RESUMO
Loss-of-function CHD2 (chromodomain helicase DNA-binding protein 2) mutations are associated with a spectrum of neurodevelopmental disorders often including early-onset generalized seizures, photosensitivity, and epileptic encephalopathies. Patients show psychomotor delay/intellectual disability (ID), autistic features, and behavior disorders, such as aggression and impulsivity. Most reported cases are sporadic with description of germline mosaicism only in two families. We detect the first case of parental gonosomal CHD2 mosaicism disclosed by two brothers showing mild ID, born to healthy parents. The eldest brother has a history of drug-controlled generalized tonic-clonic seizures and displays sleep disorder and aggressive behavior suggestive of Smith-Magenis syndrome (SMS). Analysis of brothers' DNAs by next-generation sequencing (NGS) custom gene panel for pediatric epilepsy and/or ID disclosed in both the same pathogenic CHD2 variant. Additional NGS experiment on genomic DNA from parents' peripheral blood and from buccal swab raised the suspicion of low-grade gonosomal mosaicism in the unaffected mother subsequently confirmed by digital polymerase chain reaction (dPCR). This report underlines as worthwhile CHD2 screening in individuals presenting ID/developmental delay, with/without epilepsy, and behavior and sleep disorders suggestive of SMS. Detecting a CHD2 variant should prime testing probands' parents by NGS coupled to dPCR on different tissues to exclude/confirm gonosomal mosaicism and define the recurrence risk.
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Mosaicismo , Irmãos , Síndrome de Smith-Magenis , Humanos , Masculino , Síndrome de Smith-Magenis/genética , Proteínas de Ligação a DNA/genética , Feminino , Deficiência Intelectual/genética , Criança , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Linhagem , Mutação/genética , Pré-Escolar , FenótipoRESUMO
BACKGROUND: To date, variants in the GBA gene represent the most frequent large-effect genetic factor associated with Parkinson's disease (PD). However, the reason why individuals with the same GBA variant may or may not develop neurodegeneration and PD is still unclear. OBJECTIVES: Therefore, we evaluated the contribution of rare variants in genes responsible for lysosomal storage disorders (LSDs) to GBA-PD risk, comparing the burden of deleterious variants in LSD genes in PD patients versus asymptomatic subjects, all carriers of deleterious variants in GBA. METHODS: We used a custom next-generation sequencing panel, including 50 LSD genes, to screen 305 patients and 207 controls (discovery cohort). Replication and meta-analysis were performed in two replication cohorts of GBA-variant carriers, of 250 patients and 287 controls, for whom exome or genome data were available. RESULTS: Statistical analysis in the discovery cohort revealed a significantly increased burden of deleterious variants in LSD genes in patients (P = 0.0029). Moreover, our analyses evidenced that the two strongest modifiers of GBA penetrance are a second variation in GBA (5.6% vs. 1.4%, P = 0.023) and variants in genes causing mucopolysaccharidoses (6.9% vs. 1%, P = 0.0020). These results were confirmed in the meta-analysis, where we observed pooled odds ratios of 1.42 (95% confidence interval [CI] = 1.10-1.83, P = 0.0063), 4.36 (95% CI = 2.02-9.45, P = 0.00019), and 1.83 (95% CI = 1.04-3.22, P = 0.038) for variants in LSD genes, GBA, and mucopolysaccharidosis genes, respectively. CONCLUSION: The identification of genetic lesions in lysosomal genes increasing PD risk may have important implications in terms of patient stratification for future therapeutic trials. © 2022 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson Movement Disorder Society.
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Doença de Parkinson , Humanos , Glucosilceramidase/genética , Heterozigoto , Lisossomos , Mutação , Doença de Parkinson/complicações , Doença de Parkinson/genéticaRESUMO
Factor XI (FXI) deficiency is an autosomal bleeding disorder, usually posttrauma or postsurgery, characterized by reduced levels of coagulation FXI in plasma. The disease is highly prevalent in Ashkenazi Jews (heterozygote frequency, â¼9%), whereas it is considered a rare condition in most populations (prevalence of the severe deficiency, 1 in 106 in the white population). So far, >190 causative mutations have been identified throughout the F11 gene. To have a global landscape of genetic variation of F11, we explored publicly available exome-based data obtained from >60 000 individuals belonging to different ethnicities (Exome Aggregation Consortium resource). This analysis revealed profound differences in heterozygote frequencies among populations (allele frequencies: African = 0.0016; East Asian = 0.0045; European = 0.0036; Finnish = 0.00030; Latino = 0.0021; South Asian = 0.0015), and a prevalence significantly higher than that reported so far (eg, the calculated prevalence of the severe deficiency in Europeans would be: 12.9 in 106). In addition, this analysis allowed us to evidence recurrent and ethnic-specific mutations: p.Phe223Leu in Africans (23.5% of all mutated alleles), p.Gln263X and p.Leu424CysfsX in East Asians (28.2% and 20.5%, respectively), and p.Ala412Thr in Latinos (25%).
