title: Footprint-free human fetal foreskin derived iPSCs: a tool for modeling hepatogenesis associated gene regulatory networks

city: Düsseldorf

first: Wasco

last: Wruck

address: Moorenstr. 5

institute: Universitätsklinikum Düsseldorf

summary: Induced pluripotent stem cells (iPSCs) are similar to embryonic stem cells and can be generated from somatic cells. We have generated episomal plasmid-based and integration-free iPSCs (E-iPSCs) from human fetal foreskin fibroblast cells (HFF1). E-iPSCs were fully characterized and their transcriptomes are more similar to that of hESCs (R2 = 0.9363) in comparison to viral-derived HFF1-iPSCs (R2 = 0.8176). We used an E-iPSC-line to model hepatogenesis in vitro. The differentiation of iPSCs into hepatocyte-like cells (HLCs) is a three-step process, from the undifferentiated E-iPSC to definitive endoderm (DE), hepatic endoderm (HE) and ultimately HLCs. The HLCs were characterized biochemically, i.e. glycogen storage, ICG uptake and release, UREA and bile acid production, as well as CYP3A4 activity. Ultra-structure analysis by electron microscopy revealed the presence of lipid and glycogen storage, tight junctions and bile canaliculi- all typical features of hepatocytes. Furthermore, the transcriptome of undifferentiated E-iPSC, DE, HE and HLCs were compared to that of fetal liver and primary human hepatocytes (PHH). K-means clustering identified 100 clusters which include developmental stage-specific groups of genes, e.g. OCT4 expression at the undifferentiated stage, SOX17 marking the DE stage, DLK and HNF6 the HE stage, HNF4a and Albumin is specific to HLCs, fetal liver and adult liver (PHH) stage. The lack of viral DNA integrations in these E-iPSCs endow them superior to viral-derived iPSCs for (i) modeling gene regulatory networks associated with hepatogenesis and gastrulation in general, (ii) toxicology studies and (iii) drug screening platforms.

overall_design: Total RNA obtained from induced pluripotent stem cells in several differentiation stages to hepatocyte-like cells

first: Peggy

last: Matz


title: S100A9 is a mediator of the ID1 functions in metastasis

status: Public on Aug 29 2017

city: Philadelphia

first: Louise

middle: C

last: Showe

state: PA

address: 3601 Spruce St

country: USA

institute: The Wistar Institute

summary: Metastasis is a major factor responsible for mortality in breast cancer patients. Id1 plays important roles in cell differentiation and promotes tumor angiogenesis, cell invasion and metastasis. Although Id1 is established as a critical factor for lung metastasis in breast cancer, the pathways and molecular mechanisms of Id1 functions in metastasis remains to be defined. Here we show that Id1 interacts with TFAP2A to suppress S100A9 expression. The expression of Id1 and S100A9 is inversely correlated in both breast cancer cell lines and clinical samples. We also find that S100A9 expression rescues the migratory and invasive phenotypes in vitro and metastasis in vivo induced by Id1 expression. S100A9 also suppresses the expression of known metastasis promoting factor RhoC activated by Id1 expression. Our results suggest that S100A9 mediates the functions of Id1 in breast cancer metastasis.

overall_design: MCF7 cell lines under three conditions: control, Id1 overexpression, Id2 overexpression. Each condition has 2 replicates

first: Qihong

last: Huang


title: Integrated analysis of genomic and epigenomic regulation of transcriptome identifies molecular subtypes of liver cancer (gene expression)

status: Public on Oct 05 2017

city: Suwon

first: Hyun Goo

last: Woo

address: 164 Worldcup-ro Yeongtong-gu

country: South Korea

institute: Ajou University School of Medicine

summary: We profiled DNA copy numbers, DNA methylation, and mRNA expression levels in the same HCC patients. To identify genes which transcriptional expression levels are regulated by genomic and/or epigenetic deregulation, we defined the copy number-correlated and methylation-correlated genes with their corresponding gene expression levels across the samples as genic and epigenetic deregulators, respectively.

overall_design: mRNA expression profiling of 64 hepatocellular carcinoma and 30 non-tumor were performed

first: Hyun

middle: G


title: The effects of HNF1b over-expression in PC3 cells

status: Public on Aug 25 2017

city: Cambridge

first: Chandra

last: Chilamakuri

address: Robinson Way

country: United Kingdom

institute: Cancer Research UK Cambridge Institute

summary: Genome-wide association studies (GWAS) and fine-mapping have identified several distinct variants within HNF1B associated with risk of prostate cancer, but its mechanism of action in this context is unknown.  To determine the effects of HNF1B in prostate cancer, we over-expressed HNF1B in PC3 cells to identify biological pathways affected by this change, and performed in vitro assays to validate our findings.

overall_design: Technical replicates of each of PC3 cells expressing empty vector (EV) and PC3 cells over-expressing HNF1B were compared, using Illumina HT12 microarrays.

first: Helen

last: Ross-Adams

first: Silvia

last: Halim

first: Sarah

last: Vowler


title: Synergistic antileukemic therapies in NOTCH-induced T-ALL

city: New York

first: Alberto

last: Ambesi-Impiombato

state: NY

address: 1130 St. Nicholas Avenue

department: ICG

institute: Columbia University

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

overall_design: Refer to individual Series


title: Gene expression profiling of CUTLL cell lines upon 17 drug treatments

summary: The clinical development of targeted therapies has been hampered by their limited intrinsic antitumor activity and the rapid emergence of resistance, highlighting the need to identify highly active and synergistic drug combinations. However, empirical synergistic drug screening approaches are challenging and elucidating the mechanisms that underlie such drug interactions is typically complex. Here we performed an expression based screen and network analyses to identify drugs amplyfiying the antitumor effects of NOTCH inhibition in T-ALL. These studies uncovered a novel and druggable synthetic lethal interaction between supression of protein translation and NOTCH inhibition in T-ALL. Our results illustrate the power of expression-based analyses towards the identification and functional characterization of new antitumor drug combinations for the treatment of human cancer.

overall_design: CUTLL cell lines were treated with drugs (Pyrvinium P, Vorinostat, Geldanamycin, Lanatoside C, Withaferin A, Prochlorperazine, Astemizole, Mefloquine, Trichostatin A, Rapamycin, Parthenolide, Valproic acid, Thioridazine, Trifluoperazine, Phenoxibenzamine, Wortmannin, Resveratrol) or DMSO control at 24hrs in 3 replicates.

first: Marta

last: Sanchez-Martin

first: Yue

last: Qin

first: Daniel

last: Herranz

first: Mukesh

last: Bansal

first: Tiziana

last: Girardi

first: Kim

last: De Keersmaecker

first: Andrea

last: Califano

first: Adolfo

middle: A

last: Ferrando


title: Expression data from human breast cancer cell MCF-7 and human gastric cancer cell SGC-7901

status: Public on Sep 18 2017

city: hohhot

first: xuemin

last: Cao

address: 内蒙古呼和浩特市玉泉区

country: China

institute: Inner Mongolia University

summary:
Piper longum L. is a well-known traditional antihyperlipidemic medicine，and it has ability to inhibit proliferation of cancer cells，potassium piperate (GBK) maybe have the same effect.
We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated and down-regulated genes during this process.

overall_design: treat and untreat with GBK on MCF-7 and SGC-7901 for RNA extraction and hybridization on Affymetrix microarrays. And then analysis the result to compare the express level between two cells that treat or untreat with GBK.

first: Xuemin

first: Huijuan

last: Yan


title: Expression data from DMOS- or paeoniflorin- treated human pancreatic cancer cell line Capan-1

status: Public on Sep 20 2017

city: Guangzhou

first: Lili

last: Gong

state: Guangdong

address: Jinsui Road

department: Zhongshan Ophthalmic Center

institute: Sun Yat-sen University

summary: Paeoniflorin (PF) is an active monoterpene glycoside extracted from Paeonia lactiflora Pall. Recent studies showed that PF has anti-tumor effects in various types of cancer. However, the function of PF in pancreatic cancer (PA) is largely unexplored. Here, we showed that PF suppressed growth of PA cell lines Capan-1 and MIAPaCa-2, and profoundly sensitized these cells to X-ray irradiation. Through a microarray analysis, we identified tumor-suppressor candidate gene HTRA3 as the most increased gene upon PF treatment in Capan-1 cells. Ectopic expression of HTRA3 led to reduced cell growth and increased expression of apoptotic protein Bax, suggesting a tumor suppressive role of HTRA3 in PA cells. Together, our results provide a set of genetic and biologic proofs that PF inhibited PA cell growth by upregulation of HTRA3.

overall_design: Capan-1 cells were with DMSO or 500 μM paeoniflorin. Each treatment was performed in triplicates.DMSO treatment was considered as control group.


title: Activation of human CD8+ T cells in renal cell carcinoma

city: Bari

first: Paola

last: Pontrelli

address: Piazza G.Cesare 11

department: Dept. of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J)

country: Italy

institute: University of Bari

summary:
BACKGROUND: Mammalian microRNAs (miR) regulate the expression of genes relevant for the development of adaptive and innate immunity against cancer. Since T cell dysfunction has previously been reported in patients with renal cell carcinoma (RCC; clear cell type), we aimed to analyse these immune cells for genetic and protein differences when compared to normal donor T cells freshly after isolation and 35 days after in vitro stimulation (IVS) with HLA-matched RCC tumor cells.
METHODS: We investigated gene expression profiles of tumor-reactive CD8+ T cells obtained from RCC patient and compared with their HLA-matched healthy sibling donors by microarray approach. In addition, miRNAs analysis was performed in a validation cohort of peripheral blood CD8+ T cells from 25 RCC patients compared to 15 healthy volunteers.
RESULTS: We observed that CD8+ T cells from RCC patients expressed reduced levels of anti-apoptotic and proliferation-associated gene products when compared with normal donor T cells both pre- and post-IVS. In particular, JAK3 and MCL-1 were down-regulated in patient CD8+ T cells versus their normal counterparts, likely due to defective suppressor activity of miR-29b and miR-198  in RCC CD8+ T cells. Indeed, specific inhibition of miR-29b or miR-198 in isolated peripheral blood mononuclear cells (PBMCs) from RCC patients, resulted in the up-regulation of JAK3 and MCL-1 proteins and significant improvement of cell survival in vitro.
CONCLUSIONS: Our results suggest that miR-29b and miR-198 dysregulation in RCC patient CD8+ T cells is associated with dysfunctional immunity and foreshadow the development of miR-targeted therapeutics to correct such T cell defects in vivo.

overall_design: CD8+ T cells were isolated from the PBMCs of autologous and allogeneic normal, healthy donors by negative selection using specific MACS magnetic beads (Miltenyi Biotec, Bergisch Gladbach, Germany) on MiniMACS columns, following the manufacturer's protocol and subsequently assessed for their functional and phenotypic profiles. For MLTC experiments, PBMCs from RCC patients or HLA-matched healthy donors were co-cultured in 24-well plates (Costar, Corning, USA) at 10^6 cells/well with irradiated RCC stimulator cells (10^5 cells/well) in AIM-V medium (Life Technologies, Invitrogen, Italy) supplemented with 10% heat-inactivated pooled human serum (Sigma (medium Mb)). Recombinant human IL-2 was added on day 3 (250 IU/mL; Proleukin, Chiron, and Emeryville, CA). Responder lymphocytes were restimulated weekly with 10^5 irradiated tumor cells in IL-2-containing medium for 2 weeks prior to responder CD8+ T cells isolation. Positively isolated CD8+ T cells were cultured for an additional 2 weeks. On day 0 and day 35 of culture, CD8+ T cells were analyzed for gene and miRNA expression profiles. Responder lymphocytes were restimulated weekly with 10^5 irradiated tumor cells in IL-2-containing medium for 2 weeks prior to responder CD8+ T cells isolation. Positively isolated CD8+ T cells were cultured for an additional 2 weeks. On day 0 and day 35 of culture, CD8+ T cells were analyzed for gene expression profiles. Total RNA was isolated from freshly-isolated and day 35 cultured CD8+ T cells using TRIzol© reagent (Life Technologies), according to the manufacturer's instructions. Total RNA integrity was assessed by electrophoresis using the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA). Total RNA was processed and hybridized on to the GeneChip Human Genome U133A Array (Affymetrix, Santa Clara, CA), which contains 22,283 gene probe sets, representing approximately 12,000 well-characterized human genes (Affymetrix, Santa Clara, CA).

