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1.
JCI Insight ; 7(10)2022 05 23.
Article in English | MEDLINE | ID: mdl-35603789

ABSTRACT

The eukaryotic CDC45/MCM2-7/GINS (CMG) helicase unwinds the DNA double helix during DNA replication. The GINS subcomplex is required for helicase activity and is, therefore, essential for DNA replication and cell viability. Here, we report the identification of 7 individuals from 5 unrelated families presenting with a Meier-Gorlin syndrome-like (MGS-like) phenotype associated with hypomorphic variants of GINS3, a gene not previously associated with this syndrome. We found that MGS-associated GINS3 variants affecting aspartic acid 24 (D24) compromised cell proliferation and caused accumulation of cells in S phase. These variants shortened the protein half-life, altered key protein interactions at the replisome, and negatively influenced DNA replication fork progression. Yeast expressing MGS-associated variants of PSF3 (the yeast GINS3 ortholog) also displayed impaired growth, S phase progression defects, and decreased Psf3 protein stability. We further showed that mouse embryos homozygous for a D24 variant presented intrauterine growth retardation and did not survive to birth, and that fibroblasts derived from these embryos displayed accelerated cellular senescence. Taken together, our findings implicate GINS3 in the pathogenesis of MGS and support the notion that hypomorphic variants identified in this gene impaired cell and organismal growth by compromising DNA replication.


Subject(s)
Micrognathism , Saccharomyces cerevisiae , Animals , Chromosomal Proteins, Non-Histone , Congenital Microtia , DNA Replication/genetics , Growth Disorders , Humans , Mice , Micrognathism/genetics , Minichromosome Maintenance Proteins/genetics , Patella/abnormalities
3.
J Med Genet ; 59(4): 358-365, 2022 04.
Article in English | MEDLINE | ID: mdl-33820834

ABSTRACT

BACKGROUND: Holoprosencephaly is a spectrum of developmental disorder of the embryonic forebrain in which there is failed or incomplete separation of the prosencephalon into two cerebral hemispheres. To date, dominant mutations in sonic hedgehog (SHH) pathway genes are the predominant Mendelian causes, and have marked interfamilial and intrafamilial phenotypical variabilities. METHODS: We describe two families in which offspring had holoprosencephaly spectrum and homozygous predicted-deleterious variants in phospholipase C eta-1 (PLCH1). Immunocytochemistry was used to examine the expression pattern of PLCH1 in human embryos. We used SHH as a marker of developmental stage and of early embryonic anatomy. RESULTS: In the first family, two siblings had congenital hydrocephalus, significant developmental delay and a monoventricle or fused thalami with a homozygous PLCH1 c.2065C>T, p.(Arg689*) variant. In the second family, two siblings had alobar holoprosencephaly and cyclopia with a homozygous PLCH1 c.4235delA, p.(Cys1079ValfsTer16) variant. All parents were healthy carriers, with no holoprosencephaly spectrum features. We found that the subcellular localisation of PLCH1 is cytoplasmic, but the p.(Cys1079ValfsTer16) variant was predominantly nuclear. Human embryo immunohistochemistry showed PLCH1 to be expressed in the notorcord, developing spinal cord (in a ventral to dorsal gradient), dorsal root ganglia, cerebellum and dermatomyosome, all tissues producing or responding to SHH. Furthermore, the embryonic subcellular localisation of PLCH1 was exclusively cytoplasmic, supporting protein mislocalisation contributing to the pathogenicity of the p.(Cys1079ValfsTer16) variant. CONCLUSION: Our data support the contention that PLCH1 has a role in prenatal mammalian neurodevelopment, and deleterious variants cause a clinically variable holoprosencephaly spectrum phenotype.


Subject(s)
Holoprosencephaly , Type C Phospholipases , Animals , Hedgehog Proteins/genetics , Holoprosencephaly/genetics , Holoprosencephaly/metabolism , Humans , Mammals/metabolism , Mutation , Phenotype , Type C Phospholipases/genetics
4.
Front Immunol ; 12: 707159, 2021.
Article in English | MEDLINE | ID: mdl-34966381

