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1.
PLoS Genet ; 15(2): e1007964, 2019 02.
Article in English | MEDLINE | ID: mdl-30817801

ABSTRACT

Transmission ratio distortion (TRD) by the mouse t-haplotype, a variant region on chromosome 17, is a well-studied model of non-Mendelian inheritance. It is characterized by the high transmission ratio (up to 99%) of the t-haplotype from t/+ males to their offspring. TRD is achieved by the exquisite ability of the responder (Tcr) to trigger non-Mendelian inheritance of homologous chromosomes. Several distorters (Tcd1-Tcd4), which act cumulatively, together promote the high transmission ratio of Tcr and the t-haplotype. Molecularly, TRD is brought about by deregulation of Rho signaling pathways via the distorter products, which impair sperm motility, and the t-sperm specific rescue of sperm motility by the responder. The t-sperm thus can reach the egg cells faster than +-sperm and fertilize them. Previously we have shown that the responder function is accomplished by a dominant negative form of sperm motility kinase (SMOKTCR), while the distorter functions are accomplished by the Rho G protein regulators TAGAP, FGD2 and NME3 proposed to function in two oppositely acting pathways. Here we identify the RAC1-specific guanine nucleotide exchange factor TIAM2 as modifier of t-haplotype TRD. Tiam2 is expressed in two isoforms, the full-length (Tiam2l) and a short transcript (Tiam2s). Tiam2s expression from the t-allele is strongly increased compared to the wild-type allele. By transgenic approaches we show that Tiam2s enhances t-haplotype transmission, while Tiam2l has the opposite effect. Our data show that a single modifier locus can encode different gene products exerting opposite effects on a trait. They also suggest that the expression ratio of the isoforms determines if the outcome is an enhancing or a suppressive effect on the trait.


Subject(s)
Guanine Nucleotide Exchange Factors/genetics , Guanine Nucleotide Exchange Factors/metabolism , Inheritance Patterns , t-Complex Genome Region , Alleles , Animals , Female , Gene Expression Regulation, Developmental , Guanine Nucleotide Exchange Factors/deficiency , Male , Mice , Mice, Inbred C57BL , Mice, Knockout , Mice, Transgenic , Models, Genetic , Paternal Inheritance , Protein Isoforms/genetics , Protein Isoforms/metabolism , Sperm Motility/genetics , Sperm Motility/physiology , Spermatogenesis/genetics
2.
Mol Psychiatry ; 24(7): 1027-1039, 2019 07.
Article in English | MEDLINE | ID: mdl-29302074

ABSTRACT

Autosomal recessive (AR) gene defects are the leading genetic cause of intellectual disability (ID) in countries with frequent parental consanguinity, which account for about 1/7th of the world population. Yet, compared to autosomal dominant de novo mutations, which are the predominant cause of ID in Western countries, the identification of AR-ID genes has lagged behind. Here, we report on whole exome and whole genome sequencing in 404 consanguineous predominantly Iranian families with two or more affected offspring. In 219 of these, we found likely causative variants, involving 77 known and 77 novel AR-ID (candidate) genes, 21 X-linked genes, as well as 9 genes previously implicated in diseases other than ID. This study, the largest of its kind published to date, illustrates that high-throughput DNA sequencing in consanguineous families is a superior strategy for elucidating the thousands of hitherto unknown gene defects underlying AR-ID, and it sheds light on their prevalence.


Subject(s)
Genes, Recessive/genetics , Intellectual Disability/genetics , Adult , Consanguinity , Exome/genetics , Family , Female , High-Throughput Nucleotide Sequencing/methods , Homozygote , Humans , Iran , Male , Middle Aged , Mutation/genetics , Pedigree , Protein Interaction Maps/genetics , Exome Sequencing/methods , Whole Genome Sequencing/methods
3.
Clin Genet ; 95(1): 151-159, 2019 01.
Article in English | MEDLINE | ID: mdl-30315573

ABSTRACT

In outbred Western populations, most individuals with intellectual disability (ID) are sporadic cases, dominant de novo mutations (DNM) are frequent, and autosomal recessive ID (ARID) is very rare. Because of the high rate of parental consanguinity, which raises the risk for ARID and other recessive disorders, the prevalence of ID is significantly higher in near- and middle-east countries. Indeed, homozygosity mapping and sequencing in consanguineous families have already identified a plethora of ARID genes, but because of the design of these studies, DNMs could not be systematically assessed, and the proportion of cases that are potentially preventable by avoiding consanguineous marriages or through carrier testing is hitherto unknown. This prompted us to perform whole-exome sequencing in 100 sporadic ID patients from Iran and their healthy consanguineous parents. In 61 patients, we identified apparently causative changes in known ID genes. Of these, 44 were homozygous recessive and 17 dominant DNMs. Assuming that the DNM rate is stable, these results suggest that parental consanguinity raises the ID risk about 3.6-fold, and about 4.1 to 4.25-fold for children of first-cousin unions. These results do not rhyme with recent opinions that consanguinity-related health risks are generally small and have been "overstated" in the past.


