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1.
Mol Cell ; 79(1): 30-42.e4, 2020 07 02.
Article in English | MEDLINE | ID: mdl-32473093

ABSTRACT

Autophagy is activated by prolonged fasting but cannot overcome the ensuing hepatic lipid overload, resulting in fatty liver. Here, we describe a peroxisome-lysosome metabolic link that restricts autophagic degradation of lipids. Acyl-CoA oxidase 1 (Acox1), the enzyme that catalyzes the first step in peroxisomal ß-oxidation, is enriched in liver and further increases with fasting or high-fat diet (HFD). Liver-specific Acox1 knockout (Acox1-LKO) protected mice against hepatic steatosis caused by starvation or HFD due to induction of autophagic degradation of lipid droplets. Hepatic Acox1 deficiency markedly lowered total cytosolic acetyl-CoA levels, which led to decreased Raptor acetylation and reduced lysosomal localization of mTOR, resulting in impaired activation of mTORC1, a central regulator of autophagy. Dichloroacetic acid treatment elevated acetyl-CoA levels, restored mTORC1 activation, inhibited autophagy, and increased hepatic triglycerides in Acox1-LKO mice. These results identify peroxisome-derived acetyl-CoA as a key metabolic regulator of autophagy that controls hepatic lipid homeostasis.


Subject(s)
Acetyl Coenzyme A/metabolism , Acyl-CoA Oxidase/physiology , Autophagy , Fatty Acids/chemistry , Fatty Liver/pathology , Mechanistic Target of Rapamycin Complex 1/metabolism , Peroxisomes/chemistry , Acetylation , Animals , Autophagy-Related Protein 5/physiology , Diet, High-Fat/adverse effects , Fasting , Fatty Liver/etiology , Fatty Liver/metabolism , Female , Male , Mechanistic Target of Rapamycin Complex 1/genetics , Mice , Mice, Knockout , Mitochondria/metabolism , Oxidation-Reduction , Peroxisomes/metabolism , Regulatory-Associated Protein of mTOR/genetics , Regulatory-Associated Protein of mTOR/metabolism
2.
Hum Mol Genet ; 2024 May 22.
Article in English | MEDLINE | ID: mdl-38776958

ABSTRACT

The ubiquitin-proteasome system mediates the degradation of a wide variety of proteins. Proteasome dysfunction is associated with neurodegenerative diseases and neurodevelopmental disorders in humans. Here we identified mutations in PSMC5, an AAA ATPase subunit of the proteasome 19S regulatory particle, in individuals with neurodevelopmental disorders, which were initially considered as variants of unknown significance. We have now found heterozygotes with the following mutations: P320R (6 individuals), R325W, Q160A, and one nonsense mutation at Q69. We focused on understanding the functional consequence of PSMC5 insufficiency and the P320R mutation in cells and found that both impair proteasome function and activate apoptosis. Interestingly, the P320R mutation impairs proteasome function by weakening the association between the 19S regulatory particle and the 20S core particle. Our study supports that proteasome dysfunction is the pathogenic cause of neurodevelopmental disorders in individuals carrying PSMC5 variants.

3.
Genet Med ; 26(6): 101119, 2024 06.
Article in English | MEDLINE | ID: mdl-38465576

ABSTRACT

PURPOSE: Fem1 homolog B (FEM1B) acts as a substrate recognition subunit for ubiquitin ligase complexes belonging to the CULLIN 2-based E3 family. Several biological functions have been proposed for FEM1B, including a structurally resolved function as a sensor for redox cell status by controlling mitochondrial activity, but its implication in human disease remains elusive. METHODS: To understand the involvement of FEM1B in human disease, we made use of Matchmaker exchange platforms to identify individuals with de novo variants in FEM1B and performed their clinical evaluation. We performed functional validation using primary neuronal cultures and in utero electroporation assays, as well as experiments on patient's cells. RESULTS: Five individuals with a recurrent de novo missense variant in FEM1B were identified: NM_015322.5:c.377G>A NP_056137.1:p.(Arg126Gln) (FEM1BR126Q). Affected individuals shared a severe neurodevelopmental disorder with behavioral phenotypes and a variable set of malformations, including brain anomalies, clubfeet, skeletal abnormalities, and facial dysmorphism. Overexpression of the FEM1BR126Q variant but not FEM1B wild-type protein, during mouse brain development, resulted in delayed neuronal migration of the target cells. In addition, the individuals' cells exhibited signs of oxidative stress and induction of type I interferon signaling. CONCLUSION: Overall, our data indicate that p.(Arg126Gln) induces aberrant FEM1B activation, resulting in a gain-of-function mechanism associated with a severe syndromic developmental disorder in humans.