ABSTRACT

Coronavirus disease-2019 (COVID-19) was declared as a pandemic by WHO in March 2020. SARS-CoV-2 causes a wide range of illness from asymptomatic to life-threatening. There is an essential need to identify biomarkers to predict disease severity and mortality during the earlier stages of the disease, aiding treatment and allocation of resources to improve survival. The aim of this study was to identify at the time of SARS-COV-2 infection patients at high risk of developing severe disease associated with low survival using blood parameters, including inflammation and coagulation mediators, vital signs, and pre-existing comorbidities. This cohort included 89 multi-ethnic COVID-19 patients recruited between July 14th and October 20th 2020 in Doha, Qatar. According to clinical severity, patients were grouped into severe (n=33), mild (n=33) and asymptomatic (n=23). Common routine tests such as complete blood count (CBC), glucose, electrolytes, liver and kidney function parameters and markers of inflammation, thrombosis and endothelial dysfunction including complement component split product C5a, Interleukin-6, ferritin and C-reactive protein were measured at the time COVID-19 infection was confirmed. Correlation tests suggest that C5a is a predictive marker of disease severity and mortality, in addition to 40 biological and physiological parameters that were found statistically significant between survivors and non-survivors. Survival analysis showed that high C5a levels, hypoalbuminemia, lymphopenia, elevated procalcitonin, neutrophilic leukocytosis, acute anemia along with increased acute kidney and hepatocellular injury markers were associated with a higher risk of death in COVID-19 patients. Altogether, we created a prognostic classification model, the CAL model (C5a, Albumin, and Lymphocyte count) to predict severity with significant accuracy. Stratification of patients using the CAL model could help in the identification of patients likely to develop severe symptoms in advance so that treatments can be targeted accordingly.


Subject(s)
Biomarkers/blood , COVID-19/blood , COVID-19/mortality , Complement C5a/analysis , Patient Acuity , Adult , Aged , COVID-19/complications , Cohort Studies , Female , Humans , Hypoalbuminemia/mortality , Hypoalbuminemia/virology , Lymphocyte Count , Lymphopenia/mortality , Lymphopenia/virology , Male , Middle Aged , Prognosis , Prospective Studies , Qatar , SARS-CoV-2
6.
Cancer Immunol Immunother ; 70(9): 2625-2638, 2021 Sep.
Article in English | MEDLINE | ID: mdl-33582867

ABSTRACT

There is an increased risk of colorectal cancer (CRC) development in patients with non-insulin-dependent type 2 diabetes. CD8+ T cells have been implicated in diabetes and are crucial for anti-tumor immunity. However, transcriptomic profiling for CD8+ T cells from CRC diabetic patients has not been explored. We performed RNA sequencing and compared transcriptomic profiles of CD8+ tumor-infiltrating T lymphocytes (CD8+ TILs) in CRC diabetic patients with CRC nondiabetic patients. We found that genes associated with ribogenesis, epigenetic regulations, oxidative phosphorylation and cell cycle arrest were upregulated in CD8+ TILs from diabetic patients, while genes associated with PI3K signaling pathway, cytokine response and response to lipids were downregulated. Among the significantly deregulated 1009 genes, 342 (186 upregulated and 156 downregulated) genes were selected based on their link to diabetes, and their associations with the presence of specific CRC pathological parameters were assessed using GDC TCGA colon database. The 186 upregulated genes were associated with the presence of colon polyps history (P = 0.0007) and lymphatic invasion (P = 0.0025). Moreover, CRC patients with high expression of the 186 genes were more likely to have poorer disease-specific survival (DSS) (Mantel-Cox log-rank P = 0.024) than those with low score. Our data provide novel insights into molecular pathways and biological functions, which could be altered in CD8+ TILs from CRC diabetic versus nondiabetic patients, and reveal candidate genes linked to diabetes, which could predict DSS and pathological parameters associated with CRC progression. However, further investigations using larger patient cohorts and functional studies are required to validate these findings.


Subject(s)
CD8-Positive T-Lymphocytes/immunology , CD8-Positive T-Lymphocytes/metabolism , Colorectal Neoplasms/etiology , Diabetes Mellitus, Type 2/complications , Lymphocytes, Tumor-Infiltrating/immunology , Lymphocytes, Tumor-Infiltrating/metabolism , Transcriptome , Biomarkers , Colorectal Neoplasms/metabolism , Colorectal Neoplasms/pathology , Computational Biology , Diabetes Mellitus, Type 2/diagnosis , Disease Susceptibility , Gene Expression Profiling , Gene Expression Regulation , Humans , Immunophenotyping , Prognosis , Protein Interaction Mapping
7.
Am J Hum Genet ; 108(1): 115-133, 2021 01 07.
Article in English | MEDLINE | ID: mdl-33308444

