title: Progression from actinic keratosis to cutaneous squamous cell carcinoma involves miR-204 silencing and a switch towards STAT3 activation

status: Public on Dec 31 2016

summary: Squamous cell carcinoma is the second most common skin cancer and frequently progress from an intraepithelial actinic keratosis. The role of microRNAs during the progression from actinic keratosis to cutaneous squamous cell carcinoma (cSCC) remains to be elicited. By using an Agilent microRNA expression microarray we found the expression of miR-204 to be markedly downregulated in cSCC when compared to actinic keratoses. DNA methylation of the TRPM3 promoter region upstream of miR-204-5p was identified as one of the repressive mechanisms that accounts for miR-204 silencing in cSCC. Functional studies on HaCaT cells revealed that this microRNA downregulates the Signal Transducer and Activator of Transcription 3 (STAT3) pathway and favours the MAPK signaling pathway, likely acting through PTPN11, a tyrosine phosphatase that is a direct miR-204 target. We found that activated STAT3, as detected by pY705-STAT3 immunofluorescence, is retained in the membrane and cytoplasm compartment in AK, whereas cSCC displayed STAT3 in the nuclei. Taken together, our data indicates that MiR-204 may act as a “rheostat” that controls the signaling towards the MAPK pathway or the STAT3 pathway.

overall_design: 4 samples were analyzed: HaCaT tansduced with control shRNA (n=2) and HaCaT transduced with shRNA against miR-204 (n=2)

first: Inma

last: Hernández


title: Expression data from H9 human embryonic stem cells (hESCs) infected with either lentiviral non-silencing shRNA or shRUNX1, and differentiated to early mesendoderm

status: Public on Oct 06 2016

city: New Haven

first: Jennifer

last: VanOudenhove

state: CT

address: 300 George St RM 786

department: Internal Medicine - Section of Hematology

country: USA

institute: Yale University

summary: We used microarrays to detail the global program of gene expression during early hESC differentiation to mesendoderm using FBS, with and without RUNX1 depletion.

overall_design: Samples of hESCs were taken at undifferentiated state (0h), 8h of differentiation, 24h of differentiation, and 72h of differentiation with three replicates at each time point; (A, B, and C) for the non-silencing timecourse, and (C, D, and E) for the shRUNX1 timecourse.

middle: J

first: Gary

middle: S

last: Stein


title: Expression data from MSC DDR2 KD and control cells, and from MDA-MB-231 cells primed with MSC DDR2 KD and controls

status: Public on Dec 17 2016

city: Ann Arbor

first: Maria

middle: Elena

last: Gonzalez

state: Michigan

address: 1400East Medical Ct Dr

department: Pathology

institute: University of Michigan

summary: DDR2 regulates genes in MSCs and in MDA-MD-231 cells primed with MSCs

overall_design:
MDAMB231 GFP labelled cells were primed with MSCs-DsRed sh Scramble or shDDR2, then sorted for GFP+ or double + by flow cytometry and analyzed by gene expression between pairs groups.
MSCs were treated with lentivirus containig shRNA for DDR2 to knock down DDR2 expression and compared gene expression with shScramble control.
We isolated total RNA from all samples, after culture in complete medium. Triplicate RNA of each sample were submitted for microarray analyses.

first: Celina

last: Kleer


title: Snail1 controls fibroblast action on tumor cell invasion and metastasis [MSC]

status: Public on Dec 22 2016

city: Barcelona

first: Júlia

last: Perera-Bel

address: Doctor Aiguader, 88

department: MARData-BU

country: Spain

institute: Hospital del Mar Research Institute

summary: Snail1 transcriptional factor is essential for triggering epithelial-to-mesenchymal transition (EMT) and inducing tumor cell invasion. We report here that Snail1 plays also a key role in tumor associated fibroblasts since is necessary for enhancement by these cells on epithelial cells tumor invasion. Snail1 expression in fibroblast requires signals derived from tumor cells such as TGF-b; reciprocally, in fibroblasts Snail1 organizes a complex program that favors collective invasion of epithelial cells at least in part by the secretion of diffusible signaling molecules, such as prostaglandin E2. The capability of human or murine tumor-derived cancer associated fibroblasts to promote tumor invasion is associated to Snail1 expression and obliterated by Snail1 depletion. In vivo experiments show that tumor cells co-transplanted with Snail1 depleted fibroblasts show lower invasion than those xenografted with control fibroblasts.  Finally Snail1 depletion in mice prevents the formation of breast tumors and decreased their invasion. Therefore, these results demonstrate that the role of Snail1 in tumor invasion is not limited to its effect in EMT but dependent on its expression in stromal fibroblasts where it orchestrates its activation and the crosstalk with epithelial cells.

overall_design: 4 samples were analyzed: Snail1-WT MSCs, Snail1-WT MSCs treated with TGF-b1, Snail1-KO MSCs and Snail1-KO MSCs treated with TGF-b1

first: Lorena

last: Alba-Castellon

first: Aida

last: Mestre

first: Rubén

last: Olivera

first: Antonio

last: Garcia de Herreros


title: Snail1 controls fibroblast action on tumor cell invasion and metastasis [HT29]

overall_design: 2 samples were analyzed: HT-29M6 control, HT-29M6 treated with PGE2 16h


title: Snail1 controls fibroblast action on tumor cell invasion and metastasis

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Microarray expression study of histological subtypes of intestinal metaplasia that progress to gastric cancer

status: Public on Jun 12 2017

summary:
Background: Intestinal metaplasia (IM)  is a gastric precancerous lesion that precedes the development of gastric cancer in up to 3.77 cases/1000 person-years. It consists in a trans-differentiation process of gastric to intestinal tissue. Two histological subtypes exist, complete (CIM) and incomplete (IIM), the latter having higher progression rates to gastric cancer . Our objective was to identify molecular processes responsible for the tumoral transition from intestinal metaplasia to GC and the initial steps of  this lesion
Methods: We used expression microarray to compare the transcriptome of intestinal metaplasia subtypes that progress to gastric cancer (IIM-GC and CIM-GC) after a follow-up period with respect to those that do not progress (IIM control and CIM control). Also, IM-NoGC (IM control, comprising both IIM and CIM Control) was compared with healthy gastric mucosa. Differentially expressed genes were obtained and functional analyses (GSEA and IPA softwares) were performed. Some deregulated genes were validated by qPCR.
Results: Histological subtypes of intestinal metaplasia that progress or not to GC differ less among them than to healthy mucosa. Incomplete intestinal metaplasia has a higher number of over-expressed carcinogenic genes and molecular processes than the complete subtype. Most relevant molecular processes and genes in this group include antigenic processing, inflammation, activation of cell cycle and cell proliferation, oncogenes and tumor suppressors.
When IM-NoGC is compared with healthy gastric mucosa new identified transcripts include TRIM, TMEM, homeobox, transporters and nucleolar RNAs SNORDs116. We confirm previously reported processes such us intestinal differentiation, metabolism of lipids and of xenobiotics and identify new ones such as non tumoral Warburg effect and melatonin degradation.
Conclusions: Differentially expressed genes and molecular processes have been identified for the first time in intestinal metaplasia that progress to gastric cancer. New genes and molecular processes have also been identified in intestinal metaplasia in comparison with healthy gastric mucosa.

overall_design:
Using the Almac-Xcel array (Affymetrix) we profiled total RNA of gastric mucosa from:
Incomplete Intestinal metaplasia that progress to GC (N=6) vs Incomplete Intestinal metaplasia that not progress to GC (IIM Controls, N=7)
Complete Intestinal metaplasia that progress to GC (N=8) vs Complete Intestinal metaplasia that not progress to GC (CIM controls, N=9)
Healthy controls (N=15)

first: Osmel

last: Companioni

first: Núria

last: Sala

first: José

middle: M

last: Sanz-Anquela

last: L Pardo

first: Eulalia

last: Puigdecanet

first: Lara

last: Nonell

first: Carlos

middle: A


title: MIST1 and PTF1 Collaborate in Feed-forward Regulatory Loops that Maintain the Pancreatic Acinar Phenotype in Adult Mice

status: Public on Sep 01 2016

city: Dallas

first: Galvin

last: Swift

state: TX

address: 6000 Harry Hines Blvd

department: Molecular Biology

institute: U TX Southwestern Medical Center

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing


title: Next Generation Sequencing Facilitates Quantitative Analysis of colorectal cancer cells transfected with NC siRNA or RPL9 siRNA

status: Public on Feb 23 2017

city: Rockville

first: Daekwan

last: Seo

state: MARYLAND

address: 1330 Piccard Dr., Ste 103

department: Bioinformatics

institute: Psomagen Inc

summary: Ribosomal protein L9 (RPL9), a component of the 60S subunit, is up-regulated in human colorectal cancer (CRC). We thus hypothesized if targeting of RPL9 with small interfering (si) RNA could inhibit CRC progression. We also investigated molecular mechanism to mediate CRC cell death caused by RPL9 silencing. HCT116 and HT29 human CRC cells were transfected with RPL9 siRNA and tested for growth inhibition and apoptotic induction using MTS, FACS and microscopic analysis. To obtain insights into the molecular changes in response to RPL9 knockdown, global changes in gene expression were examined using RNA sequencing. As a result, RPL9 silencing caused inhibition of CRC cell growth through induction of apoptotic cell death. RNA sequencing revealed that RPL9-specific knockdown led to dysregulation of 918 genes in HCT116 and 3178 genes in HT29 cells. Among those, 296 genes showed the same directional regulation (128 up- and 168 down-regulated genes), including up-regulation of tumor suppressors such as KLF6 and ATF3, and were considered as a common RPL9 knockdown signature. Western blotting proved that down-regulation of RPL9 was accompanied with the decrease in the levels of PARP-1 and pro-caspase 3, accelerating apoptotic signaling. Of importance, targeting RPL9 significantly inhibited CRC growth in a murine xenograft model. In conclusion, these results suggest that inhibition of RPL9 expression could be an attractive option for molecular targeted therapy of colorectal cancer.