Subject(s)
Mutation, Missense , Neurodevelopmental Disorders , Ubiquitin-Protein Ligases , Humans , Mutation, Missense/genetics , Female , Mice , Male , Animals , Neurodevelopmental Disorders/genetics , Neurodevelopmental Disorders/pathology , Ubiquitin-Protein Ligases/genetics , Child , Child, Preschool , Phenotype , Cell Cycle Proteins/genetics , Cell Cycle Proteins/metabolism , Neurons/metabolism , Neurons/pathology , Infant
4.
Anal Bioanal Chem ; 416(8): 1907-1922, 2024 Mar.
Article in English | MEDLINE | ID: mdl-38332189

ABSTRACT

Smokeless powders (SLPs) are composed of a combination of thermolabile and non-thermolabile compounds. When analysed by GC-MS, injection conditions may therefore play a fundamental role on the characterisation of forensic samples. However, no systematic investigations have ever been carried out. This casts doubt on the optimal conditions that should be adopted in advanced profiling applications (e.g. class attribution and source association), especially when a traditional split/splitless (S/SL) injector is used. Herein, a study is reported that specifically focused on the evaluation of the liner type (Ltype) and inlet temperature (Tinj). Results showed that both could affect the exhaustiveness and repeatability of the observed chemical profiles, with Ltype being particularly sensitive despite typically not being clarified in published works. Perhaps as expected, degradation effects were observed for the most thermolabile compounds (e.g. nitroglycerin) at conditions maximising the heat transfer rates (Ltype = packed and Tinj ≥ 200 °C). However, these did not seem to be as influential as, perhaps, suggested in previous studies. Indeed, the harshest injection conditions in terms of heat transfer rate (Ltype = packed and Tinj = 260 °C) were found to lead to better performances (including better overall %RSDs and LODs) compared to the mildest ones. This suggested that implementing conditions minimising heat-induced breakdowns during injection was not necessarily a good strategy for comparison purposes. The reported findings represent a concrete step forward in the field, providing a robust body of data for the development of the next generation of SLP profiling methods.

5.
Am J Hum Genet ; 106(2): 272-279, 2020 02 06.
Article in English | MEDLINE | ID: mdl-32004445

ABSTRACT

Recent studies have identified both recessive and dominant forms of mitochondrial disease that result from ATAD3A variants. The recessive form includes subjects with biallelic deletions mediated by non-allelic homologous recombination. We report five unrelated neonates with a lethal metabolic disorder characterized by cardiomyopathy, corneal opacities, encephalopathy, hypotonia, and seizures in whom a monoallelic reciprocal duplication at the ATAD3 locus was identified. Analysis of the breakpoint junction fragment indicated that these 67 kb heterozygous duplications were likely mediated by non-allelic homologous recombination at regions of high sequence identity in ATAD3A exon 11 and ATAD3C exon 7. At the recombinant junction, the duplication allele produces a fusion gene derived from ATAD3A and ATAD3C, the protein product of which lacks key functional residues. Analysis of fibroblasts derived from two affected individuals shows that the fusion gene product is expressed and stable. These cells display perturbed cholesterol and mitochondrial DNA organization similar to that observed for individuals with severe ATAD3A deficiency. We hypothesize that the fusion protein acts through a dominant-negative mechanism to cause this fatal mitochondrial disorder. Our data delineate a molecular diagnosis for this disorder, extend the clinical spectrum associated with structural variation at the ATAD3 locus, and identify a third mutational mechanism for ATAD3 gene cluster variants. These results further affirm structural variant mutagenesis mechanisms in sporadic disease traits, emphasize the importance of copy number analysis in molecular genomic diagnosis, and highlight some of the challenges of detecting and interpreting clinically relevant rare gene rearrangements from next-generation sequencing data.


