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1.
Hum Genet ; 143(1): 59-69, 2024 Jan.
Article in English | MEDLINE | ID: mdl-38180561

ABSTRACT

Perinatal stroke is associated with significant short- and long-term morbidity and has been recognized as the most common cause of cerebral palsy in term infants. The diagnosis of presumed perinatal stroke (PPS) is made in children who present with neurological deficit and/or seizures attributable to focal chronic infarction on neuroimaging and have uneventful neonatal history. The underlying mechanism of presumed perinatal stroke remains unknown and thorough investigation of potential monogenic causes has not been conducted to date. Here, we describe the use of untargeted exome sequencing to investigate a cohort of eight patients from six families with PPS. A likely deleterious variant was identified in four families. These include the well-established risk genes COL4A2 and JAM3. In addition, we report the first independent confirmation of the recently described link between ESAM and perinatal stroke. Our data also highlight NID1 as a candidate gene for the condition. This study suggests that monogenic disorders are important contributors to the pathogenesis of PPS and should be investigated by untargeted sequencing especially when traditional risk factors are excluded.


Subject(s)
Stroke , Infant , Infant, Newborn , Child , Pregnancy , Female , Humans , Saudi Arabia , Stroke/genetics , Stroke/diagnosis , Neuroimaging/adverse effects , Genomics , Risk Factors
2.
Clin Genet ; 105(5): 488-498, 2024 05.
Article in English | MEDLINE | ID: mdl-38193334

ABSTRACT

ALDH1L2, a mitochondrial enzyme in folate metabolism, converts 10-formyl-THF (10-formyltetrahydrofolate) to THF (tetrahydrofolate) and CO2. At the cellular level, deficiency of this NADP+-dependent reaction results in marked reduction in NADPH/NADP+ ratio and reduced mitochondrial ATP. Thus far, a single patient with biallelic ALDH1L2 variants and the phenotype of a neurodevelopmental disorder has been reported. Here, we describe another patient with a neurodevelopmental disorder associated with a novel homozygous missense variant in ALDH1L2, Pro133His. The variant caused marked reduction in the ALDH1L2 enzyme activity in skin fibroblasts derived from the patient as probed by 10-FDDF, a stable synthetic analog of 10-formyl-THF. Additional associated abnormalities in these fibroblasts include reduced NADPH/NADP+ ratio and pool of mitochondrial ATP, upregulated autophagy and dramatically altered metabolomic profile. Overall, our study further supports a link between ALDH1L2 deficiency and abnormal neurodevelopment in humans.


Subject(s)
Oxidoreductases Acting on CH-NH Group Donors , Humans , Adenosine Triphosphate , NADP/genetics , Oxidoreductases Acting on CH-NH Group Donors/genetics , Oxidoreductases Acting on CH-NH Group Donors/metabolism , Phenotype
3.
Brain ; 146(11): 4547-4561, 2023 11 02.
Article in English | MEDLINE | ID: mdl-37459438

ABSTRACT

SLC4A10 is a plasma-membrane bound transporter that utilizes the Na+ gradient to drive cellular HCO3- uptake, thus mediating acid extrusion. In the mammalian brain, SLC4A10 is expressed in principal neurons and interneurons, as well as in epithelial cells of the choroid plexus, the organ regulating the production of CSF. Using next generation sequencing on samples from five unrelated families encompassing nine affected individuals, we show that biallelic SLC4A10 loss-of-function variants cause a clinically recognizable neurodevelopmental disorder in humans. The cardinal clinical features of the condition include hypotonia in infancy, delayed psychomotor development across all domains and intellectual impairment. Affected individuals commonly display traits associated with autistic spectrum disorder including anxiety, hyperactivity and stereotyped movements. In two cases isolated episodes of seizures were reported in the first few years of life, and a further affected child displayed bitemporal epileptogenic discharges on EEG without overt clinical seizures. While occipitofrontal circumference was reported to be normal at birth, progressive postnatal microcephaly evolved in 7 out of 10 affected individuals. Neuroradiological features included a relative preservation of brain volume compared to occipitofrontal circumference, characteristic narrow sometimes 'slit-like' lateral ventricles and corpus callosum abnormalities. Slc4a10 -/- mice, deficient for SLC4A10, also display small lateral brain ventricles and mild behavioural abnormalities including delayed habituation and alterations in the two-object novel object recognition task. Collapsed brain ventricles in both Slc4a10-/- mice and affected individuals suggest an important role of SLC4A10 in the production of the CSF. However, it is notable that despite diverse roles of the CSF in the developing and adult brain, the cortex of Slc4a10-/- mice appears grossly intact. Co-staining with synaptic markers revealed that in neurons, SLC4A10 localizes to inhibitory, but not excitatory, presynapses. These findings are supported by our functional studies, which show the release of the inhibitory neurotransmitter GABA is compromised in Slc4a10-/- mice, while the release of the excitatory neurotransmitter glutamate is preserved. Manipulation of intracellular pH partially rescues GABA release. Together our studies define a novel neurodevelopmental disorder associated with biallelic pathogenic variants in SLC4A10 and highlight the importance of further analyses of the consequences of SLC4A10 loss-of-function for brain development, synaptic transmission and network properties.