overall_design: Examination of 2 different siRNA transfected cells in 2 cell lines.

first: In

middle: H

last: Baik

first: Yun-Han

last: Lee


title: MIST1 and PTF1 Collaborate in Feed-forward Regulatory Loops that Maintain the Pancreatic Acinar Phenotype in Adult Mice [ChIP-Seq]

overall_design: Chip-seq was performed with antibodies against Mist1, RNA Polymerase II, and Histone3-K27me3.

first: Mei

last: Jiang

first: Raymond

last: MacDonald

first: Chinh

last: Hoang

first: Tye

last: Deering

first: Ana

last: Azevedo-Pouly


title: Transcriptional Maintenance of Pancreatic Acinar Identity, Differentiation and Homeostasis by PTF1A [ChIP-Seq]

summary: Genome-wide maps of Ptf1a-bound sites in adult pancrea acinar cells.

overall_design: 2 replicates of each of 2 antibodies against Ptf1a, and input DNA


title: MIST1 and PTF1 Collaborate in Feed-forward Regulatory Loops that Maintain the Pancreatic Acinar Phenotype in Adult Mice [RNA-Seq]

overall_design: RNA-seq was done on 2 normal heterozygous Mist1(+/ko) mice and 3 Mist1(ko/ko) mice.


title: The PRC1 protein RING1B contributes to Ewing sarcoma tumorigenesis by repressing the NaV1.6 sodium channel and modulating the NF-kB pathway, independently of the fusion oncoprotein.

status: Public on Jun 30 2016

first: Júlia

last: Perera-Bel

summary: Ewing sarcoma (ES) is an aggressive tumor molecularly defined by reciprocal translocations of EWSR1 to an ETS transcription factor. The functions of EZH2 and BMI1, two proteins of the Polycomb group (PcG) of epigenetic repressors, have been previously shown to mediate specific features in EWSR1/ETS-transformed cells. Here we have characterized the expression and function of RING1B, a PcG protein with unique abilities, in ES. RING1B is highly and universally expressed in primary ES tumors. In contrast to EZH2, RING1B expression is independent of both the oncogene and of differentiation agents. RING1B depletion affects heme biosynthesis and hematopoiesis but does not result in a widespread alteration in ES differentiation. Among the unique set of genes regulated upon RING1B depletion, FGF14 and SCN8A, interacting components of the NaV1.6 channel, are two of the most up-regulated genes. Control of FGF14 and SCN8A in ES is specific of RING1B and functionally relevant. The signaling pathway most significantly modulated by RING1B is NF-κB. Indeed, RING1B depletion results in enhanced p105/p50 expression, which specifically sensitizes ES cells to apoptosis by FGFR/SHP2/STAT3 blockade. In conclusion, we show that RING1B is pivotal in ES cells, independently of the fusion oncogene, likely reflecting essential functional traits of the cell-of-origin.

overall_design: 10 samples were analyzed: A4573 transduced with control shRNA; A4573 transduced with shRING1B; A673 transduced with control shRNA; A673 transduced with shRING1B; SK-ES-1  transduced with control shRNA; SK-ES-1  transduced with shRING1B; TC71 transduced with control shRNA; TC71 transduced with shRING1B; A673 transduced with shBMI1; TC71 transduced with shBMI1

first: Inmaculada

last: Hernández-Muñoz


title: Expression data from H9 human embryonic stem cells (hESCs)  differentiated to Early Mesoendoderm

status: Public on Mar 22 2016

first: Jennifer

last: VanOudenhove

summary: We used microarrays to detail the global programme of gene expression during early hESC differentiation to Mesendoderm using FBS.

overall_design: Samples of hESCs were taken at undifferentiated state (0h), 8h of differentiation, 24h of differentiation, and 72h of differentiation with three replicates (A, B, and C) at each time point.

first: Gary

last: Stein


title: Recurrent somatic mutations in POLR2A define a distinct subset of meningiomas [RNA-seq]

status: Public on Aug 21 2016

first: Victoria

middle: Elizabeth

last: Clark

address: 300 Cedar Street TAC S330

department: Departments of Neurosurgery and Genetics

institute: Yale University School of Medicine

summary: RNA polymerase II mediates the transcription of all protein-coding genes in eukaryotic cells, a process that is fundamental to life. Genomic mutations in this enzyme have not been previously linked to any pathology in humans, a testament to its indispensable role in cell biology. Based on a combination of next-generation genomic analyses of 775 meningiomas, we report that recurrent somatic p.Gln403Lys or p.Leu438_His439del mutations in POLR2A, which encodes the catalytic subunit of RNA polymerase II, are sufficient to hijack this essential enzyme and drive neoplasia. POLR2A mutant tumors reveal dysregulation of key meningeal identity genes, including WNT6 and ZIC1/ZIC4. In addition to POLR2A, NF2, SMARCB1, TRAF7, KLF4, AKT1, PIK3CA and SMO, we also report somatic mutations in AKT3, PIK3R1, PRKAR1A, and SUFU in meningiomas. Our results identify a role for essential transcriptional machinery in driving tumorigenesis and define mutually exclusive meningioma subgroups with distinct clinical and pathological features.

overall_design: RNAseq data from 19 meningioma tumors representing major mutation groups (NF2/chr22 loss, POLR2A, KLF4/TRAF7, PI3K mutant)

middle: E

first: Akdes

last: Serin Harmancı

first: Hanwen

last: Bai

first: Mark

middle: W

last: Youngblood

first: Tong

middle: I

first: Jacob

last: Baranoski

first: Adife

middle: G

last: Ercan-Sencicek

first: Brian

last: Abraham

first: Abraham

last: Weintraub

first: Denes

last: Hnisz

first: Matthias

last: Simon

first: Boris

last: Krischek

first: E

middle: Z

last: Erson-Omay

first: Octavian

last: Henegariu

first: Geneive

last: Carrión-Grant

first: Ketu

last: Mishra-Goru

first: Daniel

last: Durán

first: Johanna

last: Goldmann

first: Johannes

last: Schramm

first: Roland

last: Goldbrunner

first: Joseph

last: Piepmeier

first: Alexander

middle: O

last: Vortmeyer

last: Günel

first: Kaya

last: Bilgüvar

first: Katsuhito

last: Yasuno

first: Richard

last: Young

first: Murat


title: Recurrent somatic mutations in POLR2A define a distinct subset of meningiomas [array]

first: Victoria

last: Clark

overall_design: Expression microarray data from 121 total samples, including 96 tumors representing the major meningioma mutation groups (NF2/chr22 loss, POLR2A, KLF4/TRAF7, PI3K mutant, Sonic Hedgehog mutant) and 25 control samples (3 dura, 13 adult meninges, and 9 embryonic meninges).

first: Akdes

last: Serin Harmancı

first: Hanwen

last: Bai

first: Mark

last: Youngblood

first: Tong

last: Lee

first: Jacob

last: Baranoski

first: Adife

last: Ercan-Sencicek

first: Brian

last: Abraham

first: Abraham

last: Weintraub

first: Denes

last: Hnisz

first: Jennifer


title: Primary Human Osteoblasts miRNA array

status: Public on Dec 21 2015

first: Júlia

last: Perera-Bel

summary: A microRNA array was performed using human primary osteoblasts (hOB) obtained from trabecular bone of postmenopausal women after knee replacement due to osteoarthritis in order to determine the miRNAs expressed in these osteoblastic cells.

platform_organism:
Homo sapiens
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Macacine alphaherpesvirus 1
Human betaherpesvirus 5
human gammaherpesvirus 4
Herpesvirus saimiri (strain 11)
JC polyomavirus
Human immunodeficiency virus 1
Human betaherpesvirus 6B
Human gammaherpesvirus 8
Merkel cell polyomavirus
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: 4 samples were analyzed: Human primary osteoblasts (hOB) were obtained from trabecular bone of postmenopausal women after knee replacement due to osteoarthritis (n=4).

first: Laura

last: de Ugarte

first: Natàlia

last: Garcia Giralt

first: Guy

last: Yoskovitz

first: Susana

last: Balcells

first: Roberto

last: Güerri Fernández

first: Santos

last: Martinez Diaz

first: Leonardo

last: Mellibovsky

first: Roser

last: Urreizti

first: Xavier

last: Nogués

first: Daniel

last: Grinberg

first: Adolfo

last: Díez Pérez


title: Recurrent somatic mutations in POLR2A define a distinct subset of meningiomas [ChIP-seq]

first: Victoria

last: Clark

overall_design:
Peak calls from H3K27ac ChIPseq data from 22 samples, including 20 tumors representing the major mutation groups (NF2/chr22 loss, POLR2A, KLF4/TRAF7, PI3K mutant, Sonic Hedgehog mutant) and 2 control samples (dura).