first: Margherita

last: Gigante

first: Wolfgang

last: Herr

first: Maddalena

first: Morena

last: D’Avenia

first: Gianluigi

last: Zaza

first: Elisabetta

last: Cavalcanti

first: Matteo

last: Accetturo

first: Giuseppe

last: Lucarelli

first: Michele

last: Battaglia

first: Walter

middle: J

last: Storkus

first: Loreto

last: Gesualdo

first: Elena

last: Ranieri


title: OCT4 and SOX2 Work as Transcriptional Activators in Reprogramming Human Fibroblasts

status: Public on Aug 30 2017

first: Mark

last: Ptashne

address: 1275 York Ave

department: Molecular Biology Program

institute: Sloan Kettering Institute

summary: SOX2 and OCT4, in conjunction with KLF4 and cMYC, are sufficient to reprogram human fibroblasts to induced pluripotent stem cells (iPSCs), but it is unclear if they function as transcriptional activators or as repressors. We now show that, like OCT4, SOX2 functions as a transcriptional activator. We substituted SOX2-VP16 (a strong activator) for wild-type (WT) SOX2, and we saw an increase in the efficiency and rate of reprogramming, whereas the SOX2-HP1 fusion (a strong repressor) eliminated reprogramming. We report that, at an early stage of reprogramming, virtually all DNA-bound OCT4, SOX2, and SOX2-VP16 were embedded in puta- tive enhancers, about half of which were created de novo. Those associated with SOX2-VP16 were, on average, stronger than those bearing WT SOX2. Many newly created putative enhancers were tran- sient, and many transcription factor locations on DNA changed as reprogramming progressed. These results are consistent with the idea that, during re- programming, there is an intermediate state that is distinct from both parental cells and iPSCs.

overall_design: 11 Samples analyzed, 4 attributes- MRC5 (mock infected) cells (2 replicates), OSKM (day 5) (3 replicates), OS(v)KM (3 replicates), hES/hiPS (3 replicates)

first: Santosh

last: Narayan


title: Patients Experiencing Statin-Induced Myalgia Exhibit a Unique Program of Skeletal Muscle Gene Expression Following Statin Re-challenge

status: Public on Aug 18 2017

city: Memphis

first: Marshall

middle: B

last: Elam

state: TN

address: 1030 Jefferson Avenue

department: Research

institute: VA Medical Center

summary: Statins, the 3-hydroxy-3-methyl-glutaryl (HMG)-CoA reductase inhibitors, are widely prescribed for treatment of hypercholesterolemia. Although statins are generally well tolerated, up to ten percent of patients taking statins experience muscle related adverse events. Myalgia, defined as muscle pain without elevated creatinine phosphokinase (CPK) levels, is the most frequent reason for discontinuation of statin therapy.  The mechanisms underlying statin-associated myalgia are not clearly understood. To elucidate changes in gene expression associated with statin-induced myalgia, we compared profiles of gene expression in the biopsied skeletal muscle from statin-intolerant patients undergoing statin re-challenge versus those of statin-tolerant controls. A robust separation of statin-intolerant and statin-tolerant cohorts was revealed by Principal Component Analysis of differentially expressed genes (DEGs). To identify putative gene expression and metabolic pathways that may be perturbed in skeletal muscles of statin intolerant patients, we subjected DEGs to Ingenuity Pathways (IPA) and DAVID (Database for Annotation, Visualization and Integrated Discovery) analyses. The most prominent pathways altered by statins included cellular stress, apoptosis, senescence and DNA repair (TP53, BARD1, Mre11 and RAD51); activation of pro-inflammatory immune response (CXCL12, CST5, POU2F1); protein catabolism, cholesterol biosynthesis, protein prenylation and RAS-GTPase activation (FDFT1, LSS, TP53, UBD, ATF2, H-ras). Based on these data we tentatively conclude that persistent myalgia in response to statins may emanate from cellular stress underpinned by mechanisms of post-inflammatory repair and regeneration. We also posit that this subset of individuals are genetically predisposed to eliciting altered statin metabolism and/or increased end-organ susceptibility that lead to a range of statin-induced myopathies. This mechanistic scenario further bolstered by the discovery that a number of single nucleotide polymorphisms (e.g., SLCO1B1, SLCO2B1 and RYR2) associated with statin myopathy were observed with increased frequency among statin-intolerant study subjects.

overall_design: Compare gene expression (RNA) in muscle biopsies from statin tolerant and  statin intolerant individuals following statin rechallenge

first: Rajendra

last: Raghow


title: iPSCs from patients with NBS as a model uncovering disease mechanisms and a screening platform for anti-oxidants modifying genomic stability [iPSCs]

first: Wasco

last: Wruck

country: Germany

summary: Nijmegen Breakage Syndrome (NBS) is a rare autosomal recessive genetic disorder, first described 1981 in Nijmegen, Holland. The characteristics of NBS include genomic instability (resulting in early onset of malignancies), premature aging, microcephaly and other growth retardations, immune deficiency, and impaired puberty and fertility in females. The consequence of these manifestations is a severe decrease in average life span, caused by cancer or infection of the respiratory and urinary tract.  We reprogrammed fibroblasts from NBS patients into induced pluripotent stem cells (iPSCS) to bypass premature senescence and to generate an unlimited cell source for modeling purposes.  We screened the influence of antioxidants on intracellular levels of ROS and DNA damage and found that EDHB was able to decrease DNA damage in the presence of high oxidative stress.  Furthermore, we found that NBS fibroblasts, but not NBS-iPSCs were more susceptible to the induction of DNA damage than their normal counterparts.  We performed global transcriptome analysis comparing NBS to normal fibroblasts and NBS-iPSCs to hESCs. There, we found, that TP53 was activated and cell cycle genes broadly down-regulated in NBS fibroblasts and up-regulation of glycolysis specifically in NBS-iPSCs.

overall_design: Total RNA obtained from fibroblasts of patients with Nijmegen-Breakage Syndrome reprogrammed to induced pluripotent stem cells

first: Barbara

last: Mlody


title: Altered expression of genes in HOXD-AS1 knockdown prostate cancer cells

first: Xu

last: Chen

address: 107. W. Yanjiang Road

department: Department of Urology

institute: Sun Yat-sen Memorial Hospital

summary: Castration-resistant prostate cancer (CRPC) that arise after the failure of androgen deprivation therapy is a leading cause of deaths in prostate cancer patients. HOXD-AS1 is reported to play a role in bladder cancer and neuroblastoma. However, its function and underlying mechanism in CRPC remains unknown. The goal of this study is to identify the target genes of HOXD-AS1 in prostate cancer. Our results inditcate that the genes regulated by HOXD-S1 involved in a variety of biological functions, such as proliferation and and Androgen Receptor signaling.

overall_design: prostate cancer cell lineLNCaP was transfected with the contol siRNA or two different HOXD-AS1 siRNA for 48h. The RNA of the transfected cells was extracted and hybridized on Affymetrix microarrays. We indentified the putative target genes of HOXD-AS1 in both HOXD-AS1 siRNAs by comparing  the diferent expressed genes among control, si-HOXD-AS1-1 and si-HOXD-AS1-2. We futher validated the data of microarray in LNCaP and PC-3 by RT-qPCR and Western bloting.

first: Peng

last: Gu

first: Tianxin

last: Lin

first: Jian

last: Huang


title: iPSCs from patients with NBS as a model uncovering disease mechanisms and a screening platform for anti-oxidants modifying genomic stability


title: SOX17 regulates cholangiocyte differentiation and acts as a tumour suppressor in cholangiocarcinoma

status: Public on Aug 31 2017

city: Derio

first: Jose

middle: Luis

last: Lavin

state: Bizkaia

address: Parque Tecnológico de Bizkaia Building 502, Floor 0

country: Spain

institute: CIC bioGUNE

summary: Background and aims: Cholangiocarcinoma (CCA) is a heterogeneous group of malignancies with features of biliary tract differentiation. Incidence is increasing worldwide and these cancers collectively represent the second most common primary liver tumour. CCAs are characterized by genetic and epigenetic alterations that determine their pathogenesis. Hypermethylation of the SOX17 promoter was recently reported in human CCA tumours. SOX17 seems to be a key transcription factor for biliary embryogenesis. Here, we evaluated the role of SOX17 in cholangiocyte differentiation and in cholangiocarcinogenesis.   Methods: SOX17 expression and function was evaluated during the differentiation of human induced pluripotent stem cells (iPSC) into cholangiocytes, in the dedifferentiation of normal human cholangiocytes (NHC) and in cholangiocarcinogenesis. Lentiviruses overexpressing or knocking-down SOX17 (Lent-SOX17 and Lent-shRNA-SOX17, respectively) were used. Gene expression arrays were performed.  Results: SOX17 expression is highly induced in the later stages of cholangiocyte differentiation from iPSC, and mediates the acquisition of the biliary markers cytokeratin (CK) 7 and 19, as well as fibronectin. In addition, SOX17 becomes progressively downregulated in NHC over serial cell passages in vitro and this event is associated with cellular senescence; however, experimental SOX17 knocking-down in differentiated NHC decreased the expression of both CK7 and 19 without affecting cellular senescence. SOX17 expression is reduced in CCA cells compared to NHC, as well as in human CCA tissue compared to human gallbladder tissue or NHC. In a murine xenograft model, overexpression of SOX17 in CCA cells decreased their tumorigenic capacity related to increased oxidative stress and apoptosis. Interestingly, overexpression of SOX17 in NHC did not affect their survival. Moreover, SOX17 overexpression inhibited the Wnt/β-catenin-dependent proliferation in CCA cells and was associated with upregulation of biliary epithelial markers and restoration of the primary cilium length. Both Wnt3a and TGFβ1 decreased SOX17 expression in NHC in a DNMT1-dependent manner. Inhibition of DNMT1 in CCA cells with siRNAs or pharmacological drugs upregulated SOX17 expression.  Conclusion: SOX17 regulates the cholangiocyte phenotype and becomes epigenetically downregulated in CCA. SOX17 acts as a tumour suppressor in CCA, and restoration of its expression may have important therapeutic value.

overall_design: Genome-wide changes in gene expression of normal human cholangiocytes (NHC) with experimental SOX17 inhibition and cholangiocarcinoma (CCA) human cells with experimental SOX17 overexpression were generated by microarray gene expression arrays.

first: Jesús

middle: M

last: Bañales Asurmendi

first: Maite

last: Azpitarte

first: Ana

last: Aransay

middle: L

last: Lavín


title: Gene expression profileing of CUTLL cell lines upon Withaferin A treatment

first: Alberto

last: Ambesi-Impiombato

overall_design: CUTLL cell lines were treated with Withaferin A or DMSO control at 24hrs in 6 replicates.

