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1.
Nucleic Acids Res ; 2024 Jun 27.
Article in English | MEDLINE | ID: mdl-38932701

ABSTRACT

Androgen receptor- (AR-) indifference is a mechanism of resistance to hormonal therapy in prostate cancer (PC). Here we demonstrate that ONECUT2 (OC2) activates resistance through multiple drivers associated with adenocarcinoma, stem-like and neuroendocrine (NE) variants. Direct OC2 gene targets include the glucocorticoid receptor (GR; NR3C1) and the NE splicing factor SRRM4, which are key drivers of lineage plasticity. Thus, OC2, despite its previously described NEPC driver function, can indirectly activate a portion of the AR cistrome through epigenetic activation of GR. Mechanisms by which OC2 regulates gene expression include promoter binding, enhancement of genome-wide chromatin accessibility, and super-enhancer reprogramming. Pharmacologic inhibition of OC2 suppresses lineage plasticity reprogramming induced by the AR signaling inhibitor enzalutamide. These results demonstrate that OC2 activation promotes a range of drug resistance mechanisms associated with treatment-emergent lineage variation in PC and support enhanced efforts to therapeutically target OC2 as a means of suppressing treatment-resistant disease.

2.
Am J Hum Genet ; 108(10): 2017-2023, 2021 10 07.
Article in English | MEDLINE | ID: mdl-34587489

ABSTRACT

ABHD16A (abhydrolase domain-containing protein 16A, phospholipase) encodes the major phosphatidylserine (PS) lipase in the brain. PS lipase synthesizes lysophosphatidylserine, an important signaling lipid that functions in the mammalian central nervous system. ABHD16A has not yet been associated with a human disease. In this report, we present a cohort of 11 affected individuals from six unrelated families with a complicated form of hereditary spastic paraplegia (HSP) who carry bi-allelic deleterious variants in ABHD16A. Affected individuals present with a similar phenotype consisting of global developmental delay/intellectual disability, progressive spasticity affecting the upper and lower limbs, and corpus callosum and white matter anomalies. Immunoblot analysis on extracts from fibroblasts from four affected individuals demonstrated little to no ABHD16A protein levels compared to controls. Our findings add ABHD16A to the growing list of lipid genes in which dysregulation can cause complicated forms of HSP and begin to describe the molecular etiology of this condition.


Subject(s)
Cerebral Palsy/pathology , Intellectual Disability/pathology , Leukoencephalopathies/pathology , Monoacylglycerol Lipases/genetics , Mutation , Spastic Paraplegia, Hereditary/pathology , Adolescent , Adult , Cerebral Palsy/etiology , Cerebral Palsy/metabolism , Child , Child, Preschool , Cohort Studies , Female , Humans , Intellectual Disability/etiology , Intellectual Disability/metabolism , Leukoencephalopathies/etiology , Leukoencephalopathies/metabolism , Male , Monoacylglycerol Lipases/deficiency , Pedigree , Phenotype , Spastic Paraplegia, Hereditary/etiology , Spastic Paraplegia, Hereditary/metabolism , Young Adult
3.
Am J Hum Genet ; 108(1): 176-185, 2021 01 07.
Article in English | MEDLINE | ID: mdl-33245860

ABSTRACT

Fibroblast growth factor homologous factors (FHFs) are intracellular proteins which regulate voltage-gated sodium (Nav) channels in the brain and other tissues. FHF dysfunction has been linked to neurological disorders including epilepsy. Here, we describe two sibling pairs and three unrelated males who presented in infancy with intractable focal seizures and severe developmental delay. Whole-exome sequencing identified hemi- and heterozygous variants in the N-terminal domain of the A isoform of FHF2 (FHF2A). The X-linked FHF2 gene (also known as FGF13) has alternative first exons which produce multiple protein isoforms that differ in their N-terminal sequence. The variants were located at highly conserved residues in the FHF2A inactivation particle that competes with the intrinsic fast inactivation mechanism of Nav channels. Functional characterization of mutant FHF2A co-expressed with wild-type Nav1.6 (SCN8A) revealed that mutant FHF2A proteins lost the ability to induce rapid-onset, long-term blockade of the channel while retaining pro-excitatory properties. These gain-of-function effects are likely to increase neuronal excitability consistent with the epileptic potential of FHF2 variants. Our findings demonstrate that FHF2 variants are a cause of infantile-onset developmental and epileptic encephalopathy and underline the critical role of the FHF2A isoform in regulating Nav channel function.


