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Ahmed I, Muzammal M, Khan MA, Ullah H, Farid A, Yasin M, Khan J, Alam K, Mir A. Identification of Four Novel Candidate Genes for Non-syndromic Intellectual Disability in Pakistani Families. Biochem Genet 2023:10.1007/s10528-023-10556-w. [PMID: 37985543 DOI: 10.1007/s10528-023-10556-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 10/21/2023] [Indexed: 11/22/2023]
Abstract
Intellectual disability, a genetically and clinically varied disorder and is a significant health problem, particularly in less developed countries due to larger family size and high ratio of consanguineous marriages. In the current genetic study, we investigate and find the novel disease causative factors in the four Pakistani families with severe type of non-syndromic intellectual disability. For genetic analysis whole-exome sequencing (WES) and Sanger sequencing was performed. I-TASSER and Cluspro tools were used for Protein modeling and Protein-protein docking. Sanger sequencing confirms the segregation of novel homozygous variants in all the families i.e., c.245 T > C; p.Leu82Pro in SLC50A1 gene in family 1, missense variant c.1037G > A; p.Arg346His in TARS2 gene in family 2, in family 3 and 4, nonsense mutation c.234G > A; p.Trp78Term and missense mutation c.2200G > A; p.Asp734Asn in TBC1D3 and ANAPC2 gene, respectively. In silico functional studies have found the drastic effect of these mutations on protein structure and its interaction properties. Substituted amino acids were highly conserved and present on highly conserved region throughout the species. The discovery of pathogenic variants in SLC50A1, TARS2, TBC1D1 and ANAPC2 shows that the specific pathways connected with these genes may be important in cognitive impairment. The decisive role of pathogenic variants in these genes cannot be determined with certainty due to lack of functional data. However, exome sequencing and segregation analysis of all filtered variants revealed that the currently reported variants were the only variations from the respective families that segregated with the phenotype in the family.
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Affiliation(s)
- Iftikhar Ahmed
- Department of Biological Sciences, International Islamic University, Islamabad, Pakistan
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan, 29050, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Muzammal
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan, 29050, Khyber Pakhtunkhwa, Pakistan
| | - Muzammil Ahmad Khan
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan, 29050, Khyber Pakhtunkhwa, Pakistan
| | - Hafiz Ullah
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan, 29050, Khyber Pakhtunkhwa, Pakistan
| | - Arshad Farid
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan, 29050, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Yasin
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan, 29050, Khyber Pakhtunkhwa, Pakistan
| | - Jabbar Khan
- Institue of Biological Science, Gomal University, Dera Ismail Khan, 29050, Khyber Pakhtunkhwa, Pakistan
| | - Khurshid Alam
- Departement of Clinical Pharmacy, School Pf Pharmaceutical Sciences, Univesiti Sains Malaysia (USM), 11800, Gelugor, Penang, Malaysia
| | - Asif Mir
- Department of Biological Sciences, International Islamic University, Islamabad, Pakistan.
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Ayaz M, Muzammal M, Siraj S, Fatima S, Fatima S, Khan J, Khan MA, Shah MI, Rehman ZU, Wei L. Genetic basis of ß-thalassemia in families of pashtun ethnicity in Dera Ismail Khan district of Khyber Pakhtun-Khwa province, Pakistan. Expert Rev Hematol 2023; 16:693-699. [PMID: 37491848 DOI: 10.1080/17474086.2023.2241639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 07/12/2023] [Indexed: 07/27/2023]
Abstract
OBJECTIVES The objective of current genetic research was to verify the genetic basis of ß-thalassemia and its pattern of inheritance in families of Pashtun ethnicity in District Dera Ismail Khan, Pakistan. METHODOLOGY Blood samples from clinically diagnosed five unrelated ß-thalassemia families were collected and target Sanger Sequencing of HBB gene was done. Moreover, in silico analysis including protein modeling and Protein-Protein docking was aslo performed. RESULTS AND DISCUSSION Clinical analysis of patients from family 1,2, 4, and 5 revealed Thalassemia Intermedia, while patient from family 3 was suffering from thalassemia major. The average Hb concentrations between the cases that were severe were found to be a little lower (6.3 mg/dl) than the patients with milder clinical manifestations (7.6 ± 1.4). Genetic analysis in family 1 identified compound heterozygous mutation of HBB (NM_000518) i.e. c.20A>T +c.92 G>A, in family 2 and 4 compound heterozygous mutations c.20A>T + c.27_28insG, in family 3 homozygous mutation c.27_28insG, while in family 5 we identified homozygous mutation c.92 + 5 G>C (IVS-1 + 5 G>C). CONCLUSION This study offers an effective incentive to establish a mutation detection as well as prenatal diagnosis (PND) centers at a larger scale in the Pashtun ethnicity residing in District Dera Ismail Khan, Pakistan.
