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Zafar R, Awais M. Molecular identification of missense variants in SLC3A1 gene; an approach leading to computer-aided drug design for cystinuria. Gene 2023; 888:147802. [PMID: 37716586 DOI: 10.1016/j.gene.2023.147802] [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: 07/09/2023] [Revised: 09/09/2023] [Accepted: 09/13/2023] [Indexed: 09/18/2023]
Abstract
Cystinuria is a rare congenital disorder characterized by the formation of cystine stones in urinary system, mainly kidneys and urinary tract. It follows the autosomal recessive inheritance pattern, where both of the parents contain the mutant allele. Cystine is an oxidized dimeric form of amino acid cysteine, shining crystal of greenish-yellow color sized greater than 5 mm. A minor genetic defect in SLC3A1 gene, downregulate the cystine transporter, rBAT protein, to absorb cystine and other dibasic amino acids in proximal tubule of nephron, causing Cystinuria. Computational and molecular analysis of SLC3A1 gene was performed to identify the deleterious missense single nucleotide variations (mSNVs) linked with Cystinuria in Pakistani population. In silico analysis of whole SLC3A1 gene nsSNPs has revealed that the exon 1, 6 and 10 are the hotspot areas, which potentially alter the protein structure and function. Three SNVs including one synonymous SNV A186C in exon 1, and two mSNVs including G314T in exon 1 and G44972A in exons 10 were identified. Both mSNVs were confirmed by ARMS PCR in all the 68 samples. The results have shown that 10% of the patients have G314T, 16% have G44972A and 74% of the patients have both of these mSNVs. Both of these mSNVs were involved in the structural and functional deterioration of rBAT protein. Additionally, computer aided drug designing tools were used to design diaminobenzylpyrimidine drug around the mutant residues which exhibit the lowest binding affinity with the target as compared to the previously reported cystine binding thiol drugs. In future, the present study could be extended to a large scale for mass screening of reported SNVs and mSNVs which, ultimately, lead to the development of knockouts for the functional studies and treatments.
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Affiliation(s)
- Rimsha Zafar
- Department of Biotechnology, Faculty of Science and Technology, University of Central Punjab, Lahore 54782, Pakistan.
| | - Muhammad Awais
- Department of Biotechnology, Faculty of Science and Technology, University of Central Punjab, Lahore 54782, Pakistan.
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Clinical Characteristics and In Silico Analysis of Cystinuria Caused by a Novel SLC3A1 Mutation. Genes (Basel) 2022; 13:genes13112173. [DOI: 10.3390/genes13112173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/27/2022] [Accepted: 11/17/2022] [Indexed: 11/23/2022] Open
Abstract
Cystinuria is a genetically inherited disorder of renal and intestinal transport, featured as a high concentration of cystine in the urine. Cumulative cystine in urine would cause the formation of kidney stones, which further leads to renal colic and dysfunction. Gene screens have found that mutations in SLC3A1 or SLC7A9 gene are responsible for most cases of cystinuria, for encoding defective cystine transporters. Here, we presented the genotypic and phenotypic characteristics of one unique case of a three-generation Chinese family. The proband developed severe urolithiasis combined with renal damage. The radiography and computed tomography (CT) scan showed calculus in the left pelvic kidney. Postoperative stone analysis revealed that the stones were mainly composed of cystine. Therefore, to explore its pathogenesis, next-generation Whole Exome Sequencing (WES) and Sanger sequencing identify the proband mutated gene of the proband’s family. In this article, we reported novel compound heterozygous mutations (c.818G>A and c.1011G>A) of the SLC3A1 gene in a 5-year-old child suffering from a cystine stone from a three-generation family. Bioinformatic analysis was used to predict the pathogenicity and conservation of the target mutation. Conservative sequence and evolutionary conservation analysis indicated that cystine273 and proline337 were highly conserved among species, and both mutations listed here (Cys273Tyr and Pro337Pro) were pathogenic. To conclude, our study expands the phenotypic and genotypic spectrum of SLC3A1 and indicates that genetic screening should be considered in the clinic to provide more effective and precise treatment for cystinuria.
