A novel Xp11.22 duplication involving HUWE1 in a male with syndromic intellectual disability and additional neurological findings

Sequence variants and duplications in the HECT, UBA and WWE domain -containing 1 (HUWE1) E3 ubiquitin ligase gene have been associated with X-linked mild to severe intellectual disability (ID), but a solid phenotype pattern among the affected males is still remaining to be established. Here, we report a male patient with sporadic, severe and syndromic ID, carrying a novel and unique 842 kb duplication at Xp11.22, including the dosage-sensitive HUWE1 gene and other fifteen curated RefSeq genes. Expression analysis in the patient and his female relatives confirmed increased HUWE1 mRNA levels, with different X-chromosome inactivation patterns among the female carriers. Our patient differs from those previously described by us and others as he presents encephalomalacia at brain Magnetic Resonance Imaging and diffuse bilaterally and synchronous intercritical irritating paroxysms at electroencephalogram. Overall, our clinical, molecular, and neurological findings sum up the previous data, expanding the phenotype spectrum in Xp11.22 copy gains involving the whole HUWE1 gene in both males and female carriers in light of X-chromosome inactivation patterns.

Skewed X-chromosome Inactivation in Women with Idiopathic Intellectual Disability is Indicative of Pathogenic Variants

Intellectual disability (ID) is an early onset impairment in cognitive functioning and adaptive behavior, affecting approximately 1% of the population worldwide. Extreme skewing of X-chromosome inactivation (XCI) can be associated with ID phenotypes caused by pathogenic variants in the X chromosome. We analyzed the XCI pattern in blood samples of 194 women with idiopathic ID, using the androgen receptor gene (AR) methylation assay. Among the 136 patients who were informative, 11 (8%) presented with extreme or total XCI skewing (≥ 90%), which was significantly higher than expected by chance. Whole-exome data obtained from these 11 patients revealed the presence of dominant pathogenic variants in eight of them, all sporadic cases, resulting in a molecular diagnostic rate of 73% (8/11 patients). All variants were mapped to ID-related genes with dominant phenotypes: four variants in the X-linked genes DDX3X (an XCI escape gene; two cases), WDR45, and PDHA1, and four variants in the autosomal genes KCNB1, CTNNB1, YY1, and ANKRD11. Three of the autosomal genes had no obvious correlation with the observed XCI skewing. However, YY1 is a known transcriptional repressor that acts in the binding of the XIST long noncoding RNA on the inactive X chromosome, providing a mechanistic link between the pathogenic variant and the detected skewed XCI in the carrier. These data confirm that extreme XCI skewing in females with ID is highly indicative of causative X-linked pathogenic variants, and point to the possibility of identifying causative variants in autosomal genes with a XCI role.

Convergent molecular mechanisms underlying cognitive impairment in mucopolysaccharidosis type II

Mucopolysaccharidosis type II (MPS II) is a lysosomal storage disorder caused by pathogenic variants in the iduronate-2-sulfatase gene (IDS), responsible for the degradation of glycosaminoglycans (GAGs) heparan and dermatan sulfate. IDS enzyme deficiency results in the accumulation of GAGs within cells and tissues, including the central nervous system (CNS). The progressive neurological outcome in a representative number of MPSII patients (neuronopathic form) involves cognitive impairment, behavioral difficulties, and regression in developmental milestones. In an attempt to dissect part of the influence of axon guidance instability over the cognitive impairment presentation in MPS II, we used brain expression data, network propagation, and clustering algorithm to prioritize in the human interactome a disease module associated with the MPS II context. We identified new candidate genes and pathways that act in focal adhesion, integrin cell surface, laminin interactions, ECM proteoglycans, cytoskeleton, and phagosome that converge into functional mechanisms involved in early neural circuit formation defects and could indicate clues about cognitive impairment in patients with MPSII. Such molecular changes during neurodevelopment may precede the morphological and clinical evidence, emphasizing the importance of an early diagnosis and directing the development of potential drug leads. Furthermore, our data also support previous hypotheses pointing to shared pathogenic mechanisms in some neurodegenerative diseases.