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Affiliation(s)
- Muhammad Ayaz
- Department of Immunology, Hebei Medical University, Shijiazhuang, Hebei, China
| | - Muhammad Muzammal
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan, Pakistan
| | - Sami Siraj
- Institute of Biomedical Sciences, Khyber Medical University, Peshawar, KP, Pakistan
| | - Sumaya Fatima
- Research Centre, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Sana Fatima
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan, Pakistan
| | - Jabbar Khan
- Institute of Biological Sciences, Gomal University, Dera Ismail Khan, Pakistan
| | - Muzammil Ahmad Khan
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan, Pakistan
| | - Muhammad Ishaq Shah
- Institute of Biological Sciences, Gomal University, Dera Ismail Khan, Pakistan
| | - Zia Ur Rehman
- Institute of Biological Sciences, Gomal University, Dera Ismail Khan, Pakistan
| | - Lin Wei
- Department of Immunology, Hebei Medical University, Shijiazhuang, Hebei, China
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Muhammad N, Hussain SI, Rehman ZU, Khan SA, Jan S, Khan N, Muzammal M, Abbasi SW, Kakar N, Rehman ZU, Khan MA, Mirza MU, Muhammad N, Khan S, Wasif N. Autosomal recessive variants c.953A>C and c.97-1G>C in NSUN2 causing intellectual disability: a molecular dynamics simulation study of loss-of-function mechanisms. Front Neurol 2023; 14:1168307. [PMID: 37305761 PMCID: PMC10249782 DOI: 10.3389/fneur.2023.1168307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 04/28/2023] [Indexed: 06/13/2023] Open
Abstract
Introduction Intellectual disability (ID) is a clinically and genetically heterogeneous disorder. It drastically affects the learning capabilities of patients and eventually reduces their IQ level below 70. Methods The current genetic study ascertained two consanguineous Pakistani families suffering from autosomal recessive intellectual developmental disorder-5 (MRT5). We have used exome sequencing followed by Sanger sequencing to identify the disease-causing variants. Results and discussion Genetic analysis using whole exome sequencing in these families identified two novel mutations in the NSUN2 (NM_017755.5). Family-A segregated a novel missense variant c.953A>C; p.Tyr318Ser in exon-9 of the NSUN2. The variant substituted an amino acid Tyr318, highly conserved among different animal species and located in the functional domain of NSUN2 known as "SAM-dependent methyltransferase RsmB/NOP2-type". Whereas in family B, we identified a novel splice site variant c.97-1G>C that affects the splice acceptor site of NSUN2. The identified splice variant (c.97-1G>C) was predicted to result in the skipping of exon-2, which would lead to a frameshift followed by a premature stop codon (p. His86Profs*16). Furthermore, it could result in the termination of translation and synthesis of dysfunctional protein, most likely leading to nonsense-mediated decay. The dynamic consequences of NSUN2 missense variant was further explored together with wildtype through molecular dynamic simulations, which uncovered the disruption of NSUN2 function due to a gain in structural flexibility. The present molecular genetic study further extends the mutational spectrum of NSUN2 to be involved in ID and its genetic heterogeneity in the Pakistani population.
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Affiliation(s)
- Nazif Muhammad
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Syeda Iqra Hussain
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Zia Ur Rehman
- Department of General Medicine, Northwest General Hospital & Research Center, Peshawar, Khyber Pakhtunkhwa, Pakistan
| | - Sher Alam Khan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Samin Jan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Niamatullah Khan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Muzammal
- Gomal Center of Biochemistry and Biotechnology, Gomal University, D.I.Khan, Khyber Pakhtunkhwa, Pakistan
| | - Sumra Wajid Abbasi
- NUMS Department of Biological Sciences, National University of Medical Sciences, The Mall, Rawalpindi, Punjab, Pakistan
| | - Naseebullah Kakar
- Department of Biotechnology, Faculty of Life Sciences and Informatics, BUITEMS, Quetta, Pakistan
- Institute of Human Genetics, Universitätsklinikum Schleswig-Holstein, Lübeck, Germany
| | - Zia Ur Rehman
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Muzammil Ahmad Khan
- Gomal Center of Biochemistry and Biotechnology, Gomal University, D.I.Khan, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Usman Mirza
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON, Canada
| | - Noor Muhammad
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Saadullah Khan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Naveed Wasif
- Institute of Human Genetics, Ulm University, and Ulm University Medical Center, Ulm, Germany
- Institute of Human Genetics, University Hospital Schleswig-Holstein, Kiel, Germany
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Ahmad S, Ali MZ, Muzammal M, Khan AU, Ikram M, Muurinen M, Hussain S, Loid P, Khan MA, Mäkitie O. Identification of GLI1 and KIAA0825 Variants in Two Families with Postaxial Polydactyly. Genes (Basel) 2023; 14:genes14040869. [PMID: 37107627 PMCID: PMC10137575 DOI: 10.3390/genes14040869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 03/27/2023] [Accepted: 03/29/2023] [Indexed: 04/29/2023] Open
Abstract
Polydactyly is a rare autosomal dominant or recessive appendicular patterning defect of the hands and feet, phenotypically characterized by the duplication of digits. Postaxial polydactyly (PAP) is the most common form and includes two main types: PAP type A (PAPA) and PAP type B (PAPB). Type A involves a well-established extra digit articulated with the fifth or sixth metacarpal, while type B presents a rudimentary or poorly developed superfluous digit. Pathogenic variants in several genes have been identified in isolated and syndromic forms of polydactyly. The current study presents two Pakistani families with autosomal recessive PAPA with intra- and inter-familial phenotype variability. Whole-exome sequencing and Sanger analysis revealed a novel missense variant in KIAA0825 (c.3572C>T: p.Pro1191Leu) in family A and a known nonsense variant in GLI1 (c.337C>T: p.Arg113*) in family B. In silico studies of mutant KIAA0825 and GLI1 proteins revealed considerable structural and interactional modifications that suggest an abnormal function of the proteins leading to the disease phenotype. The present study broadens the mutational spectrum of KIAA0825 and demonstrates the second case of a previously identified GLI1 variant with variable phenotypes. These findings facilitate genetic counseling in Pakistani families with a polydactyly-related phenotype.
