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1.
Am J Hum Genet ; 110(1): 71-91, 2023 01 05.
Artigo em Inglês | MEDLINE | ID: mdl-36493769

RESUMO

Cleft lip with or without cleft palate (CL/P) is a common birth defect with a complex, heterogeneous etiology. It is well established that common and rare sequence variants contribute to the formation of CL/P, but the contribution of copy-number variants (CNVs) to cleft formation remains relatively understudied. To fill this knowledge gap, we conducted a large-scale comparative analysis of genome-wide CNV profiles of 869 individuals from the Philippines and 233 individuals of European ancestry with CL/P with three primary goals: first, to evaluate whether differences in CNV number, amount of genomic content, or amount of coding genomic content existed within clefting subtypes; second, to assess whether CNVs in our cohort overlapped with known Mendelian clefting loci; and third, to identify unestablished Mendelian clefting genes. Significant differences in CNVs across cleft types or in individuals with non-syndromic versus syndromic clefts were not observed; however, several CNVs in our cohort overlapped with known syndromic and non-syndromic Mendelian clefting loci. Moreover, employing a filtering strategy relying on population genetics data that rare variants are on the whole more deleterious than common variants, we identify several CNV-associated gene losses likely driving non-syndromic clefting phenotypes. By prioritizing genes deleted at a rare frequency across multiple individuals with clefts yet enriched in our cohort of individuals with clefts compared to control subjects, we identify COBLL1, RIC1, and ARHGEF38 as clefting genes. CRISPR-Cas9 mutagenesis of these genes in Xenopus laevis and Danio rerio yielded craniofacial dysmorphologies, including clefts analogous to those seen in human clefting disorders.


Assuntos
Fenda Labial , Fissura Palatina , Variações do Número de Cópias de DNA , Humanos , Fenda Labial/genética , Fissura Palatina/genética , Estudo de Associação Genômica Ampla , Fatores de Troca do Nucleotídeo Guanina/genética , Fenótipo , Fatores de Transcrição/genética
2.
PLoS Comput Biol ; 20(6): e1012215, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38857308

RESUMO

New sublineages of SARS-CoV-2 variants-of-concern (VOCs) continuously emerge with mutations in the spike glycoprotein. In most cases, the sublineage-defining mutations vary between the VOCs. It is unclear whether these differences reflect lineage-specific likelihoods for mutations at each spike position or the stochastic nature of their appearance. Here we show that SARS-CoV-2 lineages have distinct evolutionary spaces (a probabilistic definition of the sequence states that can be occupied by expanding virus subpopulations). This space can be accurately inferred from the patterns of amino acid variability at the whole-protein level. Robust networks of co-variable sites identify the highest-likelihood mutations in new VOC sublineages and predict remarkably well the emergence of subvariants with resistance mutations to COVID-19 therapeutics. Our studies reveal the contribution of low frequency variant patterns at heterologous sites across the protein to accurate prediction of the changes at each position of interest.


Assuntos
COVID-19 , Farmacorresistência Viral , Evolução Molecular , Mutação , SARS-CoV-2 , Glicoproteína da Espícula de Coronavírus , SARS-CoV-2/genética , Humanos , Glicoproteína da Espícula de Coronavírus/genética , Glicoproteína da Espícula de Coronavírus/química , COVID-19/virologia , COVID-19/genética , Farmacorresistência Viral/genética , Biologia Computacional/métodos , Tratamento Farmacológico da COVID-19 , Antivirais/uso terapêutico
3.
Hum Mol Genet ; 31(14): 2307-2316, 2022 07 21.
Artigo em Inglês | MEDLINE | ID: mdl-35137044

RESUMO

Hypothalamic hamartoma with gelastic seizures is a well-established cause of drug-resistant epilepsy in early life. The development of novel surgical techniques has permitted the genomic interrogation of hypothalamic hamartoma tissue. This has revealed causative mosaic variants within GLI3, OFD1 and other key regulators of the sonic-hedgehog pathway in a minority of cases. Sonic-hedgehog signalling proteins localize to the cellular organelle primary cilia. We therefore explored the hypothesis that cilia gene variants may underlie hitherto unsolved cases of sporadic hypothalamic hamartoma. We performed high-depth exome sequencing and chromosomal microarray on surgically resected hypothalamic hamartoma tissue and paired leukocyte-derived DNA from 27 patients. We searched for both germline and somatic variants under both dominant and bi-allelic genetic models. In hamartoma-derived DNA of seven patients we identified bi-allelic (one germline, one somatic) variants within one of four cilia genes-DYNC2I1, DYNC2H1, IFT140 or SMO. In eight patients, we identified single somatic variants in the previously established hypothalamic hamartoma disease genes GLI3 or OFD1. Overall, we established a plausible molecular cause for 15/27 (56%) patients. Here, we expand the genetic architecture beyond single variants within dominant disease genes that cause sporadic hypothalamic hamartoma to bi-allelic (one germline/one somatic) variants, implicate three novel cilia genes and reconceptualize the disorder as a ciliopathy.