Subject(s)
Seizures , Sodium-Bicarbonate Symporters , Child , Mice , Humans , Animals , Sodium-Bicarbonate Symporters/genetics , Sodium-Bicarbonate Symporters/metabolism , Seizures/genetics , Mutation/genetics , Neurotransmitter Agents , gamma-Aminobutyric Acid/genetics , Mammals/metabolism , Chloride-Bicarbonate Antiporters/genetics , Chloride-Bicarbonate Antiporters/metabolism
4.
Hum Genet ; 142(4): 477-482, 2023 Apr.
Article in English | MEDLINE | ID: mdl-36715754

ABSTRACT

Ichthyosis is a genetically heterogeneous genodermatosis characterized by severely rough, dry and scaly skin. We report two consanguineous families with congenital ichthyosis. Combined positional mapping and exome sequencing of the two families revealed novel homozygous likely deleterious variants in PRSS8 (encoding prostasin) within a linkage locus on chromosome 16. One variant involved a canonical splice site and was associated with reduced abundance of the normal transcript, while the other was a missense variant that altered a highly conserved residue. The phenotype of Prss8 knockout mouse bears a striking resemblance to the one we describe in human patients, including the skin histopathology. Our data suggest a novel PRSS8-related ichthyosis disorder.


Subject(s)
Ichthyosis , Serine Endopeptidases , Animals , Humans , Mice , Ichthyosis/genetics , Mice, Knockout , Mutation , Mutation, Missense , Pedigree , Phenotype , Serine Endopeptidases/genetics
5.
Hum Genet ; 142(10): 1491-1498, 2023 Oct.
Article in English | MEDLINE | ID: mdl-37656279

ABSTRACT

DBR1 encodes the only known human lariat debranching enzyme and its deficiency has been found to cause an autosomal recessive inborn error of immunity characterized by pediatric brainstem viral-induced encephalitis (MIM 619441). We describe a distinct allelic disorder caused by a founder recessive DBR1 variant in four families (DBR1(NM_016216.4):c.200A > G (p.Tyr67Cys)). Consistent features include prematurity, severe intrauterine growth deficiency, congenital ichthyosis-like presentation (collodion membrane, severe skin peeling and xerosis), and death before the first year of life. Patient-derived fibroblasts displayed the characteristic accumulation of intron lariats in their RNA as revealed by targeted and untargeted analysis, in addition to a marked reduction of DBR1 on immunoblot analysis. We propose a novel DBR1-related developmental disorder that is distinct from DBR1-related encephalitis susceptibility and highlight the apparent lack of correlation with the degree of DBR1 deficiency.


