strasbourg, CNRS UMR7104, INSERM U1258, Illkirch, 67404, France
| | | | | | | | - Joost Raaphorst
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands; Department of Neurology, Amsterdam Neuroscience Institute, Amsterdam University Medical Center, 1105AZ Amsterdam, the Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands
| | - Ruben Portier
- Department of Neurology, Medisch Spectrum Twente, 7512KZ Enschede, the Netherlands
| | - Marwan Shinawi
- Department of Pediatrics, Divisions of Genetics and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Amelia Kirby
- Division of Medical Genetics, SSM Health Cardinal Glennon Children's Hospital, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Katherine M Christensen
- Division of Medical Genetics, SSM Health Cardinal Glennon Children's Hospital, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Lu Wang
- Howard Hughes Medical Institute, University of California San Diego and Rady Children's Hospital, La Jolla, CA 92130, USA
| | - Rasim O Rosti
- Howard Hughes Medical Institute, University of California San Diego and Rady Children's Hospital, La Jolla, CA 92130, USA
| | - Sohail A Paracha
- Institute of Basic Medical Sciences, Khyber Medical University, 25100 Peshawar, Pakistan
| | - Muhammad T Sarwar
- Institute of Basic Medical Sciences, Khyber Medical University, 25100 Peshawar, Pakistan
| | - Dagan Jenkins
- Institute of Child Health, Guilford Street and Dubowitz Neuromuscular Centre, Great Ormond Street Hospital for Children, London, WC1N 3JH, UK
| | - Jawad Ahmed
- Institute of Basic Medical Sciences, Khyber Medical University, 25100 Peshawar, Pakistan
| | - Federico A Santoni
- Department of Genetic Medicine and Development, University of Geneva, 1206 Geneva, Switzerland; Department of Endocrinology, Diabetes, and Metabolism, University Hospital of Lausanne, 1011 Lausanne, Switzerland
| | - Emmanuelle Ranza
- Department of Genetic Medicine and Development, University of Geneva, 1206 Geneva, Switzerland; Service of Genetic Medicine, University Hospitals of Geneva, 1205 Geneva, Switzerland; Medigenome, The Swiss Institute of Genomic Medicine, Geneva, CH-1207, Switzerland
| | - Justyna Iwaszkiewicz
- Swiss Institute of Bioinformatics, Molecular Modeling Group, Batiment Genopode, Unil Sorge, Lausanne, CH-1015, Switzerland
| | - Cheryl Cytrynbaum
- Hospital for Sick Children, Division of Clinical and Metabolic Genetics, 555 University Ave., Toronto, M5G 1X8, Canada
| | - Rosanna Weksberg
- Hospital for Sick Children, Division of Clinical and Metabolic Genetics, 555 University Ave., Toronto, M5G 1X8, Canada
| | | | | | - Yue Si
- GeneDx, 207 Perry Parkway Gaithersburg, MD 20877, USA
| | | | - Marisa V Andrews
- Department of Pediatrics, Divisions of Genetics and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Dustin Baldridge
- Department of Pediatrics, Divisions of Genetics and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Heinz Gabriel
- CeGaT GmbH and Praxis für Humangenetik Tuebingen, Tuebingen, 72076, Germany
| | - Julia Mohr
- CeGaT GmbH and Praxis für Humangenetik Tuebingen, Tuebingen, 72076, Germany
| | | | - Sylvain Debard
- University of Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, 67083, France
| | - Bruno Senger
- University of Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, 67083, France
| | - Frédéric Fischer
- University of Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, 67083, France
| | - Conny van Ravenwaaij
- University of Groningen, University Medical Center Groningen, Department of Neurology, Groningen, 9713, the Netherlands
| | - Annemarie J M Fock
- University of Groningen, University Medical Center Groningen, Department of Neurology, Groningen, 9713, the Netherlands
| | - Servi J C Stevens
- Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, 6211, the Netherlands
| | - Jürg Bähler
- Institute of Healthy Ageing, Department of Genetics, Evolution and Environment, University College London (UCL), London, WC1E 6BT, UK
| | - Amina Nasar
- Department of Pediatrics, Queen's University, Kingston, ON, K7L 2V7, Canada
| | - John F Mantovani
- Division of Child Neurology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Adnan Manzur
- Institute of Child Health, Guilford Street and Dubowitz Neuromuscular Centre, Great Ormond Street Hospital for Children, London, WC1N 3JH, UK
| | - Anna Sarkozy
- Institute of Child Health, Guilford Street and Dubowitz Neuromuscular Centre, Great Ormond Street Hospital for Children, London, WC1N 3JH, UK
| | - Desirée E C Smith
- Metabolic Unit, Department of Clinical Chemistry, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam, Amsterdam Neuroscience, Amsterdam Gastroenterology and Metabolism, Amsterdam, 1081 the Netherlands
| | - Gajja S Salomons
- Metabolic Unit, Department of Clinical Chemistry, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam, Amsterdam Neuroscience, Amsterdam Gastroenterology and Metabolism, Amsterdam, 1081 the Netherlands
| | - Zubair M Ahmed
- Department of Biochemistry and Molecular Biology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Shaikh Riazuddin
- Jinnah Burn and Reconstructive Surgery Center, Allama Iqbal Medical College, University of Health Sciences, Lahore 54550, Pakistan
| | - Saima Riazuddin
- Department of Biochemistry and Molecular Biology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Muhammad A Usmani
- Department of Biochemistry and Molecular Biology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Annette Seibt
- Department of General Pediatrics, Heinrich-Heine-University, Moorenstr. 5, 40225 Düsseldorf, Germany
| | - Muhammad Ansar
- Department of Genetic Medicine and Development, University of Geneva, 1206 Geneva, Switzerland; Institute of Molecular and Clinical Ophthalmology Basel, Basel Switzerland
| | - Stylianos E Antonarakis
- Department of Genetic Medicine and Development, University of Geneva, 1206 Geneva, Switzerland; Service of Genetic Medicine, University Hospitals of Geneva, 1205 Geneva, Switzerland; iGE3 Institute of Genetics and Genomics of Geneva, 1211 Geneva, Switzerland
| | - John B Vincent
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, ON, M5T 1R8, Canada; Institute of Medical Science and Department of Psychiatry, University of Toronto, Toronto, ON, M5T 1R8, Canada
| | - Muhammad Ayub
- Department of Pediatrics, Queen's University, Kingston, ON, K7L 2V7, Canada
| | - Mona Grimmel
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, 72076 Tübingen, Germany
| | - Anne Marie Jelsig
- Department of Clinical Genetics, University Hospital of Copenhagen, Rigshospitalet, 2100, Denmark
| | - Tina Duelund Hjortshøj
- Department of Clinical Genetics, University Hospital of Copenhagen, Rigshospitalet, 2100, Denmark
| | - Helena Gásdal Karstensen
- Department of Clinical Genetics, University Hospital of Copenhagen, Rigshospitalet, 2100, Denmark
| | - Marybeth Hummel
- Department of Pediatrics, Section of Medical Genetics, West Virginia University, Morgantown, WV 26506-9600, USA
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, 72076 Tübingen, Germany; Centre for Rare Diseases, University of Tuebingen, 72076 Tübingen, Germany
| | - Yalda Jamshidi
- Genetics Centre, Molecular and Clinical Sciences Institute, St George's University of London, London, SW17 0RE, UK
| | - Felix Distelmaier
- Department of General Pediatrics, Heinrich-Heine-University, Moorenstr. 5, 40225 Düsseldorf, Germany
| | - Rita Horvath
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, CB2 0QQ UK
| | - Joseph G Gleeson
- Howard Hughes Medical Institute, University of California San Diego and Rady Children's Hospital, La Jolla, CA 92130, USA
| | - Hubert Becker
- University of Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, 67083, France
| | - Jean-Louis Mandel
- Institute for Genetics and Molecular and Cellular Biology (IGBMC), University of Strasbourg, CNRS UMR7104, INSERM U1258, Illkirch, 67404, France
| | - David A Koolen
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands
| | - Henry Houlden
- Department of Neuromuscular Disorders, University College London (UCL) Institute of Neurology, Queen Square, London, WC1N 3BG, UK.