Assuntos
Ciliopatias , Hamartoma , Doenças Hipotalâmicas , Ciliopatias/genética , Hamartoma/genética , Proteínas Hedgehog/metabolismo , Humanos , Doenças Hipotalâmicas/complicações , Doenças Hipotalâmicas/genética , Imageamento por Ressonância Magnética
4.
Int J Mol Sci ; 25(9)2024 Apr 30.
Artigo em Inglês | MEDLINE | ID: mdl-38732148

RESUMO

Mutations in the LMNA gene-encoding A-type lamins can cause Limb-Girdle muscular dystrophy Type 1B (LGMD1B). This disease presents with weakness and wasting of the proximal skeletal muscles and has a variable age of onset and disease severity. This variability has been attributed to genetic background differences among individuals; however, such variants have not been well characterized. To identify such variants, we investigated a multigeneration family in which affected individuals are diagnosed with LGMD1B. The primary genetic cause of LGMD1B in this family is a dominant mutation that activates a cryptic splice site, leading to a five-nucleotide deletion in the mature mRNA. This results in a frame shift and a premature stop in translation. Skeletal muscle biopsies from the family members showed dystrophic features of variable severity, with the muscle fibers of some family members possessing cores, regions of sarcomeric disruption, and a paucity of mitochondria, not commonly associated with LGMD1B. Using whole genome sequencing (WGS), we identified 21 DNA sequence variants that segregate with the family members possessing more profound dystrophic features and muscle cores. These include a relatively common variant in coiled-coil domain containing protein 78 (CCDC78). This variant was given priority because another mutation in CCDC78 causes autosomal dominant centronuclear myopathy-4, which causes cores in addition to centrally positioned nuclei. Therefore, we analyzed muscle biopsies from family members and discovered that those with both the LMNA mutation and the CCDC78 variant contain muscle cores that accumulated both CCDC78 and RyR1. Muscle cores containing mislocalized CCDC78 and RyR1 were absent in the less profoundly affected family members possessing only the LMNA mutation. Taken together, our findings suggest that a relatively common variant in CCDC78 can impart profound muscle pathology in combination with a LMNA mutation and accounts for variability in skeletal muscle disease phenotypes.


Assuntos
Lamina Tipo A , Proteínas Associadas aos Microtúbulos , Proteínas Musculares , Músculo Esquelético , Adulto , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Lamina Tipo A/genética , Proteínas Musculares/genética , Músculo Esquelético/patologia , Músculo Esquelético/metabolismo , Distrofia Muscular do Cíngulo dos Membros/genética , Distrofia Muscular do Cíngulo dos Membros/patologia , Mutação , Linhagem , Proteínas Associadas aos Microtúbulos/genética
5.
Int J Mol Sci ; 25(14)2024 Jul 09.
Artigo em Inglês | MEDLINE | ID: mdl-39062773

RESUMO

Functional copy-number alterations (fCNAs) are DNA copy-number changes with concordant differential gene expression. These are less likely to be bystander genetic lesions and could serve as robust and reproducible tumor biomarkers. To identify candidate fCNAs in neuroendocrine tumors (NETs), we integrated chromosomal microarray (CMA) and RNA-seq differential gene-expression data from 31 pancreatic (pNETs) and 33 small-bowel neuroendocrine tumors (sbNETs). Tumors were resected from 47 early-disease-progression (<24 months) and 17 late-disease-progression (>24 months) patients. Candidate fCNAs that accurately differentiated these groups in this discovery cohort were then replicated using fluorescence in situ hybridization (FISH) on formalin-fixed, paraffin-embedded (FFPE) tissues in a larger validation cohort of 60 pNETs and 82 sbNETs (52 early- and 65 late-disease-progression samples). Logistic regression analysis revealed the predictive ability of these biomarkers, as well as the assay-performance metrics of sensitivity, specificity, and area under the curve. Our results indicate that copy-number changes at chromosomal loci 4p16.3, 7q31.2, 9p21.3, 17q12, 18q21.2, and 19q12 may be used as diagnostic and prognostic NET biomarkers. This involves a rapid, cost-effective approach to determine the primary tumor site for patients with metastatic liver NETs and to guide risk-stratified therapeutic decisions.


