Cytogenetic characterization of two new cases involving 17p13.3 and 3p26 chromosomal regions in two sisters by Array-CGH
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ABSTRACT: Array-CGH identified a cytogenetic characterization of two new cases involving 17p13.3 and 3p26 chromosomal regions in two sisters with familial history of lissencephaly.
Project description:Human cerebral cortex development is a highly complex and orchestrated process that is under tight genetic regulation. Rare mutations that alter gene expression or function can disrupt the structure of the cerebral cortex, resulting in a variety of neurological cAonditions1. Lissencephaly (“smooth brain”) spectrum disorders comprise a group of rare, genetically heterogeneous congenital brain malformations commonly associated with epilepsy and intellectual disability2. However, the molecular mechanisms underlying disease pathogenesis remain unknown. Here, we establish hypoactivity of the mammalian target of rapamycin (mTOR) pathway as a clinically relevant molecular mechanism in lissencephaly spectrum disorders. We characterized cerebral organoids from individuals with two genetically distinct lissencephalies harboring a recessive mutation in P53-Induced Death Domain Protein 1 (PIDD1) or a heterozygous chromosome 17p13.3 microdeletion leading to Miller-Dieker Lissencephaly Syndrome (MDLS). We found that PIDD1-mutant and MDLS organoids recapitulate the thickened cortex typical of human lissencephaly and demonstrated dysregulation of protein translation, metabolism, and the mTOR pathway. We found that a brain-selective activator of mTOR complex 1 (mTORC1) prevents, and even reverses, cellular and molecular defects in lissencephaly organoids. Our findings unveil an unexpected converging molecular mechanism contributing to genetically heterogeneous lissencephaly spectrum disorders.
Project description:Flenniken - Honey bee gene expression microarray experimental design<br>To minimize variability between samples all arrayed bees were obtained from a single brood comb from a naturally mated queen, therefore all the bees were age-matched half-sisters. The bees selected for microarray analysis of virus (Sindbis-eGFP) co-injected with either virus-specific-dsRNA (vs-dsRNA) or non-specific dsRNA (ns-dsRNA) exhibited the reduced virus phenotype that was seen in the majority of the bees assayed. The five representative bees from each condition (v, v+vs-dsRNA, v+ns-dsRNA, dsRNA, and mock/injected with buffer) selected for microarray analysis were free of pre-existing conditions (assessed by APM analysis) (Runckel, Flenniken et al., 2011). To facilitate gene expression comparisons between multiple treatment groups we utilized a reference-design strategy in which each Cy5-labeled experimental sample was hybridized with a standardized Cy3-labeled reference sample. A complex RNA mixture representing hundreds of bees of various ages exposed to difference treatment groups, served as the reference RNA sample.
Project description:Current therapy has turned HIV infection into a chronic condition. Clinically, some patients suffer prematurely from ailments associated with advanced age; however, the relationship between HIV and aging is unclear. Here we have collected a large cohort of HAART treated HIV+ subjects with both recent and chronic infection and recapitulated the shared phenotype of HIV and age. To further understand this signal, we applied validated models of DNA methylation-based biological age to establish a clear link between HIV infection and molecular age advancement. We then show this result to be robust to HIV duration, cellular composition, and general methylome disorder. Finally we show a pattern of hypomethylation in HIV+ individuals at the HLA locus. Together these results lead to a much-needed better understanding of the epigenetic consequences and gerontological aspects of chronic HIV infection. To determine whether HIV is associated with signs of aberrant biological aging, samples of whole blood were collected from HIV-infected, HAART-treated but otherwise healthy non-Hispanic white males (no hepatitis C co-infection, no diabetes, and strict adherence to therapy) and healthy non-Hispanic white male controls. DNA was extracted from whole blood and genome-wide methylation profiles of each sample were determined using the Illumina Infinium HumanMethylation450 BeadChip array. As a validation, a second cohort of subjects was profiled by flow-sorting cells and measuring methylation in pure-cell populations. Data were normalized and controlled for quality using standard techniques. Please note that the following samples were excluded from the data processing by quality control steps; METI-6 METI-7 352_CD4 381_CD4 however, their raw data was provided so that the full pipeline could be reproduced.