Subject(s)
Genes, Recessive , Inbreeding , Intellectual Disability/genetics , Consanguinity , Exome/genetics , Family , Female , Homozygote , Humans , Intellectual Disability/epidemiology , Intellectual Disability/pathology , Iran/epidemiology , Male , Middle East/epidemiology , Mutation , Pedigree , Exome Sequencing
4.
Hum Mutat ; 38(6): 621-636, 2017 06.
Article in English | MEDLINE | ID: mdl-28236339

ABSTRACT

Intellectual disability (ID) is the hallmark of an extremely heterogeneous group of disorders that comprises a wide variety of syndromic and non-syndromic phenotypes. Here, we report on mutations in two aminoacyl-tRNA synthetases that are associated with ID in two unrelated Iranian families. In the first family, we identified a homozygous missense mutation (c.514G>A, p.Asp172Asn) in the cytoplasmic seryl-tRNA synthetase (SARS) gene. The mutation affects the enzymatic core domain of the protein and impairs its enzymatic activity, probably leading to reduced cytoplasmic tRNASer concentrations. The mutant protein was predicted to be unstable, which could be substantiated by investigating ectopic mutant SARS in transfected HEK293T cells. In the second family, we found a compound heterozygous genotype of the mitochondrial tryptophanyl-tRNA synthetase (WARS2) gene, comprising a nonsense mutation (c.325delA, p.Ser109Alafs*15), which very likely entails nonsense-mediated mRNA decay and a missense mutation (c.37T>G, p.Trp13Gly). The latter affects the mitochondrial localization signal of WARS2, causing protein mislocalization. Including AIMP1, which we have recently implicated in the etiology of ID, three genes with a role in tRNA-aminoacylation are now associated with this condition. We therefore suggest that the functional integrity of tRNAs in general is an important factor in the development and maintenance of human cognitive functions.


Subject(s)
Amino Acyl-tRNA Synthetases/genetics , Intellectual Disability/genetics , Nonsense Mediated mRNA Decay/genetics , Adolescent , Adult , Child , Cytokines/genetics , Female , HEK293 Cells , Homozygote , Humans , Intellectual Disability/pathology , Iran , Male , Mutation, Missense/genetics , Neoplasm Proteins/genetics , Pedigree , RNA-Binding Proteins/genetics
5.
Nature ; 478(7367): 57-63, 2011 Sep 21.
Article in English | MEDLINE | ID: mdl-21937992

ABSTRACT

Common diseases are often complex because they are genetically heterogeneous, with many different genetic defects giving rise to clinically indistinguishable phenotypes. This has been amply documented for early-onset cognitive impairment, or intellectual disability, one of the most complex disorders known and a very important health care problem worldwide. More than 90 different gene defects have been identified for X-chromosome-linked intellectual disability alone, but research into the more frequent autosomal forms of intellectual disability is still in its infancy. To expedite the molecular elucidation of autosomal-recessive intellectual disability, we have now performed homozygosity mapping, exon enrichment and next-generation sequencing in 136 consanguineous families with autosomal-recessive intellectual disability from Iran and elsewhere. This study, the largest published so far, has revealed additional mutations in 23 genes previously implicated in intellectual disability or related neurological disorders, as well as single, probably disease-causing variants in 50 novel candidate genes. Proteins encoded by several of these genes interact directly with products of known intellectual disability genes, and many are involved in fundamental cellular processes such as transcription and translation, cell-cycle control, energy metabolism and fatty-acid synthesis, which seem to be pivotal for normal brain development and function.