Assuntos
Biomarcadores Tumorais , Variações do Número de Cópias de DNA , Tumores Neuroendócrinos , Humanos , Tumores Neuroendócrinos/genética , Tumores Neuroendócrinos/diagnóstico , Tumores Neuroendócrinos/patologia , Biomarcadores Tumorais/genética , Prognóstico , Neoplasias Pancreáticas/genética , Neoplasias Pancreáticas/diagnóstico , Neoplasias Pancreáticas/patologia , Hibridização in Situ Fluorescente , Feminino , Masculino , Pessoa de Meia-Idade , Regulação Neoplásica da Expressão Gênica
6.
Hum Genet ; 142(4): 523-530, 2023 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-36929416

RESUMO

Turner syndrome (TS) is a chromosomal disorder caused by complete or partial loss of the second sex chromosome and exhibits phenotypic heterogeneity, even after accounting for mosaicism and karyotypic variation. Congenital heart defects (CHD) are found in up to 45 percent of girls with TS and span a phenotypic continuum of obstructive left-sided lesions, with bicuspid aortic valve (BAV) being the most common. Several recent studies have demonstrated a genome-wide impact of X chromosome haploinsufficiency, including global hypomethylation and altered RNA expression. The presence of such broad changes to the TS epigenome and transcriptome led others to hypothesize that X chromosome haploinsufficiency sensitizes the TS genome, and several studies have demonstrated that a second genetic hit can modify disease susceptibility in TS. The objective of this study was to determine whether genetic variants in known heart developmental pathways act synergistically in this setting to increase the risk for CHD, specifically BAV, in TS. We analyzed 208 whole exomes from girls and women with TS and performed gene-based variant enrichment analysis and rare-variant association testing to identify variants associated with BAV in TS. Notably, rare variants in CRELD1 were significantly enriched in individuals with TS who had BAV compared to those with structurally normal hearts. CRELD1 is a protein that functions as a regulator of calcineurin/NFAT signaling, and rare variants in CRELD1 have been associated with both syndromic and non-syndromic CHD. This observation supports the hypothesis that genetic modifiers outside the X chromosome that lie in known heart development pathways may influence CHD risk in TS.


Assuntos
Doença da Válvula Aórtica Bicúspide , Cardiopatias Congênitas , Doenças das Valvas Cardíacas , Síndrome de Turner , Feminino , Humanos , Doença da Válvula Aórtica Bicúspide/complicações , Síndrome de Turner/genética , Valva Aórtica/anormalidades , Valva Aórtica/patologia , Doenças das Valvas Cardíacas/genética , Cardiopatias Congênitas/genética , Mosaicismo , Moléculas de Adesão Celular/genética , Proteínas da Matriz Extracelular/genética
7.
Int J Mol Sci ; 24(24)2023 Dec 12.
Artigo em Inglês | MEDLINE | ID: mdl-38139230

RESUMO

Determining neuroendocrine tumor (NET) primary sites is pivotal for patient care as pancreatic NETs (pNETs) and small bowel NETs (sbNETs) have distinct treatment approaches. The diagnostic power and prioritization of fluorescence in situ hybridization (FISH) assay biomarkers for establishing primary sites has not been thoroughly investigated using machine learning (ML) techniques. We trained ML models on FISH assay metrics from 85 sbNET and 59 pNET samples for primary site prediction. Exploring multiple methods for imputing missing data, the impute-by-median dataset coupled with a support vector machine model achieved the highest classification accuracy of 93.1% on a held-out test set, with the top importance variables originating from the ERBB2 FISH probe. Due to the greater interpretability of decision tree (DT) models, we fit DT models to ten dataset splits, achieving optimal performance with k-nearest neighbor (KNN) imputed data and a transformation to single categorical biomarker probe variables, with a mean accuracy of 81.4%, on held-out test sets. ERBB2 and MET variables ranked as top-performing features in 9 of 10 DT models and the full dataset model. These findings offer probabilistic guidance for FISH testing, emphasizing the prioritization of the ERBB2, SMAD4, and CDKN2A FISH probes in diagnosing NET primary sites.


Assuntos
Neoplasias Intestinais , Tumores Neuroendócrinos , Neoplasias Pancreáticas , Humanos , Tumores Neuroendócrinos/diagnóstico , Tumores Neuroendócrinos/genética , Tumores Neuroendócrinos/patologia , Hibridização in Situ Fluorescente , Neoplasias Intestinais/patologia , Neoplasias Pancreáticas/patologia , Aprendizado de Máquina
8.
Hum Mutat ; 43(4): 511-528, 2022 04.
Artigo em Inglês | MEDLINE | ID: mdl-35165973

RESUMO

DMD pathogenic variants for Duchenne and Becker muscular dystrophy are detectable with high sensitivity by standard clinical exome analyses of genomic DNA. However, up to 7% of DMD mutations are deep intronic and analysis of muscle-derived RNA is an important diagnostic step for patients who have negative genomic testing but abnormal dystrophin expression in muscle. In this study, muscle biopsies were evaluated from 19 patients with clinical features of a dystrophinopathy, but negative clinical DMD mutation analysis. Reverse transcription-polymerase chain reaction or high-throughput RNA sequencing methods identified 19 mutations with one of three pathogenic pseudoexon types: deep intronic point mutations, deletions or insertions, and translocations. In association with point mutations creating intronic splice acceptor sites, we observed the first examples of DMD pseudo 3'-terminal exon mutations causing high efficiency transcription termination within introns. This connection between splicing and premature transcription termination is reminiscent of U1 snRNP-mediating telescripting in sustaining RNA polymerase II elongation across large genes, such as DMD. We propose a novel classification of three distinct types of mutations identifiable by muscle RNA analysis, each of which differ in potential treatment approaches. Recognition and appropriate characterization may lead to therapies directed toward full-length dystrophin expression for some patients.