Subject(s)
ATPases Associated with Diverse Cellular Activities/genetics , Cholesterol/metabolism , Gene Duplication , Homologous Recombination , Membrane Proteins/genetics , Mitochondria/pathology , Mitochondrial Diseases/pathology , Mitochondrial Proteins/genetics , ATPases Associated with Diverse Cellular Activities/chemistry , Amino Acid Sequence , Brain Diseases/etiology , Brain Diseases/metabolism , Brain Diseases/pathology , Cardiomyopathies/etiology , Cardiomyopathies/metabolism , Cardiomyopathies/pathology , Corneal Opacity/etiology , Corneal Opacity/metabolism , Corneal Opacity/pathology , DNA Copy Number Variations , Female , Gene Rearrangement , Humans , Infant , Infant, Newborn , Male , Membrane Proteins/chemistry , Mitochondria/genetics , Mitochondria/metabolism , Mitochondrial Diseases/genetics , Mitochondrial Diseases/metabolism , Mitochondrial Proteins/chemistry , Muscle Hypotonia/etiology , Muscle Hypotonia/metabolism , Muscle Hypotonia/pathology , Mutation , Protein Conformation , Seizures/etiology , Seizures/metabolism , Seizures/pathology , Sequence Homology
6.
Chem Res Toxicol ; 36(3): 390-401, 2023 03 20.
Article in English | MEDLINE | ID: mdl-36812109

ABSTRACT

Drug-responsive T-cells are activated with the parent compound or metabolites, often via different pathways (pharmacological interaction and hapten). An obstacle to the investigation of drug hypersensitivity is the scarcity of reactive metabolites for functional studies and the absence of coculture systems to generate metabolites in situ. Thus, the aim of this study was to utilize dapsone metabolite-responsive T-cells from hypersensitive patients, alongside primary human hepatocytes to drive metabolite formation, and subsequent drug-specific T-cell responses. Nitroso dapsone-responsive T-cell clones were generated from hypersensitive patients and characterized in terms of cross-reactivity and pathways of T-cell activation. Primary human hepatocytes, antigen-presenting cells, and T-cell cocultures were established in various formats with the liver and immune cells separated to avoid cell contact. Cultures were exposed to dapsone, and metabolite formation and T-cell activation were measured by LC-MS and proliferation assessment, respectively. Nitroso dapsone-responsive CD4+ T-cell clones from hypersensitive patients were found to proliferate and secrete cytokines in a dose-dependent manner when exposed to the drug metabolite. Clones were activated with nitroso dapsone-pulsed antigen-presenting cells, while fixation of antigen-presenting cells or omission of antigen-presenting cells from the assay abrogated the nitroso dapsone-specific T-cell response. Importantly, clones displayed no cross-reactivity with the parent drug. Nitroso dapsone glutathione conjugates were detected in the supernatant of hepatocyte immune cell cocultures, indicating that hepatocyte-derived metabolites are formed and transferred to the immune cell compartment. Similarly, nitroso dapsone-responsive clones were stimulated to proliferate with dapsone, when hepatocytes were added to the coculture system. Collectively, our study demonstrates the use of hepatocyte immune cell coculture systems to detect in situ metabolite formation and metabolite-specific T-cell responses. Similar systems should be used in future diagnostic and predictive assays to detect metabolite-specific T-cell responses when synthetic metabolites are not available.


Subject(s)
Drug Hypersensitivity , Humans , Coculture Techniques , Dapsone/pharmacology , Liver , Hepatocytes , Lymphocyte Activation
7.
Am J Hum Genet ; 104(2): 246-259, 2019 02 07.
Article in English | MEDLINE | ID: mdl-30661772