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Alelos , Deficiência do Fator XI/genética , Fator XI/genética , Frequência do Gene , Mutação de Sentido Incorreto , Feminino , Humanos , Masculino , Grupos Raciais/genéticaRESUMO
Biallelic DNAJC12 mutations were described in children with hyperphenylalaninemia, neurodevelopmental delay, and dystonia. We identified DNAJC12 homozygous null variants (c.187A>T;p.K63* and c.79-2A>G;p.V27Wfs*14) in two kindreds with early-onset parkinsonism. Both probands had mild intellectual disability, mild nonprogressive, motor symptoms, sustained benefit from small dose of levodopa, and substantial worsening of symptoms after levodopa discontinuation. Neuropathology (Proband-A) revealed no alpha-synuclein pathology, and substantia nigra depigmentation with moderate cell loss. DNAJC12 transcripts were reduced in both patients. Our results suggest that DNAJC12 mutations (absent in 500 early-onset patients with Parkinson's disease) rarely cause dopa-responsive nonprogressive parkinsonism in adulthood, but broaden the clinical spectrum of DNAJC12 deficiency. Ann Neurol 2017;82:640-646.
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Antiparkinsonianos/uso terapêutico , Levodopa/uso terapêutico , Mutação/genética , Transtornos Parkinsonianos/tratamento farmacológico , Transtornos Parkinsonianos/genética , Proteínas Repressoras/genética , Adulto , Peptídeos beta-Amiloides/metabolismo , Aminas Biogênicas/metabolismo , Encéfalo/metabolismo , Encéfalo/patologia , Análise Mutacional de DNA , Proteínas de Ligação a DNA/metabolismo , Saúde da Família , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Transtornos Parkinsonianos/patologia , Fenilalanina/metabolismo , Proteína Sequestossoma-1/metabolismo , Adulto Jovem , alfa-Sinucleína/metabolismo , Proteínas tau/metabolismoRESUMO
BACKGROUND: The protein kinase C alpha (PRKCA) gene, coding for a Th17-cell-selective kinase, shows a complex splicing pattern, with at least 2 stable alternative transcripts characterized by an alternative upstream polyadenylation site. Polymorphisms in this gene were associated with several conditions, including multiple sclerosis, asthma, schizophrenia, and cancer. The presence of a microRNA (miRNA), i.e. miR-634, within intron 15 of the PRKCA gene, suggests the intriguing possibility that this miRNA might play a role in the susceptibility to these pathologies. METHODS: Here, we characterized miR-634 expression profile and searched for its putative targets using a combination of RT-PCR and gene reporter assays. RESULTS: The quantitative analysis of PRKCA and miR-634 transcripts in a panel of human tissues and cell lines revealed discordant expression profiles, suggesting the presence of an independent miR-634 promoter and/or a possible direct role of miR-634 in modulating PRKCA expression. Functional studies demonstrated the existence of a miRNA-specific promoter, which was shown to be Pol-III-dependent. Furthermore, transfection experiments showed that miR-634 is able to target its host gene by specifically down-regulating the shorter alternative-polyadenylated isoforms. CONCLUSIONS: MiR-634 is a Pol III-dependent intronic miRNA, which could target its host gene through a "first-order" negative feedback. GENERAL SIGNIFICANCE: MiR-634 is one of the few characterized examples of Pol-III-dependent intronic miRNAs. Its independent transcription from the host gene suggests caution in using expression profiles of host genes as proxies for the expression of the corresponding intronic miRNAs.
