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1.
Cell ; 184(18): 4772-4783.e15, 2021 09 02.
Artigo em Inglês | MEDLINE | ID: mdl-34388390

RESUMO

Throughout development and aging, human cells accumulate mutations resulting in genomic mosaicism and genetic diversity at the cellular level. Mosaic mutations present in the gonads can affect both the individual and the offspring and subsequent generations. Here, we explore patterns and temporal stability of clonal mosaic mutations in male gonads by sequencing ejaculated sperm. Through 300× whole-genome sequencing of blood and sperm from healthy men, we find each ejaculate carries on average 33.3 ± 12.1 (mean ± SD) clonal mosaic variants, nearly all of which are detected in serial sampling, with the majority absent from sampled somal tissues. Their temporal stability and mutational signature suggest origins during embryonic development from a largely immutable stem cell niche. Clonal mosaicism likely contributes a transmissible, predicted pathogenic exonic variant for 1 in 15 men, representing a life-long threat of transmission for these individuals and a significant burden on human population health.


Assuntos
Crescimento e Desenvolvimento , Mosaicismo , Espermatozoides/metabolismo , Adolescente , Envelhecimento/sangue , Alelos , Células Clonais , Estudos de Coortes , Humanos , Masculino , Modelos Biológicos , Mutação/genética , Fatores de Risco , Fatores de Tempo , Adulto Jovem
2.
Nature ; 629(8011): 384-392, 2024 May.
Artigo em Inglês | MEDLINE | ID: mdl-38600385

RESUMO

Debate remains around the anatomical origins of specific brain cell subtypes and lineage relationships within the human forebrain1-7. Thus, direct observation in the mature human brain is critical for a complete understanding of its structural organization and cellular origins. Here we utilize brain mosaic variation within specific cell types as distinct indicators for clonal dynamics, denoted as cell-type-specific mosaic variant barcode analysis. From four hemispheres and two different human neurotypical donors, we identified 287 and 780 mosaic variants, respectively, that were used to deconvolve clonal dynamics. Clonal spread and allele fractions within the brain reveal that local hippocampal excitatory neurons are more lineage-restricted than resident neocortical excitatory neurons or resident basal ganglia GABAergic inhibitory neurons. Furthermore, simultaneous genome transcriptome analysis at both a cell-type-specific and a single-cell level suggests a dorsal neocortical origin for a subgroup of DLX1+ inhibitory neurons that disperse radially from an origin shared with excitatory neurons. Finally, the distribution of mosaic variants across 17 locations within one parietal lobe reveals that restriction of clonal spread in the anterior-posterior axis precedes restriction in the dorsal-ventral axis for both excitatory and inhibitory neurons. Thus, cell-type-resolved somatic mosaicism can uncover lineage relationships governing the development of the human forebrain.


Assuntos
Linhagem da Célula , Células Clonais , Mosaicismo , Neurônios , Prosencéfalo , Idoso , Feminino , Humanos , Alelos , Linhagem da Célula/genética , Células Clonais/citologia , Células Clonais/metabolismo , Neurônios GABAérgicos/citologia , Neurônios GABAérgicos/metabolismo , Hipocampo/citologia , Proteínas de Homeodomínio/metabolismo , Neocórtex/citologia , Inibição Neural , Neurônios/citologia , Neurônios/metabolismo , Lobo Parietal/citologia , Prosencéfalo/anatomia & histologia , Prosencéfalo/citologia , Prosencéfalo/metabolismo , Análise de Célula Única , Transcriptoma/genética
3.
Nature ; 604(7907): 689-696, 2022 04.
Artigo em Inglês | MEDLINE | ID: mdl-35444276

RESUMO

The structure of the human neocortex underlies species-specific traits and reflects intricate developmental programs. Here we sought to reconstruct processes that occur during early development by sampling adult human tissues. We analysed neocortical clones in a post-mortem human brain through a comprehensive assessment of brain somatic mosaicism, acting as neutral lineage recorders1,2. We combined the sampling of 25 distinct anatomic locations with deep whole-genome sequencing in a neurotypical deceased individual and confirmed results with 5 samples collected from each of three additional donors. We identified 259 bona fide mosaic variants from the index case, then deconvolved distinct geographical, cell-type and clade organizations across the brain and other organs. We found that clones derived after the accumulation of 90-200 progenitors in the cerebral cortex tended to respect the midline axis, well before the anterior-posterior or ventral-dorsal axes, representing a secondary hierarchy following the overall patterning of forebrain and hindbrain domains. Clones across neocortically derived cells were consistent with a dual origin from both dorsal and ventral cellular populations, similar to rodents, whereas the microglia lineage appeared distinct from other resident brain cells. Our data provide a comprehensive analysis of brain somatic mosaicism across the neocortex and demonstrate cellular origins and progenitor distribution patterns within the human brain.