ABSTRACT

SOX4, together with SOX11 and SOX12, forms group C of SRY-related (SOX) transcription factors. They play key roles, often in redundancy, in multiple developmental pathways, including neurogenesis and skeletogenesis. De novo SOX11 heterozygous mutations have been shown to cause intellectual disability, growth deficiency, and dysmorphic features compatible with mild Coffin-Siris syndrome. Using trio-based exome sequencing, we here identify de novo SOX4 heterozygous missense variants in four children who share developmental delay, intellectual disability, and mild facial and digital morphological abnormalities. SOX4 is highly expressed in areas of active neurogenesis in human fetuses, and sox4 knockdown in Xenopus embryos diminishes brain and whole-body size. The SOX4 variants cluster in the highly conserved, SOX family-specific HMG domain, but each alters a different residue. In silico tools predict that each variant affects a distinct structural feature of this DNA-binding domain, and functional assays demonstrate that these SOX4 proteins carrying these variants are unable to bind DNA in vitro and transactivate SOX reporter genes in cultured cells. These variants are not found in the gnomAD database of individuals with presumably normal development, but 12 other SOX4 HMG-domain missense variants are recorded and all demonstrate partial to full activity in the reporter assay. Taken together, these findings point to specific SOX4 HMG-domain missense variants as the cause of a characteristic human neurodevelopmental disorder associated with mild facial and digital dysmorphism.


Subject(s)
Abnormalities, Multiple/genetics , Mutation, Missense/genetics , Neurodevelopmental Disorders/genetics , SOXC Transcription Factors/genetics , Amino Acid Sequence , Animals , Child , Child, Preschool , Coffin-Lowry Syndrome/genetics , Cohort Studies , Conserved Sequence , DNA/genetics , DNA/metabolism , Female , HMG-Box Domains/genetics , Heterozygote , Humans , Male , SOX Transcription Factors/chemistry , SOX Transcription Factors/genetics , SOXC Transcription Factors/chemistry , SOXC Transcription Factors/metabolism , Transcriptional Activation , Xenopus/anatomy & histology , Xenopus/embryology , Xenopus/genetics , Xenopus Proteins/chemistry , Xenopus Proteins/genetics
8.
Chem Res Toxicol ; 35(11): 2122-2132, 2022 11 21.
Article in English | MEDLINE | ID: mdl-36137197

ABSTRACT

ß-Lactamase inhibitors such as clavulanic acid and tazobactam were developed to overcome ß-lactam antibiotic resistance. Hypersensitivity reactions to these drugs have not been studied in detail, and the antigenic determinants that activate T-cells have not been defined. The objectives of this study were to (i) characterize clavulanate- and tazobactam-responsive T-cells from hypersensitive patients, (ii) explore clavulanate and tazobactam T-cell crossreactivity, and (iii) define the antigenic determinants that contribute to T-cell reactivity. Antigen specificity, pathways of T-cell activation, and crossreactivity with clavulanate- and tazobactam-specific T-cell clones were assessed by proliferation and cytokine release assays. Antigenic determinants were analyzed by mass spectrometry-based proteomics methods. Clavulanate- and tazobactam-responsive CD4+ T-cell clones were stimulated to proliferate and secrete IFN-γ in an MHC class II-restricted and dose-dependent manner. T-cell activation with clavulanate- and tazobactam was dependent on antigen presenting cells because their fixation prevented the T-cell response. Strong crossreactivity was observed between clavulanate- and tazobactam-T-cells; however, neither drug activated ß-lactam antibiotic-responsive T-cells. Mass spectrometric analysis revealed that both compounds form multiple antigenic determinants with lysine residues on proteins, including an overlapping aldehyde and hydrated aldehyde adduct with mass additions of 70 and 88 Da, respectively. Collectively, these data show that although clavulanate and tazobactam are structurally distinct, the antigenic determinants formed by both drugs overlap, which explains the observed T-cell cross-reactivity.


Subject(s)
T-Lymphocytes , beta-Lactamase Inhibitors , Humans , Clavulanic Acid/pharmacology , Tazobactam , Epitopes , Anti-Bacterial Agents/pharmacology , Aldehydes
9.
Am J Med Genet A ; 188(10): 2958-2968, 2022 10.
Article in English | MEDLINE | ID: mdl-35904974

ABSTRACT

Congenital diaphragmatic hernia (CDH) can occur in isolation or in conjunction with other birth defects (CDH+). A molecular etiology can only be identified in a subset of CDH cases. This is due, in part, to an incomplete understanding of the genes that contribute to diaphragm development. Here, we used clinical and molecular data from 36 individuals with CDH+ who are cataloged in the DECIPHER database to identify genes that may play a role in diaphragm development and to discover new phenotypic expansions. Among this group, we identified individuals who carried putatively deleterious sequence or copy number variants affecting CREBBP, SMARCA4, UBA2, and USP9X. The role of these genes in diaphragm development was supported by their expression in the developing mouse diaphragm, their similarity to known CDH genes using data from a previously published and validated machine learning algorithm, and/or the presence of CDH in other individuals with their associated genetic disorders. Our results demonstrate how data from DECIPHER, and other public databases, can be used to identify new phenotypic expansions and suggest that CREBBP, SMARCA4, UBA2, and USP9X play a role in diaphragm development.


