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1.
PLoS Genet ; 14(3): e1007297, 2018 03.
Article in English | MEDLINE | ID: mdl-29590114

ABSTRACT

Autosomal recessive nonsyndromic hearing loss is a genetically heterogeneous disorder. Here, we report a severe-to-profound sensorineural hearing loss locus, DFNB100 on chromosome 5q13.2-q23.2. Exome enrichment followed by massive parallel sequencing revealed a c.2510G>A transition variant in PPIP5K2 that segregated with DFNB100-associated hearing loss in two large apparently unrelated Pakistani families. PPIP5Ks enzymes interconvert 5-IP7 and IP8, two key members of the inositol pyrophosphate (PP-IP) cell-signaling family. Their actions at the interface of cell signaling and bioenergetic homeostasis can impact many biological processes. The c.2510G>A transition variant is predicted to substitute a highly invariant arginine residue with histidine (p.Arg837His) in the phosphatase domain of PPIP5K2. Biochemical studies revealed that the p.Arg837His variant reduces the phosphatase activity of PPIP5K2 and elevates its kinase activity. We found that in mouse inner ear, PPIP5K2 is expressed in the cochlear and vestibular sensory hair cells, supporting cells and spiral ganglion neurons. Mice homozygous for a targeted deletion of the Ppip5k2 phosphatase domain exhibit degeneration of cochlear outer hair cells and elevated hearing thresholds. Our demonstration that PPIP5K2 has a role in hearing in humans indicates that PP-IP signaling is important to hair cell maintenance and function within inner ear.


Subject(s)
Hearing Loss, Sensorineural/genetics , Phosphotransferases (Phosphate Group Acceptor)/genetics , Animals , Chromosomes, Human, Pair 5 , Ear, Inner/physiopathology , Exome , Female , Genes, Recessive , Genetic Linkage , Hair Cells, Auditory, Inner , Homeostasis , Humans , Male , Mice , Pedigree , Point Mutation
2.
Hum Mutat ; 40(1): 53-72, 2019 01.
Article in English | MEDLINE | ID: mdl-30303587

ABSTRACT

Consanguineous Pakistani pedigrees segregating deafness have contributed decisively to the discovery of 31 of the 68 genes associated with nonsyndromic autosomal recessive hearing loss (HL) worldwide. In this study, we utilized genome-wide genotyping, Sanger and exome sequencing to identify 163 DNA variants in 41 previously reported HL genes segregating in 321 Pakistani families. Of these, 70 (42.9%) variants identified in 29 genes are novel. As expected from genetic studies of disorders segregating in consanguineous families, the majority of affected individuals (94.4%) are homozygous for HL-associated variants, with the other variants being compound heterozygotes. The five most common HL genes in the Pakistani population are SLC26A4, MYO7A, GJB2, CIB2 and HGF, respectively. Our study provides a profile of the genetic etiology of HL in Pakistani families, which will allow for the development of more efficient genetic diagnostic tools, aid in accurate genetic counseling, and guide application of future gene-based therapies. These findings are also valuable in interpreting pathogenicity of variants that are potentially associated with HL in individuals of all ancestries. The Pakistani population, and its infrastructure for studying human genetics, will continue to be valuable to gene discovery for HL and other inherited disorders.


Subject(s)
Chromosome Segregation/genetics , Consanguinity , Hearing Loss/genetics , Family , Female , Genes, Recessive , Genetic Predisposition to Disease , Humans , Male , Mutation/genetics , Pakistan , Pedigree
3.
Cell Biol Int ; 43(2): 147-157, 2019 Feb.
Article in English | MEDLINE | ID: mdl-30443955

ABSTRACT

Conventional approaches can repair minor skin injuries; however, severe burn injuries require innovative approaches for efficient and better wound repair. Recent studies indicate that stem cell-based regenerative therapies can restore severe damaged skin both structurally and functionally. The current study aims to evaluate the wound healing potential of skin substitute derived from human neonatal stem cells (hNSCs) using a severe burn injury rat model. Amniotic epithelial cells (AECs) and mesenchymal stem cells (MSCs) were isolated from placenta (a source of neonatal stem cells) by explant culture method. After characterization, AECs and umbilical cord-MSCs were differentiated into keratinocyte and fibroblasts, respectively. Morphological changes, and expression of corresponding keratinocyte and fibroblast specific markers were used to verify differentiation into respective lineage. A skin substitute was developed by mixing hNSCs-derived skin cells (hNSCs-SCs) in plasma for transplantation in a rat model of severe burn injury. Results indicated that placenta-derived AECs and MSCs were efficiently differentiated into skin cells, that is, keratinocytes and fibroblasts, respectively, as indicated by morphological changes, immunostaining, and polymerase chain reaction analysis. Further, transplantation of hNSCs-SCs seeded in plasma significantly improved basic skin architecture, re-epithelization rate, and wound healing concurrent with reduced apoptosis. In conclusion, neonatal stem cell-derived skin substitute efficiently improved severe burn wounds in a rat model of burn injury. Unique properties of placenta-derived stem cells make them superlative candidates for the development of "off-the-shelf" artificial skin substitutes for future use.