first: Marta

last: Sanchez-Martin

first: Yue

last: Qin

first: Daniel

last: Herranz

first: Mukesh

last: Bansal

first: Tiziana

last: Girardi

first: Kim

last: De Keersmaecker

first: Andrea

last: Califano

first: Adolfo

last: Ferrando


title: HepG2 cells undergoes postmitotic neuron-like differentiation in response to inhibition of epigenetic factors

city: Nanjing

first: Ying

last: Cao

address: 12 Xuefu Rd., Pukou High-Tech Zone

institute: Nanjing University

summary:
Cancer cells are not fully differentiated cells. Re-differentiation of cancer cells is expected to drive the loss of cancer cell malignancy. We found that upon the treatment of a combination of inhibitors against class I HDACs, DNMTs, EZH2 and LSD1, the hepatocellular carcinoma cell line HepG2 shows neuron like differentiation.
We used microarray to analyze global gene expression change in HepG2 cells after differentiation induced by chemical treatment.

overall_design: HepG2 cells were treated with a combination of HDAC inhibitor TSA, DNMT inhibitor AZA, EZH2 inhibitor EPZ-6438 and LSD1 inhibitor SP2509 in appropriate doses. Cells underwent significant morphological change after eight days of treatment, as compared with HepG2 cells treated with vehicle (DMSO). Vehicle treated cells, which served as a control,  and chemical inhibitor combination treated cells were collected and subjected to microassay analysis. Two samples, one was HepG2 cells treated with DMSO and the other was HepG2 cells treated with inhibitor combination, were used for microarray assay.

first: Zan

last: Zhang


title: Transcriptional profiling of proliferating and differentiating SPC04 human neural stem cell line

city: London

first: Sylvane

last: Desrivieres

address: 16 De Crespigny Park

department: MRC-SGDP Centre

institute: King's College London

summary:
Here we used microarray expression profiling to characterise global changes in gene expression during stages of proliferation and differentiation of human neural stem cells
Comparing gene expression profiles of undifferentiated cells with pre-differentiated cells, or cells that have been induced to differentiate for 3 or 7 days, led to identification of ~3540 genes that were differentially expressed between these stages, with most of the changes in gene expression occurring 7 days after differentiation. Gene ontology clustering analyses indicated enrichment of genes downregulated at differentiation day 7 for genes involved in cell cycle  and DNA metabolic processes. Upregulated genes were mainly enriched for genes involved in cell adhesion, synaptic transmission, neuron morphogenesis and differentiation and synapse formation and organization (Desrivières et al. Mol Psychiatry. 2014 Feb 11. doi: 10.1038/mp.2013.197).

overall_design: Total RNA obtained from triplicate experiments during which SPC04 cells that had been pre-differentiated for 2 days, or further subjected to 3 or 7 days of differentiation compared to control undifferentiated (i.e., proliferating) SPC04 cells.

last: Desrivières


title: The effect of MPO-ANCA on LPS-primed human monocytes

status: Public on Aug 23 2017

first: Paul

last: Lavender

address: 5th Floor, Tower Wing, Great Maze Pond

department: School of Immunology and Microbial Sciences

summary: Human monocytes treated with LPS and MPO-ANCA  or control IgG

overall_design: total RNA isolated from monocytes

first: Michael

last: Robson


title: HIV-1 selectively targets gut-homing CCR6+CD4+ T-cells via mTOR-dependent mechanisms.

city: Montréal

first: Jean-Philippe

last: Goulet

state: Québec

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

country: Canada

institute: Université de Montréal

summary:
In an effort to identify mechanisms governing HIV-1 permissiveness in gut-homing Th17 cells, we analyzed the transcriptome of CCR6+ versus CCR6- T-cells exposed to the gut-homing inducer retinoic acid (RA) and performed functional validations in colon biopsies of HIV-infected individuals receiving ART (HIV+ART).
Together, our results identify mTOR as a druggable key regulator of HIV permissiveness in gut-homing CCR6+ T-cells.

overall_design: Total cellular RNA was extracted from Th17-polarized CD4+ T-cells from 6 donors in two experimental conditions (ATRA-stimulated and unstimulated).

first: Delphine

last: Planas

first: Yuwei

first: Patricia

last: Monteiro

first: Anni

last: Gosselin

first: Ariberto

last: Fassati

first: Jean-Pierre

last: Routy

first: Petronela

last: Ancuta


title: Ultrasonic surgical aspirate is a reliable source for adult neural progenitor cells (aNPCs)

status: Public on Aug 15 2017

city: Oslo

first: Biljana

last: Stangeland

address: Sognsvannsveien 20

department: Institute of Surgical Research

country: Norway

institute: Oslo University Hospital

summary: Adult neural progenitor cells (aNPCs) are a potential source for cell based therapy for neurodegenerative diseases and traumatic brain injuries. We show that the ultrasonic aspirate samples that are typically considered as a waste after surgery are a great source for aHNPCs.

overall_design: Total RNA isolated from the core tumor tissues (Fr-Co) was compared to that from the ultrasonic aspirates (Fr-UA). Total RNA isolated from the tumorspheres generated from core tumor tissues (Sp-Co) was compared to the total RNA isolated from tumorspheres generated from ultrasonic aspirates (Sp-UA).


title: AML cell line expression response to SY-1425 (tamibarotene)

city: Watertown

first: Eric

last: Olson

state: MA

address: 480 Arsenal Street

institute: Syros Pharmaceuticals

summary: AML cell lines were treated with either vehicle or SY-1425 (tamibarotene), a potent and selective agonist of retinoic acid receptor alpha (RARa), and assayed by microarray expression analysis.

last: McKeown

first: Emily

last: Lee

first: Chris

last: Fiore


title: Altered global gene profile in KSHV-infected siHa cells

status: Public on Aug 13 2017

city: New Orleans

first: Zhiqiang

last: Qin

state: LA

address: 1700 Tulane Ave

institute: LSUHSC-NO

summary: The Kaposi sarcoma-associated herpesvirus (KSHV) is the causative agent of Kaposi sarcoma (KS), the most common HIV/AIDS-associated tumor worldwide. Transmission routes of KSHV in the general population are poorly understood. Whereas sexual transmission appears to be common in homosexual men, the evidence for heterosexual transmission is less convincing. In fact, KSHVDNA sequences have been detected in the prostate, semen, and in the female genital tract. Persistent infection with high-risk human papillomavirus (HPV) is the major risk factor and is a requirement for the development of cervical cancer. However, it remains unknown the interaction between KSHV and HPV, and the contribution of KSHV to cervical cancer development and pathogenesis.  In the present study, we used Illumina microarray to detect the global gene profile altered in KSHV-infected siHa cervical cancer cell-line containing integrated HPV16 genome.

overall_design: SiHa cells were infected by KSHV and the gene expression signature was compared to the corresponding mock cells

first: Lu

last: Dai

first: Zhen

last: Lin

first: Zabaleta

last: Jovanny


title: Metabolic drivers of ovarian cancer tumor growth

city: Birmingham

first: Narendra

last: Wajapeyee

state: AL

address: 720 20th Street South, Kaul 540A

department: Department of Biochemistry and Molecular Genetics

institute: University of Alabama at Birmingham

summary: Effect of SHMT1 knockdown on ovarian cancer tumor growth was analyzed

overall_design: PEO4 cells expressing non-silencing shRNA or SHMT1 shRNAs were analyzed for gene expression alterations

first: Romi

last: Gupta

first: Shaillay

last: Dogra


title: Transcriptome profiling of CD44highCD24low(CSC) and CD44lowCD24high(Non-CSC) SCC25 cells

status: Public on Aug 16 2017

city: KOLKATA

first: Sangeeta

last: Ghuwalewala

state: West Bengal

address: 4, Raja S. C. Mullick Road

department: Cancer Biology and Inflammatory Disorder Division

country: India

institute: CSIR-Indian Institute of Chemical Biology

summary: In the present study, we have characterized the putative Cancer Stem Cell population of Oral Squamous Cell Carcinoma by various cellular and molecular assay. Subsequently we performed gene expression profiling of  SCC25 cell line with CD44highCD24low(CSC) and CD44lowCD24high(Non-CSC) phenotypes using illumina BeadChip Array. Further, systematic computational analysis was performed to identify CSC-like gene signatures in the oral cancer cells. Differentially expressed genes were subjected to pathway analysis in IPA.  The analysis lead to the identification of few relevant signaling pathway implicated in stemness.

overall_design: Determination of gene signature in Cancer stem-like population of  oral cancer cell line SCC25 by microarray

first: Susanta

last: Roychoudhury


title: Selective inhibition of Pin1 with a covalent small molecule   targeting its catalytic domain

status: Public on Aug 11 2017

city: Trieste

first: Silvano

last: Piazza

address: localita' Padriciano 99

institute: ICGEB

summary: From a mechanism-based screening we have identified a novel Pin1 suicide inhibitor, KPT-6566, able to selectively inhibit Pin1 and target it for degradation. We have performed a transcriptiomic analysis comparing Pin1 specific RNA interference in MDA-MB 231 cells with KPT-6566 treatment to assess specificity of the KPT-6566 towards Pin1.

overall_design: One cell line was transfected with control siRNA or Pin1 siRNA or treated with KPT-6566 or DMSO. The study comprises 10 experimental points, including duplicate experiments for each siRNA condition and triplicate experiments for the treatment with KPT-6566 or DMSO.

first: Elena

last: Campaner

first: Alessandra

last: Rustighi

first: Alessandro

last: Zannini

first: Yari

last: Ciani

first: Giannino

last: Del Sal


title: Expression data from human osteosarcoma cells after transfected with klf-4 and treated with Adriamycin

city: hangzhou

first: yangling

last: li

state: zhejiang

address: 866 Yuhangtang Road

department: College of Pharmaceutical Sciences

institute: zhejiang university

summary: The KHOS/NP osteosarcoma cells were seeded onto the 60mm cell culture plate, then treated with pccl vector, Adriamycin(50nM) and pccl-klf-4. Total RNA was collected from these cells using TRIzol® Reagent according to the manufacturer’s instructions.

overall_design: Evaluate the effect of klf-4 and Adriamycin regulated gene expression in osteosarcoma cells

first: Meidan

last: Ying

first: Qiaojun

last: He


title: Circadian expression data from muscle stem cells from adult and aged mice fed with normal diet or calorie restricted

status: Public on Aug 10 2017

city: Barcelona

first: Aikaterini

last: Symeonidi

state: Barcelona

address: Baldiri i Reixac, 10

department: Oncology

institute: Institut for Research in Biomedicine (IRB-Barcelona)

summary:
Caloric restriction (CR) enhances the function of adult stem cells and significantly extends the lifespan of many organisms including rodents. CR increases the expression of Period genes in several tissues in mice, and the circadian machinery is strongly influenced by feeding and metabolic pathways.
Importantly, Bmal1-deficient mice, or Period/Timeless-deficient Drosophila are refractory to the lifespan extension induced by CR. We therefore studied whether CR could prevent the ageing related circadian reprogramming we had observed in muscle SCs.

overall_design: Per-1 venus C57B6/J aged and adult mice were fed either ad libitum with control diet or a 30% food reduction compared to the ad libitum group intake of calorie restricted diet. The experiment was 25 week-long and started after an adaption period of 3 weeks, where calorie restricted animals were subjected to a 10% food reduction per week. The age groups were composed of 19-29 week old and 55-69 week old mice at the start of the adaption period. Four mice were used per each of the 6 time points (ZT0, ZT4, ZT8, ZT12, ZT16, ZT20) and per diet group. For sample collection, one mouse per diet group was sacrificed per day, all belonging to one time point.