Subject(s)
Cognition Disorders/genetics , Genes, Recessive/genetics , High-Throughput Nucleotide Sequencing , Intellectual Disability/genetics , Brain/metabolism , Brain/physiology , Cell Cycle , Consanguinity , DNA Mutational Analysis , Exons/genetics , Gene Regulatory Networks , Genes, Essential/genetics , Homozygote , Humans , Metabolic Networks and Pathways , Mutation/genetics , Organ Specificity , Synapses/metabolism
6.
Am J Med Genet A ; 161A(8): 1915-22, 2013 Aug.
Article in English | MEDLINE | ID: mdl-23825041

ABSTRACT

Succinic semialdehyde dehydrogenase (SSADH) deficiency is a disorder of the catabolism of the neurotransmitter gamma-aminobutyric acid (GABA) with a very variable clinical phenotype ranging from mild intellectual disability to severe neurological defects. We report here on a large Iranian family with four affected patients presenting with severe intellectual disability, developmental delay and generalized tonic-clonic seizures. Molecular genetic analysis revealed a missense mutation c.901A>G (p.K301E, RefSeq number NM_001080) in ALDH5A1 co-segregating with the disease in the family. The missense mutation affects an amino acid residue that is highly conserved across the animal kingdom. Protein modeling showed that p.K301E most likely leads to a loss of NAD(+) binding and a predicted decrease in the free energy by 6.67 kcal/mol furthermore suggests a severe destabilization of the protein. In line with these in silico observations, no SSADH enzyme activity could be detected in patient lymphoblasts.


Subject(s)
1-Pyrroline-5-Carboxylate Dehydrogenase/genetics , Amino Acid Metabolism, Inborn Errors/genetics , Intellectual Disability/genetics , Mutation, Missense/genetics , Adult , DNA/analysis , DNA/genetics , Developmental Disabilities , Humans , Iran , Male , Pedigree , Polymerase Chain Reaction , Polymorphism, Single Nucleotide , Succinate-Semialdehyde Dehydrogenase/blood , Succinate-Semialdehyde Dehydrogenase/deficiency , Succinate-Semialdehyde Dehydrogenase/genetics , Young Adult
7.
J Neurosci ; 24(26): 5982-6002, 2004 Jun 30.
Article in English | MEDLINE | ID: mdl-15229246

ABSTRACT

The molecular changes underlying neural progenitor differentiation are essentially unknown. We applied cDNA microarrays with 13,627 clones to measure dynamic gene expression changes during the in vitro differentiation of neural progenitor cells that were isolated from the subventricular zone of postnatal day 7 mice and grown in vitro as neurospheres. In two experimental series in which we withdrew epidermal growth factor and added the neurotrophins Neurotrophin-4 or BDNF, four time points were investigated: undifferentiated cells grown as neurospheres, and cells 24, 48, and 96 hr after differentiation. Expression changes of selected genes were confirmed by semiquantitative RT-PCR. Ten different groups of gene expression dynamics obtained by cluster analysis are described. To correlate selected gene expression changes to the localization of respective proteins, we performed immunostainings of cultured neurospheres and of brain sections from adult mice. Our results provide new insights into the genetic program of neural progenitor differentiation and give strong hints to as yet unknown cellular communications within the adult subventricular zone stem cell niche.


Subject(s)
Cell Differentiation/genetics , Gene Expression Profiling , Gene Expression Regulation, Developmental , Lateral Ventricles/growth & development , Nerve Tissue Proteins/biosynthesis , Neurons/cytology , Stem Cells/cytology , Animals , Brain-Derived Neurotrophic Factor/pharmacology , Cell Differentiation/drug effects , Cell Division , Cells, Cultured/cytology , Cells, Cultured/drug effects , Cells, Cultured/metabolism , Cytoskeletal Proteins/biosynthesis , Cytoskeletal Proteins/genetics , DNA, Complementary/genetics , Gene Expression Regulation, Developmental/drug effects , Lateral Ventricles/cytology , Lateral Ventricles/metabolism , Mice , Nerve Growth Factors/pharmacology , Nerve Tissue Proteins/genetics , Oligonucleotide Array Sequence Analysis , Reverse Transcriptase Polymerase Chain Reaction , Signal Transduction , Spheroids, Cellular/metabolism , Stem Cells/drug effects , Stem Cells/metabolism , Transcription Factors/biosynthesis , Transcription Factors/genetics
8.
Eur J Hum Genet ; 19(6): 717-20, 2011 Jun.
Article in English | MEDLINE | ID: mdl-21267006

ABSTRACT

X-linked intellectual disability (XLID), also known as X-linked mental retardation, is a highly genetically heterogeneous condition for which mutations in >90 different genes have been identified. In this study, we used a custom-made sequencing array based on the Affymetrix 50k platform for mutation screening in 17 known XLID genes in patients from 135 families and found eight single-nucleotide changes that were absent in controls. For four mutations affecting ATRX (p.1761M>T), PQBP1 (p.155R>X) and SLC6A8 (p.390P>L and p.477S>L), we provide evidence for a functional involvement of these changes in the aetiology of intellectual disability.