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Íntrons/genética , MicroRNAs/genética , Poliadenilação/genética , Isoformas de Proteínas/genética , Proteína Quinase C-alfa/genética , RNA Polimerase III/metabolismo , Linhagem Celular , Linhagem Celular Tumoral , Regulação para Baixo/genética , Regulação da Expressão Gênica/genética , Genes Reporter/genética , Células HEK293 , Células HeLa , Humanos , Regiões Promotoras Genéticas/genética , RNA Polimerase III/genética , Transcrição Gênica/genética , Transcriptoma/genéticaRESUMO
Abnormalities in alternative splicing (AS) are emerging as recurrent features in autoimmune diseases (AIDs). In particular, a growing body of evidence suggests the existence of a pathogenic association between a generalized defect in splicing regulatory genes and multiple sclerosis (MS). Moreover, several studies have documented an unbalance in alternatively-spliced isoforms in MS patients possibly contributing to the disease etiology. In this work, using a combination of PCR-based techniques (reverse-transcription (RT)-PCR, fluorescent-competitive, real-time, and digital RT-PCR assays), we investigated the alternatively-spliced gene encoding Gasdermin B, GSDMB, which was repeatedly associated with susceptibility to asthma and AIDs. The in-depth characterization of GSDMB AS and backsplicing profiles led us to the identification of an exonic circular RNA (ecircRNA) as well as of novel GSDMB in-frame and out-of-frame isoforms. The non-productive splicing variants were shown to be downregulated by the nonsense-mediated mRNA decay (NMD) in human cell lines, suggesting that GSDMB levels are significantly modulated by NMD. Importantly, both AS isoforms and the identified ecircRNA were significantly dysregulated in peripheral blood mononuclear cells of relapsing-remitting MS patients compared to controls, further supporting the notion that aberrant RNA metabolism is a characteristic feature of the disease.
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Regulação da Expressão Gênica , Esclerose Múltipla/genética , Proteínas de Neoplasias/genética , Splicing de RNA , RNA , Processamento Alternativo , Estudos de Casos e Controles , Éxons , Feminino , Ordem dos Genes , Humanos , Masculino , Esclerose Múltipla/sangue , Esclerose Múltipla Recidivante-Remitente/sangue , Esclerose Múltipla Recidivante-Remitente/genética , Degradação do RNAm Mediada por Códon sem Sentido , RNA CircularRESUMO
The protein kinase C alpha (PRKCA) gene, encoding a Th17-cell-selective kinase, was repeatedly associated with multiple sclerosis (MS), but the underlying pathogenic mechanism remains unknown. We replicated the association in Italians (409 cases, 723 controls), identifying a protective signal in the PRKCA promoter (P = 0.033), and a risk haplotype in intron 3 (P = 7.7 × 10(-4); meta-analysis with previously published data: P = 4.01 × 10(-8)). Expression experiments demonstrated that the protective signal is associated with alleles conferring higher PRKCA expression levels, well fitting our observation that MS patients have significantly lower PRKCA mRNA levels in blood. The risk haplotype was shown to be driven by a GGTG ins/del polymorphism influencing the heterogeneous nuclear ribonucleoprotein H-dependent inclusion/skipping of a PRKCA alternative exon 3*. Indeed, exon 3* can be present in two different versions in PRKCA mRNAs (out-of-frame 61 bp or in-frame 66 bp long), and is preferentially included in transcripts generated through a premature polyadenylation event. The GGTG insertion downregulates 3* inclusion and shifts splicing towards the 66 bp isoform. Both events reduce the nonsense-mediated mRNA-decay-induced degradation of exon 3*-containing mRNAs. Since we demonstrated that the protein isoform produced through premature polyadenylation aberrantly localizes to the plasma membrane and/or in cytoplasmic clusters, dysregulated PRKCA 3* inclusion may represent an additional mechanism relevant to MS susceptibility.