Subject(s)
Brain Diseases/genetics , Epilepsy/genetics , Fibroblast Growth Factors/genetics , Mutation, Missense/genetics , Protein Isoforms/genetics , Adolescent , Amino Acid Sequence , Child , Exons/genetics , Female , Gain of Function Mutation/genetics , Genes, X-Linked/genetics , Heterozygote , Humans , Male , NAV1.6 Voltage-Gated Sodium Channel/genetics , Neurons/physiology , Seizures/genetics
4.
Genet Med ; 26(2): 101012, 2024 Feb.
Article in English | MEDLINE | ID: mdl-37924259

ABSTRACT

PURPOSE: To evaluate the diagnostic utility of publicly funded clinical exome sequencing (ES) for patients with suspected rare genetic diseases. METHODS: We prospectively enrolled 297 probands who met eligibility criteria and received ES across 5 sites in Ontario, Canada, and extracted data from medical records and clinician surveys. Using the Fryback and Thornbury Efficacy Framework, we assessed diagnostic accuracy by examining laboratory interpretation of results and assessed diagnostic thinking by examining the clinical interpretation of results and whether clinical-molecular diagnoses would have been achieved via alternative hypothetical molecular tests. RESULTS: Laboratories reported 105 molecular diagnoses and 165 uncertain results in known and novel genes. Of these, clinicians interpreted 102 of 105 (97%) molecular diagnoses and 6 of 165 (4%) uncertain results as clinical-molecular diagnoses. The 108 clinical-molecular diagnoses were in 104 families (35% diagnostic yield). Each eligibility criteria resulted in diagnostic yields of 30% to 40%, and higher yields were achieved when >2 eligibility criteria were met (up to 45%). Hypothetical tests would have identified 61% of clinical-molecular diagnoses. CONCLUSION: We demonstrate robustness in eligibility criteria and high clinical validity of laboratory results from ES testing. The importance of ES was highlighted by the potential 40% of patients that would have gone undiagnosed without this test.


Subject(s)
Exome , Rare Diseases , Humans , Prospective Studies , Exome Sequencing , Rare Diseases/diagnosis , Rare Diseases/genetics , Genetic Testing/methods , Ontario
5.
Brain ; 146(6): 2285-2297, 2023 06 01.
Article in English | MEDLINE | ID: mdl-36477332

ABSTRACT

The blood-brain barrier ensures CNS homeostasis and protection from injury. Claudin-5 (CLDN5), an important component of tight junctions, is critical for the integrity of the blood-brain barrier. We have identified de novo heterozygous missense variants in CLDN5 in 15 unrelated patients who presented with a shared constellation of features including developmental delay, seizures (primarily infantile onset focal epilepsy), microcephaly and a recognizable pattern of pontine atrophy and brain calcifications. All variants clustered in one subregion/domain of the CLDN5 gene and the recurrent variants demonstrate genotype-phenotype correlations. We modelled both patient variants and loss of function alleles in the zebrafish to show that the variants analogous to those in patients probably result in a novel aberrant function in CLDN5. In total, human patient and zebrafish data provide parallel evidence that pathogenic sequence variants in CLDN5 cause a novel neurodevelopmental disorder involving disruption of the blood-brain barrier and impaired neuronal function.


Subject(s)
Microcephaly , Animals , Humans , Microcephaly/genetics , Claudin-5/genetics , Claudin-5/metabolism , Zebrafish/metabolism , Blood-Brain Barrier/metabolism , Seizures/genetics , Syndrome
6.
Clin Genet ; 103(3): 288-300, 2023 03.
Article in English | MEDLINE | ID: mdl-36353900

ABSTRACT

We examined the utility of clinical and research processes in the reanalysis of publicly-funded clinical exome sequencing data in Ontario, Canada. In partnership with eight sites, we recruited 287 families with suspected rare genetic diseases tested between 2014 and 2020. Data from seven laboratories was reanalyzed with the referring clinicians. Reanalysis of clinically relevant genes identified diagnoses in 4% (13/287); four were missed by clinical testing. Translational research methods, including analysis of novel candidate genes, identified candidates in 21% (61/287). Of these, 24 families have additional evidence through data sharing to support likely diagnoses (8% of cohort). This study indicates few diagnoses are missed by clinical laboratories, the incremental gain from reanalysis of clinically-relevant genes is modest, and the highest yield comes from validation of novel disease-gene associations. Future implementation of translational research methods, including continued reporting of compelling genes of uncertain significance by clinical laboratories, should be considered to maximize diagnoses.