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Affiliation(s)
- Safeer Ahmad
- Gomal Center of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan 29050, Pakistan
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
| | - Muhammad Zeeshan Ali
- Gomal Center of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan 29050, Pakistan
| | - Muhammad Muzammal
- Gomal Center of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan 29050, Pakistan
| | - Amjad Ullah Khan
- Gomal Center of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan 29050, Pakistan
| | - Muhammad Ikram
- Gomal Center of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan 29050, Pakistan
| | - Mari Muurinen
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
- Children's Hospital, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland
- Folkhälsan Research Center, Folkhälsan Institute of Genetics, 00290 Helsinki, Finland
| | - Shabir Hussain
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
| | - Petra Loid
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
- Children's Hospital, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland
- Folkhälsan Research Center, Folkhälsan Institute of Genetics, 00290 Helsinki, Finland
| | - Muzammil Ahmad Khan
- Gomal Center of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan 29050, Pakistan
| | - Outi Mäkitie
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
- Children's Hospital, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland
- Folkhälsan Research Center, Folkhälsan Institute of Genetics, 00290 Helsinki, Finland
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Hussain S, Nawaz A, Hamid M, Ullah W, Khan IN, Afshan M, Rehman A, Nawaz H, Halswick J, Rehman SU, Ahmad S, Muzammal M, Muhammad N, Jan A, Khan S, Windpassinger C, Khan MA. Mutation screening of multiple Pakistani MCPH families revealed novel and recurrent protein-truncating mutations of ASPM. Biotechnol Appl Biochem 2022; 69:2296-2303. [PMID: 34826358 DOI: 10.1002/bab.2286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 11/11/2021] [Indexed: 12/27/2022]
Abstract
Autosomal primary microcephaly (MCPH) is a heterogenetic disorder that affects brain's cerebral cortex size and leads to a reduction in the cranial vault. Along with the hallmark feature of reduced head circumference, microcephalic patients also exhibit a variable degree of intellectual disability as well. Genetic studies have reported 28 MCPH genes, most of which produce microtubule-associated proteins and are involved in cell division. Herein this study, 14 patients from seven Pashtun origin Pakistani families of primary microcephaly were analyzed. Mutation analysis was performed through targeted Sanger DNA sequencing on the basis of phenotype-linked genetic makeup. Genetic analysis in one family found a novel pathogenic DNA change in the abnormal spindle microtubule assembly (ASPM) gene (NM_018136.4:c.3871dupGA), while the rest of the families revealed recurrent nonsense mutation c.3978G>A (p.Trp1326*) in the same gene. The novel reported frameshift insertion presumably truncates the protein p.(Lys1291Glyfs*14) and deletes the N-terminus domains. Identification of novel ASPM-truncating mutation expands the mutational spectrum of the ASPM gene, while mapping of recurrent mutation c.3978G>A (p.Trp1326*) will aid in establishing its founder effect in the Khyber Pakhtunkhwa (KPK) inhabitant population of Pakistan and should be suggestively screened for premarital counseling of MCPH susceptible families. Most of the recruited families are related to first-degree consanguinity. Hence, all the family elders were counseled to avoid intrafamilial marriages.
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Affiliation(s)
- Sadam Hussain
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology, Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Amjad Nawaz
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology, Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Malaika Hamid
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology, Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Waseem Ullah
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology, Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Iqbal Nawaz Khan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology, Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Mehak Afshan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology, Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Adil Rehman
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology, Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Hamid Nawaz
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology, Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Julia Halswick
- Diagnostic and Research Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Shoaib-Ur Rehman
- Department of Biotechnology, University of Science and Technology Bannu, Bannu, Khyber Pakhtunkhwa, Pakistan
| | - Sohail Ahmad
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, D. I. Khan, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Muzammal
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, D. I. Khan, Khyber Pakhtunkhwa, Pakistan
| | - Noor Muhammad
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology, Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Abid Jan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology, Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Saadullah Khan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology, Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Christian Windpassinger
- Diagnostic and Research Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Muzammil Ahmad Khan
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, D. I. Khan, Khyber Pakhtunkhwa, Pakistan
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Khan KA, Zizzadoro C, Di Cerbo A, Pugliese N, Khan GM, Ghazanfar S, Almusalami EM, Muzammal M, Alsalman KJ, Farid A. Preparation and In Vitro Evaluation of Controlled-Release Matrices of Losartan Potassium Using Ethocel Grade 10 and Carbopol 934P NF as Rate-Controlling Polymers. Polymers (Basel) 2022; 14:polym14152993. [PMID: 35893957 PMCID: PMC9331966 DOI: 10.3390/polym14152993] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 07/14/2022] [Accepted: 07/21/2022] [Indexed: 02/04/2023] Open
Abstract
Controlled-release formulations are essential for those drugs that require fine tuning of their activity to increase the ratio between therapeutic vs. adverse effects. Losartan potassium is among those drugs whose adverse effects may somehow impair its purported benefits. Previous investigations have been carried out to ascertain the suitability of several polymers for being associated with losartan. This study is focused on the effects of Ethocel grade 10 and Carbopol 934P NF on losartan release. Flow and physical properties were assessed according to the protocols standardized by the pharmacopeia (USP-NF 29), and the drug release in phosphate buffer (pH = 6.8) was measured for 24 h. Data evidenced good to excellent flow and physical properties according to the drug/polymer ratio and the addition of co-excipients. The release rate in 24 h was found to be 63–69% to 79–82% without or with the addition of co-excipients, respectively, following zero-order kinetics. The results also suggest a significant difference with the release profile of a traditional release losartan formulation. The results suggest the suitability of Ethocel grade 10 and Carbopol 934P NF as components of a controlled-release losartan formulation.
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Affiliation(s)
- Kamran Ahmad Khan
- Gomal Center of Pharmaceutical Sciences, Faculty of Pharmacy, Gomal University, Dera Ismail Khan 29050, Pakistan;
| | - Claudia Zizzadoro
- Department of Veterinary Medicine, University of Bari, 70010 Valenzano, Italy;
| | - Alessandro Di Cerbo
- School of Biosciences and Veterinary Medicine, University of Camerino, Via Circonvallazione 93/95, 62024 Matelica, Italy;
| | - Nicola Pugliese
- Department of Veterinary Medicine, University of Bari, 70010 Valenzano, Italy;
- Correspondence: (N.P.); (A.F.)
| | - Gul Majid Khan
- Department of Pharmacy, Quaid-i-Azam University, Islamabad 45320, Pakistan;
| | - Shakira Ghazanfar
- National Agricultural Research Centre, National Institute of Genomics and Advanced Biotechnology (NIGAB), Park Road, Islamabad 45500, Pakistan;
| | | | - Muhammad Muzammal
- Gomal Center of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan 29050, Pakistan;
| | - Khaled J. Alsalman
- Pharmaceutical Care Department, Albatha General Hospital, Alodaid 36636, Saudi Arabia;
| | - Arshad Farid
- Gomal Center of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan 29050, Pakistan;
- Correspondence: (N.P.); (A.F.)