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Processamento Alternativo , Predisposição Genética para Doença , Esclerose Múltipla/genética , Proteína Quinase C-alfa/genética , RNA Mensageiro/genética , Alelos , Linhagem Celular , Cromossomos Humanos Par 17/química , Éxons , Feminino , Loci Gênicos , Humanos , Mutação INDEL , Íntrons , Masculino , Pessoa de Meia-Idade , Esclerose Múltipla/metabolismo , Esclerose Múltipla/patologia , Regiões Promotoras Genéticas , Proteína Quinase C-alfa/química , Proteína Quinase C-alfa/metabolismo , Estabilidade de RNA , RNA Mensageiro/química , RNA Mensageiro/metabolismo , Transdução de SinaisRESUMO
Oculocutaneous albinism (OCA) is characterized by hypopigmentation of the skin, hair and eye, and by ophthalmologic abnormalities caused by a deficiency in melanin biosynthesis. OCA type IV (OCA4) is one of the four commonly recognized forms of albinism, and is determined by mutation in the SLC45A2 gene. Here, we investigated the genetic basis of OCA4 in an Italian child. The mutational screening of the SLC45A2 gene identified two novel potentially pathogenic splicing mutations: a synonymous transition (c.888G>A) involving the last nucleotide of exon 3 and a single-nucleotide insertion (c.1156+2dupT) within the consensus sequence of the donor splice site of intron 5. As computer-assisted analysis for mutant splice-site prediction was not conclusive, we investigated the effects on pre-mRNA splicing of these two variants by using an in vitro minigene approach. Production of mutant transcripts in HeLa cells demonstrated that both mutations cause the almost complete abolishment of the physiologic donor splice site, with the concomitant unmasking of cryptic donor splice sites. To our knowledge, this work represents the first in-depth molecular characterization of splicing defects in a OCA4 patient.
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Albinismo Oculocutâneo/genética , Antígenos de Neoplasias/genética , Proteínas de Membrana Transportadoras/genética , Sítios de Splice de RNA/genética , Pré-Escolar , Humanos , Masculino , Mutação de Sentido Incorreto , Splicing de RNA/genéticaRESUMO
The emergence of early life must have been marked by the appearance in the prebiotic era of complex molecular structures and systems, motivating the investigation of conditions that could not only facilitate appropriate chemical synthesis, but also provide the mechanisms of molecular selection and structural templating necessary to pilot the complexification toward specific molecular patterns. We recently proposed and demonstrated that these functions could be afforded by the spontaneous ordering of ultrashort nucleic acids oligomers into Liquid Crystal (LC) phases. In such supramolecular assemblies, duplex-forming oligomers are held in average end-to-end contact to form chemically discontinuous but physically continuous double helices. Using blunt ended duplexes, we found that LC formation could both provide molecular selection mechanisms and boost inter-oligomer ligation. This paper provides an essential extension to this notion by investigating the catalytic effects of LC ordering in duplexes with mutually interacting overhangs. Specifically, we studied the influence of LC ordering of 5'-hydroxy-3'-phosphate partially self-complementary DNA 14mers with 3'-CG sticky-ends, on the efficiency of non-enzymatic ligation reaction induced by water-soluble carbodiimide EDC as condensing agent. We investigated the ligation products in mixtures of DNA with poly-ethylene glycol (PEG) at three PEG concentrations at which the system phase separates creating DNA-rich droplets that organize into isotropic, nematic LC and columnar LC phases. We observe remarkable LC-enhanced chain lengthening, and we demonstrate that such lengthening effectively promotes and stabilizes LC domains, providing the kernel of a positive feedback cycle by which LC ordering promotes elongation, in turn stabilizing the LC ordering.
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DNA/química , Evolução Química , Cristais Líquidos/química , Etildimetilaminopropil Carbodi-Imida/química , Polietilenoglicóis/químicaRESUMO
Abnormalities in RNA metabolism and alternative splicing (AS) are emerging as important players in complex disease phenotypes. In particular, accumulating evidence suggests the existence of pathogenic links between multiple sclerosis (MS) and altered AS, including functional studies showing that an imbalance in alternatively-spliced isoforms may contribute to disease etiology. Here, we tested whether the altered expression of AS-related genes represents a MS-specific signature. A comprehensive comparative analysis of gene expression profiles of publicly-available microarray datasets (190 MS cases, 182 controls), followed by gene-ontology enrichment analysis, highlighted a significant enrichment for differentially-expressed genes involved in RNA metabolism/AS. In detail, a total of 17 genes were found to be differentially expressed in MS in multiple datasets, with CELF1 being dysregulated in five out of seven studies. We confirmed CELF1 downregulation in MS (p=0.0015) by real-time RT-PCRs on RNA extracted from blood cells of 30 cases and 30 controls. As a proof of concept, we experimentally verified the unbalance in alternatively-spliced isoforms in MS of the NFAT5 gene, a putative CELF1 target. In conclusion, for the first time we provide evidence of a consistent dysregulation of splicing-related genes in MS and we discuss its possible implications in modulating specific AS events in MS susceptibility genes.