Subject(s)
Hernias, Diaphragmatic, Congenital , Animals , DNA Copy Number Variations , Diaphragm , Hernias, Diaphragmatic, Congenital/genetics , Mice
10.
Physiol Plant ; 174(5): e13780, 2022 Sep.
Article in English | MEDLINE | ID: mdl-36121340

ABSTRACT

Anthocyanins are a group of pigments that have various roles in plants including attracting pollinators and seed dispersers and protecting against various types of stress. In vegetative tissue, these anthocyanins are sequestered in the vacuole following biosynthesis in the cytoplasm, though there remain questions as to the events leading to the vacuolar sequestration. In this study, we were able to show that the uptake of acylated anthocyanins by vacuolar membrane-enriched vesicles isolated from Arabidopsis was stimulated by the addition of MgATP and was inhibited by both vanadate and glybenclamide, but not by gramicidin D or bafilomycin A1 , suggesting that uptake involves an ATP-binding cassette (ABC) transporter and not an H+ -antiporter. Membrane vesicles isolated from yeast expressing the ABC transporters designated AtABCC1, AtABCC2, and AtABCC14 are capable of MgATP-dependent uptake of acylated anthocyanins. This uptake was not dependent on glutathione as seen previously for anthocyanidin 3-O-monoglucosides. Compared to the wild-type, the transport of acylated anthocyanins was lower in vacuolar membrane-enriched vesicles isolated from atabcc1 cell cultures providing evidence that AtABCC1 may be the predominant transporter of these compounds in vivo. In addition, the pattern of anthocyanin accumulation differed between the atabcc1, atabcc2, and atabcc14 mutants and the wild-type seedlings under anthocyanin inductive conditions. We suggest that AtABCC1, AtABCC2, and AtABCC14 are involved in the vacuolar transport of acylated anthocyanins produced in the vegetative tissue of Arabidopsis and that the pattern of anthocyanin accumulation can be altered depending on the presence or absence of a specific vacuolar ABC transporter.


Subject(s)
Arabidopsis , Arabidopsis/genetics , Arabidopsis/metabolism , Anthocyanins/metabolism , ATP-Binding Cassette Transporters/genetics , Vanadates/pharmacology , Gramicidin , Glyburide , Antiporters , Saccharomyces cerevisiae/metabolism , Glutathione , Adenosine Triphosphate
11.
Anal Chem ; 93(10): 4497-4505, 2021 03 16.
Article in English | MEDLINE | ID: mdl-33660983

ABSTRACT

A microfluidic paper-based analytical device (µPAD) is a cost-effective platform to implement assays, especially for point-of-care testing. Developing µPADs with fluidic control is important to implement multistep assays and provide high sensitivities. However, current localized delays in µPADs made of sucrose have a limited ability to decrease the flow rate. In addition, existing µPADs for automatic multistep assays are limited by their need for auxiliary instruments, their false activation, or their unavoidable tradeoff between available fluid volumes and temporal differences between steps. Here, a novel µPAD composed of a localized dissolvable delay and a horizontal motion mechanical valve for use as an automatic multistep assay is reported. A mixture of fructose and sucrose was used in the localized dissolvable delay and it provided an effective decrease in the flow rate to ensure adequate sensitivity in an assay. The dissolvable delay effectively doubled the flow time. A mechanical valve using a horizontal movement was developed to automatically implement a multistep process. Two-step and four-step processes were enabled with the µPAD. Cardiac troponin I (cTnI), a gold-standard biomarker for myocardial infarction, was used as a model analyte to show the performance of the developed µPAD in an assay. The designed µPAD, with the simple-to-make localized dissolvable delay and the robust mechanical valve, provides the potential to automatically implement high-performance multistep assays toward a versatile platform for point-of-care diagnostics.