The H3k27ac ChIP-seq data for 14 benign meningiomas and 2 dura samples listed below were created by Dr. Justin Cotney in Dr. James Noonan’s lab at Yale and previously published in a paper by our group with Drs. Cotney and Noonan as co-authors (Clark et al. Science, 2013). Sample IDs: MN-297, MN-288, MN-163, MN-1037, MN-105, MN-201, MN-249, MN-191, MN-1066, MN-169, MN-291, MN-24, MN-79, MN-1044, DURA_1, DURA_2.

In this study, we used these meningioma H3k27ac ChIP-seq data as controls and compared them to the newly created ChIP-seq data. Sample IDs: MN-1200, MN-63345, MN-60355, MN-63670, MN-64273, MN-296.

This GEO entry contains ChIP-seq results for both data sets.

first: Akdes

last: Serin Harmancı

first: Hanwen

last: Bai

first: Mark

last: Youngblood

first: Tong

last: Lee

first: Jacob

last: Baranoski

first: Adife

first: Matthias

last: Simon

first: Boris

last: Krischek

first: E

last: Erson-Omay

first: Octavian

last: Henegariu

first: Geneive

last: Carrión-Grant

first: Ketu

last: Mishra-Goru

last: Durán

first: Johanna

last: Goldmann

first: Johannes

last: Schramm

first: Roland

last: Goldbrunner

first: Joseph

last: Piepmeier

first: Alexander

last: Vortmeyer

last: Günel

first: Kaya

last: Bilgüvar

first: Katsuhito

last: Yasuno

first: Richard

last: Young

first: Murat


title: Recurrent somatic mutations in POLR2A define a distinct subset of meningiomas

first: Victoria

last: Clark


title: MiRNA Profiling of Whole Trabecular Bone: Identification of Osteoporosis-Related Changes in MiRNAs in Human Hip Bones

first: Júlia

last: Perera-Bel

summary: MicroRNAs (miRNAs) are important regulators of gene expression, with documented roles in bone metabolism and osteoporosis, suggesting potential therapeutic targets. Our aim was to identify miRNAs differentially expressed in fractured vs nonfractured bones. Additionally, we performed a miRNA profiling of primary osteoblasts to assess the origin of these differentially expressed miRNAs. Total RNA was extracted from (a) fresh femoral neck trabecular bone from women undergoing hip replacement due to either osteoporotic fracture (OP group, n=6) or osteoarthritis in the absence of osteoporosis (Control group, n=6), matching the two groups by age and body mass index, and (b) primary osteoblasts obtained from knee replacement due to osteoarthritis (n=4). Samples were hybridized to a microRNA array containing more than 1900 miRNAs. Principal component analysis (PCA) plots and heat map hierarchical clustering were performed. For comparison of expression levels, the threshold was set at log fold change > 1.5 and a p-value < 0.05 (corrected for multiple testing). Both PCA and heat map analyses showed that the samples clustered according to the presence or absence of fracture. Overall, 790 and 315 different miRNAs were detected in fresh bone samples and in primary osteoblasts, respectively, 293 of which were common to both groups. A subset of 82 miRNAs was differentially expressed (p < 0.05) between osteoporotic and non-osteoporotic samples. The eight miRNAs with the lowest p-values (and for which a validated miRNA qPCR assay was available) were assayed, and two were confirmed: miR-320a and miR-483-5p. Both were over-expressed in the osteoporotic samples and expressed in primary osteoblasts. miR-320a is known to target CTNNB1 and predicted to regulate RUNX2, while miR-483-5p down-regulates IGF2. We observed a reduction trend for this target gene in the osteoporotic bone.In conclusion, we identified two osteoblast miRNAs over-expressed in osteoporotic fractures, which opens novel prospects for research and therapy.

overall_design: 12 samples were analyzed: Fresh femoral neck trabecular bone was obtained from 12 postmenopausal women undergoing hip replacement due to either osteoporotic fracture (n=6) or osteoarthritis in the absence of osteoporosis (n=6)

first: Laura

last: de Ugarte

first: Natàlia

last: Garcia Giralt

first: Guy

last: Yoskovitz

first: Susana

last: Balcells

first: Roberto

last: Güerri Fernández

first: Santos

last: Martinez Diaz

first: Leonardo

last: Mellibovsky

first: Roser

last: Urreizti

first: Xavier

last: Nogués

first: Daniel

last: Grinberg

first: Adolfo

last: Díez Pérez


title: Mammalian NET-seq reveals genome-wide nascent transcription coupled to RNA processing

status: Public on Apr 23 2015

city: Lisboa

first: Tomás

last: Gomes

address: Av. Professor Egas Moniz

country: Portugal

institute: Instituto de Medicina Molecular

summary: We have generated single-nucleotide resolution, nascent transcription profiles from HeLa cells by developing Native Elongation Transcript sequencing technology for mammalian chromatin (mNET-seq). Our extensive data sets provide a substantial resource to study mammalian nascent transcript profiles. We reveal unanticipated phosphorylation states for RNA polymerase II C-terminal domain (Pol II CTD) at both gene ends. We also observe that following 5’ splice site cleavage by the spliceosome, upstream exon transcripts are tethered to Pol II CTD phosphorylated on the serine 5 position (S5P) which is accumulated over downstream exons. We further show that depletion of termination factors  substantially reduces Pol II pausing at gene ends leading to termination defects. Remarkably termination factors play an additional promoter role by restricting non-productive RNA synthesis and redistributing Pol II CTD S2P to promoters. These data demonstrate that CTD phosphorylation is more dynamic and variably distributed across mammalian transcription units than previously envisaged.

overall_design: To monitor nascent RNA within the mammalian Pol II complex, and its association with different CTD phosphorylation states, we employed mNET-seq methodology on HeLa cells, complemented with direct sequencing of chromatin-bound RNA (ChrRNA-seq). mNET-seq was preformed using the antibodies 8WG16, CMA602, CMA603 and CMA601, which are specific for unphosphorylated CTD, Ser2 phosphorylation, Ser5 phosphorylation and all CTD isoforms, respectively. In another experiment, to evaluate the effect of transcription termination factors in nascent RNA production by Pol II, mNET-seq  and complemented with ChrRNA-seq was preformed on HeLa cells transfected with siRNA against PTBP1, CPSF73, CstF64+CstF64tau or Xrn2, and the gene profiles were compared with profiles from HeLa transfected with siRNA for Luciferase generated by the same protocol.

first: Takayuki

last: Nojima

first: Ana

middle: F

last: Grosso

first: Hiroshi

last: Kimura

first: Michael

last: Dye

first: Somdutta

last: Dhir

first: Maria

middle: C

last: Fonseca

first: Nicholas

last: Proudfoot


title: LOXL2 dependent genes in RA induced mES differentiation

first: Júlia

last: Perera-Bel

summary: Our results indicate that oxidation of TAF10 by LOXL2 induces its release from its promoters, leading to a block in TFIID-dependent gene transcription. Since TFIID complex is crucial for the expression of Nanog, Klf4, Sox2 and Oct4 and for maintaining the pluripotent state of embryonic stem cells, TAF10 oxidation by LOXL2 leads to inactivation of the pluripotency genes and a loss of pluripotent capacity in embryonic stem cells. Moreover, in vivo results demonstrate an essential role of LOXL2 in neural differentiation during zebrafish development: in the absence of LOXL2 the neural progenitor gene Sox2 is aberrantly overexpressed and neural differentiation is impaired.

overall_design: 12 samples were analyzed: mES transduced with control shRNA (n=3); mES transduced with LOXL2 shRNA (n=3), ES transduced with control shRNA and treated with RA (n=3); ES transduced with LOXL2 shRNA and treated with RA (n=3)

first: Sandra

last: Peiró


title: Expression data from mouse intestinal epithelial cells infected with Trichinella spiralis

status: Public on Mar 28 2015

city: Stanford

first: Lisa

middle: K

last: Blum

state: CA

address: 269 Campus Drive

institute: Stanford University

summary:
Trichinella spiralis is a highly destructive parasitic nematode that invades and destroys intestinal epithelial cells, injures many different tissues during its migratory phase, and occupies and transforms myotubes during the final phase of its life cycle. Mice deficient in the IL-1 family receptor for the DAMP, IL-33 (called ST2), display reduced intestinal Th2 responses and impaired mast cell activation. IL-33 was constitutively expressed in intestinal epithelial cells, where it became concentrated in nuclei within 2 days of infection. Nuclear localization was an innate response to infection that occurred in intestinal regions where worms were actively migrating. We isolated intestinal epithelial cells from uninfected mice (cytoplasmic IL-33) and mice at 2 days post-infection (nuclear IL-33) to compare global expression profiles.
We used microarrays to characterize the global gene expression that occurs in intestinal epithelial cells following T. spiralis-induced nuclear translocation of IL-33.

overall_design: Intestinal epithelial cells were isolated from Rag2-/- mice at day zero (uninfected) or two days post-infection with T. ispiralis for RNA extraction and hybridization on Affymetrix microarrays.