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Esclerose Múltipla/genética , Análise de Sequência com Séries de Oligonucleotídeos/métodos , Splicing de RNA/genética , Idoso , Processamento Alternativo/genética , Proteínas CELF1/genética , Proteínas CELF1/metabolismo , Bases de Dados Genéticas , Feminino , Redes Reguladoras de Genes , Genótipo , Humanos , Masculino , Pessoa de Meia-Idade , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , SoftwareRESUMO
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiologic agent of the coronavirus disease 2019 (COVID-19) pandemic. Clinical manifestations of the disease range from an asymptomatic condition to life-threatening events and death, with more severe courses being associated with age, male sex, and comorbidities. Besides these risk factors, intrinsic characteristics of the virus as well as genetic factors of the host are expected to account for COVID-19 clinical heterogeneity. Genetic studies have long been recognized as fundamental to identify biological mechanisms underlying congenital diseases, to pinpoint genes/proteins responsible for the susceptibility to different inherited conditions, to highlight targets of therapeutic relevance, to suggest drug repurposing, and even to clarify causal relationships that make modifiable some environmental risk factors. Though these studies usually take long time to be concluded and, above all, to translate their discoveries to patients' bedside, the scientific community moved really fast to deliver genetic signals underlying different COVID-19 phenotypes. In this Review, besides a concise description of COVID-19 symptomatology and of SARS-CoV-2 mechanism of infection, we aimed to recapitulate the current literature in terms of host genetic factors that specifically associate with an increased severity of the disease.
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COVID-19 , Masculino , Humanos , COVID-19/genética , SARS-CoV-2/genética , Predisposição Genética para Doença , Comorbidade , Fatores de RiscoRESUMO
BACKGROUND: Circular RNAs (circRNAs) are a class of non-coding RNAs increasingly emerging as crucial actors in the pathogenesis of human diseases, including autoimmune and neurological disorders as multiple sclerosis (MS). Despite several efforts, the mechanisms regulating circRNAs expression are still largely unknown and the circRNA profile and regulation in MS-relevant cell models has not been completely investigated. In this work, we aimed at exploring the global landscape of circRNA expression in MS patients, also evaluating a possible correlation with their genetic and epigenetic background. METHODS: We performed RNA-seq experiments on circRNA-enriched samples, derived from peripheral blood mononuclear cells (PBMCs) of 10 MS patients and 10 matched controls and performed differential circRNA expression. The genetic background was evaluated using array genotyping, and an expression quantitative trait loci (eQTL) analysis was carried out. RESULTS: Expression analysis revealed 166 differentially expressed circRNAs in MS patients, 125 of which are downregulated. One of the top dysregulated circRNAs, hsa_circ_0007990, derives from the PGAP3 gene, encoding a protein relevant for the control of autoimmune responses. The downregulation of this circRNA was confirmed in two independent replication cohorts, suggesting its implementation as a possible RNA-based biomarker. The eQTL analysis evidenced a significant association between 89 MS-associated loci and the expression of at least one circRNA, suggesting that MS-associated variants could impact on disease pathogenesis by altering circRNA profiles. Finally, we found a significant correlation between exon methylation and circRNA expression levels, supporting the hypothesis that epigenetic features may play an important role in the definition of the cell circRNA pool. CONCLUSION: We described the circRNA expression profile of PBMCs in MS patients, suggesting that MS-associated variants may tune the expression levels of circRNAs acting as "circ-QTLs", and proposing a role for exon-based DNA methylation in regulating circRNA expression.
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Esclerose Múltipla , RNA Circular , Humanos , RNA Circular/genética , RNA Circular/metabolismo , Leucócitos Mononucleares/metabolismo , Esclerose Múltipla/genética , Esclerose Múltipla/metabolismo , RNA/genética , RNA/metabolismo , Metilação de DNARESUMO
Alternative splicing of pre-mRNAs is a central process to the generation of proteome complexity. However, many alternative mRNA isoforms carry premature termination codons (PTCs) rendering them possible targets for the nonsense-mediated mRNA decay (NMD) pathway. The F11 gene consists of 15 exons spanning approximately 23 kb on chromosome 4q35 and codes for coagulation factor XI (FXI), a 160-kDa dimeric zymogen composed of 4 apple domains and a serine protease domain. Here, we characterized the F11 splicing pattern in human liver and platelets identifying multiple in-frame and out-of-frame splicing events. Inhibition of NMD resulted in the up-regulation of all unproductively spliced F11 transcripts, thus providing evidence that these PTC-containing mRNAs are under the control of NMD. Among in-frame alternatively spliced transcripts, the one skipping exons 6 and 7 would lead to the synthesis of a FXI protein lacking 1 apple domain (FXI-Delta6/7). Ex vivo expression in mammalian cells demonstrated that FXI-Delta6/7 is mostly retained intracellularly, and secreted only in low amounts. Traces of this FXI isoform were detectable in human plasma. Our results suggest that the coupling of alternative splicing and NMD may play a role in regulating F11 expression, and point to the existence of a novel FXI isoform.