ABSTRACT

Signal peptide-CUB-EGF domain-containing protein 3 (SCUBE3) is a member of a small family of multifunctional cell surface-anchored glycoproteins functioning as co-receptors for a variety of growth factors. Here we report that bi-allelic inactivating variants in SCUBE3 have pleiotropic consequences on development and cause a previously unrecognized syndromic disorder. Eighteen affected individuals from nine unrelated families showed a consistent phenotype characterized by reduced growth, skeletal features, distinctive craniofacial appearance, and dental anomalies. In vitro functional validation studies demonstrated a variable impact of disease-causing variants on transcript processing, protein secretion and function, and their dysregulating effect on bone morphogenetic protein (BMP) signaling. We show that SCUBE3 acts as a BMP2/BMP4 co-receptor, recruits the BMP receptor complexes into raft microdomains, and positively modulates signaling possibly by augmenting the specific interactions between BMPs and BMP type I receptors. Scube3-/- mice showed craniofacial and dental defects, reduced body size, and defective endochondral bone growth due to impaired BMP-mediated chondrogenesis and osteogenesis, recapitulating the human disorder. Our findings identify a human disease caused by defective function of a member of the SCUBE family, and link SCUBE3 to processes controlling growth, morphogenesis, and bone and teeth development through modulation of BMP signaling.


Subject(s)
Bone and Bones/metabolism , Calcium-Binding Proteins/metabolism , Developmental Disabilities/metabolism , Osteogenesis/physiology , Signal Transduction/physiology , Animals , Bone Morphogenetic Protein 2/metabolism , Bone Morphogenetic Protein 4/metabolism , Bone Morphogenetic Proteins/metabolism , Cell Line , Cell Line, Tumor , Female , Gene Expression Regulation, Developmental/physiology , HEK293 Cells , Hep G2 Cells , Humans , Intercellular Signaling Peptides and Proteins/metabolism , MCF-7 Cells , Male , Mice , Mice, Inbred C3H , Mice, Inbred C57BL
8.
Brain ; 143(10): 2911-2928, 2020 10 01.
Article in English | MEDLINE | ID: mdl-33103737

ABSTRACT

Human post-natal neurodevelopmental delay is often associated with cerebral alterations that can lead, by themselves or associated with peripheral deficits, to premature death. Here, we report the clinical features of 10 patients from six independent families with mutations in the autosomal YIF1B gene encoding a ubiquitous protein involved in anterograde traffic from the endoplasmic reticulum to the cell membrane, and in Golgi apparatus morphology. The patients displayed global developmental delay, motor delay, visual deficits with brain MRI evidence of ventricle enlargement, myelination alterations and cerebellar atrophy. A similar profile was observed in the Yif1b knockout (KO) mouse model developed to identify the cellular alterations involved in the clinical defects. In the CNS, mice lacking Yif1b displayed neuronal reduction, altered myelination of the motor cortex, cerebellar atrophy, enlargement of the ventricles, and subcellular alterations of endoplasmic reticulum and Golgi apparatus compartments. Remarkably, although YIF1B was not detected in primary cilia, biallelic YIF1B mutations caused primary cilia abnormalities in skin fibroblasts from both patients and Yif1b-KO mice, and in ciliary architectural components in the Yif1b-KO brain. Consequently, our findings identify YIF1B as an essential gene in early post-natal development in human, and provide a new genetic target that should be tested in patients developing a neurodevelopmental delay during the first year of life. Thus, our work is the first description of a functional deficit linking Golgipathies and ciliopathies, diseases so far associated exclusively to mutations in genes coding for proteins expressed within the primary cilium or related ultrastructures. We therefore propose that these pathologies should be considered as belonging to a larger class of neurodevelopmental diseases depending on proteins involved in the trafficking of proteins towards specific cell membrane compartments.


Subject(s)
Cilia/genetics , Golgi Apparatus/genetics , Mutation/genetics , Neurodevelopmental Disorders/genetics , Vesicular Transport Proteins/genetics , Animals , Cells, Cultured , Cilia/pathology , Female , Golgi Apparatus/pathology , Humans , Male , Mice , Mice, Knockout , Neurodevelopmental Disorders/diagnostic imaging
9.
J Clin Invest ; 130(8): 4423-4439, 2020 08 03.
Article in English | MEDLINE | ID: mdl-32453716