Project description:By successfully tracking individual maternal food intake and milk investment, we show that offspring gain more milk from their own mother, particularly when partner mothers are unrelated and when offspring born second experience strong competition from older pups. Unrelated partner mothers are less efficient, requiring more energy than sisters to rear communal broods of equivalent mass. Further, while unrelated partners provide more equal (but not proportional) investment in the brood, individual fitness gains from investment are much greater and more equal between sisters. Our results show that cryptic kin discrimination in maternal investment provides a strong selective advantage for the choice of close relatives as communal rearing partners, reducing costs and potential exploitation of effort when partners were closely matched.
Project description:By successfully tracking individual maternal food intake and milk investment, we show that offspring gain more milk from their own mother, particularly when partner mothers are unrelated and when offspring born second experience strong competition from older pups. Unrelated partner mothers are less efficient, requiring more energy than sisters to rear communal broods of equivalent mass. Further, while unrelated partners provide more equal (but not proportional) investment in the brood, individual fitness gains from investment are much greater and more equal between sisters. Our results show that cryptic kin discrimination in maternal investment provides a strong selective advantage for the choice of close relatives as communal rearing partners, reducing costs and potential exploitation of effort when partners were closely matched.
Project description:DNA methylation data for 479 women from 130 families including 66 monozygotic twin pairs, 66 dizygotic twin pairs and 215 sisters of twins.
Project description:Genome wide DNA methylation profiling of individuals across a large age range. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450k CpGs from human whole blood. Bisulphite converted DNA from the 656 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip
Project description:Posterior amorphous corneal dystrophy (PACD) is a rare, autosomal dominant disorder affecting the cornea and iris. After next-generation sequencing of the family in which linkage analysis identified a chromosomal locus for PACD on 12q21.33 failed to yield a pathogenic mutation, array-based copy number analysis and qPCR detected a deletion on 12q21.33 containing four genes encoding small leucine-rich proteoglycans (SLRPs): KERA, LUM, DCN, and EPYC. Two other families with PACD also demonstrated deletion of these SLRPs, which together with murine models of KERA, LUM, and DCN deficiency provide convincing evidence that PACD is caused by haploinsufficiency of these SLRPs. Copy number analysis of 750K SNP and 1.9 non-polymorphic probes present on the Affymetrix CytoScan HD array. Samples were separated by affection status. Eight unaffected and 5 affected samples from across 3 families were analyzed. Analysis was performed using the Affymetrix Chromosome Analysis Suite (ChAS) v.2.0 software.
Project description:Heterozygous and homozygous mutations were introduced to the human embryonic stem cell line H9 by using the CRISPR/Cas9-system. Since off-target effects can occur and high numbers of SNVs can be acquired during clonal selection, the generated cell lines and the parental cell line were analyzed by whole-genome sequencing.
Project description:Age-related changes in DNA methylation occurring in blood leukocytes during early childhood may reflect epigenetic maturation. We hypothesized that some of these changes involve gene networks of critical relevance in leukocyte biology and conducted a prospective study to elucidate the dynamics of DNA methylation. Serial blood samples were collected at 3, 6, 12, 24, 36, 48 and 60 months after birth in 10 healthy girls born in Finland and participating in the Type 1 Diabetes Prediction and Prevention Study. DNA methylation was measured using the HumanMethylation450 BeadChip. After filtering for the presence of polymorphisms and cell-lineage-specific signatures, 794 CpGs showed significant DNA methylation differences as a function of age in all children (41.5% age-methylated and 58.4% age-demethylated, bonferroni corrected p-value <0.001). Age-methylated CpGs were more frequently located in gene bodies and within +5 to +50 kilobases (kb) of transcription start sites (TSS), and enriched in developmental, neuronal and plasma membrane genes. Age-demethylated CpGs were associated to promoters and DNAse-I hypersensitivity sites, located within -5 to +5 kb of the nearest TSS, and enriched in genes related to immunity, antigen presentation, the polycomb-group protein complex and cytoplasm. This study reveals that susceptibility loci for complex inflammatory diseases (e.g. IRF5, NOD2, PTGER4) and genes encoding histone modifiers and chromatin remodeling factors (e.g. HDAC4, KDM2A, KDM2B, JARID2, ARID3A, SMARCD3) undergo DNA methylation changes in leukocytes during early childhood. These results open new perspectives to understand leukocyte maturation and provide a catalog of CpGs that may need to be corrected for age effects when performing DNA methylation studies in children. We analysed the longitudinal changes in DNA methylation in a total of 60 samples at 3, 6, 12, 24, 36, 48, and 60 months after birth, using serial DNA samples extracted from peripheral blood leukocytes of 10 healthy girls of the Diabetes Prediction and Prevention Study (DIPP).