Subject(s)
Burns/therapy , Mesenchymal Stem Cell Transplantation , Stem Cell Transplantation , Amnion/cytology , Animals , Cell Differentiation , Collagen Type I/genetics , Collagen Type I/metabolism , Disease Models, Animal , Female , Fibroblasts/cytology , Fibroblasts/metabolism , Humans , Keratin-10/genetics , Keratin-10/metabolism , Mesenchymal Stem Cells/cytology , Proliferating Cell Nuclear Antigen/genetics , Proliferating Cell Nuclear Antigen/metabolism , Rats , Skin/pathology , Stem Cells/cytology , Umbilical Cord/cytology , Vascular Endothelial Growth Factor A/genetics , Vascular Endothelial Growth Factor A/metabolism , bcl-2-Associated X Protein/genetics , bcl-2-Associated X Protein/metabolism
4.
J Med Genet ; 55(7): 479-488, 2018 07.
Article in English | MEDLINE | ID: mdl-29572253

ABSTRACT

BACKGROUND: Usher syndrome (USH) is a neurosensory disorder characterised by deafness, variable vestibular areflexia and vision loss. The aim of the study was to identify the genetic defect in a Pakistani family (PKDF1051) segregating USH. METHODS: Genome-wide linkage analysis was performed by using an Illumina linkage array followed by Sanger and exome sequencing. Heterologous cells and mouse organ of Corti explant-based transfection assays were used for functional evaluations. Detailed clinical evaluations were performed to characterise the USH phenotype. RESULTS: Through homozygosity mapping, we genetically linked the USH phenotype segregating in family PKDF1051 to markers on chromosome 1p36.32-p36.22. The locus was designated USH1M. Using a combination of Sanger sequencing and exome sequencing, we identified a novel homozygous 18 base pair inframe deletion in ESPN. Variants of ESPN, encoding the actin-bundling protein espin, have been previously associated with deafness and vestibular areflexia in humans with no apparent visual deficits. Our functional studies in heterologous cells and in mouse organ of Corti explant cultures revealed that the six deleted residues in affected individuals of family PKDF1051 are essential for the actin bundling function of espin demonstrated by ultracentrifugation actin binding and bundling assays. Funduscopic examination of the affected individuals of family PKDF1051 revealed irregular retinal contour, temporal flecks and disc pallor in both eyes. ERG revealed diminished rod photoreceptor function among affected individuals. CONCLUSION: Our study uncovers an additional USH gene, assigns the USH1 phenotype to a variant of ESPN and provides a 12th molecular component to the USH proteome.


Subject(s)
Benign Paroxysmal Positional Vertigo/genetics , Deafness/genetics , Microfilament Proteins/genetics , Vision Disorders/genetics , Adult , Animals , Benign Paroxysmal Positional Vertigo/physiopathology , Deafness/physiopathology , Genetic Linkage/genetics , Genetic Predisposition to Disease , Genotype , Homozygote , Humans , Mice , Mutation , Pedigree , Phenotype , Retina/metabolism , Retina/physiopathology , Sequence Deletion/genetics , Vision Disorders/physiopathology , Exome Sequencing , Young Adult
5.
Adv Exp Med Biol ; 1074: 219-228, 2018.
Article in English | MEDLINE | ID: mdl-29721947

ABSTRACT

PURPOSE: To identify the molecular basis of inherited retinal degeneration (IRD) in a familial case of Pakistani origin using whole-exome sequencing. METHODS: A thorough ophthalmic examination was completed, and genomic DNA was extracted using standard protocols. Whole exome(s) were captured with Agilent V5 + UTRs probes and sequenced on Illumina HiSeq genome analyzer. The exomeSuite software was used to filter variants, and the candidate causal variants were prioritized, examining their allele frequency and PolyPhen2, SIFT, and MutationTaster predictions. Sanger dideoxy sequencing was performed to confirm the segregation with disease phenotype and absence in ethnicity-matched control chromosomes. RESULTS: Ophthalmic examination confirmed retinal degeneration in all affected individuals that segregated as an autosomal recessive trait in the family. Whole-exome sequencing identified two homozygous missense variants: c.1304G > A; p.Arg435Gln in ZNF408 (NM_024741) and c.902G > A; p.Gly301Asp in C1QTNF4 (NM_031909). Both variants segregated with the retinal phenotype in the PKRD320 and were absent in ethnically matched control chromosomes. CONCLUSION: Whole-exome sequencing coupled with bioinformatics analysis identified potential novel variants that might be responsible for IRD.


Subject(s)
DNA-Binding Proteins/genetics , Exome Sequencing , Genes, Recessive , Polymorphism, Single Nucleotide , Retinal Degeneration/genetics , Transcription Factors/genetics , Animals , Chromosomes, Human, Pair 11/genetics , Consanguinity , Conserved Sequence , DNA Mutational Analysis , DNA-Binding Proteins/chemistry , Genetic Linkage , Humans , INDEL Mutation , Pakistan , Pedigree , Sequence Alignment , Sequence Homology, Amino Acid , Species Specificity , Transcription Factors/chemistry
6.
PLoS Genet ; 11(3): e1005097, 2015 Mar.
Article in English | MEDLINE | ID: mdl-25807530

ABSTRACT

Here we demonstrate association of variants in the mitochondrial asparaginyl-tRNA synthetase NARS2 with human hearing loss and Leigh syndrome. A homozygous missense mutation ([c.637G>T; p.Val213Phe]) is the underlying cause of nonsyndromic hearing loss (DFNB94) and compound heterozygous mutations ([c.969T>A; p.Tyr323*] + [c.1142A>G; p.Asn381Ser]) result in mitochondrial respiratory chain deficiency and Leigh syndrome, which is a neurodegenerative disease characterized by symmetric, bilateral lesions in the basal ganglia, thalamus, and brain stem. The severity of the genetic lesions and their effects on NARS2 protein structure cosegregate with the phenotype. A hypothetical truncated NARS2 protein, secondary to the Leigh syndrome mutation p.Tyr323* is not detectable and p.Asn381Ser further decreases NARS2 protein levels in patient fibroblasts. p.Asn381Ser also disrupts dimerization of NARS2, while the hearing loss p.Val213Phe variant has no effect on NARS2 oligomerization. Additionally we demonstrate decreased steady-state levels of mt-tRNAAsn in fibroblasts from the Leigh syndrome patients. In these cells we show that a decrease in oxygen consumption rates (OCR) and electron transport chain (ETC) activity can be rescued by overexpression of wild type NARS2. However, overexpression of the hearing loss associated p.Val213Phe mutant protein in these fibroblasts cannot complement the OCR and ETC defects. Our findings establish lesions in NARS2 as a new cause for nonsyndromic hearing loss and Leigh syndrome.