Assuntos
Células Clonais , Mosaicismo , Neocórtex , Linhagem da Célula , Células Cultivadas , Humanos , Microglia , Neocórtex/citologia , Neocórtex/crescimento & desenvolvimento
4.
Trends Genet ; 37(10): 890-902, 2021 10.
Artigo em Inglês | MEDLINE | ID: mdl-34158173

RESUMO

While sperm mosaicism has few consequences for men, the offspring and future generations are unwitting recipients of gonadal cell mutations, often yielding severe disease. Recent studies, fueled by emergent technologies, show that sperm mosaicism is a common source of de novo mutations (DNMs) that underlie severe pediatric disease as well as human genetic diversity. Sperm mosaicism can be divided into three types: Type I arises during sperm meiosis and is non-age dependent; Type II arises in spermatogonia and increases as men age; and Type III arises during paternal embryogenesis, spreads throughout the body, and contributes stably to sperm throughout life. Where Types I and II confer little risk of recurrence, Type III may confer identifiable risk to future offspring. These mutations are likely to be the single largest contributor to human genetic diversity. New sequencing approaches may leverage this framework to evaluate and reduce disease risk for future generations.


Assuntos
Doença/genética , Genômica , Mosaicismo , Mutação , Espermatozoides/metabolismo , Humanos , Masculino , Espermatogônias/metabolismo
5.
Am J Hum Genet ; 103(2): 296-304, 2018 08 02.
Artigo em Inglês | MEDLINE | ID: mdl-30032983

RESUMO

The dynamic shape of the endoplasmic reticulum (ER) is a reflection of its wide variety of critical cell biological functions. Consequently, perturbation of ER-shaping proteins can cause a range of human phenotypes. Here, we describe three affected children (from two consanguineous families) who carry homozygous loss-of-function mutations in LNPK (previously known as KIAA1715); this gene encodes lunapark, which is proposed to serve as a curvature-stabilizing protein within tubular three-way junctions of the ER. All individuals presented with severe psychomotor delay, intellectual disability, hypotonia, epilepsy, and corpus callosum hypoplasia, and two of three showed mild cerebellar hypoplasia and atrophy. Consistent with a proposed role in neurodevelopmental disease, LNPK was expressed during brain development in humans and mice and was present in neurite-like processes in differentiating human neural progenitor cells. Affected cells showed the absence of full-length lunapark, aberrant ER structures, and increased luminal mass density. Together, our results implicate the ER junction stabilizer lunapark in establishing the corpus callosum.


Assuntos
Retículo Endoplasmático/genética , Proteínas de Homeodomínio/genética , Mutação/genética , Adolescente , Animais , Atrofia/genética , Diferenciação Celular/genética , Criança , Corpo Caloso/patologia , Feminino , Humanos , Lactente , Deficiência Intelectual/genética , Masculino , Proteínas de Membrana , Camundongos , Hipotonia Muscular/genética , Fenótipo , Transtornos Psicomotores/genética , Células-Tronco/patologia
6.
J Med Genet ; 57(4): 274-282, 2020 04.
Artigo em Inglês | MEDLINE | ID: mdl-31586943

RESUMO

BACKGROUND: Protein disulfide isomerase (PDI) proteins are part of the thioredoxin protein superfamily. PDIs are involved in the formation and rearrangement of disulfide bonds between cysteine residues during protein folding in the endoplasmic reticulum and are implicated in stress response pathways. METHODS: Eight children from four consanguineous families residing in distinct geographies within the Middle East and Central Asia were recruited for study. All probands showed structurally similar microcephaly with lissencephaly (microlissencephaly) brain malformations. DNA samples from each family underwent whole exome sequencing, assessment for repeat expansions and confirmatory segregation analysis. RESULTS: An identical homozygous variant in TMX2 (c.500G>A), encoding thioredoxin-related transmembrane protein 2, segregated with disease in all four families. This variant changed the last coding base of exon 6, and impacted mRNA stability. All patients presented with microlissencephaly, global developmental delay, intellectual disability and epilepsy. While TMX2 is an activator of cellular C9ORF72 repeat expansion toxicity, patients showed no evidence of C9ORF72 repeat expansions. CONCLUSION: The TMX2 c.500G>A allele associates with recessive microlissencephaly, and patients show no evidence of C9ORF72 expansions. TMX2 is the first PDI implicated in a recessive disease, suggesting a protein isomerisation defect in microlissencephaly.