first: Guiomar

last: Solanas

first: Francisca

last: Peixoto

first: Eusebio

last: Perdiguero

first: Vanessa

last: Ruiz-Bonilla

first: Debayan

last: Datta

first: Purificación

last: Muñoz-Cánovas

first: Salvador

last: Aznar Benitah


title: Expression data from epidermal stem cells from young mice fed either with normal diet or high fat diet

summary:
High fat diet (HFD), if prolonged, leads to obesity thereby accelerating the development of many ageing-related pathologies including chronic inflammation, cardiovascular disease, diabetes, and a higher predisposition to develop cancer. We asked whether HFD could reprogram the circadian output of young stem cells in a manner similar to what we observed during physiological ageing.
HFD has been recently shown to induce a rewiring of the liver circadian transcriptome and metabolome, although in an obesity-independent manner. We therefore fed young (8 week old) C57Bl6 mice with HFD or its control diet for 7-weeks, a time when mice had not yet become obese, and performed circadian transcriptome analysis.

overall_design: Eight week old female C57B6/J mice were fed ad libitum either with high fat or with the respective control diet. The experiment lasted for 7 weeks, and four mice were used per each of the 6 time points (ZT0, ZT4, ZT8, ZT12, ZT16, ZT20) and per diet group. For sample collection, 4 mice per diet group were sacrificed per day, all belonging to one time point.


title: Circadian expression data from epidermal stem cells from adult and aged mice fed with normal diet or calorie restricted

summary:
Caloric restriction (CR) enhances the function of adult stem cells and significantly extends the lifespan of many organisms including rodents. CR increases the expression of Period genes in several tissues in mice, and the circadian machinery is strongly influenced by feeding and metabolic pathways.
Importantly, Bmal1-deficient mice, or Period/Timeless-deficient Drosophila are refractory to the lifespan extension induced by CR. We therefore studied whether CR could prevent the ageing related circadian reprogramming we had observed in epidermal SCs.


title: Circadian expression data from epidermal stem cells from young and aged mice

summary:
Circadian adaptation is thought to have maximized organismal fitness by anticipating and synchronizing physiological functions to the day-night oscillations imposed by the rotation of the earth.
The function of mammalian adult stem cells is under tight circadian control, and conditional deletion of the core clock component Bmal1 in murine tissues results in their premature ageing. In addition, complete Bmal1 and Clock knockout mice show a significantly shortened lifespan. However, it is not clear to what extent circadian disruption is causative of ageing. Moreover, if and how circadian oscillations are altered during physiological ageing in adult stem cells is not known.

overall_design: C57B6/J female mice were used to perform a circadian transcriptome analyses with EpSCs from 8 week old and aged mice between 102-116 week old. Four mice were used per each of the 6 time points (ZT0, ZT4, ZT8, ZT12, ZT16, ZT20) and per age group.


title: Expression data from muscle stem cells from young mice fed either with normal diet or high fat diet in a circadian manner


title: FSTL1 promotes cancer cell invasion through pro-invasive and pro-inflammatory pathways

status: Public on Aug 09 2017

city: Singapore

first: Prabha

last: Sampath

state: Singapore

address: 8A Biomedical Grove

department: Institute of Medical Biology

country: Singapore

institute: Institute of Medical Biology

summary: This study identifies FSTL1 as a key component of tumor invasion in cutaneous squamous cell carcinoma

overall_design: Total RNA from SCC13 cells stably transduced with a scrambled shRNA or shRNA against human FSTL1 were subjected to microarray analysis

first: Gopinath

last: Sundaram


title: Identification of PURPL regulated genes in HCT116 cells

status: Public on Aug 03 2017

city: Bethesda

first: Yuelin

middle: Jack

last: Zhu

state: MD

address: 9000 Rockville Pike

department: Genetics Branch, Center for Cancer Research

institute: NCI

summary: Analysis of changes in gene expression profile upon depletion of PURPL in HCT116 cells. The hypothesis in this study is that PURPL regulates gene expression in the p53 pathway.

overall_design: Total RNA was isolated from HCT116_PURPL WT and KO cells.

first: Xiao

last: Li

first: Ashish

last: Lal


title: Adult stem cells undergo circadian reprogramming during ageing

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

overall_design: Refer to individual Series


title: Gemcitabine induced TIMP-1 attenuates therapy response and promotes tumour growth and liver metastasis in pancreatic cancer

status: Public on Aug 08 2017

city: Oxford

first: Ruud

last: van Stiphout

address: Old Road Campus Research Building

institute: University of Oxford

summary: Gemcitabine constitutes one of the backbones for chemotherapy treatment in pancreatic ductal adenocarcinoma (PDAC) but patients often show poor or complete lack of response to this agent. Molecular markers downstream of Gemcitabine treatment in pre-clinical models may provide an insight into resistance mechanisms. We identified potential secretory biomarkers of Gemcitabine resistance (response) in the transgenic KRasG12D; Trp53R172H; Pdx-1 Cre (KPC) mouse model of PDAC using cytokine arrays. We validated the oncogenic role of the cytokine tissue inhibitor of matrix metalloproteinases 1 (TIMP-1) in primary pancreatic tumours and metastasis using both in vitro techniques and animal models. We identified potential pathways affected downstream of TIMP-1 using the Illumina Human H12 array. Our findings were validated in both primary and metastatic models of pancreatic cancer. Gemcitabine increases inflammatory cytokines including TIMP-1 in the KPC mouse model. TIMP-1 is upregulated in patients with pancreatic intraepithelial neoplasias grade 3 and PDAC lesions relative to matched normal pancreatic tissue. Additionally, we demonstrate that TIMP-1 plays a role in tumour proliferation and angiogenesis, while inhibition resensitises to gemcitabine and radiotherapy. Strikingly, serum TIMP-1 levels support the formation of liver metastasis through the recruitment of immunosuppressive cell populations, such as CD11b+Gr1+ myeloid cells and CD4+CD25+FOXP3+ Tregs to the hepatic microenvironment. Gemcitabine treatment results in upregulation of the pro-tumourigenic/pro-metastatic cytokine TIMP-1, which partially explains the therapeutic resistance and poor responses to this therapy in PDAC. Our study provides a rationale for the development and testing of TIMP-1 specific inhibitors in addition to chemo/radiotherapy.

overall_design: Wild-type and TIMP1 knock down PANC1cell lines are compared with in each group six replicates. Wild-type (N=6): PANC1 with a lentiviral integration of the pLKO.1 puro vector. TIMP1 knock down (N=6): PANC1 with a lentiviral integration of pLKO.1 vector containing shRNA against human TIMP1.

first: Zenobia

last: D'Costa

first: Eric

last: O'Neill

first: Emmanouil

last: Fokas


title: Expression data from KEAP1 overexpression and NRF2 siRNA knockdown of A549 NSCLC cell

status: Public on Aug 02 2017

city: HANGZHOU

first: XIUWEN

last: TANG

address: YUHANGTONG ROAD

department: BIOCHEMISTRY AND GENETICS

institute: ZHEJIANG UNIVERSITY SCHOOL OF MEDICINE

summary:
KEAP1 overexpressed and NRF2 siRNA knockdown A549 NSCLC cells were used to identify downstream genes of NRF2 pathway separately and by combinatorial analysis. We used triplicate microarrays of transfected A549 cells with mKeap1-GFP for overexpression, siRNAs targeting NRF2 for knockdown and siGFP as control respectively. As a result, we identified several genes which are involved in cancer metabolic functions in these cells.
We used microarrays to identify the gene downregulated in both KEAP1 overexpressed and NRF2 siRNA knockdown A549 NSCLC cells and found a subset of downregulated genes which are involved in metabolic functions.

overall_design: We divided microarrays into three groups. One group with A549 cells that were stably transfected with mKeap1-GFP construct for overexpression, second group with knockdown of NRF2 with specific siRNA and third group contains siGFP transfected control cells. Triplicates of both KEAP1 overexpression and NRF2 siRNA knockdown groups were analyzed and compared with control microarray data.

first: Akhileshwar

last: Namani

first: Xiu

last: Wang

first: Xiuwen

last: Tang


title: Expression profiling of 5 novel breast cancer cell lines

city: Montreal

first: Matthew

last: Annis

state: Quebec

address: 1160 Av des Pin O Rm508

department: Rosalind and Morris Goodman Cancer Research Centre

institute: McGill University

summary: The Fra-1 transcription factor promotes tumor cell growth, invasion and metastasis. While characterizing five breast cancer cell lines derived from primary human breast tumors, we identified BRC-31 as a novel basal-like cell model that expresses elevated Fra-1 levels. BRC-31 cells display elevated FAK, SRC and ERK2 phosphorylation relative to luminal breast cancer models. Inhibition of this signaling axis, through the use of pharmacological inhibitors, reduces the phosphorylation and stabilization of Fra-1. Elevated integrin αVβ3 expression in these cells suggested that integrin receptors might activate this FAK-SRC-ERK2 signaling axis to enhance Fra-1 phosphorylation. These cells also express high levels of uPAR, a GPI-anchored receptor that has been shown to enhance integrin-mediated signaling initiated by Vitronectin engagement. Transient knockdown of uPAR in BRC31 cells grown on Vitronectin reduces Fra-1 phosphorylation and stabilization and uPAR and Fra-1 are required for Vitronectin-induced cell invasion. In clinical samples, a molecular component signature consisting of Vitronectin-uPAR-uPA-Fra-1 predicts poor overall survival in patients with breast cancer and correlates with a Fra-1 transcriptional signature. Taken together, we have identified a novel-signaling axis that leads to phosphorylation and stabilization of Fra-1, a transcription factor that is emerging as an important modulator of breast cancer progression and metastasis.

overall_design: Gene expression profiling of RNA extracted from 5  human breast cancer cell lines, BRC-17,BRC-31, BRC-32, BRC-36, BRC-196.

first: Veronique

last: Ouellet

first: John

last: Rennhack

first: Claudine

last: Rancourt

first: Anne-Marie

last: Mes-Masson

first: Eran

middle: R

last: Andrechek

first: Peter

last: Siegel


title: Human monocyte subsets are transcriptionally and functionally altered in aging in response to pattern recognition receptor agonists [ExVivo]

status: Public on Jul 27 2017

city: Cleveland

last: Wilkinson

state: Ohio

address: 2103 Cornell Road

department: Pathology / Systems Biology & Bioinformatics

institute: Case Western Reserve University

summary: Age-related alterations in immunity have been linked to increased incidence of infections and decreased responses to vaccines in the aging population. Human peripheral blood monocytes are known to promote antigen presentation and antiviral activities; however, the impact of aging on monocyte functions remains an open question. We present an in-depth global analysis examining the impact of aging on classical (CD14+CD16-), intermediate (CD14+CD16+), and non-classical (CD14dimCD16+) monocytes. Monocytes sorted from non-frail healthy adults (18-40 yrs) and old (≥ 65 yrs) individuals were analyzed after stimulation with TLR4, TLR7/8, and RIG-I agonists. Our data showed under non-stimulated conditions, monocyte subsets did not reveal significant age-related alternations; however, agonist stimulated-monocytes from adults and old subjects did show differences at the transcriptional and functional levels. These alternations in many immune-related transcripts and biological processes resulted in reduced production of IFNα, IFN, IL-1β, CCL20, and CCL8, and higher expression of CX3CR1 in monocytes from old subjects. Our findings represent a comprehensive analysis of the influence of human aging on pattern recognition receptors signaling and monocyte functions, and have implications for strategies to enhance the immune response in the context of infection and immunization.

