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Deitch I, Itskov S, Panneman D, Abu Shtaya A, Saban T, Goldberg Y, Ehrenberg M, Cremers FPM, Roosing S, Ben-Yosef T. Autosomal Recessive Rod-Cone Dystrophy with Mild Extra-Ocular Manifestations Due to a Splice-Affecting Variant in BBS9. Curr Issues Mol Biol 2024; 46:2566-2575. [PMID: 38534779 DOI: 10.3390/cimb46030163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/14/2024] [Accepted: 03/14/2024] [Indexed: 03/28/2024] Open
Abstract
Bardet-Biedl syndrome (BBS), one of the most common forms of syndromic inherited retinal diseases (IRDs), is characterized by the combination of retinal degeneration with additional extra-ocular manifestations, including obesity, intellectual disability, kidney disease, polydactyly and other skeletal abnormalities. We observed an Israeli patient with autosomal recessive apparently non-syndromic rod-cone dystrophy (RCD). Extra-ocular findings were limited to epilepsy and dental problems. Genetic analysis with a single molecule molecular inversion probes-based panel that targets the exons and splice sites of 113 genes associated with retinitis pigmentosa and Leber congenital amaurosis revealed a homozygous rare missense variant in the BBS9 gene (c.263C>T;p.(Ser88Leu)). This variant, which affects a highly conserved amino acid, is also located in the last base of Exon 3, and predicted to be splice-altering. An in vitro minigene splice assay demonstrated that this variant leads to the partial aberrant splicing of Exon 3. Therefore, we suggest that this variant is likely hypomorphic. This is in agreement with the relatively mild phenotype observed in the patient. Hence, the findings in our study expand the phenotypic spectrum associated with BBS9 variants and indicate that variants in this gene should be considered not only in BBS patients but also in individuals with non-syndromic IRD or IRD with very mild extra-ocular manifestations.
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Affiliation(s)
- Iris Deitch
- Rabin Medical Center, Department of Ophthalmology, Petach Tikva 4941492, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Sofia Itskov
- Ruth & Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 3109601, Israel
| | - Daan Panneman
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Aasem Abu Shtaya
- Raphael Recanati Genetic Institute, Rabin Medical Center, Beilinson Hospital, Petach Tikva 4941492, Israel
- Unit of Gastroenterology, Carmel Medical Center, Haifa 3436212, Israel
| | - Tal Saban
- Rabin Medical Center, Department of Ophthalmology, Petach Tikva 4941492, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Yael Goldberg
- Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
- Raphael Recanati Genetic Institute, Rabin Medical Center, Beilinson Hospital, Petach Tikva 4941492, Israel
| | - Miriam Ehrenberg
- Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
- Schneider Children's Medical Center of Israel, Department of Ophthalmology, Petach Tikva 4920235, Israel
| | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Susanne Roosing
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Tamar Ben-Yosef
- Ruth & Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 3109601, Israel
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Kanwal A, Sheikh SA, Aslam F, Yaseen S, Beetham Z, Pankratz N, Clabots CR, Naz S, Pardo JV. Genome Sequencing of Consanguineous Family Implicates Ubiquitin-Specific Protease 53 ( USP53) Variant in Psychosis/Schizophrenia: Wild-Type Expression in Murine Hippocampal CA 1-3 and Granular Dentate with AMPA Synapse Interactions. Genes (Basel) 2023; 14:1921. [PMID: 37895270 PMCID: PMC10606770 DOI: 10.3390/genes14101921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 09/22/2023] [Accepted: 10/02/2023] [Indexed: 10/29/2023] Open
Abstract
Psychosis is a severe mental disorder characterized by abnormal thoughts and perceptions (e.g., hallucinations) occurring quintessentially in schizophrenia and in several other neuropsychiatric disorders. Schizophrenia is widely considered as a neurodevelopmental disorder that onsets during teenage/early adulthood. A multiplex consanguineous Pakistani family was afflicted with severe psychosis and apparent autosomal recessive transmission. The first-cousin parents and five children were healthy, whereas two teenage daughters were severely affected. Structured interviews confirmed the diagnosis of DSM-V schizophrenia. Probands and father underwent next-generation sequencing. All available relatives were subjected to confirmatory Sanger sequencing. Homozygosity mapping and directed a priori filtering identified only one rare variant [MAF < 5(10)-5] at a residue conserved across vertebrates. The variant was a non-catalytic deubiquitinase, USP53 (p.Cys228Arg), predicted in silico as damaging. Genome sequencing did not identify any other potentially pathogenic single nucleotide variant or structural variant. Since the literature on USP53 lacked relevance to mental illness or CNS expression, studies were conducted which revealed USP53 localization in regions of the hippocampus (CA 1-3) and granular dentate. The staining pattern was like that seen with GRIA2/GluA2 and GRIP2 antibodies. All three proteins coimmunoprecipitated. These findings support the glutamate hypothesis of schizophrenia as part of the AMPA-R interactome. If confirmed, USP53 appears to be one of the few Mendelian variants potentially causal to a common-appearing mental disorder that is a rare genetic form of schizophrenia.
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Affiliation(s)
- Ambreen Kanwal
- School of Biological Sciences, University of the Punjab, Lahore 54590, Pakistan; (A.K.); (F.A.); (S.Y.)
- Cognitive Neuroimaging Unit, Minneapolis Veterans Health Care System, Minneapolis, MN 55417, USA
- Department of Psychiatry, University of Minnesota, Minneapolis, MN 55454, USA
| | - Sohail A. Sheikh
- Department of Psychiatry, Hawkes Bay Hospital, Hastings 4120, New Zealand;
| | - Faiza Aslam
- School of Biological Sciences, University of the Punjab, Lahore 54590, Pakistan; (A.K.); (F.A.); (S.Y.)
| | - Samina Yaseen
- School of Biological Sciences, University of the Punjab, Lahore 54590, Pakistan; (A.K.); (F.A.); (S.Y.)
| | - Zachary Beetham
- Division of Computational Pathology, Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA; (Z.B.)
| | - Nathan Pankratz
- Division of Computational Pathology, Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA; (Z.B.)
| | - Connie R. Clabots
- Medicine Patient Service Line, Minneapolis Veterans Health Care System, Minneapolis, MN 55417, USA;
| | - Sadaf Naz
- School of Biological Sciences, University of the Punjab, Lahore 54590, Pakistan; (A.K.); (F.A.); (S.Y.)
| | - José V. Pardo
- Cognitive Neuroimaging Unit, Minneapolis Veterans Health Care System, Minneapolis, MN 55417, USA
- Department of Psychiatry, University of Minnesota, Minneapolis, MN 55454, USA
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Zafar S, Khurram H, Kamran M, Fatima M, Parvaiz A, Shaikh RS. Potential of GJA8 gene variants in predicting age-related cataract: A comparison of supervised machine learning methods. PLoS One 2023; 18:e0286243. [PMID: 37651414 PMCID: PMC10470928 DOI: 10.1371/journal.pone.0286243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 05/11/2023] [Indexed: 09/02/2023] Open
Abstract
Cataracts are the problems associated with the crystallins proteins of the eye lens. Any perturbation in the conformity of these proteins results in a cataract. Age-related cataract is the most common type among all cataracts as it accounts for almost 80% of cases of senile blindness worldwide. This research study was performed to predict the role of single nucleotide polymorphisms (SNPs) of the GJA8 gene with age-related cataracts in 718 subjects (400 age-related cataract patients and 318 healthy individuals). A comparison of supervised machine learning classification algorithm including logistic regression (LR), random forest (RF) and Artificial Neural Network (ANN) were presented to predict the age-related cataracts. The results indicated that LR is the best for predicting age-related cataracts. This successfully developed model after accounting different genetic and demographic factors to predict cataracts will help in effective disease management and decision-making medical practitioner and experts.
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Affiliation(s)
- Saba Zafar
- Department of Biochemistry and Biotechnology, The Women University, Multan, Pakistan
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan, Pakistan
| | - Haris Khurram
- Department of Sciences and Humanities, National University of Computer and Emerging Sciences, Chiniot-Faisalabad Campus, Chiniot, Pakistan
| | - Muhammad Kamran
- Department of Medical Laboratory Technology, Islamabad Medical & Dental college, Islamabad, Pakistan
| | - Madeeha Fatima
- Department of Zoology, The Women University, Multan, Pakistan
| | - Aqsa Parvaiz
- Department of Biochemistry and Biotechnology, The Women University, Multan, Pakistan
| | - Rehan Sadiq Shaikh
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan, Pakistan
- Center for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
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Apanovich N, Matveev A, Ivanova N, Burdennyy A, Apanovich P, Pronina I, Filippova E, Kazubskaya T, Loginov V, Braga E, Alimov A. Prediction of Distant Metastases in Patients with Kidney Cancer Based on Gene Expression and Methylation Analysis. Diagnostics (Basel) 2023; 13:2289. [PMID: 37443682 DOI: 10.3390/diagnostics13132289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 06/28/2023] [Accepted: 07/04/2023] [Indexed: 07/15/2023] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is the most common and aggressive histological type of cancer in this location. Distant metastases are present in approximately 30% of patients at the time of first examination. Therefore, the ability to predict the occurrence of metastases in patients at early stages of the disease is an urgent task aimed at personalized treatment. Samples of tumor and paired histologically normal kidney tissue from patients with metastatic and non-metastatic ccRCC were studied. Gene expression was analyzed using real-time PCR. The level of gene methylation was evaluated using bisulfite conversion followed by quantitative methylation-specific PCR. Two groups of genes were analyzed in this study. The first group includes genes whose expression is significantly reduced during metastasis: CA9, NDUFA4L2, EGLN3, and BHLHE41 (p < 0.001, ROC analysis). The second group includes microRNA genes: MIR125B-1, MIR137, MIR375, MIR193A, and MIR34B/C, whose increased methylation levels are associated with the development of distant metastases (p = 0.002 to <0.001, ROC analysis). Based on the data obtained, a combined panel of genes was formed to identify patients whose tumors have a high metastatic potential. The panel can estimate the probability of metastasis with an accuracy of up to 92%.
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Affiliation(s)
- Natalya Apanovich
- Research Centre for Medical Genetics, 1 Moskvorechye St., Moscow 115522, Russia
| | - Alexey Matveev
- Federal State Budgetary Institution (N.N. Blokhin National Medical Research Center of Oncology) of the Ministry of Health of the Russian Federation, 24 Kashirskoe Shosse, Moscow 115478, Russia
| | - Natalia Ivanova
- Institute of General Pathology and Pathophysiology, Baltijskaya St. 8, Moscow 125315, Russia
| | - Alexey Burdennyy
- Institute of General Pathology and Pathophysiology, Baltijskaya St. 8, Moscow 125315, Russia
| | - Pavel Apanovich
- Research Centre for Medical Genetics, 1 Moskvorechye St., Moscow 115522, Russia
| | - Irina Pronina
- Institute of General Pathology and Pathophysiology, Baltijskaya St. 8, Moscow 125315, Russia
| | - Elena Filippova
- Institute of General Pathology and Pathophysiology, Baltijskaya St. 8, Moscow 125315, Russia
| | - Tatiana Kazubskaya
- Federal State Budgetary Institution (N.N. Blokhin National Medical Research Center of Oncology) of the Ministry of Health of the Russian Federation, 24 Kashirskoe Shosse, Moscow 115478, Russia
| | - Vitaly Loginov
- Institute of General Pathology and Pathophysiology, Baltijskaya St. 8, Moscow 125315, Russia
| | - Eleonora Braga
- Research Centre for Medical Genetics, 1 Moskvorechye St., Moscow 115522, Russia
- Institute of General Pathology and Pathophysiology, Baltijskaya St. 8, Moscow 125315, Russia
| | - Andrei Alimov
- Research Centre for Medical Genetics, 1 Moskvorechye St., Moscow 115522, Russia
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Gul R, Firasat S, Schubert M, Ullah A, Peña E, Thuesen ACB, Hussain M, Staeger FF, Gjesing AP, Albrechtsen A, Hansen T. Identifying the genetic causes of phenotypically diagnosed Pakistani mucopolysaccharidoses patients by whole genome sequencing. Front Genet 2023; 14:1128850. [PMID: 37091798 PMCID: PMC10113632 DOI: 10.3389/fgene.2023.1128850] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 03/13/2023] [Indexed: 04/07/2023] Open
Abstract
Background: Lysosomal storage disorders (LSDs) are a group of inherited metabolic diseases, which encompass more than 50 different subtypes of pathologies. These disorders are caused by defects in lysosomal enzymes, transporters, and other non-lysosomal proteins. Mucopolysaccharidosis (MPS) is the most common subgroup of lysosomal storage disorders in which the body is unable to properly breakdown mucopolysaccharides. The aim of the present study was to identify novel genes and pathogenic variants in families from diverse regions of Pakistan with clinically diagnosed mucopolysaccharidosis type I and mucopolysaccharidosis type II.Methods: Clinical diagnosis identified 12 with mucopolysaccharidosis I and 2 with mucopolysaccharidosis II in 14 families and whole genome sequencing (WGS) was performed to identify the causative variations in 15 affected individuals. Twenty-two unaffected individuals including parents or normal siblings of patients were also sequenced. Putative causal variants were identified by co-segregation and functional annotation.Results: Analysis of whole genome sequencing data revealed ten novel and six previously reported variants in lysosomal storage disorders-associated genes (IDUA, GALNS, SGSH, GAA, IDS, ALDOB, TRAPPC4, MASP1, SMARCAL, KIAA1109, HERC1, RRAS2) and a novel candidate gene (ABCA5) for lysosomal storage disorder-like phenotypes, which has previously been associated with symptoms strongly related with lysosomal storage disorder in animal models.Conclusion: Multigenic inheritance was found in several families highlighting the importance of searching for homozygous pathogenic variants in several genes also in families with a high degree of consanguinity.
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Affiliation(s)
- Rutaba Gul
- Department of Zoology, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, Pakistan
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sabika Firasat
- Department of Zoology, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, Pakistan
- *Correspondence: Sabika Firasat, ; Torben Hansen,
| | - Mikkel Schubert
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Asmat Ullah
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Elionora Peña
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anne C. B. Thuesen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mulazim Hussain
- The Children Hospital, Pakistan Institute of Medical Sciences (PIMS), Islamabad, Pakistan
| | - Frederik F. Staeger
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Anette P. Gjesing
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anders Albrechtsen
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- *Correspondence: Sabika Firasat, ; Torben Hansen,
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Naeem M, Amaro-Estrada I, Taqadus A, Swelum AA, Alqhtani AH, Asif M, Sajid M, Khan AU, Tariq A, Anjum S, Khan A, Iqbal F. Molecular prevalence and associated risk factors of Anaplasma ovis in Pakistani sheep. Front Vet Sci 2023; 10:1096418. [PMID: 37065244 PMCID: PMC10095557 DOI: 10.3389/fvets.2023.1096418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 03/13/2023] [Indexed: 03/31/2023] Open
Abstract
BackgroundMajority of Pakistani population lives in rural areas and raising animals, especially the small ruminants, is their primary source of income. Anaplasma ovis is known to infect small ruminants globally and causing significant economic losses to livestock owners, however prevalence of Anaplasma ovis has been least investigated from Pakistan despite having a huge sheep population.MethodsThe present study was conducted from June 2021 till December 2021 to report the PCR based prevalence of Anaplasma ovis in the blood samples of sheep (n = 239) that were collected from District Dera Ghazi Khan in Pakistan.ResultsOut of 239 samples, 30 (12.5%) amplified a 347 bp fragment specific for the msp4 gene of Anaplasma ovis. Represented partial msp4 gene sequences were confirmed by Sanger sequencing and deposited to GenBank (OP620757-59). None of the studied epidemiological factors (age, sex, breed, size of herd, dogs with herd, and composition of herd) showed an association (P > 0.05) with the Anaplasma ovis infection in enrolled sheep. Analysis of the amplified partial mSP4 sequence of Anaplasma ovis revealed that this gene is highly conserved as all three sequences were identical and phylogenetically resembled with the msp4 sequences amplified from small ruminants in China, Kenya, and Germany, Turkey, Portugal, Tunisia and India. In conclusion, for the first time, we are reporting a moderate prevalence of Anaplasma ovis prevalence in Pakistani sheep and this data will help in developing the integrated control policies against this newly reported tick-borne disease that is infecting our sheep breeds.