Subject(s)
Genetic Testing , Humans , Genetic Testing/methods , Ontario/epidemiology , Exome Sequencing
7.
Support Care Cancer ; 31(5): 292, 2023 Apr 22.
Article in English | MEDLINE | ID: mdl-37086362

ABSTRACT

PURPOSE: All patients living with cancer, including those with metastatic cancer, are encouraged to be physically active. This paper examines the secondary endpoints of an aerobic exercise intervention for men with metastatic prostate cancer. METHODS: ExPeCT (Exercise, Prostate Cancer and Circulating Tumour Cells), was a multi-centre randomised control trial with a 6-month aerobic exercise intervention arm or a standard care control arm. Exercise adherence data was collected via heart rate monitors. Quality of life (FACT-P) and physical activity (self-administered questionnaire) assessments were completed at baseline, at 3 months and at 6 months. RESULTS: A total of 61 patients were included (69.4 ± 7.3 yr, body mass index 29.2 ± 5.8 kg/m2). The median time since diagnosis was 34 months (IQR 7-54). A total of 35 (55%) of participants had > 1 region affected by metastatic disease. No adverse events were reported by participants. There was no effect of exercise on quality of life (Cohen's d = - 0.082). Overall adherence to the supervised sessions was 83% (329 out of 396 possible sessions attended by participants). Overall adherence to the non-supervised home exercise sessions was 72% (months 1-3) and 67% (months 3-6). Modelling results for overall physical activity scores showed no significant main effect for the group (p-value = 0.25) or for time (p-value = 0.24). CONCLUSION: In a group of patients with a high burden of metastatic prostate cancer, a 6-month aerobic exercise intervention did not lead to change in quality of life. Further exercise studies examining the role of exercise for people living with metastatic prostate cancer are needed. TRIAL REGISTRATION: The trial was registered at clinicaltrials.gov (NCT02453139) on May 25th 2015.


Subject(s)
Prostatic Neoplasms , Quality of Life , Male , Humans , Exercise , Prostatic Neoplasms/therapy , Exercise Therapy/methods , Surveys and Questionnaires
8.
Proc Natl Acad Sci U S A ; 117(25): 14331-14341, 2020 06 23.
Article in English | MEDLINE | ID: mdl-32513686

ABSTRACT

Acute myeloid leukemia (AML) is the most common acute leukemia in adults, with approximately four new cases per 100,000 persons per year. Standard treatment for AML consists of induction chemotherapy with remission achieved in 50 to 75% of cases. Unfortunately, most patients will relapse and die from their disease, as 5-y survival is roughly 29%. Therefore, other treatment options are urgently needed. In recent years, immune-based therapies have led to unprecedented rates of survival among patients with some advanced cancers. Suppression of T cell function in the tumor microenvironment is commonly observed and may play a role in AML. We found that there is a significant association between T cell infiltration in the bone marrow microenvironment of newly diagnosed patients with AML and increased overall survival. Functional studies aimed at establishing the degree of T cell suppression in patients with AML revealed impaired T cell function in many patients. In most cases, T cell proliferation could be restored by blocking the immune checkpoint molecules PD-1, CTLA-4, or TIM3. Our data demonstrate that AML establishes an immune suppressive environment in the bone marrow, in part through T cell checkpoint function.


Subject(s)
Bone Marrow/metabolism , Leukemia, Myeloid, Acute/metabolism , T-Lymphocytes/metabolism , Tumor Microenvironment/physiology , Bone Marrow/immunology , CTLA-4 Antigen/metabolism , Cell Proliferation , Cytokines/metabolism , Hepatitis A Virus Cellular Receptor 2/metabolism , Humans , Leukemia, Myeloid, Acute/immunology , Leukemia, Myeloid, Acute/therapy , Programmed Cell Death 1 Receptor/metabolism , T-Lymphocytes/immunology
9.
Am J Hum Genet ; 104(4): 685-700, 2019 04 04.
Article in English | MEDLINE | ID: mdl-30929737

ABSTRACT

Conventional genetic testing of individuals with neurodevelopmental presentations and congenital anomalies (ND/CAs), i.e., the analysis of sequence and copy number variants, leaves a substantial proportion of them unexplained. Some of these cases have been shown to result from DNA methylation defects at a single locus (epi-variants), while others can exhibit syndrome-specific DNA methylation changes across multiple loci (epi-signatures). Here, we investigate the clinical diagnostic utility of genome-wide DNA methylation analysis of peripheral blood in unresolved ND/CAs. We generate a computational model enabling concurrent detection of 14 syndromes using DNA methylation data with full accuracy. We demonstrate the ability of this model in resolving 67 individuals with uncertain clinical diagnoses, some of whom had variants of unknown clinical significance (VUS) in the related genes. We show that the provisional diagnoses can be ruled out in many of the case subjects, some of whom are shown by our model to have other diseases initially not considered. By applying this model to a cohort of 965 ND/CA-affected subjects without a previous diagnostic assumption and a separate assessment of rare epi-variants in this cohort, we identify 15 case subjects with syndromic Mendelian disorders, 12 case subjects with imprinting and trinucleotide repeat expansion disorders, as well as 106 case subjects with rare epi-variants, a portion of which involved genes clinically or functionally linked to the subjects' phenotypes. This study demonstrates that genomic DNA methylation analysis can facilitate the molecular diagnosis of unresolved clinical cases and highlights the potential value of epigenomic testing in the routine clinical assessment of ND/CAs.