Assuntos
Distrofina , Distrofia Muscular de Duchenne , Distrofina/genética , Humanos , Íntrons/genética , Distrofia Muscular de Duchenne/diagnóstico , Distrofia Muscular de Duchenne/genética , Distrofia Muscular de Duchenne/patologia , Mutação , Sítios de Splice de RNA
9.
Blood ; 135(2): 108-120, 2020 01 09.
Artigo em Inglês | MEDLINE | ID: mdl-31697816

RESUMO

NF-κB and Notch signaling can be simultaneously activated in a variety of B-cell lymphomas. Patients with B-cell lymphoma occasionally develop clonally related myeloid tumors with poor prognosis. Whether concurrent activation of both pathways is sufficient to induce B-cell transformation and whether the signaling initiates B-myeloid conversion in a pathological context are largely unknown. Here, we provide genetic evidence that concurrent activation of NF-κB and Notch signaling in committed B cells is sufficient to induce B-cell lymphomatous transformation and primes common progenitor cells to convert to myeloid lineage through dedifferentiation, not transdifferentiation. Intriguingly, the converted myeloid cells can further transform, albeit at low frequency, into myeloid leukemia. Mechanistically, coactivation of NF-κB and Notch signaling endows committed B cells with the ability to self renew. Downregulation of BACH2, a lymphoma and myeloid gene suppressor, but not upregulation of CEBPα and/or downregulation of B-cell transcription factors, is an early event in both B-cell transformation and myeloid conversion. Interestingly, a DNA hypomethylating drug not only effectively eliminated the converted myeloid leukemia cells, but also restored the expression of green fluorescent protein, which had been lost in converted myeloid leukemia cells. Collectively, our results suggest that targeting NF-κB and Notch signaling will not only improve lymphoma treatment, but also prevent the lymphoma-to-myeloid tumor conversion. Importantly, DNA hypomethylating drugs might efficiently treat these converted myeloid neoplasms.


Assuntos
Linfócitos B/patologia , Transformação Celular Neoplásica/patologia , Linfoma de Zona Marginal Tipo Células B/patologia , Células Mieloides/patologia , NF-kappa B/metabolismo , Receptores Notch/metabolismo , Animais , Linfócitos B/metabolismo , Transformação Celular Neoplásica/metabolismo , Feminino , Humanos , Linfoma de Zona Marginal Tipo Células B/genética , Linfoma de Zona Marginal Tipo Células B/metabolismo , Masculino , Camundongos , Camundongos Endogâmicos C57BL , Células Mieloides/metabolismo , NF-kappa B/genética , Receptores Notch/genética , Transdução de Sinais
10.
Genesis ; 59(1-2): e23394, 2021 02.
Artigo em Inglês | MEDLINE | ID: mdl-32918369

RESUMO

The chromodomain family member chromodomain 1 (CHD1) has been shown to have numerous critical molecular functions including transcriptional regulation, splicing, and DNA repair. Complete loss of function of this gene is not compatible with life. On the other hand, missense and copy number variants of CHD1 can result in intellectual disabilities and craniofacial malformations in human patients including cleft palate and Pilarowski-Bjornsson Syndrome. We have used the aquatic developmental model organism Xenopus laevis, to determine a specific role for Chd1 in such cranioafcial disorders. Protein and gene knockdown techniques in Xenopus, including antisense oligos and mosaic Crispr/Cas9-mediated mutagenesis, recapitulated the craniofacial defects observed in humans. Further analysis indicated that embryos deficient in Chd1 had defects in cranial neural crest development and jaw cartilage morphology. Additionally, flow cytometry and immunohistochemistry revealed that decreased Chd1 resulted in increased in apoptosis in the developing head. Together, these experiments demonstrate that Chd1 is critical for fundamental processes and cell survival in craniofacial development. We also presented evidence that Chd1 is regulated by retinoic acid signaling during craniofacial development. Expression levels of chd1 mRNA, specifically in the head, were increased by RAR agonist exposure and decreased upon antagonist treatment. Subphenotypic levels of an RAR antagonist and Chd1 morpholinos synergized to result in orofacial defects. Further, RAR DNA binding sequences (RAREs) were detected in chd1 regulatory regions by bioinformatic analysis. In summary, by combining human genetics and experiments in an aquatic model we now have a better understanding of the role of CHD1 in craniofacial disorders.