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Israr M, Pugliese N, Farid A, Ghazanfar S, Di Cerbo A, Muzammal M, Alamri AS, Basheeruddin Asdaq SM, Ahmad A, Khan KA. Preparation and Characterization of Controlled-Release Floating Bilayer Tablets of Esomeprazole and Clarithromycin. Molecules 2022; 27:3242. [PMID: 35630719 PMCID: PMC9143198 DOI: 10.3390/molecules27103242] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 05/13/2022] [Accepted: 05/16/2022] [Indexed: 02/06/2023] Open
Abstract
Controlled-release effervescent floating bilayer tablets reduce dosage frequency and improve patient compliance with enhanced therapeutic outcomes. Generally, two different tablets of clarithromycin and esomeprazole, respectively, are given for the treatment of Helicobacter pylori infection and it might be worth incorporating both in a single tablet. In the current study, controlled-release floating bilayer tablets of clarithromycin and esomeprazole (F1−F4) were developed with different rates of polymeric materials by a direct compression method. During the formulation, Fourier-transform infrared spectroscopy (FTIR) analysis was performed for possible interactions between drugs and excipients. No interactions between drugs and excipients were noted. Moreover, the bilayer tablets’ thickness, diameter, friability, hardness, weight variation, dissolution, and percent purity were found within the acceptable limits. The floating lag time and total floating time of all formulations were found to be < 25 s and 24 h, respectively. The release of both the clarithromycin and esomeprazole started at the same time from the controlled-release floating bilayer tablets by anomalous non-Fickian diffusion, and the polymeric materials extended the drug release rate up to 24 h. In the case of F1, the results approached ideal zero-order kinetics. The dissolution profiles of the tested and reference tablet formulations were compared, but no significant differences were observed. It can be concluded that such controlled-release effervescent floating bilayer tablets can be efficiently used in clinical practice to reduce dosage frequency and increase patient compliance with continuous drug release for 24 h, which ultimately might enhance therapeutic efficacy.
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Affiliation(s)
- Muhammad Israr
- Gomal Centre of Pharmaceutical Sciences, Faculty of Pharmacy, Gomal University, D. I. Khan 29050, Pakistan;
| | - Nicola Pugliese
- Department of Veterinary Medicine, University of Bari, 70010 Valenzano, Italy;
| | - Arshad Farid
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, D. I. Khan 29050, Pakistan;
| | - Shakira Ghazanfar
- National Institute for Genomics Advanced Biotechnology, National Agricultural Research Centre, Park Road, Islamabad 45500, Pakistan;
| | - Alessandro Di Cerbo
- School of Biosciences and Veterinary Medicine, University of Camerino, 62024 Matelica, Italy
| | - Muhammad Muzammal
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, D. I. Khan 29050, Pakistan;
| | - Abdulhakeem S. Alamri
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Taif University, Taif 26432, Saudi Arabia;
- Centre of Biomedical Sciences Research (CBSR), Deanship of Scientific Research, Taif University, Taif 26432, Saudi Arabia
| | | | - Ashfaq Ahmad
- Department of Pharmacy, University of Swabi, Swabi 23430, Pakistan;
| | - Kamran Ahmad Khan
- Gomal Centre of Pharmaceutical Sciences, Faculty of Pharmacy, Gomal University, D. I. Khan 29050, Pakistan;
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Abid S, Farid A, Abid R, Rehman MU, Alsanie WF, Alhomrani M, Alamri AS, Asdaq SMB, Hefft DI, Saqib S, Muzammal M, Morshedy SA, Alruways MW, Ghazanfar S. Identification, Biochemical Characterization, and Safety Attributes of Locally Isolated Lactobacillus fermentum from Bubalus bubalis (buffalo) Milk as a Probiotic. Microorganisms 2022; 10:954. [PMID: 35630398 PMCID: PMC9144466 DOI: 10.3390/microorganisms10050954] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/28/2022] [Accepted: 04/28/2022] [Indexed: 12/03/2022] Open
Abstract
The demand of functional foods is on the rise, and researchers are trying to develop nutritious dairy products by using well-characterized strains of bacteria. In this study, we identified locally isolated strains of Lactobacillus fermentum from Bubalus bubalis (Nilli Ravi buffalo) milk and evaluated their potential as probiotics in food products like fermented milk. Fifteen Lactobacillus strains were initially isolated, and only four strains (NMCC-2, NMCC-14, NMCC-17, and NMCC-27) were examined for morphological and biochemical characterizations due to their ability of gas production in Durham tubes. Moreover, these strains were selected for further probiotic characterizations due to their extreme morphological resemblance with lactic acid bacteria for their antimicrobial activity, enzymatic potential, autoaggregation capability, hydrophobicity, and acid and bile tolerance. All selected isolates showed significant probiotic potential. However, NMCC-14 and NMCC-17 strains showed maximum probiotic potential. The isolates (NMCC-2, NMCC-14, NMCC-17, and NMCC-27) were identified as Lactobacillus fermentum utilizing 16S rRNA gene sequencing. The in vivo safety study of NMCC-14 (dose: 1010 CFU/day/mice; 21 days, orally) showed no histological dysfunctions in a mouse model. Pathogenic bacterial enzymes reduced the beneficial bacterial load in the host gastrointestinal tract. These results suggest that the NMCC-14 strain is safe and can be potentially used as a probiotic. Moreover, fermented milk was prepared by using the NMCC-14 strain. The results revealed that NMCC-14 strain-based fermented milk had significantly (p < 0.05) higher protein content (4.4 ± 0.06), water-holding capacity (WHC), and dynamic viscosity as compared to non-fermented milk. The results suggest that L. fermentum NMCC-14 is safe and nontoxic; hence, it can be a beneficial supplement to be used for the development of dairy products to be subjected to further clinical testing.
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Affiliation(s)
- Sana Abid
- Department of Biology, Faculty of Science & Technology, Virtual University, Lahore 54000, Pakistan;
| | - Arshad Farid
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, D.I.Khan 29050, Pakistan; (A.F.); (M.M.)
| | - Rameesha Abid
- Department of Biotechnology, University of Sialkot, Sialkot 51310, Pakistan;
- National Institute of Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre, Park Road, Islamabad 45500, Pakistan
| | - Mujeeb Ur Rehman
- Department of Pharmacy, Quaid-i-Azam University, Islamabad 45500, Pakistan;
| | - Walaa F. Alsanie
- Department of Clinical Laboratory Sciences, The Faculty of Applied Medical Sciences, Taif University, Al Hawiyah 21944, Saudi Arabia; (W.F.A.); (M.A.); (A.S.A.)