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Affiliation(s)
- Muhammad Naeem
- Institute of Zoology, Bahauddin Zakariya University, Multan, Pakistan
| | - Itzel Amaro-Estrada
- Centro Nacional de Investigación Disciplinaria en Salud Animal e Inocuidad, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias (INIFAP), Jiutepec, Morelos, Mexico
| | - Asia Taqadus
- Institute of Zoology, Bahauddin Zakariya University, Multan, Pakistan
| | - Ayman A. Swelum
- Department of Animal Production, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Abdulmohsen H. Alqhtani
- Department of Animal Production, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Muhammad Asif
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan, Pakistan
| | - Muhammad Sajid
- Institute of Zoology, Bahauddin Zakariya University, Multan, Pakistan
| | - Asmat Ullah Khan
- Shaheed Benazir Bhuto University Sheringal, District Dir, Khyber Pakhtunkhwa, Pakistan
| | - Aliza Tariq
- Institute of Zoology, Bahauddin Zakariya University, Multan, Pakistan
| | - Summaya Anjum
- Institute of Zoology, Bahauddin Zakariya University, Multan, Pakistan
| | - Adil Khan
- Department of Botany and Zoology, Bacha Khan University, Charsadda, Khyber Pakhtunkhwa, Pakistan
- Adil Khan
| | - Furhan Iqbal
- Institute of Zoology, Bahauddin Zakariya University, Multan, Pakistan
- *Correspondence: Furhan Iqbal
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A Biallelic Truncating Variant in the TPR Domain of GEMIN5 Associated with Intellectual Disability and Cerebral Atrophy. Genes (Basel) 2023; 14:genes14030707. [PMID: 36980979 PMCID: PMC10048441 DOI: 10.3390/genes14030707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/06/2023] [Accepted: 03/08/2023] [Indexed: 03/17/2023] Open
Abstract
GEMIN5 is a multifunctional RNA-binding protein required for the assembly of survival motor neurons. Several bi-allelic truncating and missense variants in this gene are reported to cause a neurodevelopmental disorder characterized by cerebellar atrophy, intellectual disability (ID), and motor dysfunction. Whole exome sequencing of a Pakistani consanguineous family with three brothers affected by ID, cerebral atrophy, mobility, and speech impairment revealed a novel homozygous 3bp-deletion NM_015465.5:c.3162_3164del that leads to the loss of NM_015465.5 (NP_056280.2):p. (Asp1054_Ala1055delinsGlu) amino acid in one of the α-helixes of the tetratricopeptide repeats of GEMIN5. In silico 3D representations of the GEMIN5 dimerization domain show that this variant likely affects the orientation of the downstream sidechains out of the helix axis, which would affect the packing with neighboring helices. The phenotype of all affected siblings overlaps well with previously reported patients, suggesting that NM_015465.5: c.3162_3164del (NP_056280.2):p. (Asp1054_Ala1055delinsGlu) is a novel GEMIN5 pathogenic variant. Overall, our data expands the molecular and clinical phenotype of the recently described neurodevelopmental disorder with cerebellar atrophy and motor dysfunction (NEDCAM) syndrome.
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Arshad MW, Shabbir MI, Asif S, Shahzad M, Leydier L, Rai SK. FRMD7 Gene Alterations in a Pakistani Family Associated with Congenital Idiopathic Nystagmus. Genes (Basel) 2023; 14:genes14020346. [PMID: 36833273 PMCID: PMC9957179 DOI: 10.3390/genes14020346] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 01/27/2023] [Accepted: 01/27/2023] [Indexed: 01/31/2023] Open
Abstract
Congenital idiopathic nystagmus (CIN) is an oculomotor disorder characterized by repetitive and rapid involuntary movement of the eye that usually develops in the first six months after birth. Unlike other forms of nystagmus, CIN is widely associated with mutations in the FRMD7 gene. This study involves the molecular genetic analysis of a consanguineous Pakistani family with individuals suffering from CIN to undermine any potential pathogenic mutations. Blood samples were taken from affected and normal individuals of the family. Genomic DNA was extracted using an in-organic method. Whole Exome Sequencing (WES) and analysis were performed to find any mutations in the causative gene. To validate the existence and co-segregation of the FRMD7 gene variant found using WES, sanger sequencing was also carried out using primers that targeted all of the FRMD7 coding exons. Additionally, the pathogenicity of the identified variant was assessed using different bioinformatic tools. The WES results identified a novel nonsense mutation in the FRMD7 (c.443T>A; p. Leu148 *) gene in affected individuals from the Pakistani family, with CIN resulting in a premature termination codon, further resulting in the formation of a destabilized protein structure that was incomplete. Co-segregation analysis revealed that affected males are hemizygous for the mutated allele c.443T>A; p. Leu148 * and the affected mother is heterozygous. Overall, such molecular genetic studies expand our current knowledge of the mutations associated with the FRMD7 gene in Pakistani families with CIN and significantly enhance our understanding of the molecular mechanisms involved in genetic disorders.
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Affiliation(s)
- Muhammad Waqar Arshad
- Department of Psychiatry, Yale School of Medicine, VA CT Healthcare Center S116A2, West Haven, CT 06516, USA
- Department of Molecular Biology, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad 44080, Pakistan
| | - Muhammad Imran Shabbir
- Department of Biological Sciences, Faculty of Basic & Applied Sciences, International Islamic University, Sector H-10, Islamabad 44000, Pakistan
- Correspondence: (M.I.S.); (S.K.R.)
| | - Saaim Asif
- Department of Biological Sciences, Faculty of Basic & Applied Sciences, International Islamic University, Sector H-10, Islamabad 44000, Pakistan
- Department of Biosciences, COMSATS University Islamabad, Islamabad Campus, Islamabad 45550, Pakistan
| | - Mohsin Shahzad
- Department of Molecular Biology, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad 44080, Pakistan
| | - Larissa Leydier
- Department of Molecular Biology, Medical University of the Americas, Charlestown KN 1102, Saint Kitts and Nevis, West Indies
| | - Sunil Kumar Rai
- Department of Molecular Biology, Medical University of the Americas, Charlestown KN 1102, Saint Kitts and Nevis, West Indies
- Correspondence: (M.I.S.); (S.K.R.)
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Thomas P, Srivastava S, Udayashankara AH, Damodaran S, Yadav L, Mathew B, Suresh SB, Mandal AK, Srikantia N. RhoC in association with TET2/WDR5 regulates cancer stem cells by epigenetically modifying the expression of pluripotency genes. Cell Mol Life Sci 2022; 80:1. [PMID: 36469134 PMCID: PMC11073244 DOI: 10.1007/s00018-022-04645-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 11/22/2022] [Accepted: 11/22/2022] [Indexed: 12/12/2022]
Abstract
Emerging evidence illustrates that RhoC has divergent roles in cervical cancer progression where it controls epithelial to mesenchymal transition (EMT), migration, angiogenesis, invasion, tumor growth, and radiation response. Cancer stem cells (CSCs) are the primary cause of recurrence and metastasis and exhibit all of the above phenotypes. It, therefore, becomes imperative to understand if RhoC regulates CSCs in cervical cancer. In this study, cell lines and clinical specimen-based findings demonstrate that RhoC regulates tumor phenotypes such as clonogenicity and anoikis resistance. Accordingly, inhibition of RhoC abrogated these phenotypes. RNA-seq analysis revealed that RhoC over-expression resulted in up-regulation of 27% of the transcriptome. Further, the Infinium MethylationEPIC array showed that RhoC over-expressing cells had a demethylated genome. Studies divulged that RhoC via TET2 signaling regulated the demethylation of the genome. Further investigations comprising ChIP-seq, reporter assays, and mass spectrometry revealed that RhoC associates with WDR5 in the nucleus and regulates the expression of pluripotency genes such as Nanog. Interestingly, clinical specimen-based investigations revealed the existence of a subset of tumor cells marked by RhoC+/Nanog+ expression. Finally, combinatorial inhibition (in vitro) of RhoC and its partners (WDR5 and TET2) resulted in increased sensitization of clinical specimen-derived cells to radiation. These findings collectively reveal a novel role for nuclear RhoC in the epigenetic regulation of Nanog and identify RhoC as a regulator of CSCs. The study nominates RhoC and associated signaling pathways as therapeutic targets.
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Affiliation(s)
- Pavana Thomas
- Translational and Molecular Biology Laboratory (TMBL), Division of Molecular Biology and Genetics, St. John's Research Institute (SJRI), St. John's Medical College, Bangalore, 560034, India
- School of Integrative Health Sciences, The University of Trans-Disciplinary Health Sciences and Technology (TDU), Bangalore, 560064, India
| | - Sweta Srivastava
- Translational and Molecular Biology Laboratory (TMBL), Division of Molecular Biology and Genetics, St. John's Medical College Hospital, Bangalore, 560034, India.
| | - Avinash H Udayashankara
- Department of Radiation Oncology, St John's Medical College Hospital, Bangalore, 560034, India
| | - Samyuktha Damodaran
- Translational and Molecular Biology Laboratory (TMBL), Division of Molecular Biology and Genetics, St. John's Research Institute (SJRI), St. John's Medical College, Bangalore, 560034, India
| | - Lokendra Yadav
- Translational and Molecular Biology Laboratory (TMBL), Division of Molecular Biology and Genetics, St. John's Medical College Hospital, Bangalore, 560034, India
| | - Boby Mathew
- Clinical Proteomics Unit, Division of Molecular Medicine, St. John's Research Institute (SJRI), St. John's Medical College, Bangalore, 560034, India
| | - Srinag Bangalore Suresh
- Translational and Molecular Biology Laboratory (TMBL), Division of Molecular Biology and Genetics, St. John's Research Institute (SJRI), St. John's Medical College, Bangalore, 560034, India
| | - Amit Kumar Mandal
- Clinical Proteomics Unit, Division of Molecular Medicine, St. John's Research Institute (SJRI), St. John's Medical College, Bangalore, 560034, India
| | - Nirmala Srikantia
- Department of Radiation Oncology, St John's Medical College Hospital, Bangalore, 560034, India
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10
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Kanwal A, Sheikh SA, Iftikhar A, Naz S, Pardo JV. Preliminary studies on apparent mendelian psychotic disorders in consanguineous families. BMC Psychiatry 2022; 22:709. [PMID: 36384485 PMCID: PMC9667425 DOI: 10.1186/s12888-022-04304-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 06/23/2022] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Psychiatric disorders are characterized by alteration in emotions, mood and behavior. Genetics is known to play a significant role in the development of psychiatric disorders. Genome-wide association studies have identified several loci associated with psychiatric illnesses. We hypothesize the existence of rare variants following Mendelian recessive mode of inheritance. These variants can be identified in families with multiple affected individuals born to unaffected consanguineous parents. METHODS We visited psychiatric outpatient departments of multiple hospitals in Lahore, Pakistan. We focused on psychosis, as it can occur in several DSM disorders such as schizophrenia, dementia and bipolar disorder. After clinical diagnosis by an American trained psychiatrist, detailed clinical assessments using Diagnostic Interview for Genetic Studies (DIGS), Diagnostic Interview for Psychosis and Affective Disorders (DI-PAD), Positive and Negative Syndrome Scale (PANSS), Hamilton Depression and Anxiety Rating Scale (HAM-D; HAM-A) were administered to all willing affected and unaffected participants. RESULTS We identified eight pedigrees with two or more psychotic individuals in each family. Clinical diagnoses determined by their psychiatrists included ten individuals with schizophrenia; four individuals with psychosis and bipolar disorder; and two patients with "unspecified psychosis." The rating instruments rigorously confirmed the diagnosis of psychosis in the affected patients from the six families as well as the absence of psychotic disorders in unaffected individuals from the six families. We obtained DNA samples from willing members of all eight families for future genetic analyses. CONCLUSION Our research highlights an alternative approach to discovery of rare recessively inherited genetic variants causing psychiatric disorders that have remained unidentified to date. These findings could illuminate underlying biological mechanisms leading toward development of targeted therapies in future.
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Affiliation(s)
- Ambreen Kanwal
- grid.11173.350000 0001 0670 519XSchool of Biological Sciences, University of the Punjab, Quaid-e-Azam campus, 54590 Lahore, Lahore Pakistan
| | | | - Amina Iftikhar
- Rainbow Obesity and Eating Disorders Centre, Lahore, Pakistan
| | - Sadaf Naz
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam campus, 54590, Lahore, Lahore, Pakistan.
| | - José V. Pardo
- grid.17635.360000000419368657Department of Psychiatry, University of Minnesota, Minneapolis, MN USA ,grid.410394.b0000 0004 0419 8667Minneapolis Veterans Affairs Health Care System, Minneapolis, MN USA
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Yaqoob Shahani M, Memon S, Ahmed Sheikh S, Bano U, Shaikh P, Gul Memon S, Begum Shahani S, din Ujjan I, Kumar Narsani A, Muhammad Waryah A. GENETIC HETEROGENEITY OF PRIMARY OPEN-ANGLE GLAUCOMA IN PAKISTAN. Saudi J Biol Sci 2022; 30:103488. [DOI: 10.1016/j.sjbs.2022.103488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 09/25/2022] [Accepted: 10/25/2022] [Indexed: 11/06/2022] Open
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Ali-Nasser T, Zayit-Soudry S, Banin E, Sharon D, Ben-Yosef T. Autosomal dominant retinitis pigmentosa with incomplete penetrance due to an intronic mutation of the PRPF31 gene. Mol Vis 2022; 28:359-368. [PMID: 36338669 PMCID: PMC9603903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 10/04/2022] [Indexed: 11/10/2022] Open
Abstract
Purpose To identify the molecular mechanisms of the development of autosomal dominant retinitis pigmentosa (adRP) with incomplete penetrance in an Israeli Muslim Arab family. Methods Two patients with adRP underwent a detailed ophthalmic evaluation, including funduscopic examination, visual field testing, optical coherence tomography, and electroretinography. Genetic analysis was performed using a combination of whole exome sequencing (WES) and Sanger sequencing. The pathogenicity of the identified intronic variant was evaluated in silico using several web-based tools, in vitro using a minigene-based assay, and in vivo using reverse transcription PCR analysis of lymphocyte-derived RNA. The relative abundance of alternatively spliced transcripts was evaluated using amplicon-based next-generation sequencing. The relative expression levels of PRPF31 and CNOT3 were measured using quantitative PCR (qPCR) analysis. Results The two patients recruited in this study had childhood-onset RP, with night blindness as the initial symptom, followed by concentric restriction of the visual field. The funduscopic findings included narrowed retinal blood vessels and peripheral bone spicule pigmentation. By the third decade of life, the full-field electroretinography findings had been remarkably attenuated. In these patients, we identified a novel heterozygous intronic variant at position +5 of PRPF31 intron 11 (c.1146+5G>T). The same variant was also detected in one asymptomatic family member. Through in silico analysis, the variant was predicted to alter the splicing of intron 11. An in vitro splicing assay and a reverse transcription PCR analysis of lymphocyte-derived RNA revealed that the mutant allele yielded mainly a shorter transcript in which exon 11 was skipped. The skipping of exon 11 was expected to cause a frameshift and an aberrant truncated protein (p.Tyr359Serfs*29). The qPCR analysis revealed reduced PRPF31 expression levels in the mutation carriers, without a significant difference between the affected patient and his asymptomatic brother. We evaluated several factors that have been suggested to correlate with non-penetrance of PRPF31 mutations, including the number of cis-acting MSR1 elements adjacent to the PRPF31 core promoter, CNOT3 expression level, and CNOT3 rs4806718 single-nucleotide polymorphism. None of these factors correlated with non-penetrance in the family in this study. Conclusions We report a novel intronic mutation in PRPF31 underlying adRP. This report expands the spectrum of pathogenic mutations in PRPF31 and further demonstrates the importance of intronic mutations. Moreover, it demonstrates the phenomenon of incomplete penetrance previously associated with PRPF31 mutations. The fact that the non-penetrance in the family in this study could not be explained by any of the known mechanisms suggests the possible contribution of a novel modifier of PRPF31 penetrance.
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Affiliation(s)
- Tahleel Ali-Nasser
- Ruth & Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Shiri Zayit-Soudry
- Ruth & Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel,Department of Ophthalmology, Rambam Health Care Campus, Haifa, Israel,Clinical Research Institute at Rambam, Rambam Health Care Campus, Haifa, Israel
| | - Eyal Banin
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Dror Sharon
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Tamar Ben-Yosef
- Ruth & Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
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13
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Iqbal A, Naz S, Kaul H, Sharif S, Khushbakht A, Naeem MA, Iqtedar M, Kaleem A, Firasat S, Manzoor F. Mutational analysis in sodium-borate cotransporter SLC4A11 in consanguineous families from Punjab, Pakistan. PLoS One 2022; 17:e0273685. [PMID: 36037197 PMCID: PMC9423612 DOI: 10.1371/journal.pone.0273685] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 08/12/2022] [Indexed: 12/02/2022] Open
Abstract
AIM To identify the molecular basis of Congenital Hereditary Endothelial Dystrophy CHED caused by mutations in SLC4A11, in the consanguineous Pakistani families. METHODS A total of 7 consanguineous families affected with Congenital Hereditary Endothelial Dystrophy were diagnosed and registered with the help of ophthalmologists. Blood samples were collected from affected and unaffected members of the enrolled families. Mutational analysis was carried out by DNA sequencing using both Sanger and Whole Exome Sequencing (WES). Probands of each pedigree from the 7 families were used for WES. Results were analyzed with the help of different bioinformatics tools. RESULTS The sequencing results demonstrated three known homozygous mutations in gene SLC4A11 in probands of 7 families. These mutations p.Glu675Ala, p.Val824Met, and p.Arg158fs include 2 missense and 1 frameshift mutation. The mutations result in amino acids that were highly conserved in SLC4A11 across different species. The mutations were segregated with the disease phenotype in the families. CONCLUSION This study reports 3 mutations in 7 families. One of the pathogenic mutations (p.R158fs) was identified for the first time in the Pakistani population. However, two mutations (p.Glu675Ala, p.Val824Met) were previously reported in two and one Pakistani family respectively. As these mutations segregate with the disease phenotype and bioinformatics tool also liable them as pathogenic, they are deemed as probable cause of underlying disease.