Assuntos
Predisposição Genética para Doença , Proteínas de Membrana/genética , Microcefalia/genética , Isomerases de Dissulfetos de Proteínas/genética , Tiorredoxinas/genética , Sequência de Aminoácidos/genética , Criança , Pré-Escolar , Consanguinidade , Retículo Endoplasmático/genética , Éxons/genética , Feminino , Homozigoto , Humanos , Masculino , Proteínas de Membrana/ultraestrutura , Microcefalia/patologia , Mutação/genética , Dobramento de Proteína , Tiorredoxinas/ultraestrutura , Sequenciamento do Exoma
7.
Hum Mol Genet ; 26(2): 258-269, 2017 01 15.
Artigo em Inglês | MEDLINE | ID: mdl-28013290

RESUMO

The integrity and dynamic properties of the microtubule cytoskeleton are indispensable for the development of the mammalian brain. Consequently, mutations in the genes that encode the structural component (the α/ß-tubulin heterodimer) can give rise to severe, sporadic neurodevelopmental disorders. These are commonly referred to as the tubulinopathies. Here we report the addition of recessive quadrupedalism, also known as Uner Tan syndrome (UTS), to the growing list of diseases caused by tubulin variants. Analysis of a consanguineous UTS family identified a biallelic TUBB2B mutation, resulting in a p.R390Q amino acid substitution. In addition to the identifying quadrupedal locomotion, all three patients showed severe cerebellar hypoplasia. None, however, displayed the basal ganglia malformations typically associated with TUBB2B mutations. Functional analysis of the R390Q substitution revealed that it did not affect the ability of ß-tubulin to fold or become assembled into the α/ß-heterodimer, nor did it influence the incorporation of mutant-containing heterodimers into microtubule polymers. The 390Q mutation in S. cerevisiae TUB2 did not affect growth under basal conditions, but did result in increased sensitivity to microtubule-depolymerizing drugs, indicative of a mild impact of this mutation on microtubule function. The TUBB2B mutation described here represents an unusual recessive mode of inheritance for missense-mediated tubulinopathies and reinforces the sensitivity of the developing cerebellum to microtubule defects.


Assuntos
Cerebelo/anormalidades , Malformações do Desenvolvimento Cortical/genética , Microtúbulos/genética , Malformações do Sistema Nervoso/genética , Tubulina (Proteína)/genética , Adulto , Substituição de Aminoácidos/genética , Gânglios da Base/patologia , Encéfalo/crescimento & desenvolvimento , Encéfalo/patologia , Cerebelo/fisiopatologia , Deficiências do Desenvolvimento/genética , Deficiências do Desenvolvimento/fisiopatologia , Feminino , Homozigoto , Humanos , Masculino , Malformações do Desenvolvimento Cortical/fisiopatologia , Microtúbulos/patologia , Mutação , Malformações do Sistema Nervoso/fisiopatologia , Fenótipo , Saccharomyces cerevisiae/genética
8.
Am J Hum Genet ; 99(1): 228-35, 2016 Jul 07.
Artigo em Inglês | MEDLINE | ID: mdl-27392077

RESUMO

The tRNA splicing endonuclease is a highly evolutionarily conserved protein complex, involved in the cleavage of intron-containing tRNAs. In human it consists of the catalytic subunits TSEN2 and TSEN34, as well as the non-catalytic TSEN54 and TSEN15. Recessive mutations in the corresponding genes of the first three are known to cause pontocerebellar hypoplasia (PCH) types 2A-C, 4, and 5. Here, we report three homozygous TSEN15 variants that cause a milder version of PCH2. The affected individuals showed progressive microcephaly, delayed developmental milestones, intellectual disability, and, in two out of four cases, epilepsy. None, however, displayed the central visual failure seen in PCH case subjects where other subunits of the TSEN are mutated, and only one was affected by the extensive motor defects that are typical in other forms of PCH2. The three amino acid substitutions impacted the protein level of TSEN15 and the stoichiometry of the interacting subunits in different ways, but all resulted in an almost complete loss of in vitro tRNA cleavage activity. Taken together, our results demonstrate that mutations in any known subunit of the TSEN complex can cause PCH and progressive microcephaly, emphasizing the importance of its function during brain development.