ABSTRACT

Joubert syndrome (JBTS) is a recessive neurodevelopmental ciliopathy characterized by a pathognomonic hindbrain malformation. All known JBTS genes encode proteins involved in the structure or function of primary cilia, ubiquitous antenna-like organelles essential for cellular signal transduction. Here, we used the recently identified JBTS-associated protein armadillo repeat motif-containing 9 (ARMC9) in tandem-affinity purification and yeast 2-hybrid screens to identify a ciliary module whose dysfunction underlies JBTS. In addition to the known JBTS-associated proteins CEP104 and CSPP1, we identified coiled-coil domain containing 66 (CCDC66) and TOG array regulator of axonemal microtubules 1 (TOGARAM1) as ARMC9 interaction partners. We found that TOGARAM1 variants cause JBTS and disrupt TOGARAM1 interaction with ARMC9. Using a combination of protein interaction analyses, characterization of patient-derived fibroblasts, and analysis of CRISPR/Cas9-engineered zebrafish and hTERT-RPE1 cells, we demonstrated that dysfunction of ARMC9 or TOGARAM1 resulted in short cilia with decreased axonemal acetylation and polyglutamylation, but relatively intact transition zone function. Aberrant serum-induced ciliary resorption and cold-induced depolymerization in ARMC9 and TOGARAM1 patient cell lines suggest a role for this new JBTS-associated protein module in ciliary stability.


Subject(s)
Abnormalities, Multiple , Armadillo Domain Proteins , Cerebellum/abnormalities , Cilia , Eye Abnormalities , Kidney Diseases, Cystic , Retina/abnormalities , Zebrafish Proteins , Zebrafish , Abnormalities, Multiple/genetics , Abnormalities, Multiple/metabolism , Acetylation , Animals , Armadillo Domain Proteins/genetics , Armadillo Domain Proteins/metabolism , CRISPR-Cas Systems , Cerebellum/metabolism , Cilia/genetics , Cilia/metabolism , Disease Models, Animal , Eye Abnormalities/genetics , Eye Abnormalities/metabolism , Humans , Kidney Diseases, Cystic/genetics , Kidney Diseases, Cystic/metabolism , Peptides/genetics , Peptides/metabolism , Retina/metabolism , Zebrafish/genetics , Zebrafish/metabolism , Zebrafish Proteins/genetics , Zebrafish Proteins/metabolism
10.
Genet Med ; 22(6): 1051-1060, 2020 06.
Article in English | MEDLINE | ID: mdl-32055034

ABSTRACT

PURPOSE: Ciliopathies are highly heterogeneous clinical disorders of the primary cilium. We aim to characterize a large cohort of ciliopathies phenotypically and molecularly. METHODS: Detailed phenotypic and genomic analysis of patients with ciliopathies, and functional characterization of novel candidate genes. RESULTS: In this study, we describe 125 families with ciliopathies and show that deleterious variants in previously reported genes, including cryptic splicing variants, account for 87% of cases. Additionally, we further support a number of previously reported candidate genes (BBIP1, MAPKBP1, PDE6D, and WDPCP), and propose nine novel candidate genes (CCDC67, CCDC96, CCDC172, CEP295, FAM166B, LRRC34, TMEM17, TTC6, and TTC23), three of which (LRRC34, TTC6, and TTC23) are supported by functional assays that we performed on available patient-derived fibroblasts. From a phenotypic perspective, we expand the phenomenon of allelism that characterizes ciliopathies by describing novel associations including WDR19-related Stargardt disease and SCLT1- and CEP164-related Bardet-Biedl syndrome. CONCLUSION: In this cohort of phenotypically and molecularly characterized ciliopathies, we draw important lessons that inform the clinical management and the diagnostics of this class of disorders as well as their basic biology.


Subject(s)
Bardet-Biedl Syndrome , Ciliopathies , Alleles , Bardet-Biedl Syndrome/genetics , Cilia/genetics , Ciliopathies/genetics , Humans , Sodium Channels
11.
Hepatology ; 71(6): 2067-2079, 2020 06.
Article in English | MEDLINE | ID: mdl-31595528