overall_design: Healthy non-frail individuals enrolled into the study were arranged into two groups:  adults (YNG) and old (OLD) subjects (n=11 per group). The average age for adults were 30 yrs (range 24-36 yrs), whereas old individuals were 73 yrs (range 67-83 yrs). Individuals with comorbid conditions including cancer (within the last 5 yrs for those greater than 65 yrs), immunocompromising disorders, and steroid usage were excluded; whereas inclusion criteria included controlled hypertension, occasional/tolerable “aching joints” from arthritis and not taking daily non-steroidal anti-inflammatory drugs (NSAIDS) or acetaminophen, and controlled diabetes (see Methods). Monocytes were first evaluated under healthy non-stimulus conditions to determine transcriptional differences between the three subsets, and the effects of aging on gene expression. Using CD14 and CD16 conjugated antibodies, monocytes were sorted from frozen PBMCs isolated from adults and old subjects (n=9 per group) into three subsets: (1) classical (CD14+CD16-), (2) intermediate (CD14+CD16+), and (3) non-classical (CD14dimCD16+).

first: T

middle: U

last: Metcalf

first: P

first: M

last: Cameron

first: K

last: Ghneim

first: C

last: Chiang

first: A

last: Wertheimer

first: J

last: Hiscott

last: Nikolich-Zugich

first: E

middle: K

last: Haddad


title: Cold atmospheric plasma reprograms the drug sensitivity of Tamoxifen-resistant MCF-7 breast cancer cell

status: Public on Jul 12 2017

city: goyang

first: seungyeon

last: lee

address: dongguk-ro 32

department: life science

institute: dongguk unversity

summary: genome-wide expression profiling of MCF-7, MCF-7/TamR and CAP-treated MCF-7/TamR cell. In result, cold atmospheric plasma re-sensitizes the Tamoxifen-resistant MCF-7 (MCF-7/TamR) breast cancer cell to the drug.

overall_design: Total RNA is obtained from MCF-7, MCF-7/TamR, and CAP treated MCF-7/TamR.

first: Seungyeon

last: Lee

first: Sunjunk

last: Kim


title: Functional antagonism between the MYT1L and MEF2 transcription factors controls neural development and the expression of schizophrenia-associated genes

city: London

first: Sylvane

last: Desrivieres

address: 16 De Crespigny Park

institute: King's College London

summary: Here we describe a novel functional antagonism between the MYT1L and MEF2 transcription factors in regulation of neural development

overall_design: Examination of global transcriptional effects of Myt1L and MEF2A knockdown by lentiviral-mediated delivery of shRNAs in differentiating human neural stem cells

last: Desrivières


title: Human monocyte subsets are transcriptionally and functionally altered in aging in response to pattern recognition receptor agonists [InVitro]

summary: Age-related alterations in immunity have been linked to increased incidence of infections and decreased responses to vaccines in the aging population. Human peripheral blood monocytes are known to promote antigen presentation and antiviral activities; however, the impact of aging on monocyte functions remains an open question. We present an in-depth global analysis examining the impact of aging on classical (CD14+CD16-), intermediate (CD14+CD16+), and non-classical (CD14dimCD16+) monocytes. Monocytes sorted from non-frail healthy adults (18-40 yrs) and OLD (≥ 65 yrs) individuals were analyzed after stimulation with TLR4, TLR7/8, and RIG-I agonists. Our data showed under non-stimulated conditions, monocyte subsets did not reveal significant age-related alternations; however, agonist stimulated-monocytes from adults and OLD subjects did show differences at the transcriptional and functional levels. These alternations in many immune-related transcripts and biological processes resulted in reduced production of IFNα, IFN, IL-1β, CCL20, and CCL8, and higher expression of CX3CR1 in monocytes from OLD subjects. Our findings represent a comprehensive analysis of the influence of human aging on pattern recognition receptors signaling and monocyte functions, and have implications for strategies to enhance the immune response in the context of infection and immunization.

overall_design: Healthy non-frail individuals enrolled into the study were arranged into two groups:  adults (YNG) and old (OLD) subjects (n=11 per group). The average age for adults were 30 yrs (range 24-36 yrs), whereas old individuals were 73 yrs (range 67-83 yrs). Individuals with comorbid conditions including cancer (within the last 5 yrs for those greater than 65 yrs), immunocompromising disorders, and steroid usage were excluded; whereas inclusion criteria included controlled hypertension, occasional/tolerable “aching joints” from arthritis and not taking daily non-steroidal anti-inflammatory drugs (NSAIDS) or acetaminophen, and controlled diabetes (see Methods). Monocytes were first evaluated under healthy non-stimulus conditions to determine transcriptional differences between the three subsets, and the effects of aging on gene expression. Using CD14 and CD16 conjugated antibodies, monocytes were sorted from frozen PBMCs isolated from adults and old subjects (n=9 per group) into three subsets: (1) classical (CD14+CD16-), (2) intermediate (CD14+CD16+), and (3) non-classical (CD14dimCD16+). We then determined the transcriptional responses of monocyte subsets following stimulation with various PRRs agonists. Monocyte subsets were sorted from adult and old subjects (n=8/age group) and stimulated for 24 hours with LPS (TLR4), CLO97 (TLR7/8), or 5’-pppRNA complexed with Lyovec (a cationic transfection reagent that facilitates intracellular delivery) (RIG-I) (see Methods).


title: Human monocyte subsets are transcriptionally and functionally altered in aging in response to pattern recognition receptor agonists

status: Public on Jul 26 2017


title: Impact of aging/caloric restriction on circadian gene expression

status: Public on Jul 21 2017

city: College Station

first: Shogo

last: Sato

state: Texas

address: 3258 TAMU, Biological Science Building West (BSBW) 309

department: Biology

institute: Texas A&M University

summary: Transcriptome analysis using the liver from young versus old mice, fed either normally or under caloric restriction reveals reorganization of distinct circadian signatures related to metabolic aging and nutrient-dependent counterbalance of aging by caloric restriction

overall_design: Livers from young versus old mice fed either a normal diet or calorie-restricted diet were harvested over the circadian cycle at ZT 0, 4, 8, 12, 16 and 20 for gene expression analysis.

first: Paolo

last: Sassone-Corsi


title: Nuclear mTOR acts as a transcriptional integrator of the androgen signaling pathway in prostate cancer progression [array]

status: Public on Jul 18 2017

city: Québec City

first: Etienne

last: Audet-Walsh

state: QC

address: 2705 boulevard Laurier

department: Molecular Medicine

institute: Université Laval

summary:
Whether the nuclear fraction of mTOR plays a role in prostate cancer (PCa) and can participate in direct transcriptional crosstalk with the androgen receptor (AR) is as yet unknown. The intersection of gene expression, DNA binding-events, and metabolic studies uncovered the existence of a nuclear mTOR-AR transcriptional axis dictating the metabolic rewiring and nutrient usage of PCa cells. In human clinical specimens, nuclear localization of mTOR was significantly associated with metastasis and castration-resistant PCa (CRPC), correlating with a sustained metabolic gene program governed by mTOR in that context. This study thus uncovers an unexpected function of mTOR and underscores a paradigm shift from AR to mTOR as being the master transcriptional regulator of cell metabolism during PCa progression.
We used microarrays to investigate the role of nuclear mTOR in prostate cancer cell transcriptional regulation by androgens in LNCaP cells.

overall_design: Cells were seeded in media deprived from steroids. 48h later, cell were treated with 10nM R1881, 100nM torin 1 (an mTOR inhibitor), or vehicles (EtOH, DMSO) for 48h. Triplicate samples were sent for each conditions.

first: Étienne

first: Vincent

last: Giguère


title: Genome-wide analysis of the effect of supressing miR-34a on urothelial cells

status: Public on Jul 05 2017

city: Lebanon

first: Angeline

last: Andrew

state: NH

address: 7927 Rubin Building

institute: Dartmouth

summary:
MiR-34a appears to be protective against cancer. Blocking miR-34a results in pro-tumorigenic phenotypic changes.
The purpose of this experiment was to identify gene expression changes that could potentially explain the  pro-tumorigenic effects of anti-miR 34a transfection.

overall_design: Transfected cells with anti-miR 34a versus negative control construct


title: Gene Expression Changes in Definitive Endoderm in response to GATA6-depletion (Affymetrix)

status: Public on Jul 13 2017

city: Charleston

first: Stephen

last: Duncan

state: SC

address: 173 Ashley Avenue, BSB 6th Floor, Room 657A

department: Regenerative Medicine and Cell Biology

institute: Medical University South Carolina

summary:
GATA6 is required for proper definitive endoderm formation.  The mechanism of this process is poorly understood
We used microarrays to identify genes whose expression is altered upon GATA6-depletion

overall_design: Stable lentiviral or control cell lines were differentiated to various stages of definitive endoderm.  Rescue lines were differentiated to definitive endodermin the presence of doxycycline to induce shRNA-resistant GATA6 transgene expression.  Using this system we identified genes whose expression was altered upon GATA6 depletion during definitive endoderm differentiation.

first: Joseph

last: Fisher


title: Integrative genomic and epigenetic analysis in cholangiocarcinoma [batch1]

status: Public on Jul 03 2017

first: Jing Quan

last: Lim

address: 30 Hospital Boulevard

department: CMR

institute: National Cancer Centre Singapore

summary:
Analysis of gene expression in cholangiocarcinoma patients.

Please download the supplementary file GSE89747_CCA_batch01_illumina_Gene_expression_noNorm_noBKGD.txt.gz (link below) to obtain gene expression matrix with sample IDs used in the publication.

overall_design: A total of 118 tumors and 2 normals were profiled (46 tumors and 2 normals in this batch 1 of 2)

first: Patrick

last: Tan

first: Teh

last: Tean

first: Steve

last: Rozen

first: Apinya

last: Jusakul

first: Lim

last: Quan


title: Integrative genomic and epigenetic analysis in cholangiocarcinoma [batch2]

summary:
Analysis of gene expression in cholangiocarcinoma patients.