Subject(s)
Congenital Abnormalities/genetics , DNA Methylation , Genetic Diseases, Inborn/diagnosis , Genome-Wide Association Study , Cohort Studies , Computer Simulation , Congenital Abnormalities/diagnosis , DNA Copy Number Variations , Epigenomics , Gene Dosage , Genetic Diseases, Inborn/genetics , Genetic Variation , Genomic Imprinting , Humans , Phenotype , Sequence Analysis, DNA , Syndrome , Trinucleotide Repeat Expansion
10.
PLoS Pathog ; 16(1): e1008261, 2020 01.
Article in English | MEDLINE | ID: mdl-31999807

ABSTRACT

Disruption of blood-brain barrier (BBB) function is a key feature of cerebral malaria. Increased barrier permeability occurs due to disassembly of tight and adherens junctions between endothelial cells, yet the mechanisms governing junction disassembly and vascular permeability during cerebral malaria remain poorly characterized. We found that EphA2 is a principal receptor tyrosine kinase mediating BBB breakdown during Plasmodium infection. Upregulated on brain microvascular endothelial cells in response to inflammatory cytokines, EphA2 is required for the loss of junction proteins on mouse and human brain microvascular endothelial cells. Furthermore, EphA2 is necessary for CD8+ T cell brain infiltration and subsequent BBB breakdown in a mouse model of cerebral malaria. Blocking EphA2 protects against BBB breakdown highlighting EphA2 as a potential therapeutic target for cerebral malaria.


Subject(s)
Blood-Brain Barrier/parasitology , Malaria, Cerebral/parasitology , Receptor, EphA2/metabolism , Adolescent , Animals , Blood-Brain Barrier/metabolism , Child , Child, Preschool , Cross-Sectional Studies , Female , Humans , Infant , Malaria, Cerebral/genetics , Malaria, Cerebral/metabolism , Male , Mice , Mice, Inbred C57BL , Mice, Knockout , Plasmodium falciparum/physiology , Receptor, EphA2/genetics
11.
J Med Genet ; 58(4): 284-288, 2021 04.
Article in English | MEDLINE | ID: mdl-32376792

ABSTRACT

Charcot-Marie-Tooth disease (CMT) is one of the most common Mendelian disorders characterised by genetic heterogeneity, progressive distal muscle weakness and atrophy, foot deformities and distal sensory loss. In this report, we describe genetic testing data including comprehensive sequencing and copy number analysis of 34 CMT-related genes in a Canadian cohort of patients with suspected CMT. We have demonstrated a notable gender testing bias, with an overall diagnostic yield of 15% in males and 21% in females. We have identified a large number of novel pathogenic variants as well as variants of unknown clinical significance in CMT-related genes. In this largest to date analysis of gene CNVs in CMT, in addition to the common PMP22 deletion/duplication, we have described a significant contribution of pathogenic CNVs in several CMT-related genes. This study significantly expand the mutational spectrum of CMT genes, while demonstrating the clinical utility of a comprehensive sequence and copy number next-generation sequencing-based clinical genetic testing in patients with suspected diagnosis of CMT.


Subject(s)
Charcot-Marie-Tooth Disease/genetics , DNA Copy Number Variations/genetics , Distal Myopathies/genetics , Genetic Testing , Adult , Aged , Canada/epidemiology , Charcot-Marie-Tooth Disease/diagnosis , Charcot-Marie-Tooth Disease/epidemiology , Charcot-Marie-Tooth Disease/pathology , Cohort Studies , Distal Myopathies/diagnosis , Distal Myopathies/epidemiology , Distal Myopathies/pathology , Female , Genetic Heterogeneity , High-Throughput Nucleotide Sequencing , Humans , Male , Middle Aged , Mutation/genetics , Phenotype
12.
Genet Med ; 23(5): 881-887, 2021 05.
Article in English | MEDLINE | ID: mdl-33473207

