title: Nashville Birth Cohort

status: Public on Mar 11 2016

first: Alicia

last: Smith

address: 101 Woodruff Circle

institute: Emory University

summary:
All subjects were recruited at Centennial Women?s Hospital and the Perinatal Research Center in Nashville, TN beginning in 2003. Pregnant women were enrolled during their first clinical visit after obtaining informed consent as described previously.  Demographic and clinical data specific to the fetus was collected from clinical records. Gestational age of the neonate was determined by maternal reporting of the last menstrual period and corroboration by ultrasound dating.

Accurate knowledge of gestational age (GA) is essential for proper monitoring and care of neonates. However, accurate GA measures are often not available. DNA methylation has previously been shown to associate with GA, and has been used to accurately predict chronological age in adults.  In the current study, we examine whether DNA methylation in cord blood can be used to predict gestational age at birth.

Results: We found that GA can be accurately predicted from DNA methylation of neonatal cord blood and blood spot samples (DNAm GA), using 148 CpG sites selected through elastic net regression in six training datasets (N=207). We evaluated predictive accuracy in six testing datasets (N=1,202), and found that the accuracy of DNAm GA meets or exceeds accuracy of gestational age estimates based on established methods.  We also found an increased DNAm GA, relative to clinical GA, was associated with increased birthweight percentile (p=.00057), adjusting for GA, sex, and ancestry, suggesting that DNAm GA could represent developmental age more accurately than clinical estimates of GA.

Conclusions: Further development of this predictor could provide a method of accurate neonatal estimation of GA for use in resource-limited populations, or in cases where GA cannot be estimated clinically. When clinical estimates are available, the predictor can be used to test hypotheses related to developmental age and other early life circumstances, and may provide increased accuracy beyond clinical estimates.

overall_design: 36 Umbilical cord blood samples were collected in EDTA tubes soon after placental delivery. Blood samples were centrifuged at 3,000 RPM to separate plasma, and buffy coats were aliquoted and stored at -80oC.  DNA was extracted using the DNeasy Kit (Qiagen). DNA methylation was interrogated for each sample using the HumanMethylation450 BeadChip (Illumina).

first: Ramkumar

last: Menon

first: Varun

last: Kilaru


title: microRNA-132/212 deficiency enhances Ab production and senile plaque deposition in Alzheimer’s disease triple transgenic mice

status: Public on Jul 17 2016

city: Quebec

first: Sebastien

last: Hebert

state: QC

address: 2705 Boul Laurier, Centre de recherche du CHU de Quebec

department: Medecine

country: Canada

institute: Lavay University

type: Expression profiling by high throughput sequencing

summary: The abnormal regulation of amyloid-b (Ab) metabolism (e.g., production, cleavage, clearance) plays a central role in Alzheimer’s disease (AD). Among endogenous factors believed to participate in AD progression are the small regulatory non-coding microRNAs (miRs). In particular, the miR-132/212 cluster is severely reduced in the AD brain. In previous studies we have shown that miR-132/212 deficiency in mice leads to impaired memory and enhanced Tau pathology as seen in AD patients. Here we demonstrate that the genetic deletion of miR-132/212 promotes Ab deposition and amyloid (senile) plaque formation in triple transgenic AD (3xTg-AD) mice. Using RNA-Seq and bioinformatics, we identified genes of the miR-132/212 network with documented roles in the regulation of Ab metabolism, including Tau, Mapk, and Sirt1.

overall_design: We used RNA-Seq to analyse the hippocampus of 3xTg-AD mice lacking the miR-132/212 cluster as well as Neuro2a cells overexpressing miR-132 mimics.