ABSTRACT

BACKGROUND AND AIMS: The clinical consequences of defective primary cilium (ciliopathies) are characterized by marked phenotypic and genetic heterogeneity. Although fibrocystic liver disease is an established ciliopathy phenotype, severe neonatal cholestasis is rarely recognized as such. APPROACH AND RESULTS: We describe seven individuals from seven families with syndromic ciliopathy clinical features, including severe neonatal cholestasis (lethal in one and necessitating liver transplant in two). Positional mapping revealed a single critical locus on chromosome 7. Whole-exome sequencing revealed three different homozygous variants in Tetratricopeptide Repeat Domain 26 (TTC26) that fully segregated with the phenotype. TTC26 (intraflagellar transport [IFT] 56/DYF13) is an atypical component of IFT-B complex, and deficiency of its highly conserved orthologs has been consistently shown to cause defective ciliary function in several model organisms. We show that cilia in TTC26-mutated patient cells display variable length and impaired function, as indicated by dysregulated sonic hedgehog signaling, abnormal staining for IFT-B components, and transcriptomic clustering with cells derived from individuals with closely related ciliopathies. We also demonstrate a strong expression of Ttc26 in the embryonic mouse liver in a pattern consistent with its proposed role in the normal development of the intrahepatic biliary system. CONCLUSIONS: In addition to establishing a TTC26-related ciliopathy phenotype in humans, our results highlight the importance of considering ciliopathies in the differential diagnosis of severe neonatal cholestasis even in the absence of more typical features.


Subject(s)
Cholestasis, Intrahepatic/genetics , Infant, Newborn, Diseases/genetics , Intracellular Signaling Peptides and Proteins/genetics , Tetratricopeptide Repeat/genetics , Animals , Ciliopathies , Diagnosis, Differential , Hedgehog Proteins , Humans , Infant, Newborn , Mice , Microtubule-Associated Proteins/genetics , Mutation , Protein Transport/genetics , Severity of Illness Index , Exome Sequencing/methods
12.
Hum Mutat ; 40(11): 2108-2120, 2019 11.
Article in English | MEDLINE | ID: mdl-31301155

ABSTRACT

The wobble position in the anticodon loop of transfer ribonucleic acid (tRNA) is subject to numerous posttranscriptional modifications. In particular, thiolation of the wobble uridine has been shown to play an important role in codon-anticodon interactions. This modification is catalyzed by a highly conserved CTU1/CTU2 complex, disruption of which has been shown to cause abnormal phenotypes in yeast, worms, and plants. We have previously suggested that a single founder splicing variant in human CTU2 causes a novel multiple congenital anomalies syndrome consisting of dysmorphic facies, renal agenesis, ambiguous genitalia, microcephaly, polydactyly, and lissencephaly (DREAM-PL). In this study, we describe five new patients with DREAM-PL phenotype and whose molecular analysis expands the allelic heterogeneity of the syndrome to five different alleles; four of which predict protein truncation. Functional characterization using patient-derived cells for each of these alleles, as well as the original founder allele; revealed a specific impairment of wobble uridine thiolation in all known thiol-containing tRNAs. Our data establish a recognizable CTU2-linked autosomal recessive syndrome in humans characterized by defective thiolation of the wobble uridine. The potential deleterious consequences for the translational efficiency and fidelity during development as a mechanism for pathogenicity represent an attractive target of future investigations.


Subject(s)
Abnormalities, Multiple/diagnosis , Abnormalities, Multiple/genetics , Alleles , Genetic Predisposition to Disease , Genetic Variation , RNA, Transfer/genetics , RNA, Transfer/metabolism , tRNA Methyltransferases/genetics , Amino Acid Sequence , Consanguinity , DNA Mutational Analysis , Facies , Female , Genetic Association Studies , Genotype , Humans , Magnetic Resonance Imaging , Male , Phenotype , RNA, Transfer/chemistry , Radiography , Sequence Analysis, DNA , Severity of Illness Index , Syndrome
13.
Am J Hum Genet ; 104(4): 731-737, 2019 04 04.
Article in English | MEDLINE | ID: mdl-30905400

ABSTRACT

Ciliopathies are clinical disorders of the primary cilium with widely recognized phenotypic and genetic heterogeneity. In two Arab consanguineous families, we mapped a ciliopathy phenotype that most closely matches Joubert syndrome (hypotonia, developmental delay, typical facies, oculomotor apraxia, polydactyly, and subtle posterior fossa abnormalities) to a single locus in which a founder homozygous truncating variant in FAM149B1 was identified by exome sequencing. We subsequently identified a third Arab consanguineous multiplex family in which the phenotype of Joubert syndrome/oral-facial-digital syndrome (OFD VI) was found to co-segregate with the same founder variant in FAM149B1. Independently, autozygosity mapping and exome sequencing in a consanguineous Turkish family with Joubert syndrome highlighted a different homozygous truncating variant in the same gene. FAM149B1 encodes a protein of unknown function. Mutant fibroblasts were found to have normal ciliogenesis potential. However, distinct cilia-related abnormalities were observed in these cells: abnormal accumulation IFT complex at the distal tips of the cilia, which assumed bulbous appearance, increased length of the primary cilium, and dysregulated SHH signaling. We conclude that FAM149B1 is required for normal ciliary biology and that its deficiency results in a range of ciliopathy phenotypes in humans along the spectrum of Joubert syndrome.