Assuntos
Doenças Cerebelares/genética , Endonucleases/genética , Genes Recessivos , Microcefalia/genética , Mutação , Sequência de Aminoácidos , Criança , Pré-Escolar , Endonucleases/química , Feminino , Humanos , Lactente , Recém-Nascido , Masculino , Modelos Moleculares , Linhagem
9.
Mol Cell Neurosci ; 84: 58-67, 2017 10.
Artigo em Inglês | MEDLINE | ID: mdl-28347630

RESUMO

The development of the vertebrate central nervous system is reliant on a complex cascade of biological processes that include mitotic division, relocation of migrating neurons, and the extension of dendritic and axonal processes. Each of these cellular events requires the diverse functional repertoire of the microtubule cytoskeleton for the generation of forces, assembly of macromolecular complexes and transport of molecules and organelles. The tubulins are a multi-gene family that encode for the constituents of microtubules, and have been implicated in a spectrum of neurological disorders. Evidence is building that different tubulins tune the functional properties of the microtubule cytoskeleton dependent on the cell type, developmental profile and subcellular localisation. Here we review of the origins of the functional specification of the tubulin gene family in the developing brain at a transcriptional, translational, and post-transcriptional level. We remind the reader that tubulins are not just loading controls for your average Western blot.


Assuntos
Encéfalo/crescimento & desenvolvimento , Citoesqueleto/metabolismo , Microtúbulos/metabolismo , Tubulina (Proteína)/metabolismo , Animais , Humanos , Processamento de Proteína Pós-Traducional/fisiologia , Proteômica
11.
Neurosci Bull ; 2023 Oct 29.
Artigo em Inglês | MEDLINE | ID: mdl-37898991

RESUMO

Genomic mosaicism describes the phenomenon where some but not all cells within a tissue harbor unique genetic mutations. Traditionally, research focused on the impact of genomic mosaicism on clinical phenotype-motivated by its involvement in cancers and overgrowth syndromes. More recently, we increasingly shifted towards the plethora of neutral mosaic variants that can act as recorders of cellular lineage and environmental exposures. Here, we summarize the current state of the field of genomic mosaicism research with a special emphasis on our current understanding of this phenomenon in brain development and homeostasis. Although the field of genomic mosaicism has a rich history, technological advances in the last decade have changed our approaches and greatly improved our knowledge. We will provide current definitions and an overview of contemporary detection approaches for genomic mosaicism. Finally, we will discuss the impact and utility of genomic mosaicism.

12.
bioRxiv ; 2023 Oct 26.
Artigo em Inglês | MEDLINE | ID: mdl-37961480

RESUMO

Debate remains around anatomic origins of specific brain cell subtypes and lineage relationships within the human forebrain. Thus, direct observation in the mature human brain is critical for a complete understanding of the structural organization and cellular origins. Here, we utilize brain mosaic variation within specific cell types as distinct indicators for clonal dynamics, denoted as cell-type-specific Mosaic Variant Barcode Analysis. From four hemispheres from two different human neurotypical donors, we identified 287 and 780 mosaic variants (MVs), respectively that were used to deconvolve clonal dynamics. Clonal spread and allelic fractions within the brain reveal that local hippocampal excitatory neurons are more lineage-restricted compared with resident neocortical excitatory neurons or resident basal ganglia GABAergic inhibitory neurons. Furthermore, simultaneous genome-transcriptome analysis at both a cell-type-specific and single-cell level suggests a dorsal neocortical origin for a subgroup of DLX1+ inhibitory neurons that disperse radially from an origin shared with excitatory neurons. Finally, the distribution of MVs across 17 locations within one parietal lobe reveals restrictions of clonal spread in the anterior-posterior axis precedes that of the dorsal-ventral axis for both excitatory and inhibitory neurons. Thus cell-type resolved somatic mosaicism can uncover lineage relationships governing the development of the human forebrain.