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Jawad Hassan M, Ali Raza M, Khan I, Ahmad Meraj T, Ahmed M, Abbas Shah G, Ansar M, Afzal Awan S, Khan N, Iqbal N, Peng Y, Li Z. Selenium and Salt Interactions in Black Gram ( Vigna mungo L): Ion Uptake, Antioxidant Defense System, and Photochemistry Efficiency. Plants (Basel) 2020; 9:E467. [PMID: 32272796 PMCID: PMC7238270 DOI: 10.3390/plants9040467] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/04/2020] [Accepted: 04/05/2020] [Indexed: 01/10/2023]
Abstract
Salinity is a major abiotic stress which limits crop production, especially under rainfed conditions. Selenium (Se), as an important micronutrient, plays a vital role in mitigating detrimental effects of different abiotic stresses. The objective of this research was to examine the effect of Se fertilization on black gram (Vigna mungo) under salt stress. Our results showed that salt stress (100 mM NaCl) in leaves significantly induced oxidative damage and caused a decline in relative water content, chlorophyll (Chl), stomatal conductance (gs), photochemical efficiency (Fv/Fm), sucrose, and reducing sugars. A low dose of Se (1.5 ppm) significantly reduced hydrogen peroxide content, malondialdehyde formation, cell membrane damage, and also improved antioxidative enzyme activities, including superoxide dismutase, catalase, ascorbate peroxidase, glutathione reductase, and glutathione peroxidase under salt stress. Se-treated plants exhibited higher Chl, gs, Fv/Fm, sucrose, and reducing sugars than untreated plants in response to salt stress. In addition, Se application enhanced Se uptake and reduced Na+ uptake, but Cl- remained unaffected. Our results indicated that a low dose of Se effectively alleviated salt damage via inhibition of Na+ uptake and enhanced antioxidant defense resulting in a significant decrease in oxidative damage, and maintained gaseous exchange and PS II function for sucrose and reducing sugars accumulation in black gram.
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Affiliation(s)
- Muhammad Jawad Hassan
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu 611130, China; (M.J.H.); (I.K.); (S.A.A.); (Y.P.)
| | - Muhammad Ali Raza
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, PR China; (M.A.R.); (T.A.M.)
| | - Imran Khan
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu 611130, China; (M.J.H.); (I.K.); (S.A.A.); (Y.P.)
| | - Tehseen Ahmad Meraj
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, PR China; (M.A.R.); (T.A.M.)
| | - Mukhtar Ahmed
- Department of Agronomy, PMAS-Arid Agriculture University, Rawalpindi 46000, Pakistan; (M.A.); (G.A.S.); (M.A.)
- Department of Agricultural Research for Northern Sweden, Swedish University of Agricultural Sciences, Umeå 90183, Sweden
| | - Ghulam Abbas Shah
- Department of Agronomy, PMAS-Arid Agriculture University, Rawalpindi 46000, Pakistan; (M.A.); (G.A.S.); (M.A.)
| | - Muhammad Ansar
- Department of Agronomy, PMAS-Arid Agriculture University, Rawalpindi 46000, Pakistan; (M.A.); (G.A.S.); (M.A.)
| | - Samrah Afzal Awan
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu 611130, China; (M.J.H.); (I.K.); (S.A.A.); (Y.P.)
| | - Nanak Khan
- Department of Agronomy, Balochistan Agriculture College, Quetta 87100, Pakistan;
| | - Nasir Iqbal
- School of Agriculture, Food & Wine, The University of Adelaide, PMB1, Glen Osmond, Adelaide 5064, Australia;
| | - Yan Peng
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu 611130, China; (M.J.H.); (I.K.); (S.A.A.); (Y.P.)
| | - Zhou Li
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu 611130, China; (M.J.H.); (I.K.); (S.A.A.); (Y.P.)