- Centre of Biomedical Sciences Research (CBSR), Deanship of Scientific Research, Taif University, Al Hawiyah 21944, Saudi Arabia
| | - Majid Alhomrani
- Department of Clinical Laboratory Sciences, The Faculty of Applied Medical Sciences, Taif University, Al Hawiyah 21944, Saudi Arabia; (W.F.A.); (M.A.); (A.S.A.)
- Centre of Biomedical Sciences Research (CBSR), Deanship of Scientific Research, Taif University, Al Hawiyah 21944, Saudi Arabia
| | - Abdulhakeem S. Alamri
- Department of Clinical Laboratory Sciences, The Faculty of Applied Medical Sciences, Taif University, Al Hawiyah 21944, Saudi Arabia; (W.F.A.); (M.A.); (A.S.A.)
- Centre of Biomedical Sciences Research (CBSR), Deanship of Scientific Research, Taif University, Al Hawiyah 21944, Saudi Arabia
| | | | - Daniel Ingo Hefft
- Reaseheath College, University Centre Reaseheath, Nantwich CW5 6DF, UK;
| | - Saddam Saqib
- Department of Biotechnology, Mohi- ud-Din Islamic University, Nerian Sharif 12080, Pakistan;
| | - Muhammad Muzammal
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, D.I.Khan 29050, Pakistan; (A.F.); (M.M.)
| | - Sabrin Abdelrahman Morshedy
- Fish and Animal Production Department, Faculty of Agriculture (Saba Basha), Alexandria University, Alexandria 21526, Egypt;
| | - Mashael W. Alruways
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Shaqra University, Shaqra 15273, Saudi Arabia;
| | - Shakira Ghazanfar
- National Institute of Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre, Park Road, Islamabad 45500, Pakistan
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Muzammal M, Di Cerbo A, Almusalami EM, Farid A, Khan MA, Ghazanfar S, Al Mohaini M, Alsalman AJ, Alhashem YN, Al Hawaj MA, Alsaleh AA. In Silico Analysis of the L-2-Hydroxyglutarate Dehydrogenase Gene Mutations and Their Biological Impact on Disease Etiology. Genes (Basel) 2022; 13:genes13040698. [PMID: 35456504 PMCID: PMC9028441 DOI: 10.3390/genes13040698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/08/2022] [Accepted: 04/12/2022] [Indexed: 02/04/2023] Open
Abstract
The L-2-hydroxyglutarate dehydrogenase (L2HGDH) gene encodes an important mitochondrial enzyme. However, its altered activity results in excessive levels of L-2-hydroxyglutarate, which results in diverse psychiatric features of intellectual disability. In the current study, we executed an in-silico analysis of all reported L2HGDH missense and nonsense variants in order to investigate their biological significance. Among the superimposed 3D models, the highest similarity index for a wild-type structure was shown by the mutant Glu336Lys (87.26%), while the lowest similarity index value was shown by Arg70* (10.00%). Three large active site pockets were determined using protein active site prediction, in which the 2nd largest pocket was shown to encompass the substrate L-2-hydroxyglutarate (L2HG) binding residues, i.e., 89Gln, 195Tyr, 402Ala, 403Gly and 404Val. Moreover, interactions of wild-type and mutant L2HGDH variants with the close functional interactor D2HGDH protein resulted in alterations in the position, number and nature of networking residues. We observed that the binding of L2HG with the L2HGDH enzyme is affected by the nature of the amino acid substitution, as well as the number and nature of bonds between the substrate and protein molecule, which are able to affect its biological activity.
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Affiliation(s)
- Muhammad Muzammal
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan 29050, Pakistan; (M.M.); (M.A.K.)
| | - Alessandro Di Cerbo
- School of Biosciences and Veterinary Medicine, University of Camerino, 62024 Matelica, Italy
- Correspondence: (A.D.C.); (A.F.)
| | | | - Arshad Farid
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan 29050, Pakistan; (M.M.); (M.A.K.)
- Correspondence: (A.D.C.); (A.F.)
| | - Muzammil Ahmad Khan
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan 29050, Pakistan; (M.M.); (M.A.K.)
- Department of Human Genetics, Precision Medicine Program, Sidra Medicine, Doha 26999, Qatar
| | - Shakira Ghazanfar
- National Institute for Genomics Advanced Biotechnology, National Agricultural Research Centre, Park Road, Islamabad 45500, Pakistan;
| | - Mohammed Al Mohaini
- Basic Sciences Department, College of Applied Medical Sciences, King Saud bin Abdulaziz University for Health Sciences, Alahsa 31982, Saudi Arabia;
- King Abdullah International Medical Research Center, Alahsa 31982, Saudi Arabia
| | - Abdulkhaliq J. Alsalman
- Department of Clinical Pharmacy, Faculty of Pharmacy, Northern Border University, Rafha 91911, Saudi Arabia;
| | - Yousef N. Alhashem
- Clinical Laboratory Sciences Department, Mohammed Al-Mana College for Medical Sciences, Dammam 34222, Saudi Arabia; (Y.N.A.); (A.A.A.)
| | - Maitham A. Al Hawaj
- Department of Pharmacy Practice, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Saudi Arabia;
| | - Abdulmonem A. Alsaleh
- Clinical Laboratory Sciences Department, Mohammed Al-Mana College for Medical Sciences, Dammam 34222, Saudi Arabia; (Y.N.A.); (A.A.A.)