first: Judith

last: Appleton


title: The Small Molecule Genistein Increases Hepcidin Expression in Human Hepatocytes

status: Public on Aug 13 2015

city: Boston

first: Paula

middle: Goodman

last: Fraenkel

state: MA

address: 330 Brookline Avenue, SLD 423B

department: Division of Hematology/Oncology

institute: Beth Israel Deaconess Medical Center

summary: Hepcidin, a peptide hormone that decreases intestinal iron absorption and macrophage iron release, is a potential drug target for patients with iron overload syndromes because its levels are inappropriately low in these individuals.  Endogenous stimulants of Hepcidin transcription include bone morphogenic protein 6 (BMP) and interleukin-6 (IL-6) via effects on Smad4 or Stat3, respectively.  We conducted a small-scale chemical screen in zebrafish embryos to identify small molecules that modulate hepcidin expression.  We found that treatment with the isoflavone genistein from 28−52 hours post-fertilization in zebrafish embryos enhanced Hepcidin transcript levels as assessed by whole mount in situ hybridization and quantitative realtime RT-PCR.  Genistein’s stimulatory effect was conserved in human hepatocytes: genistein treatment of HepG2 cells increased both Hepcidin transcript levels and Hepcidin promoter activity.  We found that genistein’s effect on Hepcidin expression did not depend on estrogen receptor signaling or increased cellular iron uptake, but was impaired by mutation of either the BMP response elements or the Stat3 binding site in the Hepcidin promoter.  RNA-sequencing of transcripts from genistein-treated hepatocytes indicated that genistein upregulated 68% of the transcripts that were upregulated by BMP6, however genistein raised the levels of several transcripts involved in Stat3 signaling that were not upregulated by BMP6.  Chromatin-immunoprecipitation and ELISA experiments revealed that genistein enhanced Stat3 binding to the Hepcidin promoter and increased phosphorylation of Stat3 in HepG2 cells.  CONCLUSION:  Genistein is the first small molecule experimental drug that stimulates Hepcidin expression in vivo and in vitro.  These experiments demonstrate the feasibility of identifying and characterizing small molecules that increase Hepcidin expression.  Genistein and other candidate molecules may subsequently be developed into new therapies for iron overload syndromes.

overall_design: RNA-seq of HepG2 cells treated with DMSO 1%, BMP6 50 ng/ml, or genistein 10 micromolar.  The numbers of biological replicates were 3, 2, and 3.

first: Aileen

last: Zhen

first: Nancy

last: Nguyen

first: Yann

last: Gibert

first: Shmulik

last: Motola

first: Peter

last: Buckett

first: Marianne

last: Wesling-Resnick

first: Ernest


title: BRAF-induced tumorigenesis is IKKalpha dependent but NFκB independent

status: Public on May 08 2015

summary: Tumor cells carrying KRAS mutations activate the NF-κB pathway by different mechanisms, which contribute to the acquisition of essential cancer properties. The BRAF kinase, a downstream mediator of KRAS, is also mutated in a subset of colorectal cancers (CRC), which predicts bad prognosis and therapy resistance. However, nothing is known on whether NF-κB participates of BRAF-mediated tumorigenesis. We here found that in CRC cells, mutant BRAF does not trigger canonical or alternative NF-κB signaling but induces p45-IKKα activation. Moreover, IKKα activity is required for BRAF-induced transformation and to support BRAF-dependent transcription in CRC cells. Activation of p45-IKKα downstream of BRAF requires the TAK1 kinase, and is associated to the endosomal compartment. Inhibition of endosomal V-ATPase abolished p45-IKKα phosphorylation, and induced apoptosis of BRAF mutated CRC cells. Pharmacologic inhibition of endosome acidification reduced the in vivo growth of tumors carrying mutant BRAF, and abrogated the metastatic capacity of a primary human CRC tumor with acquired resistance to standard chemotherapy in an orthotopic xenograft model.

overall_design: 18 samples were analyzed: HT29 controls (n=3); HT28 BRAF inhibited (n=3), WiDr controls (n=3); WiDr BRAF inhibited (n=3); WiDr transduced with control shRNA (n=3) and WiDr transduced with shRNA against IKKalpha (n=3)

first: Pol

last: Margalef

first: Lluís

last: Espinosa

first: Anna

last: Bigas


title: Cytoplasmic accumulation of NCoR in malignant melanoma: consequences of altered gene repression and prognostic significance

status: Public on Dec 31 2014

summary: Invasive malignant melanoma (MM) usually has a poor prognosis developing visceral disease with no curative therapy available so far. Nuclear corepressor (NCoR) is an essential regulator of gene transcription, and its function is commonly deregulated in different types of cancer. However, little is known on whether and how NCoR loss of function impacts in MM, which might have important diagnostic and prognostic significance. We here show that loss of nuclear NCoR is significantly associated with MM progression, but at comparable stage of the disease is predictive of patient outcome and reduced overall survival. Loss of nuclear NCoR results in upregulation of specific cancer-related genetic signature, whereas inhibition of IKK activity in melanoma cells is reverts both NCoR nuclear distribution and gene transcription. Analysis of public database demonstrated the high prevalence of inactivating NCoR mutations in MM, with characteristics of driver oncogene.

overall_design: 10 samples were analyzed: MMpos (n=4); MMneg  (n=3), Ctrl (n=3 )

first: Fernando

last: Gallardo


title: PROX1 amplification predicts better prognosis of oral cancer and overexpression is associated with reduced tumor cell aggressiveness

status: Public on Dec 30 2014

city: Sao Paulo

first: Patricia

last: Severino

state: Sao Paulo

address: Rua Comendador Elias Jafet, 755

department: Albert Einstein Research and Education Institute

country: Brazil

institute: Hospital Israelita Albert Einstein

summary: Homeobox genes are a family of transcription factors that play a pivotal role in embryogenesis. Altered expression of Prospero-related homeobox gene 1 (PROX1) was recently associated with cancer, including oral squamous cell carcinoma (OSCC). This study aimed to investigate the functional role of PROX1 in oral carcinogenesis. PROX1 mRNA and protein expression levels were first investigated in 40 samples of OSCC and non-tumour margins. Methylation and amplification analysis was also performed to assess the epigenetic mechanisms involved in controlling PROX1 expression. OSCC cell line SCC9 was also transfected to stably express the PROX1 gene. Next, SCC9-PROX1-overexpressing cells and controls were then subjected to proliferation, differentiation, apoptosis, and microarray assays in vitro. OSCC samples had reduced PROX1 expression levels compared to non-tumour margins. PROX1 amplification was associated with better overall survival. PROX1 overexpression reduces cell proliferation by down-regulating cyclin D1 and up-regulating p21. PROX1-overexpressing cells also exhibited significantly reduced K18 and K19 expression.

overall_design: We analyzed the expression levels of PROX1 transcript and protein as well as PROX1 DNA amplification and methylation status in OSCC tissues and tumor-free surgical margins Additionally, we investigated the effects of PROX1 on cell proliferation, differentiation and survival following its overexpression in a squamous cell carcinoma cell line. Global gene expression profiling of cells overexpressing PROX1 was used as a means to comprehend mechanisms underlying these effects.

first: Maria

last: Rodrigues

first: Camilac

last: de Oliveira Rodini

first: Flávia

last: Xavier

first: Lília

last: Rocha

first: Cauê

last: Pavanello

first: Andrea

last: Otake

first: Patrícia

first: Eloíza

last: Tajara

first: Fabio

middle: D

last: Nunes


title: Parp-2 is required for efficient erythropoiesis in mice by limiting replicative stress in erythroid progenitors

first: Júlia

last: Perera-Bel

summary: Erythropoiesis is a tightly regulated process in which multipotential hematopoietic stem cells give rise to mature red blood cells. Here, we show that Parp-2  deficiency in mice leads to chronic anemia, despite increased EPO plasma levels, providing a novel role for Parp-2 in erythropoiesis. Loss of Parp-2 causes shortened red blood cells lifespan and impaired differentiation of erythroid cells. Transcriptomic analyses revealed the activation of the p53-dependent-DNA damage response pathways on Parp-2-deficient erythroblasts, triggering the expression of genes involved in cell cycle checkpoints and apoptosis. Accordingly, Parp-2-deficient erythroblasts shows G2/M cell cycle arrest and increased apoptosis.

overall_design: 4 samples were analyzed: Parp-2-/- (n=2); WT  (n=2)

first: Yélamos

last: José


title: Transcriptional Maintenance of Pancreatic Acinar Identity, Differentiation and Homeostasis by PTF1A

first: Galvin

last: Swift

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

overall_design: Refer to individual Series


title: Gene expression in peripheral mononuclear cells from septic patients secondary to community acquired pneumonia: patterns of gene expression and outcomes

status: Public on Jun 20 2014

summary: Sepsis is defined as a systemic inflammatory response secondary to a proven or suspected infection. Mechanisms governing this inflammatory response have been shown to be complex and dynamic, involving cross-talking among diverse signaling pathways. However, current knowledge on mechanisms underlying sepsis is far from providing a complete picture of the syndrome, justifying additional efforts that might add to this scenario. Microarray-based expression profiling is a powerful approach for the investigation of complex clinical conditions such as sepsis: the analysis of gene transcription at the genome level potentially avoids results derived from biased assumptions. In this study we investigate whole-genome gene expression profiles of mononuclear cells from survivor and non-survivor septic patients. Blood samples were collected at the time of sepsis diagnosis and seven days later, allowing us to evaluate the role of biological processes or genes possibly involved in patient recovery. Aiming to circumvent, at least partially, the heterogeneity of septic patients we included only patients admitted with sepsis caused by community-acquired pneumonia. Global gene expression profiling allowed us to characterize early sepsis, as compared to healthy individuals. Our results corroborate literature reports on inflammation response in the early stages of sepsis but highlight great heterogeneity in gene expression during sepsis progress. Additionally, global gene expression in the early stage was also able to distinguish sepsis from septic shock and correlated with patient outcome. Differences in oxidative stress seem to be associated with clinical outcome, since significant differences in the expression profile of related genes were observed between survivors and non-survivors at the time of patient enrollment (early sepsis). However, our results substantiate current knowledge supporting that sepsis syndrome development is indeed multifaceted. Although the initial infection of enrolled patients was pneumonia, seven days later gene expression profiles seemed to be characteristic of each patient, common gene expression changes distinguishing survivors from non-survivors. This result could be associated with the underlying health status of each one of them, with complications due to sepsis itself as well as with distinct timing for response to treatment.

