title: Integrated miRNA and gene expression analysis of prostate cancer associated fibroblasts supports a prominent role for interleukin-6 in fibroblast activation [gene]

city: Milan

first: Maurizio

last: Callari

address: Via Amadeo, 42

institute: Fondazione IRCCS Istituto Nazionale dei Tumori

summary: Tumor microenvironment coevolves with and simultaneously sustains cancer progression. Reactive fibroblasts found in prostate cancer (PCa), known as cancer associated fibroblasts (CAF), have been indeed shown to fuel tumor development and metastasis by mutually interacting with PCa cells. Little is known about the molecular mechanisms that lead to activation of CAFs from tissue-resident fibroblasts, circulating marrow-derived fibroblast progenitors or mesenchymal stem cells. Through integrated gene and microRNA expression profiling, here we showed that transcriptome of CAFs isolated from prostate tumors strictly resembles that of normal fibroblasts stimulated in vitro with interleukin-6 (IL6), thus confirming the capability of the cytokine to promote acquisition of an activated and cancer-promoting phenotype, and, for the first time, proving that IL6 is able per se to induce all the complex transcriptional changes characteristic of patient-derived CAFs. Comparison with publicly available datasets, however, suggested that prostate CAFs may be alternatively characterized by IL6 and TGFβ-related signatures, indicating that either signal, depending on the context, tumor stage and etiology, may concur to fibroblast activation. Our analyses also highlighted pathways relevant for induction of reactive stroma, including genes the role of which in fibroblast activation is still to be explored. In addition, we revealed a role for muscle-specific miR-133b as a soluble factor secreted by activated fibroblasts to support paracrine activation of non-activated fibroblasts or promote tumor progression.  Overall, in this study we provided insights on the molecular mechanisms driving fibroblast activation in prostate cancer, thus contributing to identify novel hits for the development of therapeutic strategies targeting the crucial interplay between tumor cells and their microenvironment.  Tumor microenvironment coevolves with and simultaneously sustains cancer progression. Reactive fibroblasts found in prostate cancer (PCa), known as cancer associated fibroblasts (CAF), have been indeed shown to fuel tumor development and metastasis by mutually interacting with PCa cells. Little is known about the molecular mechanisms that lead to activation of CAFs from tissue-resident fibroblasts, circulating marrow-derived fibroblast progenitors or mesenchymal stem cells. Through integrated gene and microRNA expression profiling, here we showed that transcriptome of CAFs isolated from prostate tumors strictly resembles that of normal fibroblasts stimulated in vitro with interleukin-6 (IL6), thus confirming the capability of the cytokine to promote acquisition of an activated and cancer-promoting phenotype, and, for the first time, proving that IL6 is able per se to induce all the complex transcriptional changes characteristic of patient-derived CAFs. Comparison with publicly available datasets, however, suggested that prostate CAFs may be alternatively characterized by IL6 and TGFβ-related signatures, indicating that either signal, depending on the context, tumor stage and etiology, may concur to fibroblast activation. Our analyses also highlighted pathways relevant for induction of reactive stroma, including genes the role of which in fibroblast activation is still to be explored. In addition, we revealed a role for muscle-specific miR-133b as a soluble factor secreted by activated fibroblasts to support paracrine activation of non-activated fibroblasts or promote tumor progression.  Overall, in this study we provided insights on the molecular mechanisms driving fibroblast activation in prostate cancer, thus contributing to identify novel hits for the development of therapeutic strategies targeting the crucial interplay between tumor cells and their microenvironment.  Tumor microenvironment coevolves with and simultaneously sustains cancer progression. Reactive fibroblasts found in prostate cancer (PCa), known as cancer associated fibroblasts (CAF), have been indeed shown to fuel tumor development and metastasis by mutually interacting with PCa cells. Little is known about the molecular mechanisms that lead to activation of CAFs from tissue-resident fibroblasts, circulating marrow-derived fibroblast progenitors or mesenchymal stem cells. Through integrated gene and microRNA expression profiling, here we showed that transcriptome of CAFs isolated from prostate tumors strictly resembles that of normal fibroblasts stimulated in vitro with interleukin-6 (IL6), thus confirming the capability of the cytokine to promote acquisition of an activated and cancer-promoting phenotype, and, for the first time, proving that IL6 is able per se to induce all the complex transcriptional changes characteristic of patient-derived CAFs. Comparison with publicly available datasets, however, suggested that prostate CAFs may be alternatively characterized by IL6 and TGFβ-related signatures, indicating that either signal, depending on the context, tumor stage and etiology, may concur to fibroblast activation. Our analyses also highlighted pathways relevant for induction of reactive stroma, including genes the role of which in fibroblast activation is still to be explored. In addition, we revealed a role for muscle-specific miR-133b as a soluble factor secreted by activated fibroblasts to support paracrine activation of non-activated fibroblasts or promote tumor progression.  Overall, in this study we provided insights on the molecular mechanisms driving fibroblast activation in prostate cancer, thus contributing to identify novel hits for the development of therapeutic strategies targeting the crucial interplay between tumor cells and their microenvironment.

overall_design: In the present study, patient derived-CAFs and HPFs activated in vitro with either TGFβ or IL6 were comparatively analyzed for gene and microRNA (miRNA) expression profiles, with the aim to define transcriptional pathways responsible for fibroblast activation and establish whether different subpopulations of CAFs may exist in PCa.

first: Valentina

last: Doldi

first: Elisa

last: Giannoni

first: Francesca

last: D'Aiuto

first: Massimo

last: Maffezzini

first: Riccardo

last: Valdagni

first: Paola

last: Chiarugi

first: Paolo

last: Gandellini

first: Nadia

last: Zaffaroni


title: Effects of Active or Inactive PARP9/DTX3L Overexpression on ISG Expression

status: Public on Sep 01 2015

city: St. Louis

first: Anand

middle: Champak

last: Patel

state: MO

address: Campus Box 8116, 660 S. Euclid Ave.

department: Pulmonary/Critical Care Medicine

country: USA

institute: Washington University School of Medicine

summary:
U3A cells expressing Stat1 were transfected with either wild-type PARP9 and DTX3L, or inactive mutants of PARP9 and DTX3L. Stable lines were assessed for gene expression to identify effects of PARP9/DTX3L overexpression on ISG expression.
Keywords: interferon, PARP9, DTX3L, antiviral

overall_design: RNA was isolated from stable U3A-STAT1 lines overexpressing either wild-type or inactive mutants of PARP9 and DTX3L.

first: Yong

last: Zhang

middle: C

first: Dailing

last: Mao

first: Dhara

middle: A

first: William

middle: T

last: Roswit

first: Guangming

last: Huang

first: Ronald

last: McCarthy

first: Xiaohua

last: Jin

first: Jeffery

middle: J

last: Atkinson

first: Eugene

last: Agapov

first: Jinsheng

last: Yu

first: Nadezhda

middle: E

last: Yun

first: Slobodan

last: Paessler

first: T

middle: G

last: Lawson

first: Natalie

middle: S

last: Omattage

first: Tom

last: Brett

first: Michael

last: Holtzman


title: Modified Stat1 Confers Enhanced Interferon Responsiveness and Improved Baseline Antiviral Host Defense

first: Anand

summary:
U3A cells stably expressing wild-type STAT1 or STAT1-CC were treated with interferon beta (10U/ml) or control for 24 hours to assess effects of stat1 modifications, interferon, and the interaction on gene expression.
Keywords: interferon, STAT1, STAT1-CC, STAT1CC, STAT-1C, antiviral

overall_design: RNA was isolated from stable U3A-STAT1 lines stably expressing wild-type STAT1 or STAT1CC, after 24 hour treatment with interferon beta (10U/ml) or control.


title: PARP9 and DTX3L in Antiviral Host Defense

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: A protein network of common susceptibility genes provides a link in the genetic architecture of chronic inflammation and cardiovascular disease

city: Münster

first: Mona

last: Riemenschneider

address: Domagkstraße 3

country: Germany

institute: Genetic Epidemiology, University of Muenster

summary: Genome-wide association studies (GWAS) have identified hundreds of susceptibility loci for chronic and inflammatory disease phenotypes in humans. There is increasing evidence that chronic inflammation is a crucial driver in the pathogenesis of cardiovascular diseases (CVD), which may be genetically determined. To understand the genetic architecture underlying chronic inflammation and CVD we performed a systematic analysis of (1) common risk alleles coming from published GWAS, (2) of protein-protein interaction (PPI) networks informed by (3) gene expression data with a defined molecular target involved in the inflammatory processes promoting CVD, MRP8. (4) through analysis of integrated haplotype scores (iHS) and FST values in HapMap phase 2 data, we investigated whether recent selection pressure acting upon inflammatory genes affected CVD susceptibility loci. Our findings provide significant evidence for a PPI network, which connects inflammatory and cardiovascular susceptibility genes, and establish a genetic framework of inflammatory CVD. 41.59% of PPI genes are associated with immune functions. 28.3% of integrated genes can be linked to both, an inflammatory and cardiovascular disease phenotype.  Interestingly, CDKN2B, and CELSR2/PSRC1/MYBPHL/SORT1, unequivocally replicated CVD loci, are integrated within this network as are several SNPs located in transcription factor recognition sequences, i.e. NFKB1, STAT3, which are key factors in inflammation. Finally, we observed a significant enrichment of inflammatory variants within CVD cluster loci that are targets of selection. Overall, 32 genes exhibit traces of selection, 16 of which are part of the PPI, further suggesting that recent selective sweeps may have affected the genomic architecture underlying CVD.

overall_design: 6 samples, no replicates.


title: Integrated miRNA and gene expression analysis of prostate cancer associated fibroblasts supports a prominent role for interleukin-6 in fibroblast activation

first: Maurizio

last: Callari

country: Italy

type:
Expression profiling by array
Other


title: Genome-wide transcription profiling of 22q11.2 deletion syndrome reveals functional pathways related to phenotypic expression of psychosis and autism spectrum disorder

city: Los Angeles

first: Giovanni

last: Coppola

state: CA

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

summary: 22q11.2 Deletion Syndrome (22q11DS) represents one of the most common known genetic risk factors for the development of psychotic illness, and is also associated with high rates of autistic spectrum disorders (ASD) in childhood.  We performed integrated genomic analyses of 22q11DS to identify genes and pathways related to specific phenotypes.  Eighty percent of 22q11DS individuals (n=37) carried the typical 3 Mb deletion, with significant variability in the deletion characteristics in the remainder of the sample (n=9). Both analysis of differential expression and weighted gene coexpression network analysis (WGCNA) identified peripheral changes in gene expression related to psychotic symptom expression in patients, including a module of co-expressed genes which was associated with psychosis in 22q11DS and involved in pathways associated with transcriptional regulation.  Remarkably, this 22q11DS psychosis module was significantly enriched for brain-expressed genes, was not related to antipsychotic medication use, and showed significant overlap with transcriptional changes occurring in idiopathic schizophrenia in an independent dataset.  In those with 22q11DS-ASD, both differential expression and WGCNA analyses pointed towards dysregulation of immune response pathways.  The ASD-associated module showed overlap with a neuronal module enriched for known autism susceptibility genes identified in brain transcriptome data from individuals with idiopathic autism. These findings further support the use of peripheral tissue in the study of major mutational models of diseases affecting the brain, and point towards specific pathways dysregulated in 22q11DS carriers with psychosis and ASD, warranting their further investigation in idiopathic illness.

