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1.
Medicine (Baltimore) ; 98(39): e17342, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31574874

RESUMO

RATIONALE: The karyotype 49,XXXXY is a rare form of Klinefelter syndrome usually presenting with ambiguous genitalia, facial dysmorphism, mental retardation, and a combination of cardiac, skeletal, and other malformations. PATIENT CONCERNS: We describe a 19-year-old man, whose chromosomal analysis of peripheral blood revealed a karyotype of 49,XXXXY. His mental development and motor ability were significantly delayed. At the age of 19, he had failed to develop secondary sexual characteristics. His random blood glucose level was 19.61 mmol/L, and he showed dry mouth, polydipsia, and polyuria. He had a characteristic facial appearance with prognathism, widened nasal bridge, and strabismus. His bilateral elbow rotation was limited. He had atrophic testes with micropenis. Ophthalmic examination revealed a polar cataract in both eyes. DIAGNOSIS: He was diagnosed with Klinefelter syndrome associated with cleft palate, hypothyroidism, cataracts, diabetes, and other anomalies. INTERVENTIONS: After the initial diagnosis, the patient received intensive insulin therapy to correct hyperglycemia, and he received calcium and vitamin D supplements. The patient also received testosterone and thyroid hormone replacement therapy for primary hypogonadism. OUTCOMES: The patient was discharged 12 days after receiving treatment; meanwhile, there were no clinical symptoms of dry mouth, polyuria and polyuria, and his blood glucose level was controlled. LESSONS: The combination of cleft palate, hypothyroidism, cataracts, diabetes, and osteoporosis in 49,XXXXY syndrome has not yet been reported. Early treatment and appropriate care can significantly improve the patient's quality of life and prevent serious consequences.


Assuntos
Catarata/congênito , Fissura Palatina/genética , Hipotireoidismo Congênito/genética , Diabetes Mellitus/congênito , Transtornos dos Cromossomos Sexuais/complicações , Anormalidades Múltiplas/genética , Aneuploidia , Cromossomos Humanos X/genética , Humanos , Cariotipagem , Masculino , Aberrações dos Cromossomos Sexuais , Transtornos dos Cromossomos Sexuais/genética , Adulto Jovem
2.
Nat Commun ; 10(1): 2164, 2019 05 15.
Artigo em Inglês | MEDLINE | ID: mdl-31092820

RESUMO

Systemic lupus erythematosus (SLE) is an autoimmune disease, characterised by increased expression of type I interferon (IFN)-regulated genes and a striking sex imbalance towards females. Through combined genetic, in silico, in vitro, and ex vivo approaches, we define CXorf21, a gene of hitherto unknown function, which escapes X-chromosome inactivation, as a candidate underlying the Xp21.2 SLE association. We demonstrate that CXorf21 is an IFN-response gene and that the sexual dimorphism in expression is magnified by immunological challenge. Fine-mapping reveals a single haplotype as a potential causal cis-eQTL for CXorf21. We propose that expression is amplified through modification of promoter and 3'-UTR chromatin interactions. Finally, we show that the CXORF21 protein colocalises with TLR7, a pathway implicated in SLE pathogenesis. Our study reveals modulation in gene expression affected by the combination of two hallmarks of SLE: CXorf21 expression increases in a both an IFN-inducible and sex-specific manner.


Assuntos
Cromossomos Humanos X/genética , Genes Ligados ao Cromossomo X/genética , Interferon Tipo I/metabolismo , Peptídeos e Proteínas de Sinalização Intracelular/metabolismo , Lúpus Eritematoso Sistêmico/genética , Regiões 3' não Traduzidas/genética , Adulto , Fatores Etários , Estudos de Casos e Controles , Feminino , Genes Ligados ao Cromossomo X/imunologia , Predisposição Genética para Doença , Humanos , Interferon Tipo I/imunologia , Peptídeos e Proteínas de Sinalização Intracelular/genética , Lúpus Eritematoso Sistêmico/imunologia , Masculino , Regiões Promotoras Genéticas/genética , Fatores Sexuais , Receptor 7 Toll-Like/genética
3.
Scand J Immunol ; 90(2): e12776, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31069824