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Affiliation(s)
- Afia Iqbal
- Department of Zoology, Lahore College for Women University, Lahore, Pakista
| | - Shagufta Naz
- Department of Zoology, Lahore College for Women University, Lahore, Pakista
| | - Haiba Kaul
- Department of Animal Breeding and Genetics, Genetics Discipline, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Saima Sharif
- Department of Zoology, Lahore College for Women University, Lahore, Pakista
| | - Aysha Khushbakht
- Department of Zoology, Lahore College for Women University, Lahore, Pakista
| | - Muhammad Asif Naeem
- Vision Impairment Lab of Genetic Diseases Group, Center of Excellence in Molecular Biology, Lahore, Pakistan
| | - Mehwish Iqtedar
- Department of Biotechnology, Lahore College for Women University, Lahore, Pakistan
| | - Afshan Kaleem
- Department of Biotechnology, Lahore College for Women University, Lahore, Pakistan
| | - Sabika Firasat
- Department of Biological Sciences, Quaid-e-Azam University, Islamabad, Pakistan
| | - Farkhanda Manzoor
- Department of Zoology, Lahore College for Women University, Lahore, Pakista
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Khan A, Tian S, Tariq M, Khan S, Safeer M, Ullah N, Akbar N, Javed I, Asif M, Ahmad I, Ullah S, Satti HS, Khan R, Naeem M, Ali M, Rendu J, Fauré J, Dieterich K, Latypova X, Baig SM, Malik NA, Zhang F, Khan TN, Liu C. NGS-driven molecular diagnosis of heterogeneous hereditary neurological disorders reveals novel and known variants in disease-causing genes. Mol Genet Genomics 2022; 297:1601-1613. [PMID: 36002593 DOI: 10.1007/s00438-022-01945-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 08/11/2022] [Indexed: 11/28/2022]
Abstract
Hereditary neurological disorders (HNDs) are a clinically and genetically heterogeneous group of disorders. These disorders arise from the impaired function of the central or peripheral nervous system due to aberrant electrical impulses. More than 600 various neurological disorders, exhibiting a wide spectrum of overlapping clinical presentations depending on the organ(s) involved, have been documented. Owing to this clinical heterogeneity, diagnosing these disorders has been a challenge for both clinicians and geneticists and a large number of patients are either misdiagnosed or remain entirely undiagnosed. Contribution of genetics to neurological disorders has been recognized since long; however, the complete picture of the underlying molecular bases are under-explored. The aim of this study was to accurately diagnose 11 unrelated Pakistani families with various HNDs deploying NGS as a first step approach. Using exome sequencing and gene panel sequencing, we successfully identified disease-causing genomic variants these families. We report four novel variants, one each in, ECEL1, NALCN, TBR1 and PIGP in four of the pedigrees. In the rest of the seven families, we found five previously reported pathogenic variants in POGZ, FA2H, PLA2G6 and CYP27A1. Of these, three families segregate a homozygous 18 bp in-frame deletion of FA2H, indicating a likely founder mutation segregating in Pakistani population. Genotyping for this mutation can help low-cost population wide screening in the corresponding regions of the country. Our findings not only expand the existing repertoire of mutational spectrum underlying neurological disorders but will also help in genetic testing of individuals with HNDs in other populations.
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Affiliation(s)
- Ayaz Khan
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Pakistan
| | - Shixiong Tian
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai, 200438, China
| | - Muhammad Tariq
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Pakistan
| | - Sheraz Khan
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Pakistan
| | - Muhammad Safeer
- Department of Biotechnology and Genetic Engineering, Hazara University, Mansehra, Pakistan
| | - Naimat Ullah
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Pakistan
| | - Nazia Akbar
- Department of Biotechnology and Genetic Engineering, Hazara University, Mansehra, Pakistan
| | - Iram Javed
- Department of Paediatric Neurology, Children Hospital and Institute of Child Health, Faisalabad, Pakistan
| | - Mahnoor Asif
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Pakistan
| | - Ilyas Ahmad
- Institute for Cardiogenetics, University of Lübeck, DZHK (German Research Centre for Cardiovascular Research), partner site Hamburg/Lübeck/Kiel, University Heart Center Lübeck, Lübeck, Germany
| | - Shahid Ullah
- Department of General Surgery, Hayatabad Medical Complex, Peshawar, 2500, Pakistan
| | - Humayoon Shafique Satti
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, 46000, Pakistan
| | - Raees Khan
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, 46000, Pakistan.,NUMS Institute of Advance Studies and Research, National University of Medical Sciences, Rawalpindi, 46000, Pakistan
| | - Muhammad Naeem
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, 46000, Pakistan
| | - Mahwish Ali
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, 46000, Pakistan.,NUMS Institute of Advance Studies and Research, National University of Medical Sciences, Rawalpindi, 46000, Pakistan
| | - John Rendu
- Inserm, U1216, CHU Grenoble Alpes, Grenoble Institute of Neurosciences, University of Grenoble Alpes, 38000, Grenoble, France
| | - Julien Fauré
- Inserm, U1216, CHU Grenoble Alpes, Grenoble Institute of Neurosciences, University of Grenoble Alpes, 38000, Grenoble, France
| | - Klaus Dieterich
- Inserm, U1209, CHU Grenoble Alpes, Institute of Advanced Biosciences, University of Grenoble Alpes, 38000, Grenoble, France
| | - Xenia Latypova
- Inserm, U1216, CHU Grenoble Alpes, Grenoble Institute of Neurosciences, University of Grenoble Alpes, 38000, Grenoble, France
| | - Shahid Mahmood Baig
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Pakistan.,Pakistan Science Foundation, Constitution Avenue, Islamabad, Pakistan
| | - Naveed Altaf Malik
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Pakistan
| | - Feng Zhang
- Obstetrics and Gynecology Hospital, Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Institute of Reproduction and Development, Fudan University, Shanghai, 200438, China
| | - Tahir Naeem Khan
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, 46000, Pakistan. .,NUMS Institute of Advance Studies and Research, National University of Medical Sciences, Rawalpindi, 46000, Pakistan. .,Advanced Center for Translational and Genetic Medicine, Stanley Manne Children's Research Institute, Lurie Children's Hospital, Departments of Pediatrics and Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, United States.
| | - Chunyu Liu
- Obstetrics and Gynecology Hospital, Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Institute of Reproduction and Development, Fudan University, Shanghai, 200438, China.
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Hu X, Jiang N, Li Y, Zhou Y, Fan Y, Xue M, Zeng L, Liu W, Meng Y. Rapid Nucleic Acid Extraction for Aquatic Animal DNA Virus Determination Using Chelex 100 Resin via Conventional PCR and Digital Droplet PCR Detection. Animals (Basel) 2022; 12:ani12151999. [PMID: 35953988 PMCID: PMC9367309 DOI: 10.3390/ani12151999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 07/18/2022] [Accepted: 08/02/2022] [Indexed: 12/05/2022] Open
Abstract
Simple Summary Convenient, fast, and high-quality nucleic acid extraction methods are urgently needed in molecular diagnostic testing for viral pathogens in aquaculture. We developed a viral DNA extraction method from diseased tissues and cells using the Chelex 100 resin solution workflow. The only extraction reagents required are the Chelex 100 resin and phosphate-buffered saline. The whole extraction process only takes about 15 min from the tissue homogenate to obtain the DNA. The concentration of extracted DNA is at least 100 ng/µL. This methodology has clear benefits in terms of cost and time saving compared to the commercial kit extraction for aquatic animal DNA virus determination by PCR in the laboratory. In addition, the simplified method using Chelex 100 resin with a pH value of 10–11 presented excellent results in PCR application and could be a standard for the DNA extraction for DNA virus testing in the future. Abstract Molecular diagnostic testing for viral pathogens is crucial in aquaculture. The efficient and convenient preparation of pathogenic microbial nucleic acids is the basis of molecular diagnosis. Here, we developed a simplified deoxyribonucleic acid (DNA) extraction method from aquatic animal DNA viruses using the Chelex 100 resin. The nucleic acid was extracted from infected tissues and cell culture for the detection of three common aquatic viral pathogens (CEV, CyHV-2, and GSIV). We compared the extraction effects of a current commercial kit extraction method and the Chelex 100 resin extraction method according to nucleic acid concentration, conventional polymerase chain reaction (PCR), and digital droplet PCR (ddPCR). The results indicated that both extraction procedures could obtain high-quality nucleotide samples. Extracting DNA using the Chelex 100 resin led to better detective efficiency for ddPCR molecular diagnostic testing. The whole process took less than 20 min, and only Chelex 100 resin solution was added to the tissues or cells without multiple tubes being transferred several times. The extracted DNA concentration and the detection sensitivity were high. These results indicated that the Chelex 100 resin solution has the advantages of speed, efficiency, and economy compared to the commercial kit. In addition, the higher pH value (10–11) of the Chelex 100 resin solution markedly improved the detection sensitivity compared to a lower pH value (9–10). In conclusion, the comparison of the Chelex 100 Resin and commercial viral DNA extraction kits revealed the good performance of the Chelex 100 resin solution at pH 10–11 in DNA extraction for PCR amplification from aquatic animal viral samples of tissues and cells in molecular diagnostic testing. It is both rapid and cost-effective.
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Affiliation(s)
- Xi Hu
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
| | - Nan Jiang
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
| | - Yiqun Li
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
| | - Yong Zhou
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
| | - Yuding Fan
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
| | - Mingyang Xue
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
| | - Lingbing Zeng
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
| | - Wenzhi Liu
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
| | - Yan Meng
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
- Correspondence:
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Jarwar P, Waryah YM, Rafiq M, Waryah AM. Association of single nucleotide polymorphism variations in CRYAA and CRYAB genes with congenital cataract in Pakistani population. Saudi J Biol Sci 2022; 29:2727-2732. [PMID: 35531184 PMCID: PMC9073017 DOI: 10.1016/j.sjbs.2021.12.063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 12/19/2021] [Accepted: 12/28/2021] [Indexed: 12/02/2022] Open
Abstract
Background The purpose of present study was to analyze the association of single nucleotide polymorphism (SNPs) variant in CRYAA and CRYAB genes with Congenital Cataract. Method Total 196 blood samples of children were collected, out of which 102 samples were congenital cataract (case group) and 94 samples were normal individuals (control group). Genomic DNA was extracted by using optimized inorganic method. Tetra primers for SNPs were designed and TETRA-ARMs assay was performed on both groups. Genotypic, allelic frequency and haplotype analyses were obtained by using SNPstats software. Results The coordination of genotypic and allelic frequencies of CRYAA and CRYAB genes variants and the association between case and control groups showed increased risk of congenital cataract in children who contained rs13053109 G > C variant of CRYAA in all models (all P > 0.05). This depicts the evident difference between the frequencies of case and control groups. The haplotype analysis of SNPs rs3761382, rs7278468 and rs13051039 of CRYAA gene showed weak linkage disequilibrium between the 3 SNPs (r2 < 0.8). The haplotype CTC indicated the high risk of congenital cataract in infants based of its p value (OR = 1.60 95% CI = 0.11-22.64, P > 0.05). Conclusion The variation in CRYAA gene can be the risk factor for congenital cataract in infants.
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Affiliation(s)
- Priya Jarwar
- Institute of Biotechnology and Genetic Engineering, University of Sindh, Jamshoro, Pakistan
| | - Yar Muhammad Waryah
- Scientific Ophthalmic and Research Laboratory, Sindh Institute of Ophthalmology and Visual Sciences, Hyderabad 71500, Pakistan
| | - Muhammad Rafiq
- Institute of Biotechnology and Genetic Engineering, University of Sindh, Jamshoro, Pakistan
| | - Ali Muhammad Waryah
- Department of Pathology, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan
- Department Molecular Biology and Genetics, Medical Research Center, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan
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Ullah I, Murtaza K, Ammara H, Misbah, Bhinder MA, Riaz A, Shehzad W, Zahoor MY. Association study of CLDN14 variations in patients with kidney stones. Open Life Sci 2022; 17:81-92. [PMID: 35291565 PMCID: PMC8886595 DOI: 10.1515/biol-2021-0134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 10/08/2021] [Accepted: 10/10/2021] [Indexed: 11/28/2022] Open
Abstract
Claudin-14 protein plays an essential role in regulating calcium ions in the kidney and ear. Two phenotypes, hearing loss and kidney stones, were reportedly associated with variations in the CLDN14 gene. This study aimed to understand CLDN14 mutations’ contribution to hearing loss and renal stone formation in a Pakistani cohort. We analyzed CLDN14 sequence variations in 100 patients, along with healthy individuals, to assess whether specific polymorphisms were associated with the disease. Also, we performed an in silico analysis using a mutation database and protein annotation. The rs219779’s genotype CT (p = 0.0020) and rs219780’s genotype AG (p = 0.0012) were significantly associated with kidney stones. We also found that a novel haplotype, “TA” associated with kidney stone formation, has moderate linkage disequilibrium. The TA haplotype was significantly correlated with a kidney stone risk formation of 3.76-fold (OR (CI 95%) = 3.76 (1.83–7.72)) and p = 0.0016 compared to other haplotypes. In silico analysis revealed that mutations associated with hearing loss were not correlated with renal stone formation but affected claudin-14 protein stability. We structurally mapped a novel TA haplotype of CLDN14 that, based on our analysis, likely contributes to the pathogenesis of renal stones.
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Affiliation(s)
- Ihsan Ullah
- Molecular Biology and Biotechnology Section, Institute of Biochemistry & Biotechnology, University of Veterinary & Animal Sciences , Syed Abdul Qadir Jillani (Out Fall) Road , Lahore 54000 , Pakistan
| | - Khadijah Murtaza
- Molecular Biology and Biotechnology Section, Institute of Biochemistry & Biotechnology, University of Veterinary & Animal Sciences , Syed Abdul Qadir Jillani (Out Fall) Road , Lahore 54000 , Pakistan
| | - Hafiza Ammara
- Molecular Biology and Biotechnology Section, Institute of Biochemistry & Biotechnology, University of Veterinary & Animal Sciences , Syed Abdul Qadir Jillani (Out Fall) Road , Lahore 54000 , Pakistan
| | - Misbah
- Department of Medicine, Services Hospital , Lahore 54000 , Pakistan
| | - Munir Ahmad Bhinder
- Department of Human Genetics and Molecular Biology, University of Health Sciences , Lahore 54000 , Pakistan
| | - Amjad Riaz
- Department of Theriogenology, University of Veterinary & Animal Sciences , Lahore 54000 , Pakistan
| | - Wasim Shehzad
- Molecular Biology and Biotechnology Section, Institute of Biochemistry & Biotechnology, University of Veterinary & Animal Sciences , Syed Abdul Qadir Jillani (Out Fall) Road , Lahore 54000 , Pakistan
| | - Muhammad Yasir Zahoor
- Molecular Biology and Biotechnology Section, Institute of Biochemistry & Biotechnology, University of Veterinary & Animal Sciences , Syed Abdul Qadir Jillani (Out Fall) Road , Lahore 54000 , Pakistan
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18
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Bennett MF, Hildebrand MS, Kayumi S, Corbett MA, Gupta S, Ye Z, Krivanek M, Burgess R, Henry OJ, Damiano JA, Boys A, Gécz J, Bahlo M, Scheffer IE, Berkovic SF. Evidence for a Dual-Pathway, 2-Hit Genetic Model for Focal Cortical Dysplasia and Epilepsy. NEUROLOGY GENETICS 2022; 8:e652. [PMID: 35097204 PMCID: PMC8789218 DOI: 10.1212/nxg.0000000000000652] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 12/03/2021] [Indexed: 12/31/2022]
Abstract
Background and Objectives The 2-hit model of genetic disease is well established in cancer, yet has
only recently been reported to cause brain malformations associated with
epilepsy. Pathogenic germline and somatic variants in genes in the
mechanistic target of rapamycin (mTOR) pathway have been implicated in
several malformations of cortical development. We investigated the 2-hit
model by performing genetic analysis and searching for germline and somatic
variants in genes in the mTOR and related pathways. Methods We searched for germline and somatic pathogenic variants in 2 brothers with
drug-resistant focal epilepsy and surgically resected focal cortical
dysplasia (FCD) type IIA. Exome sequencing was performed on blood- and
brain-derived DNA to identify pathogenic variants, which were validated by
droplet digital PCR. In vitro functional assays of a somatic variant were
performed. Results Exome analysis revealed a novel, maternally inherited, germline pathogenic
truncation variant (c.48delG; p.Ser17Alafs*70) in
NPRL3 in both brothers. NPRL3 is a
known FCD gene that encodes a negative regulator of the mTOR pathway.
Somatic variant calling in brain-derived DNA from both brothers revealed a
low allele fraction somatic variant (c.338C>T; p.Ala113Val) in the
WNT2 gene in 1 brother, confirmed by droplet digital
PCR. In vitro functional studies suggested a loss of WNT2 function as a
consequence of this variant. A second somatic variant has not yet been found
in the other brother. Discussion We identify a pathogenic germline mTOR pathway variant
(NPRL3) and a somatic variant (WNT2)
in the intersecting WNT signaling pathway, potentially implicating the
WNT2 gene in FCD and supporting a dual-pathway 2-hit
model. If confirmed in other cases, this would extend the 2-hit model to
pathogenic variants in different genes in critical, intersecting pathways in
a malformation of cortical development. Detection of low allele fraction
somatic second hits is challenging but promises to unravel the molecular
architecture of FCDs.
