title: Characterisation of microRNA expression in post-natal mouse mammary gland development

first: Leonard

last: Goldstein

summary:
Background: The differential expression pattern of microRNAs (miRNAs) during mammary gland development might provide insights into their role in regulating the homeostasis of the breast epithelium. Our aim was to analyse these regulatory functions by deriving a comprehensive tissue-specific combined miRNA and mRNA expression profile of post-natal mouse mammary gland development. We measured the expression of 318 individual murine miRNAs by bead-based flow-cytometric profiling of whole mouse mammary glands throughout a 16-point developmental time course, including juvenile, puberty, mature virgin, gestation, lactation, and involution stages. In parallel whole-genome mRNA expression data were obtained.
Results: One third (n = 102) of all murine miRNAs analysed were present during mammary gland development. MicroRNAs were represented in seven temporally co-expressed clusters, which were enriched for both miRNAs belonging to the same family and breast cancer-associated miRNAs. Global miRNA and mRNA expression was significantly reduced during lactation and the early stages of involution after weaning. For most detected miRNA families we did not observe systematic changes in the expression of predicted targets. For miRNA families whose targets did show significant changes, we observed inverse patterns of miRNA and target expression. The datasets are made publicly available and the combined expression profiles represent an important community resource for mammary gland biology research.
Conclusions: MicroRNAs were expressed in co-regulated clusters during mammary gland development. Breast cancer-associated miRNAs were significantly enriched in these clusters. The mechanism and functional consequences of this miRNA co-regulation and its correlation with mRNA expression provide new avenues for research into mammary gland biology and generates candidates for functional validation.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Characterisation of microRNA expression in post-natal mouse mammary gland development [gene]

status: Public on Sep 30 2009

city: Darlinghurst

address: 384 Victoria St

country: Australia

institute: Garvan Institute of Medical Research

summary:
Background: The differential expression pattern of microRNAs (miRNAs) during mammary gland development might provide insights into their role in regulating the homeostasis of the breast epithelium. Our aim was to analyse these regulatory functions by deriving a comprehensive tissue-specific combined miRNA and mRNA expression profile of post-natal mouse mammary gland development. We measured the expression of 318 individual murine miRNAs by bead-based flow-cytometric profiling of whole mouse mammary glands throughout a 16-point developmental time course, including juvenile, puberty, mature virgin, gestation, lactation, and involution stages. In parallel whole-genome mRNA expression data were obtained.
Results: One third (n = 102) of all murine miRNAs analysed were present during mammary gland development. MicroRNAs were represented in seven temporally co-expressed clusters, which were enriched for both miRNAs belonging to the same family and breast cancer-associated miRNAs. Global miRNA and mRNA expression was significantly reduced during lactation and the early stages of involution after weaning. For most detected miRNA families we did not observe systematic changes in the expression of predicted targets. For miRNA families whose targets did show significant changes, we observed inverse patterns of miRNA and target expression. The datasets are made publicly available and the combined expression profiles represent an important community resource for mammary gland biology research.
Conclusions: MicroRNAs were expressed in co-regulated clusters during mammary gland development. Breast cancer-associated miRNAs were significantly enriched in these clusters. The mechanism and functional consequences of this miRNA co-regulation and its correlation with mRNA expression provide new avenues for research into mammary gland biology and generates candidates for functional validation.

overall_design: Developmental time course over 17 time points with 2-3 independent biological replicates per time point and four pairs of technical replicates, 48 samples in total

first: Stefanie

last: Sassen

middle: D

first: John

last: Stingl

first: Cherie

last: Blenkiron

last: Le Quesne

first: Inma

last: Spiteri

first: Konstantina

last: Karagavriilidou

first: Christine

middle: J

last: Watson

first: Simon

last: Tavaré

first: Eric

middle: A

last: Miska

first: Carlos

last: Caldas


title: MicroRNA expression profiling of human breast cancer identifies new markers of tumour subtype