12.
Am J Med Genet A ; 185(11): 3446-3458, 2021 11.
Article in English | MEDLINE | ID: mdl-34436830

ABSTRACT

The study aimed at widening the clinical and genetic spectrum of ASXL3-related syndrome, a neurodevelopmental disorder, caused by truncating variants in the ASXL3 gene. In this international collaborative study, we have undertaken a detailed clinical and molecular analysis of 45 previously unpublished individuals with ASXL3-related syndrome, as well as a review of all previously published individuals. We have reviewed the rather limited functional characterization of pathogenic variants in ASXL3 and discuss current understanding of the consequences of the different ASXL3 variants. In this comprehensive analysis of ASXL3-related syndrome, we define its natural history and clinical evolution occurring with age. We report familial ASXL3 pathogenic variants, characterize the phenotype in mildly affected individuals and discuss nonpenetrance. We also discuss the role of missense variants in ASXL3. We delineate a variable but consistent phenotype. The most characteristic features are neurodevelopmental delay with consistently limited speech, significant neuro-behavioral issues, hypotonia, and feeding difficulties. Distinctive features include downslanting palpebral fissures, hypertelorism, tubular nose with a prominent nasal bridge, and low-hanging columella. The presented data will inform clinical management of individuals with ASXL3-related syndrome and improve interpretation of new ASXL3 sequence variants.


Subject(s)
Developmental Disabilities/genetics , Genetic Predisposition to Disease , Neurodevelopmental Disorders/genetics , Transcription Factors/genetics , Adolescent , Adult , Child , Child, Preschool , Developmental Disabilities/epidemiology , Developmental Disabilities/physiopathology , Female , Genetic Variation/genetics , Humans , Hypertelorism/genetics , Hypertelorism/physiopathology , Intellectual Disability/genetics , Intellectual Disability/physiopathology , Male , Muscle Hypotonia/genetics , Muscle Hypotonia/physiopathology , Mutation/genetics , Neurodevelopmental Disorders/epidemiology , Neurodevelopmental Disorders/physiopathology , Phenotype , Young Adult
13.
Brain ; 143(8): 2380-2387, 2020 08 01.
Article in English | MEDLINE | ID: mdl-32658972

ABSTRACT

The SLC12 gene family consists of SLC12A1-SLC12A9, encoding electroneutral cation-coupled chloride co-transporters. SCL12A2 has been shown to play a role in corticogenesis and therefore represents a strong candidate neurodevelopmental disorder gene. Through trio exome sequencing we identified de novo mutations in SLC12A2 in six children with neurodevelopmental disorders. All had developmental delay or intellectual disability ranging from mild to severe. Two had sensorineural deafness. We also identified SLC12A2 variants in three individuals with non-syndromic bilateral sensorineural hearing loss and vestibular areflexia. The SLC12A2 de novo mutation rate was demonstrated to be significantly elevated in the deciphering developmental disorders cohort. All tested variants were shown to reduce co-transporter function in Xenopus laevis oocytes. Analysis of SLC12A2 expression in foetal brain at 16-18 weeks post-conception revealed high expression in radial glial cells, compatible with a role in neurogenesis. Gene co-expression analysis in cells robustly expressing SLC12A2 at 16-18 weeks post-conception identified a transcriptomic programme associated with active neurogenesis. We identify SLC12A2 de novo mutations as the cause of a novel neurodevelopmental disorder and bilateral non-syndromic sensorineural hearing loss and provide further data supporting a role for this gene in human neurodevelopment.


Subject(s)
Bilateral Vestibulopathy/genetics , Hearing Loss, Sensorineural/genetics , Neurodevelopmental Disorders/genetics , Solute Carrier Family 12, Member 2/genetics , Adolescent , Adult , Child , Child, Preschool , Female , Humans , Infant , Male , Mutation , Young Adult
14.
Environ Res ; 189: 109915, 2020 10.
Article in English | MEDLINE | ID: mdl-32678741