ABSTRACT

PURPOSE: Neurodevelopmental disorders (NDDs) encompass a spectrum of genetically heterogeneous disorders with features that commonly include developmental delay, intellectual disability, and autism spectrum disorders. We sought to delineate the molecular and phenotypic spectrum of a novel neurodevelopmental disorder caused by variants in the GNAI1 gene. METHODS: Through large cohort trio-based exome sequencing and international data-sharing, we identified 24 unrelated individuals with NDD phenotypes and a variant in GNAI1, which encodes the inhibitory Gαi1 subunit of heterotrimeric G-proteins. We collected detailed genotype and phenotype information for each affected individual. RESULTS: We identified 16 unique variants in GNAI1 in 24 affected individuals; 23 occurred de novo and 1 was inherited from a mosaic parent. Most affected individuals have a severe neurodevelopmental disorder. Core features include global developmental delay, intellectual disability, hypotonia, and epilepsy. CONCLUSION: This collaboration establishes GNAI1 variants as a cause of NDDs. GNAI1-related NDD is most often characterized by severe to profound delays, hypotonia, epilepsy that ranges from self-limiting to intractable, behavior problems, and variable mild dysmorphic features.


Subject(s)
Intellectual Disability , Neurodevelopmental Disorders , Child , Developmental Disabilities/genetics , Humans , Intellectual Disability/diagnosis , Intellectual Disability/genetics , Muscle Hypotonia/diagnosis , Muscle Hypotonia/genetics , Neurodevelopmental Disorders/diagnosis , Neurodevelopmental Disorders/genetics , Seizures/genetics , Exome Sequencing
13.
Genet Med ; 23(4): 740-750, 2021 04.
Article in English | MEDLINE | ID: mdl-33239752

ABSTRACT

PURPOSE: In this study we investigate the disease etiology in 12 patients with de novo variants in FAR1 all resulting in an amino acid change at position 480 (p.Arg480Cys/His/Leu). METHODS: Following next-generation sequencing and clinical phenotyping, functional characterization was performed in patients' fibroblasts using FAR1 enzyme analysis, FAR1 immunoblotting/immunofluorescence, and lipidomics. RESULTS: All patients had spastic paraparesis and bilateral congenital/juvenile cataracts, in most combined with speech and gross motor developmental delay and truncal hypotonia. FAR1 deficiency caused by biallelic variants results in defective ether lipid synthesis and plasmalogen deficiency. In contrast, patients' fibroblasts with the de novo FAR1 variants showed elevated plasmalogen levels. Further functional studies in fibroblasts showed that these variants cause a disruption of the plasmalogen-dependent feedback regulation of FAR1 protein levels leading to uncontrolled ether lipid production. CONCLUSION: Heterozygous de novo variants affecting the Arg480 residue of FAR1 lead to an autosomal dominant disorder with a different disease mechanism than that of recessive FAR1 deficiency and a diametrically opposed biochemical phenotype. Our findings show that for patients with spastic paraparesis and bilateral cataracts, FAR1 should be considered as a candidate gene and added to gene panels for hereditary spastic paraplegia, cerebral palsy, and juvenile cataracts.


Subject(s)
Aldehyde Oxidoreductases/genetics , Ethers , Lipids , Spastic Paraplegia, Hereditary/genetics , Humans , Phenotype
14.
Am J Med Genet A ; 185(3): 766-773, 2021 03.
Article in English | MEDLINE | ID: mdl-33369152

ABSTRACT

Reports of patients with concomitant diagnoses of two inherited genetic disorders, sometimes referred to as "double trouble," have appeared intermittently in the medical literature. We report eight additional cases with dual diagnoses of two genetic conditions. All cases had a phenotype atypical for their primary diagnosis, leading to the search for a second genetic diagnosis. These cases highlight the importance of the history, physical examination and continued work-up if the phenotype of the patient falls drastically outside what has been reported with their primary diagnosis. Some of the diagnoses of the patients presented here (e.g., Myotonic Dystrophy Type 1, fascioscapulohumeral muscular dystrophy) would not have been identified by genetic testing done on a next generation sequencing backbone (e.g., panel or exome sequencing). When the clinical picture is atypical or more severe than expected the possibility of a dual diagnosis (double trouble) should be considered. Identification of a second genetic condition can impact management and genetic counseling.