Assuntos
Anormalidades Craniofaciais/genética , DNA Helicases/genética , Proteínas de Xenopus/genética , Animais , Apoptose , Cartilagem/embriologia , Cartilagem/metabolismo , DNA Helicases/metabolismo , Arcada Osseodentária/embriologia , Crista Neural/embriologia , Crista Neural/metabolismo , Proteínas de Xenopus/metabolismo , Xenopus laevis
11.
Am J Med Genet A ; 185(5): 1582-1588, 2021 05.
Artigo em Inglês | MEDLINE | ID: mdl-33650152

RESUMO

Currarino syndrome (CS) is an autosomal dominant syndrome caused by mutations in MNX1 and characterized by anorectal abnormalities, partial sacral agenesis, and presacral masses. The presacral masses are typically benign; however, malignant degeneration can occur, and presacral neuroendocrine tumors (NETs) have been reported in six cases. We report three individuals from two families affected by CS in which multiple individuals developed presacral NETs. The first family, 491, had six members with features of CS, including two siblings who presented with presacral, Grade 2 NETs, one of which had metastasized to bone and lymph nodes. A germline c.874C>T (p.Arg292Trp) mutation was found in a highly conserved region of MNX1 in three affected members who underwent sequencing. A second somatic variant/deletion in MNX1 was not detected in either patient's tumor. In the second family, 342, the proband presented with an incidentally discovered presacral NET. The proband's father had previously undergone resection of a presacral NET, and so genetic testing was performed, which did not reveal an MNX1 mutation or copy number variants. The lack of a second, somatic mutation in the tumors from family 491 argues against MNX1 acting as a tumor suppressor, and the absence of a germline MNX1 mutation in family 342 suggests that other genetic and anatomic factors contribute to the development of presacral NETs. These cases highlight the variable presentation of CS, and the potential for malignancy in these patients.


Assuntos
Anormalidades Múltiplas/genética , Canal Anal/anormalidades , Anormalidades do Sistema Digestório/genética , Proteínas de Homeodomínio/genética , Meningocele/genética , Tumores Neuroendócrinos/genética , Reto/anormalidades , Região Sacrococcígea/anormalidades , Sacro/anormalidades , Siringomielia/genética , Fatores de Transcrição/genética , Anormalidades Múltiplas/patologia , Adulto , Idoso , Canal Anal/patologia , Malformações Anorretais/complicações , Malformações Anorretais/genética , Malformações Anorretais/patologia , Anormalidades do Sistema Digestório/complicações , Anormalidades do Sistema Digestório/patologia , Feminino , Testes Genéticos , Mutação em Linhagem Germinativa/genética , Humanos , Masculino , Meningocele/complicações , Meningocele/patologia , Pessoa de Meia-Idade , Tumores Neuroendócrinos/complicações , Tumores Neuroendócrinos/patologia , Reto/patologia , Região Sacrococcígea/patologia , Sacro/patologia , Siringomielia/complicações , Siringomielia/patologia
12.
Transpl Int ; 34(12): 2696-2705, 2021 12.
Artigo em Inglês | MEDLINE | ID: mdl-34632641

RESUMO

Living kidney donors (LKDs) with a family history of renal disease are at risk of kidney disease as compared to LKDs without such history suggesting that some LKDs may be pre-symptomatic for monogenic kidney disease. LKDs with related transplant candidates whose kidney disease was considered genetic in origin were selected for genetic testing. In each case, the transplant candidate was first tested to verify the genetic diagnosis. A genetic diagnosis was confirmed in 12 of 24 transplant candidates (ADPKD-PKD1: 6, ALPORT-COL4A3: 2, ALPORT-COL4A5: 1: nephronophthisis-SDCCAG8: 1; CAKUT-HNF1B and ADTKD-MUC1: 1 each) and 2 had variants of unknown significance (VUS) in phenotype-relevant genes. Focused genetic testing was then done in 20 of 34 LKDs. 12 LKDs screened negative for the familial variant and were permitted to donate; seven screened positive and were counseled against donation. One, the heterozygous carrier of a recessive disorder was also cleared. Six of seven LKDs with a family history of ADPKD were under 30 years and in 5, by excluding ADPKD, allowed donation to safely proceed. The inclusion of genetic testing clarified the diagnosis in recipient candidates, improving safety or informed decision-making in LKDs.