overall_design: In this study we investigate whole-genome gene expression profiles of mononuclear cells from survivor (n=5)  and non-survivor (n=5) septic patients, as well as from 3 healthy controls. Blood samples were collected at the time of sepsis diagnosis and seven days later, allowing us to evaluate the role of biological processes or genes possibly involved in patient recovery. Aiming to circumvent, at least partially, the heterogeneity of septic patients we included only patients admitted with sepsis caused by community-acquired pneumonia.

first: Eliézer

last: Silva

first: Giovana

middle: L

last: Baggio-Zappia

first: Milena

last: Brunialti

first: Otelo

last: Rigato Junior

first: Ismael

last: Guerreiro da Silva

middle: R

last: Machado

first: Reinaldo

last: Salomao


title: Adipose transcriptome and microRNA profiles after surgery-induced weight loss [mRNA]

summary: Molecular mechanisms associated with pathophysiological variations in adipose tissue (AT) are not fully recognized. The main aim of this study was to identify novel candidate genes and miRNAs that may contribute to the pathophysiology of hyperplastic AT. Therefore, wide gene and microRNA (miRNA) expression patterns were assessed in subcutaneous AT of 16 morbidly obese women before and after surgery-induced weight loss. Validation of microarray data was performed by quantitative real-time PCR both longitudinally (n=25 paired samples) and cross-sectionally (25 obese vs. 26 age-matched lean women). Analyses in macrophages and differentiated human adipocytes were also performed to try to comprehend the associations found in AT. 5,018 different probe sets identified significant variations in gene expression after treatment (adjusted p-value<0.05). A set of 16 miRNAs also showed significant modifications. Functional analysis revealed changes in genes and miRNAs associated with cell cycle, development and proliferation, lipid metabolism, and the inflammatory response. Canonical affected pathways included TREM1, PI3K, and EIF2 signaling, hepatic stellate cell activation, and mitochondrial function. Increased expression of SLC27A2, ELOVL6, FASN, GYS2, LGALS12, PKP2, ACLY, and miR-575, as well as decreased FOS, EGFL6, PRG4, AQP9, DUSP1, RGS1, EGR1, SPP1, LYZ, miR-130b, miR-221, and miR-155, were further validated. The clustering of similar expression patterns for gene products with related functions revealed molecular footprints, some of them described for the first time, which elucidate changes in biological processes after the surgery-induced weight loss.

overall_design: 32 samples were analyzed: PRE (n=16) and POST (n=16).

first: Francisco

middle: J

last: Ortega

first: José

middle: M

last: Fernández-Real


title: Gene expression change induced by TIM-3/galectin-9 interaction in primary AML

status: Public on Oct 10 2014

city: Fukuoka

first: Yoshikane

last: Kikushige

address: 3-1-1 Maidashi, Higashiku

country: Japan

institute: Kyushu University

summary: Analysis of gene expression change after galectin-9 stimulation in primary CD34+TIM-3+ AML cells

overall_design: Total RNA obtained from purified CD34+TIM-3+ primary AML cells with or without recombinant human galectin-9 stimulation (20hrs) was subjected to transcriptome analysis

first: Koichi

last: Akashi


title: Adipose transcriptome and microRNA profiles after surgery-induced weight loss

type:
Expression profiling by array
Non-coding RNA profiling by array

platform_organism:
Homo sapiens
synthetic construct


title: Adipose transcriptome and microRNA profiles after surgery-induced weight loss [miRNA]


title: MicroRNA expression profile in Head and Neck Cancer: HOX-cluster embedded microRNA-196 and microRNA-10b dysregulation is implicated in cell proliferation

status: Public on Jun 08 2014

first: Patricia

last: Severino

summary: Current evidence implicates aberrant microRNA expression patterns in human malignancies; measurement of microRNA expression may have diagnostic and prognostic applications. Roles for microRNAs in head and neck squamous cell carcinomas (HNSCC) are largely unknown. HNSCC, a smoking-related cancer, is one of the most common malignancies worldwide but reliable diagnostic and prognostic markers have not been discovered so far. Some studies have evaluated the potential use of miRNAs as biomarkers with clinical application in HNSCC. MicroRNA expression profile of oral squamous cell carcinoma samples was determined by means of DNA microarrays. We also performed gain-of-function assays for two differentially expressed miRNAs using two squamous cell carcinoma cell lines and normal oral keratinocytes. The effect of the over-expression of these molecules was evaluated by means of global gene expression profiling and cell proliferation assessment. Altered microRNA expression was detected for a total of 72 microRNAs. Among these we found well studied molecules,  such as the miR-17-92 cluster, comprising potent oncogenic miRNAs, and miR-34, recently found to interact with p53. HOX-cluster embedded miR-196a/b and miR-10b were up- and down-regulated, respectively, in tumor samples. Since validated HOX gene targets for these microRNAs are not consistently deregulated in HNSCC, we performed gain-of-function experiments, in an attempt to outline their possible role. Our results suggest that both molecules interfere in cell proliferation through distinct processes, possibly targeting a small set of genes involved in cell cycle progression.Functional data on miRNAs  in HNSCC is still scarce. Our data corroborate current literature and brings new insights into the role of microRNAs in HNSCC. We also show that miR-196a and miR-10b, not previously associated with HNSCC, may play an oncogenic role in this disease through the deregulation of cell proliferation. The study of microRNA alterations in HNSCC is an essential step to the mechanistic understanding of tumor formation and could lead to the discovery of clinically relevant biomarkers.

overall_design:
[miRNA] Sixteen patients with Oral Squamous Cell Carcinoma (OSCC) were selected for microarray experiments. Tumor and corresponding cancer free surgical margins were collected from patients submitted to surgical resection of primary tumor. MiR expression profiling was performed using the Illumina miR arrays version 1.0. The preparation and hybridization of the samples was done using the reagents and instructions supplied by the manufacturer.
[mRNA] We performed gain-of-function experiments in two human squamous cell carcinoma cell lines formicroRNAs miR-10b and in nomral keratinocytes for miR-196. In an attempt to outline their function we employed whole genome microarray expression profiling in order to identify genes affected by the over-expression of each microRNA. Cells transfected with synthetic precursor molecules were compared with transfection controls in terms of gene expression levels.

first: Holger

last: Brüggemann

first: Flavio

last: Borges

first: Welbert

last: Pereira

first: Flavia

last: Andreghetto

first: Carme

last: Camps

first: Maria

last: de Fatima Garrido Klingbeil

last: de Oliveira Pereira

first: Renata

last: Soares

first: Raquel

last: Moyses

first: Victor

last: Wünsch-Filho

first: Monica

middle: B

last: Mathor

first: Jiannis

last: Ragoussis

first: Eloiza

middle: H


title: Histone Deacetylase Inhibitor prevents cell growth in Burkitt's lymphoma by regulating PI3K/Akt pathways and leading to up regulation of micro RNA-143, -145 and -101

summary: In this study we analyzed gene expression profiles in a well-characterized BL cell line upon treatment with HDACi combined with chemotherapy. The impact on gene expression regulation was broader when HDACi was combined with chemotherapy, than when either therapy was used alone. As expected, treatment interfered in the regulation of cell cycle progression and enhanced cell death. Noteworthy was the effect on members of p53 signaling pathway. The down regulation of PI3KCA and up regulation of p16 were observed at the gene and protein levels, while the inhibition of Akt phosphorylation and the down regulation of c-Myc were confirmed through the analysis of protein levels. As a complementary approach we investigated if HDACi combined with chemotherapy treatment would enhance mir-101, mir-143 and mir-145 levels in BL cell line. This hypothesis was confirmed and we also observed that levels of mir-101, mir-143 and mir-145 were extremely down regulated in BL patients' samples. In this study we demonstrate mechanisms involved in cell cycle arrest upon cell treatment using a combination of HDACi and chemotherapy. We highlight the fact that effective combinations of HDACis with other cytotoxic drugs could improve BL therapy in the future.

overall_design: DNA microarrays were used to access global gene expression modulation upon treatment of Raji BL cell line with VP-16 or NaB and a combination of NaB and VP-16 for 24 hours. Total RNA was extracted using Trizol®. Gene expression of treated cells was compared with controls consisting of untreated cells. Microarray analysis was performed using Agilent Whole Human Genome Microarray 4×44K arrays and labeled using the One Color Quick Amp Labeling Kit (Agilent Technologies). Two biological replicates were included for each experimental condition.