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Henry LK, Ansar M, Ranza E, Shetty M, Paracha SA, Azam M, Kern I, Iwaszkiewicz J, Farooq O, Pournaras CJ, Malcles A, Kecik M, Muzaffar W, Qurban A, Ali L, Aggoun Y, Santoni FA, Makrythanasis P, Ahmed J, Qamar R, Rivolta C, Sarwar MT, Antonarakis SE. Identification, Characterization, and Treatment for a Taurine Transporter (SLC6A6) Variant Resulting in Taurine Deficiency and Pathologies in a Consanguineous Family. FASEB J 2020. [DOI: 10.1096/fasebj.2020.34.s1.06466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- L. Keith Henry
- University of North Dakota School of Medicine and Health Sciences
| | | | | | - Madhur Shetty
- University of North Dakota School of Medicine and Health Sciences
| | | | | | - Ilse Kern
- Geneva University Childrens Hospitals
| | | | - Omer Farooq
- Bahria University Medical and Dental College
| | | | | | | | | | | | | | | | | | | | | | | | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel
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Ansar M, Paracha SA, Serretti A, Sarwar MT, Khan J, Ranza E, Falconnet E, Iwaszkiewicz J, Shah SF, Qaisar AA, Santoni FA, Zoete V, Megarbane A, Ahmed J, Colombo R, Makrythanasis P, Antonarakis SE. Biallelic variants in FBXL3 cause intellectual disability, delayed motor development and short stature. Hum Mol Genet 2020; 28:972-979. [PMID: 30481285 DOI: 10.1093/hmg/ddy406] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 11/13/2018] [Accepted: 11/14/2018] [Indexed: 12/20/2022] Open
Abstract
FBXL3 (F-Box and Leucine Rich Repeat Protein 3) encodes a protein that contains an F-box and several tandem leucine-rich repeats (LRR) domains. FBXL3 is part of the SCF (Skp1-Cullin-F box protein) ubiquitin ligase complex that binds and leads to phosphorylation-dependent degradation of the central clock protein cryptochromes (CRY1 and CRY2) by the proteasome and its absence causes circadian phenotypes in mice and behavioral problems. No FBXL3-related phenotypes have been described in humans. By a combination of exome sequencing and homozygosity mapping, we analyzed two consanguineous families with intellectual disability and identified homozygous loss-of-function (LoF) variants in FBXL3. In the first family, from Pakistan, an FBXL3 frameshift variant [NM_012158.2:c.885delT:p.(Leu295Phefs*25)] was the onlysegregating variant in five affected individuals in two family loops (LOD score: 3.12). In the second family, from Lebanon, we identified a nonsense variant [NM_012158.2:c.445C>T:p.(Arg149*)]. In a third patient from Italy, a likely deleterious non-synonymous variant [NM_012158.2:c.1072T>C:p.(Cys358Arg)] was identified in homozygosity. Protein 3D modeling predicted that the Cys358Arg change influences the binding with CRY2 by destabilizing the structure of the FBXL3, suggesting that this variant is also likely to be LoF. The eight affected individuals from the three families presented with a similar phenotype that included intellectual disability, developmental delay, short stature and mild facial dysmorphism, mainly large nose with a bulbous tip. The phenotypic similarity and the segregation analysis suggest that FBXL3 biallelic, LoF variants link this gene with syndromic autosomal recessive developmental delay/intellectual disability.
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Affiliation(s)
- Muhammad Ansar
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
| | - Sohail Aziz Paracha
- Institute of Basic Medical Sciences, Khyber Medical University, Peshawar, Pakistan
| | - Alessandro Serretti
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Muhammad T Sarwar
- Institute of Basic Medical Sciences, Khyber Medical University, Peshawar, Pakistan
| | - Jamshed Khan
- Institute of Basic Medical Sciences, Khyber Medical University, Peshawar, Pakistan
| | - Emmanuelle Ranza
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland.,Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland
| | - Emilie Falconnet
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
| | - Justyna Iwaszkiewicz
- Swiss Institute of Bioinformatics, Molecular Modeling Group, Batiment Genopode, Unil Sorge, Lausanne, Switzerland
| | - Sayyed Fahim Shah
- Department of Medicine, KMU Institute of Medical Sciences, Kohat, Pakistan
| | | | - Federico A Santoni
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland.,Department of Endocrinology Diabetes and Metabolism, University Hospital of Lausanne, Lausanne, Switzerland
| | - Vincent Zoete
- Swiss Institute of Bioinformatics, Molecular Modeling Group, Batiment Genopode, Unil Sorge, Lausanne, Switzerland.,Department of Fundamental Oncology, Lausanne University, Ludwig Institute for Cancer Research, Route de la Corniche 9A, Epalinges, Switzerland
| | | | - Jawad Ahmed
- Institute of Basic Medical Sciences, Khyber Medical University, Peshawar, Pakistan
| | - Roberto Colombo
- Institute of Clinical Biochemistry, Faculty of Medicine, Catholic University IRCCS Policlinico Gemelli, Rome, Italy.,Center for the Study of Rare Hereditary Diseases, Niguarda Ca' Granda Metropolitan Hospital, Milan, Italy
| | - Periklis Makrythanasis
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland.,Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Stylianos E Antonarakis
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland.,Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland.,iGE3 Institute of Genetics and Genomics of Geneva, Geneva, Switzerland
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Beck DB, Petracovici A, He C, Moore HW, Louie RJ, Ansar M, Douzgou S, Sithambaram S, Cottrell T, Santos-Cortez RLP, Prijoles EJ, Bend R, Keren B, Mignot C, Nougues MC, Õunap K, Reimand T, Pajusalu S, Zahid M, Saqib MAN, Buratti J, Seaby EG, McWalter K, Telegrafi A, Baldridge D, Shinawi M, Leal SM, Schaefer GB, Stevenson RE, Banka S, Bonasio R, Fahrner JA. Delineation of a Human Mendelian Disorder of the DNA Demethylation Machinery: TET3 Deficiency. Am J Hum Genet 2020; 106:234-245. [PMID: 31928709 DOI: 10.1016/j.ajhg.2019.12.007] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 12/11/2019] [Indexed: 12/11/2022] Open
Abstract
Germline pathogenic variants in chromatin-modifying enzymes are a common cause of pediatric developmental disorders. These enzymes catalyze reactions that regulate epigenetic inheritance via histone post-translational modifications and DNA methylation. Cytosine methylation (5-methylcytosine [5mC]) of DNA is the quintessential epigenetic mark, yet no human Mendelian disorder of DNA demethylation has yet been delineated. Here, we describe in detail a Mendelian disorder caused by the disruption of DNA demethylation. TET3 is a methylcytosine dioxygenase that initiates DNA demethylation during early zygote formation, embryogenesis, and neuronal differentiation and is intolerant to haploinsufficiency in mice and humans. We identify and characterize 11 cases of human TET3 deficiency in eight families with the common phenotypic features of intellectual disability and/or global developmental delay; hypotonia; autistic traits; movement disorders; growth abnormalities; and facial dysmorphism. Mono-allelic frameshift and nonsense variants in TET3 occur throughout the coding region. Mono-allelic and bi-allelic missense variants localize to conserved residues; all but one such variant occur within the catalytic domain, and most display hypomorphic function in an assay of catalytic activity. TET3 deficiency and other Mendelian disorders of the epigenetic machinery show substantial phenotypic overlap, including features of intellectual disability and abnormal growth, underscoring shared disease mechanisms.