Assuntos
Transplante de Rim , Rim Policístico Autossômico Dominante , Testes Genéticos , Humanos , Doadores Vivos , Fenótipo , Rim Policístico Autossômico Dominante/diagnóstico , Rim Policístico Autossômico Dominante/genética
13.
Hum Mutat ; 41(9): 1615-1628, 2020 09.
Artigo em Inglês | MEDLINE | ID: mdl-32579715

RESUMO

Serine biosynthesis disorders comprise a spectrum of very rare autosomal recessive inborn errors of metabolism with wide phenotypic variability. Neu-Laxova syndrome represents the most severe expression and is characterized by multiple congenital anomalies and pre- or perinatal lethality. Here, we present the mutation spectrum and a detailed phenotypic analysis in 15 unrelated families with severe types of serine biosynthesis disorders. We identified likely disease-causing variants in the PHGDH and PSAT1 genes, several of which have not been reported previously. Phenotype analysis and a comprehensive review of the literature corroborates the evidence that serine biosynthesis disorders represent a continuum with varying degrees of phenotypic expression and suggest that even gradual differences at the severe end of the spectrum may be correlated with particular genotypes. We postulate that the individual residual enzyme activity of mutant proteins is the major determinant of the phenotypic variability, but further functional studies are needed to explore effects at the enzyme protein level.


Assuntos
Anormalidades Múltiplas/genética , Encefalopatias/genética , Retardo do Crescimento Fetal/genética , Estudos de Associação Genética , Ictiose/genética , Deformidades Congênitas dos Membros/genética , Microcefalia/genética , Fosfoglicerato Desidrogenase/genética , Transaminases/genética , Feminino , Feto , Humanos , Recém-Nascido , Masculino , Mutação , Serina/biossíntese
14.
Am J Hum Genet ; 99(2): 423-9, 2016 08 04.
Artigo em Inglês | MEDLINE | ID: mdl-27453577

RESUMO

Hypothalamic hamartoma (HH) with gelastic epilepsy is a well-recognized drug-resistant epilepsy syndrome of early life.(1) Surgical resection allows limited access to the small deep-seated lesions that cause the disease. Here, we report the results of a search for somatic mutations in paired hamartoma- and leukocyte-derived DNA samples from 38 individuals which we conducted by using whole-exome sequencing (WES), chromosomal microarray (CMA), and targeted resequencing (TRS) of candidate genes. Somatic mutations were identified in genes involving regulation of the sonic hedgehog (Shh) pathway in 14/38 individuals (37%). Three individuals had somatic mutations in PRKACA, which encodes a cAMP-dependent protein kinase that acts as a repressor protein in the Shh pathway, and four subjects had somatic mutations in GLI3, an Shh pathway gene associated with HH. In seven other individuals, we identified two recurrent and three single brain-tissue-specific, large copy-number or loss-of-heterozygosity (LOH) variants involving multiple Shh genes, as well as other genes without an obvious biological link to the Shh pathway. The Shh pathway genes in these large somatic lesions include the ligand itself (SHH and IHH), the receptor SMO, and several other Shh downstream pathway members, including CREBBP and GLI2. Taken together, our data implicate perturbation of the Shh pathway in at least 37% of individuals with the HH epilepsy syndrome, consistent with the concept of a developmental pathway brain disease.


Assuntos
Epilepsias Parciais/genética , Hamartoma/genética , Proteínas Hedgehog/metabolismo , Doenças Hipotalâmicas/genética , Mutação/genética , Transdução de Sinais/genética , Proteína de Ligação a CREB/genética , Subunidades Catalíticas da Proteína Quinase Dependente de AMP Cíclico/genética , Exoma/genética , Feminino , Humanos , Fatores de Transcrição Kruppel-Like/genética , Perda de Heterozigosidade , Masculino , Proteínas do Tecido Nervoso/genética , Proteínas Nucleares/genética , Proteína Gli2 com Dedos de Zinco , Proteína Gli3 com Dedos de Zinco
15.
Genet Res (Camb) ; 101: e8, 2019 06 13.
Artigo em Inglês | MEDLINE | ID: mdl-31190668

RESUMO

Compound heterozygotes occur when different variants at the same locus on both maternal and paternal chromosomes produce a recessive trait. Here we present the tool VarCount for the quantification of variants at the individual level. We used VarCount to characterize compound heterozygous coding variants in patients with epileptic encephalopathy and in the 1000 Genomes Project participants. The Epi4k data contains variants identified by whole exome sequencing in patients with either Lennox-Gastaut Syndrome (LGS) or infantile spasms (IS), as well as their parents. We queried the Epi4k dataset (264 trios) and the phased 1000 Genomes Project data (2504 participants) for recessive variants. To assess enrichment, transcript counts were compared between the Epi4k and 1000 Genomes Project participants using minor allele frequency (MAF) cutoffs of 0.5 and 1.0%, and including all ancestries or only probands of European ancestry. In the Epi4k participants, we found enrichment for rare, compound heterozygous variants in six genes, including three involved in neuronal growth and development - PRTG (p = 0.00086, 1% MAF, combined ancestries), TNC (p = 0.022, 1% MAF, combined ancestries) and MACF1 (p = 0.0245, 0.5% MAF, EU ancestry). Due to the total number of transcripts considered in these analyses, the enrichment detected was not significant after correction for multiple testing and higher powered or prospective studies are necessary to validate the candidacy of these genes. However, PRTG, TNC and MACF1 are potential novel recessive epilepsy genes and our results highlight that compound heterozygous variants should be considered in sporadic epilepsy.