Subject(s)
Aspartate-tRNA Ligase/genetics , Leigh Disease/genetics , RNA, Transfer, Amino Acyl/genetics , Adult , Amino Acid Sequence/genetics , Animals , Aspartate-tRNA Ligase/biosynthesis , Deafness/genetics , Deafness/pathology , Ear, Inner/metabolism , Ear, Inner/pathology , Female , Fibroblasts , Gene Expression/genetics , Genetic Predisposition to Disease , Humans , Leigh Disease/pathology , Male , Mice , Middle Aged , Mitochondria/genetics , Mitochondria/pathology , Mutation, Missense/genetics , Oxygen Consumption/genetics , Pedigree
7.
Growth Factors ; 35(2-3): 88-99, 2017 06.
Article in English | MEDLINE | ID: mdl-28835141

ABSTRACT

The defective insulin production is associated with severely reduced islet cell mass leading to diabetes. Growth factors preconditioned stem cells have arisen as an effective therapy to treat many diseases including diabetes. The current study was designed to assess the effect of pretreatment of ASCs derived IPCs with combination of stromal cell derived factor 1 alpha (SDF1α) and basic fibroblast growth factor (bFGF) in improving glucose tolerance in streptozotocin induced diabetic rats. The results showed maximally significant reduction in hyperglycaemia and fibrosis, while up-regulation of survival and pancreas-specific genes, insulin levels and homing of transplanted cells in SDF-1α + bFGF IPCs transplanted rats as compared with other groups. Moreover, increased expression of insulin, glucagon and Glut-2 in pancreas of the SDF-1α + bFGF IPCs transplanted group indicated more regeneration of pancreas. Hence, the use of IPCs preconditioned with SDF-1α + bFGF would be more effective for treating diabetes.


Subject(s)
Chemokine CXCL12/metabolism , Diabetes Mellitus, Experimental/therapy , Fibroblast Growth Factors/metabolism , Hyperglycemia/therapy , Islets of Langerhans Transplantation/methods , Animals , Blood Glucose/metabolism , Cells, Cultured , Chemokine CXCL12/genetics , Female , Fibroblast Growth Factors/genetics , Glucagon/metabolism , Insulin/blood , Insulin-Secreting Cells/metabolism , Male , Rats , Rats, Sprague-Dawley
8.
Growth Factors ; 35(4-5): 144-160, 2017 10.
Article in English | MEDLINE | ID: mdl-29110545

ABSTRACT

Cellular therapies hold promise to alleviate liver diseases. This study explored the potential of allogenic serum isolated from rat with acute CCl4 injury to differentiate adipose derived stem cells (ADSCs) towards hepatic lineage. Acute liver injury was induced by CCl4 which caused significant increase in serum levels of VEGF, SDF1α and EGF. ADSCs were preconditioned with 3% serum isolated from normal and acute liver injury models. ADSCs showed enhanced expression of hepatic markers (AFP, albumin, CK8 and CK19). These differentiated ADSCs were transplanted intra-hepatically in CCl4-induced liver fibrosis model. After one month of transplantation, fibrosis and liver functions (alkaline phosphatase, ALAT and bilirubin) showed marked improvement in acute injury group. Elevated expression of hepatic (AFP, albumin, CK 18 and HNF4a) and pro survival markers (PCNA and VEGF) and improvement in liver architecture as deduced from results of alpha smooth muscle actin, Sirius red and Masson's trichome staining was observed.


Subject(s)
Cell Differentiation , Chemokine CCL4/blood , Culture Media, Conditioned/pharmacology , Intercellular Signaling Peptides and Proteins/pharmacology , Liver Cirrhosis/therapy , Mesenchymal Stem Cell Transplantation/methods , Mesenchymal Stem Cells/cytology , Adipose Tissue/cytology , Animals , Chemokine CCL4/toxicity , Hepatocytes/cytology , Hepatocytes/drug effects , Intercellular Signaling Peptides and Proteins/metabolism , Liver Cirrhosis/etiology , Mesenchymal Stem Cells/drug effects , Rats , Rats, Sprague-Dawley
9.
Am J Hum Genet ; 94(1): 144-52, 2014 Jan 02.
Article in English | MEDLINE | ID: mdl-24387994

ABSTRACT

Inherited deafness is clinically and genetically heterogeneous. We recently mapped DFNB86, a locus associated with nonsyndromic deafness, to chromosome 16p. In this study, whole-exome sequencing was performed with genomic DNA from affected individuals from three large consanguineous families in which markers linked to DFNB86 segregate with profound deafness. Analyses of these data revealed homozygous mutation c.208G>T (p.Asp70Tyr) or c.878G>C (p.Arg293Pro) in TBC1D24 as the underlying cause of deafness in the three families. Sanger sequence analysis of TBC1D24 in an additional large family in which deafness segregates with DFNB86 identified the c.208G>T (p.Asp70Tyr) substitution. These mutations affect TBC1D24 amino acid residues that are conserved in orthologs ranging from fruit fly to human. Neither variant was observed in databases of single-nucleotide variants or in 634 chromosomes from ethnically matched control subjects. TBC1D24 in the mouse inner ear was immunolocalized predominantly to spiral ganglion neurons, indicating that DFNB86 deafness might be an auditory neuropathy spectrum disorder. Previously, six recessive mutations in TBC1D24 were reported to cause seizures (hearing loss was not reported) ranging in severity from epilepsy with otherwise normal development to epileptic encephalopathy resulting in childhood death. Two of our four families in which deafness segregates with mutant alleles of TBC1D24 were available for neurological examination. Cosegregation of epilepsy and deafness was not observed in these two families. Although the causal relationship between genotype and phenotype is not presently understood, our findings, combined with published data, indicate that recessive alleles of TBC1D24 can cause either epilepsy or nonsyndromic deafness.