Please download the supplementary file GSE89748_CCA_batch02_illumina_Gene_expression_noNorm_noBKGD.txt.gz (link below) to obtain gene expression matrix with sample IDs used in the publication.

overall_design: A total of 118 tumors and 2 normals were profiled (72 tumors in this batch 2 of 2)


title: Integrative genomic and epigenetic analysis in cholangiocarcinoma

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

Please click through to the individual SubSeries to obtain gene expression matrix files with sample IDs used in the publication.


title: Sensitivity to PI3K and AKT inhibitors is mediated by divergent molecular mechanisms in subtypes of diffuse large B-cell lymphoma

status: Public on Jul 01 2017

city: Münster

first: Michael

last: Grau

state: Nordrhein-Westfalen

address: Albert-Schweitzer-Campus 1

department: Faculty of Medicine

institute: University of Münster

summary: Activated B-cell-like (ABC) and germinal center B-cell-like (GCB) diffuse large B-cell lymphoma (DLBCL) represent the two major molecular DLBCL subtypes. They are characterized by differences in clinical course and by divergent addiction to oncogenic pathways. To determine activity of novel compounds in these two subtypes, we conducted an unbiased pharmacologic in vitro screen. The phosphatidylinositol-3-kinase (PI3K) alpha/delta (PI3Ka/d) inhibitor AZD8835 showed marked potency in ABC DLBCL models, whereas the protein kinase B (AKT) inhibitor AZD5363 induced apoptosis in PTEN-deficient DLBCLs. These in vitro results were confirmed in various cell line xenograft and patient-derived xenograft mouse models in vivo. Treatment with AZD8835 induced inhibition of nuclear factor kappa-B (NF-kB) signaling, prompting us to combine AZD8835 with the Bruton’s tyrosine kinase (BTK) inhibitor ibrutinib. This combination was highly synergistic and effective both in vitro and in vivo. In contrast, the AKT inhibitor AZD5363 was effective in PTEN-deficient DLBCLs through downregulation of the oncogenic transcription factor MYC. Collectively our data suggest that patients should be stratified according to their oncogenic dependencies when treated with PI3K and AKT inhibitors.

overall_design:
(a) Gene expression in HBL-1, OCI-Ly10 and U2932 cells after treatment with AZD8835 was compared to that of cells treated with DMSO.
(b) Furthermore gene expression in K422 and U2932 cells after treatment with AZD5363 was compared to that of cells treated with DMSO.

first: Georg

last: Lenz


title: Gene expression data in Huh-7 cell line transfected with HBeAg-expression vector

city: New Delhi

first: Perumal

last: Vivekanandan

state: Delhi

address: Kusuma School of Biological Sciences, IIT Delhi, Hauz Khas, New Delhi-110016

department: Kusuma School of biological Sciences, IIT Delhi

institute: Indian Institute of technology Delhi

summary:
The presence of HBeAg has been linked to an increased risk of HBV-realted HCC. However, the biological role of HBeAg in modulating host gene expression is poorly understood. Therefore, we performed a cDNA microarray in response to presence of HBeAg in Huh-7 cells.
We used human primeview gene expression microarray chips to assess the host cellular mRNA expression profile in response to HBeAg in Huh7 cells

overall_design: The total RNA from Huh-7 cells transfected with control and HBeAg-expression vector was harvested 48 hours post transfection and mRNA profiling was done human primeview gene chips.

first: Jasmine

last: Samal

first: Manish

last: Kandpal

last: Vivekanadan


title: Expression data in Huh-7 cell line transfected with HBeAg-expression vector

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

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

platform_organism:
Homo sapiens
synthetic construct


title: Genome-wide analysis of glucose deprivation-responsive gene expression in parental and KAP1 knockdown MDA-MB-231 cells

city: Duarte

first: David

middle: Kong

last: Ann

state: CA

address: 1500 E. Duarte Rd.

institute: City of Hope

summary: Analysis of the alteration of gene expression in response to 8-h glucose depletion in parental or KAP1 knockdown MDA-MB-231 cells. The results provide important information for KAP1-regulated gene response upon metabolic stress such as glucose starvation.

overall_design: Total RNA obtained from MDA-MB-231 or MDA-MB-231/shKAP1 cells subjected to 0 or 8 hours of glucose starvation.

first: Chun-Ting

last: Cheng


title: Rhinovirus Infection Induces a Differential Gene Expression Pattern in Pulmonary Epithelial Cells

status: Public on Jun 29 2017

city: Serdang

first: Mohammad Reza

last: Etemadi

state: Selangor

department: Medical Microbiology and Parasitology

country: Malaysia

institute: UPM

summary:
We aimed to investigate whether HRV infection induces a specific gene expression pattern in airway epithelial cells.
The study suggests the underlying molecular regulatory networks genes which might be involved in pathogenicity of the HRV-B and potential targets for further validations and development of effective treatment.

overall_design: Human alveolar epithelial cell monolayers were infected with HRV species B (HRV-B). Total RNA was extracted from both supernatants and infected monolayer cells at 6, 12, 24 and 48 hours post infection (hpi) and transcriptional profile was analyzed using high-density oligonucleotide Affymetrix GeneChip and the results were subsequently validated by using quantitative Real-time PCR method.

first: King-Hwa

last: LING

first: Chee

middle: H

last: Yee

first: Zamberi

last: Sekawi


title: Integrated transcriptomic and histologic analysis of cholangiolar differentiation trait in intrahepatic cholangiocarcinoma

city: Suwon

first: Hyun Goo

last: Woo

address: 164 Worldcup-ro Yeongtong-gu

institute: Ajou University School of Medicine

summary:
Background & Aims: Intrahepatic cholangiocarcinoma (ICC) is known to heterogeneous with diverse etiology, morphology, and clinical outcomes. Recently, cholangiolar differentiation of ICC has been suggested to associate with prognostic outcomes, however, its molecular patho-biological features and clinical significances were not evaluated extensively.
Methods:Integrative analysis was performed using transcriptomic profiles (n=27) and tissue microarrays (n=142) from ICC specimens.
Results:ICCs were classified into ICC with cholangiolar differentiation (ICC-CD, n=20) and ICC with bile duct differentiation (ICC-BD, n=122). ICC-CD showed favorable overall survival (OS) compared to ICC-BD (Hazard Ratio=0.38, P=0.020, log-rank test). Transcriptomic profiling of ICC-CD and ICC-BD revealed a cholangiolar differentiation signature (CD signature, n=794), which could predict prognostic outcomes of ICC in an independent data. Interestingly, the expression of CD signature demonstrated that the ICC-BD but not ICC-CD harbored pancreatic ductal adenocarcinoma (PDAC) like expression trait, implying its cellular origin from multipotent biliary tree stem cells or the cells committed to differentiate into pancreatic lineage cells. The CD signature might be a key determinant for ICC heterogeneity indicating spectral continuum of cellular differentiation of ICC-CD → ICC-BD → PDAC. In addition, we identified four genes (i.e., CRP, CDH2, TFF1, and S100P) from integrated analysis of tissue microarrays and transcriptome profiles as prognostic as well as differential histologic markers for ICC-CD and ICC-BD. Strikingly, combined expression status of the four genes were more beneficial in predicting prognostic outcomes of ICC.
Conclusions:Our integrative genomic-pathologic analysis could reveal new molecular and clinical significance of cholangiolar differentiation in association with PDAC-like expression traits, which might play pivotal roles in heterogeneous progression of ICC.

overall_design: The analysis of gene expression profiling among cholangiocarcinoma samples


title: Shrinking the Psoriasis assessment gap: Early gene-expression profiling accurately predicts response to long-term treatment

city: New York

first: Joel

last: Correa da Rosa

state: New York

address: 1230 York Avenue

department: CTSA

institute: Rockefeller University

summary: Prediction of response to adalimumab and methotrexate treatments based on gene expression profiles at baseline, weeks 1, 2, 4 and 16

overall_design: Total RNA obtained from isolated from skin tissue at baseline - non-lesional and lesional - weeks 1,2,4 and 16 in subjects with moderate to severe psoriasis

first: Mayte

last: Suárez-Fariñas


title: Identifiation and characterisation of human fetal antigen presenting cells subsets.

status: Public on Jun 28 2017

city: Singapore

first: Kaibo

last: Duan

address: 8A Biomedical Grove, Immunos Building, Level 4

institute: Singapore Immunology Network

summary: The human immune system evolves gradually from the embryo to adult, continuously adapting to the ever-changing environment of the human body. The ability of our immune system to sense external cues and adapt as we develop is as important in the early tolerogenic environment of the fetus, as it is in the constantly pathogen-challenged adult. Dendritic cells (DC), professional antigen sensing and presenting cells, play a crucial role in such processes as sentinels of the immune system, initiating and regulating immune responses. We have previously characterised CD14+ DC, CD1c+DC and CD141+DC subset by flow cytometry and microarray transcriptome analysis in adult mucosal tissues, and have described their superior abilities to either induce IL-17 responses or to cross-present external antigens respectively. However, the role of such DC subsets in the tolerogenic environment of the fetus remains undefined, prompting us to investigate the ontogeny and functional significance of human fetal DCs.

overall_design: APC were isolated from fetal (17-22 wk EGA) skin and spleen that was collagenase digeseted for 1hr by FACS.  Gene expression analysis using total RNA from specific human APC subsets purified by FACS was performed.

first: Naomi

last: Mc Govern

first: Florent

last: Ginhoux

last: Poidinger


title: Genome-wide expression profiling of prostate specimens from a clinical trial of genistein supplementation prior to prostatectomy.

status: Public on Jun 23 2017

city: Atlanta

first: Carlos

middle: S.

last: Moreno

state: GA

address: Michael Street

department: Pathology & Laboratory Medicine

institute: Emory University

summary: To identify molecular effects of genistein on mRNA levels in prostate cancer, we compared gene expression profiles of genistein-treated tumors with placebo-treated samples. There were 628 probes that reached nominally significant p-values. The genes that were differentially expressed between genistein and placebo samples were involved in angiogenesis, apoptosis, epithelial to mesenchymal transition, and tumor progression. Gene enrichment analysis suggested that PTEN and PDGF were activated, while MYC, beta-estradiol, glucocorticoid receptor NR3C1, and interferon-gamma were repressed in response to genistein treatment. These findings highlight the effects of genistein on global changes in gene expression in prostate cancer and its effects on molecular pathways involved in prostate tumorigenesis.

overall_design: We analyzed prostate tissue samples from a clinical trial, which was a randomized, placebo-controlled, double-blind Phase 2 study on Norwegian patients with localized prostate cancer who received 30 mg synthetic genistein or placebo capsules daily for 3-6 weeks before radical prostatectomy. We investigated the gene expression levels of prostate tumor samples from 10 patients who received genistein and 10 patients who received placebo. Four adjacent normal prostate tissue samples were also analyzed.

middle: S

first: Aud

last: Svindland


title: Effect of Intradermal Immunotherapy (IDIT) injections on gene expression profiles of activated T cells derived from skin biopsy explants

city: Leicester

middle: John

last: Cousins

address: NIHR BRC Respiratory, Glenfield Hospital

department: Respiratory Sciences

institute: University of Leicester

summary:
A Randomized, Placebo-Controlled Trial of Intradermal Allergen Immunotherapy for Grass Pollen Allergy
Background: Repeated intradermal injection of grass pollen (nanograms of allergen) suppresses allergen-induced cutaneous late phase responses, in keeping with effects of conventional high dose subcutaneous and sublingual immunotherapy. We evaluated the efficacy and safety of grass pollen intradermal immunotherapy for treatment of allergic rhinitis.Methods: We randomly assigned 93 adults with grass pollen allergic rhinitis to receive 7 pre-seasonal Intradermal allergen immunotherapy injections (containing 7 ng of Phl p 5 major allergen) or histamine control. The primary end point was daily combined symptom-medication scores during the 2013 pollen season. Skin biopsies were taken after the pollen season following an intradermal allergen challenge. Cutaneous late phase responses were measured 4 and either 7, 10 or 13 months post-treatment.     Results  No difference in the primary endpoint was observed between treatment arms (median difference, 14; 95% confidence interval [CI], -172.5 to 215.1; P=0.80). Amongst secondary endpoints, nasal symptoms measured with daily scores (median difference, 35; 95% CI, 4.0 to 67.5; P=0.03) and visual-analogue scales (median difference, 53; 95% CI, -11.6 to 125.2; P=0.05) were higher in the intradermal treatment group. Intradermal immunotherapy increased serum Phl p-specific IgE (P=0.001) compared to the control arm and T cells cultured from biopsies showed higher and lower surface of surface markers for Type 2 (P=0.04) and Type 1 (P=0.01) T-helper cells, respectively, Interleukin-5 was differentially expressed by microarray (P=0.03). Late phase responses were still inhibited 7 months after treatment (P=0.03) but not at 10-13 months.     Conclusions  Grass pollen intradermal allergen immunotherapy was not clinically effective but resulted in immunological priming and worsening of allergic rhinitis symptoms.

overall_design: T-cells were isolated from skin biopsy by explant culture from control subjects (8) and subjects undergoing IDIT (7). After 7 days T-cells were activated with PMA/Ionomycin. Control subjects were compared with IDIT subjects.