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Fairweather SJ, Shah N, Brӧer S. Heteromeric Solute Carriers: Function, Structure, Pathology and Pharmacology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 21:13-127. [PMID: 33052588 DOI: 10.1007/5584_2020_584] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Solute carriers form one of three major superfamilies of membrane transporters in humans, and include uniporters, exchangers and symporters. Following several decades of molecular characterisation, multiple solute carriers that form obligatory heteromers with unrelated subunits are emerging as a distinctive principle of membrane transporter assembly. Here we comprehensively review experimentally established heteromeric solute carriers: SLC3-SLC7 amino acid exchangers, SLC16 monocarboxylate/H+ symporters and basigin/embigin, SLC4A1 (AE1) and glycophorin A exchanger, SLC51 heteromer Ost α-Ost β uniporter, and SLC6 heteromeric symporters. The review covers the history of the heteromer discovery, transporter physiology, structure, disease associations and pharmacology - all with a focus on the heteromeric assembly. The cellular locations, requirements for complex formation, and the functional role of dimerization are extensively detailed, including analysis of the first complete heteromer structures, the SLC7-SLC3 family transporters LAT1-4F2hc, b0,+AT-rBAT and the SLC6 family heteromer B0AT1-ACE2. We present a systematic analysis of the structural and functional aspects of heteromeric solute carriers and conclude with common principles of their functional roles and structural architecture.
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Affiliation(s)
- Stephen J Fairweather
- Research School of Biology, Australian National University, Canberra, ACT, Australia. .,Resarch School of Chemistry, Australian National University, Canberra, ACT, Australia.
| | - Nishank Shah
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Stefan Brӧer
- Research School of Biology, Australian National University, Canberra, ACT, Australia.
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Curi RA, Pereira GL, Alvarez MVN, Baldassini WA, Machado Neto OR, Chardulo LAL. Exome analysis and functional classification of identified variants in racing Quarter Horses. Anim Genet 2020; 51:716-721. [PMID: 32696541 DOI: 10.1111/age.12976] [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: 03/25/2020] [Revised: 04/27/2020] [Accepted: 06/15/2020] [Indexed: 11/26/2022]
Abstract
The main objectives of this study were to identify and functionally classify SNPs and indels by exome sequencing of animals of the racing line of Quarter Horses. Based on the individual genomic estimated breeding values (GEBVs) for maximum speed index (SImax) obtained for 349 animals, two groups of 20 extreme animals were formed. Of these individuals, 20 animals with high GEBVs for SImax and 19 with low GEBVs for SImax had their exons and 5' and 3' UTRs sequenced. Considering SNPs and indels, 105 182 variants were identified in the expressed regions of the Quarter Horse genome. Of these, 72 166 variants were already known and 33 016 are new variants and were deposited in a database. The analysis of the set of gene variants significantly related (Padjusted < 0.05) to extreme animals in conjunction with the predicted impact of the changes and the physiological role of protein product pointed to two candidate genes potentially related to racing performance: SLC3A1 on ECA15 and CCN6 on ECA10.
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Affiliation(s)
- R A Curi
- Department of Animal Breeding and Nutrition, College of Veterinary and Animal Science, São Paulo State University, Rubião Junior District, Botucatu, São Paulo, 18618-970, Brazil
| | - G L Pereira
- Department of Animal Breeding and Nutrition, College of Veterinary and Animal Science, São Paulo State University, Rubião Junior District, Botucatu, São Paulo, 18618-970, Brazil
| | - M V N Alvarez
- Department of Parasitology, Institute of Biosciences, São Paulo State University, Rubião Junior District, Botucatu, São Paulo, 18618-970, Brazil
| | - W A Baldassini
- Department of Animal Breeding and Nutrition, College of Veterinary and Animal Science, São Paulo State University, Rubião Junior District, Botucatu, São Paulo, 18618-970, Brazil
| | - O R Machado Neto
- Department of Animal Breeding and Nutrition, College of Veterinary and Animal Science, São Paulo State University, Rubião Junior District, Botucatu, São Paulo, 18618-970, Brazil
| | - L A L Chardulo
- Department of Animal Breeding and Nutrition, College of Veterinary and Animal Science, São Paulo State University, Rubião Junior District, Botucatu, São Paulo, 18618-970, Brazil
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Fu Y, Jia J, Yue L, Yang R, Guo Y, Ni X, Shi T. Systematically Analyzing the Pathogenic Variations for Acute Intermittent Porphyria. Front Pharmacol 2019; 10:1018. [PMID: 31572191 PMCID: PMC6753391 DOI: 10.3389/fphar.2019.01018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 08/09/2019] [Indexed: 12/18/2022] Open
Abstract