Subject(s)
Abnormalities, Multiple/genetics , Cerebellum/abnormalities , Cilia/pathology , Ciliopathies/diagnosis , Ciliopathies/genetics , Cytoskeletal Proteins/genetics , Eye Abnormalities/genetics , Kidney Diseases, Cystic/genetics , Mutation , Retina/abnormalities , Adolescent , Alleles , Child, Preschool , Cilia/genetics , Consanguinity , Exome , Genes, Recessive , Homozygote , Humans , Male , Nervous System Malformations/genetics , Orofaciodigital Syndromes/genetics , Phenotype , Sequence Analysis, DNA , Signal Transduction , Turkey
14.
Am J Med Genet A ; 179(6): 1053-1057, 2019 06.
Article in English | MEDLINE | ID: mdl-30912300

ABSTRACT

We report two siblings with microcephaly, early infantile onset seizures, and cerebellar vermis hypoplasia, in whom whole exome sequencing revealed a novel homozygous missense (c.770T>C, p.[Leu257Pro]) variant in the hedgehog acyl-transferase gene (HHAT), encoding an enzyme required for the attachment of palmitoyl residues that are critical for multimerization and long and short range hedgehog signaling. There is a report of one family with Nivelon-Nivelon-Mabille syndrome in which HHAT was proposed as the likely candidate gene. The phenotypic overlap with the family we report herein provides further evidence implicating HHAT in cerebellar development and the pathogenesis of this rare spectrum.


Subject(s)
Acyltransferases/genetics , Alleles , Cerebellar Vermis/abnormalities , Microcephaly/diagnosis , Microcephaly/genetics , Mutation, Missense , Phenotype , Child , Child, Preschool , DNA Mutational Analysis , Facies , Female , Genetic Association Studies , Genetic Predisposition to Disease , Humans , Infant, Newborn , Magnetic Resonance Imaging
15.
Hum Genet ; 138(3): 231-239, 2019 Mar.
Article in English | MEDLINE | ID: mdl-30778726

ABSTRACT

Pseudouridylation is the most common post-transcriptional modification, wherein uridine is isomerized into 5-ribosyluracil (pseudouridine, Ψ). The resulting increase in base stacking and creation of additional hydrogen bonds are thought to enhance RNA stability. Pseudouridine synthases are encoded in humans by 13 genes, two of which are linked to Mendelian diseases: PUS1 and PUS3. Very recently, PUS7 mutations were reported to cause intellectual disability with growth retardation. We describe two families in which two different homozygous PUS7 mutations (missense and frameshift deletion) segregate with a phenotype comprising intellectual disability and progressive microcephaly. Short stature and hearing loss were variable in these patients. Functional characterization of the two mutations confirmed that both result in decreased levels of Ψ13 in tRNAs. Furthermore, the missense variant of the S. cerevisiae ortholog failed to complement the growth defect of S. cerevisiae pus7Δ trm8Δ mutants. Our results confirm that PUS7 is a bona fide Mendelian disease gene and expand the list of human diseases caused by impaired pseudouridylation.


Subject(s)
Genetic Association Studies , Genetic Predisposition to Disease , Intellectual Disability/genetics , Microcephaly/genetics , Mutation , Pseudouridine/genetics , Adolescent , Amino Acid Sequence , Child , Chromosome Mapping , Consanguinity , Female , Genes, Recessive , Humans , Male , Microcephaly/diagnosis , Pedigree , Phenotype , RNA, Transfer/genetics , Exome Sequencing
16.
Genet Med ; 21(3): 545-552, 2019 03.
Article in English | MEDLINE | ID: mdl-30214071

ABSTRACT

PURPOSE: Congenital microcephaly (CM) is an important birth defect with long term neurological sequelae. We aimed to perform detailed phenotypic and genomic analysis of patients with Mendelian forms of CM. METHODS: Clinical phenotyping, targeted or exome sequencing, and autozygome analysis. RESULTS: We describe 150 patients (104 families) with 56 Mendelian forms of CM. Our data show little overlap with the genetic causes of postnatal microcephaly. We also show that a broad definition of primary microcephaly -as an autosomal recessive form of nonsyndromic CM with severe postnatal deceleration of occipitofrontal circumference-is highly sensitive but has a limited specificity. In addition, we expand the overlap between primary microcephaly and microcephalic primordial dwarfism both clinically (short stature in >52% of patients with primary microcephaly) and molecularly (e.g., we report the first instance of CEP135-related microcephalic primordial dwarfism). We expand the allelic and locus heterogeneity of CM by reporting 37 novel likely disease-causing variants in 27 disease genes, confirming the candidacy of ANKLE2, YARS, FRMD4A, and THG1L, and proposing the candidacy of BPTF, MAP1B, CCNH, and PPFIBP1. CONCLUSION: Our study refines the phenotype of CM, expands its genetics heterogeneity, and informs the workup of children born with this developmental brain defect.