status: Public on Oct 09 2007

summary:
MicroRNAs (miRNAs), a class of short non-coding RNAs, often act post-transcriptionally to inhibit gene expression. We used a bead-based flow cytometric profiling method to obtain miRNA expression data for 93 primary human breast tumours, 21 cell lines and five normal breast samples. Of 309 human miRNAs assayed we identify 133 miRNAs expressed in human breast and breast tumours. We used mRNA expression profiling to classify the breast tumours into Luminal A, Luminal B, Basal-like, HER2+/ER- and Normal-like. A number of miRNAs are differentially expressed between these molecular tumour subtypes and individual miRNAs are associated with clinicopathological factors. Furthermore, we find that miRNAs could classify basal versus luminal tumour subtypes in an independent data set.
Keywords = miRNA
Keywords = microRNA
Keywords = normal
Keywords = tumour
Keywords = cell line
Keywords = breast
Keywords = cancer
Keywords: Bead-based flow cytometric profiling

first: Natalie

middle: P

last: Thorne

first: M

middle: I

first: Suet-Feung

last: Chin

first: Mark

last: Dunning

first: Nuno

middle: L

last: Barbosa-Morais

first: Andrew

middle: E

last: Teschendorff

middle: R

last: Green

first: Ian

middle: O

last: Ellis


title: The microRNA miR-124 controls gene expression in the sensory nervous system of Caenorhabditis elegans

status: Public on Mar 22 2010

first: Leonard

last: Goldstein

summary: We generated animals carrying a genomically integrated mir-124 promoter::gfp transgene and identified mir-124 promoter::GFP labelled cells as a subset of the C. elegans sensory neurons. We used fluorescence activated cell sorting (FACS) to isolate four distinct cell populations: mir-124 expressing (GFP+) and non-expressing (GFP-) cells from both wild-type and mutant animals. RNA samples obtained from the four cell populations were used for Affymetrix gene expression analysis to study the effect of mir-124 deletion on the transcriptome of mir-124 expressing (GFP+) and non-expressing (GFP-) cells.

overall_design: Affymetrix gene expression data from isolated populations of mir-124 expressing (GFP+) and non-expressing (GFP-) cells obtained from wild-type and mir-124 mutant C. elegans (in biological triplicates)

first: Alejandra

middle: M

last: Clark

first: Maya

last: Tevlin

first: Shai

last: Shaham


title: Identification of differentially expressed genes in runx1-/- primitive erythroid

status: Public on Feb 02 2008

city: Stanford

first: Kazuteru

last: Hasegawa

address: Lorry Lokey Stem Cell Research Building (SIM1), G2165 265 Campus Drive

country: USA

institute: Stanford University

summary:
Targeted disruption of the Runx1/ AML1 gene in mice has demonstrated that it is required for the emergence of definitive hematopoietic cells, but that it is not essential for the formation of primitive erythrocytes. These findings led to the conclusion that Runx1 is a stage-specific transcription factor acting only during definitive hematopoiesis. However, the zebrafish and Xenopus homologues of Runx1 have been shown to play roles in primitive hematopoiesis, suggesting that mouse Runx1 might also be involved in the development of primitive lineages. In order to identify differentially expressed genes in runx1-/- primitive erythroid, we carried out microarray analysis.
Keywords: genetic modification

overall_design: Total RNA from E10.5 wild type and Runx1–/– yolk sacs was extracted, and gene expression patterns were compared.

first: Tomomasa

last: Yokomizo

first: Masatsugu

last: Ema

first: Satoru

last: Takahashi


title: Evaluation of the effects of Lactobacillus sp. (ostrich) on body weight, the intestinal microbiome and metabolism in mice