Assuntos
Epilepsia/genética , Epilepsia/metabolismo , Análise de Sequência de DNA/métodos , Adulto , Alelos , Exoma , Feminino , Frequência do Gene/genética , Genes Recessivos/genética , Predisposição Genética para Doença/genética , Variação Genética/genética , Heterozigoto , Humanos , Lactente , Recém-Nascido , Síndrome de Lennox-Gastaut/genética , Síndrome de Lennox-Gastaut/metabolismo , Masculino , Proteínas de Membrana/genética , Proteínas dos Microfilamentos/genética , Mutação , Fenótipo , Estudos Prospectivos , Espasmos Infantis/genética , Espasmos Infantis/metabolismo , Tenascina/genética
16.
J Cutan Pathol ; 46(3): 238-241, 2019 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-30582191

RESUMO

Primary cutaneous Ewing sarcoma is a rare clinical presentation of Ewing sarcoma, usually occurring as a small, localized tumor on the extremities of young adults and associated with favorable prognosis. We report a case of primary cutaneous Ewing sarcoma, which presented on the sole of the foot of a 27-year-old patient with relapsed acute myeloid leukemia and neutropenia. Diagnosis was determined through histological features and staining, as well as fluorescence in situ hybridization and molecular testing. The patient underwent wide-local excision with plan to begin targeted chemotherapy, but unfortunately died from adenovirus pneumonia while neutropenic before targeted chemotherapy was initiated.


Assuntos
Hospedeiro Imunocomprometido , Leucemia Mieloide Aguda/complicações , Neutropenia/complicações , Sarcoma de Ewing/imunologia , Neoplasias Cutâneas/imunologia , Adulto , Feminino , Humanos
17.
PLoS Genet ; 11(3): e1005022, 2015 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-25763846

RESUMO

Epilepsy is a common disabling disease with complex, multifactorial genetic and environmental etiology. The small fraction of epilepsies subject to Mendelian inheritance offers key insight into epilepsy disease mechanisms; and pathologies brought on by mutations in a single gene can point the way to generalizable therapeutic strategies. Mutations in the PRICKLE genes can cause seizures in humans, zebrafish, mice, and flies, suggesting the seizure-suppression pathway is evolutionarily conserved. This pathway has never been targeted for novel anti-seizure treatments. Here, the mammalian PRICKLE-interactome was defined, identifying prickle-interacting proteins that localize to synapses and a novel interacting partner, USP9X, a substrate-specific de-ubiquitinase. PRICKLE and USP9X interact through their carboxy-termini; and USP9X de-ubiquitinates PRICKLE, protecting it from proteasomal degradation. In forebrain neurons of mice, USP9X deficiency reduced levels of Prickle2 protein. Genetic analysis suggests the same pathway regulates Prickle-mediated seizures. The seizure phenotype was suppressed in prickle mutant flies by the small-molecule USP9X inhibitor, Degrasyn/WP1130, or by reducing the dose of fat facets a USP9X orthologue. USP9X mutations were identified by resequencing a cohort of patients with epileptic encephalopathy, one patient harbored a de novo missense mutation and another a novel coding mutation. Both USP9X variants were outside the PRICKLE-interacting domain. These findings demonstrate that USP9X inhibition can suppress prickle-mediated seizure activity, and that USP9X variants may predispose to seizures. These studies point to a new target for anti-seizure therapy and illustrate the translational power of studying diseases in species across the evolutionary spectrum.


Assuntos
Convulsões/metabolismo , Ubiquitina Tiolesterase/metabolismo , Animais , Drosophila melanogaster , Humanos , Espectrometria de Massas , Camundongos , Convulsões/tratamento farmacológico , Ubiquitina Tiolesterase/genética
18.
Hum Mol Genet ; 24(22): 6473-84, 2015 Nov 15.
Artigo em Inglês | MEDLINE | ID: mdl-26374845