Subject(s)
Encephalitis , Ichthyosis , Child , Humans , Alleles , Causality , Fibroblasts , Ichthyosis/genetics
6.
Am J Hum Genet ; 106(2): 246-255, 2020 02 06.
Article in English | MEDLINE | ID: mdl-32004447

ABSTRACT

Ral (Ras-like) GTPases play an important role in the control of cell migration and have been implicated in Ras-mediated tumorigenicity. Recently, variants in RALA were also described as a cause of intellectual disability and developmental delay, indicating the relevance of this pathway to neuropediatric diseases. Here, we report the identification of bi-allelic variants in RALGAPA1 (encoding Ral GTPase activating protein catalytic alpha subunit 1) in four unrelated individuals with profound neurodevelopmental disability, muscular hypotonia, feeding abnormalities, recurrent fever episodes, and infantile spasms . Dysplasia of corpus callosum with focal thinning of the posterior part and characteristic facial features appeared to be unifying findings. RalGAPA1 was absent in the fibroblasts derived from two affected individuals suggesting a loss-of-function effect of the RALGAPA1 variants. Consequently, RalA activity was increased in these cell lines, which is in keeping with the idea that RalGAPA1 deficiency causes a constitutive activation of RalA. Additionally, levels of RalGAPB, a scaffolding subunit of the RalGAP complex, were dramatically reduced, indicating a dysfunctional RalGAP complex. Moreover, RalGAPA1 deficiency clearly increased cell-surface levels of lipid raft components in detached fibroblasts, which might indicate that anchorage-dependence of cell growth signaling is disturbed. Our findings indicate that the dysregulation of the RalA pathway has an important impact on neuronal function and brain development. In light of the partially overlapping phenotype between RALA- and RALGAPA1-associated diseases, it appears likely that dysregulation of the RalA signaling pathway leads to a distinct group of genetic syndromes that we suggest could be named RALopathies.


Subject(s)
Feeding and Eating Disorders/etiology , GTPase-Activating Proteins/genetics , Muscle Hypotonia/etiology , Mutation , Nerve Tissue Proteins/genetics , Neurodevelopmental Disorders/etiology , Spasms, Infantile/etiology , Alleles , Cell Movement , Cell Proliferation , Child, Preschool , Family , Feeding and Eating Disorders/pathology , Female , Humans , Infant , Male , Muscle Hypotonia/pathology , Neurodevelopmental Disorders/pathology , Phenotype , Spasms, Infantile/pathology
7.
Hum Genet ; 141(1): 55-64, 2022 Jan.
Article in English | MEDLINE | ID: mdl-34750646

ABSTRACT

Mitochondrial disorders are challenging to diagnose. Exome sequencing has greatly enhanced the diagnostic precision of these disorders although interpreting variants of uncertain significance (VUS) remains a formidable obstacle. Whether specific mitochondrial morphological changes can aid in the classification of these variants is unknown. Here, we describe two families (four patients), each with a VUS in a gene known to affect the morphology of mitochondria through a specific role in the fission-fusion balance. In the first, the missense variant in MFF, encoding a fission factor, was associated with impaired fission giving rise to a characteristically over-tubular appearance of mitochondria. In the second, the missense variant in DNAJA3, which has no listed OMIM phenotype, was associated with fragmented appearance of mitochondria consistent with its published deficiency states. In both instances, the highly specific phenotypes allowed us to upgrade the classification of the variants. Our results suggest that, in select cases, mitochondrial "dysmorphology" can be helpful in interpreting variants to reach a molecular diagnosis.


Subject(s)
HSP40 Heat-Shock Proteins/genetics , Membrane Proteins/genetics , Mitochondria/physiology , Mitochondrial Diseases/genetics , Mitochondrial Dynamics , Mitochondrial Proteins/genetics , Cell Line , Child , Child, Preschool , Female , Genetic Variation , Humans , Male , Microscopy, Electron, Transmission , Mitochondria/ultrastructure , Mitochondrial Diseases/diagnosis , Molecular Diagnostic Techniques/methods , Mutation, Missense , Exome Sequencing
8.
Am J Hum Genet ; 102(1): 116-132, 2018 01 04.
Article in English | MEDLINE | ID: mdl-29290337