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Mohan V, Ashwani K. Pro-apoptotic, anti-metastatic, and anti-telomerase activity of Tinospora cordifolia and its active polysaccharide arabinogalactan during Benzo(a)pyrene-induced lung carcinogenesis. Indian J Pharmacol 2022; 54:198-207. [PMID: 35848691 PMCID: PMC9396687 DOI: 10.4103/ijp.ijp_962_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
BACKGROUND The present study aims to unravel the pro-apoptotic, anti-metastatic, and anti-telomerase activity of aqueous extract of Tinospora cordifolia stem (Aq.Tc) and its active component arabinogalactan (AG) during Benzo(a)pyrene [B(a)P]-induced lung tumorigenesis in mice. MATERIALS AND METHODS Lung tumors were induced in male BALB/c mice using B(a)P as a carcinogen. Animals were administered twice with 50 mg/kg b.wt (i.p.) dosage of B(a)P at the 2nd and 4th week of the study. Mice were orally treated with Aq.Tc and AG on alternate days at a dose of 200 mg/kg b.wt and 7.5 mg/kg b.wt, respectively, for continuous 22 weeks. RESULTS Oral administration of animals with Aq.Tc and AG suppressed the development of lung carcinogenesis by modulating the mRNA and protein expressions of different apoptotic genes; bcl-2, bax, caspase 3, and caspase 9. The pro-apoptotic proficiency of Aq.Tc and AG was further confirmed by DNA agarose gel electrophoresis showing fragmentation in B(a)P + Aq.Tc group and smear formation in B(a)P + AG group. In contrast to the control group, an increase in tumor invasion factors such as matrix metalloproteinases-2 (MMP-2) and MMP-9 was also observed in B(a)P treated animals. Nevertheless, Aq.Tc and AG treatment effectively mitigated the B(a)P-induced upregulation of MMP-2 and MMP-9. The activity of the telomerase enzyme was also observed to be upregulated in B(a)P treated animals which consecutively found to get normalized with the parallel administration of Aq.Tc and AG. CONCLUSION Aq.Tc and AG successfully mitigated the altered expression of apoptosis, metastasis, and telomerase activity-associated genes during pulmonary carcinogenesis.
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Affiliation(s)
- Vandana Mohan
- Department of Biophysics, Basic Medical Sciences Block, Panjab University South Campus, Chandigarh, India
| | - Koul Ashwani
- Department of Biophysics, Basic Medical Sciences Block, Panjab University South Campus, Chandigarh, India,Address for correspondence: Prof. Koul Ashwani, Department of Biophysics, Basic Medical Sciences Block, Panjab University, South Campus, Sector 25, Chandigarh - 160 014, India. E-mail:
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Narsani AK, Waryah AM, Rafiq M, Shaikh H, Naqvi SHA, Kumar R, Kumar P. Mutational analysis of CYP1B1 (rs56010818) variant in primary open angle glaucoma (POAG) affected patients of Pakistan. Saudi J Biol Sci 2022; 29:96-101. [PMID: 35002398 PMCID: PMC8716894 DOI: 10.1016/j.sjbs.2021.08.066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/02/2021] [Accepted: 08/19/2021] [Indexed: 11/24/2022] Open
Abstract
Background Primary open angle glaucoma (POAG) occurs due to the discrepancies in the angle of anterior chamber characterized by the alterations in intraocular pressure, optic nerves head changes and central loss of visual field. In molecular research, CYP1B1 mutations modulates an integral role in association with glaucoma. Current study was undertaken to reveal the homozygous and heterozygous patterns of CYP1B1 c.1169 G > A variant (rs56010818) in POAG patients of Pakistan. Methods After consent, total n = 88 POAG patients undergone through standard ophthalmological investigations before their recruitment in this study. The blood samples were utilized for DNA isolation. The genotyping of CYP1B1 c.1169 G > A variant was carried out by Sanger sequencing. The mutational patterns and its association with clinical variables were demonstrated by statistical and bioinformatic tools. Results It was evident that the frequencies of heterozygous G/A and homozygous mutants A/A genotypes were higher in males (36.5%, 7.7%) than females (30.6%, 2.8%) of POAG population. Furthermore, the juvenile patients exhibit high manifestation of carrier genotype (66.6%) in comparison to adult patients (31.7%). The results also indicated the significant relationship of intraocular pressure with homozygous mutant A/A genotype of CYP1B1 variant in POAG patients (p < 0.05). Conclusions Our study provided the mutational data of CYP1B1 R390H variant and the patterns of homozygosity and heterozygosity along with clinical associations. Overall, this study revealed the genetic predisposition of CYP1B1 c.1169 G > A variant in the patients of POAG in Pakistan. The findings could be helpful for genetic screening and in-depth understanding of underlying causes in the pathogenesis of POAG.
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Affiliation(s)
- Ashok Kumar Narsani
- Institute of Biotechnology & Genetic Engineering, University of Sindh, Jamshoro, Pakistan.,Department of Ophthalmology, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan
| | - Ali Muhammad Waryah
- Department Molecular Biology and Genetics, Medical Research Center, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan
| | - Muhammad Rafiq
- Institute of Biotechnology & Genetic Engineering, University of Sindh, Jamshoro, Pakistan
| | - Hina Shaikh
- Department Molecular Biology and Genetics, Medical Research Center, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan
| | - Syed Habib Ahmed Naqvi
- Institute of Biotechnology & Genetic Engineering, University of Sindh, Jamshoro, Pakistan
| | - Raveet Kumar
- Department of Ophthalmology, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan
| | - Pawan Kumar
- Department of Ophthalmology, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan
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Iqbal F, Shabbir MI. Genetic analysis with pyrosequencing using loop pipetting and a light dependent resistor. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:5035-5047. [PMID: 34647115 DOI: 10.1039/d1ay01123e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
DNA sequencing is among the most important techniques in biology to decipher the key genetic players of health and disease. The existing laboratory instruments for DNA sequencing are well established and reliable. However, these instruments are still out of reach of most laboratories in the world due to very high equipment and running costs and require trained personnel to keep them running. These instruments are also large and bulky making them unsuitable for analysis in remote settings away from laboratories. Here we describe a proof-of-concept of a DNA sequencing device LoopSeeq using a simple approach to address the said problems without minimizing the quality of results. The device was designed to perform pyrosequencing by iterative addition of dNTPs by contact dispensing through a loop pipette (loopette) and detection of chemiluminiscence with the cheapest sensor in the market, a light dependent resistor (LDR). Two small geared motors drive the moving parts in a controlled and coordinated manner with the help of a motor driver circuit, an Arduino Nano microcontroller and two small neodymium magnets. The real-time light intensity data from the LDR were transferred to a laptop computer for further analysis. Pyrosequencing was optimized using 55 nt self-primed oligo. In order to demonstrate the DNA sequencing ability with real samples, molecular genetic analysis was performed for a previously identified novel mutation from our lab in exon4 of the OCA2 gene. LoopSeeq successfully identified the homozygous normal (c.408-409_AA), homozygous mutant (c.408-409_delAA) and heterozygous carrier (c.408-409_AA/delAA) alleles in three individuals of a family affected with oculocutaneous albinism (OCA). Further, this can be implemented for molecular diagnostic applications for bacterial, viral or other pathogen detection and genotyping among different subtypes following some reports described earlier. A few drawbacks in the current implementation including the evaporation of liquid reagents, possible loopette contamination, etc. associated with use for longer times are also described along with suggestions to rectify these problems in future designs. With the described capabilities, the LoopSeeq device can be implemented in routine labs as well as in several real-world situations where conventional DNA sequencing instruments are unfeasible, for example, diagnostic testing at remote settings or at the point-of-care.
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Affiliation(s)
- Faisal Iqbal
- Department of Biological Sciences, Faculty of Basic & Applied Sciences, International Islamic University, Sector H-10, Islamabad, Pakistan.
| | - Muhammad Imran Shabbir
- Department of Biological Sciences, Faculty of Basic & Applied Sciences, International Islamic University, Sector H-10, Islamabad, Pakistan.
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Kausar N, Haque A, Masoud MS, Nahid N, Ashfaq UA, Waryah AM, Bhatti R, Qasim M. Disease-associated variants of Gap Junction Beta 2 protein (GJB2) in the deaf population of Southern Punjab of Pakistan. PLoS One 2021; 16:e0259083. [PMID: 34695157 PMCID: PMC8544867 DOI: 10.1371/journal.pone.0259083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 10/12/2021] [Indexed: 02/03/2023] Open
Abstract
Hearing impairment (HI) is a highly heterogeneous genetic disorder and is classified into nonsyndromic (without any other clinical manifestations) and syndromic (if combined with other clinical presentations) forms. Variations in GJB2 gene are the leading cause of autosomal recessive nonsyndromic hearing loss (ARNSHL) in several populations worldwide. This study was carried out to investigate the prevalence of GJB2 variations in severe-to-profound hearing impaired families of Southern Punjab of Pakistan. Ten families segregating ARNSHL were recruited from different areas of the region. Sanger sequencing of GJB2 coding region was carried out. In two out of ten families, NM_004004:c.*71G>A (p.(Trp24*)) and NM_004004:c.358_360del (p.(Glu120del)) homozygous variants were identified as the cause of hearing loss. Our study showed that GJB2-related hearing loss accounts for at least 20% of all cases with severe-to-profound hearing loss in the Southern Punjab population of Pakistan.
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Affiliation(s)
- Nabila Kausar
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
- Department of Molecular Biology and Biochemistry, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad, Pakistan
| | - Asma Haque
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Muhammad Shareef Masoud
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Nazia Nahid
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
- * E-mail: (NN); (MQ)
| | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Ali Muhammad Waryah
- Molecular Biology and Genetics Department, Medical Research Center, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan
| | - Rashid Bhatti
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Muhammad Qasim
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
- * E-mail: (NN); (MQ)
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Ain NU, Fatima Z, Naz S, Makitie O. RAB33B and PCNT variants in two Pakistani families with skeletal dysplasia and short stature. BMC Musculoskelet Disord 2021; 22:630. [PMID: 34284742 PMCID: PMC8293541 DOI: 10.1186/s12891-021-04503-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 07/01/2021] [Indexed: 11/12/2022] Open
Abstract
Background Skeletal dysplasia is a heterogeneous group of disorders resulting from different genetic variants in humans. The current study was designed to identify the genetic causes of skeletal dysplasia and short stature in two consanguineous families from Pakistan, both comprised of multiple affected individuals. Patients in one family had proportionate short stature with reduced head circumference while affected individuals in the other family had disproportionate short stature. Methods Clinical data were obtained and radiological examinations of the index patients were completed. Whole genome sequencing for probands from both families were performed followed by Sanger sequencing to confirm segregation of identified variants in the respective families. In-silico pathogenicity score prediction for identified variant and amino acid conservation analysis was completed. Results Whole Genome Sequencing identified a known biallelic variant c.6176_6189delGTCAGCTGCCGAAG; p.(Gln2060ArgfsTer48) in PCNT gene and a novel biallelic variant c.174delC; p.(Asp60ThrfsTer7) in RAB33B gene respectively in affected members of the two families. Clinical imaging revealed platyspondyly and varus deformity in the legs of the affected members in the first family. Radiographs indicated severe platyspondyly, genu valgus deformity of legs and pectus carinatum for the patients in the second family. Conclusion In this study we report the phenotypes and genetic variants in two unrelated families with two distinct forms of skeletal dysplasia. This study strengthens the previous findings that patients harboring PCNT variants are phenotypically homogeneous and also extends the genotypic spectrum of RAB33B variants. Supplementary Information The online version contains supplementary material available at 10.1186/s12891-021-04503-2.
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Affiliation(s)
- Noor Ul Ain
- School of Biological Sciences, University of the Punjab, Quaid-i-Azam Campus, Lahore, 54590, Pakistan.,Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Present address: Institute of Biomedical and Genetic Engineering, Islamabad, Pakistan
| | - Zunaira Fatima
- School of Biological Sciences, University of the Punjab, Quaid-i-Azam Campus, Lahore, 54590, Pakistan
| | - Sadaf Naz
- School of Biological Sciences, University of the Punjab, Quaid-i-Azam Campus, Lahore, 54590, Pakistan.
| | - Outi Makitie
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden. .,Folkhälsan Institute of Genetics, Helsinki, Finland. .,Children's Hospital, University of Helsinki and Helsinki University Hospital, P.O. Box 63, 00014, Helsinki, Finland.
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Benhsaien I, Essadssi S, Elkhattabi L, Bakhchane A, Abdelghaffar H, Bousfiha AA, Badou A, Barakat A. Omenn syndrome caused by a novel homozygous mutation in recombination activating gene 1. Immunobiology 2021; 226:152090. [PMID: 33964732 DOI: 10.1016/j.imbio.2021.152090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 02/12/2021] [Accepted: 03/29/2021] [Indexed: 11/20/2022]
Abstract
Omenn syndrome (OS) is a type of severe combined immunodeficiency (SCID) that is distinguished by, lymphadenopathy, hepatosplenomegaly, erythroderma, alopecia with normal to elevated T-cell counts, eosinophilia, and elevated serum IgE levels. Recombination activation gene (RAG) 1 or RAG2 mutations that result in partial V(D)J recombination activity are known to be the main cause of OS. Other genes (DCLRE1C, LIG4, IL7RA, common gamma chain, ADA, RMRP, and CHD7) have also been linked to OS, although with low frequency. Here, we report a two-month-old Moroccan girl from consanguineous marriage with chronic diarrhea, recurrent and opportunistic infections, failure to thrive, desquamative erythroderma, hepatosplenomegaly, and axillary lymphadenitis. The immunological assessment showed normal lymphocyte and NK cell counts but an absence of B cells, agammaglobulinemia contrasting with a high level of IgE. On the other hand, Sanger sequencing of RAG1 and RAG2 exon 2 regions revealed a new homozygous deleterious mutation in the RAG1 gene. This c.1184C > T mutation caused a change from Proline to Leucine at position 395 of the protein, leading to a partial loss of function. Early and rapid diagnosis of the disease may facilitate urgent life-saving treatment.
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Affiliation(s)
- Ibtihal Benhsaien
- Clinical Immunology Unit, Infectious Disease Department, Children Hospital, Ibn Rochd University Hospital, Casablanca, Morocco; Cellular and Molecular Pathology Laboratory, Faculty of Medicine and Pharmacy, Hassan II University, Casablanca, Morocco; Clinical Immunology, Autoimmunity and Inflammation Laboratory (LICIA), Faculty of Medicine and Pharmacy, Hassan II University, Casablanca, Morocco
| | - Soukaina Essadssi
- Laboratory of Genomics and Human Genetics,Institut Pasteur du Maroc, 1 Place Louis Pasteur, 20360 Casablanca, Morocco; Laboratory of Biosciences, Integrated and Molecular Functional Exploration (LBEFIM), Faculty of Science and Technology of Mohammedia, Hassan II University of Casablanca, Casablanca, Morocco
| | - Lamiae Elkhattabi
- Laboratory of Genomics and Human Genetics,Institut Pasteur du Maroc, 1 Place Louis Pasteur, 20360 Casablanca, Morocco
| | - Amina Bakhchane
- Laboratory of Genomics and Human Genetics,Institut Pasteur du Maroc, 1 Place Louis Pasteur, 20360 Casablanca, Morocco
| | - Houria Abdelghaffar
- Laboratory of Biosciences, Integrated and Molecular Functional Exploration (LBEFIM), Faculty of Science and Technology of Mohammedia, Hassan II University of Casablanca, Casablanca, Morocco
| | - Ahmed Aziz Bousfiha
- Clinical Immunology Unit, Infectious Disease Department, Children Hospital, Ibn Rochd University Hospital, Casablanca, Morocco; Clinical Immunology, Autoimmunity and Inflammation Laboratory (LICIA), Faculty of Medicine and Pharmacy, Hassan II University, Casablanca, Morocco
| | - Abdallah Badou
- Cellular and Molecular Pathology Laboratory, Faculty of Medicine and Pharmacy, Hassan II University, Casablanca, Morocco
| | - Abdelhamid Barakat
- Laboratory of Genomics and Human Genetics,Institut Pasteur du Maroc, 1 Place Louis Pasteur, 20360 Casablanca, Morocco.
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Genetic association of ERAP1 and ERAP2 with eclampsia and preeclampsia in northeastern Brazilian women. Sci Rep 2021; 11:6764. [PMID: 33762660 PMCID: PMC7990956 DOI: 10.1038/s41598-021-86240-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 03/09/2021] [Indexed: 01/28/2023] Open
Abstract
The clinical spectrum of hypertensive disorders of pregnancy (HDP) is determined by the interplay between environmental and genetic factors, most of which remains unknown. ERAP1, ERAP2 and LNPEP genes code for multifunctional aminopeptidases involved with antigen processing and degradation of small peptides such as angiotensin II (Ang II), vasopressin and oxytocin. We aimed to test for associations between genetic variants in aminopeptidases and HDP. A total of 1282 pregnant women (normotensive controls, n = 693; preeclampsia, n = 342; chronic hypertension with superimposed preeclampsia, n = 61; eclampsia, n = 74; and HELLP syndrome, n = 112) were genotyped for variants in LNPEP (rs27300, rs38034, rs2303138), ERAP1 (rs27044, rs30187) and ERAP2 (rs2549796 rs2927609 rs11135484). We also evaluated the effect of ERAP1 rs30187 on plasma Ang II levels in an additional cohort of 65 pregnant women. The genotype C/C, in ERAP1 rs30187 variant (c.1583 T > C, p.Lys528Arg), was associated with increased risk of eclampsia (OR = 1.85, p = 0.019) whereas ERAP2 haplotype rs2549796(C)–rs2927609(C)–rs11135484(G) was associated with preeclampsia (OR = 1.96, corrected p-value = 0.01). Ang II plasma levels did not differ across rs30187 genotypic groups (p = 0.895). In conclusion, ERAP1 gene is associated with eclampsia whereas ERAP2 is associated with preeclampsia, although the mechanism by which genetic variants in ERAPs influence the risk of preeclampsia and eclampsia remain to be elucidated.