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Affiliation(s)
- David B Beck
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ana Petracovici
- Graduate Group in Genetics and Epigenetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Chongsheng He
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Current address: Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082 Hunan, P.R. China
| | | | | | - Muhammad Ansar
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-I-Azam University, 45320 Islamabad, Pakistan
| | - Sofia Douzgou
- Division of Evolution & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK; Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Sivagamy Sithambaram
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Trudie Cottrell
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | | | | | - Renee Bend
- Greenwood Genetic Center, Greenwood, SC 29646, USA
| | - Boris Keren
- Assistance Publique-Hôpitaux de Paris, Groupe Hospitalier Pitié-Salpêtrière, Département de Génétique, Paris 75013, France
| | - Cyril Mignot
- Assistance Publique-Hôpitaux de Paris, Groupe Hospitalier Pitié-Salpêtrière, Département de Génétique, Paris 75013, France; Centre de Référence Déficiences Intellectuelles de Causes Rares, Paris 75013, France
| | - Marie-Christine Nougues
- Assistance Publique-Hôpitaux de Paris, Armand Trousseau Hospital, Department of Neuropediatrics, Paris 75012, France
| | - Katrin Õunap
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu 50406, Estonia; Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu 50406, Estonia
| | - Tiia Reimand
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu 50406, Estonia; Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu 50406, Estonia; Chair of Human Genetics, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu 50406, Estonia
| | - Sander Pajusalu
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu 50406, Estonia; Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu 50406, Estonia; Yale University School of Medicine, Department of Genetics, New Haven, CT 06510, USA
| | - Muhammad Zahid
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-I-Azam University, 45320 Islamabad, Pakistan
| | | | - Julien Buratti
- Assistance Publique-Hôpitaux de Paris, Groupe Hospitalier Pitié-Salpêtrière, Département de Génétique, Paris 75013, France
| | - Eleanor G Seaby
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | | | - Dustin Baldridge
- Department of Pediatrics, Division of Genetics and Genomic Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Marwan Shinawi
- Department of Pediatrics, Division of Genetics and Genomic Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Suzanne M Leal
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, Taub Institute for Alzheimer's D disease and the Aging Brain, Department of Neurology, Columbia University Medical Center, 630 W 168th St, New York, NY 10032, USA
| | | | | | - Siddharth Banka
- Division of Evolution & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK; Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Roberto Bonasio
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Jill A Fahrner
- Department of Pediatrics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD 21205, USA.
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Khan A, Wang R, Han S, Umair M, Alshabeeb MA, Ansar M, Ahmad W, Alaamery M, Zhang X. A Novel Homozygous Nonsense Mutation p.Cys366* in the WNT10B Gene Underlying Split-Hand/Split Foot Malformation in a Consanguineous Pakistani Family. Front Pediatr 2020; 7:526. [PMID: 31998667 PMCID: PMC6970189 DOI: 10.3389/fped.2019.00526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 12/04/2019] [Indexed: 02/04/2023] Open
Abstract
Split hand/split foot malformation (SHFM) or ectrodactyly is characterized by a deep median cleft of the hand or foot, hypoplasia or aplasia of the metacarpals, metatarsals, and phalanges. It is a clinically and genetically heterogeneous group of limb malformations. This study aimed to identify the pathogenic variant in a consanguineous Pakistani family with autosomal recessive SHFM. Peripheral blood samples were obtained, DNA was extracted, WNT10B coding and noncoding regions were PCR amplified and Sanger sequencing was performed using workflow suggested by Thermo Fisher Scientific. A novel homozygous nonsense variant (c.1098C>A; p.Cys366*) was identified in the WNT10B gene in the index patients, which probably explains SHFM type 6 in this family in comparison with similar data from the literature.
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Affiliation(s)
- Amjad Khan
- McKusick-Zhang Center for Genetic Medicine, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
- The Research Center for Medical Genomics, China Medical University, Shenyang, China
- Developmental Medicine Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard-Health Affairs (MNGHA), Riyadh, Saudi Arabia
| | - Rongrong Wang
- McKusick-Zhang Center for Genetic Medicine, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Shirui Han
- The Research Center for Medical Genomics, China Medical University, Shenyang, China
| | - Muhammad Umair
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Science, Ministry of National Guard-Health Affairs (MNGHA), Riyadh, Saudi Arabia
| | - Mohammad A. Alshabeeb
- Developmental Medicine Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard-Health Affairs (MNGHA), Riyadh, Saudi Arabia
| | - Muhammad Ansar
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Wasim Ahmad
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Manal Alaamery
- Developmental Medicine Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard-Health Affairs (MNGHA), Riyadh, Saudi Arabia
| | - Xue Zhang
- McKusick-Zhang Center for Genetic Medicine, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
- The Research Center for Medical Genomics, China Medical University, Shenyang, China
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Riazuddin S, Hussain M, Razzaq A, Iqbal Z, Shahzad M, Polla DL, Song Y, van Beusekom E, Khan AA, Tomas-Roca L, Rashid M, Zahoor MY, Wissink-Lindhout WM, Basra MAR, Ansar M, Agha Z, van Heeswijk K, Rasheed F, Van de Vorst M, Veltman JA, Gilissen C, Akram J, Kleefstra T, Assir MZ, Grozeva D, Carss K, Raymond FL, O’Connor TD, Riazuddin SA, Khan SN, Ahmed ZM, de Brouwer APM, van Bokhoven H, Riazuddin S. Correction: Exome sequencing of Pakistani consanguineous families identifies 30 novel candidate genes for recessive intellectual disability. Mol Psychiatry 2020; 25:3101-3102. [PMID: 30171209 PMCID: PMC7962566 DOI: 10.1038/s41380-018-0128-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This Article was originally published under a CC BY-NC-SA 4.0 license, but has now been made available under a CC BY 4.0 license. The PDF and HTML versions of the Article have been modified accordingly.