Shared Neurodevelopmental Perturbations Can Lead to Intellectual Disability in Individuals with Distinct Rare Chromosome Duplications

Chromosomal duplications are associated with a large group of human diseases that arise mainly from dosage imbalance of genes within the rearrangements. Phenotypes range widely but are often associated with global development delay, intellectual disability, autism spectrum disorders, and multiple congenital abnormalities. How different contiguous genes from a duplicated genomic region interact and dynamically affect the expression of each other remains unclear in most cases. Here, we report a genomic comparative delineation of genes located in duplicated chromosomal regions 8q24.13q24.3, 18p11.32p11.21, and Xq22.3q27.2 in three patients followed up at our genetics service who has the intellectual disability (ID) as a common phenotype. We integrated several genomic data levels by identification of gene content within the duplications, protein-protein interactions, and functional analysis on specific tissues. We found functional relationships among genes from three different duplicated chromosomal regions, reflecting interactions of protein-coding genes and their involvement in common cellular subnetworks. Furthermore, the sharing of common significant biological processes associated with ID has been demonstrated between proteins from the different chromosomal regions. Finally, we elaborated a shared model of pathways directly or indirectly related to the central nervous system (CNS), which could perturb cognitive function and lead to ID in the three duplication conditions.

XRCC4 rs28360071 intronic variant is associated with increased risk for infant acute lymphoblastic leukemia with KMT2A rearrangements

Early age acute leukemia (EAL) shows a high frequency of KMT2A-rearrangements (KMT2A-r). Previous investigations highlighted double-strand breaks arising from maternal exposure to xenobiotics during pregnancy as a risk factor for EAL and KMT2A-r. In this case-control study, we investigated the relationship between EAL and genetic variants of the nonhomologous end-joining (XRCC6 rs5751129, XRCC4 rs6869366 and rs28360071), since they might affect DNA repair capacity, leading to KMT2A-r and leukemogenesis. Samples from 577 individuals (acute lymphoblastic leukemia-ALL, n=164; acute myeloid leukemia-AML, n=113; controls, n=300) were genotyped. No significant association was found for rs5751129 and rs6869366, whereas rs28360071 was associated with an increased risk for ALL with KMT2A-r (IIxID: OR - Odds ratio 2.23, CI 1.17-4.25, p=0.014). Bone marrow samples from ALL patients showed a higher expression of XRCC4 compared to AML patients (p=0.025). Human Splicing Finder 3.1 predicted that the deleted allele of rs28360071 is potentially associated with the activation of a 5’ cryptic splice site in intron 3 of XRCC4. The sequencing of cDNA did not show any differences on the splicing process for the rs28360071 genotypes. Our results suggest that the deleted allele for rs28360071 increases the risk for ALL with KMT2A-r, but not by modifying the XRCC4 expression levels or its structure.

Association between socioeconomic markers and adult telomere length differs according to sex: Pro-Saúde study

Understanding the social determinants of telomere length is critical to evaluate the risk of early biological aging. We investigated sex differences on the association between socioeconomic status (SES) and demographic markers and leukocyte telomere length (LTL) in Brazilian adults. This cross-sectional study was conducted in a subsample (women=228; men=200) nested within the Pro-Saúde study, a prospective cohort study of university civil servants in Rio de Janeiro, Brazil (2012-2013). Adjusted multivariate models were used to test the relationship between SES markers (marital status, educational attainment, father's educational attainment, race/skin color, household income, and childhood experience of food deprivation) and LTL. After adjusting for age and potential health-related confounders, lower educational attainment was associated with shorter LTL among men (β=-0.05, 95% confidence interval (CI)=95%CI: -0.10, 0.00, P=0.03). In women, LTL was inversely associated with unmarried status (β=-0.05, 95%CI: -0.09, 0.00, P=0.03), lower father's educational attainment (β=-0.05, 95%CI: -0.13, 0.00, P=0.04), and childhood experience of food deprivation (β=-0.07, 95%CI: -0.13, 0.00, P=0.04). Our findings suggested that the association between SES markers and LTL differs according to sex. SES markers able to induce lifelong stress, reflected in LTL, appeared to be more related to individual factors in men, whereas in women they were family-related.