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Processamento Alternativo/genética , Fator XI/genética , Precursores de RNA/genética , Processamento Alternativo/efeitos dos fármacos , Processamento Alternativo/fisiologia , Animais , Células COS , Chlorocebus aethiops , Códon sem Sentido/genética , Códon sem Sentido/metabolismo , Feminino , Células Hep G2 , Humanos , Modelos Biológicos , Fases de Leitura Aberta/genética , Isoformas de Proteínas/análise , Isoformas de Proteínas/genética , Isoformas de Proteínas/metabolismo , Inibidores da Síntese de Proteínas/farmacologia , Puromicina/farmacologia , Precursores de RNA/análise , Processamento Pós-Transcricional do RNA/efeitos dos fármacos , Processamento Pós-Transcricional do RNA/fisiologia , Regulação para CimaRESUMO
INTRODUCTION: Parkinson's disease (PD) belongs to a family of neurodegenerative diseases characterized by alpha-synuclein accumulation in neurons, whose etiopathogenesis remains largely uncovered. Recently, LRP10 has been associated with PD, Parkinson's disease Dementia (PDD) and Dementia with Lewy Bodies (DLB) by linkage analysis and positional cloning in an Italian family with late-onset PD. After the first characterization of a LRP10 pathogenic variant, other eight mutations have been detected in an international series of 660 probands with either a clinical or pathological diagnosis of PD, PDD or DLB. However, the results of following replication studies were inconclusive and the pathogenic role of LRP10 is still debated. The aim of this study is to sequence the LRP10 gene in an Italian cohort of clinically-diagnosed PD patients and to compare the frequency of the identified variants with the ones found in a large cohort of Italian exomes. METHODS: A cohort of 664 PD patients was analyzed by targeted Next Generation Sequencing approach. Identified LRP10 variants were subsequently confirmed by Sanger sequencing and searched for in an in-house database including 3596 Italian exomes. RESULTS: We identified three PD patients carrying a rare heterozygous, potentially pathogenic variant (p.R296C, p.R549Q, p.R661C). None of them was detected in 3596 Italian exomes. Two of them (p.R296C and p.R661C) have been previously reported in one sporadic PD and one definite Progressive supranuclear palsy patients respectively. All three carriers had late-onset PD responsive to levodopa, characterized by both motor and non-motor features, but no cognitive impairment. CONCLUSION: We report three rare possibly-pathogenic LRP10 variants in PD patients from Italy. Further investigations are required to definitively establish their role in alpha-synucleinopathies.
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Proteínas Relacionadas a Receptor de LDL/genética , Doença de Parkinson/genética , Idoso , Feminino , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Itália , Masculino , Pessoa de Meia-Idade , Sequenciamento do ExomaRESUMO
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiologic agent of the coronavirus disease 2019 (COVID-19) pandemic. Besides virus intrinsic characteristics, the host genetic makeup is predicted to account for the extreme clinical heterogeneity of the disease, which is characterized, among other manifestations, by a derangement of hemostasis associated with thromboembolic events. To date, large-scale studies confirmed that genetic predisposition plays a role in COVID-19 severity, pinpointing several susceptibility genes, often characterized by immunologic functions. With these premises, we performed an association study of common variants in 32 hemostatic genes with COVID-19 severity. We investigated 49,845 single-nucleotide polymorphism in a cohort of 332 Italian severe COVID-19 patients and 1668 controls from the general population. The study was conducted engaging a class of students attending the second year of the MEDTEC school (a six-year program, held in collaboration between Humanitas University and the Politecnico of Milan, allowing students to gain an MD in Medicine and a Bachelor's Degree in Biomedical Engineering). Thanks to their willingness to participate in the fight against the pandemic, we evidenced several suggestive hits (p < 0.001), involving the PROC, MTHFR, MTR, ADAMTS13, and THBS2 genes (top signal in PROC: chr2:127192625:G:A, OR = 2.23, 95%CI = 1.50-3.34, p = 8.77 × 10-5). The top signals in PROC, MTHFR, MTR, ADAMTS13 were instrumental for the construction of a polygenic risk score, whose distribution was significantly different between cases and controls (p = 1.62 × 10-8 for difference in median levels). Finally, a meta-analysis performed using data from the Regeneron database confirmed the contribution of the MTHFR variant chr1:11753033:G:A to the predisposition to severe COVID-19 (pooled OR = 1.21, 95%CI = 1.09-1.33, p = 4.34 × 10-14 in the weighted analysis).