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Affiliation(s)
- S. Riazuddin
- grid.411024.20000 0001 2175 4264Department of Otorhinolaryngology—Head and Neck Surgery, University of Maryland, School of Medicine, Baltimore, MD USA ,grid.417348.d0000 0000 9687 8141Center for Genetic Diseases, Shaheed Zulfiqar Ali Bhutto Medical University, Pakistan Institute of Medical Sciences, Islamabad, Pakistan
| | - M. Hussain
- grid.411024.20000 0001 2175 4264Department of Otorhinolaryngology—Head and Neck Surgery, University of Maryland, School of Medicine, Baltimore, MD USA ,grid.10417.330000 0004 0444 9382Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands ,grid.412956.dAllama Iqbal Medical College, University of Health Sciences, Lahore, Pakistan ,grid.11173.350000 0001 0670 519XNational Centre of Excellence in Molecular Biology, University of The Punjab, Lahore, Pakistan
| | - A. Razzaq
- grid.10417.330000 0004 0444 9382Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands ,grid.412956.dAllama Iqbal Medical College, University of Health Sciences, Lahore, Pakistan ,grid.11173.350000 0001 0670 519XNational Centre of Excellence in Molecular Biology, University of The Punjab, Lahore, Pakistan
| | - Z. Iqbal
- grid.10417.330000 0004 0444 9382Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands ,grid.55325.340000 0004 0389 8485Present Address: Department of Neurology, Oslo University Hospital, Oslo, Norway
| | - M. Shahzad
- grid.411024.20000 0001 2175 4264Department of Otorhinolaryngology—Head and Neck Surgery, University of Maryland, School of Medicine, Baltimore, MD USA ,grid.417348.d0000 0000 9687 8141Center for Genetic Diseases, Shaheed Zulfiqar Ali Bhutto Medical University, Pakistan Institute of Medical Sciences, Islamabad, Pakistan
| | - D. L. Polla
- grid.10417.330000 0004 0444 9382Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands ,grid.456760.60000 0004 0603 2599Center for Genetic Diseases, CAPES Foundation, Ministry of Education of Brazil, Brasília, Brazil
| | - Y. Song
- grid.411024.20000 0001 2175 4264Institute for Genome Sciences and Program in Personalized and Genomic Medicine, University of Maryland, School of Medicine, Baltimore, MD USA
| | - E. van Beusekom
- grid.10417.330000 0004 0444 9382Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - A. A. Khan
- grid.11173.350000 0001 0670 519XNational Centre of Excellence in Molecular Biology, University of The Punjab, Lahore, Pakistan
| | - L. Tomas-Roca
- grid.10417.330000 0004 0444 9382Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - M. Rashid
- grid.10417.330000 0004 0444 9382Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands ,grid.412956.dAllama Iqbal Medical College, University of Health Sciences, Lahore, Pakistan ,grid.11173.350000 0001 0670 519XNational Centre of Excellence in Molecular Biology, University of The Punjab, Lahore, Pakistan
| | - M. Y. Zahoor
- grid.11173.350000 0001 0670 519XNational Centre of Excellence in Molecular Biology, University of The Punjab, Lahore, Pakistan
| | - W. M. Wissink-Lindhout
- grid.10417.330000 0004 0444 9382Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - M. A. R. Basra
- grid.11173.350000 0001 0670 519XNational Centre of Excellence in Molecular Biology, University of The Punjab, Lahore, Pakistan
| | - M. Ansar
- grid.10417.330000 0004 0444 9382Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands ,grid.11173.350000 0001 0670 519XNational Centre of Excellence in Molecular Biology, University of The Punjab, Lahore, Pakistan ,grid.8591.50000 0001 2322 4988Present Address: Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
| | - Z. Agha
- grid.10417.330000 0004 0444 9382Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands ,grid.418920.60000 0004 0607 0704Department of Biosciences, Faculty of Science, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - K. van Heeswijk
- grid.10417.330000 0004 0444 9382Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - F. Rasheed
- grid.11173.350000 0001 0670 519XNational Centre of Excellence in Molecular Biology, University of The Punjab, Lahore, Pakistan
| | - M. Van de Vorst
- grid.10417.330000 0004 0444 9382Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - J. A. Veltman
- grid.10417.330000 0004 0444 9382Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands ,grid.412966.e0000 0004 0480 1382Department of Clinical Genetics, GROW School for Oncology and Developmental Biology, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - C. Gilissen
- grid.10417.330000 0004 0444 9382Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - J. Akram
- grid.417348.d0000 0000 9687 8141Center for Genetic Diseases, Shaheed Zulfiqar Ali Bhutto Medical University, Pakistan Institute of Medical Sciences, Islamabad, Pakistan
| | - T. Kleefstra
- grid.10417.330000 0004 0444 9382Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - M. Z. Assir
- grid.412956.dAllama Iqbal Medical College, University of Health Sciences, Lahore, Pakistan
| | - UK10K
- grid.10306.340000 0004 0606 5382The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - D. Grozeva
- grid.5335.00000000121885934Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - K. Carss
- grid.5335.00000000121885934Department of Haematology, University of Cambridge, Cambridge, UK
| | - F. L. Raymond
- grid.5335.00000000121885934Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - T. D. O’Connor
- grid.411024.20000 0001 2175 4264Institute for Genome Sciences and Program in Personalized and Genomic Medicine, University of Maryland, School of Medicine, Baltimore, MD USA
| | - S. A. Riazuddin
- grid.21107.350000 0001 2171 9311Department of Ophthalmology, The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - S. N. Khan
- grid.11173.350000 0001 0670 519XNational Centre of Excellence in Molecular Biology, University of The Punjab, Lahore, Pakistan
| | - Z. M. Ahmed
- grid.411024.20000 0001 2175 4264Department of Otorhinolaryngology—Head and Neck Surgery, University of Maryland, School of Medicine, Baltimore, MD USA
| | - A. P. M. de Brouwer
- grid.10417.330000 0004 0444 9382Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - H. van Bokhoven
- grid.10417.330000 0004 0444 9382Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - S. Riazuddin
- grid.417348.d0000 0000 9687 8141Center for Genetic Diseases, Shaheed Zulfiqar Ali Bhutto Medical University, Pakistan Institute of Medical Sciences, Islamabad, Pakistan ,grid.412956.dAllama Iqbal Medical College, University of Health Sciences, Lahore, Pakistan
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45
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Ansar M, Chung H, Waryah YM, Makrythanasis P, Falconnet E, Rao AR, Guipponi M, Narsani AK, Fingerhut R, Santoni FA, Ranza E, Waryah AM, Bellen HJ, Antonarakis SE. Visual impairment and progressive phthisis bulbi caused by recessive pathogenic variant in MARK3. Hum Mol Genet 2019; 27:2703-2711. [PMID: 29771303 DOI: 10.1093/hmg/ddy180] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 05/02/2018] [Accepted: 05/06/2018] [Indexed: 12/20/2022] Open
Abstract
Developmental eye defects often severely reduce vision. Despite extensive efforts, for a substantial fraction of these cases the molecular causes are unknown. Recessive eye disorders are frequent in consanguineous populations and such large families with multiple affected individuals provide an opportunity to identify recessive causative genes. We studied a Pakistani consanguineous family with three affected individuals with congenital vision loss and progressive eye degeneration. The family was analyzed by exome sequencing of one affected individual and genotyping of all family members. We have identified a non-synonymous homozygous variant (NM_001128918.2: c.1708C > G: p.Arg570Gly) in the MARK3 gene as the likely cause of the phenotype. Given that MARK3 is highly conserved in flies (I: 55%; S: 67%) we knocked down the MARK3 homologue, par-1, in the eye during development. This leads to a significant reduction in eye size, a severe loss of photoreceptors and loss of vision based on electroretinogram (ERG) recordings. Expression of the par-1 p.Arg792Gly mutation (equivalent to the MARK3 variant found in patients) in developing fly eyes also induces loss of eye tissue and reduces the ERG signals. The data in flies and human indicate that the MARK3 variant corresponds to a loss of function. We conclude that the identified mutation in MARK3 establishes a new gene-disease link, since it likely causes structural abnormalities during eye development and visual impairment in humans, and that the function of MARK3/par-1 is evolutionarily conserved in eye development.