first: Julia

last: Hernandez-Rapp

first: Sara

last: Rainone

first: Sébastien

middle: S

last: Hébert


title: Epigenomic Profiling of Primary Gastric Adenocarcinoma Reveals Super-enhancer Heterogeneity

status: Public on Sep 28 2016

city: Singapore

first: Aditi

last: Qamra

address: 60 Biopolis Street, Genome, #02-01

country: Singapore

institute: GIS

type: Methylation profiling by genome tiling array

type: Genome binding/occupancy profiling by high throughput sequencing

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Development and application of a new immunophenotypic algorithm for molecular subtype classification of Diffuse Large B-Cell Lymphoma (DLBCL): Report from an International DLBCL Rituximab-CHOP Consortium Program Study

status: Public on Aug 01 2012

city: Pleasanton

first: Yan

last: Li

state: CA

address: 4300 Hacienda Dr

department: Bioinformatics

country: USA

institute: Roche Molecular Systems

summary:
We studied 498 de-novo adult DLBCL cases, which had been diagnosed between January 2002 and October 2009, as part of the International DLBCL Rituximab-CHOP Consortium Program Study
We perform global gene expression profiling from formalin fixed paraffin embedded 498 DLBCL tissues RNA by SPIA mediated microarray detection and identified the distinct subgroups of the disease within DLBCL, known as germinal-center-B-cell-like (GCB), activated B-cell-like (ABC), and unclassified DLBCL (UC).

overall_design:
RNA of 498 FFPET DLBCL patient samples were extracted, amplified using a novel RNA amplicfication method, Single Primer Isothermal Amplification (SPIA, NuGen Inc.), and hybridized to Affymetrix HG-U133 Plus 2.0 GeneChips.
This dataset is the collaboration between The University of Texas at MD Anderson Cancer Center and Roche Molecular Systems, Inc.


title: Sex-related differences in lactotroph tumor aggressiveness are associated with a specific gene-expression signature and genome instability

status: Public on Dec 26 2018

city: Lyon

first: Anne

last: Wierinckx

state: select a state

address: 8, av Rockefeller

country: France

institute: University Lyon1

summary: we aimed to explore the molecular importance of the estrogen pathway through a detailed analysis of the transcriptomic profile of lactotroph tumors from 20 men and 10 women. We undertook gene expression analysis of the 30 selected lactotroph tumors following their pathological grading using the five-tiered classification.

overall_design: Thirty frozen tumors stored at the Neurobiotec Bank (Lyon, France) were selected from a series of 89 lactotroph pituitary tumors we had previously used to report the existence of ERalpha-associated sex-related differences among men and women

first: Catherine

last: Rey

first: Joël

last: Lachuer

first: Jacqueline

last: Trouillas

first: Gérald

last: Raverot


title: Expression data of pmr1∆ mutants

status: Public on Jun 18 2012

city: Seville

first: Nestor

last: Garcia-Rodriguez

state: Seville

address: Av Americo Vespucio

country: Spain

institute: CABIMER

summary: The yeast PMR1 (ATP2C1) gene codes for the eukaryotic prototype of a high affinity P-type ATPase required for Ca2+/Mn2+ transport into the Golgi. Cells lacking PMR1 exhibit multiple genetic interactions with genes involved in DNA recombination and replication, a fact that is not yet understood. We find that deletion of PMR1 causes a delay in DNA replication initiation, progression and G2/M transition and induces the transcriptional up-regulation of genes involved in cell cycle regulation, including CLB5 and SWE1. Interestingly, pmr1∆ clb5∆ double mutants exhibit a dramatic delay in DNA replication and increased DNA breakage, while endoreplication and the formation of multi-nucleated, giant yeast is observed in pmr1∆ swe1∆ cells. Because these phenotypes can be attributed to impeded Mn2+-pump function, we provide a model in which Mn2+ interferes with Mg2+ in the nucleus, and vice versa, Mg2+ interferes with Mn2+ in the Golgi. Consequently, cell cycle progression is challenged by aberrant catalytic activities of enzymes involved in replication and protein glycosylation.