first: Anna

last: Slovic

first: S

last: Till


title: Gene expression profiles of mouse CIC-DUX4 sarcoma

status: Public on Jun 21 2017

city: Tokyo

first: Takuro

last: Nakamura

address: 3-8-31 Ariake, Koto-ku

department: The Cancer Institute

country: Japan

institute: Japanese Foundation for Cancer Research

summary:
CIC-DUX4 sarcoma (CDS) or CIC-rearranged sarcoma is a  subcategory of small round cell sarcoma resembling the morphological phenotypes of Ewing sarcoma (ES). Recent clinicopathologic and molecular genetic analyses indicate that CDS is an independent disease entity from ES. Although a few ancillary markers have been used in the differential diagnosis of CDS, additional CDS-specific biomarkers are needed in challenging diagnosis for a more definitive classification. Here we have generated an ex vivo mouse model for CDS by transducing embryonic mesenchymal cells (eMCs) with human CIC-DUX4 cDNA. The recipient mice transplanted with eMCs expressing CIC-DUX4 rapidly developed an aggressive, undifferentiated sarcoma composed of small round to short spindle cells. Gene expression profiles of CDS and eMCs revealed upregulation of CIC-DUX4 downstream genes such as PEA3 family genes, Ccnd2, Crh and Zic1. Immunohistochemical analyses for both mouse and human tumors showed that CCND2 and MUC5AC are reliable biomarkers to distinguish CDS from ES. Gene silencing of CIC-DUX4 as well as Ccnd2, Ret, and Bcl2, that are upregulated in CDS, effectively inhibited tumor growth in vitro. Palbociclib, a CDK4/6 inhibitor, also showed growth inhibition of mouse CDS cells in vitro, while trabectedin induced tumor suppressive effects both in vitro and in vivo. In summary, the CDS mouse model provides important biological information of CDS and is a useful platform to explore novel biomarkers and therapeutic agents for CDS.
We used microarrays to detail the global program of gene expression in mouse CDS.

overall_design: Murine embryonic mesenchymal cells were transduced with the CIC-DUX4 and transplanted into nude mice. Tumor developed as a subcutaneous mass and histological examination was performed to confirm the CDS phenotypes. Individual tumor tissues and embryonic mesenchymal cells (eMCs) transduced with the CIC-DUX4 retrovirus were subjected to microarray analyses. eMCs introduced with an empty vector was used as a control. In addition, mouse ES tumors were also subjected to microarray analyses and expression profiles were compared between CDS and ES.

first: Toyoki

last: Yoshimoto

first: Miwa

last: Tanaka


title: Elevated acid ceramidase promotes acute myeloid leukemia blast survival through sphingolipid dysregulation and Mcl-1 upregulation

status: Public on Jun 19 2017

city: Charlottesville

first: Stephen

last: Turner

state: VA

address: 1670 Discovery Drive

institute: Signature Science, LLC

summary: Gene expression of patient samples with acute myeloid leukemia (AML) were compared to normal controls to study dysregulated signalling pathways. Peripheral blood mononuclear cells (PBMCs) from primary AML patient samples were isolated using the Ficoll-Paque gradient separation method. RNA from CD34+ bone marrow cells of healthy donors were purchased from AllCells LLC (Alameda, CA; catalog number RNA-BM003C). Total RNA were harvested from patient samples using Trizol and subjected to microarray-based gene expression analysis.

overall_design: Total RNA from patient PBMCs and healthy donor CD34+ bone marrow cells.

first: Su

middle: F

last: Tan

first: Brian

last: Barth

first: Mark

last: Kester

first: Myles

middle: C

last: Cabot

first: Nikki

last: Keasey

first: Xin

last: Liu

first: Mithun

last: Shah

first: David

last: Claxton

last: Feith

first: Todd

middle: E

last: Fox

first: Kathleen

last: Broeg

first: Hong

last: Wang

first: Thomas

middle: P

last: Loughran Jr.


title: CRIS, a superior predictive and prognostic classification system of colorectal cancer based on high-resolution analysis of cancer cell-autonomous traits

city: Candiolo

first: Enzo

last: Medico

state: TO

address: Strada Prov. 142, km 3,95

department: Oncology

institute: Candiolo Cancer Institute, University of Torino

summary: Recent work built on published transcriptional subtypes of colorectal cancer (CRC) has shown that tumor stromal content impacts CRC classification, with both clinical and biological implications. To Tackle the issue of intrinsic epithelial gene profiles, we assembled a dataset of matched liver metastatic colorectal cancer and Patients Derived Xenografts. in which the stroma of the original tumor is substituted by murine tissue, we deployed a molecularly annotated collection of 515 PDXs from 244 patients as a resource for species (human)-specific assessment of cancer-cell intrinsic transcriptional features. We identified five ColoRectal cancer Intrinsic Subtypes (CRIS) endowed with functional and phenotypic characteristics related to specific genetic traits, most of which were not evidenced in the transcriptional subgroups reported in previous studies.

overall_design: Expression profiling of frozen liver metastasis samples

first: Andrea

last: Bertotti

first: Claudio

last: Isella

first: Sara

last: Bellomo

first: Francesco

last: Brundu


title: Expression data from Yellow Fever 17D vaccine immunized healthy subjects

status: Public on Jun 25 2017

city: Beijing

first: Yiming

last: Shao

state: Beijing

address: No. 155 Changbai Road, Changping District

department: National Center for AIDS/STD Control and Prevention

institute: Chinese Center for Disease Control and Prevention

summary: To better understand how innate immunity to vaccination can lead to lasting protective immunity, we have used systemic bioinformatics approaches to define the signature of the yellow fever specific immune response in a cohort of 21 volunteers.

overall_design: In this study, we have 21 subjects in the final enrollment. Nine time points had been set as a time-course, which one time point (Day0) before inoculation, and eight time points covered serveal time points after immunization from Hour 4 to Day 28 (Hour4, Day1, Day2, Day3, Day5, Day7, Day14 and Day28). The goal is to indentify some gene expression signature from the microarray data that correlate with immune responses.

first: Jue

last: Hou


title: Mitochondrial dynamics mediated by Mitofusin 1 is required for POMC neurons glucose-sensing and insulin release control

status: Public on Jun 27 2017

city: Barcelona

first: Joan Marc

last: Servitja

state: Catalonia

address: Rosselló, 153

institute: IDIBAPS

summary:
Mitofusin 1 (Mfn1) is a transmembrane GTPase protein implicated in mitochondrial fusion. To investigate the potential role of Mfn1 in energy balance and metabolism control we generated mice lacking Mfn1 specifically in hypothalamic POMC neurons (POMCMfn1KO).
We used microarrays to determine gene expression changes resulting from deletion of Mfn1 in POMC neurons under fed and fasting conditions

overall_design: Total hypothalamic mRNA was isolated from control and conditional knock-out mice under ad libitum fed or fasting (16h) conditions. RNA was hybridized on Affymetrix microarrays.

first: M

last: Claret

first: J


title: Assessing the developmental potential of human pluripotent stem cells using Pluritest

status: Public on Jun 20 2017

city: Sheffield

first: Paul

last: Gokhale

address: Western Bank

department: Biomedical Science

institute: University of Sheffield

summary: The International Stem Cell Initiative compared three common approaches for assessing pluripotent stem cells (PSC).  The formation of teratomas in vivo, or embryoid bodies (EB) in vitro, provide direct tests of differentiation, whereas PluriTest predicts pluripotency through bioinformatic analysis of transcriptomes of undifferentiated cells.  Here we studied the starting poulations of pluripotent stem cells  using an Illumina HumanHT-12 V4.0 expression beadchip assays

overall_design: Undifferentiated samples from 16 pluripotent stem cell lines, consisting of 10 embryonic stem cell (ES) and six induced pluripotent stem cell (iPS) lines, from four laboratories were analysed by Illumina  HumanHT-12 V4.0 expression beadchip array to asess the degree of pluripotency

first: Franz-Josef

last: Müller

first: Bernhard

last: Schuldt


title: Expression data from MCF-7 breast cancer cells treated with Wild Type Tomato fruit  extract (WT) and transgenic lines tomato fruit extract (L6 and L7)

status: Public on Jun 12 2017

city: Little Rock

first: Mariya

last: Khodakovskaya

state: AR

address: 2801 S. University Avenue

institute: University of Arkansas at Little Rock

summary:
To investigate the effects of transgenic lines L6 and L7 tomato fruits on total expression profile of MCF-7 breast cancer cells, we treated MCF-7 cells with 1 ug/ml of tomato fruit extract for 24 hours and compare it with wild type tomato fruit extract
Objectives for this study included the identification of genes that were up or down-regulated at the transcriptional level in MCF-7 cells treated with transgenic lines L6 and L7 tomatofruit  extract and compare it to wild type tomato fruit extract.

overall_design:
MCF-7 breast cancer cells were incubated with wild type (WT)  tomatofruit  extract (1 ug/ml),  line 6 (L6) transgenic line tomato fruit extract (1 ug/ml) and line 7 (L7) transgenic line tomato fruit extract (1 ug/ml) for 24 hours  and selected for RNA extraction and hybridization on Affymetrix microarrays.
cell death responses


title: Genomic characterization of liver metastases from colorectal cancer patients

city: Salamanca

first: Jose

middle: María

last: Sayagués

state: Salamanca

address: Campus Miguel de Unamuno

department: Department of Medicine

institute: Cancer Research Center (IBMCC-CSIC/USAL)

overall_design: Refer to individual Series


title: Correlates of self-reported symptom scores in a human H1N1 influenza challenge trial

status: Public on Jun 10 2017

city: Oxford

first: Julius

last: Muller

state: Oxfordshire

address: ORCRB, Roosevelt Drive

department: Nuffield Department of Medicine

institute: The Jenner Institute, University of Oxford

summary: Influenza challenge trials are important for vaccine efficacy testing. Currently, disease severity is determined by self-reported scores to a list of symptoms which can be highly subjective. A more objective measure would allow for improved data analysis. Twenty one volunteers participated in an influenza challenge trial. We calculated the Daily Sum of Scores (DSS) for a list of 16 influenza symptoms. Whole blood collected at baseline and 24, 48, 72 and 96 hours post challenge was profiled on Illumina HT12v4 microarrays. We selected 19 genes with the largest fold change to train a random forest model with out of bag sampling cross validation. We observed good concordance between predicted and actual scores in an independent test set (overall Pearson correlation, r = 0.57; RMSE = -16.1%).

overall_design: Twenty one volunteers participated in an H1N1 influenza challenge trial. Whole blood collected at baseline and 24, 48, 72 and 96 hours post challenge was profiled on Illumina HT12v4 microarrays.