first: Ana

last: dos Santos Ferreira

first: Marcela

last: Robaina

first: Lidia

last: Magalh‹es de Rezende

first: Claudete

middle: E

last: Klumb


title: Gene expression from human fibroblasts

status: Public on Dec 31 2013

first: Júlia

last: Perera-Bel

summary: Since the initial discovery that OCT4, SOX2, KLF4 and c-MYC overexpression sufficed for the induction of pluripotency in somatic cells, methodologies replacing the original factors have enhanced our understanding of the reprogramming process. However, unlike in mouse, OCT4 has not been replaced successfully during reprogramming of human cells. Here we report on a strategy to do so. Through a combination of transcriptome and bioinformatic analysis we have identified factors previously characterized as being lineage specifiers that are able to replace OCT4 and SOX2 in the reprogramming of human fibroblasts. Our results show that is possible to replace OCT4 and SOX2 simultaneously with alternative lineage specifiers in the reprogramming of human cells.  At a broader level, they also support a model in which counteracting lineage specification networks underlie the induction of pluripotency,

overall_design: We analyzed 3 arrays from human fibroblats; 1 array from 4F iPSC;  1 array from 4F iPSC; 1  array for GATA3SOX2, KLF4 and cMYC iPS; 1  array for GATA3vP16,SOX2VP16, KLF4 and cMYC iPS;1  array for GATA3vP16SOX2VP16, KLF4 and cMYC iPS; 1  array for GATA3vP16SOX2VP16, KLF4 and cMYC iPS;  1 array for hES4;1 array for hES10; 1 arrays for iPS generated with OCT4, ZIC2, ZNF521, ASCL1, HESX1,FOXD5,KLF4 and cMYC; 1 arrays for iPS generated with OCT4, ZIC2, ZNF521, ASCL1, HESX1,FOXD5,KLF4 and cMYC; 1 array for iPS generated with  OCT4, SOX1, KLF4 and cMYC;1 array for iPS generated with  OCT4, SOX1, KLF4 and cMYC;1 array  for iPS generated with OCT4, ZNF521, KLF4 and cMYC: 1 array for iPS generated with  OCT4, SOX3, KLF4 and cMYC

first: Nuria

last: Montserrat

first: Emmanuel

last: Nivet

first: Ignacio

last: Martínez

first: Juan

last: Izpisua Belmonte


title: Expression data from MALD1 and MCL cases

status: Public on Dec 23 2013

summary:
Patients with conventional mantle cell lymphoma (MCL) show an aggressive clinical behavior. However, cases fulfilling the WHO criteria for MCL, but that remain asymptomatic without treatment, have been reported. In an attempt to understand this heterogeneity, we have compared 17 typical cases of MCL with a homogeneous group of 13 asymptomatic individuals with monoclonal expansion of t(11;14)(q13;q32) cyclin D1-positive B-cells in peripheral blood (MALD1). None of these cases have received treatment (minimum follow-up of 26 months; median, 71 months).
Gene expression analysis has shown enrichment of signatures associated to neoplastic behavior and cell proliferation in MCL but not in MALD1. In contrast, MALD1 was highly enriched in gene sets related to immune activation and inflammatory responses. CD38 and CD200 genes were differentially expressed between MCL and MALD1. The combined assessment of both proteins by flow cytometry allowed classifying 85% of MALD1 cases. In summary, we have shown for the first time that MALD1, in contrast to MCL, is characterized by immune activation and driven by inflammatory cues. We have also shown that CD38 and CD200 flow cytometry assessment is useful to discern most cases of MALD1 from MCL in the clinical setting. MALD1 should be identified and segregated from the current MCL category to avoid overdiagnosis and unnecessary treatment.

overall_design: 18 samples were analyzed: 5 MALD1, 5 MCL and 8 Healthy Controls

first: Blanca

last: Espinet

first: Lara

last: Nonell

first: Sergi

last: Serrano


title: Single-nucleotide polymorphism array analysis reveals distinct chromosomal aberrations in breast cancer tumors according to the circulating tumor cells status

status: Public on Nov 19 2014

summary: Recent technological advances have made it possible to detect circulating breast cancer cells as precursors of distant metastasis and as prognosis marker in nonmetastatic breast cancer patients. Association of circulating tumor cells (CTCs) with molecular alteration in the primary tumor is not widely explored. We reported differential profile of altered genome, copy number alteration and copy-neutral loss of heterogeneity in 14 primary tumors when comparing patients with CTCs+ versus CTCs- using single-nucleotide polymorphism array. The most prevalent copy number alteration in CTCs+ patients was at 8q and particularly at the cytoband 8q24 (MYC loci). As the role of MYC in the process of tumor cell invasion and migration is controversial, we further validated in a larger series of patients whether altered MYC (amplification or gained) in primary tumors was correlated with the presence of CTCs in peripheral blood (as a surrogate of micrometastais).  No correlation between MYC alteration and presence of CTCs was observed, providing clinical support to the recent data that MYC suppresses cancer metastasis or at least suggesting that MYC alteration could be contributory but insufficient for the generation of CTCs. This molecular association needs to be further characterized in preclinical model and especially clinically.

overall_design: We analyzed CN and LOH of CTC+ and CTC-

first: Rosa

last: Nadal

first: Marta

last: Salido

first: Eulalia

last: Puigdecanet

first: Maria

last: Rodriguez-Rivera

first: Josep

last: Corominas

first: Francesc

last: Solé


title: Expression data from dormant and after-ripened wheat seeds and after-ripened seeds imbibed in ABA.

status: Public on Jun 05 2013

city: Winnipeg

first: Belay

middle: T.

last: Ayele

state: MB

address: 222 Agriculture Building

department: Plant Science

country: Canada

institute: University of Manitoba

summary:
Wheat seed dormancy is released by after-ripening, and germination and seminal root growth of after-ripened/non-dormant seeds can be inhibited by treatment with exogenous ABA.
We used Affymetrix GeneChip Wheat Genome Array to detail transcriptional programs affected by after-ripening of dormant seeds and imbibition of after-ripened seeds in ABA.

overall_design: Dry and imbibed (in water for 12 h and 24 h) dormant and after-ripened seeds, and after-ripened seeds imbibed in ABA for 24 h were used for RNA extraction and hybridization on Affymetrix GeneChip. After-ripened seeds were generated by storing dormant seeds at room temperature for 10 months.

middle: T

first: Mark

last: Jordan

first: Feng

last: Gao


title: High-throughput sequencing of small RNA transcriptomes and DNA microarrays reveal critical biological features targeted by microRNAs in cell models used for squamous cell cancer research

status: Public on Dec 30 2013

first: Patricia

last: Severino

summary:
Background
The implication of post-transcriptional regulation by microRNAs in molecular mechanisms underlying cancer disease is well documented. However, their interference at the cellular level is not fully explored. Functional in vitro studies are fundamental for the comprehension of their role; nevertheless results are highly dependable on the adopted cellular model. Next generation small RNA transcriptomic sequencing data of a tumor cell line and keratinocytes derived from primary culture was generated in order to characterize the microRNA content of these systems, thus helping in their understanding. Both constitute cell models for functional studies of microRNAs in head and neck squamous cell carcinoma (HNSCC), a smoking-related cancer. Known microRNAs were quantified and analyzed in the context of gene regulation. New microRNAs were investigated using similarity and structural search, ab initio classification, and prediction of the location of mature microRNAs within would-be precursor sequences. Results were compared with small RNA transcriptomic sequences from HNSCC samples in order to access the applicability of these cell models for cancer phenotype comprehension and for novel molecule discovery.
Results
Ten miRNAs represented over 70% of the mature molecules present in each of the cell types. The most expressed molecules were miR-21, miR-24 and miR-205, Accordingly; miR-21 and miR-205 have been previously shown to play a role in epithelial cell biology. Although miR-21 has been implicated in cancer development, and evaluated as a biomarker in HNSCC progression, no significant expression differences were seen between cell types. We demonstrate that differentially expressed mature miRNAs target cell cycle progression and apoptosis related biological processes, indicating that they might represent, with acceptable accuracy, the genetic context from which they derive. Most miRNAs identified in the cancer cell line and in keratinocytes were present in tumor samples and cancer-free samples, respectively, with miR-21, miR-24 and miR-205 still among the most prevalent molecules at all instances. Thirteen miRNA-like structures, containing reads identified by the deep sequencing, were predicted from putative miRNA precursor sequences. Strong evidences suggest that one of them could be a new miRNA. This molecule was mostly expressed in the tumor cell line and HNSCC samples indicating a possible biological function in cancer.
Conclusions
Critical biological features of cells must be fully understood before they can be chosen as models for functional studies. Expression levels of miRNAs relate to cell type and tissue context. This study provides insights on miRNA content of two cell models used for cancer research. Pathways commonly deregulated in HNSCC were targeted by most expressed and also by differentially expressed miRNAs. Results indicate that the use of cell models for cancer research demands careful assessment of underlying molecular characteristics for proper data interpretation. Additionally, one new miRNA-like molecule with a potential role in cancer was identified in the cell lines and clinical samples.