overall_design: Participants. Forty-six patients with a molecularly confirmed diagnosis of a 22q11.2 deletion and 66 controls (24 unrelated controls and 42 first-degree relatives of 22q11DS patients) were recruited from an ongoing longitudinal study.  Comparative Genomic Hybridization Arrays.  To characterize the boundaries of the 22q11.2 deletion, we designed a custom NimbleGen 12*135 HX12 array. Microarray-based gene expression analysis. Whole-genome transcriptional profiling was performed using Illumina Human HT-12 microarrays.Gene ontology annotation was performed using DAVID (http://david.abcc.ncifcrf.gov/) and pathway analysis was performed by using the Functional Analysis Annotation tool in the Ingenuity Pathways Analysis (IPA) software (Ingenuity Systems, www.ingenuity.com). Because the healthy control group included parents of 22q11DS patients, there were significant age differences between groups (Table 1, p<.001); thus, we corrected for age in all analyses.Weighted Gene Co-expression Network Analysis (WGCNA). We conducted WGCNA, a systems biology approach used to identify networks of co-expressed genes in relation to phenotypic data, using the R package.   Phenotypic traits examined within the 22q11DS group included: categorical and dimensional indicators of psychosis (i.e. psychosis diagnosis and SIPS psychotic symptom severity score), ASD, and gender. For modules that showed a statistically significant relationship with any phenotypic trait (p<.05), GO analyses and IPA were conducted. Validation with published datasets.  In order to validate our gene expression and WGCNA results, we overlapped gene lists obtained from microarray differential expression analysis for 22q11DS vs. Controls,

first: Maria

last: Jalbrzikowski

last: Lazaro

first: Fuying

last: Gao

first: Alden

first: Carolyn

last: Chow

first: Daniel

middle: H

last: Geschwind

first: Carrie

last: Bearden


title: Cohesin recruits the Esco1 acetyltransferase genomewide to repress transcription and promote cohesion in somatic cells

status: Public on Aug 25 2015

city: New York

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

summary: The cohesin complex links DNA molecules and plays key roles in the organization, expression, repair, and segregation of eukaryotic genomes. In vertebrates the Esco1 and Esco2 acetyltransferases both modify cohesin’s Smc3 subunit to establish sister chromatid cohesion during S phase, but differ in their N-terminal domains and expression during development and across the cell cycle. Here we show that Esco1 and Esco2 also differ dramatically in their interaction with chromatin, as Esco1 is recruited by cohesin to over 11,000 sites, whereas Esco2 is infrequently enriched at REST/NRSF target genes. Esco1’s colocalization with cohesin occurs throughout the cell cycle and depends on two short motifs (the A-box and B-box) present in and unique to all Esco1 orthologs. Deleting either motif led to the derepression of Esco1-proximal genes and functional uncoupling of cohesion from Smc3 acetylation. In contrast, other mutations that preserved Esco1’s recruitment separated its roles in cohesion establishment and gene silencing. We conclude that Esco1 uses cohesin as both a substrate and a scaffold for coordinating multiple chromatin-based transactions in somatic cells.

overall_design: Total RNA was isolated after treatment with indicated siRNAs, or transfection reagent only for control samples. Samples for each group in triplicate were processed for Illumina bead arrays (Illumina HT-12) by the MSKCC genomics core facility according to manufacturer instructions.

first: Sadia

last: Rahman

first: Prasad

middle: V

last: Jallepalli


title: Differences in the transcriptomic response of human adult, neonatal, and older adult monocytes to Listeria monocytogenes infection

city: Vancouver

first: Kathleen

last: Wee

state: BC

address: 938 W 28th Ave.

country: Canada

institute: University of British Columbia

summary: Listeria monocytogenes (Lm) kills up to 60% of infected newborns and adults >60 years of age but is asymptomic is most young adults. Monocytes are central to effective host defense against Lm. We hypothesize that age-dependent, pathway-specific differences in the ability of the monocyte to respond to Lm explain the increased risk of the newborn and older adult to severely suffer or die from Lm infection. To delineate age-dependent differences in innate responses that lead to differential infectious outcome, monocytes were isolated from cord blood (newborn) and peripheral blood (young and older adults) and infected with Lm. RNA was collected to determine age-dependent transcriptomic changes upon infection.

overall_design: Total RNA was isolated from purified human monocytes from 6 adult, 6 cord , 6 older adult blood donors that were infected with wild-type Listeria monocytogenes at a multiplicity of infected (MOI)=5 for 2 and 6 hr.


title: Characterisation of Two New Th17-Subsets with Distinct Contribution to HIV-1 Persistence under Antiretroviral Therapy

status: Public on Aug 31 2015

city: Montréal

first: Jean-Philippe

last: Goulet

state: Québec

address: C.P. 6128, succursale Centre-ville

institute: Université de Montréal

summary:
Th17 cells act as the first line of defense against pathogens at mucosal surfaces. Their paucity during HIV infection causes disease progression.
Here, we reveal the existence of two new CCR6+CD161+ subsets, CCR4-CXCR3- (DN; double negative) and CCR4+CXCR3+ (DP; double positive), expressing typical Th17 transcripts (e.g., RORγt, RORα, PTPN13, ARNTL), C. albicans specificity, and exhibiting Th17-lineage commitment versus flexibility.

overall_design: 4 cell populations from up to 6 donors for a total of 20 samples.

first: Vanessa

last: Wacleche

first: Annie

last: Gosselin

first: Patricia

last: Monteiro

first: Hugo

last: Soudeyns

first: Mohammad-Ali

last: Jenabian

first: Jean-Pierre

last: Routy

first: Petronela

last: Ancuta


title: Gene expression analysis of Neoechinulin B (NeoB)-treated Huh7.5.1 cells

city: Yokohama

first: Piero

last: Carninci

department: Center for Life Science Technologies

country: Japan

institute: RIKEN

summary: Huh-7.5.1 cells were treated with 0.2% DMSO, 20 microM NeoB for 24 h.  Treatment with 0.2% DMSO for 24h was prepared as non-treated Huh7.5.1 cells. Huh7.5.1 cells were kindly provided by Prof. Francis Chisari at The Scripps Research Institute.

overall_design: Total RNA obtained from NeoB-treated and un-treated Huh7.5.1 cells

first: Syo

last: Nakajima

first: Koichi

last: Watashi

first: Shinji

last: Kamisuki

first: Jesus

last: Izaguirre-Carbonell

first: Andrew

last: Kwon

first: Harukazu

last: Suzuki

first: Senko

last: Tsukuda

first: Maiko

last: Okada

first: Meng

middle: L

last: Moi

first: Ryosuke

first: Hideki

last: Aizaki

first: Takanobu

last: Kato

first: Tomohiko

last: Takasaki

first: Fumio

last: Sugawara

first: Takaji

last: Wakita


title: Microarray data for Rheumatoid arthritis synovial fibroblast (RASF) after C5orf30 and HDAC1 knockdown

status: Public on Aug 22 2015

city: Sheffield

first: Munitta

last: Muthana

address: Beech Hill Rd

country: United Kingdom

institute: University of Sheffield

summary:
The variant rs26232, in the first intron of the C5orf30 locus, has recently been associated with both risk of developing rheumatoid arthritis (RA) and severity of tissue damage. The biological activities of human C5orf30 are unknown, and neither the gene nor protein show significant homology to any other characterized human sequences. The C5orf30 gene is present only in vertebrate genomes with a high degree of conservation implying a central function in these organisms. Here we report that C5orf30 is highly expressed in the synovium of RA patients compared with control synovial tissue, and that it is predominately expressed by synovial fibroblast (RASF) and macrophages in the lining and sublining layer of the tissue. These cells play a central role in the initiation and perpetuation of RA and are implicated in cartilage destruction. RASFs lacking C5orf30 exhibit increased cell migration and invasion in vitro and gene-profiling following C5orf30 inhibition confirmed upregulation of genes involved in cell migration, adhesion, angiogenesis, and immune and inflammatory pathways. Importantly, loss of C5orf30 contributes to the pathology of inflammatory arthritis in vivo, since inhibition of C5orf30 in the collagen-induced arthritis model markedly accentuated joint inflammation and tissue damage.  Our study reveal C5orf30 to be a novel negative regulator of tissue damage in RA and this may act by modulating the autoaggressive phenotype that is characteristic of RASFs.
Rheumatoid arthritis (RA) is a chronic, autoimmune, inflammatory disease that affects synovial joints. A key characteristic of RA is hyperplasia of fibroblast-like synoviocytes (FLS) which develop a stable, auto-aggressive phenotype that augments tissue destruction. It is unknown how this phenotype is stably maintained; however, epigenetic changes have been implicated. Histone deacetylation is one proposed method; a process controlled by histone deacetylases (HDACs). However, there have recently been reports publishing conflicting data regarding the expression of HDACs in RA synovium and FLS. The objective of this thesis is to determine the role of HDACs in regulating the auto-aggressive phenotype of RA through studies in FLS and in mice.  Real time-quantitative PCR was used to assess the levels of HDAC1-11 in RA compared to osteoarthritis (OA) FLS. Immunohistochemistry and western blotting were used to assess protein expression of HDAC1 in RA and OA synovial tissue and FLS. HDAC1 was found to be overexpressed in RA compared to OA. HDAC1 was knocked down in RA FLS, then cell proliferation, migration and invasion were assessed by using tritiated thymidine, a scratch assay and a Matrigel invasion assay respectively. All three functions were significantly reduced following HDAC1 knockdown. An Illumina BeadChip (47,000 transcripts) was used to analyse global gene expression changes after knockdown. This revealed significant gene changes in important functional clusters, such as proliferation and migration. HDAC1 knockout is embryonic lethal in mice, so the in vivo role of HDAC1 was investigated in a mouse model of collagen-induced arthritis (CIA) using in vivo siRNAs. Clinical scores of CIA were measured daily and HDAC1 knockdown mice showed a significantly reduced clinical score compared to controls, comparable to dexamethasone-treated mice. The bones were analysed using a microCT scanner and histology. Knocking down HDAC1 showed reduced bone erosion, joint inflammation and cartilage degradation compared to controls.  Overall, this study shows that HDAC1 is dysregulated in RA and it has a significant role in the autoaggressive phenotype shown in RA FLS and collagen-induced arthritis. The novel data shown in this thesis demonstrates that inhibiting HDAC1 may provide a powerful new target for treating RA.

overall_design: Three independent patient RASF samples were analysed in this study for each siRNA gene knockdown. Also a non targerting control siRNA was also used for each of the patient RASFs

first: Sarah

last: Hawtree


title: Differential role of IL-23 and IL-17 in intestinal regulation

status: Public on Aug 20 2015

city: San Francisco

first: Antony

last: Symons

address: 1120 Veterans Boulevard

department: Inflammation TA

institute: Amgen Inc.

summary: Interleukin-23 (IL-23) and IL-17 are cytokines currently being targeted in clinical trials. Although inhibition of these cytokines is effective for treating psoriasis, IL-12/23 inhibition attenuates Crohn's disease, while IL-17A or IL-17RA inhibition exacerbates disease. This dichotomy between IL-23 and IL-17 was effectively modeled in the mdr1a- /- mouse model of colitis. IL-23 inhibition attenuated disease by decreasing colonic inflammation while enhancing Treg accumulation. Exacerbation of colitis by IL-17A or IL-17RA inhibition was associated with severe weakening of the intestinal epithelial barrier, culminating in increased colonic inflammation and accelerated mortality. These data show that IL-17A acts on intestinal epithelium to promote barrier function and provides insight into mechanisms underlying exacerbation of Crohn's disease when IL-17A or IL-17RA is inhibited.