RESUMO

The number of the X chromosome-linked genes has been previously suggested to influence immune responses and the development of autoimmune diseases. In the present study, we aimed at evaluating the level of expression of CD40L (an X-linked gene involved in adaptive immunity) and TLR7 (an X-linked gene involved in innate immunity) in a variety of different karyotypes. Those included males, females and patients with X chromosome aneuploidy. Healthy females (46, XX; n = 10) and healthy males (46, XY; n = 10) were compared to females with Turner syndrome (TS) (45, X; n = 11) and males with Klinefelter syndrome (KS) (47, XXY; n = 5). Stimulation of peripheral blood mononuclear cells (PBMCs) with PMA and ionomycin resulted in higher percentage of CD3 + CD40L+ T cells (P < 0.001) and higher level expression of CD40L in T cell (P < 0.001) in female and KS patients compared with male and TS patients. TLR7-mediated IFN-alpha production by HLADR + CD3- CD19- cells was significantly upregulated in healthy women compared with healthy males, TS and KS patients (P < 0.001). TLR7 agonist-stimulated PBMCs from healthy females and KS patients expressed significantly higher levels of TLR7 mRNA than those from male and TS patients (P < 0.05). The increased expression of the X-linked genes TLR7 and CD40L in healthy females and KS patients suggests that the presence of two X chromosomes plays a major role in enhancing both innate and adaptive immune responses. These results may contribute to the explanation of sex-based differences in immune biology and the sex bias in predisposition to autoimmune diseases.


Assuntos
Imunidade Adaptativa/genética , Ligante de CD40/biossíntese , Ligante de CD40/genética , Cromossomos Humanos X/genética , Dosagem de Genes/genética , Imunidade Inata/genética , Receptor 7 Toll-Like/biossíntese , Receptor 7 Toll-Like/genética , Imunidade Adaptativa/imunologia , Antígenos CD19/biossíntese , Complexo CD3/biossíntese , Células Cultivadas , Variações do Número de Cópias de DNA/genética , Feminino , Humanos , Imunidade Inata/imunologia , Interferon-alfa/biossíntese , Ionomicina/farmacologia , Síndrome de Klinefelter/genética , Leucócitos Mononucleares/metabolismo , Ativação Linfocitária/efeitos dos fármacos , Ativação Linfocitária/imunologia , Masculino , Ácidos Polimetacrílicos/farmacologia , RNA Mensageiro/biossíntese , Linfócitos T/efeitos dos fármacos , Linfócitos T/imunologia , Síndrome de Turner/genética
4.
J Pediatr Endocrinol Metab ; 32(5): 479-488, 2019 May 27.
Artigo em Inglês | MEDLINE | ID: mdl-31075085

RESUMO

Background Females with Turner syndrome (TS) are prone to develop autoimmune diseases (AIDs). The X chromosome contains several immune-related genes. Growth hormone (GH) and estrogens modulate the immune system. We aimed to clarify whether the loss of a specific X chromosome gene locus and the administration of GH and estradiol facilitate the development of AIDs in TS females. Methods Retrospective data on clinical course, AIDs, karyotype and treatment were analyzed from a cohort of 286 Czech females with TS (current age 2.8-43.3 years; median age 18.7 years). The karyotypes were sorted using two different classification systems: a mosaicism-focused and an isochromosome (isoXq)-focused approach. Karyotype subgroups with a significantly higher prevalence of AIDs were further evaluated. Data of common therapies were correlated with the prevalence of AIDs. Results The most frequent AIDs were autoimmune thyroid disease (AITD; 37.4%; n = 107) and celiac disease (CD; 8.7%; n = 25). All karyotype subgroups were prone to develop AIDs. Females with an isolated Xp deletion had a significantly higher prevalence of AITD and CD compared to all other individuals with TS (AITD: 66.0% vs. 31.5%, p < 0.0001; CD: 17.4% vs. 7.2%; p = 0.04, respectively). We observed no link between the mean age at initiation as well as the duration of GH and/or estrogen administration and the occurrence of AIDs. Conclusions Isolated Xp deletion contributes to the development of AIDs in TS patients. The haploinsufficiency of genes located in Xpter-p11.2 may explain this observation. Common therapies used in TS do not modify the risk of AIDs.


Assuntos
Doenças Autoimunes/etiologia , Deleção Cromossômica , Cromossomos Humanos X/genética , Síndrome de Turner/genética , Adolescente , Adulto , Doenças Autoimunes/epidemiologia , Criança , Pré-Escolar , República Tcheca/epidemiologia , Feminino , Seguimentos , Humanos , Cariotipagem , Prevalência , Prognóstico , Estudos Retrospectivos , Síndrome de Turner/complicações , Adulto Jovem
5.
Eur J Endocrinol ; 180(6): 397-406, 2019 06 01.
Artigo em Inglês | MEDLINE | ID: mdl-30991358