Subject(s)
Carrier Proteins/genetics , Epilepsy/genetics , Mutation , Alleles , Amino Acid Sequence , Chromosomes, Human, Pair 16/genetics , Consanguinity , Deafness/genetics , Exome , Exons , Female , GTPase-Activating Proteins , Genes, Recessive , Genetic Loci , Genome-Wide Association Study , Heterozygote , Homozygote , Humans , Male , Membrane Proteins , Molecular Sequence Data , Nerve Tissue Proteins , Pakistan , Pedigree , Phenotype , Polymorphism, Single Nucleotide , RNA, Messenger/genetics , RNA, Messenger/metabolism , Sequence Analysis, DNA
10.
Hum Mutat ; 37(10): 991-1003, 2016 10.
Article in English | MEDLINE | ID: mdl-27375115

ABSTRACT

Deafness in humans is a common neurosensory disorder and is genetically heterogeneous. Across diverse ethnic groups, mutations of MYO15A at the DFNB3 locus appear to be the third or fourth most common cause of autosomal-recessive, nonsyndromic deafness. In 49 of the 67 exons of MYO15A, there are currently 192 recessive mutations identified, including 14 novel mutations reported here. These mutations are distributed uniformly across MYO15A with one enigmatic exception; the alternatively spliced giant exon 2, encoding 1,233 residues, has 17 truncating mutations but no convincing deafness-causing missense mutations. MYO15A encodes three distinct isoform classes, one of which is 395 kDa (3,530 residues), the largest member of the myosin superfamily of molecular motors. Studies of Myo15 mouse models that recapitulate DFNB3 revealed two different pathogenic mechanisms of hearing loss. In the inner ear, myosin 15 is necessary both for the development and the long-term maintenance of stereocilia, mechanosensory sound-transducing organelles that extend from the apical surface of hair cells. The goal of this Mutation Update is to provide a comprehensive review of mutations and functions of MYO15A.


Subject(s)
Deafness/genetics , Deafness/pathology , Mutation , Myosins/genetics , Myosins/metabolism , Alternative Splicing , Animals , Deafness/metabolism , Disease Models, Animal , Ear, Inner/growth & development , Ear, Inner/metabolism , Ear, Inner/pathology , Exons , Gene Expression Regulation, Developmental , Humans , Mice , Stereocilia/metabolism , Stereocilia/pathology
11.
Am J Hum Genet ; 92(4): 605-13, 2013 Apr 04.
Article in English | MEDLINE | ID: mdl-23541340

ABSTRACT

Perrault syndrome is a genetically and clinically heterogeneous autosomal-recessive condition characterized by sensorineural hearing loss and ovarian failure. By a combination of linkage analysis, homozygosity mapping, and exome sequencing in three families, we identified mutations in CLPP as the likely cause of this phenotype. In each family, affected individuals were homozygous for a different pathogenic CLPP allele: c.433A>C (p.Thr145Pro), c.440G>C (p.Cys147Ser), or an experimentally demonstrated splice-donor-site mutation, c.270+4A>G. CLPP, a component of a mitochondrial ATP-dependent proteolytic complex, is a highly conserved endopeptidase encoded by CLPP and forms an element of the evolutionarily ancient mitochondrial unfolded-protein response (UPR(mt)) stress signaling pathway. Crystal-structure modeling suggests that both substitutions would alter the structure of the CLPP barrel chamber that captures unfolded proteins and exposes them to proteolysis. Together with the previous identification of mutations in HARS2, encoding mitochondrial histidyl-tRNA synthetase, mutations in CLPP expose dysfunction of mitochondrial protein homeostasis as a cause of Perrault syndrome.


Subject(s)
ATP-Dependent Proteases/genetics , Endopeptidase Clp/genetics , Exome/genetics , Genes, Recessive , Gonadal Dysgenesis, 46,XX/etiology , Hearing Loss, Sensorineural/etiology , Mitochondria/enzymology , Mutation/genetics , ATP-Dependent Proteases/metabolism , Adenosine Triphosphate/metabolism , Adolescent , Adult , Female , Homozygote , Humans , In Situ Hybridization , Male , Mitochondria/genetics , Pedigree , Phenotype , Young Adult
12.
Mol Vis ; 22: 797-815, 2016.
Article in English | MEDLINE | ID: mdl-27440997