ABSTRACT

With the now widescale reporting of oral bioaccessibility data at contaminated sites, following our investigation of three sites (one public open space and two residential) for As and Pb contamination, a critical evaluation of the application and utility of such bioaccessibility testing was undertaken to better inform future use. Mean As and Pb soil levels across the sites varied between 12.5 and 24,900 mg/kg and 149-5930 mg/kg, respectively. Using the Unified Bioaccessibility Method (UBM) for in vitro bioaccessibility testing the highest bioaccessible concentrations were identified in the gastric phase. At site 1, a residential urban garden site the maximum bioaccessible As was 50.2% while the maximum bioaccessible Pb was 64.8%; similarly in site 2, also a residential urban garden site the maximum bioaccessible As was 38.72% while the maximum bioaccessible Pb was 66.0%. However, at site 3, a public open space site, the maximum bioaccessible As was 29.7% while the maximum bioaccessible Pb was 38.4%. Using the appropriate soil screening values and recommended statistical testing, we highlight that the use of bioaccessibility testing was unnecessary at sites 1 and 2 (residential urban garden sites), while at site 3 the value of oral bioaccessibility testing is highlighted as part of a 'lines of evidence approach' to support the site's specific risk assessment. We need to move away from the uncritical, blanket application of oral bioacessibility testing and strategically target where the results of these data add real value to site determination.


Subject(s)
Lead , Soil Pollutants , Biological Availability , Environment , Humans , Risk Assessment , Soil , Soil Pollutants/analysis
15.
Am J Med Genet C Semin Med Genet ; 181(4): 557-564, 2019 12.
Article in English | MEDLINE | ID: mdl-31721432

ABSTRACT

CHD8 has been reported as an autism susceptibility/intellectual disability gene but emerging evidence suggests that it additionally causes an overgrowth phenotype. This study reports 27 unrelated patients with pathogenic or likely pathogenic CHD8 variants (25 null variants, two missense variants) and a male:female ratio of 21:6 (3.5:1, p < .01). All patients presented with intellectual disability, with 85% in the mild or moderate range, and 85% had a height and/or head circumference ≥2 standard deviations above the mean, meeting our clinical criteria for overgrowth. Behavioral problems were reported in the majority of patients (78%), with over half (56%) either formally diagnosed with an autistic spectrum disorder or described as having autistic traits. Additional clinical features included neonatal hypotonia (33%), and less frequently seizures, pes planus, scoliosis, fifth finger clinodactyly, umbilical hernia, and glabellar hemangioma (≤15% each). These results suggest that, in addition to its established link with autism and intellectual disability, CHD8 causes an overgrowth phenotype, and should be considered in the differential diagnosis of patients presenting with increased height and/or head circumference in association with intellectual disability.


Subject(s)
Cadherins/genetics , Growth Disorders/genetics , Phenotype , Adolescent , Adult , Child , Child, Preschool , Female , Humans , Infant , Intellectual Disability/genetics , Male , Syndrome , Young Adult
16.
Genet Med ; 21(3): 663-675, 2019 03.
Article in English | MEDLINE | ID: mdl-30158690

ABSTRACT

PURPOSE: Defects in the cohesin pathway are associated with cohesinopathies, notably Cornelia de Lange syndrome (CdLS). We aimed to delineate pathogenic variants in known and candidate cohesinopathy genes from a clinical exome perspective. METHODS: We retrospectively studied patients referred for clinical exome sequencing (CES, N = 10,698). Patients with causative variants in novel or recently described cohesinopathy genes were enrolled for phenotypic characterization. RESULTS: Pathogenic or likely pathogenic single-nucleotide and insertion/deletion variants (SNVs/indels) were identified in established disease genes including NIPBL (N = 5), SMC1A (N = 14), SMC3 (N = 4), RAD21 (N = 2), and HDAC8 (N = 8). The phenotypes in this genetically defined cohort skew towards the mild end of CdLS spectrum as compared with phenotype-driven cohorts. Candidate or recently reported cohesinopathy genes were supported by de novo SNVs/indels in STAG1 (N = 3), STAG2 (N = 5), PDS5A (N = 1), and WAPL (N = 1), and one inherited SNV in PDS5A. We also identified copy-number deletions affecting STAG1 (two de novo, one of unknown inheritance) and STAG2 (one of unknown inheritance). Patients with STAG1 and STAG2 variants presented with overlapping features yet without characteristic facial features of CdLS. CONCLUSION: CES effectively identified disease-causing alleles at the mild end of the cohensinopathy spectrum and enabled characterization of candidate disease genes.