Subject(s)
Microcephaly/genetics , Microcephaly/physiopathology , Adult , Child , Child, Preschool , Dwarfism/genetics , Female , Genomics/methods , Genotype , Humans , Infant , Infant, Newborn , Male , Mutation/genetics , Pedigree , Phenotype , Exome Sequencing/methods
17.
Genet Med ; 21(3): 736-742, 2019 03.
Article in English | MEDLINE | ID: mdl-30237576

ABSTRACT

PURPOSE: Establishing links between Mendelian phenotypes and genes enables the proper interpretation of variants therein. Autozygome, a rich source of homozygous variants, has been successfully utilized for the high throughput identification of novel autosomal recessive disease genes. Here, we highlight the utility of the autozygome for the high throughput confirmation of previously published tentative links to diseases. METHODS: Autozygome and exome analysis of patients with suspected Mendelian phenotypes. All variants were classified according to the American College of Medical Genetics and Genomics guidelines. RESULTS: We highlight 30 published candidate genes (ACTL6B, ADAM22, AGTPBP1, APC, C12orf4, C3orf17 (NEPRO), CENPF, CNPY3, COL27A1, DMBX1, FUT8, GOLGA2, KIAA0556, LENG8, MCIDAS, MTMR9, MYH11, QRSL1, RUBCN, SLC25A42, SLC9A1, TBXT, TFG, THUMPD1, TRAF3IP2, UFC1, UFM1, WDR81, XRCC2, ZAK) in which we identified homozygous likely deleterious variants in patients with compatible phenotypes. We also identified homozygous likely deleterious variants in 18 published candidate genes (ABCA2, ARL6IP1, ATP8A2, CDK9, CNKSR1, DGAT1, DMXL2, GEMIN4, HCN2, HCRT, MYO9A, PARS2, PLOD3, PREPL, SCLT1, STX3, TXNRD2, WIPI2) although the associated phenotypes are sufficiently different from the original reports that they represent phenotypic expansion or potentially distinct allelic disorders. CONCLUSIONS: Our results should facilitate the timely relabeling of these candidate disease genes in relevant databases to improve the yield of clinical genomic sequencing.


Subject(s)
Disease/genetics , Genomics/methods , Sequence Analysis, DNA/methods , Biological Variation, Population/genetics , Child , Child, Preschool , Diagnosis , Diagnostic Techniques and Procedures , Female , Genetic Testing/standards , Genetic Variation , Genotype , Heredity/genetics , High-Throughput Nucleotide Sequencing/methods , Homozygote , Humans , Infant , Infant, Newborn , Male , Mutation , Phenotype
18.
Clin Genet ; 95(2): 310-319, 2019 02.
Article in English | MEDLINE | ID: mdl-30561787

ABSTRACT

Defects in the peroxisomes biogenesis and/or function result in peroxisomal disorders. In this study, we describe the largest Arab cohort to date (72 families) of clinically, biochemically and molecularly characterized patients with peroxisomal disorders. At the molecular level, we identified 43 disease-causing variants, half of which are novel. The founder nature of many of the variants allowed us to calculate the minimum disease burden for these disorders in our population ~1:30 000, which is much higher than previous estimates in other populations. Clinically, we found an interesting trend toward genotype/phenotype correlation in terms of long-term survival. Nearly half (40/75) of our peroxisomal disorders patients had documented survival beyond 1 year of age. Most unusual among the long-term survivors was a multiplex family in which the affected members presented as adults with non-specific intellectual disability and epilepsy. Other unusual presentations included the very recently described peroxisomal fatty acyl-CoA reductase 1 disorder as well as CRD, spastic paraparesis, white matter (CRSPW) syndrome. We conclude that peroxisomal disorders are highly heterogeneous in their clinical presentation. Our data also confirm the demonstration that milder forms of Zellweger spectrum disorders cannot be ruled out by the "gold standard" very long chain fatty acids assay, which highlights the value of a genomics-first approach in these cases.