RESUMO

Objective Turner Syndrome is associated with several phenotypic conditions associated with a higher risk of subsequent comorbidity. We aimed to evaluate the prevalence of congenital malformations and the occurrence of age-related comorbid conditions and to determine whether the frequencies of congenital and acquired conditions depend on X chromosome gene dosage, as a function of karyotype subgroup. Design and methods This national retrospective observational cohort study includes 1501 patients. We evaluated the prevalence of congenital malformations and the cumulative incidence of subsequent specific comorbidities at five-year intervals, from the ages of 10 to 30 years, with stratification by karyotype subgroup: 45,X (n = 549), 45,X/46,isoXq (n = 280), 46,X,r(X)/46,XX (n = 106), 45,X/46,XX (n = 221), presence of Y (n = 87). Results Median age was 9.4 (3.7-13.7) years at first evaluation and 16.8 (11.2-21.4) years at last evaluation. Congenital heart (18.9%) malformations were more frequent in 45,X patients, and congenital renal (17.2%) malformations were more frequent in 45,X, 45,X/46,isoXq and 46,X,r(X)/46,XX patients than in those with 45,X/46,XX mosaicism or a Y chromosome (P < 0.0001). The cumulative incidence of subsequent acquired conditions, such as thyroid disease, hearing loss, overweight/obesity, dyslipidemia and, to a lesser extent, celiac disease, glucose intolerance/type 2 diabetes, hypertension and liver dysfunction increased with age, but less markedly for patients with mosaicism than for those with other karyotypes. Patients with a ring chromosome were more prone to metabolic disorders. Conclusion These data suggest that X gene chromosome dosage, particularly for Xp genes, contributes to the risk of developing comorbidities.


Assuntos
Cromossomos Humanos X/genética , Anormalidades Congênitas/genética , Dosagem de Genes , Síndrome de Turner/genética , Adolescente , Adulto , Fatores Etários , Criança , Estudos de Coortes , Comorbidade , Anormalidades Congênitas/epidemiologia , Feminino , Cardiopatias Congênitas/epidemiologia , Cardiopatias Congênitas/genética , Humanos , Cariótipo , Rim/anormalidades , Nefropatias/congênito , Nefropatias/epidemiologia , Nefropatias/genética , Mosaicismo , Estudos Retrospectivos , Fatores de Risco , Síndrome de Turner/classificação , Síndrome de Turner/complicações , Adulto Jovem
6.
J Genet ; 982019 03.
Artigo em Inglês | MEDLINE | ID: mdl-30945684

RESUMO

Microduplications of the X chromosome are a rare cause of X-linked intellectual disability (XLID), a clinically and genetically heterogeneous spectrum of disorders. In the present study, a 950-kb Xp22.12 microduplication including the RPS6KA3 gene was detected in affected members of a family, including the proband (male), his mother and one maternal uncle. Four female carriers had major depression and one of them also had mild intellectual disability. The present and previous cases with overlapping microduplications suggest that Xp22.12 microduplications can be included in the neuropsychiatric copy number variations.


Assuntos
Cromossomos Humanos X/genética , Doenças Genéticas Ligadas ao Cromossomo X/genética , Deficiência Intelectual/genética , Proteínas Quinases S6 Ribossômicas 90-kDa/genética , Esquizofrenia/genética , Adulto , Duplicação Cromossômica , Variações do Número de Cópias de DNA , Feminino , Doenças Genéticas Ligadas ao Cromossomo X/diagnóstico , Humanos , Deficiência Intelectual/diagnóstico , Masculino , Pessoa de Meia-Idade , Linhagem , Esquizofrenia/diagnóstico
7.
Cancer Sci ; 110(6): 1897-1908, 2019 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-31006167

RESUMO

Xp11.2 translocation renal cell carcinoma (Xp11 tRCC) is a rare sporadic pediatric kidney cancer caused by constitutively active TFE3 fusion proteins. Tumors in patients with Xp11 tRCC tend to recur and undergo frequent metastasis, in part due to lack of methods available to detect early-stage disease. Here we generated transgenic (Tg) mice overexpressing the human PRCC-TFE3 fusion gene in renal tubular epithelial cells, as an Xp11 tRCC mouse model. At 20 weeks of age, mice showed no histological abnormalities in kidney but by 40 weeks showed Xp11 tRCC development and related morphological and histological changes. MicroRNA (miR)-204-5p levels in urinary exosomes of 40-week-old Tg mice showing tRCC were significantly elevated compared with levels in control mice. MicroRNA-204-5p expression also significantly increased in primary renal cell carcinoma cell lines established both from Tg mouse tumors and from tumor tissue from 2 Xp11 tRCC patients. All of these lines secreted miR-204-5p-containing exosomes. Notably, we also observed increased miR-204-5p levels in urinary exosomes in 20-week-old renal PRCC-TFE3 Tg mice prior to tRCC development, and those levels were equivalent to those in 40-week-old Tg mice, suggesting that miR-204-5p increases follow expression of constitutively active TFE3 fusion proteins in renal tubular epithelial cells prior to overt tRCC development. Finally, we confirmed that miR-204-5p expression significantly increases in noncancerous human kidney cells after overexpression of a PRCC-TFE3 fusion gene. These findings suggest that miR-204-5p in urinary exosomes could be a useful biomarker for early diagnosis of patients with Xp11 tRCC.