Subject(s)
Biological Variation, Population/genetics , Cell Cycle Proteins/genetics , Chromosomal Proteins, Non-Histone/genetics , Adolescent , Alleles , Antigens, Nuclear/genetics , Carrier Proteins/genetics , Child , Child, Preschool , Cohort Studies , De Lange Syndrome/diagnosis , De Lange Syndrome/genetics , Exome/genetics , Female , Gene Frequency/genetics , Genetic Heterogeneity , Humans , INDEL Mutation/genetics , Male , Mutation , Nuclear Proteins/genetics , Phenotype , Polymorphism, Single Nucleotide/genetics , Proto-Oncogene Proteins/genetics , Retrospective Studies , Exome Sequencing/methods , Cohesins
17.
Anal Bioanal Chem ; 411(13): 2839-2853, 2019 May.
Article in English | MEDLINE | ID: mdl-31079177

ABSTRACT

A new and improved method was developed for the determination and quantification of four "free" thyroid hormones (i.e. 3,5-diiodothyronine (T2), 3,3',5-triiodothyronine (T3), 3,3',5'-triiodothyrone (rT3) and 3,5,3',5'-tetraiodothyronine (T4)) in human serum by low- and high-resolution liquid chromatography-mass spectrometry (LC-MS). Several sample preparation strategies were investigated to obtain matrix-independent results. These strategies included solid phase extraction and matrix dilution. The developed analytical methods were then directly compared, in a blind study using patient-derived human blood serum samples, to the current clinical routine testing methods, i.e. electrochemiluminescence immunoassay and enzyme-linked immunosorbent assay. Chromatographic separation was achieved on a pentafluorophenyl (F5) column with an isocratic method of 30% aqueous phase, 70% organic phase where mobile phase A is 0.1% formic acid in water (pH 4) and mobile phase B is 0.1% formic acid in methanol (pH 4) (v/v). The high-resolution LC-MS was able to give a significant improvement in sensitivity with limits of quantification of 0.002 to 0.008 pmol/L for all four "free" thyroid hormones, as well as reduced sample preparation, making this the preferred method. However, the increase in capital cost may be beyond the capabilities of some laboratories. The LC-MS methods allow for the analysis of "free" thyroid hormones to be carried out in a significantly reduced analysis time. Clinical sample analysis showed that there was no statistical difference between the results obtained by ECLIA/ELISA and both LC-MS methods. Graphical abstract.


Subject(s)
Chromatography, High Pressure Liquid/methods , Mass Spectrometry/methods , Thyroid Hormones/blood , Animals , Horses , Humans , Immunoassay/methods , Limit of Detection
19.
Am J Med Genet A ; 176(5): 1108-1114, 2018 05.
Article in English | MEDLINE | ID: mdl-29383814

ABSTRACT

Variants in the Protein Kinase CK2 alpha subunit, encoding the CSNK2A1 gene, have previously been reported in children with an intellectual disability and dysmorphic facial features syndrome: now termed the Okur-Chung neurodevelopmental syndrome. More recently, through trio-based exome sequencing undertaken by the Deciphering Developmental Disorders Study (DDD study), a further 11 children with de novo CSNK2A1 variants have been identified. We have undertaken detailed phenotyping of these patients. Consistent with previously reported patients, patients in this series had apparent intellectual disability, swallowing difficulties, and hypotonia. While there are some shared facial characteristics, the gestalt is neither consistent nor readily recognized. Congenital heart abnormalities were identified in nearly 30% of the patients, representing a newly recognized CSNK2A1 clinical association. Based upon the clinical findings from this study and the previously reported patients, we suggest an initial approach to the management of patients with this recently described intellectual disability syndrome.


Subject(s)
Mutation , Neurodevelopmental Disorders/diagnosis , Neurodevelopmental Disorders/genetics , Phenotype , Alleles , Amino Acid Motifs , Amino Acid Sequence , Amino Acid Substitution , Casein Kinase II/chemistry , Casein Kinase II/genetics , Child , Exons , Facies , Female , Humans , Male , Protein Binding , Protein Interaction Domains and Motifs
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