overall_design: Mdr1a-deficient mice were infected with Helicobacter bilis to induce colitis and the role of different cytokines in disease compared by treatment with blocking antibodies. To that end, H. bilis-infected mice were treated with IL-23-, IL-23-/12- and IL-17RA-blocking antibodies and isotype control antibody and PBS control as well as an uninfected group in experiment 1. In a second experiment, H. bilis-infected mice were treated with IL-17A- and IL-17RA-blocking antibodies, isotype control antibody and PBS control as well as an uninfected group. Total RNA was extracted from the colon of each mouse and Affymetrix microarray profiles of each cytokine-blocking antibody group compared to control groups to understand the different effects of inhibiting IL-17A, IL-23, IL-23/12 and IL-17RA in this model of colitis. There were 3 to 5 mice in each antibody treatment group for a total of 42 samples across the 2 studies.

first: Joseph

middle: R

last: Maxwell

first: Jennifer

last: Towne


title: Dose-Responsive Gene Expression in Suberoylanilide Hydroxamic Acid (SAHA) Treated Resting CD4+ T Cells

status: Public on Aug 13 2015

city: La Jolla

first: Brian

last: Reardon

address: 9500 Gilman Drive

department: Medicine

institute: UCSD

summary: Design: Persistent latently infected CD4+ T cells represent a major obstacle to HIV eradication.  Histone deacetylase inhibitors (HDACis) are a promising activation therapy in a “shock and kill” strategy.  However, off-target effects of HDACis on host gene expression are poorly understood in primary cells of the immune system.  We hypothesized that HDACi-modulated genes would be best identified with a dose response analysis.  Methods: Resting primary CD4+ T cells were treated with increasing concentrations (0.34, 1, 3, or 10 μM) of the HDACi, suberoylanilide hydroxamic acid (SAHA), for 24 hours and then subjected to microarray gene expression analysis.  Genes with dose-correlated expression were identified with a likelihood ratio test using Isogene GX and a subset of these genes with a consistent trend of up or downregulation at each dose of SAHA were identified as dose-responsive.  Histone modifications were characterized in promoter regions of the top 6 SAHA dose-responsive genes by RT-qPCR analysis of immunopreciptated chromatin (ChIP).  Results: A large number of genes were shown to be up (N=657) or down (N=725) regulated by SAHA in a dose-responsive manner (FDR p-value < 0.05 and fold change ≥ |2|).  Several of these genes (CTNNAL1, DPEP2, H1F0, IRGM, PHF15, and SELL) are potential in vivo biomarkers of SAHA activity.  SAHA dose-responsive gene categories included transcription factors, HIV restriction factors, histone methyltransferases, and host proteins that interact with HIV proteins or the HIV LTR.  Pathway analysis suggested net downregulation of T cell activation with increasing SAHA dose.  Histone acetylation was not correlated with host expression, but plausible alternative mechanisms for SAHA-modulated expression were identified.   Conclusions: Numerous host genes in CD4+ T cells are modulated by SAHA in a dose-responsive manner, including genes that may negatively influence HIV activation from latency.  Our study suggests that SAHA influences gene expression through a confluence of several mechanisms, including histone acetylation, histone methylation, and altered expression and activity of transcription factors.

overall_design: Primary CD4+ T cells were isolated from human peripheral blood drawn from 6 healthy HIV-seronegative donors.  For each donor sample, CD4+ T cells were counted and aliquoted into 6-well plates; 5 million cells per well at a concentration of 2.5 million cells per mL of media (RPMI 1640 with 5% human serum AB).  Wells containing CD4+ T cells were treated with SAHA (Merck) at 0.34 μM, 1 μM, 3 μM, or 10 μM in 0.1% DMSO, or with only 0.1% DMSO (vehicle control).  Treated cells were incubated at 37°C, 5% CO2 for 24 hours.  Treated cells were then collected for microarray analysis of mRNA in SAHA treated cells versus DMSO treated cells.

first: Nadia

last: Beliakova-Bethell

first: Celsa

last: Spina

first: Akul

last: Singhania

first: Douglas

last: Richman

first: Christopher

last: Woelk


title: Reactivation of multipotency by oncogenic PIK3CA induces breast tumor heterogeneity

city: Bruxelles

first: Alexandra

last: Van Keymeulen

address: 808, route de Lennik CP602

department: IRIBHM

country: Belgium

institute: Université Libre de Bruxelles

summary: Breast cancer is the most frequent cancer in women and consists of heterogeneous types of tumours that are classified into different histological and molecular subtypes1-3. Pik3ca and p53 are the two most frequently mutated genes and are associated with different types of human breast cancers4. The cellular origin and the mechanisms leading to Pik3ca-induced tumour heterogeneity remain unknown. Here, we used a genetic approach in mice to define the cellular origin of Pik3ca-derived tumours and its impact on tumour heterogeneity. Surprisingly, oncogenic Pik3ca-H1047R expression at physiological levels5 in basal cells (BCs) using K5CREERT2 induced the formation of luminal ER+PR+ tumours, while its expression in luminal cells (LCs) using K8CREERT2 gave rise to luminal ER+PR+ tumours or basal-like ER-PR- tumours. Concomitant deletion of p53 and expression of Pik3ca-H1047R accelerated tumour development and induced more aggressive mammary tumours. Interestingly, expression of Pik3ca-H1047R in unipotent BCs gave rise to luminal-like cells, while its expression in unipotent LCs gave rise to basal-like cells before progressing into invasive tumours. Transcriptional profiling of cells that have undergone cell fate transition upon Pik3ca-H1047R expression in unipotent progenitors demonstrate a profound oncogene-induced reprogramming of these newly formed cells and identified gene signatures, characteristic of the different cell fate switches that occur upon Pik3ca-H1047R expression in BC and LCs, which correlated with the cell of origin, tumour type and different clinical outcomes. Altogether our study identifies the cellular origin of Pik3ca-induced tumours and reveals that oncogenic Pik3ca-H1047R activates a multipotent genetic program in normally lineage-restricted populations at the early stage of tumour initiation, setting the stage for future intratumoural heterogeneity. These results have important implications for our understanding of the mechanisms controlling tumour heterogeneity and the development of new strategies to block PIK3CA breast cancer initiation.

overall_design: Luminal and basal cells, or tumour cells,  from mice in which expression of PIK3CA-H1047R and YFP (and in some conditions loss of p53) was targeted in basal cells using K5CREERT2 or in luminal cells using K8CREERT2 were FACS isolated and RNA was extracted before being hybridized Affymetrix microarrays.

first: Cédric

last: Blanpain


title: Starvation and chemotherapy

status: Public on Aug 11 2015

city: Genova

first: Ulrich

last: Pfeffer

address: L. Benzi 10

institute: IRCCS AOU San Martino - IST

summary: Tumor chemoresistance is often associated to high aerobic glycolysis rates and reduced oxidative phosphorylation by cancer cells,  a phenomenon called the “Warburg effect”. Thus, a treatment reversing the Warburg effect could decrease tumor cell survival both in the presence or absence of chemotherapy. Short-term starvation (STS) could accomplish this task since it is accompanied by a glucose and amino acid decrease and fatty acid increase, which require respiration for energy production.   We tested the cytotoxicity of STS+Oxaliplatin on colon cancer cells by Trypan Blue,  Carboxyfluorescein Succinimidyl ester and  Annexin V staining. Reactive oxygen species production was measured by 2',7'-dichlorodihydrofluorescein diacetate staining. In vitro glucose consumption was evaluated by 18F-Fluoro-deoxyglucose uptake. Gene expression was tested by microarray analysis.  Protein expression and activity were studied by western blot, proteomic analyses and spectrophotometric assays. CT26 bearing mice consumed only water for 48 hours (STS) before oxaliplatin treatment. Dynamic micro-Positron Emission Tomography and tumor growth measurements were performed. STS+Oxaliplatin cause a potent suppression of colon carcinoma growth and glucose consumption in in vitro and in vivo models. In CT26 cells, STS down-regulates aerobic glycolysis, and glutaminolysis, while increasing oxidative phosphorylation.  STS-dependent increase in  O2 consumption is associated with reduced ATP synthesis and increased oxidation. In combination with chemotherapy, these effects of STS cause additive toxicity to cancer cells. Our findings indicate that during and following STS the decreased glucose levels promote an anti-Warburg effect characterized by increased oxygen consumption but failure to generate ATP, resulting in oxidative damage and apoptosis.

overall_design: The experiment comprised for conditions: Control, Starvation, Oxaliplatin, and Starvation plus Oxaliplatin


title: Temporal Response to seasonal and pandemic H1N1 infection in human DCs - Donor2

city: New Haven

first: Hailong

last: Meng

state: CT

address: 300 George Str

institute: Yale University

summary: An 8 hours timecourse was performed with human DCs infected either with A/California/7/2009 and A/Brevig Mission/1/1918 (pandemic) or A/New Caledonia/20/99  and A/Texas/36/91 seosonal.

overall_design: Human monocyte derived dendritic cells (DCs) were infected either with chicken egg grown  A/California/7/2009, A/Brevig Mission/1/1918, A/New Caledonia/20/99or A/Texas/36/91. Samples were taken and fixed in RNA stabilizing regaent at 2, 2.7, 3.3, 4, 5, 6, 7 and 8 hours. Cells exposed to chicken egg alantoic fluid served as a control. Infections with A/California/7/2009,  A/New Caledonia/20/99 or A/Texas/36/91 were carried out at a BSL2 enviroment. Infections with  A/Brevig Mission/1/1918 were carried out in a BSL3 enviroment in parralel to the BSL2 infections with cells from the same donor and cell preparation.

first: Boris

middle: M

last: Hartmann

first: Randy

last: Albrecht

first: Steven

last: Kleinstein


title: Temporal Response to seasonal and pandemic H1N1 infection in human DCs- Donor 1


title: Genome-wide analysis of colon cancer cell SW480_Control, _BOP1, _CKS2 and _NFIL3 treated with different inhibitors

status: Public on Aug 04 2015

city: Berlin

first: Jingjing

last: Qi

state: Outside the US or Canada

address: Robert-Roessle-str. 10

institute: Max-Delbrueck-Center for Molecular Medicine

summary: SW480 cells overexpressing BOP1, CKS2 or NFIL3 migrated more actively compared to Control cells. Migration induced by BOP1, CKS2 or NFIL3 was repressed by interfering with distinct signaling systems using small- molecular-weight inhibitors, i.e., interference with PI3K, JNK and Notch in the case of BOP1, with PI3K and p38 MAPK in the case of CKS2, as well as with PI3K, p38 and mTOR in the case of NFIL3. Gene expression profilings suggest that BOP1, CKS2 and NFIL3 overexpression are associated functionally with a series of migration-related genes, which can be repressed transcriptionally by specific pathway inhibitors.

overall_design: SW480 stable cells were grown in DMEM, 10% FCS, and treated for 24 hr with the following inhibitors or with solvent (DMSO): SW480_Control with DMSO; SW480_BOP1 with DMSO, LY294002 (3.3 uM), SP600125 (33.3 nM) and DAPT (667 nM); SW480_CKS2 with DMSO, LY294002 (3.3 uM) and SB203580 (3.3 uM); SW480_NFIL3 with DMSO, LY294002 (3.3 uM), SB203580 (3.3 uM) and Rapamycin (33.3 nM).

first: Walter

last: Birchmeier


title: Molecular changes induced in melanoma cells by stromal cells and anti-BRAF therapy.