This submission represents the gene expression component of the study only

overall_design: Microarray analysis was performed using Agilent Whole Human Genome Microarray 4×44K arrays and labeled using the One Color Quick Amp Labeling Kit (Agilent Technologies). A total of four samples were analyzed: two biological replicates of SCC25 and two biological replicates of normal keratinocytes. Hybridization and washing followed protocols described by the manufacturer (Agilent Technologies).  The one-color arrays were scanned by GenePix 4000B Scanner (Axon), and analyzed using the Agilent Feature extraction software (version 9.5). The quality control of the microarrays was assessed using the standard Agilent controls to verify that the arrays met the expected criteria.

first: Liliane

middle: S

last: Oliveira

first: Natalia

last: Torres

first: Flavia

last: Andreghetto

last: de Fatima Guarizo Klingbeil

first: Monica

last: Mathor

first: Alexandre

last: Paschoal

first: Alan

last: Durham

first: Raquel

last: Moyses

first: Victor

last: Wunsch-Filho

first: Fabio

last: Nunes


title: Monocyte-Derived Dendritic Cells Differ in Cytoskeleton and Cell Adhesion-Related Expression Depending on VEGF Exposure

status: Public on Dec 30 2011

summary:
The inadequate function of the antigen presenting cells, such as dendritic cells (DCs) in cancer is one of the major factors leading to compromised anti-tumor immune response. Cell-to-cell interactions and cell migration are essential features of the immunological response in cancer. Vascular endothelial growth factor (VEGF) has been shown to affect DCs differentiation and maturation processes, thus leading to impaired DCs function. This study aimed to compare the expression of adherence and cytoskeleton-related genes between mature monocyte-derived dendritic cells (mDCs) and mDCs previously exposed to VEGF (mDCVs). VEGF is known to stimulate cell migration and actin rearrangement, but its association with adhesion molecules has not been largely explored in the context of DCs. Our results show that immature human DCs exposed to VEGF up-regulated CD80 and CD86, typical cell surface markers of DC maturation. However, unlike mDCs, mDCVs showed alterations in cell morphology, with broad changes in the characteristic cytoplasmic processes. DNA microarray analysis revealed that mDCVs up-regulated a significant subset of genes related to cell migration, including cell adhesion molecules and related signaling pathways as well as cytoskeleton-related genes. Our results suggest that VEGF, known to be involved in the inhibition of DC maturation, interferes in cell mechanisms leading to cytoskeleton reorganization and the expression of cell adhesion molecules. Cell morphology is associated with DC maturation and migration, both impaired in pathological conditions such as cancer.

Keywords: Gene expression profiling

overall_design: Gene expression profiling was carried out in freshly isolated CD14+ cells prior to cultivation (“D0” samples) and in DCs after 6 days (“D6” samples) and 7 days in culture, with or without VEGF treatment (“D7V” and “D7” samples, respectively). Blood samples were collected on the same day and processed concomitantly. Cell culture, RNA extraction, and microarray hybridization were also carried out simultaneously in an attempt to minimize technical inconsistencies. A total of 14 independent microarray hybridizations were carried out with oligonucleotide microarrays, covering approximately 55,000 human transcripts (Whole Genome CodeLink™ Bioarrays, GE Healthcare). Target preparation and hybridization procedures strictly followed protocols provided by the manufacturer.Arrays were scanned following the recommended scanning procedure and settings for use with CodeLink bioarrays (GE Healthcare) on GenePix 4000B Array Scanner/GenePix Pro 4.1 software (Axon Instruments).


title: Genetic Heterogeneity in Mouse Mammary Tumors

status: Public on Aug 28 2009

city: East Lansing

first: Eran

last: Andrechek

state: MI

address: 2120 BPS Building

department: Physiology

institute: Michigan State University

summary:
Human cancers result from a complex series of genetic alterations resulting in heterogeneous disease states. Dissecting this heterogeneity is critical for understanding underlying mechanisms and providing opportunities for therapeutics matching the complexity. Mouse models of cancer have generally been employed to reduce this complexity and focus on the role of single genes. Nevertheless, our analysis of tumors arising in the MMTV-Myc model of mammary carcinogenesis reveals substantial heterogeneity, seen in both histological and expression phenotypes. One contribution to this heterogeneity is the substantial frequency of activating Ras mutations, the frequency of which can be changed by alterations in Myc. Additionally, we show that these Myc-induced mammary tumors exhibit even greater heterogeneity, revealed by distinct histological subtypes as well as distinct patterns of gene expression, than many other mouse models of tumorigenesis. Two of the major histological subtypes are characterized by differential patterns of cellular signaling pathways, including B-Catenin and Stat3 activities.  We also demonstrate the predictive nature of this approach though examining metastatic potential. Together, these data reveal that a combination of histological and genomic analyses can uncover substantial heterogeneity in mammary tumor formation and therefore highlight aspects of tumor phenotype not evident in the population as a whole.

Keywords: Transcription factor expression analysis

overall_design: 20 MMTV-Neu Tumors, 25 Papillary MMTV-Myc T58A and 81 MMTV-Myc tumors of various histological subtypes were arrayed.

first: Robert

last: Cardiff

first: Chaitanya

last: Acharya

first: Anil

last: Potti

first: Joseph

last: Nevins


title: Gene expression profiling of oral squamous cell carcinoma

status: Public on Nov 24 2008

summary:
Abstract
BACKGROUND:
Oral squamous cell carcinoma (OSCC) is a frequent neoplasm, which is usually aggressive and has unpredictable biological behavior and unfavorable prognosis. The comprehension of the molecular basis of this variability should lead to the development of targeted therapies as well as to improvements in specificity and sensitivity of diagnosis.
RESULTS:
Samples of primary OSCCs and their corresponding surgical margins were obtained from male patients during surgery and their gene expression profiles were screened using whole-genome microarray technology. Hierarchical clustering and Principal Components Analysis were used for data visualization and One-way Analysis of Variance was used to identify differentially expressed genes. Samples clustered mostly according to disease subsite, suggesting molecular heterogeneity within tumor stages. In order to corroborate our results, two publicly available datasets of microarray experiments were assessed. We found significant molecular differences between OSCC anatomic subsites concerning groups of genes presently or potentially important for drug development, including mRNA processing, cytoskeleton organization and biogenesis, metabolic process, cell cycle and apoptosis.
CONCLUSION:
Our results corroborate literature data on molecular heterogeneity of OSCCs. Differences between disease subsites and among samples belonging to the same TNM class highlight the importance of gene expression-based classification and challenge the development of targeted therapies.

overall_design: Nine tumor samples differing in their TNM classification and their respective surgical margins were used in this study. They were obtained from individual patients during tongue and floor of the mouth tumor resection surgery. Microarray experiments were carried out using the microarray platform CodeLink (GE Healthcare). This platform utilizes bioarrays consisting of 30-base, single pre-validated oligonucleotide probe per gene target. CodeLink Whole-Genome  bioarrays, containing 55,000 human transcripts, were used for all experiments. Hybridization procedures strictly followed protocols provided by the manufacturer (GE Healthcare). A total of 11 arrays were hybridized in this study. Arrays were scanned following the recommended scanning procedure and settings for use with CodeLink bioarrays (GE Healthcare) on GenePix 4000B Array Scanner/GenePix Pro 4.0 software (Axon Instruments).


title: Gene expression data from myocardial infarction porcine samples

status: Public on Mar 01 2013

first: Júlia

last: Perera-Bel

summary: The use of cDNA microarrays has made it possible to analyze expression of thousands of genes simultaneously. We employed microarray gene expression profiling of porcine cDNA to compare myocardial gene expression in infarct core and remote myocardium at 1 week (n=3), 4 weeks (n=3), and 6 weeks (n=3) after surgically induced myocardial infarction (MI) and in sham-operated controls (n=3). More than 8,000 cDNA sequences were identified in myocardium that showed differential expression in response to MI. Different temporal and spatial patterns of gene expression were recognized in the infarct core tissue within this large set of data. Microarray gene profiling revealed candidate genes, some of them described for the first time, which elucidate changes in biological processes at different stages after MI.

overall_design: We evaluated temporal gene expression in a porcine model of myocardial infarction by microarray technology. Nine female pigs (Sus scrofa crossbreed Landrace x Large White) weighing 30-40 kg were subjected to experimental MI by a double-ligation of the first marginal branch of the circumflex artery. Animals were randomly sacrificed at 1 week (n=3), 4 weeks (n=3), or 6 weeks (n=3) after MI. Three paired myocardial samples from the infarct core and remote myocardium were analyzed at each time point. Myocardial samples from sham-operated animals (open-chest cardiac exposure without coronary artery ligation; n=3) were included as physiological controls.

first: Gálvez-Montón

last: Carolina

first: Prat-Vidal

last: Cristina


title: Identification of Dynamically Regulated MicroRNA and mRNA Networks in Oligodendrocytes

status: Public on Jun 01 2008

city: Bethesda

first: Joe

middle: A

last: Nielsen

state: MD

address: 49 Convent Drive BD49,5A75

institute: NIH/NINDS

summary:
MicroRNAs (miRNAs) play important roles in modulating gene expression at the post-transcriptional level. In postnatal oligodendrocytes, the miRNA expression profile -“microRNAome” - consists of 98 miRNAs whose expression dynamically changes during the transition from A2B5+ oligodendrocyte progenitor cells to premyelinating GalC+ cells. The combination of microRNAome profiling with analyses of the oligodendrocyte transcriptome reveals a target bias for a class of miRNAs which includes miR-9. We show that miR-9 is down-regulated during oligodendrocyte differentiation. In addition, miR-9 expression levels inversely correlate with the expression of its predicted targets, among which is the peripheral myelin protein, PMP22. PMP22 mRNA but not protein is detectable in oligodendrocytes, while Schwann cells producing PMP22 protein lack miR-9. We demonstrate that miR-9 interacts with the 3’ untranslated region of PMP22 and down-regulates its expression. Our results support models in which miRNAs can act as guardians of the transcriptome.
Keywords: developmental stage

overall_design: Flow cytometry was used to isolate single A2B5+ and single GalC+ oligodedrocytes from postnatal day 7 rat whole brain.  4 biological replicates were obtained for each group using a pooled litter of 10 pups per biological replicate

first: Pierre

last: lau

first: Jonathan

last: Verrier

first: Lucia

last: Notterpek

first: Lynn

last: Hudson


title: Insights on PRAME and osteosarcoma by means of gene expression profiling

status: Public on May 31 2009

first: Patricia

last: Severino

summary:
Abstract
BACKGROUND:
Osteosarcoma (OS) is the most frequent bone tumor in children and adolescents. Tumor antigens are encoded by genes that are expressed in many types of solid tumors but are silent in normal tissues, with the exception of placenta and male germ-line cells. It has been proposed that antigen tumors are potential tumor markers.
OBJECTIVES:
The premise of this study is that the identification of novel OS-associated transcripts will lead to a better understanding of the events involved in OS pathogenesis and biology.
METHODS:
We analyzed the expression of a panel of seven tumor antigens in OS samples to identify possible tumor markers. After selecting the tumor antigen expressed in most samples of the panel, gene expression profiling was used to identify osteosarcoma-associated molecular alterations. A microarray was employed because of its ability to accurately produce comprehensive expression profiles.
RESULTS:
PRAME was identified as the tumor antigen expressed in most OS samples; it was detected in 68% of the cases. Microarray results showed differences in expression for genes functioning in cell signaling and adhesion as well as extracellular matrix-related genes, implying that such tumors could indeed differ in regard to distinct patterns of tumorigenesis.
CONCLUSIONS:
The hypothesis inferred in this study was gathered mostly from available data concerning other kinds of tumors. There is circumstantial evidence that PRAME expression might be related to distinct patterns of tumorigenesis. Further investigation is needed to validate the differential expression of genes belonging to tumorigenesis-related pathways in PRAME-positive and PRAME-negative tumors.

