Next-generation sequencing profiling of miRNAs in individuals with 22q11.2 deletion syndrome revealed altered expression of miR-185-5p.

BACKGROUND: The 22q11.2 deletion syndrome (22q11.2DS) is a microdeletion syndrome with highly variable phenotypic manifestations, even though most patients present the typical 3 Mb microdeletion, usually affecting the same ~ 106 genes. One of the genes affected by this deletion is DGCR8, which plays a crucial role in miRNA biogenesis. Therefore, the haploinsufficiency of DGCR8 due to this microdeletion can alter the modulation of the expression of several miRNAs involved in a range of biological processes. RESULTS: In this study, we used next-generation sequencing to evaluate the miRNAs profiles in the peripheral blood of 12 individuals with typical 22q11DS compared to 12 healthy matched controls. We used the DESeq2 package for differential gene expression analysis and the DIANA-miTED dataset to verify the expression of differentially expressed miRNAs in other tissues. We used miRWalk to predict the target genes of differentially expressed miRNAs. Here, we described two differentially expressed miRNAs in patients compared to controls: hsa-miR-1304-3p, located outside the 22q11.2 region, upregulated in patients, and hsa-miR-185-5p, located in the 22q11.2 region, which showed downregulation. Expression of miR-185-5p is observed in tissues frequently affected in patients with 22q11DS, and previous studies have reported its downregulation in individuals with 22q11DS. hsa-miR-1304-3p has low expression in blood and, thus, needs more validation, though using a sensitive technology allowed us to identify differences in expression between patients and controls. CONCLUSIONS: Thus, lower expression of miR-185-5p can be related to the 22q11.2 deletion and DGCR8 haploinsufficiency, leading to phenotypic consequences in 22q11.2DS patients, while higher expression of hsa-miR-1304-3p might be related to individual genomic variances due to the heterogeneous background of the Brazilian population.

Downregulation of genes outside the deleted region in individuals with 22q11.2 deletion syndrome.

The 22q11.2 deletion syndrome (22q11.2DS) is caused by recurrent hemizygous deletions of chromosome 22q11.2. The phenotype of the syndrome is complex and varies widely among individuals. Little is known about the role of the different genes located in 22q11.2, and we hypothesized that genetic risk factors lying elsewhere in the genome might contribute to the phenotype. Here, we present the whole-genome gene expression data of 11 patients with approximately 3 Mb deletions. Apart from the hemizygous genes mapped to the 22q11.2 region, the TUBA8 and GNAZ genes, neighboring the deleted interval but in normal copy number, showed altered expression. When genes mapped to other chromosomes were considered in the gene expression analysis, a genome-wide dysregulation was observed, with increased or decreased expression levels. The enriched pathways of these genes were related to immune response, a deficiency that is frequently observed in 22q11.2DS patients. We also used the hypothesis-free weighted gene co-expression network analysis (WGCNA), which revealed the co-expression gene network modules with clear connection to mechanisms associated with 22q11.2DS such as immune response and schizophrenia. These findings, combined with the traditional gene expression profile, can be used for the identification of potential pathways and genes not previously considered to be related to the 22q11.2 deletion syndrome.

Duplication 9p and their implication to phenotype.

BACKGROUND: Trisomy 9p is one of the most common partial trisomies found in newborns. We report the clinical features and cytogenomic findings in five patients with different chromosome rearrangements resulting in complete 9p duplication, three of them involving 9p centromere alterations. METHODS: The rearrangements in the patients were characterized by G-banding, SNP-array and fluorescent in situ hybridization (FISH) with different probes. RESULTS: Two patients presented de novo dicentric chromosomes: der(9;15)t(9;15)(p11.2;p13) and der(9;21)t(9;21)(p13.1;p13.1). One patient presented two concomitant rearranged chromosomes: a der(12)t(9;12)(q21.13;p13.33) and an psu i(9)(p10) which showed FISH centromeric signal smaller than in the normal chromosome 9. Besides the duplication 9p24.3p13.1, array revealed a 7.3 Mb deletion in 9q13q21.13 in this patient. The break in the psu i(9)(p10) probably occurred in the centromere resulting in a smaller centromere and with part of the 9q translocated to the distal 12p with the deletion 9q occurring during this rearrangement. Two patients, brother and sister, present 9p duplication concomitant to 18p deletion due to an inherited der(18)t(9;18)(p11.2;p11.31)mat. CONCLUSIONS: The patients with trisomy 9p present a well-recognizable phenotype due to facial appearance, although the genotype-phenotype correlation can be difficult due to concomitant partial monosomy of other chromosomes. The chromosome 9 is rich in segmental duplication, especially in pericentromeric region, with high degree of sequence identity to sequences in 15p, 18p and 21p, chromosomes involved in our rearrangements. Thus, we suggest that chromosome 9 is prone to illegitimate recombination, either intrachromosomal or interchromosomal, which predisposes it to rearrangements, frequently involving pericentromeric regions.

Neuropsychological Profile of 25 Brazilian Patients with 22q11.2 Deletion Syndrome: Effects of Clinical and Socioeconomic Variables.