ABSTRACT

PURPOSE: To identify pathogenic mutations responsible for autosomal recessive retinitis pigmentosa (arRP) in consanguineous familial cases. METHODS: Seven large familial cases with multiple individuals diagnosed with retinitis pigmentosa were included in the study. Affected individuals in these families underwent ophthalmic examinations to document the symptoms and confirm the initial diagnosis. Blood samples were collected from all participating members, and genomic DNA was extracted. An exclusion analysis with microsatellite markers spanning the TULP1 locus on chromosome 6p was performed, and two-point logarithm of odds (LOD) scores were calculated. All coding exons along with the exon-intron boundaries of TULP1 were sequenced bidirectionally. We constructed a single nucleotide polymorphism (SNP) haplotype for the four familial cases harboring the K489R allele and estimated the likelihood of a founder effect. RESULTS: The ophthalmic examinations of the affected individuals in these familial cases were suggestive of RP. Exclusion analyses confirmed linkage to chromosome 6p harboring TULP1 with positive two-point LOD scores. Subsequent Sanger sequencing identified the single base pair substitution in exon14, c.1466A>G (p.K489R), in four families. Additionally, we identified a two-base deletion in exon 4, c.286_287delGA (p.E96Gfs77*); a homozygous splice site variant in intron 14, c.1495+4A>C; and a novel missense variation in exon 15, c.1561C>T (p.P521S). All mutations segregated with the disease phenotype in the respective families and were absent in ethnically matched control chromosomes. Haplotype analysis suggested (p<10(-6)) that affected individuals inherited the causal mutation from a common ancestor. CONCLUSIONS: Pathogenic mutations in TULP1 are responsible for the RP phenotype in seven familial cases with a common ancestral mutation responsible for the disease phenotype in four of the seven families.


Subject(s)
Consanguinity , Eye Proteins/genetics , Mutation/genetics , Retinitis Pigmentosa/genetics , Adolescent , Adult , Alleles , Base Sequence , Child , Chromosomes, Human, Pair 6/genetics , Computer Simulation , Conserved Sequence/genetics , DNA Mutational Analysis , Family , Female , Genetic Markers , Haplotypes/genetics , Humans , Lod Score , Male , Microsatellite Repeats/genetics , Middle Aged , Pedigree , Polymorphism, Single Nucleotide/genetics , RNA Splice Sites/genetics , Young Adult
13.
Mol Vis ; 22: 610-25, 2016.
Article in English | MEDLINE | ID: mdl-27307693

ABSTRACT

PURPOSE: This study was undertaken to identify causal mutations responsible for autosomal recessive retinitis pigmentosa (arRP) in consanguineous families. METHODS: Large consanguineous families were ascertained from the Punjab province of Pakistan. An ophthalmic examination consisting of a fundus evaluation and electroretinography (ERG) was completed, and small aliquots of blood were collected from all participating individuals. Genomic DNA was extracted from white blood cells, and a genome-wide linkage or a locus-specific exclusion analysis was completed with polymorphic short tandem repeats (STRs). Two-point logarithm of odds (LOD) scores were calculated, and all coding exons and exon-intron boundaries of RP1 were sequenced to identify the causal mutation. RESULTS: The ophthalmic examination showed that affected individuals in all families manifest cardinal symptoms of RP. Genome-wide scans localized the disease phenotype to chromosome 8q, a region harboring RP1, a gene previously implicated in the pathogenesis of RP. Sanger sequencing identified a homozygous single base deletion in exon 4: c.3697delT (p.S1233Pfs22*), a single base substitution in intron 3: c.787+1G>A (p.I263Nfs8*), a 2 bp duplication in exon 2: c.551_552dupTA (p.Q185Yfs4*) and an 11,117 bp deletion that removes all three coding exons of RP1. These variations segregated with the disease phenotype within the respective families and were not present in ethnically matched control samples. CONCLUSIONS: These results strongly suggest that these mutations in RP1 are responsible for the retinal phenotype in affected individuals of all four consanguineous families.


Subject(s)
Eye Proteins/genetics , Loss of Function Mutation , Retinitis Pigmentosa/genetics , Base Sequence , Consanguinity , DNA Mutational Analysis , Electroretinography , Exons , Female , Genetic Linkage , Genome-Wide Association Study , Humans , Lod Score , Male , Microtubule-Associated Proteins , Mutation , Pedigree , Polymerase Chain Reaction , Retinitis Pigmentosa/diagnosis , Young Adult
14.
Cell Biol Int ; 40(5): 579-88, 2016 May.
Article in English | MEDLINE | ID: mdl-26888708

ABSTRACT

Transplantation of mesenchymal stem cells (MSCs) or autologous chondrocytes has been shown to repair damages to articular cartilage due to osteoarthritis (OA). However, survival of transplanted cells is considerably reduced in the osteoarthritic environment and it affects successful outcome of the transplantation of the cells. Differentiated chrondroytes derived from adipose stem cells have been proposed as an alternative source and our study investigated this possibility in rats. We investigated the regenerative potential of ADSCs and DCs in osteoarthritic environment in the repair of cartilage in rats. We found that ADSCs maintained fibroblast morphology in vitro and also expressed CD90 and CD29. Furthermore, ADSCs differentiated into chondrocytes, accompanied by increased level of proteoglycans and expression of chondrocytes specific genes, such as, Acan, and Col2a1. Histological examination of transplanted knee joints showed regeneration of cartilage tissue compared to control OA knee joints. Increase in gene expression for Acan, Col2a1 with concomitant decrease in the expression of Col1a1 suggested formation of hyaline like cartilage. A significant increase in differentiation index was observed in DCs and ADSCs transplanted knee joints (P = 0.0110 vs. P = 0.0429) when compared to that in OA control knee joints. Furthermore, transplanted DCs showed increased proliferation along with reduction in apoptosis as compared to untreated control. In conclusion, DCs showed better survival and regeneration potential as compared with ADSCs in rat model of OA and thus may serve a better option for regeneration of osteoarthritic cartilage.