The rare autosomal dominant disorder acute intermittent porphyria (AIP) is caused by the deficient activity of hydroxymethylbilane synthase (HMBS). The symptoms of AIP are acute neurovisceral attacks which are induced by the dysfunction of heme biosynthesis. To better interpret the underlying mechanism of clinical phenotypes, we collected 117 HMBS gene mutations from reported individuals with AIP and evaluated the mutations' impacts on the corresponding protein structure and function. We found that several mutations with most severe clinical symptoms are located at dipyromethane cofactor (DPM) binding domain of HMBS. Mutations on these residues likely significantly influence the catalytic reaction. To infer new pathogenic mutations, we evaluated the pathogenicity for all the possible missense mutations of HMBS gene with different bioinformatic prediction algorithms, and identified 34 mutations with serious pathogenicity and low allele frequency. In addition, we found that gene PPARA may also play an important role in the mechanisms of AIP attacks. Our analysis about the distribution frequencies of the 23 variations revealed different distribution patterns among eight ethnic populations, which could help to explain the genetic basis that may contribute to population disparities in AIP prevalence. Our systematic analysis provides a better understanding for this disease and helps for the diagnosis and treatment of AIP.
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Affiliation(s)
- Yibao Fu
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Jinmeng Jia
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Lishu Yue
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Ruiying Yang
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Yongli Guo
- Big Data and Engineering Research Center, Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, MOE Key Laboratory of Major Diseases in Children, Beijing Children’s Hospital, National Center for Children’s Health, Beijing Pediatric Research Institute, Capital Medical University, Beijing, China
- Biobank for Clinical Data and Samples in Pediatrics, Beijing Children’s Hospital, National Center for Children’s Health, Beijing Pediatric Research Institute, Capital Medical University, Beijing, China
- Department of Otolaryngology, Head and Neck Surgery, Beijing Children’s Hospital, National Center for Children’s Health, Capital Medical University, Beijing, China
| | - Xin Ni
- Big Data and Engineering Research Center, Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, MOE Key Laboratory of Major Diseases in Children, Beijing Children’s Hospital, National Center for Children’s Health, Beijing Pediatric Research Institute, Capital Medical University, Beijing, China
- Biobank for Clinical Data and Samples in Pediatrics, Beijing Children’s Hospital, National Center for Children’s Health, Beijing Pediatric Research Institute, Capital Medical University, Beijing, China
- Department of Otolaryngology, Head and Neck Surgery, Beijing Children’s Hospital, National Center for Children’s Health, Capital Medical University, Beijing, China
| | - Tieliu Shi
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
- National Center for International Research of Biological Targeting Diagnosis and Therapy, Guangxi Key Laboratory of Biological Targeting Diagnosis and Therapy Research, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, China
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Reis ST, Leite KRM, Marchini GS, Guimarães RM, Viana NI, Pimenta RCA, Torricelli FC, Danilovic A, Vicentini FC, Nahas WC, Srougi M, Mazzucchi E. Polymorphism in the PBX1 gene is related to cystinuria in Brazilian families. J Cell Mol Med 2019; 23:1593-1597. [PMID: 30450686 PMCID: PMC6349145 DOI: 10.1111/jcmm.13981] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 10/02/2018] [Indexed: 11/27/2022] Open
Abstract
The aim of our study was to determine regions of loss of heterozygosity, copy number variation analysis, and single nucleotide polymorphisms (SNPs) in Brazilian patients with cystinuria. A linkage study was performed using DNA samples from six patients with cystinuria and six healthy individuals. Genotyping was done with the Genome-Wide Human SNP 6.0 arrays (Affymetrix, Inc., Santa Clara, CA, USA). For validation, SNPs were genotyped using a TaqMan® SNP Genotyping Assay Kit. The homozygote polymorphic genotype of SNP rs17383719 in the gene PBX1 was more frequent (P = 0.015) in cystinuric patients. The presence of the polymorphic allele for this SNP increased the chance of cystinuria by 3.0-fold (P = 0.036). Pre-B-cell leukaemia transcription factor 1 (PBX1) was overexpressed 3.3-fold in patients with cystinuria. However, when we compared the gene expression findings with the genotyping, patients with a polymorphic homozygote genotype had underexpression of PBX1, while patients with a heterozygote or wild-type homozygote genotype had overexpression of PBX1. There is a 3-fold increase in the risk of the development of cystinuria among individuals with this particular SNP in the PBX1 gene. We postulate that the presence of this SNP alters the expression of PBX1, thus affecting the renal absorption of cystine and other amino acids, predisposing to nephrolithiasis.