Assuntos
Biomarcadores Tumorais/genética , Carcinoma de Células Renais/genética , Cromossomos Humanos X/genética , Neoplasias Renais/genética , MicroRNAs/genética , Translocação Genética , Animais , Fatores de Transcrição de Zíper de Leucina e Hélice-Alça-Hélix Básicos/genética , Fatores de Transcrição de Zíper de Leucina e Hélice-Alça-Hélix Básicos/metabolismo , Biomarcadores Tumorais/urina , Carcinoma de Células Renais/metabolismo , Carcinoma de Células Renais/urina , Proteínas de Ciclo Celular/genética , Proteínas de Ciclo Celular/metabolismo , Exossomos/genética , Humanos , Rim/anormalidades , Rim/metabolismo , Neoplasias Renais/metabolismo , Neoplasias Renais/urina , Camundongos Endogâmicos C57BL , Camundongos Transgênicos , MicroRNAs/urina , Proteínas de Neoplasias/genética , Proteínas de Neoplasias/metabolismo , Proteínas de Fusão Oncogênica/genética , Proteínas de Fusão Oncogênica/metabolismo
8.
J Exp Clin Cancer Res ; 38(1): 119, 2019 Mar 08.
Artigo em Inglês | MEDLINE | ID: mdl-30849994

RESUMO

BACKGROUND: Xp11.2 translocation renal cell carcinoma (tRCC) is mainly caused by translocation of the TFE3 gene located on chromosome Xp11.2 and is characterized by overexpression of the TFE3 fusion gene. Patients are diagnosed with tRCC usually before 45 years of age with poor prognosis. We investigated this disease using two tRCC cell lines, UOK109 and UOK120, in this study. METHODS: The purpose of this study was to investigate the pathogenic mechanism of TFE3 fusions in tRCC based on its subcellular localization, nuclear translocation and transcriptional activity. The expression of TFE3 fusions and other related genes were analyzed by quantitative reverse transcription PCR (qRT-PCR) and Western blot. The subcellular localization of TFE3 was determined using immunofluorescence. The transcriptional activity of TFE3 fusions was measured using a luciferase reporter assay and ChIP analysis. In some experiments, TFE3 fusions were depleted by RNAi or gene knockdown. The TFE3 fusion segments were cloned into a plasmid expression system for expression in cells. RESULTS: Our results demonstrated that TFE3 fusions were overexpressed in tRCC with a strong nuclear retention irrespective of treatment with an mTORC1 inhibitor or not. TFE3 fusions lost its co-localization with lysosomal proteins and decreased its interaction with the chaperone 14-3-3 proteins in UOK109 and UOK120 cells. However, the fusion segments of TFE3 could not translocate to the nucleus and inhibition of Gsk3ß could increase the cytoplasmic retention of TFE3 fusions. Both the luciferase reporter assay and ChIP analysis demonstrated that TFE3 fusions could bind to the promoters of the target genes as a wild-type TFE3 protein. Knockdown of TFE3 results in decreased expression of those genes responsible for lysosomal biogenesis and other target genes. The ChIP-seq data further verified that, in addition to lysosomal genes, TFE3 fusions could regulate genes involved in cellular responses to hypoxic stress and transcription. CONCLUSIONS: Our results indicated that the overexpressed TFE3 fusions were capable of escaping from the control by the mTOR signaling pathway and were accumulated in the nucleus in UOK109 and UOK120 cells. The nuclear retention of TFE3 fusions promoted the expression of lysosomal genes and other target genes, facilitating cancer cell resistance against an extreme environment.


Assuntos
Fatores de Transcrição de Zíper de Leucina e Hélice-Alça-Hélix Básicos/genética , Carcinoma de Células Renais/genética , Proteínas de Fusão Oncogênica/genética , Serina-Treonina Quinases TOR/genética , Adulto , Carcinoma de Células Renais/patologia , Linhagem Celular Tumoral , Núcleo Celular/genética , Cromossomos Humanos X/genética , Regulação Neoplásica da Expressão Gênica/genética , Humanos , Masculino , Transdução de Sinais , Translocação Genética/genética
9.
Leg Med (Tokyo) ; 37: 95-102, 2019 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-30831559

RESUMO

The unknown origin of DNA samples derived from crime scenes generates a considerable amount of uncertainty, as do unexpected short tandem repeat (STR) results caused by sample mix-ups, contamination, medical interventions, and transgender individuals (broad meaning). Genetic abnormalities such as somatic/germline mutations, mosaicism or chimerism, sex reversal cases, aneuploidies, and chromosomal structural rearrangements are also possible causes of such results. The evidence offered by the present study suggested that additional DYS385 alleles, as seen in mixed stain samples and in the potentially single-source DNA profile of a female, originated from the female DNA source only. For the case reported here, we propose an interchromosomal insertion hypothesis, in which a 768-kb segment including the P4 palindrome of the azoospermia factor (AZFb) region was deleted from the Y chromosome and inserted into the X chromosome or an autosome during male meiosis. Y-SNP data points from the AccuID platform and in-house PCR assays narrowed down the expected length of the target region. Bioinformatics analysis followed by whole genome amplification and whole genome sequencing showed that a 529-kb segment including the P4 palindrome (HSFY/DYS385)/DYS460 region from the female sample mapped to the Y reference sequence (GRCh37). To our knowledge, the interchromosomal insertional translocation event was identified as an unknown type of genomic rearrangement in the forensic genetic field.