status: Public on Aug 01 2015

city: Oslo

first: Lina

last: Prasmickaite

address: Ullernchausseen 70

department: Department of Tumor Biology

country: Norway

institute: Oslo University Hospital

summary: Tumor-associated stromal cells can enable cancer cells to become insensitive to therapy. They can promote aggressive phenotype in cancer cells, which become less responsive to drugs such as BRAF inhibitors (BRAFi) used to treat melanomas. To clarify potential mechanism behind stromal influence on melanoma, we analyzed gene expression in Melmet 5 melanoma cells grown as mono-cultures or co-cultures with lung fibroblasts with/without BRAFi. We have shown that Melmet 5 growing as co-cultures gained a de-differentiated, invasive transcriptional state, which is known to be linked to BRAFi-resistance. The transcriptional changes induced by BRAFi were much larger in Melmet 5 mono-cultures compared to co-cultures, indicating a much dampened transcriptional response to BRAFi in melanoma under the influence of fibroblasts. We conclude that interaction with the stromal cells stimulate melanoma cell transition to the invasive de-differentiated phenotype, leading to a worse response to BRAF inhibitors.

overall_design: Total RNA was isolated from Melmet 5 cell line growing as mono- or co-cultures with fibroblasts for 72 hours and treated with BRAFi for the last 24 hours.

first: Kotryna

last: Seip

first: Gunhild

last: Mælandsmo

first: Vigdis

last: Nygaard


title: Gene expression in subcutaneous and visceral fat predicts liver histology in morbidly obese patients

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

institute: VIB

summary: Nonalcoholic fatty liver disease (NAFLD) has become the most common cause of liver disease affecting 20-30% of the population in developed countries. NAFLD is strongly associated with abdominal obesity and is recognized as the hepatic manifestation of the metabolic syndrome. In a subgroup of patients with NAFLD inflammation and fibrosis develops, this so-called Non-Alcoholic Steatohepatitis (NASH) may progress to cirrhosis and hepatocellular carcinoma. A multi-hit hypothesis has been proposed in which during the first “hit” fat accumulation occurs in hepatocytes from excessive delivery of fatty acids from adipose tissue, in addition there is an imbalance in lipid synthesis and export. However, the reason why fat accumulation is subsequently followed by inflammation and fibrosis in some patients is poorly understood. We studied the role of inflammatory processes in visceral and subcutaneous fat at the transcriptional level using microarray in bariatric patients from whom the liver histology was available.

overall_design:
Patients scheduled for bariatric surgery were recruited in two centers (Pretoria/South-Africa and Antwerpen/Belgium). At the time of the procedure, tissue samples of the visceral and subcutaneous fat were taken for molecular analysis as well as liver tissue for histology, also full biochemical data was collected. Patients were grouped according histology: group I (<5% steatosis), group II (NAFLD, 30-50% steatosis), group III (NASH) and group IV (NASH + fibrosis F2-F3).
The following samples were used for microarray (number of 'patients' respectively for stages I-II-III-IV): visceral fat (9-7-7-5), subcutaneous fat (6-6-6-5). Microarrays were run in two batches (15xxx versus 17xxx CEL file samples; indicated in the description field). Samples from two patients (FN61; FN76) were put twice on array (15078+17881; 15064+17877) to verify and exclude batch effects.

Please note that, due to technical repeats with two patient samples, the number of 'visceral fat samples' for stages I-II-III-IV is 10-7-8-5.

first: Johannie

last: Du Plessis

first: Jos

last: van Pelt

first: Schalk

last: van der Merwe


title: CCR-5 using HIV-1 induces an anti-inflammatory profile in primary macrophages

city: Guildford

first: Fernando

middle: O

last: Martinez Estrada

state: Surrey

address: Stag Hill

department: Faculty of Health & Medical Sciences

institute: University of Surrey

summary: Macrophages are important effector cells of the immune system and play an important role in mounting inflammatory responses.  Macrophages can be activated by different stimuli in the tissue, either by cytokines produced by T helper cells (M1 or M2 polarization) or by the pathogens they encounter. Macrophages are also important target cells of HIV-1 and are preferentially infected by CCR5-using viruses. In this study, we investigated the ability of HIV-1 to induce changes in gene expression in unpolarized macrophages as well as in M1 or M2 polarized cells. We observed that CCR5-using HIV-1 regulates the expression of genes that are also regulated by IL-4 in macrophages. Genes regulated by HIV-1 infection and IL-4 polarization are involved in dampening pro-inflammatory responses in macrophages, which may facilitate HIV-1 to escape from detection by other immune cells. We also observed that changes in macrophage gene expression triggered by CCR5-using HIV-1 differed from those regulated by a CXCR4-using virus. This indicates that CCR5-using HIV-1 may be able to modulate macrophage gene expression to achieve successful replication. Our results provide insight in the complex interplay between HIV-1 and cells of the immune system.

overall_design: Polarized macrophages were obtained by stimulation of primary human monocytes with IFN-gamma (250 U/ml) in combination with TNF-alpha (12.5 ng/ml) (M1), IL-4 (50 ng/ml) (M2a), IL-10 (50 ng/ml) (M2c) for 5 days. Cells were inoculated for 24 hours with one of two HIV-1 strains (CCR5 or CXCR4 using HIV1) or their non replicating counterparts (heat inactivated virus). Macrophages that were not stimulated wiht cyokines or inoculates with HIV-1 were used as control. A total of 16 treatment conditions were tested in triplicate, for a total of 48 samples analysed.

first: Viviana

last: Cobos Jimenez

last: Martinez

first: Siamon

last: Gordon

first: Neeltje

last: Kootstra


title: Temporal Response to seasonal and pandemic H1N1 infection in human DCs

first: Hailong

last: Meng

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

overall_design: Refer to individual Series


title: Genome-wide analysis of the genetic regulation of gene expression in human neutrophils

status: Public on Aug 10 2015

first: Bernett

last: Lee

address: 8A Biomedical Grove #03-06 Immunos

country: Singapore

institute: Singapore Immunology Network

summary: Here we report an expression dataset of isolated neutrophils from 114 healthy individuals of Chinese ethnicity collected in Singapore.

overall_design: A total of 114 individuals with no case control stratification.

first: Anand

middle: K

last: Andiappan

first: Rossella

last: Melchiotti

first: Tuang

middle: Y

last: Poh

first: Michelle

last: Nah

first: Kia

last: Puan

first: Elena

last: Vigano

first: Doreen

last: Haase

first: Nurhashikin

last: Yusof

first: Boris

last: San Luis

first: Josephine

last: Lum

first: Dilip

last: Kumar

first: Shihui

last: Foo

first: Li

last: Zhuang

first: Anusha

last: Vasudev

first: Astrid

last: Irwanto

first: Alessandra

last: Nardin

first: Hong

last: Liu

first: Furen

last: Zhang

first: John

last: Connolly

first: Jianjun

last: Mortellaro

first: De

last: Wang

first: Michael

last: Poidinger

first: Anis

last: Larbi

first: Francesca

last: Zolezzi

first: Olaf

last: Rotzschke


title: Slug-dependent upregulation of L1CAM is responsible for the increased invasion potential of pancreatic cancer cells following long-term 5-FU-treatment

first: Ian

last: Mills

address: Gaustadalleen 21

department: Centre for Molecular Medicine Norway

institute: University of Oslo

summary: In pancreatic cancer the survival rate is low, as the available treatment options usually only extend survival and seldom produce a cure. Drug resistance and disease reoccurrence is the typical reason for death after cancer diagnosis. 5-Fluorouracil (5-FU) is the main chemostatic used in first line therapy.  However the majority of the tumors become resistant to treatment. To investigate acquired 5-FU resistance in pancreatic adenocarcinoma, we established chemoresistant monoclonal cell lines from the Panc03.27 cell line by long-term exposure to 5-FU.   In addition to increased expression of markers associated with multidrug resistance, the 5-FU resistant clones showed alterations typical of the process of epithelial-to-mesenchymal transition (EMT), including upregulation of mesenchymal markers and increased invasiveness. Microarray analysis revealed the L1CAM pathway as one of the most upregulated pathways in the chemoresistant clones, which was confirmed on RNA and protein levels. Expression of the adhesion molecule L1CAM is associated with a chemoresistant and migratory phenotype of pancreatic cancer. Using esiRNA targeting L1CAM, or by blocking the extracellular part of L1CAM with monoclonal antibodies, we discovered that the increased invasiveness observed in the chemoresistant cells depends on L1CAM. Using esiRNA targeting β-catenin and/or Slug, we discovered that L1CAM expression depends on Slug rather than β-catenin in the 5-FU resistant cells. We demonstrate a functional link between Slug and the expression level of L1CAM in pancreatic cancer cells having undergone EMT following long-term exposure to 5-FU. Our findings provide further insight into the molecular mechanisms leading to a chemoresistant and migratory phenotype in pancreatic cancer cells and indicate the importance of Slug-induced L1CAM in refractory pancreatic cancer.

overall_design: Examination of expression of 5-Fluorouracil (5-FU) Panc03.27 cell line resistant clone versus expression of 5-FU sensitive clones (NT) in 4 replicates per cell lines

first: Jennifer

last: Dembinski

first: Kaja

last: Lund

first: Nina

last: Solberg

first: Alfonso

last: Urbanucci

first: Stefan

last: Krauss


title: Prostate cancer stratification using molecular profiles [Stockholm ExpressionArray]

status: Public on Jul 30 2015

city: Cambridge

first: Chandra

last: Chilamakuri

address: Robinson Way

institute: Cancer Research UK Cambridge Institute

summary:
Background
Understanding the heterogeneous genotypes and phenotypes of prostate cancer is fundamental to improving the way we treat this disease.  As yet, there are no validated descriptions of prostate cancer subgroups derived from integrated genomics linked with clinical outcome.
Methods
In a study of 482 tumour, benign and germline samples from 259 men with primary prostate cancer, we used integrative analysis of copy number alterations (CNA) and array transcriptomics to identify genomic loci that affect expression levels of mRNA in an expression quantitative trait loci (eQTL) approach, to stratify patients into subgroups that we then associated with future clinical behavior, and compared with either CNA or transcriptomics alone.
Findings
We identified five separate patient subgroups with distinct genomic alterations and expression profiles based on 100 discriminating genes in our separate discovery and validation sets of 125 and 99 men. These subgroups were able to consistently predict biochemical relapse (p=0.0017 and p=0.016 respectively)  and were further validated in a third cohort with long-term follow-up (p=0.027). We show the relative contributions of gene expression and copy number data on phenotype, and demonstrate the improved power gained from integrative analyses. We confirm alterations in six genes previously associated with prostate cancer (MAP3K7, MELK, RCBTB2, ELAC2, TPD52, ZBTB4) in prostate cancer, and also identify 94 genes not previously linked to prostate cancer progression that would not have been detected using either transcript or copy number data alone. We confirm a number of previously published molecular changes associated with high risk disease, including MYC amplification, and NKX3-1, RB1 and PTEN deletions, as well as over-expression of PCA3 and AMACR, and loss of MSMB in tumour tissue. A subset of the 100 genes  outperforms established clinical predictors of poor prognosis (PSA, Gleason score), as well as previously published gene signatures (p=0•0001). We further show how our molecular profiles can be used for the early detection  of aggressive cases in a clinical setting, and inform treatment decisions.
Interpretation
For the first time this study demonstrates the importance of integrated genomic analyses incorporating both benign and tumour tissue data in identifying molecular alterations leading to generation of robust gene sets that are predictive of clinical outcome in independent patient cohorts.