Subject(s)
Arabs , Peroxisomal Disorders/epidemiology , Peroxisomal Disorders/etiology , Arabs/genetics , Biomarkers , Brain/abnormalities , Brain/diagnostic imaging , Cohort Studies , Consanguinity , Cost of Illness , Disease Management , Disease Susceptibility , Facies , Female , Genetic Association Studies , Genetic Predisposition to Disease , Humans , Magnetic Resonance Imaging , Male , Mutation , Pedigree , Peroxisomal Disorders/diagnosis , Peroxisomal Disorders/therapy , Phenotype , Population Surveillance , Prognosis
19.
Am J Hum Genet ; 103(4): 612-620, 2018 10 04.
Article in English | MEDLINE | ID: mdl-30269812

ABSTRACT

Joubert syndrome (JBTS) is a genetically heterogeneous autosomal-recessive neurodevelopmental ciliopathy. We investigated further the underlying genetic etiology of Joubert syndrome by studying two unrelated families in whom JBTS was not associated with pathogenic variants in known JBTS-associated genes. Combined autozygosity mapping of both families highlighted a candidate locus on chromosome 10 (chr10: 101569997-109106128, UCSC Genome Browser hg 19), and exome sequencing revealed two missense variants in ARL3 within the candidate locus. The encoded protein, ADP ribosylation factor-like GTPase 3 (ARL3), is a small GTP-binding protein that is involved in directing lipid-modified proteins into the cilium in a GTP-dependent manner. Both missense variants replace the highly conserved Arg149 residue, which we show to be necessary for the interaction with its guanine nucleotide exchange factor ARL13B, such that the mutant protein is associated with reduced INPP5E and NPHP3 localization in cilia. We propose that ARL3 provides a potential hub in the network of proteins implicated in ciliopathies, whereby perturbation of ARL3 leads to the mislocalization of multiple ciliary proteins as a result of abnormal displacement of lipidated protein cargo.


Subject(s)
ADP-Ribosylation Factors/genetics , Abnormalities, Multiple/genetics , Cerebellum/abnormalities , Cilia/genetics , Eye Abnormalities/genetics , Kidney Diseases, Cystic/genetics , Mutation, Missense/genetics , Retina/abnormalities , Adult , Child , Child, Preschool , Chromosomes, Human, Pair 10/genetics , Exome/genetics , Female , GTP-Binding Proteins/genetics , Guanine Nucleotide Exchange Factors/genetics , Humans , Male , Protein Transport/genetics , Young Adult
20.
Am J Med Genet A ; 176(11): 2404-2418, 2018 11.
Article in English | MEDLINE | ID: mdl-30216658

ABSTRACT

Warsaw breakage syndrome (WBS) is a recently recognized DDX11-related rare cohesinopathy, characterized by severe prenatal and postnatal growth restriction, microcephaly, developmental delay, cochlear anomalies, and sensorineural hearing loss. Only seven cases have been reported in the English literature, and thus the information on the phenotype and genotype of this interesting condition is limited. We provide clinical and molecular information on five additional unrelated patients carrying novel bi-allelic variants in the DDX11 gene, identified via whole exome sequencing. One of the variants was found to be a novel Saudi founder variant. All identified variants were classified as pathogenic or likely pathogenic except for one that was initially classified as a variant of unknown significance (VOUS) (p.Arg378Pro). Functional characterization of this VOUS using heterologous expression of wild type and mutant DDX11 revealed a marked effect on protein stability, thus confirming pathogenicity of this variant. The phenotypic data of the seven WBS reported patients were compared to our patients for further phenotypic delineation. Although all the reported patients had cochlear hypoplasia, one patient also had posterior labyrinthine anomaly. We conclude that while the cardinal clinical features in WBS (microcephaly, growth retardation, and cochlear anomalies) are almost universally present, the breakage phenotype is highly variable and can be absent in some cases. This report further expands the knowledge of the phenotypic and molecular features of WBS.


Subject(s)
Abnormalities, Multiple/genetics , Chromosome Breakage , Amino Acid Sequence , Child , Child, Preschool , DEAD-box RNA Helicases/chemistry , DEAD-box RNA Helicases/genetics , DNA Helicases/chemistry , DNA Helicases/genetics , Ear, Inner/diagnostic imaging , Facies , Female , Gene Expression Regulation , Humans , Infant , Infant, Newborn , Magnetic Resonance Imaging , Male , Models, Molecular , Phenotype , Proteasome Inhibitors/pharmacology , Protein Stability , Syndrome , Tomography, X-Ray Computed
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