first: Eneida

last: Parizotto

first: Richard

last: Antrobus

first: James

last: Francis

first: Campbell

last: Bunce

first: Adrian

last: Hill

first: Adaikalavan

last: Ramasamy

first: Sarah

last: Gilbert


title: CRIS, a superior predictive and prognostic classification system of colorectal cancer based on high-resolution analysis of cancer cell-autonomous traits II

first: Enzo

last: Medico

overall_design:
Expression profiling of CRC patients derived Xenografts
----------------------------------
Submitters did not include information pertaining to "functional and phenotypic characteristics related to specific genetic traits"

first: Andrea

last: Bertotti

first: Claudio

last: Isella

first: Sara

last: Bellomo

first: Francesco

last: Brundu


title: Genomic characterization of liver metastases from colorectal cancer patients [PrimeView]

summary: Metastatic dissemination is the most frequent cause of death sporadic colorectal cancer (sCRC) patients. The genomic abnormalities which are potentially characteristic of such advanced stages of the disease are complex and so far, they have been poorly described and only partially understood. We evaluate the molecular heterogeneity of sCRC tumors based on simultaneous assessment of the overall GEP of both coding mRNA and non-coding RNA genes in primary sCRC tumor samples from 23 consecutive patients and their paired liver metastases. Liver metastases from the sCRC patients analyzed, systematically showed deregulated transcripts of those genes identified as also deregulated in their paired primary colorectal carcinomas. However, some transcripts were found to be specifically deregulated in liver metastases while expressed at normal levels in their primary tumors, suggesting an increased genomic instability of neoplastic cells from metastatic versus primary tumor samples. Of note, once tumoral samples were normalized vs. non-tumoral colorectal tissue, only three mRNAS (i.e.: DEFB1, COL12A and PTGER3) and one miRNA (i.e.: miR-572) emerged as significantly deregulated in the liver metastases vs. the primary tumor. Canonical pathways found to be specifically deregulated in liver metastatic samples included multiple genes related with intercellular adhesion and the metastatic processes (e.g., IGF1R, PIK3CA, PTEN and EGFR), endocytosis (e.g., the PDGFRA, SMAD2, ERBB3, PML and FGFR2), and cell cycle (e.g., SMAD2, CCND2, E2F5 and MYC). Our results also highlight the activation of genes associated with the TGFβ signaling pathway, which thereby emerge as candidate genes to play an important role in CRC tumor metastasis.

overall_design: Tissue specimens from 23 sporadic colorectal adenocarcinomas and 19 liver metastases (n=42 samples) were obtained from 23 patients with metastatic lesions susceptible of being resected (16 males and 7 females; median age of 66 years, ranging from 48 to 80 years) after informed consent had been given by each subject. The studied cases corresponded to 23 consecutive metastatic colorectal cancer patients.

first: José

last: Sayagues

first: Luis

last: Corchete

first: María

last: Gutierrez

last: del Mar Abad

first: Oscar

last: Bengoechea

first: Encarna

last: Fermiñan

first: Maria

last: Anduaga

first: Manuel

last: Iglesias

first: Carmen

last: Esteban

last: Angoso

middle: A

last: Alcazar

first: Jacinto

last: Garcia

first: Alberto

last: Orfão

last: Muñoz-Bellvis


title: mRNA Expression data from sodium butyrate or sodium phenylbutyrate treated A549 cells

city: Wenzhou

first: xiaoqiang

last: xiao

state: zhejiang

address: No 270.Xueyuan road

institute: Wenzhou Medical University

summary:
As a histone deacetylase inhibitor, sodium butyrate and its derivative sodium phenylbutyrate involve in cellular events such as proliferation, differentiation, apoptosis and cell cycle control via reprogramming gene expression. However, the gene associated with the cell cycle control and molecular signaling triggering cell apopotosis and death are not well elucidated.
Here, we treated A549 cells,a cell line belong to the non-small cells lung cancer,with high concentration of sodium butyrate or sodium phenylbutyrate and then used microarray identified differentially-expressed mRNA during this process.

overall_design: time point


title: PARP1 expression predicts and determines synergy between PARP1 inhibitors and trabectedin.

first: ymera

last: pignochino

address: str provinciale 142

institute: IRCCS Candiolo cancer center

summary: Trabectedin is a DNA-damaging agent with a peculiar mechanism of action; it traps the DNA repair machinery leading to DNA single- and double-strand breaks, particularly in BRCA1/2-deficient tumors. We hypothesized that trabectedin-induced DNA damage might activate PARP1 (a DNA-repair machinery key player), and consequently, PARP1 inhibition would perpetuate trabectedin-induced DNA damage. In several tumor histotypes, we demonstrated a different degree of synergism between trabectedin and PARP1 inhibitors (PARP1-Is). Independent of BRCA1/2 status, PARP1 expression dictated the degree of synergism. Namely, silenced PARP1 reduced trabectedin-PARP1-Is synergism, whereas overexpressed PARP1 increased combination efficacy. High-PARP1 expression and specific gene signatures associated with DNA damage response and repair (DDR-R) were predictive of trabectedin+PARP1-I synergy. These findings pave the way for the clinical development of this novel combination therapy, as well as evaluation of PARP1 expression and DDR-R signatures in tumor samples as predictive biomarkers of response.

overall_design: six bone and soft tissue sarcoma cell lines treated with trabectedin, olaparib and combination

first: Ymera

last: Pignochino

first: Giovanni

last: Grignani


title: Gene-expression profile of triple negative breast cancer cells stimulated with post-surgery wound-healing fluids

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

institute: IRCSS Istituto Nazionale Tumori

summary: Triple-negative breast cancer (TNBC) is an aggressive breast cancer subtype showing high recurrences and mortality rate, for which no therapies besides chemotherapy are available to date. Lacking specific markers for an effective targeted therapy, TNBCs still represent the most important challenge for clinical oncologists.TNBC definition for lack of expression markers underscored the urgent need of discover the “drivers” for this disease and their role in aggressiveness to develop specific targeted therapies. In the effort to identify drivers responsible of early TNBC relapse, we choose to take advantage of the pro-tumorigenic activity of post-surgery wound healing fluids (WHFs) of breast cancer patients that represents the microenvironment constituted of peripheral blood of patients in which disseminated tumor cells reside and that can strongly influence the survival of tumor cells allowing distant relapses. . The stimulus of this enriched microenvironment created immediately post-surgery can determine a selecting pressure for the survival of most aggressive tumor cells modulating the expression of existing or new molecules on TNBC surface driving the develop of distant metastases. By using WHF to stimulate human TNBC cell models prior gene expression profile, we identify the significant up-modulation of the plasma membrane receptor CUB-domain containing protein 1 (CDCP1).

overall_design: Five triple negative breast cancer cell lines, MDA-MB-231, BT549, MDA-MB-468, SUM149, MDA-MB-157, were seeded in 10 cm petri dishes, grown at 70% of confluence, starved for 24 h in RPMI medium without FBS and then stimulated or not with RPMI containing pool of post-surgery wound healing fluids from breast cancer patients at final concentration of 5% for 48 h. Two independent replicates were collected for each cell line.

first: Manuela

last: Campiglio


title: Altered global gene profile in KSHV+ PEL cells exposure to dhC16-Cer

city: New Orleans

first: Zhiqiang

last: Qin

state: LA

address: 1700 Tulane Ave

institute: LSUHSC-NO

summary: Primary effusion lymphoma (PEL) is a rare B-cell malignancy that originates from B cells latently infected with Kaposi’s sarcoma-associated herpesvirus (KSHV, also known as human herpesvirus-8, HHV8). Our previous data indicated that several exogenous ceramide and dh-ceramide species, such as C18-Cer and dhC16-Cer, also displayed effective anti-cancer activities for KSHV+ PEL in vitro and in vivo. However, the underlying mechanisms for exogenous ceramide “killing” PEL cells still require further investigation, which will be helpful to better understand PEL pathogenesis and identify more potential therapeutic targets. In the current study, we used Illumina microarray to determine the altered gene profile in KSHV+ PEL cell-line, BCBL-1 exposure to dhC16-Cer.

overall_design: PEL cell-line BCBL-1 were treated with vehicle control or dhC16-Cer (40 µM) for 24 h, and the gene expression signature was compared to the corresponding vehicle controls

first: Lu

last: Dai

first: Zabaleta

last: Jovanny


title: Isolation of Mex3a / Lgr5 cell population in mouse small intestine

status: Public on Jun 01 2017

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

institute: IRB Barcelona

summary:
Proximal mouse small intestine from mice bearing the Lgr5 GFP/+ and Mex3a Tom/+ alleles were used to obtain single cell preparations.
Cells were selected for GFP expression and different levels of tdTomato were defined. Sorted cells were lysed and processed for transcriptomic analysis

overall_design: 6 populations (Mex3a-high Lgr5-high; Mex3a-low Lgr5-high; Mex3a-neg Lgr5-high; Mex3a-high Lgr5-low; Mex3a-low Lgr5-low; Mex3a-neg Lgr5-low) were obtained from two biological replicates for analysis.

first: Eduard

last: Battle

last: Attolini


title: Expression profiling of WM9 and 1205Lu with shILEI.

city: Charleston

first: Philip

last: Howe

state: South Carolina

address: 173 Ashley Avenue

department: Biochemistry

institute: Medical University of South Carolina

overall_design: Melanoma cell lines characterized by a low-MITF invasive state express high levels of ILEI. We have used lentiviral shRNA vectors to generate pools of melanoma cells (1205Lu and WM9) stably knocked down for ILEI (FAM3C). In vitro measures of invasion show that ILEI knockdown attenuate invasive potential.

first: Ken

last: Noguchi

first: Annamarie

last: Dalton

first: Breege

middle: V

last: Howley

first: Buckley

middle: J

last: McCall

first: Akihiro

last: Yoshida

first: J

last: Diehl


title: Molecular profiling of 159 primary lung carcinomas

status: Public on Jun 07 2017

city: Lund

first: Johan

last: Staaf

address: Medicon Village

country: Sweden

institute: SCIBLU - Swegene Centre for Integrative Biology at Lund University

summary: Molecular profiling of 159 lung cancers of different histological subtypes. A primary objective is to identify gene expression differences between histological subtypes. Sample overlap exist with GSE60644

overall_design: Gene expression profiling of 159 lung carcinomas using Illumina HT-12 V4.0 microarrays.

first: Maria

last: Planck

first: Anna

last: Karlsson


title: Potential biomarker genes for acute and gradual temperature stress in maraena whitefish Coregonus lavaretus

status: Public on Jun 04 2017

city: Dummerstorf

first: Alexander

last: Rebl

address: Wilhelm-Stahl-Allee 2

department: Institute of Genome Biology

institute: Research Institute for Farm Animal Biology

summary: Stress represents a major factor negatively affecting fish welfare in aquaculture. The objective of the present study was to identify and evaluate informative indicators for the welfare of maraena whitefish (Coregonus maraena) exposed to inconvenient temperatures. The present study compares the physiological impact of either acute or gradual temperature rise from 18 °C to 24 °C on maraena whitefish in aquaculture. We analysed microarray-based transcriptome profiles in liver, spleen and kidney and identified a common set of diagnostic biomarkers each indicating thermal stress induced by acute or gradual temperature rise in the selected tissues. We identified common and unique tissue- and stress mode-specific pathways reflecting metabolic, cell signalling and immunologic crossroads to cope with thermal stress.

first: Simone

last: Altmann

first: Mareen

last: Nipkow

first: Tom

last: Goldammer


title: Genome-wide analysis of human prostate epithelial cell lines

city: Peking

first: wang

middle: li

last: yong

state: Peking

address: No 10 xi tou tiao, you an gate

department: medical school

institute: Capital Medical University

summary: Human prostate epithelial cell line of 8 cases having different metastatics were examined, such as  up- or down-regulated specific cellular functions.

overall_design: Total RNA obtained from human prostate epithelial cell line, Illumina HumanHT-12 v4 Expression BeadChip being used.

first: Lei

last: Ding

first: Lu

last: Kong

first: Liyong

last: Wang


title: miR-193b-regulated signaling networks inhibit adipogenesis and promote oncogenesis in liposarcoma

city: New York

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

summary: miR-193b functions as a tumor suppressor in liposarcoma cells. Microarray was used to identify the targets of miR-193b. The functions of identified miR-193b targets were further investigated in liposarcoma cells.

overall_design: Total RNA was isolated after treatment with control miRNA or miR-193b for 72 hours in DDLS and WDLS liposarcoma cells. 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: Ying

middle: Z

last: Mazzu

first: Samuel

last: Singer