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Affiliation(s)
- Muhammad Ansar
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Hyunglok Chung
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Yar M Waryah
- Molecular Biology and Genetics Department, Medical Research Center, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan
| | - Periklis Makrythanasis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Emilie Falconnet
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Ali Raza Rao
- Molecular Biology and Genetics Department, Medical Research Center, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan
| | - Michel Guipponi
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.,Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland
| | - Ashok K Narsani
- Institute of Ophthalmology, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan
| | - Ralph Fingerhut
- Swiss Newborn Screening Laboratory, University Children's Hospital, Zurich, Switzerland
| | - Federico A Santoni
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Emmanuelle Ranza
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.,Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland
| | - Ali M Waryah
- Molecular Biology and Genetics Department, Medical Research Center, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA.,Howard Hughes Medical Institute, Houston, TX, USA
| | - Stylianos E Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.,Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland.,iGE3 Institute of Genetics and Genomics of Geneva, Geneva, Switzerland
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46
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Ansar M, Chung HL, Al-Otaibi A, Elagabani MN, Ravenscroft TA, Paracha SA, Scholz R, Abdel Magid T, Sarwar MT, Shah SF, Qaisar AA, Makrythanasis P, Marcogliese PC, Kamsteeg EJ, Falconnet E, Ranza E, Santoni FA, Aldhalaan H, Al-Asmari A, Faqeih EA, Ahmed J, Kornau HC, Bellen HJ, Antonarakis SE. Bi-allelic Variants in IQSEC1 Cause Intellectual Disability, Developmental Delay, and Short Stature. Am J Hum Genet 2019; 105:907-920. [PMID: 31607425 DOI: 10.1016/j.ajhg.2019.09.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 09/11/2019] [Indexed: 12/30/2022] Open
Abstract
We report two consanguineous families with probands that exhibit intellectual disability, developmental delay, short stature, aphasia, and hypotonia in which homozygous non-synonymous variants were identified in IQSEC1 (GenBank: NM_001134382.3). In a Pakistani family, the IQSEC1 segregating variant is c.1028C>T (p.Thr343Met), while in a Saudi Arabian family the variant is c.962G>A (p.Arg321Gln). IQSEC1-3 encode guanine nucleotide exchange factors for the small GTPase ARF6 and their loss affects a variety of actin-dependent cellular processes, including AMPA receptor trafficking at synapses. The ortholog of IQSECs in the fly is schizo and its loss affects growth cone guidance at the midline in the CNS, also an actin-dependent process. Overexpression of the reference IQSEC1 cDNA in wild-type flies is lethal, but overexpression of the two variant IQSEC1 cDNAs did not affect viability. Loss of schizo caused embryonic lethality that could be rescued to 2nd instar larvae by moderate expression of the human reference cDNA. However, the p.Arg321Gln and p.Thr343Met variants failed to rescue embryonic lethality. These data indicate that the variants behave as loss-of-function mutations. We also show that schizo in photoreceptors is required for phototransduction. Finally, mice with a conditional Iqsec1 deletion in cortical neurons exhibited an increased density of dendritic spines with an immature morphology. The phenotypic similarity of the affecteds and the functional experiments in flies and mice indicate that IQSEC1 variants are the cause of a recessive disease with intellectual disability, developmental delay, and short stature, and that axonal guidance and dendritic projection defects as well as dendritic spine dysgenesis may underlie disease pathogenesis.
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47
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Khan A, Han S, Wang R, Ansar M, Ahmad W, Zhang X. Sequence variants in genes causing nonsyndromic hearing loss in a Pakistani cohort. Mol Genet Genomic Med 2019; 7:e917. [PMID: 31389194 PMCID: PMC6732339 DOI: 10.1002/mgg3.917] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 07/14/2019] [Accepted: 07/23/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Hearing loss or hearing impairment is a clinically and genetically heterogeneous disorder. More than 117 genes were discovered to date in hereditary, nonsyndromic hearing loss (NSHL). Identifying novel gene variants and their frequency in specific populations is valuable for public health and potentially for genetic screening of NSHL. AIMS To identify the gene variants underlying NSHL in a Pakistani cohort. METHODS AND RESULTS A cohort of 40 school-aged children with NSHL was initially screened for variants in GJB2, the gene with the highest incidence of variants in other populations with NSHL. We found known homozygous as well as compound heterozygous GJB variants in 15 individuals. Next, we used targeted next generation sequencing (TNGS) for the remaining 25 individuals and identified 20 different variants in 14 genes (SLC26A4, KCNQ4, MYO7A, MYO15A, TMPRSS3, ESPN, TMC1, GIPC3, LHFPL5, WFS1, DFNB59, GRXCR1, ESRRB, and LRTOMT). CONCLUSIONS We described common and novel variants in 15 genes in a Pakistani cohort of NSHL.
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Affiliation(s)
- Amjad Khan
- McKusick-Zhang Center for Genetic Medicine, Institute of Basic Medical Sciences, School of Basic Medicine, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.,The Research Center for Medical Genomics, China Medical University, Shenyang, China.,Department of Developmental Medicine, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard-Health Affairs (MNGHA), Riyadh, Saudi Arabia
| | - Shirui Han
- McKusick-Zhang Center for Genetic Medicine, Institute of Basic Medical Sciences, School of Basic Medicine, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.,The Research Center for Medical Genomics, China Medical University, Shenyang, China
| | - Rongrong Wang
- McKusick-Zhang Center for Genetic Medicine, Institute of Basic Medical Sciences, School of Basic Medicine, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Muhammad Ansar
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Wasim Ahmad
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Xue Zhang
- McKusick-Zhang Center for Genetic Medicine, Institute of Basic Medical Sciences, School of Basic Medicine, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.,The Research Center for Medical Genomics, China Medical University, Shenyang, China
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48
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Parveen A, Mirza MU, Vanmeert M, Akhtar J, Bashir H, Khan S, Shehzad S, Froeyen M, Ahmed W, Ansar M, Wasif N. A novel pathogenic missense variant in CNNM4 underlying Jalili syndrome: Insights from molecular dynamics simulations. Mol Genet Genomic Med 2019; 7:e902. [PMID: 31347285 PMCID: PMC6732295 DOI: 10.1002/mgg3.902] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 06/04/2019] [Accepted: 07/08/2019] [Indexed: 12/24/2022] Open
Abstract
Background Jalili syndrome (JS) is a rare cone‐rod dystrophy (CRD) associated with amelogenesis imperfecta (AI). The first clinical presentation of JS patients was published in 1988 by Jalili and Smith. Pathogenic mutations in the Cyclin and CBS Domain Divalent Metal Cation Transport Mediator 4 (CNNM4) magnesium transporter protein have been reported as the leading cause of this anomaly. Methods In the present study, a clinical and genetic investigation was performed in a consanguineous family of Pakistani origin, showing characteristic features of JS. Sanger sequencing was successfully used to identify the causative variant in CNNM4. Molecular dynamics (MD) simulations were performed to study the effect of amino acid change over CNNM4 protein. Results Sequence analysis of CNNM4 revealed a novel missense variant (c.1220G>T, p.Arg407Leu) in exon‐1 encoding cystathionine‐β‐synthase (CBS) domain. To comprehend the mutational consequences in the structure, the mutant p.Arg407Leu was modeled together with a previously reported variant (c.1484C>T, p.Thr495Ile) in the same domain. Additionally, docking analysis deciphered the binding mode of the adenosine triphosphate (ATP) cofactor. Furthermore, 60ns MD simulations were carried out on wild type (p.Arg407/p.Thr495) and mutants (p.Arg407Leu/p.Thr495Ile) to understand the structural and energetic changes in protein structure and its dynamic behavior. An evident conformational shift of ATP in the binding site was observed in simulated mutants disrupting the native ATP‐binding mode. Conclusion The novel identified variant in CNNM4 is the first report from the Pakistani population. Overall, the study is valuable and may give a novel insight into metal transport in visual function and biomineralization.