Assuntos
Azoospermia/genética , Cromossomos Humanos Y/genética , Cromossomos Humanos/genética , Genética Forense/métodos , Técnicas de Genotipagem/métodos , Sequências Repetidas Invertidas/genética , Repetições de Microssatélites/genética , Análise para Determinação do Sexo/métodos , Translocação Genética/genética , Alelos , Cromossomos Humanos X/genética , Feminino , Loci Gênicos/genética , Humanos , Masculino , Meiose/genética , Sequenciamento Completo do Genoma
10.
Andrologia ; 51(5): e13253, 2019 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-30746732

RESUMO

BACKGROUND: Klinefelter syndrome(KS), affecting 1 in 500-1,000 newborn males, is the most common sex chromosome aneuploidy among males with primary hypogonadism. Isochromosome Xq on the other hand is a rare variant of Klinefelter syndrome, accounting approximately 0.3% of all KS and associated with normal height and androgenisation compared to classical KS. Here, we present a case of isochromosome Xq variant of KS with similar clinical and cytogenetic findings with the few cases reported before. MATERIALS AND METHODS: A 25-year-old male patient referred to our clinic with complaint of infertility. He is the son of a consanguineous couple who are first cousins and there was no family history of reproductive difficulty. In physical examination synophrys, prominent ear and small testicles noted. The patient's spermiogram showed azoospermia and scrotal USG revealed testicular atrophy. RESULTS: Karyotype analysis using G-banding resulted as 47,X,i(X)(q10),Y, and STR analysis showed no deletion in AZF and SRY loci of interest. CONCLUSION: Although several isochromosome Xq variant of KS cases can be found in literature, it is our duty to emphasise the importance of karyotyping for patients with reproductive difficulty who may not have all features of classical Klinefelter syndrome.


Assuntos
Cromossomos Humanos X/genética , Isocromossomos/genética , Síndrome de Klinefelter/genética , Adulto , Humanos , Cariotipagem , Síndrome de Klinefelter/diagnóstico , Masculino
11.
Int J Hematol ; 109(6): 744-750, 2019 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-30706328

RESUMO

Aggressive natural killer cell leukemia (ANKL) is a rare neoplasm characterized by the systemic infiltration of Epstein-Barr virus (EBV)-associated NK cells, and rapidly progressive clinical course. We report the case of a 45-year-old man with intellectual disability who developed ANKL, and describe the identification of a novel genetic mutation of coiled-coil domain-containing 22 (CCDC22). He presented with persistent fever, severe pancytopenia, and hepatosplenomegary. Following bone marrow aspiration, numerous hemophagocytes were identified. High EBV viral load was detected in NK cells fractionation by qPCR. The initial diagnosis was EBV-related hemophagocytic lymphohistiocytosis (EBV-HLH). A combination of immunosuppressive drugs and chemotherapy was administered, but was unsuccessful in controlling the disease. Therefore, he was treated with HLA-matched related allogeneic hematopoietic stem cell transplantation. However, his condition deteriorated within 30 days, resulting in fatal outcome. Autopsy revealed many EBV-infected NK cells infiltrating major organs, consistent with ANKL. Furthermore, whole-exome sequencing identified a novel missense mutation of the CCDC22 gene (c.112G>A, p.V38M), responsible for X-linked intellectual disability (XLID). CCDC22 has been shown to play a role in NF-κB activation. Our case suggests that CCDC22 mutation might be implicated in pathogenesis of EBV-HLH and NK-cell neoplasms as well as XLID via possibly affecting NF-κB signaling.


Assuntos
Infecções por Vírus Epstein-Barr/genética , Leucemia Linfocítica Granular Grande/genética , Linfo-Histiocitose Hemofagocítica/genética , Mutação de Sentido Incorreto , Proteínas/genética , Aloenxertos , Cromossomos Humanos X/genética , Transplante de Células-Tronco Hematopoéticas , Humanos , Deficiência Intelectual/genética , Leucemia Linfocítica Granular Grande/terapia , Linfo-Histiocitose Hemofagocítica/terapia , Masculino , Pessoa de Meia-Idade , NF-kappa B/metabolismo , Índice de Gravidade de Doença , Transdução de Sinais/genética
12.
BMC Bioinformatics ; 20(1): 64, 2019 Feb 06.
Artigo em Inglês | MEDLINE | ID: mdl-30727948