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Affiliation(s)
- Sabrina T. Reis
- Laboratory of Medical Investigation (LIM55)Division of UrologyUniversity of Sao Paulo Medical SchoolSao PauloBrazil
- Endourology and Stone Disease SectionDivision of UrologyUniversity of Sao Paulo Medical SchoolSao PauloBrazil
| | - Katia R. M. Leite
- Laboratory of Medical Investigation (LIM55)Division of UrologyUniversity of Sao Paulo Medical SchoolSao PauloBrazil
| | - Giovanni S. Marchini
- Endourology and Stone Disease SectionDivision of UrologyUniversity of Sao Paulo Medical SchoolSao PauloBrazil
| | - Ronaldo M. Guimarães
- Endourology and Stone Disease SectionDivision of UrologyUniversity of Sao Paulo Medical SchoolSao PauloBrazil
| | - Nayara I. Viana
- Laboratory of Medical Investigation (LIM55)Division of UrologyUniversity of Sao Paulo Medical SchoolSao PauloBrazil
| | - Ruan C. A. Pimenta
- Laboratory of Medical Investigation (LIM55)Division of UrologyUniversity of Sao Paulo Medical SchoolSao PauloBrazil
| | - Fabio C. Torricelli
- Endourology and Stone Disease SectionDivision of UrologyUniversity of Sao Paulo Medical SchoolSao PauloBrazil
| | - Alexandre Danilovic
- Endourology and Stone Disease SectionDivision of UrologyUniversity of Sao Paulo Medical SchoolSao PauloBrazil
| | - Fábio Carvalho Vicentini
- Endourology and Stone Disease SectionDivision of UrologyUniversity of Sao Paulo Medical SchoolSao PauloBrazil
| | - William Carlos Nahas
- Laboratory of Medical Investigation (LIM55)Division of UrologyUniversity of Sao Paulo Medical SchoolSao PauloBrazil
| | - Miguel Srougi
- Laboratory of Medical Investigation (LIM55)Division of UrologyUniversity of Sao Paulo Medical SchoolSao PauloBrazil
| | - Eduardo Mazzucchi
- Endourology and Stone Disease SectionDivision of UrologyUniversity of Sao Paulo Medical SchoolSao PauloBrazil
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Cystinuria: genetic aspects, mouse models, and a new approach to therapy. Urolithiasis 2018; 47:57-66. [PMID: 30515543 DOI: 10.1007/s00240-018-1101-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 11/27/2018] [Indexed: 01/07/2023]
Abstract
Cystinuria, a genetic disorder of cystine transport, is characterized by excessive excretion of cystine in the urine and recurrent cystine stones in the kidneys and, to a lesser extent, in the bladder. Males generally are more severely affected than females. The disorder may lead to chronic kidney disease in many patients. The cystine transporter (b0,+) is a heterodimer consisting of the rBAT (encoded by SLC3A1) and b0,+AT (encoded by SLC7A9) subunits joined by a disulfide bridge. The molecular basis of cystinuria is known in great detail, and this information is now being used to define genotype-phenotype correlations. Current treatments for cystinuria include increased fluid intake to increase cystine solubility and the administration of thiol drugs for more severe cases. These drugs, however, have poor patient compliance due to adverse effects. Thus, there is a need to reduce or eliminate the risks associated with therapy for cystinuria. Four mouse models for cystinuria have been described and these models provide a resource for evaluating the safety and efficacy of new therapies for cystinuria. We are evaluating a new approach for the treatment of cystine stones based on the inhibition of cystine crystal growth by cystine analogs. Our ongoing studies indicate that cystine diamides are effective in preventing cystine stone formation in the Slc3a1 knockout mouse model for cystinuria. In addition to crystal growth, crystal aggregation is required for stone formation. Male and female mice with cystinuria have comparable levels of crystalluria, but very few female mice form stones. The identification of factors that inhibit cystine crystal aggregation in female mice may provide insight into the gender difference in disease severity in patients with cystinuria.
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