Subject(s)
Genetic Markers , Genetic Testing/methods , Muscular Dystrophy, Facioscapulohumeral/diagnosis , Mutation , Myotonic Dystrophy/diagnosis , Adolescent , Adult , Child , Child, Preschool , Female , Follow-Up Studies , High-Throughput Nucleotide Sequencing , Humans , Infant, Newborn , Male , Muscular Dystrophy, Facioscapulohumeral/genetics , Myotonic Dystrophy/genetics , Phenotype , Prognosis , Retrospective Studies , Exome Sequencing , Young Adult
15.
Am J Med Genet A ; 185(2): 486-499, 2021 02.
Article in English | MEDLINE | ID: mdl-33300680

ABSTRACT

Diagnosing mitochondrial disorders is a challenge due to the heterogeneous clinical presentation and large number of associated genes. A custom next generation sequencing (NGS) panel was developed incorporating the full mitochondrial genome (mtDNA) plus 19 nuclear genes involved in structural mitochondrial defects and mtDNA maintenance. This assay is capable of simultaneously detecting small gene sequence variations and larger copy number variants (CNVs) in both the nuclear and mitochondrial components along with heteroplasmy detection down to 5%. We describe technical validations of this panel and its implementation for clinical testing in a Canadian reference laboratory, and report its clinical performance in the initial 950 patients tested. Using this assay, we demonstrate a diagnostic yield of 18.1% of patients with known pathogenic variants. In addition to the common 5 kb mtDNA deletion, we describe significant contribution of pathogenic CNVs in both the mitochondrial genome and nuclear genes in this patient population.


Subject(s)
DNA Copy Number Variations/genetics , Genetics, Population , High-Throughput Nucleotide Sequencing , Mitochondrial Diseases/genetics , Adolescent , Adult , Aged , Aged, 80 and over , Canada/epidemiology , Cell Nucleus/genetics , Child , Child, Preschool , DNA, Mitochondrial/genetics , Female , Humans , Infant , Male , Middle Aged , Mitochondria/genetics , Mitochondrial Diseases/diagnosis , Mitochondrial Diseases/epidemiology , Mitochondrial Diseases/pathology , Young Adult
16.
Brain ; 143(1): 94-111, 2020 01 01.
Article in English | MEDLINE | ID: mdl-31855247

ABSTRACT

Cerebral choline metabolism is crucial for normal brain function, and its homoeostasis depends on carrier-mediated transport. Here, we report on four individuals from three families with neurodegenerative disease and homozygous frameshift mutations (Asp517Metfs*19, Ser126Metfs*8, and Lys90Metfs*18) in the SLC44A1 gene encoding choline transporter-like protein 1. Clinical features included progressive ataxia, tremor, cognitive decline, dysphagia, optic atrophy, dysarthria, as well as urinary and bowel incontinence. Brain MRI demonstrated cerebellar atrophy and leukoencephalopathy. Moreover, low signal intensity in globus pallidus with hyperintensive streaking and low signal intensity in substantia nigra were seen in two individuals. The Asp517Metfs*19 and Ser126Metfs*8 fibroblasts were structurally and functionally indistinguishable. The most prominent ultrastructural changes of the mutant fibroblasts were reduced presence of free ribosomes, the appearance of elongated endoplasmic reticulum and strikingly increased number of mitochondria and small vesicles. When chronically treated with choline, those characteristics disappeared and mutant ultrastructure resembled healthy control cells. Functional analysis revealed diminished choline transport yet the membrane phosphatidylcholine content remained unchanged. As part of the mechanism to preserve choline and phosphatidylcholine, choline transporter deficiency was implicated in impaired membrane homeostasis of other phospholipids. Choline treatments could restore the membrane lipids, repair cellular organelles and protect mutant cells from acute iron overload. In conclusion, we describe a novel childhood-onset neurometabolic disease caused by choline transporter deficiency with autosomal recessive inheritance.


Subject(s)
Antigens, CD/genetics , Heredodegenerative Disorders, Nervous System/genetics , Organic Cation Transport Proteins/genetics , Adolescent , Ataxia/genetics , Ataxia/physiopathology , Atrophy , Cerebellum/diagnostic imaging , Cerebellum/pathology , Choline/pharmacology , Cognitive Dysfunction/genetics , Cognitive Dysfunction/physiopathology , Cytoplasmic Vesicles/drug effects , Cytoplasmic Vesicles/ultrastructure , Deglutition Disorders/genetics , Deglutition Disorders/physiopathology , Dysarthria/genetics , Dysarthria/physiopathology , Endoplasmic Reticulum/drug effects , Endoplasmic Reticulum/ultrastructure , Fecal Incontinence/genetics , Fecal Incontinence/physiopathology , Female , Fibroblasts/drug effects , Fibroblasts/ultrastructure , Frameshift Mutation , Globus Pallidus/diagnostic imaging , Heredodegenerative Disorders, Nervous System/diagnostic imaging , Heredodegenerative Disorders, Nervous System/pathology , Heredodegenerative Disorders, Nervous System/physiopathology , Homozygote , Humans , Leukoencephalopathies/diagnostic imaging , Leukoencephalopathies/genetics , Leukoencephalopathies/physiopathology , Magnetic Resonance Imaging , Male , Microscopy, Electron , Mitochondria/drug effects , Mitochondria/ultrastructure , Nootropic Agents/pharmacology , Optic Atrophy/genetics , Optic Atrophy/physiopathology , Pedigree , Ribosomes/drug effects , Ribosomes/ultrastructure , Substantia Nigra/diagnostic imaging , Syndrome , Tremor/genetics , Tremor/physiopathology , Urinary Incontinence/genetics , Urinary Incontinence/physiopathology
17.
Hum Mol Genet ; 27(21): 3710-3719, 2018 11 01.
Article in English | MEDLINE | ID: mdl-30085106