overall_design:
A total of 482 samples from 289 men with prostate cancer from two cohorts were included in this study.  The discovery cohort comprised 125 tumour samples from radical prostatectomy (RP) with 118 matched benign samples, and 85 matched blood samples.  An additional 4 benign samples from men undergoing Holmium laser enucleation of the prostate (HoLEP) and 16 radical prostatectomy samples from men with castrate-resistant prostate cancer, with 13 matched blood samples were also included.  These were assayed on several platforms, including Illumina HT12v4 gene expression arrays, Illumina OMNI2.5M genotyping arrays and Affymetrix SNP6 genotyping arrays.  The validation cohort comprised 103 tumour tissue samples from men with prostate cancer, with 99 matched benign tissue samples and 103 matched blood samples.  This datasheet describes samples in the VALIDATION COHORT only, with complete, QCd Illumina HT12v4 data for 94 RP samples.
Extensive clinical metadata is available in the associated publication Ross-Adams et al. (2015, Suppl. Table 2)

first: Helen

last: Ross-Adams

first: Alastair

last: Lamb

first: Silvia

last: Halim

first: Mark

last: Dunning


title: Genome-wide expression microarray analysis of seminoma-like TCam-2 cells during transition into an embryonal carcinoma-like state

city: Düsseldorf

first: Daniel

last: Nettersheim

state: NRW

address: Universitätsstr. 1

department: Urology

institute: University Hospital Düsseldorf

summary: Illumina expression microarray analysis of seminoma-like TCam-2 cells xenografted in nude mice. 2120EP embryonal carcinoma cells served as control. TCam-2 cells acquire pluripotency and become epigenetically reprogrammed to an embryonal carcinoma-like state during in vivo growth. This analysis is part of the article 'BMP inhibition in seminomas initiates acquisition of pluripotency via NODAL signaling resulting in reprogramming to an embryonal carcinoma' by Nettersheim et al., 2015. PLoS Genetics

overall_design: Total RNA was isolated from tumors of TCam-2 and 2102EP cells xenografted for 1, 2, 4 and 6 weeks as well as 4 and 8 weeks, respectively. 1x10^7 cells were xenografted. In vivo samples of TCam-2 cells were analyzed in biological duplicates. In vitro cultivated TCam-2 / 2102EP cells as well as 2102EP xenografted for 4 and 8 weeks were analyzed once.

first: Hubert

last: Schorle


title: Prostate cancer stratification using molecular profiles [CamCap ExpressionArray]

overall_design:
A total of 482 samples from 289 men with prostate cancer from two cohorts were included in this study.  The discovery cohort comprised 125 tumour samples from radical prostatectomy (RP) with 118 matched benign samples, and 85 matched blood samples.  An additional 4 benign samples from men undergoing Holmium laser enucleation of the prostate (HoLEP) and 16 radical prostatectomy samples from men with castrate-resistant prostate cancer, with 13 matched blood samples were also included.  These were assayed on several platforms, including Illumina HT12v4 gene expression arrays, Illumina OMNI2.5M genotyping arrays and Affymetrix SNP6 genotyping arrays.  The validation cohort comprised 103 tumour tissue samples from men with prostate cancer, with 99 matched benign tissue samples and 103 matched blood samples.  This datasheet describes samples in the DISCOVERY COHORT only, with complete, QCd Illumina HT12v4 data for 13 CRPC samples, 113 tumour samples and 73 matched benign samples.
Extensive clinical metadata is available in the associated publication Ross-Adams et al. (2015, Suppl. Table 2)


title: Explosure of breast cancer cells promotes estrogen-dependent and -independent cell proliferation mechanisms tied to clinical outcomes identified in ER+ breast cancers

status: Public on Jul 31 2015

city: Houston

first: Nicholes

last: Candelaria

state: Texas

address: 3605 Cullen Boulevard SERC (Building 545), Rm 3023

department: Cellular and Molecular Biology

institute: University of Houston

summary: Differentially expressed genes identified in MCF-7 cells treated to 0.1% ethanol concentration.

overall_design: Total RNA was generated from MCF-7 breast cancer cells starved of estrogen in 5% charcoal filtered FBS. Cells were treated to either a 0.1% ethanol concentration or left untreated.


title: Gene expression analysis of monocytes and monocyte derived cells (MDCs) in CLL patients with differing antibody sensitivity

status: Public on Jul 29 2015

city: Brisbane

first: Nicholas

last: Saunders

address: 37 Kent Street

country: Australia

institute: University of Queensland Diamantina Institute

summary: RNA from CD14 positive monocytes isolated from CLL patient PBMCs on day 0 and from MDCs from CLL PBMCs cultured for seven days were hybridised to an RNA microarray to identify differences between the MDCs derived from sensitive or resistant CLL patients and differences in MDCs pre and post in vitro culture.

overall_design: Total RNA isolated from CD14 positive monocytes from 2 sensitive and 2 resistant CLL patients and total RNA isolated from MDCs from 4 sensitive and 3 resistant CLL patients

first: Melinda

last: Burgess


title: Direct conversion of normal and patient human fibroblasts into neuronal cells

status: Public on Jul 28 2015

city: Shanghai

first: Wenxiang

last: Hu

address: Yueyang Road 320

country: China

institute: Shanghai institutes for Biological Sciences, CAS

summary:
Neuronal conversion from human fibroblasts can be induced by lineage-specific transcription factors, holding great promise for human neurological disease modeling and regenerative medicine. However, the introduction of ectopic genes limits their therapeutic applications. Here, we report that neuronal cells could be directly induced from human fibroblasts by a chemical cocktail of seven small molecules bypassing neural progenitor stage. These chemical-induced neuronal cells (hciN cells) resembled hES-derived neurons regarding morphology, gene expression profiles, and electrophysiological properties. Our further experiments show that hciN cells were able to develop into mature neurons in vivo in embryonic mouse brain. Moreover, this approach was further applied to induce hciN cells from fibroblasts of familial Alzheimer’s disease patients and the hciN cells showed abnormal Aβ production. Together, we established a transgene-free chemical approach to directly induce neuronal cells from human fibroblasts, thus providing alternative strategies for modeling of related neurological diseases and regenerative medicine.
We used microarray to comparethe global gene expression patterns of hES-derived neurons (control neurons), HAFs, pre-hciN cells (VCRFSGY-treated HAFs at day 3 and 7) and hciN cells (induced with VCRFSGY for 14 days)

overall_design: hciNs RNA samples were selected at different time points, i.e. pre-hciN cells (VCRFSGY-treated HAFs at day 3 and 7) and hciN cells (induced with VCRFSGY for 14 days), to study molecular mechanism and marker gene expression happened at the early stage of chemical induction by compared with hES-neurons (positve control) and HAFs (negtive control).

first: Binlong

last: Qiu

first: Wuqiang

last: Guan

first: Qinying

last: Wang

first: Min

first: Yin

last: Huang

first: Gangcai

last: Xie

first: Longfei

last: Gao

first: Hanzhi

last: Zhao

first: Ying

last: Jin

first: Beisha

last: Tang

first: Lu

last: Shen

first: Yongchun

last: Yu

first: Jian

first: Gang

last: Pei


title: Study the effect of calreticulin knockdown on genome-wide transcript expression in HepG2 cells

status: Public on Jul 23 2015

city: Delhi

first: Malabika

last: Datta

address: Mall Road

country: India

institute: Institute of Genomics and Integrative Biology

summary: The objective was to evaluate the status of the global hepatic transcriptome in the presence of inhibited calreticulin levels. Results identify a total of 324 genes were altered of which 245 genes were downregulated and 79 genes were upregulated. This suggests that such altered genes might be associated with altered hepatic physiology that are observed during calreticulin deficiency.

overall_design: Total RNA was isolated from HepG2 cells subjected to calreticulin (CRT) siRNA for 24 hours compared to control HepG2 cells subjected to scramble siRNA for 24 hours. This was then hybridized to Illumina HumanHT-12 v4 Expression BeadChip arrays.

first: Saurabh

last: Vig


title: The Senescent Methylome and its relationship with cancer, ageing, and germline genetic variation in humans (gene expression)

status: Public on Jul 26 2015

city: London

first: Robert

last: Lowe

address: 4 Newark Street

department: Blizard Institute

institute: QMUL

summary: Cellular senescence is a stable arrest of proliferation and is considered a key component of processes associated with carcinogenesis and other ageing-related phenotypes. However, till now, biological markers that define senescence on a genome-wide scale have been limited. Here, we report a DNA methylomic analysis of actively dividing and deeply senescent normal human epithelial cells, identifying 3,852 senescence-associated differentially methylated positions (senDMPs). We find that this human senDMP signature is positively and significantly correlated with both cancer and ageing-associated methylomic dynamics. We also identify germline genetic variants, including those associated with the p16INK4A locus, that are associated with the presence of in vivo senDMP signatures. Importantly, we also demonstrate that the senDMP signature can be effectively reversed in a newly-developed protocol of transient cellular rejuvenation. The senDMP signature has significant potential for understanding some of the key (epi)genetic etiological factors that lead to cancer and age-related diseases in humans.

overall_design: Total RNA obtained from the HMECs at early passage (EP) and deep senescence (DS)


title: Effects of bromodomain inhibitors on CD4 T+ cells under Th17-promoting conditions

city: Oxford

first: Paul

last: Bowness

address: Windmill Road

department: Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences (NDORMS)

institute: University of Oxford

summary: The human dataset includes the gene expression profile of CD4+ T cells isolated from blood of healthy controls and plated on TCP in RPMI-1640 containing 10% FCS, Penicillin-Streptomycin (50,000 units-50 mg) and L-glutamine (2 mM). Cells were stimulated for 4 days with 20 ng/ml of IL-1beta, 100 IU/ml of IL-2, 20 ng/ml of IL-6, 20 ng/ml IL-23 plus anti-CD2/3/28 beads at a ratio of 1 bead per 10 cells. RNA samples were isolated using the RNeasy Mini Kit (Qiagen) with on-column DNA digestion. The transcriptional profile was evaluated in three different donors using the HT12v4.1 BeadChip arrays from Illumina.

overall_design: Total RNA obtained from CD4+ T cells exposed to Th17-promoting cytokines.

first: Ariane

last: Hammitzsch

first: Fernando

last: Martinez

first: Stefan

last: Knapp


title: Effect of NDRG3 expression on cell response to hypoxia

status: Public on Jul 24 2015

city: Daejeon

first: Minho

last: Kang

address: 125 Gwahak-ro, Yuseong-gu

department: Medical Genomics Research Center

country: South Korea

institute: KRIBB

summary: Analysis of Huh-7 hepatocarcinoma cell line depleted of NDRG3 or HIF-1α under hypoxic condition. HIF-1α and NDRG3 have distinct functions in hypoxia responses. Results provide insight into molecular basis of HIF-independent signaling in the development and progression of hypoxic tumors

overall_design: Gene expression profiles of Huh-7 cells stably expressing NDRG3-shRNA or HIF-1α-shRNA under normoxia were compared to gene expression profiles of Huh-7 stable cells under  hypoxia for 3, 6, 12 and 24 hours.

first: Dong

last: Lee

first: Suk-Jin

last: Yang

first: Young

middle: I

last: Yeom


title: An RNAi screen probing signalling control of human embryonic stem cells establishes the cell cycle-regulated restriction of the exit from pluripotency (DNA damage checkpoint)

city: Singapore

first: Kevin Andrew

last: Gonzales

address: 60 Biopolis Street

institute: Genome Institute of Singapore

summary: Analysis of effect of S-phase arrest and replication checkpoint activation on differentiating hESCs at the gene expression level. The hypothesis tested in the present study was that replication checkpoint activation prevents the exit from pluripotency in hESCs. Results provide important information of the response of hESCs to replication arrest, such as upregulation of genes involved in the TGF-beta signaling pathway, and subsequent maintenance of pluripotency marker expression.