ABSTRACT

Whole-exome and targeted sequencing of 13 individuals from 10 unrelated families with overlapping clinical manifestations identified loss-of-function and missense variants in KIAA1109 allowing delineation of an autosomal-recessive multi-system syndrome, which we suggest to name Alkuraya-Kucinskas syndrome (MIM 617822). Shared phenotypic features representing the cardinal characteristics of this syndrome combine brain atrophy with clubfoot and arthrogryposis. Affected individuals present with cerebral parenchymal underdevelopment, ranging from major cerebral parenchymal thinning with lissencephalic aspect to moderate parenchymal rarefaction, severe to mild ventriculomegaly, cerebellar hypoplasia with brainstem dysgenesis, and cardiac and ophthalmologic anomalies, such as microphthalmia and cataract. Severe loss-of-function cases were incompatible with life, whereas those individuals with milder missense variants presented with severe global developmental delay, syndactyly of 2nd and 3rd toes, and severe muscle hypotonia resulting in incapacity to stand without support. Consistent with a causative role for KIAA1109 loss-of-function/hypomorphic variants in this syndrome, knockdowns of the zebrafish orthologous gene resulted in embryos with hydrocephaly and abnormally curved notochords and overall body shape, whereas published knockouts of the fruit fly and mouse orthologous genes resulted in lethality or severe neurological defects reminiscent of the probands' features.


Subject(s)
Arthrogryposis/genetics , Brain/embryology , Mutation/genetics , Proteins/genetics , Adolescent , Animals , Brain/diagnostic imaging , Brain/pathology , Child , Female , Gene Knockdown Techniques , Humans , Infant , Infant, Newborn , Magnetic Resonance Imaging , Male , Pedigree , Zebrafish , Zebrafish Proteins/genetics
9.
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
10.
Am J Med Genet A ; 185(12): 3859-3865, 2021 12.
Article in English | MEDLINE | ID: mdl-34327814

ABSTRACT

Intellectual disability (ID) is one of the most common disabilities in humans. In an effort to contribute to the expanding genetic landscape of ID, we describe a novel autosomal recessive ID candidate gene. Combined autozygome/exome analysis was performed in two unrelated consanguineous families with ID. Each of the two families had a novel homozygous likely deleterious variant in PLXNA2 and displayed the core phenotype of ID. PLXNA2 belongs to a family of transmembrane proteins that function as semaphorin receptors. Sema5A-PlexinA2 is known to regulate brain development in mouse, and Plxna2-/- mice display defective associative learning, sociability, and sensorimotor gating. We note the existence of variability in the phenotype among the three patients, including the existence of variable degree of ID, ranging from borderline intellectual functioning to moderate-severe ID, and the presence of cardiac anomalies in only one of the patients. We propose incomplete penetrance as a possible explanation of the observed difference in phenotypes. Future cases will be needed to support the proposed link between PLXNA2 and ID in humans.


Subject(s)
Genetic Predisposition to Disease , Intellectual Disability/genetics , Nerve Tissue Proteins/genetics , Receptors, Cell Surface/genetics , Animals , Child , Child, Preschool , Consanguinity , Exome/genetics , Female , Genetic Association Studies , Homozygote , Humans , Infant , Intellectual Disability/pathology , Male , Mice , Mice, Knockout , Mutation/genetics , Pedigree
11.
Hum Genet ; 139(10): 1273-1283, 2020 Oct.
Article in English | MEDLINE | ID: mdl-32367404

ABSTRACT

Unlike disorders of primary cilium, primary ciliary dyskinesia (PCD) has a much narrower clinical spectrum consistent with the limited tissue distribution of motile cilia. Nonetheless, PCD diagnosis can be challenging due to the overlapping features with other disorders and the requirement for sophisticated tests that are only available in specialized centers. We performed exome sequencing on all patients with a clinical suspicion of PCD but for whom no nasal nitric oxide test or ciliary functional assessment could be ordered. Among 81 patients (56 families), in whom PCD was suspected, 68% had pathogenic or likely pathogenic variants in established PCD-related genes that fully explain the phenotype (20 variants in 11 genes). The major clinical presentations were sinopulmonary infections (SPI) (n = 58), neonatal respiratory distress (NRD) (n = 2), laterality defect (LD) (n = 6), and combined LD/SPI (n = 15). Biallelic likely deleterious variants were also encountered in AKNA and GOLGA3, which we propose as novel candidates in a lung phenotype that overlaps clinically with PCD. We also encountered a PCD phenocopy caused by a pathogenic variant in ITCH, and a pathogenic variant in CEP164 causing Bardet-Biedl syndrome and PCD presentation as a very rare example of the dual presentation of these two disorders of the primary and motile cilia. Exome sequencing is a powerful tool that can help "democratize" the diagnosis of PCD, which is currently limited to highly specialized centers.