ABSTRACT

Mitochondrial dynamics, including mitochondrial division, fusion and transport, are integral parts of mitochondrial and cellular function. DNM1L encodes dynamin-related protein 1 (Drp1), a member of the dynamin-related protein family that is required for mitochondrial division. Several de novo mutations in DNM1L are associated with a range of disease states. Here we report the identification of five patients with pathogenic or likely pathogenic variants of DNM1L, including two novel variants. Interestingly, all of the positions identified in these Drp1 variants are fully conserved among all members of the dynamin-related protein family that are involved in membrane division and organelle division events. This work builds upon and expands the clinical spectrum associated with Drp1 variants in patients and their impact on mitochondrial division in model cells.


Subject(s)
GTP Phosphohydrolases/genetics , Microtubule-Associated Proteins/genetics , Mitochondrial Diseases/enzymology , Mitochondrial Dynamics , Mitochondrial Proteins/genetics , Mutation , Cell Line , Child , DNA Mutational Analysis , Dynamins , Female , GTP Phosphohydrolases/physiology , Humans , Infant , Male , Microtubule-Associated Proteins/physiology , Mitochondrial Diseases/physiopathology , Mitochondrial Proteins/physiology
18.
Prostate ; 80(6): 491-499, 2020 05.
Article in English | MEDLINE | ID: mdl-32068909

ABSTRACT

BACKGROUND: Prostate cancer (PC) research has relied heavily on patient-derived cell lines, which may be used for in vitro (two-dimensional [2D]) studies or cultivated as three-dimensional (3D) xenografts in mice. These approaches are likely to have differential impacts on cell phenotypes, with implications for experimental outcomes. Therefore, defining and comparing the transcriptional signatures associated with 2D and 3D approaches may be useful for designing experiments and interpreting research results. METHODS: In this study, LNCaP, VCaP, and 22Rv1 human PC cells were either cultivated in monolayers or as xenografts in NOD SCID mice, and their gene transcription profiles were quantitated and compared using microarray and real-time polymerase chain reaction techniques. Immunohistochemistry was used to evaluate protein expression in cancer cell xenografts. RESULTS: Comparisons of gene expression profiles of tumor cells grown in 2D vs 3D environments identified gene sets featuring similar expression patterns in all three cancer cell lines and unique transcriptional signatures associated with 3D vs 2D growth. Pathways related to cell-cell interactions, differentiation, and the extracellular matrix were enriched in 3D conditions. Immunohistochemical analyses confirmed that gene upregulation in xenografts occurred in implanted cancer cells and not in mouse stromal cells. Cultivating cells in vitro in the presence of mouse, rather than bovine serum failed to elicit the gene transcription profile observed in xenografts, further supporting the hypothesis that this profile reflects 3D growth and enhanced microenvironmental interactions, rather than exposure to species-specific serum factors. CONCLUSIONS: Overall, these findings define the expression profiles observed in PC cells cultivated in 2D monolayers and in 3D xenografts, highlighting differentially regulated pathways in each setting and providing information for interpreting research results in model systems.


Subject(s)
Prostatic Neoplasms/genetics , Prostatic Neoplasms/pathology , Animals , Cell Line, Tumor , Gene Expression Regulation, Neoplastic , Genome, Human , Heterografts , Humans , Immunohistochemistry , Male , Mice , Mice, Inbred NOD , Mice, SCID , Oligonucleotide Array Sequence Analysis/methods , Transcriptome , Tumor Cells, Cultured , Tumor Microenvironment/genetics
19.
Am J Hum Genet ; 100(1): 117-127, 2017 Jan 05.
Article in English | MEDLINE | ID: mdl-28017373