13.
Nat Biotechnol ; 41(6): 870-877, 2023 06.
Artigo em Inglês | MEDLINE | ID: mdl-36593400

RESUMO

Mosaic variants (MVs) reflect mutagenic processes during embryonic development and environmental exposure, accumulate with aging and underlie diseases such as cancer and autism. The detection of noncancer MVs has been computationally challenging due to the sparse representation of nonclonally expanded MVs. Here we present DeepMosaic, combining an image-based visualization module for single nucleotide MVs and a convolutional neural network-based classification module for control-independent MV detection. DeepMosaic was trained on 180,000 simulated or experimentally assessed MVs, and was benchmarked on 619,740 simulated MVs and 530 independent biologically tested MVs from 16 genomes and 181 exomes. DeepMosaic achieved higher accuracy compared with existing methods on biological data, with a sensitivity of 0.78, specificity of 0.83 and positive predictive value of 0.96 on noncancer whole-genome sequencing data, as well as doubling the validation rate over previous best-practice methods on noncancer whole-exome sequencing data (0.43 versus 0.18). DeepMosaic represents an accurate MV classifier for noncancer samples that can be implemented as an alternative or complement to existing methods.


Assuntos
Exoma , Software , Sequenciamento Completo do Genoma/métodos , Sequenciamento do Exoma , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Polimorfismo de Nucleotídeo Único/genética , Nucleotídeos
14.
Nat Genet ; 55(2): 209-220, 2023 02.
Artigo em Inglês | MEDLINE | ID: mdl-36635388

RESUMO

Malformations of cortical development (MCD) are neurological conditions involving focal disruptions of cortical architecture and cellular organization that arise during embryogenesis, largely from somatic mosaic mutations, and cause intractable epilepsy. Identifying the genetic causes of MCD has been a challenge, as mutations remain at low allelic fractions in brain tissue resected to treat condition-related epilepsy. Here we report a genetic landscape from 283 brain resections, identifying 69 mutated genes through intensive profiling of somatic mutations, combining whole-exome and targeted-amplicon sequencing with functional validation including in utero electroporation of mice and single-nucleus RNA sequencing. Genotype-phenotype correlation analysis elucidated specific MCD gene sets associated with distinct pathophysiological and clinical phenotypes. The unique single-cell level spatiotemporal expression patterns of mutated genes in control and patient brains indicate critical roles in excitatory neurogenic pools during brain development and in promoting neuronal hyperexcitability after birth.


Assuntos
Epilepsia , Malformações do Desenvolvimento Cortical , Humanos , Multiômica , Encéfalo/metabolismo , Epilepsia/genética , Mutação , Malformações do Desenvolvimento Cortical/genética , Malformações do Desenvolvimento Cortical/metabolismo
15.
Elife ; 112022 07 05.
Artigo em Inglês | MEDLINE | ID: mdl-35787314

RESUMO

Background: De novo mutations underlie individually rare but collectively common pediatric congenital disorders. Some of these mutations can also be detected in tissues and from cells in a parent, where their abundance and tissue distribution can be measured. We previously reported that a subset of these mutations is detectable in sperm from the father, predicted to impact the health of offspring. Methods: As a cohort study, in three independent couples undergoing in vitro fertilization, we first identified male gonadal mosaicism through deep whole genome sequencing. We then confirmed variants and assessed their transmission to preimplantation blastocysts (32 total) through targeted ultra-deep genotyping. Results: Across 55 gonadal mosaic variants, 15 were transmitted to blastocysts for a total of 19 transmission events. This represented an overall predictable but slight undertransmission based upon the measured mutational abundance in sperm. We replicated this conclusion in an independent, previously published family-based cohort. Conclusions: Unbiased preimplantation genetic testing for gonadal mosaicism may represent a feasible approach to reduce the transmission of potentially harmful de novo mutations. This-in turn-could help to reduce their impact on miscarriages and pediatric disease. Funding: No external funding was received for this work.