status: Public on Sep 21 2010

city: marseille

first: adil

last: ef

address: 27 bd jean Moulin

country: France

institute: URMITE

summary:
Background. Food can affect the microbial balance in the human intestine, and the ingestion of probiotics may play a role in the current obesity pandemic. The objective of our study was to determine if increased Lactobacillus spp. in the intestinal microflora of mice can promote growth and if changes in the intestinal microflora are associated with modifications in metabolism.
Methodology. Female BALBc mice were divided between one control and two experimental groups and inoculated either once or twice with 4×1010 Lactobacillus per animal in PBS or with PBS alone. Fecal samples were collected and tested using qPCR to detect and quantify Lactobacillus spp., Bacteroidetes and Firmicutes. Gene expression by microarray and RT-PCR was studied in liver and adipose tissue. Finally, metabolic parameters in the plasma were tested.
Principal Findings. In three independent experiments, we observed an increase in both weight gain and liver weight in mice inoculated with 4×1010 Lactobacillus. Inoculation with Lactobacillus sp. (ostrich) increased the Lactobacillus spp. and Firmicutes DNA copy number in feces. The transcriptional profile of liver tissue from mice inoculated with Lactobacillus sp. (ostrich) was enriched for Gene Ontology terms related to the immune response and metabolic modifications. The mRNA levels of fatty acyl synthase (Fas), sterol regulatory element binding factor 1 (Srebp1c), tumor necrosis factor alpha (Tnf), cytochrome P450 2E1 (Cyp2e1) and 3-phosphoinositide-dependent protein kinase-1 (Pdpk1) were significantly elevated in liver tissue in experimental group animals. In gonadal adipose tissue, the expression of leptin, peroxisome proliferator-activated receptor gamma (Pparg and Srebp1c was significantly higher in experimental group animals, whereas the expression of adiponectin was significantly lower.
Conclusions. Alterations in the intestinal microbiota resulted in increased weight gain. Furthermore, increased Lactobacillus spp. in the intestinal microflora of mice inoculated with Lactobacillus sp. (ostrich) resulted in accelerated weight gain, liver enlargement and metabolic changes in the plasma, liver and adipose tissue.

overall_design:
For microarray analysis, we used the livers from two LB1 and two control mice that had been euthanized 20 days after inoculation. We used a whole mouse genome oligomicroarray 4x44K kit (44,000 60-mer oligonucleotides) and performed a one-color microarray-based gene expression analysis, as previously described. Labeled RNAs (Low RNA Input Fluorescent Amplification Kit, Perkin Elmer) were deposited on slides and hybridized using an in situ Hybridization Plus Kit (Agilent Technologies) for 17 h. The arrays were scanned using a DNA Microarray Scanner G2505B (Agilent Technologies), and the image analysis and correction of intra-array signals were performed using Feature Extraction Software A.9.1.3 (Agilent Technologies). Microarray data analysis was performed using GeneSpring 10.01 with the default setting for inter-array normalization and inter-replicate corrections. To identify genes that were differentially expressed, we used a Student’s t-test with p<0.05, and an absolute fold change (FC) greater than 2.0 considered significant. An analysis of Gene Ontology (GO) terms was performed to identify any altered biological processes. Additional data analysis was performed using R software, version 2.8.1.
RNA extraction and cDNA synthesis were performed as described above. Primers and probes to target the mouse genes for cytochrome P450 2E1 (Cyp2e1), 3-phosphoinositide-dependent protein kinase-1 (Pdpk1) and glyceraldehyde 3-phosphate dehydrogenase (Gapdh, used as a housekeeping gene) were purchased from Applied Biosystems. qPCR reactions were performed as described above. The relative amount of each examined mRNA was normalized to the Gapdh mRNA expression level and is expressed relative to the mean amount of the same mRNA in the control group.

first: Emmanouil

last: Angelakis

first: Delphine

last: Bastelica

first: Amira

last: Ben Amara

first: Anne

last: Dutour

first: Jean-Louis

last: Mege

first: Marie-Christine

last: Alessi

first: Didier

last: Raoult


title: Browning of human adipocytes requires KLF11 and reprogramming of PPARγ super-enhancers

status: Public on Dec 12 2014

city: Odense M

last: Loft

address: Campusvej 55

department: Biochemistry & Molecular Biology

country: Denmark

institute: University of Southern Denmark

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Here we have characterized the transcriptional processes underlying the formation of human brown in white (i.e. brite) adipocytes using a genome-wide approach. We show that the browning process is associated with reprogramming of peroxisome proliferator-activated receptor γ (PPARγ) binding to form brite adipocyte-selective PPARγ super-enhancers that appear to play a key role in activation of brite adipocyte-selective genes. We identify the KLF11 gene based on its association with a PPARγ super-enhancer and show that KLF11 is a novel browning factor directly induced by rosiglitazone and required for the activation of brite adipocyte-selective gene program by rosiglitazone.