RESUMO

Ataxia telangiectasia (AT) is a progressive multisystem disorder caused by mutations in the AT-mutated (ATM) gene. AT is a neurodegenerative disease primarily characterized by cerebellar degeneration in children leading to motor impairment. The disease progresses with other clinical manifestations including oculocutaneous telangiectasia, immune disorders, increased susceptibly to cancer and respiratory infections. Although genetic investigations and physiological models have established the linkage of ATM with AT onset, the mechanisms linking ATM to neurodegeneration remain undetermined, hindering therapeutic development. Several murine models of AT have been successfully generated showing some of the clinical manifestations of the disease, however they do not fully recapitulate the hallmark neurological phenotype, thus highlighting the need for a more suitable animal model. We engineered a novel porcine model of AT to better phenocopy the disease and bridge the gap between human and current animal models. The initial characterization of AT pigs revealed early cerebellar lesions including loss of Purkinje cells (PCs) and altered cytoarchitecture suggesting a developmental etiology for AT and could advocate for early therapies for AT patients. In addition, similar to patients, AT pigs show growth retardation and develop motor deficit phenotypes. By using the porcine system to model human AT, we established the first animal model showing PC loss and motor features of the human disease. The novel AT pig provides new opportunities to unmask functions and roles of ATM in AT disease and in physiological conditions.


Assuntos
Ataxia Telangiectasia/patologia , Modelos Animais de Doenças , Animais , Animais Geneticamente Modificados , Ataxia Telangiectasia/genética , Ataxia Telangiectasia/metabolismo , Proteínas Mutadas de Ataxia Telangiectasia/genética , Proteínas Mutadas de Ataxia Telangiectasia/metabolismo , Feminino , Estudos de Associação Genética , Humanos , Masculino , Mutação , Técnicas de Transferência Nuclear , Células de Purkinje/patologia , Suínos
19.
J Pediatr Hematol Oncol ; 39(7): e370-e372, 2017 10.
Artigo em Inglês | MEDLINE | ID: mdl-28816792

RESUMO

Ewing sarcoma is a pediatric bone and soft tissue sarcoma that requires intensive therapy, which can cause secondary malignancies. We present a rare case of early, treatment-related AML in a pediatric patient concurrently receiving primary therapy for Ewing sarcoma. Despite AML-directed therapy, our patient died secondary to complications of hyperleukocytosis. Cytogenetic and mutation profiling of the leukemia cells revealed the DNA-topoisomerase-II-inhibitor-associated t(9;11)(p22;q23) translocation and clonal KRAS and BRAF mutations. This report highlights the importance of monitoring for treatment-related effects in cancer therapy, as well as the need for novel, less toxic approaches in Ewing sarcoma therapy.


Assuntos
Leucemia Mieloide Aguda/induzido quimicamente , Segunda Neoplasia Primária , Sarcoma de Ewing/tratamento farmacológico , Adolescente , Evolução Fatal , Feminino , Humanos , Leucemia Mieloide Aguda/genética , Leucocitose , Mutação , Sarcoma de Ewing/patologia , Prevenção Secundária , Translocação Genética
20.
Transfusion ; 55(6): 1178-85, 2015 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-25644965

RESUMO

BACKGROUND: The transfusion of red blood cells (RBCs) with maximum therapeutic efficacy is a major goal in transfusion medicine. One of the criteria used in determining stored RBC quality is end-of-storage hemolysis. Between donors, a wide range of hemolysis is observed under identical storage conditions. Here, a potential mechanism for this wide range is investigated. We hypothesize that the magnitude of hemolysis is a heritable trait. Also, we investigated correlations between hemolysis and RBC metabolites; this will establish pathways influencing hemolysis as future targets for genetic analysis. STUDY DESIGN AND METHODS: Units of RBCs from identical and nonidentical twins were collected and stored under standard conditions for 56 days. Hemolysis, adenosine triphosphate (ATP), and total glutathione (tGSH) were measured throughout storage. Nontargeted metabolic analyses were performed on RBCs that had been stored for 28 days. Heritability was determined by comparing values between identical and nonidentical twins. RESULTS: Hemolysis was found to be heritable (mean > 45%) throughout the storage period. Potential correlations were observed between hemolysis and metabolites from the purine metabolism, lysolipid, and glycolysis pathways. These also exhibited heritability (>20%). No correlation was found with ATP or tGSH. CONCLUSION: The susceptibility of RBCs to lysis during storage is partly determined by inheritance. We have also uncovered several pathways that are candidate targets for future genomewide association studies. These findings will aid in the design of better storage solutions and the development of donor screening tools that minimize hemolysis during storage.


Assuntos
Doadores de Sangue , Preservação de Sangue , Eritrócitos/fisiologia , Hemólise/genética , Adulto , Estatura/genética , Índice de Massa Corporal , Peso Corporal/genética , Índices de Eritrócitos , Eritrócitos/química , Feminino , Hemoglobinas/análise , Humanos , Procedimentos de Redução de Leucócitos , Masculino , Metaboloma/genética , Polimorfismo de Nucleotídeo Único , Fatores de Tempo , Gêmeos Dizigóticos , Gêmeos Monozigóticos , Adulto Jovem
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