Subject(s)
Adipocytes/transplantation , Chondrocytes/physiology , Mesenchymal Stem Cell Transplantation/methods , Osteoarthritis, Knee/therapy , Regeneration/physiology , Adipocytes/metabolism , Adipocytes/physiology , Animals , Cartilage, Articular/metabolism , Cell Differentiation/physiology , Cells, Cultured , Chondrocytes/metabolism , Chondrogenesis , Disease Models, Animal , Female , Mesenchymal Stem Cells/cytology , Osteoarthritis, Knee/pathology , Proteoglycans/metabolism , Rats , Rats, Sprague-Dawley
15.
PLoS Genet ; 9(9): e1003774, 2013.
Article in English | MEDLINE | ID: mdl-24039609

ABSTRACT

Exome sequencing coupled with homozygosity mapping was used to identify a transition mutation (c.794T>C; p.Leu265Ser) in ELMOD3 at the DFNB88 locus that is associated with nonsyndromic deafness in a large Pakistani family, PKDF468. The affected individuals of this family exhibited pre-lingual, severe-to-profound degrees of mixed hearing loss. ELMOD3 belongs to the engulfment and cell motility (ELMO) family, which consists of six paralogs in mammals. Several members of the ELMO family have been shown to regulate a subset of GTPases within the Ras superfamily. However, ELMOD3 is a largely uncharacterized protein that has no previously known biochemical activities. We found that in rodents, within the sensory epithelia of the inner ear, ELMOD3 appears most pronounced in the stereocilia of cochlear hair cells. Fluorescently tagged ELMOD3 co-localized with the actin cytoskeleton in MDCK cells and actin-based microvilli of LLC-PK1-CL4 epithelial cells. The p.Leu265Ser mutation in the ELMO domain impaired each of these activities. Super-resolution imaging revealed instances of close association of ELMOD3 with actin at the plasma membrane of MDCK cells. Furthermore, recombinant human GST-ELMOD3 exhibited GTPase activating protein (GAP) activity against the Arl2 GTPase, which was completely abolished by the p.Leu265Ser mutation. Collectively, our data provide the first insights into the expression and biochemical properties of ELMOD3 and highlight its functional links to sound perception and actin cytoskeleton.


Subject(s)
Ear, Inner/metabolism , GTP-Binding Proteins/genetics , GTPase-Activating Proteins/genetics , Hearing Loss/genetics , Actin Cytoskeleton/genetics , Actin Cytoskeleton/metabolism , Animals , Cell Membrane/genetics , Cell Movement/genetics , Ear, Inner/pathology , GTP-Binding Proteins/metabolism , HEK293 Cells , Hair Cells, Auditory/metabolism , Humans , Mice , Mutation/genetics
16.
Hum Genet ; 134(4): 423-37, 2015 Apr.
Article in English | MEDLINE | ID: mdl-25666562

ABSTRACT

Pathogenic mutations of MARVELD2, encoding tricellulin, a tricelluar tight junction protein, cause autosomal recessive non-syndromic hearing loss (DFNB49) in families of Pakistan and Czech Roma origin. In fact, they are a significant cause of prelingual hearing loss in the Czech Roma, second only to GJB2 variants. Previously, we reported that mice homozygous for p.Arg497* variant of Marveld2 had a broad phenotypic spectrum, where defects were observed in the inner ear, heart, mandibular salivary gland, thyroid gland and olfactory epithelium. The current study describes the types and frequencies of MARVELD2 alleles and clinically reexamines members of DFNB49 families. We found that MARVELD2 variants are responsible for about 1.5 % (95 % CI 0.8-2.6) of non-syndromic hearing loss in our cohort of 800 Pakistani families. The c.1331+2T>C allele is recurrent. In addition, we identified a novel large deletion in a single family, which appears to have resulted from non-allelic homologous recombination between two similar Alu short interspersed elements. Finally, we observed no other clinical manifestations co-segregating with hearing loss in DFNB49 human families, and hypothesize that the additional abnormalities in the Marveld2 mutant mouse indicates a critical non-redundant function for tricellulin in other organ systems.


Subject(s)
Hearing Loss, Sensorineural/genetics , MARVEL Domain Containing 2 Protein/genetics , Adolescent , Animals , Cells, Cultured , Child , Connexin 26 , Connexins , DNA Mutational Analysis , Dogs , Female , Genetic Association Studies , Genetic Predisposition to Disease , Humans , Male , Pakistan , Pedigree , Phenotype , Polymorphism, Single Nucleotide , Slovakia
17.
Mol Vis ; 21: 871-82, 2015.
Article in English | MEDLINE | ID: mdl-26321862

ABSTRACT

PURPOSE: This study was conducted to localize and identify causal mutations associated with autosomal recessive retinitis pigmentosa (RP) in consanguineous familial cases of Pakistani origin. METHODS: Ophthalmic examinations that included funduscopy and electroretinography (ERG) were performed to confirm the affectation status. Blood samples were collected from all participating individuals, and genomic DNA was extracted. A genome-wide scan was performed, and two-point logarithm of odds (LOD) scores were calculated. Sanger sequencing was performed to identify the causative variants. Subsequently, we performed whole exome sequencing to rule out the possibility of a second causal variant within the linkage interval. Sequence conservation was performed with alignment analyses of PDE6A orthologs, and in silico splicing analysis was completed with Human Splicing Finder version 2.4.1. RESULTS: A large multigenerational consanguineous family diagnosed with early-onset RP was ascertained. An ophthalmic clinical examination consisting of fundus photography and electroretinography confirmed the diagnosis of RP. A genome-wide scan was performed, and suggestive two-point LOD scores were observed with markers on chromosome 5q. Haplotype analyses identified the region; however, the region did not segregate with the disease phenotype in the family. Subsequently, we performed a second genome-wide scan that excluded the entire genome except the chromosome 5q region harboring PDE6A. Next-generation whole exome sequencing identified a splice acceptor site mutation in intron 16: c.2028-1G>A, which was completely conserved in PDE6A orthologs and was absent in ethnically matched 350 control chromosomes, the 1000 Genomes database, and the NHLBI Exome Sequencing Project. Subsequently, we investigated our entire cohort of RP familial cases and identified a second family who harbored a splice acceptor site mutation in intron 10: c.1408-2A>G. In silico analysis suggested that these mutations will result in the elimination of wild-type splice acceptor sites that would result in either skipping of the respective exon or the creation of a new cryptic splice acceptor site; both possibilities would result in retinal photoreceptor cells that lack PDE6A wild-type protein. CONCLUSIONS: we report two splice acceptor site variations in PDE6A in consanguineous Pakistani families who manifested cardinal symptoms of RP. Taken together with our previously published work, our data suggest that mutations in PDE6A account for about 2% of the total genetic load of RP in our cohort and possibly in the Pakistani population as well.