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Ali MZ, Farid A, Ahmad S, Muzammal M, Mohaini MA, Alsalman AJ, Al Hawaj MA, Alhashem YN, Alsaleh AA, Almusalami EM, Maryam M, Khan MA. In Silico Analysis Identified Putative Pathogenic Missense nsSNPs in Human SLITRK1 Gene. Genes (Basel) 2022; 13:672. [PMID: 35456478 PMCID: PMC9030497 DOI: 10.3390/genes13040672] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 04/05/2022] [Accepted: 04/07/2022] [Indexed: 02/04/2023] Open
Abstract
Human DNA contains several variations, which can affect the structure and normal functioning of a protein. These variations could be single nucleotide polymorphisms (SNPs) or insertion-deletions (InDels). SNPs, as opposed to InDels, are more commonly present in DNA and may cause genetic disorders. In the current study, several bioinformatic tools were used to prioritize the pathogenic variants in the SLITRK1 gene. Out of all of the variants, 16 were commonly predicted to be pathogenic by these tools. All the variants had very low frequency, i.e., <0.0001 in the global population. The secondary structure of all filtered variants was predicted, but no structural change was observed at the site of variation in any variant. Protein stability analysis of these variants was then performed, which determined a decrease in protein stability of 10 of the variants. Amino acid conservation analysis revealed that all the amino acids were highly conserved, indicating their structural and functional importance. Protein 3D structure of wildtype SLITRK1 and all of its variants was predicted using I-TASSER, and the effect of variation on 3D structure of the protein was observed using the Missense3D tool, which presented the probable structural loss in three variants, i.e., Asn529Lys, Leu496Pro and Leu94Phe. The wildtype SLITRK1 protein and these three variants were independently docked with their close interactor protein PTPRD, and remarkable differences were observed in the docking sites of normal and variants, which will ultimately affect the functional activity of the SLITRK1 protein. Previous studies have shown that mutations in SLITRK1 are involved in Tourette syndrome. The present study may assist a molecular geneticist in interpreting the variant pathogenicity in research as well as diagnostic setup.
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Affiliation(s)
- Muhammad Zeeshan Ali
- Gomal Center of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan 29111, Pakistan; (M.Z.A.); (A.F.); (S.A.); (M.M.)
| | - Arshad Farid
- Gomal Center of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan 29111, Pakistan; (M.Z.A.); (A.F.); (S.A.); (M.M.)
| | - Safeer Ahmad
- Gomal Center of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan 29111, Pakistan; (M.Z.A.); (A.F.); (S.A.); (M.M.)
| | - Muhammad Muzammal
- Gomal Center of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan 29111, Pakistan; (M.Z.A.); (A.F.); (S.A.); (M.M.)
| | - Mohammed Al Mohaini
- Basic Sciences Department, College of Applied Medical Sciences, King Saud Bin Abdulaziz University for Health Sciences, Al Ahsa 31982, Saudi Arabia;
- King Abdullah International Medical Research Center, Al Ahsa 31982, Saudi Arabia
| | - Abdulkhaliq J. Alsalman
- Department of Clinical Pharmacy, Faculty of Pharmacy, Northern Border University, Rafha 91911, Saudi Arabia;
| | - Maitham A. Al Hawaj
- Department of Pharmacy Practice, College of Clinical Pharmacy, King Faisal University, Al Ahsa 31982, Saudi Arabia;
| | - Yousef N. Alhashem
- Clinical Laboratory Sciences Department, Mohammed Al-Mana College for Medical Sciences, Dammam 34222, Saudi Arabia; (Y.N.A.); (A.A.A.)
| | - Abdulmonem A. Alsaleh
- Clinical Laboratory Sciences Department, Mohammed Al-Mana College for Medical Sciences, Dammam 34222, Saudi Arabia; (Y.N.A.); (A.A.A.)
| | | | - Mahpara Maryam
- Department of Zoology, Government College No.1, Dera Ismail Khan 29111, Pakistan;
| | - Muzammil Ahmad Khan
- Gomal Center of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan 29111, Pakistan; (M.Z.A.); (A.F.); (S.A.); (M.M.)
- Department of Human Genetics, Sidra Medical and Research Centre, Doha 26999, Qatar
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Muzammal M, Ali MZ, Ahmad S, Huma S, Ahmad S, Abbasi AA, Khan S, Khan MA. The molecular genetics of UV-Sensitive syndrome: A rare dermal anomaly. J PAK MED ASSOC 2022; 71:2391-2396. [PMID: 34974577 DOI: 10.47391/jpma.03-476] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Ultraviolet-sensitive syndrome is a rare skin disorder characterised by heterogeneous phenotypic spectrum of skin freckling, telangiectasia and acute sunburn. It usually has an autosomal recessive pattern. So far, only 18 patients from nine different families (Japanese, French, Israeli, Iranian and Pakistani) have been reported in scientific literature. Its precise prevalence is still unknown, but, according to an estimate, its prevalence ratio is 1:100,000 worldwide. Until now, only three genes have been reported to be involved in the syndrome; the Excision Repair Cross-Complementing, Group 6, the Excision Repair Cross-Complementing, Group 8 and the UV-Stimulated Scaffold Protein A (UVSSA). Among these genes, the last one is reported to be more prevalent among different ethnicities, including Pakistani. Physiologically, most of the syndrome genes are involved in the transcription-coupled nucleotide excision pathway. In order to reduce the disease severity, the patients are advised to use medicated skin moisturisers or sun-blocks, sunglasses and gloves, while going out in the sun to avoid sun exposure. The current narrative review was planned to discuss the molecular genetics and the mutational spectrum of the syndrome, and to describe the differential diagnosis of various related disorders in order to facilitate clinical researchers.