Skewed X-Chromosome Inactivation and Compensatory Upregulation of Escape Genes Precludes Major Clinical Symptoms in a Female With a Large Xq Deletion

In mammalian females, X-chromosome inactivation (XCI) acts as a dosage compensation mechanism that equalizes X-linked genes expression between homo- and heterogametic sexes. However, approximately 12–23% of X-linked genes escape from XCI, being bi-allelic expressed. Herein, we report on genetic and functional data from an asymptomatic female of a Fragile X syndrome family, who harbors a large deletion on the X-chromosome. Array-CGH uncovered that the de novo, terminal, paternally originated 32 Mb deletion on Xq25-q28 spans 598 RefSeq genes, including escape and variable escape genes. Androgen receptor (AR) and retinitis pigmentosa 2 (RP2) methylation assays showed extreme skewed XCI ratios from both peripheral blood and buccal mucosa, silencing the abnormal X-chromosome. Surprisingly, transcriptome-wide analysis revealed that escape and variable escape genes spanning the deletion are mostly upregulated on the active X-chromosome, precluding major clinical/cognitive phenotypes in the female. Metaphase high count, hemizygosity concordance for microsatellite markers, and monoallelic expression of genes within the deletion suggest the absence of mosaicism in both blood and buccal mucosa. Taken together, our data suggest that an additional protective gene-by-gene mechanism occurs at the transcriptional level in the active X-chromosome to counterbalance detrimental phenotype effects of large Xq deletions.

Clinical profiles associated with LRRK2 and GBA mutations in Brazilians with Parkinson's disease

BACKGROUND

Parkinson's disease (PD) is a neurodegenerative disorder characterized by remarkable phenotypic variability. Accumulated evidence points that the manifestation of PD clinical signs might be differentially modified by genetic factors, as mutations in LRRK2 and GBA genes. In this sense, the clarification of the genotype-phenotype correlations in PD has important implications in predicting prognosis and can contribute to the development of specific therapeutic approaches.

METHODS

Here, we conducted the first comparative analysis of motor and non-motor features in 17 LRRK2 and 22 GBA mutation carriers and 93 non-carriers unrelated PD patients from Brazil, a highly admixed population.

RESULTS

Significant differences were found between the three groups. LRRK2 PD patients presented more occurrence of familiar history. Resting tremor was observed in a lower frequency in GBA mutation carries. In contrast, gait freezing and dysautonomia was present in lower frequencies in LRRK2 carriers. Besides that, LRRK2 and GBA mutation carriers showed a higher incidence of depressive symptoms and a younger age at onset, when compared to non-carriers.

CONCLUSION

Our results suggest that specific mutations in GBA and LRRK2 influence the clinical signs of the disease, with significant implications for handling of specific patient groups.

Autosomal dominant Parkinson's disease: Incidence of mutations in LRRK2, SNCA, VPS35 and GBA genes in Brazil

INTRODUCTION

Amongst Parkinson's disease (PD) genetic factors, mutations in LRRK2, SNCA, VPS35 and GBA genes are recognized causes of PD. Nonetheless, few genetic screenings have been conducted in families with a history of PD consistent with autosomal dominant inheritance (ADPD), and their relevance to the etiology of PD has been poorly explored in Latin American populations, such as the Brazilian one, with a high degree of admixture.

METHODS

In order to assess the contribution of specific mutations in LRRK2, SNCA, VPS35 and GBA genes to ADPD in Brazil, we conducted the first molecular evaluation in a cohort of 141 index cases from families with ADPD. Genomic DNA was isolated from peripheral blood or saliva, and the molecular analysis was performed by TaqMan allelic discrimination assays or bidirectional sequencing.

RESULTS

Heterozygous mutations in LRRK2 and GBA genes were identified in 10 (7.0%) probands, and all presented typical signs of classical PD. No mutations were found in SNCA or VPS35 genes.

CONCLUSION

Our findings in a representative series of index cases from families with ADPD emphasize the important contribution of LRRK2 G2019S and GBA (L444P and N370S) mutations to parkinsonism in Brazilian families. The absence of mutations in VPS35 and SNCA genes reveals that they are uncommon causes of PD in Brazil, corroborating previous studies that also failed to detect these genetic variants in PD patients from other populations. Recent discoveries of novel causative genes of autosomal dominant forms of PD expand the investigative possibilities and should be targeted on future studies.

MicroRNAs: macro challenges on understanding human biological functions and neurological diseases

MicroRNAS (miRNAs) are a class of endogenously single-stranded non-coding RNA molecules that can negatively modulate the expression of target messenger RNAs by 3' UTR base pairing. During the processing of a miRNA, a network of orchestrated molecular events provides a dynamic manner to posttranscriptionally modulate gene expression. Recent research has demonstrated that although these molecules are small, they are involved in several crucial biological functions, as well as, in a broad spectrum of human diseases. In this review, we highlighted the current knowledge on the miRNA pathway field, focusing on how the disruption of the miRNA-mediated silencing pathways could lead to the pathogenesis of neurological disorders. The potential use of miRNAs as diagnostic/prognostic markers and the possibility of reversing the effects of some miRNA polymorphisms/mutations by promising therapeutics procedures have brought new perspectives into the treatment of human pathologies.