The 22q11.2 deletion syndrome (22q11.2DS) is associated with a heterogeneous neurocognitive phenotype, which includes psychiatric disorders. However, few studies have investigated the influence of socioeconomic variables on intellectual variability. The aim of this study was to investigate the cognitive profile of 25 patients, aged 7 to 32 years, with a typical ≈3 Mb 22q11.2 deletion, considering intellectual, adaptive, and neuropsychological functioning. Univariate linear regression analysis explored the influence of socioeconomic variables on intellectual quotient (IQ) and global adaptive behavior. Associations with relevant clinical conditions such as seizures, recurrent infections, and heart diseases were also considered. Results showed IQ scores ranging from 42 to 104. Communication, executive functions, attention, and visuoconstructive skills were the most impaired in the sample. The study found effects of access to quality education, family socioeconomic status (SES), and caregiver education level on IQ. Conversely, age at diagnosis and language delay were associated with outcomes in adaptive behavior. This characterization may be useful for better understanding the influence of social-environmental factors on the development of patients with 22q11.2 deletion syndrome, as well as for intervention processes aimed at improving their quality of life.

CEDNIK syndrome in a Brazilian patient with compound heterozygous pathogenic variants.

CEDNIK (Cerebral Dysgenesis, Neuropathy, Ichthyosis, and Keratoderma) syndrome is a neuro ichthyotic syndrome characterized by a clinical constellation of features including severe developmental delay, microcephaly, and facial dysmorphism. Here, we report the clinical and molecular characterization of a patient with CEDNIK syndrome harboring two compound heterozygous variants in the SNAP29 gene. The patient presents a combination of a loss-of-function SNAP29 mutation and a ∼370 kb 22q11.2 deletion, each of these genetic variants inherited from one of the parents. This report provides detailed data of a patient with unprecedented genetic events leading to the CEDNIK phenotype and may contribute to the elucidation of this rare condition.

Position effect modifying gene expression in a patient with ring chromosome 14.

The clinical phenotype of patients with ring chromosomes usually reflects the loss of genomic material during ring formation. However, phenotypic alterations can also be found in the presence of complete ring chromosomes, in which the breakage and rejoining in terminal regions of both chromosome arms result in no gene loss. Here, we present a patient with a ring chromosome 14 that lost nothing but the telomeres. Since he and other patients with a similar chromosome abnormality present certain abnormal characteristics, we investigated the gene expression of eight chromosome 14 genes to find out whether the configuration of the ring had changed it, possibly producing some of these clinical features. The expression of these eight genes was studied by quantitative real-time polymerase chain reaction (qPCR) in the patient and in seven controls matched for gender and age. Two of them were found to be downregulated in the patient compared to the controls, indicating that his phenotype might be related to alterations in the expression of genes located in the abnormal chromosome, even when the copy number is normal. Thus, the phenotypic alterations found in the presence of complete ring chromosomes may be related to changes in the chromatin architecture, bringing about a change of expression by position effect. These results may explain some of the characteristics presented by our patient.

Genetic mechanisms leading to primary amenorrhea in balanced X-autosome translocations.

OBJECTIVE: To map the X-chromosome and autosome breakpoints in women with balanced X-autosome translocations and primary amenorrhea, searching candidate genomic loci for female infertility. DESIGN: Retrospective and case-control study. SETTING: University-based research laboratory. PATIENT(S): Three women with balanced X-autosome translocation and primary amenorrhea. INTERVENTION(S): Conventional cytogenetic methods, genomic array, array painting, fluorescence in situ hybridization, and quantitative reverse transcription-polymerase chain reaction. MAIN OUTCOME MEASURE(S): Karyotype, copy number variation, breakpoint mapping, and gene expression levels. RESULT(S): All patients presented with breakpoints in the Xq13q21 region. In two patients, the X-chromosome breakpoint disrupted coding sequences (KIAA2022 and ZDHHC15 genes). Although both gene disruptions caused absence of transcription in peripheral blood, there is no evidence that supports the involvement of these genes with ovarian function. The ZDHHC15 gene belongs to a conserved syntenic region that encompasses the FGF16 gene, which plays a role in female germ line development. The break in the FGF16 syntenic block may have disrupted the interaction between the FGF16 promoter and its cis-regulatory element. In the third patient, although both breakpoints are intergenic, a gene that plays a role in the DAX1 pathway (FHL2 gene) flanks distally the autosome breakpoint. The FHL2 gene may be subject to position effect due to the attachment of an autosome segment in Xq21 region. CONCLUSION(S): The etiology of primary amenorrhea in balanced X-autosome translocation patients may underlie more complex mechanisms than interruption of specific X-linked candidate genes, such as position effect. The fine mapping of the rearrangement breakpoints may be a tool for identifying genetic pathogenic mechanisms for primary amenorrhea.