overall_design: Total RNA obtained from hESCs incubated in medium without bFGF and TGF-beta supplemented with either DMSO, Aphidicolin or Aphidicolin+AZD7762 for 0, 48 and 96 hours.


title: Comparative analysis of gene expression profiles in lymphoma cells after treatment by Dexamethasone or CpdA

status: Public on Jul 21 2015

city: Moscow

first: Ekaterina

last: Lesovaya

address: Kashirskoe shosse 24-15

department: Chemical Carcinogenesis

country: Russia

institute: N.N. Blokhin Cancer Research Center

summary: The project is directed to the development of selective glucocorticoid receptor agonists for anticancer therapy. Glucocorticoids (GC) are widely used in treatment of many types of cancer due to its ability to induce apoptosis in malignant cells (in blood cancer therapy) and to prevent nausea and emesis (in the chemotherapy of solid tumors). However, severe dose-limiting side effects occur, including osteoporosis, muscle wasting, diabetes and other metabolic complications.   Both beneficial and harmful effects of glucocorticoids are due to selective activation or repression of particular genes by glucocorticoid receptor (GR). GR regulates gene expression via transactivation that requires GR homodimer binding to gene promoters and transrepression mediated via negative interaction between GR and other transcription factors as well as binding with negative glucocorticoid response elements (nGRE) in genes. GR transactivation is linked to metabolic side effects, while GR transrepression underlies glucocorticoid therapeutic action. Novel selective GR agonist Compound A (CpdA) prevents GR dimerization and transactivation, specifically activates GR transrepression, and has fewer side effects compared to glucocorticoids. Here we compare the gene expression profiles in lymphoma cells treated with glucocorticoid Dexamethasone (Dex) or CpdA

overall_design: B-cell mantle cell lymphoma cells Granta-519 were treated with Dexamethasone (1 uM), Compound A (1 uM) or solvent (Ethanol) for 16 h. Then cells were pelleted and total RNA was isolated with RiboPure kit (Ambion) according to manufacturer's protocol. The RNA samples were treated with TURBOTM DNase (Ambion). Quality control was performed with Agilent Bioanalyser.

first: Irina

last: Budunova


title: Transcriptome of human foetal heart for comparison with cardiomyocytes from pluripotent stem cells

status: Public on Jul 22 2015

city: Leiden

first: Cathelijne

middle: W

last: van den Berg

address: Einthovenweg 20

country: Netherlands

institute: Leiden University Medical Center

summary: Gene expression in the human foetal heart for a comparison with cardiomyocytes derived from human pluripotent stem cells. Human foetal heart samples were collected from the individual chambers of the heart at various stages of development. This provided the opportunity to perform gene expression analysis and identify genes involved in the formation of the heart in each of the four chambers and at different stages of development. The dataset can be used to benchmark human pluripotent stem cell derived cardiomyocytes (hPSC-CMs) in terms of their maturation state by comparing it to the foetal heart samples. Two commercially available reference RNA sets are included in the analysis in order to characterize future sets of hPSC-CMs.

overall_design: Microarray experiments were performed on human foetal heart samples from first and second trimester hearts, separated in atria and ventricles.

first: C

first: R

middle: P

last: Davis

last: Mummery


title: Identification and molecular characterization of distinct glioblastoma cancer stem cell populations

status: Public on Jul 01 2015

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

summary: Malignant glioblastoma (GBM) is a highly aggressive brain tumor with a dismal prognosis and limited therapeutic options. Genomic profiling of GBM samples in the TCGA database has identified four molecular subtypes (Proneural, Neural, Classical and Mesenchymal), which may arise from different glioblastoma stem-like cell (GSC) populations. In the present study, we identify two GSC populations that produce GBM tumors by subcutaneous and intracranial injection with identical histological features. Gene expression analysis revealed that xenografts of GSCs grown as spheroid cultures had a Classical molecular subtype similar to that of bulk tumor cells.  In contrast xenografts of GSCs grown as adherent cultures on laminin-coated plates expressed a Mesenchymal gene signature. Adherent GSC-derived xenografts had high STAT3 and ANGPTL4 expression as well as enrichment for stem cell markers, transcriptional networks and pro-angiogenic markers characteristic of the Mesenchymal subtype. Examination of clinical samples from GBM patients showed that STAT3 expression was directly correlated with ANGPTL4 expression, and that increased expression of these genes correlated with poor patient survival and performance. A pharmacological STAT3 inhibitor abrogated STAT3 binding to the ANGPTL4 promoter and exhibited anticancer activity in vivo. Taken together, we identified two distinct GSC populations that produce histologically identical tumors but with very different gene expression patterns, and a STAT3/ ANGPTL4 pathway in glioblastoma that may serve as a target for therapeutic intervention.

overall_design: 2 samples of each variable were analyzed. Cells were cultured under normal adherent conditon (Bulk tumor cells), non-adherent plates with stem cell medium (Sp-GSC) or laminin-coated plates with stem cell medium (Ad-GSC). Xenografts were generated in NSG mice by subcutaneous inoculation.

first: Jo

last: Garner

last: Ellison

first: Debolina

last: Ganguly

first: Ziyun

last: Du

first: Michelle

last: Sims

first: Chuan

first: Rodrigo

middle: B

last: Interiano

first: Andrew

last: Davidoff

first: Lawrence

last: Pfeffer


title: Gene expression profiling of healthy controls upon Interferon-beta stimulation

status: Public on Aug 03 2015

city: Milan

first: Ferdinando

last: Clarelli

address: Via Olgettina 58

department: INSPE

institute: San Raffaele Scientific Institute

summary: This experiment was carried out in the context of a pharmacogenetic study of long-term (4-year follow-up) response to Interferon-beta treatment in two cohorts of Italian Multiple Sclerosis patients, to identify genetic variants (SNPs) that may influence response to IFN-beta. We integrated results from meta-analysis of the two cohorts with gene expression profiling of IFNβ stimulated PBMCs from 20 healthy controls and eQTL analyses, to look at possible enrichment of IFN-beta induced genes with genes mapped by top-ranking meta-analyzed SNPs.

overall_design: Total RNA obtained from isolated PBMC extracted from healthy subjects and in vitro stimulated or not with Interferon-β (100IU/mL) for 18h

first: Giuseppe

last: Liberatore

first: Melissa

last: Sorosina

first: Ana

last: Osiceanu

first: Federica

last: Esposito

first: Elisabetta

last: Mascia

first: Silvia

last: Santoro

first: Filippo

last: Martinelli Boneschi


title: Gene expression in liver of morbidly obese patients

status: Public on Jul 02 2015

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

institute: VIB

summary: Nonalcoholic fatty liver disease (NAFLD) has become the most common cause of liver disease affecting 20-30% of the population in developed countries. NAFLD is strongly associated with abdominal obesity and is recognized as the hepatic manifestation of the metabolic syndrome. In a subgroup of patients with NAFLD inflammation and fibrosis develops, this so-called Non-Alcoholic Steatohepatitis (NASH) may progress to cirrhosis and hepatocellular carcinoma. A multi-hit hypothesis has been proposed in which during the first “hit” fat accumulation occurs in hepatocytes from excessive delivery of fatty acids from adipose tissue, in addition there is an imbalance in lipid synthesis and export. However, the reason why fat accumulation is subsequently followed by inflammation and fibrosis in some patients is poorly understood. We studied the role of gene expression at the transcriptional level using microarray in bariatric patients from whom the liver histology was available.

overall_design: Patients scheduled for bariatric surgery were recruited in Pretoria/South-Africa. At the time of the procedure, tissue samples of the visceral and subcutaneous fat were taken for molecular analysis as well as liver tissue for histology, also full biochemical data was collected. Patients were grouped according histology: group I (<5% steatosis), group II (NAFLD, 30-50% steatosis) and group III (NASH). The 15 samples were used for microarray (nr patients respectively for stages I-II-III: 6-4-5).

first: Johannie

last: Du Plessis

first: Jos

last: van Pelt

first: Schalk

last: van der Merwe


title: An integrative analysis of reprogramming in human isogenic system identified a clone selection criterion

status: Public on Jul 15 2015

first: Maria

last: Shutova

state: Russia

address: Gubkina 3

department: Epigenetics

institute: Vavilov Institute of General Genetics, Russian Academy of Sciences

summary: The pluripotency of newly developed human induced pluripotent stem cells (iPSCs) is usually characterized by physiological parameters; i.e., by their ability to maintain the undifferentiated state and to differentiate into derivatives of the three germ layers. Nevertheless, a molecular comparison of physiologically normal iPSCs to the “gold standard” of pluripotency, embryonic stem cells (ESCs), often reveals a set of genes with different expression and/or methylation patterns in iPSCs and ESCs. To evaluate the contribution of the reprogramming process, parental cell type, and fortuity in the signature of human iPSCs, we developed a complete isogenic reprogramming system. We performed a genome-wide comparison of the transcriptome and the methylome of human isogenic ESCs, three types of ESC-derived somatic cells (fibroblasts, retinal pigment epithelium and neural cells), and three pairs of iPSC lines derived from these somatic cells. Our analysis revealed a high input of stochasticity in the iPSC signature that does not retain specific traces of the parental cell type and reprogramming process. We showed that five iPSC clones are sufficient to find with 95% confidence at least one iPSC clone indistinguishable from their hypothetical isogenic ESC line. Additionally, on the basis of a small set of genes that are characteristic of all iPSC lines and isogenic ESCs, we formulated an approach of “the best iPSC line” selection and confirmed it on an independent dataset.

overall_design: Total RNA obtained from isogenic cell lines compared to each other. For each line there are a biological (different passages) or technical (same passage) replicate.

first: Anastasia

last: Surdina

first: Dmitry

last: Ischenko

first: Vladimir

middle: A

last: Naumov

first: Aleksandra

middle: N

last: Bogomazova

first: Ekaterina

last: Vassina

last: Alekseev

last: Lagarkova

first: Sergey

last: Kiselev


title: Accurate prediction and validation of response to endocrine therapy in breast cancer

status: Public on Jul 06 2015

city: Carrington Crescent

first: Andrew

last: Sims

state: Edinburgh

address: Systems Medicine Building

department: Institute of Genetics and Molecular Medicine

institute: University of Edinburgh

summary:
Purpose Aromatase inhibitors (AIs) have an established role in  breast cancer treatment. Response rates are only 50-70% in the neoadjuvant setting and lower in advanced disease. Accurate biomarkers are urgently needed to predict response in these settings and to determine which individuals will benefit from adjuvant AI therapy.
Participants and Methods Pre- and on-treatment (after 2 weeks and 3 months) biopsies were obtained from 89 post-menopausal women with ER+ breast cancer receiving neoadjuvant letrozole for transcript profiling. Dynamic clinical response was assessed by three-dimensional ultrasound measurements.
Results The molecular response to letrozole was characterised and a four gene classifier of clinical response was established (accuracy of 96%) based upon the level of two genes prior to treatment (one associated with immune signalling, IL6ST and the other with apoptosis, NGFRAP1) and two proliferation genes (ASPM, MCM4) at 2 weeks of therapy. The four gene signature was found to be 91% accurate in a blinded, completely independent validation dataset of patients treated with anastrozole. Matched 2 week on-treatment biopsies improved predictive power over pre-treatment biopsies alone. This signature also significantly predicted recurrence free survival (p=0.029) and breast cancer specific survival (p=0.009). We demonstrate that the test can also be performed using quantitative PCR or immunohistochemistry.
Conclusion A four gene predictive model of clinical response to AIs by two weeks has been generated and validated. Deregulated immune and apoptotic responses before treatment and a failure to reduce proliferation by 2 weeks are functional characteristics of breast tumours that do not respond to AIs.