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Halder T, Verma SP, Raj J, Pandey S, Singh RK, Sharma V, Joshi D, Das P. Identification & characterization of leucine-rich repeat kinase 2 & parkin RBR E3 ubiquitin protein ligase variants in patients with Parkinson's disease. Indian J Med Res 2021; 152:498-507. [PMID: 33707392 PMCID: PMC8157902 DOI: 10.4103/ijmr.ijmr_730_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Background & objectives: Parkinson's disease (PD) is a motor disorder that affects movement. More than 24 loci and 28 associated genes have been identified to be associated with this disease. The present study accounts for the contribution of two candidates, leucine-rich repeat kinase 2 (LRRK2) and parkin RBR E3 ubiquitin protein ligase (PRKN) in the PD patients, and their characterization in silico and in vitro. Methods: A total of 145 sporadic PD cases and 120 ethnically matched healthy controls were enrolled with their informed consent. Mutation screening was performed by direct DNA sequencing of the targeted exons of LRRK2 and all exons flanking introns of PRKN. The effect of the pathogenic PRKN variants on a drug (MG-132) induced loss of mitochondrial membrane potential (△ΨM) was measured by a fluorescent dye tetramethylrhodamine methyl ester (TMRM). Results: Twelve and 20 genetic variants were identified in LRRK2 and PRKN, respectively. Interestingly, five out of seven exonic LRRK2 variants were synonymous. Further assessment in controls confirmed the rarity of two such p.Y1527 and p.V1615. Among the pathogenic missense variations (as predicted in silico) in PRKN, two were selected (p.R42H and p.A82E) for their functional study in vitro, which revealed the reduced fluorescence intensity of TMRM as compared to wild type, in case of p.R42H but not the other. Interpretation & conclusions: About 6.2 per cent of the cases (9/145) in the studied patient cohort were found to carry pathogenic (as predicted in silico) missense variations in PRKN in heterozygous condition but not in case of LRRK2 which was rare. The presence of two rare synonymous variants of LRRK2 (p.Y1527 and p.V1615) may support the phenomenon of codon bias. Functional characterization of selected PRKN variations revealed p.R42H to cause disruption of mitochondrial membrane potential (△ΨM) rendering cells more susceptible to cellular stress.
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Affiliation(s)
- Tamali Halder
- Centre for Genetic Disorders, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Shiv Prakash Verma
- Centre for Genetic Disorders, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Janak Raj
- Department of Neurosurgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Sharad Pandey
- Department of Neurosurgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Ranjeet Kumar Singh
- Department of Neurology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Vivek Sharma
- Department of Neurosurgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Deepika Joshi
- Department of Neurology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Parimal Das
- Centre for Genetic Disorders, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, India
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Kar B, Sharma M, Peter A, Chetia P, Neog B, Borah A, Pati S, Bhattacharya D. Prevalence and molecular characterization of β-lactamase producers and fluoroquinolone resistant clinical isolates from North East India. J Infect Public Health 2021; 14:628-637. [PMID: 33848892 DOI: 10.1016/j.jiph.2021.02.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 01/26/2021] [Accepted: 02/14/2021] [Indexed: 11/29/2022] Open
Abstract
INTRODUCTION The rapid emergence and variations of antibiotic resistance among common gram negative bacteria cause a significant concern specially in India and all over the world because of high mortality and morbidity rates. METHODS In our study, we screened 189 bacterial isolates from Assam Medical College & Hospital, Dibrugarh for antibiotic resistance pattern and tried to identify the resistant genes causing responsible for β-lactam and fluoroquinolones resistance. RESULTS More than 80% and 45% strains were resistant to all the 3rd generation cephalosporins, fluoroquinolones respectively. Among the 3rd generation cephalosporin resistant strains, 38% and 24% isolates were only ESBL and MBL producers respectively and 11% were reported to have both ESBL and MBL genes. The ESBL positive isolates have shown the dominance of CTX-M3 gene. VIM-1 gene was mostly reported in MBL producers. Our study probably for the first time reporting SIM-1 and SPM-1 MBL gene from India. Mutations in QRDR is found to be the primary cause of fluoroquinolone resistance along with efflux pump and PMQR presence. CONCLUSION The study represents the first detailed study on antibiotic resistance from NE India this could help to take control measures for the emerging antibiotic resistance in hospital and community based infections in North East India.
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Affiliation(s)
- Bipasa Kar
- Department of Bacteriology, ICMR-Regional Medical Research Centre (Dept. of Health Research, Ministry of Health & Family Welfare, Govt. of India), Chandrasekharpur, Bhubaneswar 751023, India.
| | - Mohan Sharma
- Department of Life Sciences, Dibrugarh University, Dibrugarh 786004, Assam, India.
| | - Annalisha Peter
- Department of Bacteriology, ICMR-Regional Medical Research Centre (Dept. of Health Research, Ministry of Health & Family Welfare, Govt. of India), Chandrasekharpur, Bhubaneswar 751023, India.
| | - Pankaj Chetia
- Department of Life Sciences, Dibrugarh University, Dibrugarh 786004, Assam, India.
| | - Bijoy Neog
- Department of Life Sciences, Dibrugarh University, Dibrugarh 786004, Assam, India.
| | - Amrit Borah
- Department of Microbiology, Assam Medical College & Hospital, Dibrugarh 786002, Assam, India.
| | - Sanghamitra Pati
- Department of Bacteriology, ICMR-Regional Medical Research Centre (Dept. of Health Research, Ministry of Health & Family Welfare, Govt. of India), Chandrasekharpur, Bhubaneswar 751023, India.
| | - Debdutta Bhattacharya
- Department of Bacteriology, ICMR-Regional Medical Research Centre (Dept. of Health Research, Ministry of Health & Family Welfare, Govt. of India), Chandrasekharpur, Bhubaneswar 751023, India.
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Ben-Yosef T, Asia Batsir N, Ali Nasser T, Ehrenberg M. Retinal dystrophy as part of TTC21B-associated ciliopathy. Ophthalmic Genet 2021; 42:329-333. [PMID: 33599192 DOI: 10.1080/13816810.2021.1888131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Background: TCC21B is a ciliary protein. The most common phenotypic features associated with TCC21B biallelic mutations are nephronophthisis and skeletal abnormalities. To date, retinal dystrophy has been reported in only one patient.Materials and Methods: Clinical evaluation included best-corrected visual acuity, cycloplegic refraction, fundus examination, fundus photography, retinal imaging by optical coherence tomography, full-field electroretinography, multifocal electroretinography, and visual evoked potentials. Genetic analysis included Whole Exome Sequencing and confirmation of the identified mutations in the patient and his parents by PCR amplification and direct sequencing.Results: A ten-year-old Caucasian male presented with nephronophthisis, high myopia and nycatalopia. Best-corrected visual acuity was preserved to 20/20 in each eye with significant myopic correction. Visual fields were constricted. Optical coherence tomography confirmed the lack of outer retinal layers in the perifoveal area on both eyes. Electroretinography confirmed significant retinal dystrophy. Whole Exome Sequencing revealed compound heterozygous mutations in the TTC21B gene.Conclusions: TTC21B is associated with ciliopathy, but retinal dystrophy is a rare finding in these patients. We report retinal dystrophy secondary to TTC21B mutations, and provide for the first time detailed clinical information of the ophthalmic phenotype.
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Affiliation(s)
- Tamar Ben-Yosef
- The Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
| | - Nurit Asia Batsir
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.,Pediatric Genetics Clinic, Schneider Children's Medical Center of Israel, Petach Tikva, Israel
| | - Tahleel Ali Nasser
- The Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
| | - Miriam Ehrenberg
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.,Department of Ophthalmology, Schneider Children's Medical Center of Israel, Petach Tikva, Israel
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Khan NM, Hussain B, Zheng C, Khan A, Masoud MS, Gu Q, Qiu L, Malik NA, Qasim M, Tariq M, Chang J. Updates on Clinical and Genetic Heterogeneity of ASPM in 12 Autosomal Recessive Primary Microcephaly Families in Pakistani Population. Front Pediatr 2021; 9:695133. [PMID: 34295862 PMCID: PMC8290066 DOI: 10.3389/fped.2021.695133] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 05/27/2021] [Indexed: 12/24/2022] Open
Abstract
Microcephaly (MCPH) is a genetically heterogeneous disorder characterized by non-progressive intellectual disability, small head circumference, and small brain size compared with the age- and sex-matched population. MCPH manifests as an isolated condition or part of another clinical syndrome; so far, 25 genes have been linked with MCPH. Many of these genes are reported in Pakistani population, but due to a high rate of consanguinity, a significant proportion of MCPH cohort is yet to be explored. MCPH5 is the most frequently reported type, accounting for up to 68.75% alone in a genetically constrained population like Pakistan. In the current study, whole exome sequencing (WES) was performed on probands from 10 families sampled from South Waziristan and two families from rural areas of the Pakistani Punjab. Candidate variants were validated through Sanger sequencing in all available family members. Variant filtering and in silico analysis identified three known mutations in ASPM, a MCPH5-associated gene. The founder mutation p.Trp1326* was segregating in 10 families, which further confirmed the evidence that it is the most prominent mutation in Pashtun ethnicity living in Pakistan and Afghanistan. Furthermore, the previously known mutations p.Arg3244* and p.Arg1019* were inherited in two families with Punjab ethnic profile. Collectively, this study added 12 more families to the mutational paradigm of ASPM and expanded the Pakistani MCPH cohort.
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Affiliation(s)
- Niaz Muhammad Khan
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Basharat Hussain
- Shenzhen Key Laboratory of Biomimetic Materials and Cellular Immunomodulation, Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.,University of Chinese Academy of Sciences, Beijing, China
| | | | - Ayaz Khan
- National Institute for Biotechnology and Genetic Engineering (NIBGE-C), Faisalabad, Pakistan; Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
| | - Muhammad Shareef Masoud
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Qingquan Gu
- Shenzhen Real Omics Biotech Co., Ltd., Shenzhen, China
| | - Linhui Qiu
- Shenzhen Key Laboratory of Biomimetic Materials and Cellular Immunomodulation, Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Naveed Altaf Malik
- National Institute for Biotechnology and Genetic Engineering (NIBGE-C), Faisalabad, Pakistan; Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
| | - Muhammad Qasim
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Muhammad Tariq
- National Institute for Biotechnology and Genetic Engineering (NIBGE-C), Faisalabad, Pakistan; Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
| | - Junlei Chang
- Shenzhen Key Laboratory of Biomimetic Materials and Cellular Immunomodulation, Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
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Khan MA, Afshan K, Nazar M, Firasat S, Chaudhry U, Sargison ND. Molecular confirmation of Dicrocoelium dendriticum in the Himalayan ranges of Pakistan. Parasitol Int 2020; 81:102276. [PMID: 33370606 DOI: 10.1016/j.parint.2020.102276] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/13/2020] [Accepted: 12/16/2020] [Indexed: 11/29/2022]
Abstract
Lancet liver flukes of the genus Dicrocoelium (Trematoda: Digenea) are recognised parasites of domestic and wild herbivores. The aim of the present study was to confirm the species identity of Dicrocoeliid flukes collected from the Chitral valley in the Himalayan ranges of Pakistan. The morphology of 48 flukes belonging to eight host populations was examined; but overlapping traits prevented accurate species designation. Phylogenetic comparison of published D. dendriticum ribosomal cistron DNA, and cytochrome oxidase-1 (COX-1) mitochondrial DNA sequences with those from D. chinensis was performed to assess within and between species variation and re-affirm the use of species-specific single nucleotide polymorphism markers. PCR and sequencing of 34 corresponding fragments of ribosomal DNA and 14 corresponding fragments of mitochondrial DNA from the Chitral valley flukes, revealed 10 and 4 unique haplotypes, respectively. These confirmed for the first time the molecular species identity of Pakistani lancet liver flukes as D. dendriticum. This work provides a preliminary illustration of a phylogenetic approach that could be developed to study the ecology, biological diversity, and epidemiology of Dicrocoeliid lancet flukes when they are identified in new settings.
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Affiliation(s)
- Muhammad Asim Khan
- Department of Zoology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Kiran Afshan
- Department of Zoology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan.
| | - Muddassar Nazar
- Department of Zoology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Sabika Firasat
- Department of Zoology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Umer Chaudhry
- University of Edinburgh, Royal (Dick) School of Veterinary Studies and Roslin Institute, Easter Bush Veterinary Centre, EH25 9RG, UK
| | - Neil D Sargison
- University of Edinburgh, Royal (Dick) School of Veterinary Studies and Roslin Institute, Easter Bush Veterinary Centre, EH25 9RG, UK.
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31
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Bouzid F, Sebbar MS, El Mousadik A, Alif N. IDUA gene polymorphisms among mucopolysaccharidosis and healthy Moroccan subjects. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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32
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Alves R, Rodrigues A, Santos V, Damasceno E, Prado G, Souza K, Nunes Neto T, Pinheiro A, Cruz M, Pinheiro R. Bases para um programa de controle da artrite encefalite caprina em rebanho leiteiro. ARQ BRAS MED VET ZOO 2020. [DOI: 10.1590/1678-4162-11695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
RESUMO Objetivou-se avaliar um programa de controle da artrite encefalite caprina (AEC), por meio de testes diagnósticos sensíveis, separação de mãe e cria após o parto e medidas de manejo, com o intuito de formar rebanho livre do vírus. Utilizou-se um total de 47 cabritos da raça Saanen, mantidos isoladamente até o resultado dos primeiros testes de reação em cadeia de polimerase nested (PCR nested) e Western Blotting (WB), com base na coleta de sangue no momento do nascimento (M0). No PCR nested, quatro animais foram positivos, no M0, e foram eutanasiados. Posteriormente, os demais 43 cabritos foram submetidos à coleta de sangue aos 60 (M60) e 270 (M270) dias de vida para realização de novos testes de WB e PCR nested, que não detectaram animais positivos. Pode-se afirmar que a metodologia adotada neste estudo foi efetiva no controle da doença, nas fases de aleitamento e pós-aleitamento, e que a combinação do sistema de manejo, a fim de propiciar diminuição de risco de transmissão horizontal, com técnicas de diagnóstico mais apuradas, como o WB e a PCR nested, é relevante para elaboração de plano estratégico de controle da enfermidade.
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Affiliation(s)
| | | | | | | | - G.M. Prado
- Instituto Superior de Teologia Aplicada, Brazil
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Novel association of genetic variants in non-coding regulatory regions with HIV-1 infection. INFECTION GENETICS AND EVOLUTION 2020; 85:104514. [PMID: 32861908 DOI: 10.1016/j.meegid.2020.104514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 07/23/2020] [Accepted: 08/22/2020] [Indexed: 11/22/2022]
Abstract
Host genetic variability interplays with the environment and variegating viral factors to determine the outcome in HIV-1/AIDS. Several GWAS studies have reported that genetic heterogeneity of individuals leads to differential HIV susceptibility. Proxy SNPs that are in Linkage Disequilibrium to the GWAS SNPs could be important targets in HIV pathogenesis and need to be analyzed further for their potential regulatory role. Current study thus aimed to identify novel proxy SNPs that may play a critical role in HIV susceptibility and disease progression. 372 SNPs, associated with HIV-1/AIDS pathogenesis, were retrieved via GWAS catalogue. 1854 proxy SNPs, in Linkage Disequilibrium (r2 = 0.8) to the GWAS reported SNPs, were identified using the SNAP web tool. Regulatory functions of aforementioned 1854 polymorphic sites (GWAS SNPs and their proxy SNPs) were acquired from RegulomeDB. 178 of the proxy SNPs showed evidence of strong regulatory potential returning a score of ≤3. Among these regulatory SNPs, 22 had already been reported for their association with HIV/AIDS while 156 SNPs showed novel association. Three of these novel SNPs (g.rs6457282T>C, g.rs17064977C>T and g.rs3130350G>T) were validated using sequence specific PCR (SSP-PCR) on HIV-infected patients. For g.rs6457282T>C and rs17064977C>T, CT genotype was determined to be significantly associated with increased risk of HIV-1 infection (rs6457282T>C: OR = 9.5, 95% CI = 3.0792-29.3099, p = 0.0001; rs17064977C>T: OR = 8.1077, 95% CI = 3.1125-21.119, p = 0.0001). Moreover, the association of interacting protein partners of affected genes with HIV-1 elucidates the significance of corresponding SNPs in HIV disease outcome that further needs to be functionally deciphered.
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Novel Mutations in CLPP, LARS2, CDH23, and COL4A5 Identified in Familial Cases of Prelingual Hearing Loss. Genes (Basel) 2020; 11:genes11090978. [PMID: 32842620 PMCID: PMC7564084 DOI: 10.3390/genes11090978] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 08/12/2020] [Accepted: 08/18/2020] [Indexed: 12/30/2022] Open
Abstract
We report the underlying genetic causes of prelingual hearing loss (HL) segregating in eight large consanguineous families, ascertained from the Punjab province of Pakistan. Exome sequencing followed by segregation analysis revealed seven potentially pathogenic variants, including four novel alleles c.257G>A, c.6083A>C, c.89A>G, and c.1249A>G of CLPP, CDH23, COL4A5, and LARS2, respectively. We also identified three previously reported HL-causing variants (c.4528C>T, c.35delG, and c.1219T>C) of MYO15A, GJB2, and TMPRSS3 segregating in four families. All identified variants were either absent or had very low frequencies in the control databases. Our in silico analyses and 3-dimensional (3D) molecular modeling support the deleterious impact of these variants on the encoded proteins. Variants identified in MYO15A, GJB2, TMPRSS3, and CDH23 were classified as “pathogenic” or “likely pathogenic”, while the variants in CLPP and LARS2 fall in the category of “uncertain significance” based on the American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) variant pathogenicity guidelines. This paper highlights the genetic diversity of hearing disorders in the Pakistani population and reports the identification of four novel mutations in four HL families.