ABSTRACT

From a GeneMatcher-enabled international collaboration, we identified ten individuals affected by intellectual disability, speech delay, ataxia, and facial dysmorphism and carrying a deleterious EBF3 variant detected by whole-exome sequencing. One 9-bp duplication and one splice-site, five missense, and two nonsense variants in EBF3 were found; the mutations occurred de novo in eight individuals, and the missense variant c.625C>T (p.Arg209Trp) was inherited by two affected siblings from their healthy mother, who is mosaic. EBF3 belongs to the early B cell factor family (also known as Olf, COE, or O/E) and is a transcription factor involved in neuronal differentiation and maturation. Structural assessment predicted that the five amino acid substitutions have damaging effects on DNA binding of EBF3. Transient expression of EBF3 mutant proteins in HEK293T cells revealed mislocalization of all but one mutant in the cytoplasm, as well as nuclear localization. By transactivation assays, all EBF3 mutants showed significantly reduced or no ability to activate transcription of the reporter gene CDKN1A, and in situ subcellular fractionation experiments demonstrated that EBF3 mutant proteins were less tightly associated with chromatin. Finally, in RNA-seq and ChIP-seq experiments, EBF3 acted as a transcriptional regulator, and mutant EBF3 had reduced genome-wide DNA binding and gene-regulatory activity. Our findings demonstrate that variants disrupting EBF3-mediated transcriptional regulation cause intellectual disability and developmental delay and are present in ∼0.1% of individuals with unexplained neurodevelopmental disorders.


Subject(s)
Ataxia/genetics , Face/abnormalities , Intellectual Disability/genetics , Language Development Disorders/genetics , Mutation , Neurodevelopmental Disorders/genetics , Transcription Factors/genetics , Transcription, Genetic/genetics , Adolescent , Adult , Amino Acid Substitution , Child , Child, Preschool , Chromatin/genetics , Chromatin/metabolism , Cyclin-Dependent Kinase Inhibitor p21/genetics , Developmental Disabilities/genetics , Exome/genetics , Female , Gene Expression Regulation/genetics , Genes, Reporter , HEK293 Cells , Humans , Male , Models, Molecular , Mosaicism , Protein Transport/genetics , Syndrome , Transcription Factors/chemistry , Transcription Factors/metabolism
20.
PLoS Biol ; 15(9): e2002623, 2017 Sep.
Article in English | MEDLINE | ID: mdl-28961236

ABSTRACT

Cells adjust to hypoxic stress within the tumor microenvironment by downregulating energy-consuming processes including translation. To delineate mechanisms of cellular adaptation to hypoxia, we performed RNA-Seq of normoxic and hypoxic head and neck cancer cells. These data revealed a significant down regulation of genes known to regulate RNA processing and splicing. Exon-level analyses classified > 1,000 mRNAs as alternatively spliced under hypoxia and uncovered a unique retained intron (RI) in the master regulator of translation initiation, EIF2B5. Notably, this intron was expressed in solid tumors in a stage-dependent manner. We investigated the biological consequence of this RI and demonstrate that its inclusion creates a premature termination codon (PTC), that leads to a 65kDa truncated protein isoform that opposes full-length eIF2Bε to inhibit global translation. Furthermore, expression of 65kDa eIF2Bε led to increased survival of head and neck cancer cells under hypoxia, providing evidence that this isoform enables cells to adapt to conditions of low oxygen. Additional work to uncover -cis and -trans regulators of EIF2B5 splicing identified several factors that influence intron retention in EIF2B5: a weak splicing potential at the RI, hypoxia-induced expression and binding of the splicing factor SRSF3, and increased binding of total and phospho-Ser2 RNA polymerase II specifically at the intron retained under hypoxia. Altogether, these data reveal differential splicing as a previously uncharacterized mode of translational control under hypoxia and are supported by a model in which hypoxia-induced changes to cotranscriptional processing lead to selective retention of a PTC-containing intron in EIF2B5.


Subject(s)
Eukaryotic Initiation Factor-2B/genetics , Gene Expression Profiling/methods , Introns/genetics , Protein Biosynthesis/genetics , Tumor Hypoxia/genetics , Alternative Splicing/genetics , Base Sequence , Cell Line, Tumor , Gene Expression Regulation, Neoplastic , Genetic Loci , Head and Neck Neoplasms/genetics , Head and Neck Neoplasms/pathology , Humans , Models, Biological , Nucleotide Motifs/genetics , Phosphorylation , Polymerase Chain Reaction , Protein Binding , Protein Isoforms/genetics , Protein Isoforms/metabolism , RNA Polymerase II/metabolism , RNA, Messenger/genetics , RNA, Messenger/metabolism , Regulatory Sequences, Nucleic Acid/genetics , Reproducibility of Results
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