Epigenetic alterations of p15(INK4B) and p16(INK4A) genes in pediatric primary myelodysplastic syndrome

We studied the methylation status of the p15(INK4B) and p16(INK4A) genes in 47 pediatric patients with primary MDS, its correlation with subtype, and the role of p15(INK4B) and p16(INK4A) in the evolution of MDS toward AML. Aberrant methylation of the p15(INK4B) gene was detected in 15 of 47 patients (32%), whereas only four patients demonstrated methylation of the p16(INK4A) gene (8%). The frequency of p15(INK4B) methylation was significantly higher in RAEB and RAEB-t subtypes (p<0.003). Aberrant methylation of the p16(INK4A) gene was also more frequent in the subtypes that characterize advanced stages of the disease (p<0.05). Evolution of disease was verified in 17 (36%) of the 47 patients. The association of p15(INK4B) and p16(INK4A) methylation status with evolution of disease was clearly significant (p<0.008 and p<0.05, respectively). These results suggest that methylation of the p15(INK4B) and p16(INK4A) genes is an epigenetic biomarker of pediatric disease evolution.

Investigation of CBS, MTR, RFC-1 and TC polymorphisms as maternal risk factors for Down syndrome

Recent evidence shows that almost 92% of the DS children are born from young mothers, suggesting that other risk factors than advanced maternal age must be involved. In this context, some studies demonstrated a possible link between DS and maternal polymorphisms in genes involved in folate metabolism. These polymorphisms, as well as low intake of folate could generate genomic instability, DNA hypomethylation and abnormal segregation, leading to trisomy 21. We compared the frequency of CBS 844ins68, MTR 2756A>G, RFC-1 80G&gt A and TC 776C>G polymorphisms among 114 case mothers and 110 matched controls, in order to observe whether these variants act as risk factors for DS. The genotype distributions revealed that there were not significant differences between both samples. However, when we proceed the multiplicative interaction analyses between the four polymorphisms described above together with the previously studied MTHFR 677C>T, MTHFR 1298A>C and MTRR 66A>G polymorphisms, our results show that the combined genotype TC 776CC / MTHFR 677TT and TC 776CC / MTR 2756AG were significantly higher in the control sample. Nevertheless, there was no significant association after Bonferroni correction. Our results suggest that maternal folate-related polymorphisms studied here have no influence on trisomy 21 susceptibility in subjects of Brazilian population.

Co-occurrence of sporadic parkinsonism and late-onset Alzheimer's disease in a Brazilian male with the LRRK2 p.G2019S mutation

Mutations in the leucine-rich repeat kinase 2 (LRRK2) gene represent the most common known genetic cause of inherited and idiopathic Parkinson's disease (PD) in different populations. The predicted multifunctionality of LRRK2 product and the pleomorphic pathology associated with LRRK2 mutations place this gene as a potential candidate for other neurodegenerative disorders, mainly Alzheimer's disease (AD). We report a Brazilian male expressing both late-onset AD and slowly progressive parkinsonism signs, and who presented the most frequent LRRK2 mutation (p.G2019S). Although the co-occurrence of PD and AD would be expected occasionally, the shared mechanisms between the two complex disorders are still unclear and are discussed herein. In light of recent findings about the wide role of LRRK2 under normal and pathological conditions, it is tempting to speculate that LRRK2 mutations might play an upstream influence on the etiology of not just PD but also several alpha-synuclein and tau pathologies, including AD.

Implication of abnormal epigenetic patterns for human diseases

Significant evidences have brought new insights on the mechanisms by which epigenetic machinery proteins regulate gene expression, leading to a redefinition of chromatin regulation in terms of modification of core histones, DNA methylation, RNA-mediated silencing pathways, action of methylation-dependent sensitive insulators and Polycomb/Trithorax group proteins. Consistent with these fundamental aspects, an increasing number of human pathologies have been found to be associated with aberrant epigenetics regulation, including cancer, mental retardation, neurodegenerative symptoms, imprinting disorders, syndromes involving chromosomal instabilities and a great number of human life-threatening diseases. The possibility of reversing epigenetic marks, in contrast to genetic code, may provide new pharmacological targets for emerging therapeutic intervention.