Assuntos
Mosaicismo , Sêmen , Criança , Estudos de Coortes , Humanos , Masculino , Software , Espermatozoides
16.
Eur J Hum Genet ; 29(6): 957-964, 2021 06.
Artigo em Inglês | MEDLINE | ID: mdl-33824466

RESUMO

HEAT repeats are 37-47 amino acid flexible tandem repeat structural motifs occurring in a wide variety of eukaryotic proteins with diverse functions. Due to their ability to undergo elastic conformational changes, they often serve as scaffolds at sites of protein interactions. Here, we describe four affected children from two families presenting with pontocerebellar hypoplasia manifest clinically with neonatal seizures, severe intellectual disability, and motor delay. Whole exome sequencing identified biallelic variants at predicted splice sites in intron 31 of HEATR5B, encoding the HEAT repeat-containing protein 5B segregating in a recessive fashion. Aberrant splicing was found in patient fibroblasts, which correlated with reduced levels of HEATR5B protein. HEATR5B is expressed during brain development in human, and we failed to recover live-born homozygous Heatr5b knockout mice. Taken together, our results implicate loss of HEATR5B in pontocerebellar hypoplasia.


Assuntos
Doenças Cerebelares/genética , Deficiências do Desenvolvimento/genética , Proteínas de Transporte Vesicular/genética , Animais , Encéfalo/metabolismo , Encéfalo/patologia , Células Cultivadas , Doenças Cerebelares/metabolismo , Doenças Cerebelares/patologia , Criança , Deficiências do Desenvolvimento/metabolismo , Deficiências do Desenvolvimento/patologia , Feminino , Fibroblastos/metabolismo , Homozigoto , Humanos , Masculino , Camundongos , Camundongos Endogâmicos C57BL , Mutação , Síndrome
17.
Neuron ; 109(2): 241-256.e9, 2021 01 20.
Artigo em Inglês | MEDLINE | ID: mdl-33220177

RESUMO

Autosomal-recessive cerebellar hypoplasia and ataxia constitute a group of heterogeneous brain disorders caused by disruption of several fundamental cellular processes. Here, we identified 10 families showing a neurodegenerative condition involving pontocerebellar hypoplasia with microcephaly (PCHM). Patients harbored biallelic mutations in genes encoding the spliceosome components Peptidyl-Prolyl Isomerase Like-1 (PPIL1) or Pre-RNA Processing-17 (PRP17). Mouse knockouts of either gene were lethal in early embryogenesis, whereas PPIL1 patient mutation knockin mice showed neuron-specific apoptosis. Loss of either protein affected splicing integrity, predominantly affecting short and high GC-content introns and genes involved in brain disorders. PPIL1 and PRP17 form an active isomerase-substrate interaction, but we found that isomerase activity is not critical for function. Thus, we establish disrupted splicing integrity and "major spliceosome-opathies" as a new mechanism underlying PCHM and neurodegeneration and uncover a non-enzymatic function of a spliceosomal proline isomerase.


Assuntos
Proteínas de Ciclo Celular/genética , Doenças Cerebelares/genética , Microcefalia/genética , Mutação/genética , Peptidilprolil Isomerase/genética , Fatores de Processamento de RNA/genética , Spliceossomos/genética , Sequência de Aminoácidos , Animais , Proteínas de Ciclo Celular/química , Doenças Cerebelares/complicações , Doenças Cerebelares/diagnóstico por imagem , Estudos de Coortes , Feminino , Técnicas de Inativação de Genes/métodos , Células HEK293 , Transtornos Heredodegenerativos do Sistema Nervoso/complicações , Transtornos Heredodegenerativos do Sistema Nervoso/diagnóstico por imagem , Transtornos Heredodegenerativos do Sistema Nervoso/genética , Humanos , Masculino , Camundongos , Camundongos Endogâmicos C57BL , Camundongos Transgênicos , Microcefalia/complicações , Microcefalia/diagnóstico por imagem , Linhagem , Peptidilprolil Isomerase/química , Estrutura Secundária de Proteína , Estrutura Terciária de Proteína , Fatores de Processamento de RNA/química
18.
Eur J Hum Genet ; 29(2): 271-279, 2021 02.
Artigo em Inglês | MEDLINE | ID: mdl-32901138