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Affiliation(s)
- Muhammad Muzammal
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan, Pakistan
| | - Muhammad Zeeshan Ali
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan, KPK, Pakistan
| | - Safeer Ahmad
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan, Pakistan
| | - Shawana Huma
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan, Pakistan
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- Gomal Centre of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan, Pakistan
| | - Sohail Ahmad
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan, Pakistan
| | - Ansar Ahmad Abbasi
- Department of Zoology, Mirpur University of Science and Technology, Azad Kashmir, Pakistan
| | - Saadullah Khan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology, Kohat, KPK, Pakistan
| | - Muzammil Ahmad Khan
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan, KPK, Pakistan
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Muzammal M, Ali MZ, Brugger B, Blatterer J, Ahmad S, Taj S, Shah SK, Khan S, Enzinger C, Petek E, Wagner K, Khan MA, Windpassinger C. A novel protein truncating mutation in L2HGDH causes L-2-hydroxyglutaric aciduria in a consanguineous Pakistani family. Metab Brain Dis 2022; 37:243-252. [PMID: 34719772 PMCID: PMC8748340 DOI: 10.1007/s11011-021-00832-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 08/23/2021] [Indexed: 01/20/2023]
Abstract
BACKGROUND L-2-hydroxyglutaric aciduria (L2HGA) is a rare neurometabolic disorder that occurs due to accumulation of L-2-hydroxyglutaric acid in the cerebrospinal fluid (CSF), plasma and urine. The clinical manifestation of L2HGA includes intellectual disability, cerebellar ataxia, epilepsy, speech problems and macrocephaly. METHODS In the present study, we ascertained a multigenerational consanguineous Pakistani family with 5 affected individuals. Clinical studies were performed through biochemical tests and brain CT scan. Locus mapping was carried out through genome-wide SNP genotyping, whole exome sequencing and Sanger sequencing. For in silico studies protein structural modeling and docking was done using I-TASSER, Cluspro and AutoDock VINA tools. RESULTS Affected individuals presented with cognitive impairment, gait disturbance, speech difficulties and psychomotor delay. Radiologic analysis of a male patient revealed leukoaraiosis with hypoattenuation of cerebral white matter, suggestive of hypomyelination. Homozygosity mapping in this family revealed a linkage region on chromosome 14 between markers rs2039791 and rs781354. Subsequent whole exome analysis identified a novel frameshift mutation NM_024884.3:c.180delG, p.(Ala62Profs*24) in the second exon of L2HGDH. Sanger sequencing confirmed segregation of this mutation with the disease phenotype. The identification of the most N-terminal loss of function mutation published thus far further expands the mutational spectrum of L2HGDH.
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Affiliation(s)
- Muhammad Muzammal
- Gomal Center of Biochemistry and Biotechnology, Gomal University, D.I.Khan, Pakistan
| | - Muhammad Zeeshan Ali
- Gomal Center of Biochemistry and Biotechnology, Gomal University, D.I.Khan, Pakistan
| | - Beatrice Brugger
- Diagnostic and Research Institute of Human Genetics, Medical University of Graz, 8010, Graz, Austria
| | - Jasmin Blatterer
- Diagnostic and Research Institute of Human Genetics, Medical University of Graz, 8010, Graz, Austria
| | - Safeer Ahmad
- Gomal Center of Biochemistry and Biotechnology, Gomal University, D.I.Khan, Pakistan
| | - Sundas Taj
- Gomal Center of Biochemistry and Biotechnology, Gomal University, D.I.Khan, Pakistan
| | - Syed Khizar Shah
- Gomal Center of Biochemistry and Biotechnology, Gomal University, D.I.Khan, Pakistan
| | - Saadullah Khan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, 26000, Khyber Pakhtunkhwa, Pakistan
| | - Christian Enzinger
- Department of Neurology, Medical University of Graz, 8010, Graz, Austria
| | - Erwin Petek
- Diagnostic and Research Institute of Human Genetics, Medical University of Graz, 8010, Graz, Austria
| | - Klaus Wagner
- Diagnostic and Research Institute of Human Genetics, Medical University of Graz, 8010, Graz, Austria
| | - Muzammil Ahmad Khan
- Gomal Center of Biochemistry and Biotechnology, Gomal University, D.I.Khan, Pakistan.
| | - Christian Windpassinger
- Diagnostic and Research Institute of Human Genetics, Medical University of Graz, 8010, Graz, Austria.
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Muzammal M, Ahmad S, Ali MZ, Khan MA. Alopecia-mental retardation syndrome: Molecular genetics of a rare neuro-dermal disorder. Ann Hum Genet 2021; 85:147-154. [PMID: 33881165 DOI: 10.1111/ahg.12425] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 04/08/2021] [Accepted: 04/09/2021] [Indexed: 11/27/2022]
Abstract
Alopecia-mental retardation syndrome (APMR) is a rare autosomal recessive neuro-dermal disorder. It is characterized by heterogeneous phenotypic features, that is, absence of hair on the scalp, eyelashes, and eyebrows and mild to severe intellectual disability. So far, approximately 14 families (i.e., Iranian, Pakistani, and Swiss) with APMR have been reported in the scientific literature. Its precise prevalence is still unknown, but according to a predictive estimate, it prevails with the ratio of 1 in 1,000,000 persons worldwide. Until now, only four loci (two characterized and two uncharacterized) have been reported to be involved in APMR. The pathogenic variants in alpha-2-HS-glycoprotein [AHSG; APMR1 (MIM#203650)] and lanosterol synthase [LSS; APMR4 (MIM#618840)] are the characterized genetic factors associated with APMR. Among them, AHSG was reported in a consanguineous Iranian family and LSS gene in a Swiss origin family, while the remaining two uncharacterized loci, that is, APMR2 and APMR3, are reported in the Pakistani population. The current mini-report discusses the molecular genetics and mutational spectrum of APMR syndrome, its differential diagnosis from related disorders, and prediction of plausible candidate genes in two uncharacterized loci.
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Affiliation(s)
- Muhammad Muzammal
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan, KPK, Pakistan
| | - Safeer Ahmad
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan, KPK, Pakistan
| | - Muhammad Zeeshan Ali
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan, KPK, Pakistan
| | - Muzammil Ahmad Khan
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan, KPK, Pakistan
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Gul H, Haleem Shah A, Harripaul R, Wajid Abbasi S, Faheem M, Zubair M, Muzammal M, Khan S, B Vincent J, Ahmad Khan M. Homozygosity mapping coupled with whole-exome sequencing and protein modelling identified a novel missense mutation in GUCY2D in a consanguineous Pakistani family with Leber congenital amaurosis. J Genet 2021; 100:57. [PMID: 34470921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Leber congenital amaurosis (LCA) is a rare form of early onset vision loss or blindness due to retinal dystrophy. This condition is characterized by early vision loss, nystagmus and severe retinal dysfunction. To date, genetic studies have reported 19 genes to be associated with autosomal recessive LCA, most of which are involved in the retinal morphology and the physiology of the phototransduction pathway. In the current study, a large consanguineous family segregating congenital blindness was ascertained from the Dera Ismail Khan region of Pakistan. Genetic analysis was performed through genomewide SNP genotyping (for homozygosity-by-descent mapping), whole-exome sequencing (for mutation identification) and Sanger sequencing (for segregation analysis). In silico structural predictions were performed through SWISS-Model (structure prediction) and ClusPro (molecular docking). Molecular investigation of the present LCA family identified a novel homozygous missense mutation p.Asp306Val in GUCY2D gene (NM_000180.3:c.917A>T). In silico structural modelling and interaction studies predicted significant changes in protein folding and interacting residues. The present molecular genetic study further extends the mutational spectrum of GUCY2D in LCA, and its genetic heterogeneity in the Pakistani population. The findings of the computational studies on protein structure and interaction profile predicted pathogenic consequences of p.Asp306Val on GUCY2D function.