Subject(s)
Cyclic Nucleotide Phosphodiesterases, Type 6/genetics , Eye Proteins/genetics , Mutation , Retinitis Pigmentosa/genetics , Adult , Chromosomes, Human, Pair 5/genetics , Consanguinity , DNA Mutational Analysis , Female , Genes, Recessive , Genetic Markers , Humans , Lod Score , Male , Middle Aged , Pakistan , Pedigree , RNA Splice Sites , Retinitis Pigmentosa/pathology , Retinitis Pigmentosa/physiopathology , Young Adult
18.
Mol Vis ; 21: 1261-71, 2015.
Article in English | MEDLINE | ID: mdl-26628857

ABSTRACT

PURPOSE: This study was undertaken to investigate the causal mutations responsible for autosomal recessive congenital stationary night blindness (CSNB) in consanguineous Pakistani families. METHODS: Two consanguineous families with multiple individuals manifesting symptoms of stationary night blindness were recruited. Affected individuals underwent a detailed ophthalmological examination, including fundus examination and electroretinography. Blood samples were collected and genomic DNA was extracted. Exclusion analyses were completed by genotyping closely spaced microsatellite markers, and two-point logarithm of odds (LOD) scores were calculated. All coding exons, along with the exon-intron boundaries of GRM6, were sequenced bidirectionally. RESULTS: According to the medical history available to us, affected individuals in both families had experienced night blindness from the early years of their lives. Fundus photographs of affected individuals in both the families appeared normal, with no signs of attenuated arteries or bone spicule pigmentation. The scotopic electroretinogram (ERG) response were absent in all of the affected individuals, while the photopic measurements show reduced b-waves. During exclusion analyses, both families localized to a region on chromosome 5q that harbors GRM6, a gene previously associated with autosomal recessive CSNB. Bidirectional sequencing of GRM6 identified homozygous single base pair changes, specifically c.1336C>T (p.R446X) and c.2267G>A (p.G756D) in families PKRP170 and PKRP172, respectively. CONCLUSIONS: We identified a novel nonsense and a previously reported missense mutation in GRM6 that were responsible for autosomal recessive CSNB in patients of Pakistani decent.


Subject(s)
Chromosomes, Human, Pair 5 , Consanguinity , Eye Diseases, Hereditary/genetics , Genetic Diseases, X-Linked/genetics , Mutation , Myopia/genetics , Night Blindness/genetics , Receptors, Glutamate/genetics , Adult , Aged , Amino Acid Sequence , Animals , Base Sequence , Electroretinography , Exons , Eye Diseases, Hereditary/pathology , Female , Gene Expression , Genes, Recessive , Genetic Diseases, X-Linked/pathology , Homozygote , Humans , Male , Molecular Sequence Data , Myopia/pathology , Night Blindness/pathology , Pakistan , Pedigree , Sequence Alignment , Sequence Analysis, DNA
19.
Mol Cell Biochem ; 410(1-2): 267-79, 2015 Dec.
Article in English | MEDLINE | ID: mdl-26359087

ABSTRACT

Type 1 diabetes mellitus (DM) is a strong risk factor for the development of diabetic cardiomyopathy (DCM) which is the leading cause of morbidity and mortality in the type 1 diabetic patients. Stem cells may act as a therapeutic agent for the repair of DCM. However, deteriorated functional abilities and survival of stem cells derived from type 1 diabetic subjects need to be overcome for obtaining potential outcome of the stem cell therapy. Diazoxide (DZ) a highly selective mitochondrial ATP-sensitive K(+) channel opener has been previously shown to improve the ability of mesenchymal stem cells for the repair of heart failure. In the present study, we evaluated the effects of DZ preconditioning in improving the ability of streptozotocin-induced type 1 diabetes affected bone marrow-derived endothelial progenitor cells (DM-EPCs) for the repair of DCM in the type 1 diabetic rats. DM-EPCs were characterized by immunocytochemistry, flow cytometry, and reverse transcriptase PCR for endothelial cell-specific markers like vWF, VE cadherin, VEGFR2, PECAM, CD34, and eNOS. In vitro studies included preconditioning of DM-EPCs with 200 µM DZ for 30 min followed by exposure to either 200 µM H2O2 for 2 h (for oxidative stress induction) or 30 mM glucose media (for induction of hyperglycemic stress) for 48 h. Non-preconditioned EPCs with and without exposure to H2O2 and 30 mM high glucose served as controls. These cells were then evaluated for survival (by MTT and XTT cell viability assays), senescence, paracrine potential (by ELISA for VEGF), and alteration in gene expression [VEGF, stromal derived factor-1α (SDF-1α), HGF, bFGF, Bcl2, and Caspase-3]. DZ preconditioned DM-EPCs demonstrated significantly increased survival and VEGF release while reduced cell injury and senescence. Furthermore, DZ preconditioned DM-EPCs exhibited up-regulated expression of prosurvival genes (VEGF, SDF-1α, HGF, bFGF, and Bcl2) on exposure to H2O2, and VEGF and Bcl2 on exposure to hyperglycemia while down regulation of Caspase-3 gene. Eight weeks after type 1 diabetes induction, DZ preconditioned, and non-preconditioned DM-EPCs were transplanted into left ventricle of diabetic rats (at a dose of 2 × 10(6) DM-EPCs/70 µl serum free medium). After 4 weeks, DZ preconditioned DM-EPCs transplantation improved cardiac function as assessed by Millar's apparatus. There was decrease in collagen content estimated by Masson's trichrome and sirius red staining. Furthermore, reduced cell injury was observed as evidenced by decreased expression of Caspase-3 and increased expression of prosurvival genes Bcl2, VEGF, and bFGF by semi-quantitative real-time PCR. In conclusion, the present study demonstrated that DZ preconditioning enhanced EPCs survival under oxidative and hyperglycemic stress and their ability to treat DCM.