overall_design: 25 Pre treatment, 25 two week and 25 three month on-treatment primary breast tumour samples from the same patients. Data was analysed with two previously generated datasets, GSE55374 which was also processed on Illumina HT-12v4 BeadChips (GPL10558) and  GSE20181 on Affymetrix U133A GeneChips (GPL96)


title: Genome-wide bisulfite sequencing reveal enhancer as main target of DNA methylation in neural conversion [gene expression]

first: Gang

last: Liu

address: 320 Yueyang Rd, Shanghai

institute: Shanghai Institutes for Biological Sciences

summary: Genome-wide bisulfite sequencing and corresponding transcriptome are analyzed together to seek for methylation target during neural differentiation

overall_design: H1 human embryonic stem cells are able to differentiated into neural stem cells with induction of compound C in 72h. We extracted RNA from 0, 12, 24, 36, 48, 72h samples during dinduction and measured their expression level with Illumina microarray, with 4 replicates each time point.

first: Jiaxi

last: Zhou

first: Yang

last: Bai

first: Lei


title: IL-10+ T cells compared to IFNg+/IL-10- T cells induced by IL-10 tolerogenic dendritic cells

status: Public on Jul 03 2015

city: Amsterdam

first: Anja

last: ten Brinke

address: Plesmanlaan 125

department: Immunopathology

institute: Sanquin Blood Supply Foundation

summary: Ex vivo generated tolerogenic dendritic cells (tDCs) have a strong therapeutic potential to induce antigen-specific iTreg upon infusion in patients. We previously demonstrated that IL-10 tDC-primed T cells are very suppressive and produce IL-10. Here, we show that the majority of the IL-10+ T cells co-express IFNγ, giving rise to the question whether these cells are proinflammatory or regulatory. Whole genome gene expression analysis revealed a strong regulatory gene profile and a suppressed Th1 gene profile for the IL-10/ IFNγ co-expressing CD4+ T cells.

overall_design: Naïve CD4+ T cells were co-cultured for 13 days with allogeneic IL-10 dendritic cells in the presence of anti-TNFα agents. After 13 days, T cells were restimulated with PMA and ionomycin. The total IL-10+ T cell population and the IFNγ+/ IL-10- T cell population were isolated with an IL-10/ IFNγ combined cytokine secretion assay and subsequent FACS sorting. Micro arrays were performed on samples of three independent donors.

first: Martine

last: Boks

first: Judith

last: Kager-Groenland

first: S

last: van Ham


title: Identification of p38 beta as a therapeutic target for the treatment of Sézary Syndrome

city: Des Moines

first: Chunfa

last: Jie

state: IA

address: 3200 Grand Ave

institute: Des Moines University

summary: Cutaneous T-Cell Lymphomas (CTCL) represent a group of hematopoietic malignancies that home to the skin and have no known molecular basis for disease pathogenesis.  Sézary syndrome (SS) is the leukemic variant of CTCL. Currently, CTCL is incurable, highlighting the need for new therapeutic modalities.  We have previously observed that combined small-molecule inhibition of protein kinase C (PKC) β and glycogen synthase kinase 3 (GSK3) causes synergistic apoptosis in CTCL cell lines and patient cells.  Through microarray analysis of a SS cell line, we surveyed global gene expression following combined PKCβ-GSK3 treatment to elucidate therapeutic targets responsible for cell death. Clinically relevant targets were defined as genes differentially expressed in SS patients that were modulated by combination-drug treatment of SS cells.  Gene set enrichment analysis uncovered candidate genes enriched for an immune cell signature, specifically the T-cell receptor and MAPK signaling pathways.  Further analysis identified p38 as a potential therapeutic target that is over-expressed in SS patients and decreased by synergistic-inhibitor treatment.  This target was verified through small-molecule inhibition of p38 leading to cell death in both SS cell lines and patient cells. These data establish p38 as a new SS biomarker and potential therapeutic target for the treatment of CTCL.

overall_design: Hut78 cells were treated with 4μM Enzastaurin, 5μM AR-A014418, 4μM Enzastaurin & 5μM AR-A014418, DMSO, or no treatment for three days.  RNA was extracted and hybridized to Illumina microarrays.

first: Meghan

last: Bliss-Moreau

first: Cristian

last: Coarfa

first: Preethi

last: Gunaratne

first: Joan

last: Guitart

first: Nancy

last: Krett

first: Steven

middle: T

last: Rosen


title: Differential Gene Expression of Phenazine biosynthesis-like domain-containing protein (PBLD) in HepG2 cells

city: Guangzhou

first: Aimin

last: Li

state: Guangdong

address: Department of Gastroenterology and Hepatology, Guangzhou First Municipal People's Hospital, Guangzhou Medical University

department: Gastroenterology

institute: Guangzhou Medical University

summary:
Our objective was to elucidate patterns of gene expression underlying the PBLD overexpression in HepG2 cells.
The transcript profiles of PBLD overexpressed HepG2 cells were compared to the gene expression profiles of HepG2 cells control.

overall_design: Gene expression is compared at a global level using total RNA from PBLD overexpressed HepG2 cells  and controls using the Illumina microarray platform.


title: Expression analysis of human PBMCs stimulated with Borrelia, MDP or Pam3cys.

status: Public on Jun 30 2015

city: Boston

first: Aylwin

last: Ng

state: MA

address: 185 Cambridge Street

institute: CCIB, MGH

summary: Analysis examining the effect of the Crohn's disease-associated ATG16L1 polymorphism on the responses to stimulation components derived from various bacteria classes.

overall_design: Expression analysis was performed on RNA extracted from peripheral blood mononuclear cells (PBMCs) from healthy genotyped volunteers were stimulated for 24h with RPMI alone, or RPMI containing heat-killed Borrelia burgdorferi , muramyl dipeptide (MDP) or Pam3Cys.

first: Jakob

last: Begun

first: Kara

middle: G

last: Lassen

first: Humberto

last: Jijon

first: Leigh

last: Baxt

first: Gautam

last: Goel

first: Robert

middle: J

last: Heath

first: Jenny

last: Tam

first: Szu-Yu

last: Kuo

first: Eduardo

last: Villablanca

first: Lola

last: Fagbami

first: Marije

last: Oosting

first: Vinod

last: Kumar

first: Monica

last: Schenone

last: Carr

first: Leo

last: Joosten

first: Jatin

last: Vyas

first: Mark

last: Daly

first: Mihai

last: Netea

first: Gordon

middle: D

last: Brown

first: Cisca

last: Wijmenga

first: Ramnik

last: Xavier


title: Inflammatory environment and oxidized LDL convert circulating human proangiogenic cells (PACs) into functional antigen presenting cells (APCs)

city: Milano

first: Gualtiero

middle: Ivanoe

last: Colombo

address: Via Carlo Parea, 4

institute: Centro Cardiologico Monzino IRCCS

summary: The function of human circulating proangiogenic cells (PACs) has been described extensively. However, little focus has been placed on understanding how these cells differ in their functions in the presence of microenvironments mimicking vascular inflammation. We hypothesized that exposure to proinflammatory cytokines or the oxLDL, an autoantigen abundant in advanced atherosclerotic plaques, converts PACs into immune-modulating/proinflammatory cells. Hence, we examined the effect of oxLDL and inflammatory stimuli on their phenotype by use of a functional genomics model based on secretome and whole genome transcriptome profiling. PACs obtained from culturing a PBMC fraction in angiogenic medium were primed with DC differentiation cytokines for 3 days and then exposed to proinflammatory cytokines or oxLDL for 2 days. Under these conditions, PACs converted into APCs (APCcy and APCox, respectively), expressed maturation markers CD80 and CD83, and showed an up-regulation of CD86. APCcy and APCox induced a robust T cell BrdU incorporation. Despite a similar ability to induce lymphocyte proliferation, APCcy and APCox differed for the secretory pathway and mRNA expression. Analysis of the differentially expressed genes identified 4 gene "clusters", showing reciprocal modulation in APCcy vs. APCox justifying, according to functional genomics analyses, a different putative function of the cells in antigen processing. Together, these data show that treatment with inflammatory cytokines or oxLDL converts human PAC phenotype and function into that of APCs with similar lymphocyte-activating ability but distinct maturation degree and paracrine functions.

overall_design: PBMC-derived PACs were committed with GM-CSF and IL-4 to a dendritic phenotype, and then exposed to proinflammatory cytokines (IL-1β and TNF-α) or to the oxidized form of LDL (oxLDL). Functional assays and whole genome gene expression profiling were performed both on PACs (n=6) and or resulting cytokine- (APCcy, n=6) and oxLDL-induced APCs (APCox, n=6). RNA was reverse transcribed, labeled, and linearly amplified, and then hybridized to HumanHT-12 v.4 Expression BeadChip microarrays. To estimate technical variability, ≈20% of the samples (n=4) were hybridized in duplicate.

first: Luca

last: Piacentini

first: Mattia

last: Chiesa


title: AKT antagonist AZD5363 influences estrogen receptor function in endocrine resistant breast cancer and synergizes with fulvestrant (ICI182780) in vivo

status: Public on Jun 29 2015

first: Alice

last: Gao

state: London

address: 237 Fulham Road

department: Breast Cancer Now

institute: The Institute of Cancer Research

summary: Phosphoinositide-3-kinase/protein-kinaseB/mammalian target of rapamycin (PI3K/AKT/mTOR) signalling plays an important role in breast cancer (BC). Its interaction with estrogen receptor (ER) signalling becomes more complex and inter-dependent with acquired endocrine resistance. Targeting mTOR combined with endocrine therapy has shown clinical utility, however, a negative feedback-loop exists downstream of PI3K/AKT/mTOR. Direct blockade of AKT together with endocrine therapy may improve BC treatment. AZD5363, a novel pan-AKT kinase catalytic inhibitor, was examined in a panel of ER+ BC cell lines (MCF7, HCC1428, T47D, ZR75.1) adapted to long-term-estrogen-deprivation (LTED) or tamoxifen (TamR). AZD5363 caused a dose-dependent decrease in proliferation in all cell lines tested (GI50<500nM) except HCC1428 and HCC1428-LTED. T47D-LTED and ZR75-LTED were the most sensitive of the lines (GI50~100nM). AZD5363 re-sensitised TamR cells to tamoxifen and acted synergistically with fulvestrant. AZD5363 decreased p-AKT/mTOR targets leading to a reduction in ERα-mediated transcription in a context specific manner and concomitant decrease in recruitment of ER and CREB-binding protein (CBP) to estrogen-response-elements located on the TFF1, PGR and GREB1 promoters. Furthermore, AZD5363 reduced expression of cell-cycle-regulatory proteins. Global gene expression highlighted ERBB2-ERBB3, ERK5 and IGF1 signaling pathways driven by MYC as potential feedback-loops. Combined treatment with AZD5363 and fulvestrant showed synergy in an ER+ patient derived xenograft and delayed tumour progression post-cessation of therapy. These data support the combination of AZD5363 with fulvestrant as a potential therapy for BC that is sensitive or resistant to E-deprivation or tamoxifen and that activated AKT is a determinant of response, supporting the need for clinical evaluation.