overall_design: Genome-wide profiling of Dnase I hypersenstive (DHS) sites, epigenomic marks, transcription factor and co-factor binding, and gene expression in hMADS white and brite adipocytes

first: Susanne

last: Mandrup


title: Vector Control vs SNAIL vs SNAIL/FBXO11

status: Public on Dec 01 2014

city: Plainsboro

first: Yong

last: Wei

state: NJ

address: LTL227 Wathington Road

department: Molecular Biology

institute: Princeton University

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Allele-specific NKX2-5 binding underlies multiple genetic associations with human electrocardiographic traits

status: Public on Jul 12 2019

city: La Jolla

first: Kelly

middle: Ann

last: Frazer

state: CA

address: 9500 Gilman Drive

department: Pediatrics

institute: UC San Diego

summary: We conducted a genome-wide analysis to identify regulatory variants affecting the binding of NKX2-5, a core cardiac development transcription factor, and investigated their role in cardiac gene expression and EKG phenotypes. We generated iPSC-derived cardiomyocytes (iPSC-CMs) from a pedigree of seven whole-genome sequenced individuals, and profiled them with a variety of functional genomic assays including RNA-Seq, ATAC-Seq, and ChIP-Seq of both histone modification H3K27ac and NKX2-5. After establishing that iPSC-CMs recapitulated cardiomyocyte-specific expression and epigenetic signatures, and that genetic variants affected the variability of molecular phenotypes across the iPSC-CM lines, we identified heterozygous sites that showed allele-specific effects (ASE). We then investigated NKX2-5 ASE variants in detail by examining whether they altered cardiac TF motifs, and whether they were enriched for eQTLs and EKG GWAS-SNPs. Our data reveal that variation affecting the binding of NKX2-5 and other cardiac TFs likely serves as a molecular mechanism underlying control of numerous EKG loci across the genome, and that fine-mapping approaches, combined with molecular phenotype data from iPSC-CMs, can be used to prioritize causal variants in EKG GWAS loci.

overall_design: We selected seven individuals of Asian and European descent in the iPSCORE resource that are part of a three-generational family. Our study design included three genetically unrelated subjects and two parent-offspring quartets, which enabled us to examine the inheritance of genetic effects.We generated and analyzed 56 RNA-Seq (iPSCs: 29 independent samples; iPSC-CMs: 26 independent samples and 1 technical replicate), 48 ChIP-Seq of histone modification H3K27ac (iPSCs: 17 samples and 4 technical replicates; iPSC-CMs: 25 samples and 2 technical replicates), 15 ChIP-seq of NKX2-5 (iPSC-CMs: 12 samples and 3 technical replicates and 37 ATAC-Seq (iPSCs: 12 samples and 5 technical replicates; iPSC-CMs: 11 samples and 9 technical replicates). Raw data requires controlled access and is deposited at dbGaP (phs000924 and phs001325). Data for RNA-Seq, H3K7ac ChIP-Seq and 21/37 ATAC-Seq samples were deposited under the accession GSE125540.

first: Paola

last: Benaglio

first: Agnieszka

last: D'Antonio-Chronowska

first: Wubin

last: Ma

first: Feng

last: Yang

first: William

middle: W

last: Greenwald

first: Margaret

middle: K

last: Donovan

first: Christopher

last: DeBoever

first: He

last: Li

first: Frauke

last: Drees

first: Sanghamitra

last: Singhal

first: Hiroko

last: Matsui

first: Jessica

last: van Setten

first: Nona

last: Sotoodehnia

first: Kyle

last: Gaulton

first: Erin

middle: N

last: Smith

first: Matteo

last: D’Antonio

first: Michael

middle: G

last: Rosenfeld