RESUMO
INTRODUCTION: Deleterious variants in the GBA gene confer a 2- to 20-fold increased risk of Parkinson's disease (PD) and are associated with a more severe disease course. The presence of a highly-similar pseudogene complicates genetic screening, both by Sanger and next-generation sequencing (NGS). Among PD-associated GBA variants, four missense substitutions (p.L444P, p.N370S, p.T369M, p.E326K) account for the majority of cases. Here, we aimed at developing an allele-specific PCR (AS-PCR) able to concomitantly detect the most common PD-related GBA variants. METHODS: A multiplex PCR assay was designed using allele-specific oligonucleotides that distinguish the gene from the pseudogene and can exclusively amplify the variant alleles. Primer sequences and molarity, and thermal profiles were empirically optimized. The assay was validated on 4016 DNAs extracted by standard salting-out and previously analyzed by whole-exome sequencing (WES) followed by Sanger validation. RESULTS: AS-PCRs performed on 4016 DNAs detected 103 variants; among them, 97 were true positives and 6 false positives. When comparing the results with the original WES data, for the "difficult" p.L444P, the number of false positives was 2/9 and 18/24 for multiplex-AS-PCR and WES, respectively. As we could have missed some p.L444P alleles by NGS, we verified the test performance on 50 DNAs from Sanger-validated p.L444P heterozygotes. All samples tested correctly. CONCLUSION: We set up and validated a rapid and inexpensive test for screening large cohorts of individuals for variants conferring a significant PD risk. This screening method is particularly interesting to identify patients who could benefit most from early access to personalized therapies.
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Testes Genéticos , Glucosilceramidase/genética , Doença de Parkinson/diagnóstico , Doença de Parkinson/genética , Idoso , Estudos de Coortes , Feminino , Testes Genéticos/economia , Testes Genéticos/métodos , Testes Genéticos/normas , Humanos , Masculino , Pessoa de Meia-Idade , Reprodutibilidade dos Testes , Sensibilidade e EspecificidadeRESUMO
OBJECTIVE: To provide a variant-specific estimate of incidence, penetrance, sex distribution, and association with dementia of the 4 most common Parkinson disease (PD)-associated GBA variants, we analyzed a large cohort of 4,923 Italian unrelated patients with primary degenerative parkinsonism (including 3,832 PD) enrolled in a single tertiary care center and 7,757 ethnically matched controls. METHODS: The p.E326K, p.T369M, p.N370S, and p.L444P variants were screened using an allele-specific multiplexed PCR approach. All statistical procedures were performed using R or Plink v1.07. RESULTS: Among the 4 analyzed variants, the p.L444P confirmed to be the most strongly associated with disease risk for PD, PD dementia (PDD), and dementia with Lewy bodies (DLB) (odds ratio [OR] for PD 15.63, 95% confidence interval [CI] = 8.04-30.37, p = 4.97*10-16; OR for PDD 29.57, 95% CI = 14.07-62.13, p = 3.86*10-19; OR for DLB 102.7, 95% CI = 31.38-336.1, p = 1.91*10-14). However, an unexpectedly high risk for dementia was conferred by p.E326K (OR for PDD 4.80, 95% CI = 2.87-8.02, p = 2.12*10-9; OR for DLB 12.24, 95% CI = 4.95-30.24, p = 5.71*10-8), which, on the basis of the impact on glucocerebrosidase activity, would be expected to be mild. The 1.5-2:1 male sex bias described in sporadic PD was lost in p.T369M carriers. We also showed that PD penetrance for p.L444P could reach the 15% at age 75 years. CONCLUSIONS: We report a large monocentric study on GBA-PD assessing mutation-specific data on the sex distribution, penetrance, incidence, and association with dementia of the 4 most frequent deleterious variants in GBA.