Subject(s)
Cilia/metabolism , Ciliary Motility Disorders/genetics , Genetic Predisposition to Disease , Pneumonia/genetics , Respiratory Distress Syndrome, Newborn/genetics , Sinusitis/genetics , Autoantigens/genetics , Cilia/pathology , Ciliary Motility Disorders/complications , Ciliary Motility Disorders/diagnosis , Ciliary Motility Disorders/pathology , Consanguinity , DNA-Binding Proteins/genetics , Female , Gene Expression , Golgi Matrix Proteins/genetics , Humans , Male , Microtubule Proteins/genetics , Mutation , Nuclear Proteins/genetics , Pedigree , Phenotype , Pneumonia/complications , Pneumonia/diagnosis , Pneumonia/pathology , Repressor Proteins/genetics , Respiratory Distress Syndrome, Newborn/complications , Respiratory Distress Syndrome, Newborn/diagnosis , Respiratory Distress Syndrome, Newborn/pathology , Respiratory Mucosa/metabolism , Respiratory Mucosa/pathology , Saudi Arabia , Sinusitis/complications , Sinusitis/diagnosis , Sinusitis/pathology , Transcription Factors/genetics , Ubiquitin-Protein Ligases/genetics , Exome Sequencing
12.
Am J Hum Genet ; 100(5): 831-836, 2017 May 04.
Article in English | MEDLINE | ID: mdl-28475863

ABSTRACT

Larsen syndrome is characterized by the dislocation of large joints and other less consistent clinical findings. Heterozygous FLNB mutations account for the majority of Larsen syndrome cases, but biallelic mutations in CHST3 and B4GALT7 have been more recently described, thus confirming the existence of recessive forms of the disease. In a multiplex consanguineous Saudi family affected by severe and recurrent large joint dislocation and severe myopia, we identified a homozygous truncating variant in GZF1 through a combined autozygome and exome approach. Independently, the same approach identified a second homozygous truncating GZF1 variant in another multiplex consanguineous family affected by severe myopia, retinal detachment, and milder skeletal involvement. GZF1 encodes GDNF-inducible zinc finger protein 1, a transcription factor of unknown developmental function, which we found to be expressed in the eyes and limbs of developing mice. Global transcriptional profiling of cells from affected individuals revealed a shared pattern of gene dysregulation and significant enrichment of genes encoding matrix proteins, including P3H2, which hints at a potential disease mechanism. Our results suggest that GZF1 mutations cause a phenotype of severe myopia and significant articular involvement not previously described in Larsen syndrome.


Subject(s)
Genetic Heterogeneity , Kruppel-Like Transcription Factors/genetics , Osteochondrodysplasias/genetics , Adolescent , Alleles , Child , Child, Preschool , Exome , Female , Gene Expression Regulation , Genes, Recessive , Homozygote , Humans , Male , Mutation , Pedigree , Phenotype , Sequence Analysis, DNA , Young Adult
13.
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
14.
Clin Genet ; 97(4): 661-665, 2020 04.
Article in English | MEDLINE | ID: mdl-31898316

ABSTRACT

Erythrokeratoderma (EK) is heterogeneous clinical entity characterized by excessive scaling with resulting erythrokeratotic plaques. Several genes have been linked to EK and they encode a number of proteins that are important for the integrity of the keratinocyte layer of the epidermis. PERP is a transcription factor that is activated by both p53 and p63. However, its deficiency in a mouse model appears to only recapitulate p63-mediated role in skin development and organization. We report an extended multiplex consanguineous family in which an EK phenotype with a striking similarity to that observed in Perp-/- mice, is mapped to an autozygous region on chromosome 6 that spans PERP. Whole-exome sequencing revealed a novel variant in PERP that fully segregated with the phenotype. Functional analysis of patient- and control-derived keratinocytes revealed a deleterious effect of the identified variant on the intracellular localization of PERP. A previous report showed that PERP mutation causes a dominant form of keratoderma but a single patient in that report with a homozygous variant in PERP suggests that recessive inheritance is also possible. Our results, therefore, support the establishment of an autosomal recessive PERP-related EK phenotype in humans.