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Gul R, Firasat S, Hussain M, Afshan K, Nawaz D. IDUA gene mutations in mucopolysaccharidosis type-1 patients from two Pakistani inbred families. Congenit Anom (Kyoto) 2020; 60:126-127. [PMID: 31400021 DOI: 10.1111/cga.12354] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 07/25/2019] [Accepted: 07/31/2019] [Indexed: 01/10/2023]
Affiliation(s)
- Rutaba Gul
- Department of Animal Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islambad, Pakistan
| | - Sabika Firasat
- Department of Animal Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islambad, Pakistan
| | - Mulazim Hussain
- The Children Hospital, Pakistan Institute of Medical Sciences, Islamabad, Pakistan
| | - Kiran Afshan
- Department of Animal Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islambad, Pakistan
| | - Dil Nawaz
- Department of Animal Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islambad, Pakistan
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Shahid M, Firasat S, Satti HS, Satti TM, Ghafoor T, Sharif I, Afshan K. Screening of the FANCA gene mutational hotspots in the Pakistani fanconi anemia patients revealed 19 sequence variations. Congenit Anom (Kyoto) 2020; 60:32-39. [PMID: 30809872 DOI: 10.1111/cga.12331] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 02/04/2019] [Accepted: 02/21/2019] [Indexed: 02/06/2023]
Abstract
Fanconi anemia (FA) is a recessive disorder that predispose to bone marrow failure and multiple congenital anomalies in affected individuals worldwide. To date, 22 FA genes are known to harbor sequence variations in disease phenotype. Among these, mutations in the FANCA gene are associated with 60% to 70% of FA cases. The aim of the present study was to screen FA cases belonging to consanguineous Pakistani families for selected exons of FANCA gene which are known mutational hotspots for Asian populations. Blood samples were collected from 20 FA cases and 20 controls. RNA was extracted and cDNA was synthesized from blood samples of cases. DNA was extracted from blood samples of cases and ethnically matched healthy controls. Sanger's sequencing of the nine selected exons of FANCA gene in FA cases revealed 19 genetic alterations of which 15 were single nucleotide variants, three were insertions and one was microdeletion. Of the total 19 sequence changes, 13 were novel and six were previously reported. All identified variants were evaluated by computational programs including SIFT, PolyPhen-2 and Mutation taster. Seven out of 20 analyzed patients were carrying homozygous novel sequence variations, predicted to be associated with FA. These disease associated novel variants were not detected in ethnically matched controls and depict genetic heterogeneity of disease.
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Affiliation(s)
- Muhammad Shahid
- Department of Animal Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Sabika Firasat
- Department of Animal Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Humayoon Shafique Satti
- Armed Forces Bone Marrow Transplant Centre (AFBMTC), CMH Medical Complex, Rawalpindi, Pakistan
| | - Tariq Mahmood Satti
- Armed Forces Bone Marrow Transplant Centre (AFBMTC), CMH Medical Complex, Rawalpindi, Pakistan
| | - Tariq Ghafoor
- Armed Forces Bone Marrow Transplant Centre (AFBMTC), CMH Medical Complex, Rawalpindi, Pakistan
| | - Imtenan Sharif
- Department of Community Medicine, Army Medical College (AMC), National University of Medical Sciences, Rawalpindi, Pakistan
| | - Kiran Afshan
- Department of Animal Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
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Ehrenberg M, Weiss S, Orenstein N, Goldenberg-Cohen N, Ben-Yosef T. The co-occurrence of rare non-ocular phenotypes in patients with inherited retinal degenerations. Mol Vis 2019; 25:691-702. [PMID: 31814694 PMCID: PMC6857777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 11/10/2019] [Indexed: 11/01/2022] Open
Abstract
Purpose To describe the coexistence of additional non-ocular genetic diseases in patients diagnosed with inherited retinal degenerations (IRDs). Methods The study was based on a retrospective chart review of patients diagnosed with IRD and additional rare systemic diseases. The chart review included the ophthalmic and genetic aspects of each patient. The ophthalmic examination included best-corrected visual acuity, biomicroscopic examination, cycloplegic refraction, retinal imaging (fundus photos, optical coherence tomography, and fundus autofluorescence), and electroretinography. Genetic testing included homozygosity mapping, whole exome sequencing, and Sanger sequencing. Results Fifteen index cases diagnosed with IRDs and one or more rare systemic diseases were identified. Six of the families were consanguineous. Of six patients with complete molecular diagnosis, four (66%) had pathogenic variants in two autosomal recessive (AR) disease genes, and of the total pathogenic variants identified, AR mutations were the most common (16/22, 72%). One patient was diagnosed with mutations in three different genes, underlying three distinct genetic conditions. Nine patients could have had an incorrect clinical diagnosis based on the clinical evaluation only (e.g., retinitis pigmentosa and hearing loss could have been diagnosed as Usher syndrome). Conclusions The common working paradigm for the ophthalmologist is combining the different symptoms observed in a patient into one unifying diagnosis. However, IRD is a strikingly heterogeneous condition, and may coincide with other genetic (and non-genetic) rare conditions. Establishing a correct diagnosis is important for the patients and their family members, as it enables prediction of disease prognosis, aids in tailoring the correct follow-up and treatment, and allows patients to pursue prenatal counseling and reproductive planning.
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Affiliation(s)
- Miriam Ehrenberg
- Department of Ophthalmology, Schneider Children’s Medical Center of Israel, Petach Tikva, Israel
| | - Shirel Weiss
- The Krieger Eye Laboratory, Felsenstein Medical Research Center, Petach Tikva, Israel
| | - Naama Orenstein
- Pediatric Genetics Clinic, Schneider Children’s Medical Center of Israel, Petach Tikva, Israel
| | - Nitza Goldenberg-Cohen
- The Krieger Eye Laboratory, Felsenstein Medical Research Center, Petach Tikva, Israel,Department of Ophthalmology, Bnai Zion Medical Center, Haifa, Israel,The Rappaport Faculty of Medicine, Technion – Israel Institute of Technology, Haifa, Israel
| | - Tamar Ben-Yosef
- The Rappaport Faculty of Medicine, Technion – Israel Institute of Technology, Haifa, Israel
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Akram N, Mustafa G, Hanif AA, Tawwab S, Hussain S, Kaul H, Mohsin S. Cytochrome 2C19 and paraoxonase-1 polymorphisms and clopidogrel resistance in ischemic heart disease patients. Per Med 2019; 16:379-386. [PMID: 31591927 DOI: 10.2217/pme-2018-0030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Aim: Polymorphisms in cytochrome P450 (CYP) 2C19 and paraoxonase-1 (PON-1) genes are thought to be involved in clopidogrel high on treatment reactivity in ischemic heart disease (IHD) patients. Methods: A total of 240 patients with IHD were screened for CYP2C19 loss-of-function alleles (LOF; *2, *3) and PON-1 Q192R. Patients were classified as responders and nonresponders to clopidogrel based upon platelet aggregation studies. Genotyping of the CYP2C19 and PON-1 allele was carried out by PCR-RFLP. Results: Results showed that 14.3% of the patients were nonresponders, whereas 85.7% were responders to the clopidogrel therapy. CYP2C19*3 allele showed significant association with clopidogrel high on treatment reactivity in IHD patients. Conclusion: Result of our study demonstrate that IHD patients with CYP2C19*3 allele can face the problem of clopidogrel high on treatment reactivity in Punjabi Pakistani population.
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Affiliation(s)
- Nabila Akram
- Department of Haematology, University of Health Sciences, Lahore, Pakistan
| | - Ghulam Mustafa
- Department of Haematology, University of Health Sciences, Lahore, Pakistan
| | - Anum A Hanif
- Department of Haematology, University of Health Sciences, Lahore, Pakistan
| | | | - Shabbir Hussain
- Department of Biochemistry, University of Health Sciences, Lahore, Pakistan
| | - Haiba Kaul
- Department of Biochemistry, University of Health Sciences, Lahore, Pakistan.,Genetics Division, Department of Livestock Production, University of Veterinary & Animal Sciences, Ravi Campus, Pattoki, Pakistan
| | - Shahida Mohsin
- Department of Haematology, University of Health Sciences, Lahore, Pakistan
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39
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Sharon D, Ben-Yosef T, Goldenberg-Cohen N, Pras E, Gradstein L, Soudry S, Mezer E, Zur D, Abbasi AH, Zeitz C, Cremers FPM, Khan MI, Levy J, Rotenstreich Y, Birk OS, Ehrenberg M, Leibu R, Newman H, Shomron N, Banin E, Perlman I. A nationwide genetic analysis of inherited retinal diseases in Israel as assessed by the Israeli inherited retinal disease consortium (IIRDC). Hum Mutat 2019; 41:140-149. [PMID: 31456290 DOI: 10.1002/humu.23903] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 08/21/2019] [Accepted: 08/22/2019] [Indexed: 01/13/2023]
Abstract
Inherited retinal diseases (IRDs) cause visual loss due to dysfunction or progressive degeneration of photoreceptors. These diseases show marked phenotypic and genetic heterogeneity. The Israeli IRD consortium (IIRDC) was established in 2013 with the goal of performing clinical and genetic mapping of the majority of Israeli IRD patients. To date, we recruited 2,420 families including 3,413 individuals with IRDs. On the basis of our estimation, these patients represent approximately 40% of Israeli IRD patients. To the best of our knowledge, this is, by far, the largest reported IRD cohort, and one of the first studies addressing the genetic analysis of IRD patients on a nationwide scale. The most common inheritance pattern in our cohort is autosomal recessive (60% of families). The most common retinal phenotype is retinitis pigmentosa (43%), followed by Stargardt disease and cone/cone-rod dystrophy. We identified the cause of disease in 56% of the families. Overall, 605 distinct mutations were identified, of which 12% represent prevalent founder mutations. The most frequently mutated genes were ABCA4, USH2A, FAM161A, CNGA3, and EYS. The results of this study have important implications for molecular diagnosis, genetic screening, and counseling, as well as for the development of new therapeutic strategies for retinal diseases.
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Affiliation(s)
- Dror Sharon
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Tamar Ben-Yosef
- Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Nitza Goldenberg-Cohen
- Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel.,Department of Ophthalmology, Bnai Zion Medical Center, Haifa, Israel.,The Krieger Eye Research Laboratory, Felsenstein Medical Research Center (FMRC), Petach Tikva, Israel
| | - Eran Pras
- Department of Ophthalmology, Assaf-Harofeh Medical Center, Zerifin, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Libe Gradstein
- Department of Ophthalmology, Soroka Medical Center and Clalit Health Services, Faculty of Health Sciences, Ben-Gurion University, Beer Sheva, Israel
| | - Shiri Soudry
- Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel.,Department of Ophthalmology, Rambam Healthcare Campus, Haifa, Israel
| | - Eedy Mezer
- Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel.,Department of Ophthalmology, Rambam Healthcare Campus, Haifa, Israel
| | - Dinah Zur
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Ophthalmology Division, Tel Aviv Medical Center, Tel Aviv, Israel
| | - Anan H Abbasi
- Ziv Medical Center, Safed, Israel.,The Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Christina Zeitz
- INSERM, CNRS, Institut de la Vision, Sorbonne Université, Paris, France
| | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Muhammad I Khan
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jaime Levy
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ygal Rotenstreich
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,The Goldschleger Eye Institute, Sheba Medical Center, Tel-Hashomer, Israel
| | - Ohad S Birk
- The Morris Kahn Laboratory of Human Genetics at the National Institute of Biotechnology in the Negev, Ben-Gurion University, Beer Sheva, Israel.,Genetics Institute, Soroka Medical Center, Faculty of Health Sciences, Ben-Gurion University, Beer Sheva, Israel
| | - Miriam Ehrenberg
- Ophthalmology Unit, Schneider Children's Medical Center in Israel, Petach Tikva, Israel
| | - Rina Leibu
- Department of Ophthalmology, Rambam Healthcare Campus, Haifa, Israel
| | - Hadas Newman
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Ophthalmology Division, Tel Aviv Medical Center, Tel Aviv, Israel
| | - Noam Shomron
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Eyal Banin
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ido Perlman
- Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel.,Ophthalmology Division, Tel Aviv Medical Center, Tel Aviv, Israel
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40
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Afzal R, Firasat S, Kaul H, Ahmed B, Siddiqui SN, Zafar SN, Shahzadi M, Afshan K. Mutational analysis of the CYP1B1 gene in Pakistani primary congenital glaucoma patients: Identification of four known and a novel causative variant at the 3' splice acceptor site of intron 2. Congenit Anom (Kyoto) 2019; 59:152-161. [PMID: 30270463 DOI: 10.1111/cga.12312] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 09/25/2018] [Accepted: 09/25/2018] [Indexed: 01/06/2023]
Abstract
Primary congenital glaucoma (PCG) causes blindness in early age. It has an autosomal recessive pattern of inheritance, hence is more prevalent in populations with frequent consanguineous marriages that occur in the Pakistani population. Mutations in the CYP1B1 gene are commonly associated with PCG. The aim of the present study was to identify genetic mutations in the CYP1B1 gene in PCG cases belonging to 38 Pakistani families. DNA was extracted using blood samples collected from all enrolled patients, their available unaffected family members and controls. Direct sequencing of the CYP1B1 gene revealed a novel 3' splice acceptor site causative variant segregating in an autosomal recessive manner in a large consanguineous family with four PCG-affected individuals. The novel variant was not detected in 93 ethnically matched controls. Furthermore, four already reported mutations, including p.G61E, p.R355X, p.R368H, and p.R390H were also detected in patients belonging to nine different families. All identified causative variants were evaluated by computational programs, that is, SIFT, PolyPhen-2, and MutationTaster. Pathogenicity of the novel splice site variant identified in this study was analyzed by Human Splicing Finder and MaxEntScan. Ten out of 38 families with PCG had the disease due to CYP1B1 mutations, suggesting CYP1B1 was contributing to PCG in these Pakistani patients. Identification of this novel 3' splice acceptor site variant in intron 2 is the first report for the CYP1B1 gene contributing to genetic heterogeneity of disease.
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Affiliation(s)
- Rabia Afzal
- Department of Animal Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Sabika Firasat
- Department of Animal Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Haiba Kaul
- Genetics Division, Department of Livestock Production, University of Veterinary and Animal Sciences, Pattoki, Pakistan
| | - Bashir Ahmed
- Department of Animal Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Sorath N Siddiqui
- Department of Pediatric Ophthalmology and Strabismus, Al-Shifa Trust Eye Hospital, Rawalpindi, Pakistan
| | - Saemah N Zafar
- Department of Pediatric Ophthalmology and Strabismus, Al-Shifa Trust Eye Hospital, Rawalpindi, Pakistan
| | - Misbah Shahzadi
- Department of Animal Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Kiran Afshan
- Department of Animal Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
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41
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Mokhber M, Shahrbabak MM, Sadeghi M, Shahrbabak HM, Stella A, Nicolzzi E, Williams JL. Study of whole genome linkage disequilibrium patterns of Iranian water buffalo breeds using the Axiom Buffalo Genotyping 90K Array. PLoS One 2019; 14:e0217687. [PMID: 31150486 PMCID: PMC6544294 DOI: 10.1371/journal.pone.0217687] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 05/16/2019] [Indexed: 01/21/2023] Open
Abstract
Accuracy of genome-wide association studies, and the successful implementation of genomic selection depends on the level of linkage disequilibrium (LD) across the genome and also the persistence of LD phase between populations. In the present study LD between adjacent SNPs and LD decay between SNPs was calculated in three Iranian water buffalo populations. Persistence of LD phase was evaluated across these populations and effective population size (Ne) was estimated from corrected r2 information. A set of 404 individuals from three Iranian buffalo populations were genotyped with the Axiom Buffalo Genotyping 90K Array. Average r2 and |D'| between adjacent SNP pairs across all chromosomes was 0.27 and 0.66 for AZI, 0.29 and 0.68 for KHU, and 0.32 and 0.72 for MAZ. The LD between the SNPs decreased with increasing physical distance from 100Kb to 1Mb between markers, from 0.234 to 0.018 for AZI, 0.254 to 0.034 for KHU, and 0.297 to 0.119 for MAZ, respectively. These results indicate that a density of 90K SNP is sufficient for genomic analyses relying on long range LD (e.g. GWAS and genomic selection). The persistence of LD phase decreased with increasing marker distances across all the populations, but remained above 0.8 for AZI and KHU for marker distances up to 100Kb. For multi-breed genomic evaluation, the 90K SNP panel is suitable for AZI and KHU buffalo breeds. Estimated effective population sizes for AZI, KHU and MAZ were 477, 212 and 32, respectively, for recent generations. The estimated effective population sizes indicate that the MAZ is at risk and requires careful management.