overall_design: Cell lines were treated in biological triplicates in the absence of estrogen with or without AZD5363 for 24hours in order to identify gene changes associated with perturbation of AKT signalling

first: Qiong

first: Ricardo

last: Santos

first: Lesley

last: Martin


title: Differentially expressed genes analysis between dihydroberberine, sunitinib and dihydroberberine plus sunitinib.

status: Public on Jun 26 2015

city: Xi’an

first: Yanmin

last: Zhang

address: No. 76, Yanta West Street, #54

department: School of Pharmacy

institute: Xi’an Jiaotong University

summary: To gain insights into the mechanisms of dihydroberberine, sunitinib and dihydroberberine plus sunitinib on inhibition to A549 cells, we have employed whole genome microarray expression profiling as a discovery platform to identify different genes between dihydroberberine, sunitinib and dihydroberberine plus sunitinib-treated sample and control.

overall_design: A549 cells were cultivated in the absence or presence of 25μmol/L dihydroberberine, 2μmol/L sunitinib, 25μmol/L dihydroberberine plus 2μmol/L sunitinib for 48 h, followed by the Agilent Whole Human Genome Oligo Microarray

first: Bingling

last: Dai


title: Rare variants affecting the Fanconi Anemia/homologous recombination DNA repair gene network confer increased risk for AML and are associated with abnormal karyotype

status: Public on Jul 14 2015

city: Adelaide

first: Richard

last: D'Andrea

address: P4-40, City East Campus

institute: University of South Australia

summary: This study was to compare gene expression profiles of human AMLs that either carry or lack potentially deleterious variants in genes of the Fanconi Anemia-Homologous Recombination DNA repair network” . Variants were identified by whole exome sequencing of the relevant genes.

overall_design:
In total, 145 AML Diagnosis Samples were arrayed with no duplicates. CD34+ cells were used as normal controls.  CML and normal Mono-nuclear cells (MNC) samples were not used for analysis.
Adelaide Samples were sourced from the South Australian Cancer Research Biobank, ALLG Samples were sourced from the Australian Leukaemia an Lymphoma Group

first: Kyaw

last: Maung

first: Mahmoud

last: Bassal

first: Stephen

last: Pederson

first: Anna

first: Grant

last: Englar

first: Ian

last: Lewis

last: D’Andrea

first: Thomas

last: Gonda


title: Correlation between DNase I hypersensitive site distribution and gene expression in HeLa S3 cells [Illumina arrays]

status: Public on Jun 19 2015

city: Beijing

first: Yu-Xiang

address: Fengtai-District,You-An-Men-Wai

department: Biochemistry

institute: Capital Medical University, China

summary: We explored the relationship between the distribution of DNase I hypersensitive site(DHSs) and levels of gene expression. Expression values from 5 to 11 are raw log2 ratio-transformed data from gene expression arrays. We found that the distribution of DHSs in promoter region and CpG islands is positively correlated with gene expression levels and 3’UTR DHSs are negatively correlated with active expression of genes.

overall_design: Total RNA obtained from HeLa S3 cells.

first: Yuxiang

first: Yamei

last: Wang


title: Microtubule Affinity-Regulating Kinase 2 is associated with DNA damage response and cisplatin resistance in non-small cell lung cancer.

status: Public on Jun 22 2015

city: Isnes Gembloux

first: Roland

last: Hubaux

state: Namur

address: rue Jean Sonet 10

department: R&D

institute: StratiCELL

summary:
MARK2 expression is associated with the malignant phenotype, expression of DNA repair components, NF-κB inhibition and cell cycle transcription factors in lung cancer cells
We used microarrays to determine the global gene expression pattern associated with knockdown of MARK2

overall_design: 3 lung cancer cell lines overexpressing MARK2 have been selected to assess the gene expression pattern after MARK2 knockdown. RNA extraction and hybridization on Affymetrix microarrays have been done on 2 biological replicates for each line (H1993, H1693 and H1650) after shRNA lentiviral transduction and compared with respective contols using the empty vector pLKO.

first: Kelsie

middle: L

last: Thu

first: Emily

last: Vucic

first: Larissa

last: Pikor

first: Sonia

middle: H

last: Kung

first: Victor

last: Martinez

first: Mitra

last: Mosslemi

first: Daiana

last: Becker-Santos

first: Adi

middle: F

last: Gazdar

last: Lam

first: Wan


title: Gene expression patterns and TP53 mutations are associated with HPV RNA status, lymph node metastasis, and survival in head and neck cancer

status: Public on Jun 24 2015

city: Leipzig

first: Maciej

last: Rosolowski

address: Härtelstr. 16-18

institute: Institute for Medical Informatics, Statistics and Epidemiology (IMISE)

summary: A growing proportion of head and neck squamous cell carcinomas (HNSCC) is associated with the human papilloma virus (HPV), particularly HPV16. We compare tumors with different HPV16 DNA and RNA (E6*I) status from 290 consecutively recruited HNSCC patients by gene expression profiling and targeted sequencing of 50 genes. We confirm that the HPV16 DNA+ RNA+ tumors are molecularly distinct from the HPV-negative (DNA-) HNSCC and have elevated expression of cell cycle genes and rare TP53 mutations (3.6%, 1/28). We show that tumors with non-transcriptionally active HPV16 (DNA+ RNA-) are similar to HPV DNA- tumors regarding gene expression and frequency of TP53 mutations (47%, 8/17 and 43%, 72/167, respectively). Furthermore, we identify four gene expression clusters. They moderately but significantly differ in overall survival. One cluster exhibits high expression of immune response genes (IR) and contains most of the HPV16 DNA+ RNA+ patients. The IR cluster and disruptive TP53 mutations are associated with lymph node metastasis independent of HPV16 status and we validate each of these associations in another large data set. Consistent with earlier studies, disruptive TP53 mutations are prognostically unfavorable. Our findings underscore the importance of measuring the HPV16 RNA (E6*I) and TP53-mutation status for patient stratification and for the first time identify associations of an immune response-related gene expression cluster and TP53 mutations with lymph node metastasis in HNSCC.

overall_design: A total of 300 samples were considered. Quality control procedures were applied to microarray probe-level intensity files. A total of 270 tumor arrays remained after removing low-quality arrays, duplicate arrays, and arrays from non-HNSCC samples. Expression values were log2-transformed and normalized using RSN.

first: Gunnar

last: Wichmann


title: Genome wide transcriptomic analysis of sarcomatoid (E/S), rhabdoid (E/R) and non-sarcomatoid (E*) clear cell renal cell carcinoma

status: Public on Jun 18 2015

city: Houston

first: Kanishka

last: Sircar

state: TX

address: 1515 Holcombe Blvd., G1.3623

institute: MD Anderson Cancer Center

summary: An analysis of the biphasic epithelioid (E-) and sarcomatoid(S-) components of sarcomatoid RCC and advanced stage non-sarcomatoid RCC (E*) showed that: the E- and S- components shared a similar transcriptomic signature, despite morphologic differences; and that the transcriptome of sarcomatoid RCC was sharply distinct from non-sarcomatoid RCC.  The E- and R- components of rhabdoid RCC were also transcriptomically similar but distinct from RCC lacking rhabdoid/sarcomatoid features (E*).

overall_design: Total RNA processed and spotted on Illumina microarrays from the following patient samples: 38 sarcomatoid RCC (37 paired E- and S and 1 unpaired S-), 4 rhabdoid RCC (paired E- and R-) and 56 non-sarcomatoid RCC.  There are 8 replicate samples (7 sarcomatoid RCC and 1 rhabdoid RCC).


title: Genome wide analysis of sarcomatoid and non-sarcomatoid clear cell renal cell carcinoma

type:
Expression profiling by array
Genome variation profiling by SNP array

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

overall_design: Refer to individual Series


title: The UBC-40 Urothelial Bladder Cancer Cell Line Index [gene expression]

city: Madrid

first: Enrique

last: Carrillo de Santa Pau

address: C/ Melchor Fernández Almagro, 3

department: Cancer Cell Biology Programme

country: Spain

institute: Spanish National Cancer Research Centre (CNIO)

summary: This is a comprehensive genomic characterization of 40 urothelial bladder carcinoma (UBC) cell lines including information on origin, mutation status of genes implicated in bladder cancer (FGFR3, PIK3CA, TP53, and RAS), copy number alterations assessed using high density SNP arrays, uniparental disomy (UPD) events, and gene expression. Based on gene mutation patterns and genomic changes we identify lines representative of the FGFR3-driven tumor pathway and of the TP53/RB tumor suppressor-driven pathway. High-density array copy number analysis identified significant focal gains (1q32, 5p13.1-12, 7q11, and 7q33) and losses (i.e. 6p22.1) in regions altered in tumors but not previously described as affected in bladder cell lines. We also identify new evidence for frequent regions of UPD, often coinciding with regions reported to be lost in tumors. Previously undescribed chromosome X losses found in UBC lines also point to potential tumor suppressor genes. Cell lines representative of the FGFR3-driven pathway showed a lower number of UPD events. Overall, there is a predominance of more aggressive tumor subtypes among the cell lines. We provide a cell line classification that establishes their relatedness to the major molecularly-defined bladder tumor subtypes. The compiled information should serve as a useful reference to the bladder cancer research community and should help to select cell lines appropriate for the functional analysis of bladder cancer genes, for example those being identified through massive parallel sequencing.

overall_design: Expression levels were assessed in 20 bladder cell lines, included in the UBC-40 Urothelial Bladder Cell Line Index, with Affymetrix U133 array platform

first: Julie

last: Earl

first: Daniel

last: Rico

last: Carrillo-de-Santa-Pau

first: Benjamín

last: Rodríguez-Santiago

first: Marinela

last: Méndez-Pertuz

first: Herbert

last: Auer

first: Gonzalo

last: Gómez

first: H

last: Grossman

first: David

last: Pisano

first: Wolfgang

last: Schulz

first: Luis

last: Pérez-Jurado

first: Alfredo

last: Carrato

first: Dan

last: Theodorescu

first: Stephen

last: Chanock

first: Alfonso

last: Valencia

first: Francisco

middle: X

last: Real


title: Modulation of the cancer cell transcriptome by culture media formulations and cell density

status: Public on Jun 17 2015

first: Mark

middle: Seungwook

last: Kim

address: 7777 Knnight rd

department: Cancer Biology

summary: We investigated how varying the composition of cell culture formulations and growing cancer cells at different densities might affect tumor cells genotype.  Specifically, we compared gene expression profiles generated by human MDA-MB-231 human breast cancer cells cultured in different media (MEM, DMEM, or RPMI 1640) containing different concentrations of fetal bovine serum (FBS) or different sera (equine or bovine) that were grown at different cell densities.

overall_design: We have 6 different group (1. MDA-MB-231; MEM-10% FBS-90% confluence (MEM-1 and MEM-2). 2. MDA-MB-231; DMEM-10% FBS-90% confluence (DMEM-1 and DMEM-2). 3. MDA-MB-231; RPMI1640-10% FBS-90% confluence (RPMI-1 and RPMI-2) 4. MDA-MB-231; MEM-10% Horse serum-90% confluence (Horse-1 and Horse-2). 5. MDA-MB-231; MEM-0.1% FBS-90% confluence (FBS0.1-1 and FBS0.1-2). 6. MDA-MB-231; MEM-10% FBS-50% confluence (Con50-1 and Con50-2). Each group has duplicated. We analyzed; 1. Cell density (90% vs 50% confluence). 2. FBS concentration (10% FBS vs 0.1% FBS). 3. Sera (10% FBS vs 10% Horse serum). 4. Media (MEM vs DMEM vs RPMI1640)

first: Seung

first: Isaiah

last: Fidler