Sowell J.,South Carolina Center for the Treatment of Genetic Disorders |
Norris J.,JC Self Research Institute |
Jones K.,JC Self Research Institute |
Schwartz C.,JC Self Research Institute |
Wood T.,South Carolina Center for the Treatment of Genetic Disorders
Clinica Chimica Acta | Year: 2011
Background: Snyder-Robinson syndrome is an X-linked genetic disorder characterized by intellectual disability, facial asymmetry, thickened lower lip, long hands with hyper extendable fingers, slow speech, and hyposcoliosis. The disorder is caused by a mutation in the spermine synthase (SMS) gene. The SMS gene encodes an enzyme involved in polyamine metabolism. Specifically, individuals with Snyder-Robinson have lack or have diminished capability to covert spermidine to spermine. Methods: We developed a liquid chromatography tandem mass spectrometry (LC-MS/MS) based screen for Snyder-Robinson syndrome. Results: Since individuals with Snyder-Robinson syndrome have diminished capacity to convert spermidine to spermine, we utilize this characteristic as a screening metric. Spermine to spermidine ratios were measured by LC-MS/MS in both normal controls and individuals with Snyder-Robinson syndrome. Polyamine ratios in subjects with Snyder-Robinson syndrome (n = 20) were significantly different from controls (n = 11) and carriers (n = 5), with p values of 0.0001 and 0.0075, respectively. Conclusions: We developed an effective LC-MS/MS diagnostic test for Snyder-Robinson syndrome. © 2011 Elsevier B.V.
Homan C.C.,University of Adelaide |
Kumar R.,Womens and Childrens Health Research Institute |
Kumar R.,University of Adelaide |
Nguyen L.S.,University of Adelaide |
And 11 more authors.
American Journal of Human Genetics | Year: 2014
With a wealth of disease-associated DNA variants being recently reported, the challenges of providing their functional characterization are mounting. Previously, as part of a large systematic resequencing of the X chromosome in 208 unrelated families with nonsyndromic X-linked intellectual disability, we identified three unique variants (two missense and one protein truncating) in USP9X. To assess the functional significance of these variants, we took advantage of the Usp9x knockout mouse we generated. Loss of Usp9x causes reduction in both axonal growth and neuronal cell migration. Although overexpression of wild-type human USP9X rescued these defects, all three USP9X variants failed to rescue axonal growth, caused reduced USP9X protein localization in axonal growth cones, and (in 2/3 variants) failed to rescue neuronal cell migration. Interestingly, in one of these families, the proband was subsequently identified to have a microdeletion encompassing ARID1B, a known ID gene. Given our findings it is plausible that loss of function of both genes contributes to the individual's phenotype. This case highlights the complexity of the interpretations of genetic findings from genome-wide investigations. We also performed proteomics analysis of neurons from both the wild-type and Usp9x knockout embryos and identified disruption of the cytoskeleton as the main underlying consequence of the loss of Usp9x. Detailed clinical assessment of all three families with USP9X variants identified hypotonia and behavioral and morphological defects as common features in addition to ID. Together our data support involvement of all three USP9X variants in ID in these families and provide likely cellular and molecular mechanisms involved. © 2014 The American Society of Human Genetics.
Birnbaum R.Y.,University of California at San Francisco |
Everman D.B.,JC Self Research Institute |
Murphy K.K.,University of California at San Francisco |
Gurrieri F.,University Cattolica ore |
And 2 more authors.
Human Molecular Genetics | Year: 2012
Disruption of distaless homeobox 5 and 6 (Dlx5/6) in mice results in brain, craniofacial, genital, ear and limb defects. In humans, chromosomal aberrations in the DLX5/6 region, some of which do not encompass DLX5/6, are associated with split hand/foot malformation 1 (SHFM1) as well as intellectual disability, craniofacial anomalies and hearing loss, suggesting that the disruption of DLX5/6 regulatory elements could lead to these abnormalities. Here, we characterized enhancers in the DLX5/6 locus whose tissue-specific expression and genomic location along with previously characterized enhancers correlate with phenotypes observed in individuals with chromosomal abnormalities. By analyzing chromosomal aberrations at 7q21, we refined the minimal SHFM1 critical region and used comparative genomics to select 26 evolutionary conserved non-coding sequences in this critical region for zebrafish enhancer assays. Eight of these sequences were shown to function as brain, olfactory bulb, branchial arch, otic vesicle and fin enhancers, recapitulating dlx5a/6a expression. Using a mouse enhancer assay, several of these zebrafish enhancers showed comparable expression patterns in the branchial arch, otic vesicle, forebrain and/or limb at embryonic day 11.5. Examination of the coordinates of various chromosomal rearrangements in conjunction with the genomic location of these tissue-specific enhancers showed a correlation with the observed clinical abnormalities. Our findings suggest that chromosomal abnormalities that disrupt the function of these tissue-specific enhancers could be the cause of SHFM1 and its associated phenotypes. In addition, they highlight specific enhancers in which mutations could lead to non-syndromic hearing loss, craniofacial defects or limb malformations. © The Author 2012. Published by Oxford University Press. All rights reserved.