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Affiliation(s)
- Mahdi Mokhber
- Department of Animal Science, Faculty of Agriculture, Urmia University, Urmia, Iran
- * E-mail:
| | - Mohammad Moradi Shahrbabak
- Department of Animal Science, Faculty of Agricultural Science and Engineering, University College of Agriculture and Natural Resources (UTCAN), University of Tehran, Karaj, Iran
| | - Mostafa Sadeghi
- Department of Animal Science, Faculty of Agricultural Science and Engineering, University College of Agriculture and Natural Resources (UTCAN), University of Tehran, Karaj, Iran
| | - Hossein Moradi Shahrbabak
- Department of Animal Science, Faculty of Agricultural Science and Engineering, University College of Agriculture and Natural Resources (UTCAN), University of Tehran, Karaj, Iran
| | | | | | - John L. Williams
- Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, South Australia, Australia
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42
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Nabais Sá MJ, Jensik PJ, McGee SR, Parker MJ, Lahiri N, McNeil EP, Kroes HY, Hagerman RJ, Harrison RE, Montgomery T, Splitt M, Palmer EE, Sachdev RK, Mefford HC, Scott AA, Martinez-Agosto JA, Lorenz R, Orenstein N, Berg JN, Amiel J, Heron D, Keren B, Cobben JM, Menke LA, Marco EJ, Graham JM, Pierson TM, Karimiani EG, Maroofian R, Manzini MC, Cauley ES, Colombo R, Odent S, Dubourg C, Phornphutkul C, de Brouwer APM, de Vries BBA, Vulto-vanSilfhout AT. De novo and biallelic DEAF1 variants cause a phenotypic spectrum. Genet Med 2019; 21:2059-2069. [PMID: 30923367 DOI: 10.1038/s41436-019-0473-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 02/15/2019] [Indexed: 01/24/2023] Open
Abstract
PURPOSE To investigate the effect of different DEAF1 variants on the phenotype of patients with autosomal dominant and recessive inheritance patterns and on DEAF1 activity in vitro. METHODS We assembled a cohort of 23 patients with de novo and biallelic DEAF1 variants, described the genotype-phenotype correlation, and investigated the differential effect of de novo and recessive variants on transcription assays using DEAF1 and Eif4g3 promoter luciferase constructs. RESULTS The proportion of the most prevalent phenotypic features, including intellectual disability, speech delay, motor delay, autism, sleep disturbances, and a high pain threshold, were not significantly different in patients with biallelic and pathogenic de novo DEAF1 variants. However, microcephaly was exclusively observed in patients with recessive variants (p < 0.0001). CONCLUSION We propose that different variants in the DEAF1 gene result in a phenotypic spectrum centered around neurodevelopmental delay. While a pathogenic de novo dominant variant would also incapacitate the product of the wild-type allele and result in a dominant-negative effect, a combination of two recessive variants would result in a partial loss of function. Because the clinical picture can be nonspecific, detailed phenotype information, segregation, and functional analysis are fundamental to determine the pathogenicity of novel variants and to improve the care of these patients.
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Affiliation(s)
- Maria J Nabais Sá
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Philip J Jensik
- Department of Physiology, Southern Illinois University School of Medicine, Carbondale, IL, USA
| | - Stacey R McGee
- Department of Physiology, Southern Illinois University School of Medicine, Carbondale, IL, USA
| | - Michael J Parker
- Sheffield Clinical Genetics Service, OPD2 Northern General Hospital, Sheffield, UK
| | - Nayana Lahiri
- Department of Clinical Genetics, St George's University Hospitals NHS Foundation Trust & St George's, University of London, London, UK
| | - Evan P McNeil
- Dartmouth Geisel School of Medicine, Hanover, NH, USA
| | - Hester Y Kroes
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Randi J Hagerman
- Medical Investigation of Neurodevelopmental Disorders (MIND) Institute, University of California Davis School of Medicine, Sacramento, Sacramento, CA, USA.,Department of Pediatrics, University of California Davis Medical Center, Sacramento, Sacramento, CA, USA
| | - Rachel E Harrison
- Department of Clinical Genetics, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Tara Montgomery
- Northern Genetics Service, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Miranda Splitt
- Northern Genetics Service, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Elizabeth E Palmer
- Sydney Children's Hospital, Randwick, NSW, Australia.,School of Women's and Children's Health, UNSW Medicine, The University of New South Wales, Sydney, NSW, Australia
| | - Rani K Sachdev
- Sydney Children's Hospital, Randwick, NSW, Australia.,School of Women's and Children's Health, UNSW Medicine, The University of New South Wales, Sydney, NSW, Australia
| | - Heather C Mefford
- Department of Pediatrics, Division of Genetic Medicine, University of Washington-Seattle, Seattle, WA, USA
| | - Abbey A Scott
- Division of Genetic Medicine, Seattle Children's Hospital, Seattle, WA, USA
| | - Julian A Martinez-Agosto
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.,Division of Medical Genetics, Department of Pediatrics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | | | - Naama Orenstein
- Pediatric Genetics Clinic, Schneider Children's Medical Center of Israel, Petach Tikva, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Jonathan N Berg
- Department of Clinical Genetics, Ninewells Hospital and Medical School, Dundee, Angus, UK.,Clinical Genetics, University of Dundee, Dundee, Angus, UK
| | - Jeanne Amiel
- Département de Génétique, Hôpital Necker-Enfants Malades, Assistance Publique, INSERM UMR 1163, Institut Imagine, Paris, France
| | - Delphine Heron
- Département de Génétique, Hôpital Pitié-Salpêtrière, Assistance publique-Hôpitaux de Paris, Paris, France
| | - Boris Keren
- Département de Génétique, Hôpital Pitié-Salpêtrière, Assistance publique-Hôpitaux de Paris, Paris, France
| | - Jan-Maarten Cobben
- Department of Pediatrics, Amsterdam University Medical Centers, Amsterdam, The Netherlands.,North West Thames Genetics NHS, Northwick Park Hospital, London, UK
| | - Leonie A Menke
- Department of Pediatrics, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Elysa J Marco
- Department of Child Neurology, Cortica Healthcare, San Rafael, CA, USA
| | - John M Graham
- Division of Clinical Genetics and Dysmorphology, Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Tyler Mark Pierson
- Department of Pediatrics, Department of Neurology, and the Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ehsan Ghayoor Karimiani
- Genetics Research Centre, Molecular and Clinical Sciences Institute, St George's, University of London, London, UK
| | - Reza Maroofian
- Genetics Research Centre, Molecular and Clinical Sciences Institute, St George's, University of London, London, UK
| | - M Chiara Manzini
- GW Institute for Neuroscience, Department of Pharmacology and Physiology, The George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Edmund S Cauley
- GW Institute for Neuroscience, Department of Pharmacology and Physiology, The George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Roberto Colombo
- Faculty of Medicine"Agostino Gemelli"Catholic University of the Sacred Heart, Rome, Italy.,Center for the Study of Rare Inherited Diseases (CeSMER), Niguarda Ca' Granda Metropolitan Hospital, Milan, Italy
| | - Sylvie Odent
- Service de Génétique Clinique, CLAD-Ouest CHU Rennes, Univ Rennes, CNRS 6290 Institut de Génétique et Développement de Rennes (IGDR), Rennes, France
| | | | - Chanika Phornphutkul
- Division of Human Genetics, Department of Pediatrics, Hasbro Children's Hospital, Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Arjan P M de Brouwer
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Bert B A de Vries
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.
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Tatour Y, Tamaiev J, Shamaly S, Colombo R, Bril E, Rabinowitz T, Yaakobi A, Mezer E, Leibu R, Tiosano B, Shomron N, Chowers I, Banin E, Sharon D, Ben-Yosef T. A novel intronic mutation of PDE6B is a major cause of autosomal recessive retinitis pigmentosa among Caucasus Jews. Mol Vis 2019; 25:155-164. [PMID: 30820151 PMCID: PMC6386512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Accepted: 02/20/2019] [Indexed: 12/02/2022] Open
Abstract
PURPOSE To identify the genetic basis for retinitis pigmentosa (RP) in a cohort of Jewish patients from Caucasia. METHODS Patients underwent a detailed ophthalmic evaluation, including funduscopic examination, visual field testing, optical coherence tomography (OCT), and electrophysiological tests, electroretinography (ERG) and visual evoked potentials (VEP). Genetic analysis was performed with a combination of whole exome sequencing (WES) and Sanger sequencing. Bioinformatic analysis of the WES results was performed via a customized pipeline. Pathogenicity of the identified intronic variant was evaluated in silico using the web tool Human Splicing Finder, and in vitro, using a minigene-based splicing assay. Linkage disequilibrium (LD) analysis was used to demonstrate a founder effect, and the decay of LD over generations around the mutation in Caucasus Jewish chromosomes was modeled to estimate the age of the most recent common ancestor. RESULTS In eight patients with RP from six unrelated families, all of Caucasus Jewish ancestry, we identified a novel homozygous intronic variant, located at position -9 of PDE6B intron 15. The c.1921-9C>G variant was predicted to generate a novel acceptor splice site, nine bases upstream of the original splice site of intron 15. In vitro splicing assay demonstrated that this novel acceptor splice site is used instead of the wild-type site, leading to an 8-bp insertion into exon 16, which is predicted to cause a frameshift. The presence of a common ancestral haplotype in mutation-bearing chromosomes was compatible with a founder effect. CONCLUSIONS The PDE6B c.1921-9C>G intronic mutation is a founder mutation that accounts for at least 40% (6/15 families) of autosomal recessive RP among Caucasus Jews. This result is highly important for molecular diagnosis, carrier screening, and genetic counseling in this population.
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Affiliation(s)
- Yasmin Tatour
- Ruth & Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Jonathan Tamaiev
- Ruth & Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Shamaly Shamaly
- Department of Ophthalmology, Bnai Zion Medical Center, Haifa, Israel
| | - Roberto Colombo
- Institute of Clinical Biochemistry, Faculty of Medicine, Catholic University of the Sacred Heart, Milan, Italy,Center for the Study of Rare Hereditary Diseases, Niguarda Ca' Granda Metropolitan Hospital, Milan, Italy
| | - Ephrat Bril
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Tom Rabinowitz
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Alona Yaakobi
- Department of Ophthalmology, Hillel Yaffe Medical Center, Hadera, Israel
| | - Eedy Mezer
- Ruth & Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel,Alberto Moscona Department of Ophthalmology, Rambam Health Care Center, Haifa, Israel
| | - Rina Leibu
- Alberto Moscona Department of Ophthalmology, Rambam Health Care Center, Haifa, Israel
| | - Beatrice Tiosano
- Ruth & Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel,Department of Ophthalmology, Hillel Yaffe Medical Center, Hadera, Israel
| | - Noam Shomron
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Itay Chowers
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Eyal Banin
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Dror Sharon
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Tamar Ben-Yosef
- Ruth & Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
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44
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Rashid M, Yousaf S, Sheikh SA, Sajid Z, Shabbir AS, Kausar T, Tariq N, Usman M, Shaikh RS, Ali M, Bukhari SA, Waryah AM, Qasim M, Riazuddin S, Ahmed ZM. Identities and frequencies of variants in CYP1B1 causing primary congenital glaucoma in Pakistan. Mol Vis 2019; 25:144-154. [PMID: 30820150 PMCID: PMC6386514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 02/20/2019] [Indexed: 11/11/2022] Open
Abstract
Purpose Primary congenital glaucoma (PCG) is a clinically and genetically heterogeneous disease. The present study was undertaken to find the genetic causes of PCG segregating in 36 large consanguineous Pakistani families. Methods Ophthalmic examination including fundoscopy, or slit-lamp microscopy was performed to clinically characterize the PCG phenotype. Genomic nucleotide sequences of the CYP1B1 and LTBP2 genes were analyzed with either Sanger or whole exome sequencing. In silico prediction programs were used to assess the pathogenicity of identified alleles. ClustalW alignments were performed to determine evolutionary conservation, and three-dimensional (3D) modeling was performed using HOPE and Phyre2 software. Results Among the known loci, mutations in CYP1B1 and LTBP2 are the common causes of PCG. Therefore, we analyzed the genomic nucleotide sequences of CYP1B1 and LTBP2, and detected probable pathogenic variants cosegregating with PCG in 14 families. These included the three novel (c.542T>A, c.1436A>G, and c.1325delC) and five known (c.868dupC, c.1168C>T, c.1169G>A, c.1209InsTCATGCCACC, and c.1310C>T) variants in CYP1B1. Two of the novel variants are missense substitutions [p.(Leu181Gln), p.(Gln479Arg)], which replaced evolutionary conserved amino acids, and are predicted to be pathogenic by various in silico programs, while the third variant (c.1325delC) is predicted to cause reading frameshift and premature truncation of the protein. A single mutation, p.(Arg390His), causes PCG in six (~43%) of the 14 CYP1B1 mutations harboring families, and thus, is the most common variant in this cohort. Surprisingly, we did not find any LTBP2 pathogenic variants in the families, which further supports the genetic heterogeneity of PCG in the Pakistani population. Conclusions In conclusion, results of the present study enhance our understanding of the genetic basis of PCG, support the notion of a genetic modifier of CYP1B1, and contribute to the development of genetic testing protocols and genetic counseling for PCG in Pakistani families.
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Affiliation(s)
- Muhammad Rashid
- Department of Otorhinolaryngology Head and Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD,Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Sairah Yousaf
- Department of Otorhinolaryngology Head and Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD
| | - Shakeel A. Sheikh
- Molecular Biology & Genetics Department, Liaquat University of Medical & Health Sciences, Jamshoro, Pakistan
| | - Zureesha Sajid
- Department of Otorhinolaryngology Head and Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD,Institute of Molecular Biology & Biotechnology, Bahauddin Zakariya University, Multan, Pakistan
| | - Asra S. Shabbir
- University College of Pharmacy, Punjab University, Lahore, Pakistan
| | - Tasleem Kausar
- Zoology Department, Government Sadiq College Women University, Bahawalpur, Pakistan
| | - Nabeela Tariq
- Zoology Department, Sardar Bahadur Khan Women University, Quetta, Pakistan
| | - Muhammad Usman
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Rehan S. Shaikh
- Institute of Molecular Biology & Biotechnology, Bahauddin Zakariya University, Multan, Pakistan
| | - Muhammad Ali
- Department of Biochemistry, Government College University, Faisalabad, Pakistan
| | - Shazia A. Bukhari
- Department of Biochemistry, Government College University, Faisalabad, Pakistan
| | - Ali M. Waryah
- Molecular Biology & Genetics Department, Liaquat University of Medical & Health Sciences, Jamshoro, Pakistan
| | - Muhammad Qasim
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Saima Riazuddin
- Department of Otorhinolaryngology Head and Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD
| | - Zubair M. Ahmed
- Department of Otorhinolaryngology Head and Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD
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Waryah YM, Iqbal M, Sheikh SA, Baig MA, Narsani AK, Atif M, Bhinder MA, Ur Rahman A, Memon AI, Pirzado MS, Waryah AM. Two novel variants in CYP1B1 gene: a major contributor of autosomal recessive primary congenital glaucoma with allelic heterogeneity in Pakistani patients. Int J Ophthalmol 2019; 12:8-15. [PMID: 30662834 DOI: 10.18240/ijo.2019.01.02] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 09/10/2018] [Indexed: 11/23/2022] Open
Abstract
AIM To find the CYP1B1 mutations associated with primary congenital glaucoma (PCG) in Pakistani consanguineous pedigrees. METHODS After getting informed consent, 11 consanguineous pedigrees belonging to different ethnic groups were enrolled. Detailed medical history was recorded and pedigrees were drawn. The standard ophthalmological examination was done to characterize the phenotype. Genomic DNA was extracted from 10 mL whole blood and coding exons and exon intron boundaries of CYP1B1 gene were directly sequenced. Bioinformatics tools were used to model the mutant protein and predict the effect of novel variants on protein structure and function. RESULTS Sequencing analysis revealed 5 different CYP1B1 variants in 7 families (7/11; 64%), including two novel variants. A common mutation, p.R390H was found in four families, whereas p.P437L was found once in a family. Two novel variants, a homozygous non sense variant p.L13* and a compound heterozygous variant, p.P350T along with p.V364M were segregating with PCG in two families. All the patients had the variable onset and severity of the disease. The success rate of early clinical interventions was observed dependent on mutation types and position. Two different haplotypes were associated with frequently found mutation, p.R390H. CONCLUSION Identification of novel CYP1B1 variants reassert the genetic heterogeneity of Pakistani PCG patients. The patients with missense mutations show severe phenotypic presentations and poor vision after surgical interventions as compare to patients with null variants. This may help to better understand the role of CYP1B1 mutations in the development of PCG and its course of pathogenicity.
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Affiliation(s)
- Yar Muhammad Waryah
- Molecular Biology and Genetics Department, Liaquat University of Medical and Health Sciences, Jamshoro, Sindh 76090, Pakistan
| | - Muhammad Iqbal
- Department of Biochemistry, Islamia University, Bahawalpur, Punjab 63100, Pakistan
| | - Shakeel Ahmed Sheikh
- Molecular Biology and Genetics Department, Liaquat University of Medical and Health Sciences, Jamshoro, Sindh 76090, Pakistan
| | - Muhammad Azhar Baig
- Department of Biochemistry, Islamia University, Bahawalpur, Punjab 63100, Pakistan
| | - Ashok Kumar Narsani
- Institute of Ophthalmology, Liaquat University of Medical and Health Sciences Jamshoro, Sindh 76090, Pakistan
| | - Muhammad Atif
- Department of Biochemistry, Islamia University, Bahawalpur, Punjab 63100, Pakistan
| | - Munir Ahmad Bhinder
- Department of Human Genetics, University of Health Sciences, Lahore, Punjab 54000, Pakistan
| | - Attiq Ur Rahman
- Center of Excellence in Marine Biology, University of Karachi, Karachi District 75270, Pakistan
| | - Azam Iqbal Memon
- Molecular Biology and Genetics Department, Liaquat University of Medical and Health Sciences, Jamshoro, Sindh 76090, Pakistan
| | - Muhammad Suleman Pirzado
- Molecular Biology and Genetics Department, Liaquat University of Medical and Health Sciences, Jamshoro, Sindh 76090, Pakistan
| | - Ali Muhammad Waryah
- Molecular Biology and Genetics Department, Liaquat University of Medical and Health Sciences, Jamshoro, Sindh 76090, Pakistan
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Su W, Wang RC, Lohano MK, Wang L, Zhu P, Luo Y, Guo LJ, Lv Q, Jiang H, Wang JH, Mei L, Weng J, Su L, Dong NG. Identification of Two Mutations in PCDHGA4 and SLFN14 Genes in an Atrial Septal Defect Family. Curr Med Sci 2018; 38:989-996. [PMID: 30536060 DOI: 10.1007/s11596-018-1974-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 05/22/2018] [Indexed: 01/01/2023]
Abstract
Atrial septal defect (ASD) is a common acyanotic congenital cardiac disorder associated with genetic mutations. The objective of this study was to identify the genetic factors in a Chinese family with ASD patients by a whole exome sequencing approach. Causative ASD gene mutations were examined in 16 members from a three-generation family, among which 6 individuals were diagnosed as having ASD. One hundred and eighty-three unrelated healthy Chinese were recruited as a normal control group. Peripheral venous blood was collected from every subject for genetic analysis. Exome sequencing was performed in the ASD patients. Potential causal mutations were detected in non-ASD family members and normal controls by polymerase chain reaction and sequencing analysis. The results showed that all affected family members carried two novel compound mutations, c.1187delT of PCDHGA4 and c.2557insC of SLFN14, and these two mutations were considered to have synergetic function on ASD. In conclusion, the mutations of c.1187delT of PCDHGA4 and c.2557insC of SLFN14 may be pathogenic factors contributing to the development of ASD.