Subject(s)
Diabetes Mellitus, Experimental/metabolism , Diabetes Mellitus, Type 1/metabolism , Diabetic Cardiomyopathies/surgery , Diazoxide/pharmacology , Endothelial Progenitor Cells/drug effects , Endothelial Progenitor Cells/transplantation , Myocardium/metabolism , Streptozocin , Animals , Apoptosis/drug effects , Apoptosis Regulatory Proteins/metabolism , Biomarkers/metabolism , Blood Glucose/metabolism , Cell Proliferation/drug effects , Cell Survival/drug effects , Cells, Cultured , Cellular Senescence/drug effects , Diabetes Mellitus, Experimental/blood , Diabetes Mellitus, Experimental/chemically induced , Diabetes Mellitus, Experimental/genetics , Diabetes Mellitus, Experimental/pathology , Diabetes Mellitus, Type 1/blood , Diabetes Mellitus, Type 1/chemically induced , Diabetes Mellitus, Type 1/genetics , Diabetes Mellitus, Type 1/pathology , Diabetic Cardiomyopathies/chemically induced , Diabetic Cardiomyopathies/genetics , Diabetic Cardiomyopathies/metabolism , Diabetic Cardiomyopathies/pathology , Diabetic Cardiomyopathies/physiopathology , Dose-Response Relationship, Drug , Endothelial Progenitor Cells/metabolism , Endothelial Progenitor Cells/pathology , Fibrosis , Gene Expression Regulation , Hydrogen Peroxide/pharmacology , Myocardium/pathology , Neovascularization, Physiologic/drug effects , Oxidative Stress/drug effects , Phenotype , Rats, Wistar , Recovery of Function , Time Factors , Vascular Endothelial Growth Factor A/metabolism , Ventricular Function, Left/drug effects
20.
Cell Biol Int ; 39(11): 1251-63, 2015 Nov.
Article in English | MEDLINE | ID: mdl-26032287

ABSTRACT

Reduced survival and homing of the transplanted cells in the oxidative stressed ischemic environment limits the potential outcome of cell therapies for myocardial ischemia. Diazoxide (DZ), a highly selective mitochondrial ATP sensitive K(+) channel opener, is known to improve the survival and therapeutic ability of mesenchymal stem cells and skeletal myoblasts for the repair of heart failure. The current study explored the effect of DZ preconditioning in improving the ability of endothelial progenitor cells (EPCs) to counteract, in vitro oxidative stress, and to repair the infarcted myocardium. The EPCs were preconditioned by 30 min incubation with 200 µM DZ followed by exposure to 200 µM hydrogen peroxide (H2 O2 ) for 2 h. Non-preconditioned EPCs with and without exposure to H2 O2 were used as control. DZ preconditioning of EPCs resulted in significantly reduced cell injury as shown by reduced lactate dehydrogenase release and expression of annexin V-PE in comparison to untreated EPCs. Furthermore, DZ preconditioned EPCs exhibited upregulated expression of prosurvival genes (VEGF, SDF-1α, PCNA, and Bcl2 ), improved chemokines release (VEGF, IGF, and SDF-1α), viability, Akt phosphorylation and tube formation. In vivo experiments involved transplantation of DZ preconditioned and untreated EPCs in the left ventricle after permanent ligation of left anterior descending coronary artery in rats. The results demonstrated that DZ EPCs transplanted group showed significant reduction in infarct size along with robust cell proliferation, angiogenesis and improvement in cardiac function. The current study demonstrates that DZ preconditioning enhances EPCs survival under oxidative stress in vitro and their ability to treat myocardial infarction.


Subject(s)
Diazoxide/pharmacology , Endothelial Progenitor Cells/drug effects , Endothelial Progenitor Cells/transplantation , Mesenchymal Stem Cell Transplantation/methods , Myocardial Infarction/therapy , Transplantation Conditioning/methods , Animals , Apoptosis/drug effects , Cell Culture Techniques , Cell Survival/drug effects , Chemokine CXCL12/metabolism , Endothelial Progenitor Cells/cytology , Insulin-Like Growth Factor I/metabolism , Male , Mesenchymal Stem Cells/cytology , Mesenchymal Stem Cells/drug effects , Myocardial Infarction/metabolism , Myocardial Infarction/pathology , Myocardium/metabolism , Neovascularization, Physiologic/drug effects , Oxidative Stress/physiology , Rats , Rats, Wistar , Vascular Endothelial Growth Factor A/metabolism
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