Birnbaum R.Y.,University of California at San Francisco |
Clowney E.J.,University of California at San Francisco |
Agamy O.,Ben - Gurion University of the Negev |
Kim M.J.,University of California at San Francisco |
And 15 more authors.
Genome Research | Year: 2012
Enhancers are essential gene regulatory elements whose alteration can lead to morphological differences between species, developmental abnormalities, and human disease. Current strategies to identify enhancers focus primarily on noncoding sequences and tend to exclude protein coding sequences. Here, we analyzed 25 available ChIP-seq data sets that identify enhancers in an unbiased manner (H3K4me1, H3K27ac, and EP300) for peaks that overlap exons. We find that, on average, 7% of all ChIP-seq peaks overlap coding exons (after excluding for peaks that overlap with first exons). By using mouse and zebrafish enhancer assays, we demonstrate that several of these exonic enhancer (eExons) candidates can function as enhancers of their neighboring genes and that the exonic sequence is necessary for enhancer activity. Using ChIP, 3C, and DNA FISH, we further show that one of these exonic limb enhancers, Dync1i1 exon 15, has active enhancer marks and physically interacts with Dlx5/6 promoter regions 900 kb away. In addition, its removal by chromosomal abnormalities in humans could cause split hand and foot malformation 1 (SHFM1), a disorder associated with DLX5/6. These results demonstrate that DNA sequences can have a dual function, operating as coding exons in one tissue and enhancers of nearby gene(s) in another tissue, suggesting that phenotypes resulting from coding mutations could be caused not only by protein alteration but also by disrupting the regulation of another gene.
Takano K.,JC Self Research Institute |
Takano K.,Kanagawa Childrens Medical Center |
Liu D.,Australian National University |
Tarpey P.,Wellcome Trust Sanger Institute |
And 9 more authors.
Human Molecular Genetics | Year: 2012
Chloride intracellular channel 2 (CLIC2) protein is a member of the glutathione transferase class of proteins. Its' only known function is the regulation of ryanodine receptor (RyR) intracellular Ca. 2+ release channels. These RyR proteins play a major role in the regulation of Ca. 2+ signaling in many cells. Utilizing exome capture and deep sequencing of genes on the X-chromosome, we have identified a mutation in CLIC2 (c.303C>G, p.H101Q) which is associated with X-linked intellectual disability (ID), atrial fibrillation, cardiomegaly, congestive heart failure (CHF), some somatic features and seizures. Functional studies of the H101Q variant indicated that it stimulated rather than inhibited the action of RyR channels, with channels remaining open for longer times and potentially amplifying Ca. 2+ signals dependent on RyR channel activity. The overly active RyRs in cardiac and skeletal muscle cells and neuronal cells would result in abnormal cardiac function and trigger post-synaptic pathways and neurotransmitter release. The presence of both cardiomegaly and CHF in the two affected males and atrial fibrillation in one are consistent with abnormal RyR2 channel function. Since the dysfunction of RyR2 channels in the brain via 'leaky mutations' can result in mild developmental delay and seizures, our data also suggest a vital role for the CLIC2 protein in maintaining normal cognitive function via its interaction with RyRs in the brain. Therefore, our patients appear to suffer from a new channelopathy comprised of ID, seizures and cardiac problems because of enhanced Ca. 2+ release through RyRs in neuronal cells and cardiac muscle cells. © The Author 2012. Published by Oxford University Press. All rights reserved.
Kerzendorfer C.,University of Sussex |
Whibley A.,University of Cambridge |
Carpenter G.,University of Sussex |
Outwin E.,University of Sussex |
And 6 more authors.
Human Molecular Genetics | Year: 2010
CUL4A and B encode subunits of E3-ubiquitin ligases implicated in diverse processes including nucleotide excision repair, regulating gene expression and controlling DNA replication fork licensing. But, the functional distinction between CUL4A and CUL4B, if any, is unclear. Recently, mutations in CUL4B were identified in humans associated with mental retardation, relative macrocephaly, tremor and a peripheral neuropathy. Cells from these patients offer a unique system to help define at the molecular level the consequences of defective CUL4B specifically. We show that these patient-derived cells exhibit sensitivity to camptothecin (CPT), impaired CPT-induced topoisomerase I (Topo I) degradation and ubiquitination, thereby suggesting Topo I to be a novel Cul4-dependent substrate. Consistent with this, we also find that these cells exhibit increased levels of CPT-induced DNA breaks. Furthermore, over-expression of known CUL4-dependent sub- strates including Cdt1 and p21 appear to be a feature of these patient-derived cells. Collectively, our findings highlight the interplay between CUL4A and CUL4B and provide insight into the pathogenesis of CUL4B- deficiency in humans. © The Author 2010. Published by Oxford University Press. All rights reserved. For Permissions, please email: firstname.lastname@example.org.