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Affiliation(s)
- Hadia Gul
- Institute of Biological Sciences, Gomal University, D.I.Khan 29050, Khyber Pakhtunkhwa, Pakistan
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Muzammal M, Zubair M, Bierbaumer S, Blatterer J, Graf R, Gul A, Abbas S, Badar M, Abbasi AA, Khan MA, Windpassinger C. Exome sequence analysis in consanguineous Pakistani families inheriting Bardet-Biedle syndrome determined founder effect of mutation c.299delC (p.Ser100Leufs*24) in BBS9 gene. Mol Genet Genomic Med 2019; 7:e834. [PMID: 31294530 PMCID: PMC6687644 DOI: 10.1002/mgg3.834] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 05/11/2019] [Accepted: 05/22/2019] [Indexed: 12/29/2022] Open
Abstract
Background Bardet‐Biedl syndrome (BBS) is characterized by a heterogeneous phenotypic spectrum of retinopathy, intellectual disability (ID), obesity, polydactyly, and kidney dysfunctions as the major clinical features. Genetic investigations have reported 21 BBS genes, the products of which are mostly located at the centrosome, basal body or the ciliary transition zone. Methods In the present genetic report, we analyzed two apparently unrelated consanguineous BBS families from Dera Ismail Khan (D.I.Khan) district, Pakistan. Genetic mapping was performed using Whole exome sequencing and Sanger sequencing. Results Whole exome sequencing identified a recently reported single base deletion NM_001033604.1:c.299delC in the fourth exon of BBS9 in both families. The identified frameshift mutation is predicted to cause premature truncation of the expressed protein (p.Ser100Leufs*24). This mutation has previously been mapped in a consanguineous Pakistani family; therefore this is the second report of this particular mutation in two additional BBS families originating from different locations. Conclusion We speculate the evolutionary significance of this mutation and assume its strong founder effect in the Khaisoori tribe of D.I.Khan. Based on these findings, we suggest developing a molecular diagnostic test that may be used for premarital and prenatal screening of families at risk of BBS.
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Affiliation(s)
- Muhammad Muzammal
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan, Pakistan
| | - Muhammad Zubair
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan, Pakistan
| | - Sophie Bierbaumer
- Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Jasmin Blatterer
- Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Ricarda Graf
- Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Aisha Gul
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan, Pakistan
| | - Safdar Abbas
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan, Pakistan
| | - Muhammad Badar
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan, Pakistan
| | - Ansar Ahmad Abbasi
- Department of Zoology, Mirpur University of Science and Technology (MUST), Mirpur, Pakistan
| | - Muzammil Ahmad Khan
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan, Pakistan
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Mushtaq H, Khawaja SG, Akram MU, Yasin A, Muzammal M, Khalid S, Khan SA. A Parallel Architecture for the Partitioning Around Medoids (PAM) Algorithm for Scalable Multi-Core Processor Implementation with Applications in Healthcare. Sensors (Basel) 2018; 18:s18124129. [PMID: 30477277 PMCID: PMC6308709 DOI: 10.3390/s18124129] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 11/01/2018] [Accepted: 11/01/2018] [Indexed: 11/16/2022]
Abstract
Clustering is the most common method for organizing unlabeled data into its natural groups (called clusters), based on similarity (in some sense or another) among data objects. The Partitioning Around Medoids (PAM) algorithm belongs to the partitioning-based methods of clustering widely used for objects categorization, image analysis, bioinformatics and data compression, but due to its high time complexity, the PAM algorithm cannot be used with large datasets or in any embedded or real-time application. In this work, we propose a simple and scalable parallel architecture for the PAM algorithm to reduce its running time. This architecture can easily be implemented either on a multi-core processor system to deal with big data or on a reconfigurable hardware platform, such as FPGA and MPSoCs, which makes it suitable for real-time clustering applications. Our proposed model partitions data equally among multiple processing cores. Each core executes the same sequence of tasks simultaneously on its respective data subset and shares intermediate results with other cores to produce results. Experiments show that the computational complexity of the PAM algorithm is reduced exponentially as we increase the number of cores working in parallel. It is also observed that the speedup graph of our proposed model becomes more linear with the increase in number of data points and as the clusters become more uniform. The results also demonstrate that the proposed architecture produces the same results as the actual PAM algorithm, but with reduced computational complexity.
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Affiliation(s)
- Hassan Mushtaq
- Department of Electrical & Computer Engineering, Sir Syed CASE Institute of Technology, Islamabad 44000, Pakistan.
| | - Sajid Gul Khawaja
- Department of Computer & Software Engineering, CE&ME, National University of Sciences & Technology, Islamabad 44000, Pakistan.
| | - Muhammad Usman Akram
- Department of Computer & Software Engineering, CE&ME, National University of Sciences & Technology, Islamabad 44000, Pakistan.
| | - Amanullah Yasin
- Department of Electrical & Computer Engineering, Sir Syed CASE Institute of Technology, Islamabad 44000, Pakistan.
| | - Muhammad Muzammal
- Department of Computer Science, Bahria University, Islamabad 44000, Pakistan.
| | - Shehzad Khalid
- Department of Computer Engineering, Bahria University, Islamabad 44000, Pakistan.
| | - Shoab Ahmad Khan
- Department of Computer & Software Engineering, CE&ME, National University of Sciences & Technology, Islamabad 44000, Pakistan.
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