overall_design: Six tumor samples representing distinct histological classes of osteosarcoma (telangiectatic, giant cell, anaplastic, osteoblastic and chondroblastic) were included in this study. They were obtained from individual patients ranging from 5 to 29 years old. Microarray experiments were carried out using the microarray platform CodeLink (GE Healthcare). This platform utilizes bioarrays consisting of 30-base, single pre-validated oligonucleotide probe per gene target. CodeLink UniSet Human I bioarrays, containing 10,000 human transcripts, were used for all experiments. Hybridization procedures strictly followed protocols provided by the manufacturer (GE Healthcare). A total of 12 arrays were hybridized, including 6 tumor samples (3 PRAME-positive and 3 PRAME-negative) and their respective technical replicates. Arrays were scanned following the recommended scanning procedure and settings for use with CodeLink bioarrays (GE Healthcare) on GenePix 4000B Array Scanner/GenePix Pro 4.0 software (Axon Instruments).


title: Effect of the silencing of WT1 expression on HCC transcriptome

status: Public on Oct 03 2008

city: Pamplona

first: Carmen

last: Berasain

state: Navarra

address: Avda. Pio XII 55

institute: CIMA

summary:
The Wilms´ tumor 1 gene (WT1) encodes a transcription factor involved in cell growth and development. As we previously reported WT1 expression is hardly detectable in normal hepatic tissue but is induced in liver cirrhosis. Although WT1 has been found to be overexpressed in a number of malignancies, the role of WT1 in hepatocarcinogenesis has not been clarified. We found that WT1 is expressed in several human hepatocellular carcinoma (HCC) cell lines including PLC/PRF/5 and HepG2, and in HCC tumor tissue in 42% of patients. WT1 small interfering RNAs did not affect proliferation rate of HCC cells but abrogated their resistance to anoikis. Transcriptome analysis of PLC/PRF/5 cells after WT1 knockdown demonstrated upregulation of 251 genes and downregulation of 321. Ninety per cent of the former corresponded to metabolic genes mostly those characterizing the mature hepatocyte phenotype. On the contrary, genes that decreased upon WT1 inhibition were mainly related to defense against apoptosis, cell cycle and tumor progression. In agreement with these findings WT1 expression increased the resistance of liver tumor cells to doxorubicin, a compound used to treat HCC. Interestingly, doxorubicin strongly enhanced WT1 expression in both HCC cells and normal human hepatocytes. Among different chemotherapeutics, induction of WT1 transcription was restricted to topoisomerase 2 inhibitors. When WT1 expression was prohibited doxorubicin caused a marked increase in caspase-3 activation. In conclusion, WT1 is expressed in a substantial proportion of HCC contributing to tumor progression and resistance to chemotherapy, suggesting that WT1 may be an important target for HCC treatment.

Keywords: Cell type comparison

overall_design: PLC/PRF/5 were transfected in triplicate with WT1 specific siRNAs (siWT) and siRNAs control (siGL)

first: Maria

last: Perugorria

first: Josefa

last: Castillo

first: Ujue

last: Latasa

first: Saioa

last: Goñi

last: Segura

first: Bruno

last: Sangro

first: Jesús

last: Prieto

first: Matías

last: Avila


title: Gene Expression Profiling of Primary Rat Oligodendrocytes

status: Public on Sep 30 2006

summary:
Oligodendrocytes undergo extensive changes as they differentiate from progenitors into myelinating cells. To better understand the
molecular mechanisms underlying this transformation, we performed a comparative analysis using gene expression profiling of A2B5+
oligodendrocyte progenitors and O4+ oligodendrocytes. Cells were sort-purified ex vivo from postnatal rat brain using flow cytometry.
Using Affymetrix microarrays, 1707 transcripts were identified with a more than twofold increase in expression inO4+oligodendrocytes.
Many genes required for oligodendrocyte differentiation were upregulated in O4+ oligodendrocytes, including numerous genes encoding
myelin proteins. Transcriptional changes included genes required for cell adhesion, actin cytoskeleton regulation, and fatty acid and
cholesterol biosynthesis. At the O4+ stage, there was an increase in expression of a novel proline-rich transmembrane protein (Prmp).
Localized to the plasma membrane, Prmp displays adhesive properties that may be important for linking the extracellular matrix to the
actin cytoskeleton. Together, our results highlight the usefulness of this discovery-driven experimental strategy to identify genes relevant
to oligodendrocyte differentiation and myelination.
Keywords: develepmental stage, oligodendrocyte differentiation

overall_design: Whole brain dissociates were prepared from one litter of 10 male postnatal day 7 rat pups for each of the 5 A2B5 bioligcal replicates and the 4 O4+ bioligical replicates.  Total RNA was extracted from single A2B5+ and single O4+ cells sorted directly from postnatal day7 rat whole brain dissociates using flow cytometry.

first: Joseph

first: Dragan

last: Maric

last: Lau

first: Jeffery

last: Barker


title: Gene expression profiling in the heart following exposure of rats to heat acclimation, its loss and re-induction.

status: Public on Dec 31 2007

city: Jerusalem

first: Michal

last: Horowitz

country: Israel

institute: The hebrew University

summary:
To understand faster reinduction of heat acclimation,  in this investigation we studied global stress associated genomic response during acclimation, following its loss and re-induction. Nylon cDNA Atlas Array was used.  Collectively, the study comprised nine experimental groups of which six characterized experimental basal conditions: Controls-untreated, Short and Long term heat acclimated groups ( exposure to environmental heat at 34oC for 2 or 30 days respectively), Deacclimated group (24oC for 1mo) and Reacclimated groups (2d at 34oC following the deacclimation protocol). Three additional experimental groups: Controls, Short and Long term and Reacclimated rats (as above) were tested for genomic responses following subjection to heat stress at 41oC. Because of a dichotomy between genomic and physiological responses we hypothesize thst rapid reacclimation is linked to reprograming of gene expression.
Keywords: heart, Left ventricle

overall_design:
Overall design: 27 samples, 9 treatments, 3 pooled samples for each:
1) Control untreated rats
2) Control, heat stressed rats
3) Short term heat acclimated rats
4) Short term, heat stressed-heat acclimated rats
5) Long-term heat acclimated rats
6) Long-term, heat stressed-heat acclimated rats
7) One mo deacclimated rats
8) Rats exposed to long-term heat acclimation, deacclimation and reacclimation for two days
9) Rats exposed to heat stress following long-term heat acclimation, deacclimation and reacclimation for two days

Series data table appended below represents the normalized log2 ratio of geomeans defined as treatment divided by control.

first: Anna

last: Tetievsky

first: Omer

last: Cohen

first: Luba

last: Eli-Berchoer

first: Gary

last: Gerstenblith

first: Michael

last: Stern

last: Horowit


title: Her2/Neu tumorigenesis and metastasis is regulated by E2F transcription factors

status: Public on Dec 29 2014

first: Eran

last: Andrechek

summary: HER2 / Neu is amplified and overexpressed in a large proportion of human breast cancers, but the signaling pathways that contribute to tumor development and metastatic progression are not completely understood.  Using gene expression data and pathway signatures we predicted a role for activator E2F transcription factors in Neu induced tumors.  This was genetically tested by interbreeding Neu transgenics with knockouts of the three activator E2Fs.  Loss of any E2F delayed Neu induced tumor onset. E2F1 loss accelerated tumor growth while E2F2 and E2F3 loss did not.  Strikingly, it was observed that loss of E2F1 or E2F2 significantly reduced the metastatic capacity of the tumor and this was associated with a reduction in circulating tumor cells in the E2F2 knockout.  Gene expression analysis between the tumors in the various E2F mutant backgrounds revealed that there was extensive compensation by other E2F family members in the individual knockouts, underscoring the importance of the E2Fs in HER2 / Neu induced tumors.  Extension to HER2 positive human breast cancer revealed a number of HER2+ subtypes based on E2F activity with differences in relapse free survival times.  Taken together these data demonstrate that the E2F transcription factors are integral to HER2+ tumor development and progression.

overall_design: MMTV-Neu tumors in a wild type E2F background and E2F1 knockout, E2F2 knockout and E2F3 +/- backgrounds were analyzed for their gene expression changes.