Robinson A.,University College London |
Escuin S.,University College London |
Vekemans K.D.,University College London |
Vekemans K.D.,University of Paris Descartes |
And 5 more authors.
Human Mutation | Year: 2012
Craniorachischisis (CRN) is a severe neural tube defect (NTD) resulting from failure to initiate closure, leaving the hindbrain and spinal neural tube entirely open. Clues to the genetic basis of this condition come from several mouse models, which harbor mutations in core members of the planar cell polarity (PCP) signaling pathway. Previous studies of humans with CRN failed to identify mutations in the core PCP genes, VANGL1 and VANGL2. Here, we analyzed other key PCP genes: CELSR1, PRICKLE1, PTK7, and SCRIB, with the finding of eight potentially causative mutations in both CELSR1 and SCRIB. Functional effects of these unique or rare human variants were evaluated using known protein- protein interactions as well as subcellular protein localization. While protein interactions were not affected, variants from five of the 36 patients exhibited a profound alteration in subcellular protein localization, with diminution or abolition of trafficking to the plasma membrane. Comparable effects were seen in the crash and spin cycle mouse Celsr1 mutants, and the line-90 mouse Scrib mutant. We conclude that missense variants in CELSR1 and SCRIB may represent a cause of CRN in humans, as in mice, with defective PCP protein trafficking to the plasma membrane a likely pathogenic mechanism.
Schwartz C.E.,Jc Self Research Institute
Methods in molecular biology (Clifton, N.J.) | Year: 2011
Polyamines, small positively charged molecules, are vital for cell proliferation and differentiation. They are found ubiquitously in eukaryotic cells. Additionally, they interact with a wide range of other molecules and some membrane associated receptors. Polyamines, spermidine and spermine, are synthesized by two aminopropyltransferases, spermidine synthase and spermine synthase. Recently, mutations in the latter enzyme have been shown to be responsible for an X-linked intellectual disability condition known as Snyder-Robinson syndrome. Spermine synthase deficiency is thus far the only known polyamine deficiency syndrome in humans.
Srivastava A.K.,Jc Self Research Institute |
Schwartz C.E.,Jc Self Research Institute
Neuroscience and Biobehavioral Reviews | Year: 2014
Intellectual disability (ID) and autism spectrum disorder (ASD) are the most common developmental disorders present in humans. Combined, they affect between 3 and 5% of the population. Additionally, they can be found together in the same individual thereby complicating treatment.The causative factors (genes, epigenetic and environmental) are quite varied and likely interact so as to further complicate the assessment of an individual patient. Nonetheless, much valuable information has been gained by identifying candidate genes for ID or ASD. Understanding the etiology of either ID or ASD is of utmost importance for families. It allows a determination of the risk of recurrence, the possibility of other comorbidity medical problems, the molecular and cellular nature of the pathobiology and hopefully potential therapeutic approaches. © 2014 Elsevier Ltd.
Hunter A.G.,JC Self Research Institute |
Seaver L.H.,Kapiolani Medical Specialists |
Stevenson R.E.,JC Self Research Institute
American Journal of Medical Genetics, Part A | Year: 2011
Aside from gastroschisis and omphalocele, major defects of the ventral body (thoracoabdominal) wall are relatively uncommon and almost universally lethal. They are most often associated with other anomalies including those of the limbs that may range from amelia to mild positional deformations, unusual craniofacial malformations, and a variety of visceral abnormalities that include the heart, lungs, genitourinary system, and gut. This complex of ventral wall anomalies has been discussed under a broad and changing nomenclature that has included amniotic band disruption complex, amnion rupture sequence, limb-body wall defect (or complex), and simply body wall complex. Three major theories have been suggested to explain this complex: early amnion rupture (operating through uterine pressure and/or disruption by amniotic bands), vascular compromise (primarily hypoperfusion), and an early intrinsic defect of the developing embryo. We present four patients that illustrate the spectrum of ventral body wall defects, and from there critique the current hypotheses of pathogenesis. We conclude that this association of malformations originates as early as the embryonic disc stage, and that some of the observed associated anomalies are secondary complications of the primary disturbance in embryogenesis. We propose a new explanation for the atypical facial clefts and cranial malformations that are often observed. © 2011 Wiley-Liss, Inc.