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Affiliation(s)
- Asia Parveen
- Institute of Molecular Biology and Biotechnology (IMBB), Centre for Research in Molecular Medicine (CRiMM), The University of Lahore, Lahore, Pakistan.,Faculty of Life Sciences, University of Central Punjab (UCP), Lahore, Pakistan
| | - Muhammad U Mirza
- Department of Pharmaceutical Sciences, REGA Institute for Medical Research, Medicinal Chemistry, University of Leuven, Leuven, Belgium
| | - Michiel Vanmeert
- Department of Pharmaceutical Sciences, REGA Institute for Medical Research, Medicinal Chemistry, University of Leuven, Leuven, Belgium
| | - Javed Akhtar
- Institute of Molecular Biology and Biotechnology (IMBB), Centre for Research in Molecular Medicine (CRiMM), The University of Lahore, Lahore, Pakistan
| | - Hina Bashir
- Institute of Molecular Biology and Biotechnology (IMBB), Centre for Research in Molecular Medicine (CRiMM), The University of Lahore, Lahore, Pakistan.,Department of Biochemistry, Sharif Medical and Dental College, Lahore, Pakistan
| | - Saadullah Khan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, Pakistan
| | - Saqib Shehzad
- Faculty of Life Sciences, University of Central Punjab (UCP), Lahore, Pakistan
| | - Matheus Froeyen
- Department of Pharmaceutical Sciences, REGA Institute for Medical Research, Medicinal Chemistry, University of Leuven, Leuven, Belgium
| | - Wasim Ahmed
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Muhammad Ansar
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Naveed Wasif
- Institute of Molecular Biology and Biotechnology (IMBB), Centre for Research in Molecular Medicine (CRiMM), The University of Lahore, Lahore, Pakistan.,Institute of Human Genetics, University of Ulm & University Hospital, Ulm, Germany.,Institute of Human Genetics, University Hospital Schleswig-Holstein, Kiel, Germany
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49
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Raza MA, Feng LY, Iqbal N, Ahmed M, Chen YK, Khalid MHB, Mohi Ud Din A, Khan A, Ijaz W, Hussain A, Jamil MA, Naeem M, Bhutto SH, Ansar M, Yang F, Yang W. Growth and development of soybean under changing light environments in relay intercropping system. PeerJ 2019; 7:e7262. [PMID: 31372317 PMCID: PMC6659667 DOI: 10.7717/peerj.7262] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 06/06/2019] [Indexed: 12/31/2022] Open
Abstract
Background Maize-soybean relay-intercropping (MSR) is a famous system of crop production in developing countries. However, maize shading under this system directly affects the light quality and intensity of soybean canopy. This is a challenging scenario in which to implement the MSR system, in terms of varieties selection, planting pattern, and crop management since the duration of crop resource utilization clearly differs. Methods Therefore, this experiment aimed to elucidate the effect of leaf excising treatments from maize top to fully clarify the needs and balance of light quality and intensity of intercrop-soybean under MSR in field conditions. The effects of different leaf excising treatments (T0, no removal of leaves; T2, removal of two topmost leaves; T4, removal of four topmost leaves; T6, removal of six topmost leaves from maize plants were applied at first-trifoliate stage (V1) of soybean) on photosynthetically active radiation transmittance (PART), red to far-red ratio (R:FR), morphological and photosynthetic characteristics and total biomass production at second-trifoliate stage (V2), fifth-trifoliate stage (V5), and flowering-stage (R1) of soybean were investigated through field experiments for 2-years under MSR. Results As compared to T0, treatment T6 increased the PART and R:FR ratio at soybean canopy by 77% and 37% (V2), 70% and 34% (V5), and 41% and 36% (R1), respectively. This improved light environment in T6 considerably enhanced the leaf area index, SPAD values and photosynthetic rate of soybean plants by 66%, 25% and 49% at R1, respectively than T0. Similarly, relative to control, T6 also increased the stem diameter (by 29%) but decreased the plant height (by 23%) which in turn significantly increased stem breaking strength (by 87%) by reducing the lodging rate (by 59%) of soybean plants. Overall, under T6, relay-cropped soybean produced 78% of sole soybean seed-yield, and relay-cropped maize produced 81% of sole maize seed-yield. Our findings implied that by maintaining the optimum level of PART (from 60% to 80%) and R:FR ratio (0.9 to 1.1), we can improve morphological and photosynthetic characteristics of soybean plants in MSR. Therefore, more attention should be paid to the light environment when considering the sustainability of MSR via appropriate planting pattern selection.