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: Three repeats of pmr1∆ mutant. Total RNA levels in pmr1∆ mutants were analyzed and compared to the wild type submitted to the GEO database under the accession number GSE29334 (C. Gonzalez-Aguilera and A. Aguilera), which has been superseded by GSE56702.

first: Néstor

first: Ralf

middle: E

last: Wellinger


title: Cyclosporine on fibroblast

status: Public on Nov 09 2010

city: Seidai

first: NAO

last: Hirota

state: Miyagi

address: Aoba-ku, Seiryo-machi 2-1

department: Respratory medicine

country: Japan

institute: Tohoku university

summary: To elucidate the gene profile of anti-fibroproliferative effects of cyclosporine, we added TGF-b and/or CsA to MRC5 (fetal human lung fibroblast) cell line. After 24 hours serum starvation, fibroblasts were treated with 3 ng/ml TGF-β1 and were treated with or without 2μg/ml Cyclosporine and effects were examined at 48 hours after treatment.  Expression of three genes (IGFBP3, ID1 and PPARG) from this signature was quantified in the same RNA samples by real-time PCR.

overall_design: TGF-β and cyclosporine induced gene expression data was measured in MRC5 (fetal human fibroblast cell line) at 48h after treatments. The dose of TGF-β was 3 ng/ml and cyclosporine was 2 μg/ml. The comparison was done between four groups (control, TGF-β, cyclosporine and TGF-β plus cyclosporine).Three independent experiments were performed at each treatments using different samples for each experiment.

first: Nao

first: Masahito

last: Ebina


title: DNA methylation-based classification of human central nervous system tumors

status: Public on Jan 18 2018

city: Heidelberg

first: Martin

last: Sill

address: Im Neuenheimer Feld 280

department: Division of Pediatric Neurooncology

country: Germany

institute: DKFZ


title: Molecular characteristics and improved survival prediction in a cohort of 2023 ependymomas

status: Public on Jan 31 2024

city: Hamburg

first: Michael

last: Bockmayr

address: Martinistr. 52

department: Pediatric Hematology and Oncology

institute: University Medical Center Hamburg-Eppendorf

type:
Methylation profiling by array
Third-party reanalysis

summary: The diagnosis of ependymoma has moved from a purely histopathological review with limited prognostic value to an integrated diagnosis, relying heavily on molecular information. However, as the integrated approach is still novel and some molecular ependymoma subtypes are quite rare, few studies have correlated integrated pathology and clinical outcome, often focusing on small series of single molecular types. We collected data from 2023 ependymomas as classified by DNA methylation profiling, consisting of 1736 previously published and 287 unpublished methylation profiles. Methylation data and clinical information were correlated, and an integrated model was developed to predict progression-free survival. Patients with EPN-PFA, EPN-ZFTA, and EPN-MYCN tumors showed the worst outcome with 10-year overall survival rates of 56%, 62%, and 32%, respectively. EPN-PFA harbored chromosome 1q gains and/or 6q losses as markers for worse survival. In supratentorial EPN-ZFTA, a combined loss of CDKN2A and B indicated worse survival, whereas a single loss did not. Twelve out of 200 EPN-ZFTA (6%) were located in the posterior fossa, and these tumors relapsed or progressed even earlier than supratentorial tumors with a combined loss of CDKN2A/B. Patients with MPE and PF-SE, generally regarded as non-aggressive tumors, only had a 10-year progression-free survival of 59% and 65%, respectively. For the prediction of the 5-year progression-free survival, Kaplan-Meier estimators based on the molecular subtype, a Support Vector Machine based on methylation, and an integrated model based on clinical factors, CNV data, and predicted methylation scores achieved balanced accuracies of 66%, 68%, and 73%, respectively. Excluding samples with low prediction scores resulted in balanced accuracies of over 80%.

overall_design: 2,023 specicmens were analyzed using the Illumina Infinium HumanMethylation450 or the MethylationEPIC BeadChip.

first: Lara

last: Pohl