Subject(s)
Leukemia, Myeloid, Acute/genetics , Membrane Proteins/genetics , Adolescent , Adult , Animals , Child , Child, Preschool , Epidermis/metabolism , Epidermis/pathology , Gene Expression Regulation/genetics , Genes, Recessive/genetics , Genes, Tumor Suppressor , Homozygote , Humans , Keratinocytes/metabolism , Keratinocytes/pathology , Leukemia, Myeloid, Acute/pathology , Mice , Exome Sequencing , Young Adult
15.
J Allergy Clin Immunol ; 144(2): 574-583.e5, 2019 08.
Article in English | MEDLINE | ID: mdl-30872117

ABSTRACT

BACKGROUND: The tumor TNF receptor family member 4-1BB (CD137) is encoded by TNFRSF9 and expressed on activated T cells. 4-1BB provides a costimulatory signal that enhances CD8+ T-cell survival, cytotoxicity, and mitochondrial activity, thereby promoting immunity against viruses and tumors. The ligand for 4-1BB is expressed on antigen-presenting cells and EBV-transformed B cells. OBJECTIVE: We investigated the genetic basis of recurrent sinopulmonary infections, persistent EBV viremia, and EBV-induced lymphoproliferation in 2 unrelated patients. METHODS: Whole-exome sequencing, immunoblotting, immunophenotyping, and in vitro assays of lymphocyte and mitochondrial function were performed. RESULTS: The 2 patients shared a homozygous G109S missense mutation in 4-1BB that abolished protein expression and ligand binding. The patients' CD8+ T cells had reduced proliferation, impaired expression of IFN-γ and perforin, and diminished cytotoxicity against allogeneic and HLA-matched EBV-B cells. Mitochondrial biogenesis, membrane potential, and function were significantly reduced in the patients' activated T cells. An inhibitory antibody against 4-1BB recapitulated the patients' defective CD8+ T-cell activation and cytotoxicity against EBV-infected B cells in vitro. CONCLUSION: This novel immunodeficiency demonstrates the critical role of 4-1BB costimulation in host immunity against EBV infection.


Subject(s)
Epstein-Barr Virus Infections/immunology , Herpesvirus 4, Human/immunology , Lymphoproliferative Disorders/immunology , Mutation, Missense , Primary Immunodeficiency Diseases/immunology , Tumor Necrosis Factor Receptor Superfamily, Member 9/immunology , B-Lymphocytes/immunology , B-Lymphocytes/pathology , CD8-Positive T-Lymphocytes/immunology , CD8-Positive T-Lymphocytes/pathology , Child, Preschool , Epstein-Barr Virus Infections/genetics , Epstein-Barr Virus Infections/pathology , Female , Herpesvirus 4, Human/genetics , Humans , Lymphoproliferative Disorders/genetics , Lymphoproliferative Disorders/pathology , Lymphoproliferative Disorders/virology , Male , Primary Immunodeficiency Diseases/genetics , Primary Immunodeficiency Diseases/pathology , Primary Immunodeficiency Diseases/virology , Tumor Necrosis Factor Receptor Superfamily, Member 9/genetics , Exome Sequencing
16.
Hum Genet ; 138(3): 221-229, 2019 Mar.
Article in English | MEDLINE | ID: mdl-30758658

ABSTRACT

Nuclear pore complex (NPC) is a fundamental component of the nuclear envelope and is key to the nucleocytoplasmic transport. Mutations in several NUP genes that encode individual components of NPC known as nucleoporins have been identified in recent years among patients with static encephalopathies characterized by developmental delay and microcephaly. We describe a multiplex consanguineous family in which four affected members presented with severe neonatal hypotonia, profound global developmental delay, progressive microcephaly and early death. Autozygome and linkage analysis revealed that this phenotype is linked to a founder disease haplotype (chr9:127,113,732-135,288,807) in which whole exome sequencing revealed the presence of a novel homozygous missense variant in NUP214. Functional analysis of patient-derived fibroblasts recapitulated the dysmorphic phenotype of nuclei that was previously described in NUP214 knockdown cells. In addition, the typical rim staining of NUP214 is largely displaced, further supporting the deleterious effect of the variant. Our data expand the list of NUP genes that are mutated in encephalopathy disorders in humans.