Intellectual performance profi le of a sample of children and adolescents from Brazil with 22q11. 2 Deletion Syndrome (22q11. 2DS) based on the Wechsler Scale / Perfil de desempenho intelectual de uma amostra brasileira de crianças e adolescentes com Síndrome da Deleção 22q11. 2 (22q11. 2DS)com base na Escala Wechsler

The 22q11.2 Deletion Syndrome (22q11.2DS), the most common human chromosome microdeletion syndrome, is associated with a very heterogeneous neurocognitive phenotype. One of the main characteristics of the syndrome spectrum is the intellectual variability, which encompasses average performance and intellectual disability and discrepancies between Verbal Intelligence Quotient and Performance Verbal Intelligence Quotient, with greater impairment in nonverbal tasks. The present study aimed at investigating the intellectual performance aspects of a 21children and adolescents sample from Brazil who had been diagnosed with 22q11.2DS, based on the Wechsler Intelligence Scale for Children - 4th edition. The samples were reviewed considering the differences between indices. The results revealed an Full Scale Intelligence Quotient predominant in the borderline range (42 to 104) and a significant discrepancy between the indices of Verbal Comprehension and Perceptual Reasoning in 42% of the sample. With regard to the performance in the subtests alone, a better performance was found in Similarities, whereas block design, matrix reasoning, digit span and letter-number sequencing subtests were the most challenging. These findings indicate that a comprehensive assessment of intellectual performance aspects covering the different measures of the Wechsler Intelligence Scale may contribute to a broader understanding of the neurocognitive phenotype associated with 22q11.2DS.

A Síndrome da Deleção 22q11.2 (SD22q11.2), microdeleção cromossômica mais frequente em humanos, é associada a um fenótipo neurocognitivo muito heterogêneo. Uma das principais características do espectro da síndrome é a variabilidade intelectual, que abrange de desempenho médio a deficiência intelectual, bem como discrepâncias entre Quociente de Inteligência Verbal e de Quociente de Inteligência de Execução, com maior prejuízo nas tarefas não verbais. O presente estudo teve por objetivo investigar aspectos do desempenho intelectual de uma amostra brasileira de 21 crianças e adolescentes diagnosticados com SD22q11.2, com base nos indicadores da Wechsler Intelligence Scale for Children - 4th edition. As amostras foram analisadas considerando diferenças entre os índices. Os resultados revelaram predomínio de Quociente de Inteligência Total na faixa limítrofe, entre 42 e 104, assim como discrepância significativa entre os índices de compreensão verbal e organização perceptual em 42% da amostra. No que concerne ao desempenho nos subtestes de forma isolada, um melhor resultado foi verificado em semelhanças, ao passo que cubos, raciocínio matricial, dígitos e sequência de números e letras foram os mais desafiadores. Esses achados indicam que uma avaliação abrangente de aspectos do desempenho intelectual contemplando as diversas medidas da Escala Wechsler de Inteligência pode contribuir para uma compreensão mais ampla do fenótipo neurocognitivo associado à SD22q11.2.

Aspectos genético clínico moleculares da síndrome de cat eye: relato de caso de um paciente do serviço de genética do Hospital do Servidor Público Estadual "Francisco Morato de Oliveira" - IAMSPE, portador de cromossomo marcador extranumerário

Cromossomos marcadores extranumerários são estruturas que aparecem como um cromossomo adicional no cariótipo humano, presente em todas as células ou em forma de mosaico. A identificação inequívoca dos cromossomos marcadores é uma difícil tarefa quando são utilizadas técnicas citogenéticas convencionais, como por exemplo, a cariotipagem com bandamento G onde o padrão de bandas pode ser ambíguo ou inaparente, dependendo da sua origem genética, complexidade do rearranjo genômico e do seu tamanho. Com o advento das técnicas de análise citogenômicas, como a Fluorescence in situ hybridization (FISH), a Multiplex ligation-dependent probe amplification (MLPA) e técnicas de array, o delineamento citogenético molecular destes cromossomos marcadores tornou-se possível. Este trabalho teve por objetivo relatar o caso de um paciente do departamento de Genética Médica do HSPE - IAMSPE que apresentou cariótipo alterado, portando um cromossomo marcador extranumerário. O presente caso foi encaminhado para a UNIFESP – Universidade Federal de São Paulo, para que fosse efetuado o estudo e investigação sobre a origem do cromossomo marcador extranumerário. O estudo com uso de técnicas de citogenética molecular como FISH (Fluorescence in situ Hybridization), SNP Array (Single Nucleotide Polimorfism) e MLPA (Multiplex Ligation Probe Amplificatioin) mostrou que o cromossomo marcador que o paciente portava era derivado de um cromossomo 22, no qual havia uma duplicação da região 22q11.2, concluindo que este paciente era portador de uma tetrassomia da região 22q11.2. Efetuando a correlação genótipo-fenótipo, o paciente foi diagosticado como portador da Síndrome Cat Eye. A importância do estudo de pacientes com alterações raras e relato destes casos destacam o impacto de técnicas de citogenética clássica e molecular, possibilitando melhora no atendimento e conhecimento da evolução de determinadas doenças genéticas.