RESUMO

BACKGROUND: Tandem repeat sequences are common in the genomes of many organisms and are known to cause important phenomena such as gene silencing and rapid morphological changes. Due to the presence of multiple copies of the same pattern in tandem repeats and their high variability, they contain a wealth of information about the mutations that have led to their formation. The ability to extract this information can enhance our understanding of evolutionary mechanisms. RESULTS: We present a stochastic model for the formation of tandem repeats via tandem duplication and substitution mutations. Based on the analysis of this model, we develop a method for estimating the relative mutation rates of duplications and substitutions, as well as the total number of mutations, in the history of a tandem repeat sequence. We validate our estimation method via Monte Carlo simulation and show that it outperforms the state-of-the-art algorithm for discovering the duplication history. We also apply our method to tandem repeat sequences in the human genome, where it demonstrates the different behaviors of micro- and mini-satellites and can be used to compare mutation rates across chromosomes. It is observed that chromosomes that exhibit the highest mutation activity in tandem repeat regions are the same as those thought to have the highest overall mutation rates. However, unlike previous works that rely on comparing human and chimpanzee genomes to measure mutation rates, the proposed method allows us to find chromosomes with the highest mutation activity based on a single genome, in essence by comparing (approximate) copies of the pattern in tandem repeats. CONCLUSION: The prevalence of tandem repeats in most organisms and the efficiency of the proposed method enable studying various aspects of the formation of tandem repeats and the surrounding sequences in a wide range of settings. AVAILABILITY: The implementation of the estimation method is available at http://ips.lab.virginia.edu/smtr .


Assuntos
Duplicação Gênica , Sequências de Repetição em Tandem/genética , Algoritmos , Cromossomos Humanos X/genética , Simulação por Computador , Genoma Humano , Humanos , Método de Monte Carlo , Mutação/genética , Taxa de Mutação , Processos Estocásticos
13.
Leg Med (Tokyo) ; 37: 64-66, 2019 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-30711876

RESUMO

We presented allele frequencies of 27 X-chromosomal short tandem repeats (DXS6807, DXS9902, DXS6795, DXS6810, DXS10076, DXS10077, DXS10078, DXS10162, DXS10163, DXS10164, DXS7132, DXS981, DXS6800, DXS6803, DXS6809, DXS6789, DXS6799, DXS7424, DXS101, DXS7133, GATA172D05, DXS10103, HPRTB, GATA31E08, DXS8377, DXS10147, and DXS7423) obtained from 352 unrelated individuals in Egypt. No deviation from Hardy-Weinberg equilibrium was detected. Two pairs of adjacent loci showed significant linkage disequilibrium. In the principal component analysis plot, the Egyptian data were located between Europe and sub-Saharan Africa, away from Asia.


Assuntos
Cromossomos Humanos X/genética , Frequência do Gene/genética , Repetições de Microssatélites/genética , Polimorfismo Genético/genética , Egito , Feminino , Loci Gênicos/genética , Humanos , Desequilíbrio de Ligação/genética , Masculino
14.
Genet Epidemiol ; 43(4): 427-439, 2019 06.
Artigo em Inglês | MEDLINE | ID: mdl-30657195

RESUMO

Analysis of the X chromosome has been largely neglected in genetic studies mainly because of complex underlying biological mechanisms. On the other hand, the study of human microbiome data (typically over-dispersed counts with an excess of zeros) has generated great interest recently because of advancements in next-generation sequencing technologies. We propose a novel approach to infer the association between host genetic variants in the X-chromosome and microbiome data. The method accounts for random X-chromosome inactivation (XCI), skewed (or nonrandom) XCI (XCI-S), and escape of XCI (XCI-E). The inference is performed through a finite mixture model (FMM), in which an indicator variable denoting the "true" biological mechanism is treated as missing data. An expectation-maximization algorithm on zero-inflated and two-part models is implemented to estimate genetic effects. We investigate the performance of the FMM along with strategies that assume XCI and XCI-E mechanisms for all subjects compared with alternative approaches. Briefly, an XCI mechanism codes males' genotypes as homozygous females, whereas under XCI-E, males are treated as heterozygous females. By comprehensive simulations, we evaluate tests of the hypothesis under a computationally efficient score statistic. In summary, the FMM renders reduced bias and commensurate power compared to XCI, XCI-E, and alternative strategies while maintaining adequate Type 1 error control. The proposed method has far-reaching applications. In particular, we illustrate its usage on a large-scale human microbiome study, the Genetic, Environmental and Microbial (GEM) project, to test for the genetic association on the X chromosome.