RESUMO

Trafficking protein particle (TRAPP) complexes, which include the TRAPPC4 protein, regulate membrane trafficking between lipid organelles in a process termed vesicular tethering. TRAPPC4 was recently implicated in a recessive neurodevelopmental condition in four unrelated families due to a shared c.454+3A>G splice variant. Here, we report 23 patients from 17 independent families with an early-infantile-onset neurodegenerative presentation, where we also identified the homozygous variant hg38:11:119020256 A>G (NM_016146.5:c.454+3A>G) in TRAPPC4 through exome or genome sequencing. No other clinically relevant TRAPPC4 variants were identified among any of over 10,000 patients with neurodevelopmental conditions. We found the carrier frequency of TRAPPC4 c.454+3A>G was 2.4-5.4 per 10,000 healthy individuals. Affected individuals with the homozygous TRAPPC4 c.454+3A>G variant showed profound psychomotor delay, developmental regression, early-onset epilepsy, microcephaly and progressive spastic tetraplegia. Based upon RNA sequencing, the variant resulted in partial exon 3 skipping and generation of an aberrant transcript owing to use of a downstream cryptic splice donor site, predicting a premature stop codon and nonsense mediated decay. These data confirm the pathogenicity of the TRAPPC4 c.454+3A>G variant, and refine the clinical presentation of TRAPPC4-related encephalopathy.


Assuntos
Homozigoto , Proteínas do Tecido Nervoso/genética , Transtornos do Neurodesenvolvimento/genética , Splicing de RNA , Proteínas de Transporte Vesicular/genética , Criança , Pré-Escolar , Códon sem Sentido , Exoma , Éxons , Feminino , Humanos , Masculino , Microcefalia/genética , Transtornos do Neurodesenvolvimento/diagnóstico por imagem , Linhagem , Sítios de Splice de RNA , Síndrome
19.
Genome Biol Evol ; 12(11): 2093-2106, 2020 11 03.
Artigo em Inglês | MEDLINE | ID: mdl-32877505

RESUMO

ABC membrane transporters are a large and complex superfamily of ATP-binding cassette transporters that are present in all domains of life. Both their essential function and complexity are reflected by their retention across large expanses of organismal diversity and by the extensive expansion of individual members and subfamilies during evolutionary history. This expansion has resulted in the diverse ABCA transporter family that has in turn evolved into multiple subfamilies. Here, we focus on the ABCA6-like subfamily of ABCA transporters with the goal of understanding their evolutionary history including potential functional changes in, or loss of, individual members. Our analysis finds that ABCA6-like genes, consisting of ABCA6, 8, 9, and 10, are absent from representatives of both monotremes and marsupials and thus the duplications that generated these families most likely occurred at the base of the Eutherian or placental mammals. We have found evidence of both positive and relaxed selection among the ABCA6-like genes, suggesting dynamic changes in function and the potential of gene redundancy. Analysis of the ABCA10 genes further suggests that this gene has undergone relaxed selection only within the human lineage. These findings are complemented by human population data, where we observe an excess of deactivating homozygous mutations. We describe the complex evolutionary history of this ABCA transporter subfamily and demonstrate through the combination of evolutionary and population genetic analysis that ABCA10 is undergoing pseudogenization within humans.


Assuntos
Transportadores de Cassetes de Ligação de ATP/genética , Evolução Molecular , Mamíferos/genética , Seleção Genética , Animais , Duplicação Gênica , Expressão Gênica , Variação Genética , Humanos , Família Multigênica , Filogenia
20.
Epilepsia Open ; 5(1): 97-106, 2020 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-32140648

RESUMO

OBJECTIVES: Recently, defects in the protein kinase mTOR (mammalian target of rapamycin) and its associated pathway have been correlated with hemimegalencephaly (HME). mTOR acts as a central regulator of important physiological cellular functions such as growth and proliferation, metabolism, autophagy, death, and survival. This study was aimed at identifying specific variants in mTOR signaling pathway genes in patients diagnosed with HME. METHODS: Using amplicon and whole exome sequencing (WES) of resected brain and paired blood samples from five HME patients, we were able to identify pathogenic mosaic variants in the mTOR pathway genes MTOR, PIK3CA, and DEPDC5. RESULTS: These results strengthen the hypothesis that somatic variants in PI3K-Akt-mTOR pathway genes contribute to HME. We also describe one patient presenting with a pathogenic variant on DEPDC5 gene, which reinforces the role of DEPDC5 on cortical structural changes due to mTORC1 hyperactivation. These findings also provide insights into when in brain development these variants occurred. An early developmental variant is expected to affect a larger number of cells and to result in a larger malformation, whereas the same variant occurring later in development would cause a minor malformation. SIGNIFICANCE: In the future, numerous somatic variants in known or new genes will undoubtedly be revealed in resected brain samples, making it possible to draw correlations between genotypes and phenotypes and allow for a genetic clinical diagnosis that may help to predict a given patient's outcome.

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