Subject(s)
Brain Diseases/diagnosis , Brain Diseases/genetics , Genetic Association Studies , Genetic Predisposition to Disease , Microcephaly/diagnosis , Microcephaly/genetics , Nuclear Pore Complex Proteins/deficiency , Amino Acid Sequence , Consanguinity , Female , Genes, Recessive , Genetic Linkage , Homozygote , Humans , Infant , Mutation , Pedigree , Phenotype , Severity of Illness Index , Exome Sequencing
17.
Hum Genet ; 138(11-12): 1247-1257, 2019 Dec.
Article in English | MEDLINE | ID: mdl-31538237

ABSTRACT

The reversible oxidation of L-malate to oxaloacetate is catalyzed by NAD(H)-dependent malate dehydrogenase (MDH). MDH plays essential roles in the malate-aspartate shuttle and the tricarboxylic acid cycle. These metabolic processes are important in mitochondrial NADH supply for oxidative phosphorylation. Recently, bi-allelic mutations in mitochondrial MDH2 were identified in patients with global developmental delay, epilepsy and lactic acidosis. We now report two patients from an extended consanguineous family with a deleterious variant in the cytosolic isoenzyme of MDH (MDH1). The homozygous missense variant in the NAD+-binding domain of MDH1 led to severely diminished MDH protein expression. The patients presented with global developmental delay, epilepsy and progressive microcephaly. Both patients had normal concentrations of plasma amino acids, acylcarnitines, lactate, and urine organic acids. To identify the metabolic consequences of MDH1 deficiency, untargeted metabolomics was performed on dried blood spots (DBS) from the patients and in MDH1 knockout HEK293 cells that were generated by Crispr/Cas9. Increased levels of glutamate and glycerol-3-phosphate were found in DBS of both patients. In MDH1 KO HEK293 cells, increased levels of glycerol-3-phosphate were also observed, as well as increased levels of aspartate and decreased levels of fumarate. The consistent finding of increased concentrations of glycerol-3-phosphate may represent a compensatory mechanism to enhance cytosolic oxidation of NADH by the glycerol-P-shuttle. In conclusion, MDH1 deficiency is a new metabolic defect in the malate-aspartate shuttle characterized by a severe neurodevelopmental phenotype with elevated concentrations of glycerol-3-phosphate as a potential biomarker.


Subject(s)
Aspartic Acid/metabolism , Brain Diseases/metabolism , Brain Diseases/pathology , Malate Dehydrogenase/deficiency , Malates/metabolism , Metabolic Diseases/etiology , Age of Onset , Brain Diseases/complications , Child, Preschool , Female , Humans , Male , Metabolic Diseases/metabolism , Metabolic Diseases/pathology , Metabolome , Pedigree
18.
Am J Hum Genet ; 98(1): 210-5, 2016 Jan 07.
Article in English | MEDLINE | ID: mdl-26708753

ABSTRACT

Brain channelopathies represent a growing class of brain disorders that usually result in paroxysmal disorders, although their role in other neurological phenotypes, including the recently described NALCN-related infantile encephalopathy, is increasingly recognized. In three Saudi Arabian families and one Egyptian family all affected by a remarkably similar phenotype (infantile encephalopathy and largely normal brain MRI) to that of NALCN-related infantile encephalopathy, we identified a locus on 2q34 in which whole-exome sequencing revealed three, including two apparently loss-of-function, recessive mutations in UNC80. UNC80 encodes a large protein that is necessary for the stability and function of NALCN and for bridging NALCN to UNC79 to form a functional complex. Our results expand the clinical relevance of the UNC79-UNC80-NALCN channel complex.


Subject(s)
Brain Diseases/genetics , Carrier Proteins/genetics , Membrane Proteins/genetics , Mutation , Sodium Channels/genetics , Child , Child, Preschool , Female , Genes, Recessive , Humans , Infant , Infant, Newborn , Ion Channels , Male , Severity of Illness Index
19.
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
20.
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
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