Assuntos
Cromossomos Humanos X , Microbiota/genética , Cromossomos Humanos X/genética , Estudos de Coortes , Doença de Crohn/epidemiologia , Doença de Crohn/genética , Doença de Crohn/microbiologia , Análise de Dados , Família , Feminino , Análise de Elementos Finitos , Interação Gene-Ambiente , Estudos de Associação Genética/estatística & dados numéricos , Genótipo , Heterozigoto , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Masculino , Modelos Genéticos , Inativação do Cromossomo X
15.
J Assist Reprod Genet ; 36(4): 769-775, 2019 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-30675680

RESUMO

PURPOSE: Male carriers of an X-autosome translocation are generally infertile, regardless of the position of the breakpoint on the X chromosome while the pathogenicity of Xp22.3 subtelomeric duplications is under debate. To shed light into this controversy, we present a rare case, of an azoospermic male with no other significant clinical findings, in whom classical cytogenetics revealed additional unbalanced chromosomal material, at the telomere of the long arm of one homolog of chromosome 9. METHODS: In peripheral blood specimens of the index case and his parents, we performed GBanding, Inverted-DAPI Banding, AgNOR staining, Telomere specific Fluorescence in Situ Hybridization (FISH), Molecular karyotyping by Multi-color FISH, whole genome SNP microarrays, sub-telomeric MLPA, and transcription analysis of the expression of KAL1 gene by RT-PCR. RESULTS: Multi-color FISH revealed an unbalanced translocation involving the short arm of chromosome X. SNP microarray analysis combined to classical cytogenetics and MLPA demonstrated a de novo 8.796 Mb duplication of Xp22.31-p22.33. Compared to three control specimens, the patient presented significantly elevated expression levels of KAL1 mRNA in peripheral blood, suggesting transcriptional functionality of the duplicated segment. CONCLUSIONS: The duplicated segment contains the pseudo-autosomal region PAR1 and more than 30 genes including SHOX, ARSE, STS, KAL1, and FAM9A and is not listed as polymorphic. Our data advocate that duplications of the Xp22.3 region may not be associated with a clinical consequence.


Assuntos
Cromossomos Humanos Par 9/genética , Cromossomos Humanos X/genética , Infertilidade Masculina/genética , Translocação Genética/genética , Adulto , Criança , Bandeamento Cromossômico/métodos , Duplicação Cromossômica/genética , Proteínas da Matriz Extracelular/genética , Feminino , Humanos , Hibridização in Situ Fluorescente , Infertilidade Masculina/patologia , Cariotipagem , Masculino , Proteínas do Tecido Nervoso/genética , Polimorfismo de Nucleotídeo Único/genética , Gravidez , Telômero/genética
16.
BMC Bioinformatics ; 20(1): 11, 2019 Jan 07.
Artigo em Inglês | MEDLINE | ID: mdl-30616589

RESUMO

BACKGROUND: Skewed X chromosome inactivation (XCI), which is a non-random process, is frequently observed in both healthy and affected females. Furthermore, skewed XCI has been reported to be related to many X-linked diseases. However, no statistical method is available in the literature to measure the degree of the skewness of XCI for case-control design. Therefore, it is necessary to develop methods for such a task. RESULTS: In this article, we first proposed a statistical measure for the degree of XCI skewing by using a case-control design, which is a ratio of two logistic regression coefficients after a simple reparameterization. Based on the point estimate of the ratio, we further developed three types of confidence intervals (the likelihood ratio, Fieller's and delta methods) to evaluate its variation. Simulation results demonstrated that the likelihood ratio method and the Fieller's method have more accurate coverage probability and more balanced tail errors than the delta method. We also applied these proposed methods to analyze the Graves' disease data for their practical use and found that rs3827440 probably undergoes a skewed XCI pattern with 68.7% of cells in heterozygous females having the risk allele T active, while the other 31.3% of cells keeping the normal allele C active. CONCLUSIONS: For practical application, we suggest using the Fieller's method in large samples due to the non-iterative computation procedure and using the LR method otherwise for its robustness despite its slightly heavy computational burden.


Assuntos
Cromossomos Humanos X/genética , Genes Ligados ao Cromossomo X , Heterozigoto , Modelos Estatísticos , Inativação do Cromossomo X , Alelos , Estudos de Casos e Controles , Feminino , Humanos
17.
J Mol Neurosci ; 67(2): 295-304, 2019 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-30604382

RESUMO

MicroRNAs are endogenous non-protein-coding RNA molecules that regulate post-transcriptional gene expression. The majority of human miRNAs are brain-expressed and chromosome X is enriched in miRNA genes. We analyzed the genomic regions of 12 brain-expressed pre-miRNAs located on chromosome X coding for 18 mature miRNAs, aiming to investigate the involvement of miRNA sequence variants on X-linked intellectual disability (XLID). Genomic DNA samples from 135 unrelated Brazilian males with intellectual disability, suggestive of X-linked inheritance, were amplified through polymerase chain reaction and sequenced by Sanger sequencing. Although no sequence variations have been identified, suggesting an intense selective pressure, further computational analysis evidenced that eight mature miRNAs (miR-221-3p/222-3p, miR-223-3p, miR-361-5p, miR-362-5p, miR-504-5p.1, miR-505-3p.1, and miR-505-3p.2) act as critical regulators of X-linked and autosomal ID genes in a fully connected network. Enrichment approaches identify transcription regulation, nervous system development, and regulation of cell proliferation as the main common biological processes among the target ID genes. Besides, a clustered chromosomal coverage of the imputed miRNAs target genes and related regulators was found on X chromosome. Considering the role of miRNAs as fine-tuning regulators of gene expression, a systematic analysis of miRNAs' expression could uncover part of the genetic landscape subjacent to ID, being urgently necessary in patients with this condition, particularly XLID.