Subject(s)
Carrier Proteins/genetics , DNA Helicases/genetics , Mental Retardation, X-Linked/genetics , Nerve Tissue Proteins/genetics , Nuclear Proteins/genetics , Plasma Membrane Neurotransmitter Transport Proteins/genetics , Polymorphism, Single Nucleotide , Carrier Proteins/biosynthesis , Chromosomes, Human, X/chemistry , DNA Helicases/biosynthesis , DNA-Binding Proteins , Female , Genes, X-Linked , Genetic Association Studies , Genetic Testing , High-Throughput Nucleotide Sequencing , Humans , Hybridization, Genetic , Male , Nerve Tissue Proteins/biosynthesis , Nuclear Proteins/biosynthesis , Pedigree , Plasma Membrane Neurotransmitter Transport Proteins/biosynthesis , Reverse Transcriptase Polymerase Chain Reaction , X-linked Nuclear Protein
9.
Hum Mol Genet ; 14(15): 2247-56, 2005 Aug 01.
Article in English | MEDLINE | ID: mdl-16002417

ABSTRACT

Rett syndrome (RTT) is a severe form of mental retardation, which is caused by spontaneous mutations in the X-linked gene MECP2. How the loss of MeCP2 function leads to RTT is currently unknown. Mice lacking the Mecp2 gene initially show normal postnatal development but later acquire neurological phenotypes, including heightened anxiety, that resemble RTT. The MECP2 gene encodes a methyl-CpG-binding protein that can act as a transcriptional repressor. Using cDNA microarrays, we found that Mecp2-null animals differentially express several genes that are induced during the stress response by glucocorticoids. Increased levels of mRNAs for serum glucocorticoid-inducible kinase 1 (Sgk) and FK506-binding protein 51 (Fkbp5) were observed before and after onset of neurological symptoms, but plasma glucocorticoid was not significantly elevated in Mecp2-null mice. MeCP2 is bound to the Fkbp5 and Sgk genes in brain and may function as a modulator of glucocorticoid-inducible gene expression. Given the known deleterious effect of glucocorticoid exposure on brain development, our data raise the possibility that disruption of MeCP2-dependent regulation of stress-responsive genes contributes to the symptoms of RTT.


Subject(s)
Corticosterone/blood , Gene Expression Regulation , Immediate-Early Proteins/metabolism , Protein Serine-Threonine Kinases/metabolism , Rett Syndrome/metabolism , Stress, Physiological/blood , Tacrolimus Binding Proteins/metabolism , Animals , Brain/metabolism , Female , Mice , Mice, Inbred C57BL , Mice, Knockout , Oligonucleotide Array Sequence Analysis , Phenotype , Rett Syndrome/genetics , Signal Transduction , Up-Regulation
10.
Dev Dyn ; 230(1): 149-64, 2004 May.
Article in English | MEDLINE | ID: mdl-15108320

ABSTRACT

To obtain a deeper insight into the genes and gene networks involved in the development of placentopathies, we have assessed global gene expression in three different models of placental hyperplasia caused by interspecies hybridization (IHPD), cloning by nuclear transfer, and mutation of the Esx1 gene, respectively. Comparison of gene expression profiles of approximately 13,000 expressed sequence tags (ESTs) identified specific subsets of genes with changed expression levels in IHPD, cloned, and Esx1 mutant placentas. Of interest, only one gene of known function and one EST of unknown function were found common to all three placentopathies; however, a significant number of ESTs were common to IHPD and cloned placentas. In contrast, only one gene was shared between IHPD and Esx1 mutant, and cloned and Esx1 mutant placentas, respectively. These genes common to different abnormal placental growth genotypes are likely to be important in the occurrence of placentopathy.


Subject(s)
Gene Expression Regulation, Developmental , Homeodomain Proteins/genetics , Placenta/metabolism , Placenta/pathology , Proto-Oncogene Proteins/genetics , Transcription Factors/genetics , Animals , Blotting, Northern , Cell Nucleus/metabolism , Cloning, Molecular , DNA/metabolism , DNA, Complementary/metabolism , Expressed Sequence Tags , Genomic Imprinting , Genotype , Hyperplasia , Image Processing, Computer-Assisted , In Situ Hybridization , Mice , Mutation , Nucleic Acid Hybridization , Oligonucleotide Array Sequence Analysis , Phenotype , RNA, Messenger/metabolism , Reverse Transcriptase Polymerase Chain Reaction
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