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Affiliation(s)
- Muhammad Ali Raza
- College of Agronomy, Sichuan Agricultural University, Chengdu, China, China
| | - Ling Yang Feng
- College of Agronomy, Sichuan Agricultural University, Chengdu, China, China
| | - Nasir Iqbal
- College of Agronomy, Sichuan Agricultural University, Chengdu, China, China
| | - Mukhtar Ahmed
- Department of Agronomy, University of Arid Agriculture Rawalpindi, Rwalpindi, Punjab, Pakistan.,Department of Northern Agricultural Sciences, Swedish University of Agricultural Sciences, Umea, Sweden
| | - Yuan Kai Chen
- College of Agronomy, Sichuan Agricultural University, Chengdu, China, China
| | | | - Atta Mohi Ud Din
- College of Life Sciences, Sichuan Agricultural University, Yaan, China, China
| | - Ahsin Khan
- College of Life Sciences, Sichuan Agricultural University, Yaan, China, China
| | - Waqas Ijaz
- Chinese Academy of Agricultural Sciences, Institute of Environment and Sustainable Development in Agriculture, Beijing, China
| | - Anwaar Hussain
- Northeast Forestry University, School of Forestry, Harbin, China
| | | | - Muhammd Naeem
- College of Agronomy, Sichuan Agricultural University, Chengdu, China, China
| | | | - Muhammad Ansar
- Department of Agronomy, University of Arid Agriculture Rawalpindi, Rwalpindi, Punjab, Pakistan
| | - Feng Yang
- College of Agronomy, Sichuan Agricultural University, Chengdu, China, China
| | - Wenyu Yang
- College of Agronomy, Sichuan Agricultural University, Chengdu, China, China
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Ansar M, Ullah F, Paracha SA, Adams DJ, Lai A, Pais L, Iwaszkiewicz J, Millan F, Sarwar MT, Agha Z, Shah SF, Qaisar AA, Falconnet E, Zoete V, Ranza E, Makrythanasis P, Santoni FA, Ahmed J, Katsanis N, Walsh C, Davis EE, Antonarakis SE. Bi-allelic Variants in DYNC1I2 Cause Syndromic Microcephaly with Intellectual Disability, Cerebral Malformations, and Dysmorphic Facial Features. Am J Hum Genet 2019; 104:1073-1087. [PMID: 31079899 PMCID: PMC6556908 DOI: 10.1016/j.ajhg.2019.04.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 04/01/2019] [Indexed: 12/30/2022] Open
Abstract
Cargo transport along the cytoplasmic microtubular network is essential for neuronal function, and cytoplasmic dynein-1 is an established molecular motor that is critical for neurogenesis and homeostasis. We performed whole-exome sequencing, homozygosity mapping, and chromosomal microarray studies in five individuals from three independent pedigrees and identified likely-pathogenic variants in DYNC1I2 (Dynein Cytoplasmic 1 Intermediate Chain 2), encoding a component of the cytoplasmic dynein 1 complex. In a consanguineous Pakistani family with three affected individuals presenting with microcephaly, severe intellectual disability, simplification of cerebral gyration, corpus callosum hypoplasia, and dysmorphic facial features, we identified a homozygous splice donor site variant (GenBank: NM_001378.2:c.607+1G>A). We report two additional individuals who have similar neurodevelopmental deficits and craniofacial features and harbor deleterious variants; one individual bears a c.740A>G (p.Tyr247Cys) change in trans with a 374 kb deletion encompassing DYNC1I2, and an unrelated individual harbors the compound-heterozygous variants c.868C>T (p.Gln290∗) and c.740A>G (p.Tyr247Cys). Zebrafish larvae subjected to CRISPR-Cas9 gene disruption or transient suppression of dync1i2a displayed significantly altered craniofacial patterning with concomitant reduction in head size. We monitored cell death and cell cycle progression in dync1i2a zebrafish models and observed significantly increased apoptosis, likely due to prolonged mitosis caused by abnormal spindle morphology, and this finding offers initial insights into the cellular basis of microcephaly. Additionally, complementation studies in zebrafish demonstrate that p.Tyr247Cys attenuates gene function, consistent with protein structural analysis. Our genetic and functional data indicate that DYNC1I2 dysfunction probably causes an autosomal-recessive microcephaly syndrome and highlight further the critical roles of the dynein-1 complex in neurodevelopment.
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Affiliation(s)
- Muhammad Ansar
- Department of Genetic Medicine and Development, University of Geneva, 1206 Geneva, Switzerland
| | - Farid Ullah
- Center for Human Disease Modeling, Duke University Medical Center, Durham, NC 27701, USA; Human Molecular Genetics Laboratory, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, 38000 Faisalabad, Pakistan; Pakistan Institute of Engineering and Applied Sciences, 45650 Islamabad, Pakistan
| | - Sohail A Paracha
- Institute of Basic Medical Sciences, Khyber Medical University, 25100 Peshawar, Pakistan
| | - Darius J Adams
- Atlantic Health System, Goryeb Children's Hospital, Morristown, NJ 07960, USA
| | - Abbe Lai
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Neurology and Pediatrics, Harvard Medical School, Center for Life Sciences, Blackfan Circle, Boston, MA 02115, USA
| | - Lynn Pais
- Medical and Population Genetics Program, Broad Institute of MIT, Cambridge, MA 02142, USA; Center for Mendelian Genomics, Harvard University, Cambridge, MA 02142, USA
| | - Justyna Iwaszkiewicz
- Swiss Institute of Bioinformatics, Molecular Modeling Group, Batiment Genopode, Unil Sorge, 1015 Lausanne, Switzerland
| | | | - Muhammad T Sarwar
- Institute of Basic Medical Sciences, Khyber Medical University, 25100 Peshawar, Pakistan
| | - Zehra Agha
- Department of Biosciences, COMSATS University, 45500 Islamabad, Pakistan
| | - Sayyed Fahim Shah
- Department of Medicine, KMU Institute of Medical Sciences, 26000 Kohat, Pakistan
| | - Azhar Ali Qaisar
- Radiology Department, Lady Reading Hospital, 25000 Peshawar, Pakistan
| | - Emilie Falconnet
- Department of Genetic Medicine and Development, University of Geneva, 1206 Geneva, Switzerland
| | - Vincent Zoete
- Swiss Institute of Bioinformatics, Molecular Modeling Group, Batiment Genopode, Unil Sorge, 1015 Lausanne, Switzerland; Department of Fundamental Oncology, Lausanne University, Ludwig Institute for Cancer Research, Route de la Corniche 9A, 1066 Epalinges, Switzerland
| | - Emmanuelle Ranza
- Department of Genetic Medicine and Development, University of Geneva, 1206 Geneva, Switzerland; Service of Genetic Medicine, University Hospitals of Geneva, 1205 Geneva, Switzerland
| | - Periklis Makrythanasis
- Department of Genetic Medicine and Development, University of Geneva, 1206 Geneva, Switzerland; Biomedical Research Foundation of the Academy of Athens, 115 27 Athens, Greece
| | - Federico A Santoni
- Department of Genetic Medicine and Development, University of Geneva, 1206 Geneva, Switzerland; Department of Endocrinology Diabetes and Metabolism, University Hospital of Lausanne, 1011 Lausanne, Switzerland
| | - Jawad Ahmed
- Institute of Basic Medical Sciences, Khyber Medical University, 25100 Peshawar, Pakistan
| | - Nicholas Katsanis
- Center for Human Disease Modeling, Duke University Medical Center, Durham, NC 27701, USA
| | - Christopher Walsh
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Neurology and Pediatrics, Harvard Medical School, Center for Life Sciences, Blackfan Circle, Boston, MA 02115, USA; Medical and Population Genetics Program, Broad Institute of MIT, Cambridge, MA 02142, USA; Center for Mendelian Genomics, Harvard University, Cambridge, MA 02142, USA
| | - Erica E Davis
- Center for Human Disease Modeling, Duke University Medical Center, Durham, NC 27701, USA.
| | - Stylianos E Antonarakis
- Department of Genetic Medicine and Development, University of Geneva, 1206 Geneva, Switzerland; Service of Genetic Medicine, University Hospitals of Geneva, 1205 Geneva, Switzerland; iGE3 Institute of Genetics and Genomics of Geneva, 1211 Geneva, Switzerland.
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