Assuntos
Encéfalo/metabolismo , Redes Reguladoras de Genes , Doenças Genéticas Ligadas ao Cromossomo X/genética , Deficiência Intelectual/genética , MicroRNAs/genética , Adolescente , Adulto , Criança , Pré-Escolar , Cromossomos Humanos X/genética , Humanos , Masculino , MicroRNAs/metabolismo , Polimorfismo Genético
19.
Orphanet J Rare Dis ; 14(1): 16, 2019 01 14.
Artigo em Inglês | MEDLINE | ID: mdl-30642344

RESUMO

BACKGROUND: Knowledge on the prevalence of sex chromosome abnormalities (SCAs) is limited, and delayed diagnosis or non-diagnosis of SCAs are a continuous concern. We aimed to investigate change over time in incidence, prevalence and age at diagnosis among Turner syndrome (TS), Klinefelter syndrome (KS), Triple X syndrome (Triple X) and Double Y syndrome (Double Y). METHODS: This study is a nationwide cohort study in a public health care system. The Danish Cytogenetic Central Registry (DCCR) holds information on all karyotypes performed in Denmark since 1961. We identified all individuals in the DCCR with a relevant SCA during 1961-2014; TS: n = 1156; KS: n = 1235; Triple X: n = 197; and Double Y: n = 287. From Statistics Denmark, which holds an extensive collection of data on the Danish population, complete data concerning dates of death and migrations in and out of Denmark were retrieved for all individuals. RESULTS: The prevalence among newborns was as follows: TS: 59 per 100,000 females; KS: 57 per 100,000 males; Triple X: 11 per 100,000 females; and Double Y: 18 per 100,000 males. Compared with the expected number among newborns, all TS, 38% of KS, 13% of Triple X, and 18% of Double Y did eventually receive a diagnosis. The incidence of TS with other karyotypes than 45,X (P < 0.0001), KS (P = 0.02), and Double Y (P = 0.03) increased during the study period whereas the incidence of 45,X TS decreased (P = 0.0006). The incidence of Triple X was stable (P = 0.22). CONCLUSIONS: The prevalence of TS is higher than previously identified, and the karyotypic composition of the TS population is changing. Non-diagnosis is extensive among KS, Triple X and Double Y, whereas all TS seem to become diagnosed. The diagnostic activity has increased among TS with other karyotypes than 45,X as well as among KS and Double Y.


Assuntos
Síndrome de Turner/genética , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , Criança , Pré-Escolar , Cromossomos Humanos X/genética , Estudos de Coortes , Feminino , Humanos , Incidência , Lactente , Recém-Nascido , Cariotipagem , Síndrome de Klinefelter/genética , Masculino , Pessoa de Meia-Idade , Aberrações dos Cromossomos Sexuais , Transtornos dos Cromossomos Sexuais/genética , Transtornos do Cromossomo Sexual no Desenvolvimento Sexual/genética , Trissomia/genética , Cariótipo XYY/genética , Adulto Jovem
20.
Hum Genomics ; 13(1): 2, 2019 01 08.
Artigo em Inglês | MEDLINE | ID: mdl-30621780

RESUMO

The X chromosome and X-linked variants have largely been ignored in genome-wide and candidate association studies of infectious diseases due to the complexity of statistical analysis of the X chromosome. This exclusion is significant, since the X chromosome contains a high density of immune-related genes and regulatory elements that are extensively involved in both the innate and adaptive immune responses. Many diseases present with a clear sex bias, and apart from the influence of sex hormones and socioeconomic and behavioural factors, the X chromosome, X-linked genes and X chromosome inactivation mechanisms contribute to this difference. Females are functional mosaics for X-linked genes due to X chromosome inactivation and this, combined with other X chromosome inactivation mechanisms such as genes that escape silencing and skewed inactivation, could contribute to an immunological advantage for females in many infections. In this review, we discuss the involvement of the X chromosome and X inactivation in immunity and address its role in sexual dimorphism of infectious diseases using tuberculosis susceptibility as an example, in which male sex bias is clear, yet not fully explored.


Assuntos
Cromossomos Humanos X/genética , Predisposição Genética para Doença , Infecção/genética , Feminino , Humanos , Masculino , Tuberculose/genética , Inativação do Cromossomo X
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