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Affiliation(s)
- Wei Su
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Ruo-Chen Wang
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Wuhan, 430074, China
| | - Mahesh Kumar Lohano
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Wuhan, 430074, China
| | - Li Wang
- Department of Internal Medicine, Affiliated Hospital of Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Peng Zhu
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Yue Luo
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Wuhan, 430074, China
| | - Li-Juan Guo
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Wuhan, 430074, China
| | - Qing Lv
- Department of Ultrasonography, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Hong Jiang
- Department of Internal Medicine, Affiliated Hospital of Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Jun-Han Wang
- Department of Internal Medicine, Affiliated Hospital of Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Li Mei
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Jun Weng
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Wuhan, 430074, China
| | - Li Su
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Wuhan, 430074, China.
| | - Nian-Guo Dong
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
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He L, Xiong L, Zhang A, Li Y, Huang R, Liao L, Zhu Z, Wang Y. Changes in gene and genotype frequencies during the development of the grass carp Ctenopharyngodon idella. JOURNAL OF FISH BIOLOGY 2018; 93:1113-1120. [PMID: 30281158 DOI: 10.1111/jfb.13828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 09/28/2018] [Indexed: 06/08/2023]
Abstract
In this study, a full-sib population of Ctenopharyngodon idella was constructed and approximately 500 C. idella individuals were sampled at four early developmental stages (hatching, first feeding, juvenile fish and young fish). Four DNA pools were constructed and subjected to next-generation sequencing. On the basis of the identification of single nucleotide polymorphisms (SNP), changes in gene and genotype frequencies during the developmental progress of C. idella were revealed, which indicates that death during the early developmental stage is not a random process. These findings will establish the basis for further studies performed for identifying superior alleles or genotypes as target markers for molecular breeding.
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Affiliation(s)
- LiB He
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Lv Xiong
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - AiD Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - YongM Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Rong Huang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - LanJ Liao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - ZuoY Zhu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - YaP Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
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48
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The synthetic peptide LyeTxI-b derived from Lycosa erythrognatha spider venom is cytotoxic to U-87 MG glioblastoma cells. Amino Acids 2018; 51:433-449. [PMID: 30449002 DOI: 10.1007/s00726-018-2678-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 11/08/2018] [Indexed: 01/04/2023]
Abstract
Antimicrobial peptides present a broad spectrum of therapeutic applications, including their use as anticancer peptides. These peptides have as target microbial, normal, and cancerous cells. The oncological properties of these peptides may occur by membranolytic mechanisms or non-membranolytics. In this work, we demonstrate for the first time the cytotoxic effects of the cationic alpha-helical antimicrobial peptide LyeTx I-b on glioblastoma lineage U87-MG. The anticancer property of this peptide was associated with a membranolytic mechanism. Loss of membrane integrity occurred after incubation with the peptide for 15 min, as shown by trypan blue uptake, reduction of calcein-AM conversion, and LDH release. Morphological studies using scanning electron microscopy demonstrated disruption of the plasma membrane from cells treated with LyeTx I-b, including the formation of holes or pores. Transmission electron microscopy analyses showed swollen nuclei with mild DNA condensation, cell volume increase with an electron-lucent cytoplasm and organelle vacuolization, but without the rupture of nuclear or plasmatic membranes. Morphometric analyses revealed a high percentage of cells in necroptosis stages, followed by necrosis and apoptosis at lower levels. Necrostatin-1, a known inhibitor of necroptosis, partially protected the cells from the toxicity of the peptide in a concentration-dependent manner. Imaging flow cytometry confirmed that 59% of the cells underwent necroptosis after 3-h incubation with the peptide. It is noteworthy that LyeTx I-b showed only mild cytotoxicity against normal fibroblasts of human and monkey cell lines and low hemolytic activity in human erythrocytes. All data together point out the anticancer potential of this peptide.
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Girard E, Eon-Marchais S, Olaso R, Renault AL, Damiola F, Dondon MG, Barjhoux L, Goidin D, Meyer V, Le Gal D, Beauvallet J, Mebirouk N, Lonjou C, Coignard J, Marcou M, Cavaciuti E, Baulard C, Bihoreau MT, Cohen-Haguenauer O, Leroux D, Penet C, Fert-Ferrer S, Colas C, Frebourg T, Eisinger F, Adenis C, Fajac A, Gladieff L, Tinat J, Floquet A, Chiesa J, Giraud S, Mortemousque I, Soubrier F, Audebert-Bellanger S, Limacher JM, Lasset C, Lejeune-Dumoulin S, Dreyfus H, Bignon YJ, Longy M, Pujol P, Venat-Bouvet L, Bonadona V, Berthet P, Luporsi E, Maugard CM, Noguès C, Delnatte C, Fricker JP, Gesta P, Faivre L, Lortholary A, Buecher B, Caron O, Gauthier-Villars M, Coupier I, Servant N, Boland A, Mazoyer S, Deleuze JF, Stoppa-Lyonnet D, Andrieu N, Lesueur F. Familial breast cancer and DNA repair genes: Insights into known and novel susceptibility genes from the GENESIS study, and implications for multigene panel testing. Int J Cancer 2018; 144:1962-1974. [PMID: 30303537 PMCID: PMC6587727 DOI: 10.1002/ijc.31921] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Revised: 09/11/2018] [Accepted: 09/25/2018] [Indexed: 12/16/2022]
Abstract
Pathogenic variants in BRCA1 and BRCA2 only explain the underlying genetic cause of about 10% of hereditary breast and ovarian cancer families. Because of cost‐effectiveness, multigene panel testing is often performed even if the clinical utility of testing most of the genes remains questionable. The purpose of our study was to assess the contribution of rare, deleterious‐predicted variants in DNA repair genes in familial breast cancer (BC) in a well‐characterized and homogeneous population. We analyzed 113 DNA repair genes selected from either an exome sequencing or a candidate gene approach in the GENESIS study, which includes familial BC cases with no BRCA1 or BRCA2 mutation and having a sister with BC (N = 1,207), and general population controls (N = 1,199). Sequencing data were filtered for rare loss‐of‐function variants (LoF) and likely deleterious missense variants (MV). We confirmed associations between LoF and MV in PALB2, ATM and CHEK2 and BC occurrence. We also identified for the first time associations between FANCI, MAST1, POLH and RTEL1 and BC susceptibility. Unlike other associated genes, carriers of an ATM LoF had a significantly higher risk of developing BC than carriers of an ATM MV (ORLoF = 17.4 vs. ORMV = 1.6; pHet = 0.002). Hence, our approach allowed us to specify BC relative risks associated with deleterious‐predicted variants in PALB2, ATM and CHEK2 and to add MAST1, POLH, RTEL1 and FANCI to the list of DNA repair genes possibly involved in BC susceptibility. We also highlight that different types of variants within the same gene can lead to different risk estimates. What's new? Pathogenic variants in BRCA1 and BRCA2 only explain the genetic cause of about 10% of hereditary breast and ovarian cancer families, and the clinical usefulness of testing other genes following the recent introduction of cost‐effective multigene panel sequencing in diagnostics laboratories remains questionable. This large case‐control study describes genetic variation in 113 DNA repair genes and specifies breast cancer relative risks associated with rare deleterious‐predicted variants in PALB2, ATM, and CHEK2. Importantly, different types of variants within the same gene can lead to different risk estimates. The results may help improve risk prediction models and define gene‐specific consensus management guidelines.
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Affiliation(s)
- Elodie Girard
- Inserm, Paris, France.,Institut Curie, Paris, France.,Mines ParisTech, Fontainebleau, France.,PSL Research University, Paris, France
| | - Séverine Eon-Marchais
- Inserm, Paris, France.,Institut Curie, Paris, France.,Mines ParisTech, Fontainebleau, France.,PSL Research University, Paris, France
| | - Robert Olaso
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, CEA, Evry, France
| | - Anne-Laure Renault
- Inserm, Paris, France.,Institut Curie, Paris, France.,Mines ParisTech, Fontainebleau, France.,PSL Research University, Paris, France
| | | | - Marie-Gabrielle Dondon
- Inserm, Paris, France.,Institut Curie, Paris, France.,Mines ParisTech, Fontainebleau, France.,PSL Research University, Paris, France
| | - Laure Barjhoux
- Département de Biopathologie, Centre Léon Bérard, Lyon, France
| | - Didier Goidin
- Life Sciences and Diagnostics Group, Agilent Technologies France, Les Ulis, France
| | - Vincent Meyer
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, CEA, Evry, France
| | - Dorothée Le Gal
- Inserm, Paris, France.,Institut Curie, Paris, France.,Mines ParisTech, Fontainebleau, France.,PSL Research University, Paris, France
| | - Juana Beauvallet
- Inserm, Paris, France.,Institut Curie, Paris, France.,Mines ParisTech, Fontainebleau, France.,PSL Research University, Paris, France
| | - Noura Mebirouk
- Inserm, Paris, France.,Institut Curie, Paris, France.,Mines ParisTech, Fontainebleau, France.,PSL Research University, Paris, France
| | - Christine Lonjou
- Inserm, Paris, France.,Institut Curie, Paris, France.,Mines ParisTech, Fontainebleau, France.,PSL Research University, Paris, France
| | - Juliette Coignard
- Inserm, Paris, France.,Institut Curie, Paris, France.,Mines ParisTech, Fontainebleau, France.,PSL Research University, Paris, France.,Université Paris Sud, Paris, France
| | - Morgane Marcou
- Inserm, Paris, France.,Institut Curie, Paris, France.,Mines ParisTech, Fontainebleau, France.,PSL Research University, Paris, France
| | - Eve Cavaciuti
- Inserm, Paris, France.,Institut Curie, Paris, France.,Mines ParisTech, Fontainebleau, France.,PSL Research University, Paris, France
| | - Céline Baulard
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, CEA, Evry, France
| | - Marie-Thérèse Bihoreau
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, CEA, Evry, France
| | | | - Dominique Leroux
- Département de Génétique, CHU de Grenoble, Hôpital Couple-Enfant, Grenoble, France
| | - Clotilde Penet
- Consultation d'Oncogénétique, Institut Jean-Godinot & ICC Courlancy, Reims, France
| | | | - Chrystelle Colas
- Département de Génétique Groupe Hospitalier Pitié-Salpêtrière, APHP, Paris, France.,Service de Génétique, Institut Curie, Paris, France
| | - Thierry Frebourg
- Département de Génétique, Hôpital Universitaire de Rouen, Rouen, France
| | - François Eisinger
- Institut Paoli Calmette, Département d'Anticipation et de Suivi des Cancers, Oncogénétique Clinique, Institut Paoli-Calmettes & Aix Marseille Université, Inserm, IRD, SESSTIM, Marseille, France
| | - Claude Adenis
- Service de Génétique, Centre Oscar-Lambret, Lille, France
| | - Anne Fajac
- Service d'Oncogénétique, Hôpital Tenon, Paris, France
| | - Laurence Gladieff
- Service d'Oncologie Médicale, Institut Claudius Regaud - IUCT-Oncopole, Toulouse, France
| | - Julie Tinat
- Département de Génétique, Hôpital Universitaire de Rouen, Rouen, France
| | | | | | - Sophie Giraud
- Service de Génétique, Hospices Civils de Lyon, Groupement Hospitalier EST, Bron, France
| | | | | | | | | | - Christine Lasset
- Université Claude Bernard Lyon 1, Villeurbanne; CNRS UMR 5558, Unité de Prévention et Epidémiologie Génétique, Lyon, Centre, Léon Bérard, France
| | | | - Hélène Dreyfus
- Clinique Sainte Catherine, Avignon & CHU de Grenoble, Département de Génétique, Hôpital Couple-Enfant, Grenoble, France
| | - Yves-Jean Bignon
- Université Clermont Auvergne; Inserm, U1240, Centre Jean Perrin, Clermont-Ferrand, France
| | | | - Pascal Pujol
- Service de Génétique Médicale et Oncogénétique, Hôpital Arnaud de Villeneuve, CHU Montpellier & INSERM 896, CRCM Val d'Aurelle, Montpellier, France
| | | | - Valérie Bonadona
- Université Claude Bernard Lyon 1, Villeurbanne; CNRS UMR 5558, Unité de Prévention et Epidémiologie Génétique, Lyon, Centre, Léon Bérard, France
| | - Pascaline Berthet
- Unité de Pathologie Gynécologique, Centre François Baclesse, Caen, France
| | - Elisabeth Luporsi
- Service de Génétique UF4128 CHR Metz-Thionville, Hôpital de Mercy, Metz, France
| | - Christine M Maugard
- Hôpitaux Universitaires de Strasbourg, UF1422 Oncogénétique moléculaire, Laboratoire d'Oncobiologie & UF6948 Oncogénétique Evaluation familiale et suivi, Strasbourg, France
| | - Catherine Noguès
- Institut Paoli Calmette, Département d'Anticipation et de Suivi des Cancers, Oncogénétique Clinique, Institut Paoli-Calmettes & Aix Marseille Université, Inserm, IRD, SESSTIM, Marseille, France
| | - Capucine Delnatte
- Unité d'Oncogénétique, Centre René Gauducheau, Nantes, Saint Herblain, France
| | | | - Paul Gesta
- Service d'Oncogénétique Régional Poitou-Charentes, Niort, France
| | - Laurence Faivre
- Institut GIMI, CHU de Dijon, Hôpital d'Enfants, Oncogénétique & Centre de Lutte contre le Cancer Georges François Leclerc, Dijon, France
| | - Alain Lortholary
- Service d'Oncologie Médicale, Centre Catherine de Sienne, Nantes, France
| | | | - Olivier Caron
- Gustave Roussy, Université Paris-Saclay, Département de Médecine Oncologique, Villejuif, France
| | | | - Isabelle Coupier
- Service de Génétique Médicale et Oncogénétique, Hôpital Arnaud de Villeneuve, CHU Montpellier & INSERM 896, CRCM Val d'Aurelle, Montpellier, France
| | - Nicolas Servant
- Inserm, Paris, France.,Institut Curie, Paris, France.,Mines ParisTech, Fontainebleau, France.,PSL Research University, Paris, France
| | - Anne Boland
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, CEA, Evry, France
| | - Sylvie Mazoyer
- Inserm, U1028, CNRS UMR5292, Centre de Recherche en Neurosciences de Lyon, France
| | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, CEA, Evry, France
| | - Dominique Stoppa-Lyonnet
- Service de Génétique, Institut Curie, Paris, France.,Inserm, U830, Institut Curie, Paris, France.,Université Paris Descartes, Paris, France
| | - Nadine Andrieu
- Inserm, Paris, France.,Institut Curie, Paris, France.,Mines ParisTech, Fontainebleau, France.,PSL Research University, Paris, France
| | - Fabienne Lesueur
- Inserm, Paris, France.,Institut Curie, Paris, France.,Mines ParisTech, Fontainebleau, France.,PSL Research University, Paris, France
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50
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Souza TSD, Pinheiro RR, Lima CCVD, Brito RLLD, Azevedo DAAD, Dias RP, Santos VWSD, Andrioli A, Costa JN. Sheep infection by caprine lentivirus. REVISTA BRASILEIRA DE SAÚDE E PRODUÇÃO ANIMAL 2018. [DOI: 10.1590/s1519-99402018000300004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
SUMMARY The objective of this study was to demonstrate iatrogenic transmission of small ruminant lentivirus (SRLV) from goats to sheep and horizontal transmission between sheep. The study was conducted on a farm with separate goat and sheep rearing, and animals were monitored for lentivirus occurrence by clinical examination and testing by immunoblotting (IB), agar gel immunodiffusion (AGID), and nested polymerase chain reaction (nPCR). Positive results had not been observed in the sheep flock until this study. Conversely, virus positive dairy goats were known. For this reason, the farm performed the caprine arthritis-encephalitis (CAE) control program. The study was designed with a sheep group that presented positive animals for SRLV by nPCR. It was verified that three newborn animals in this group were rejected by their mothers and consequently received milk from the goat herd. These three animals remained with another 20 sheep of the same age, totaling 23 animals. After one year, during monitoring, 11 of the 23 animals in the group presented positive results in the nPCR and three demonstrated seroconversion by IB. Of the animals that had received goat milk, two had positive results in the nPCR and IB. The 11 animals positive in the nPCR were followed and it was verified that five animals did not present further positive results in the nPCR, nor seroconversion; two continued presenting positive results in the nPCR but were negative in the IB and AGID and four were positive in the nPCR, IB, and AGID. Thus, it was possible to demonstrate iatrogenic interspecific infection and the occurrence of horizontal caprine lentivirus transmission among sheep.
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