title: caArray_vince-00013: Integrated Genomics and Transcriptomic Analyses of Ductal Carcinoma In situ of the Breast

summary:
Purpose: To gain insight into genomic and trancriptomic subtypes of ductal carcinomas in situ of the breast (DCIS).
Results: Thirty-two DCIS exhibited a luminal phenotype; 21were ERBB2 positive, and 4 were ERBB2/estrogen receptor (ER) negativewith1harboring a bona fide basal-like phenotype.Based on a CGHanalysis, genomic types were identified in this series of DCISwith the 1q gain/16q loss combination observed in 3 luminal DCIS, themixed amplifier pattern including all ERBB2,12 luminal and 1ERBB2/ER- DCIS, and the complex copy number alteration profile encompassing 14 luminal and 1ERBB2/ER- DCIS. Eight cases (8 of 57; 14%) presented aTP53 mutation, all being amplifiers. Unsupervised analysis of gene expression profiles of 26 of the 57 DCIS showed that luminal and ERBB2-amplified, ER-negative cases clustered separately.We further investigated the effect of high and low copy number changes on gene expression. Strikingly, amplicons but also low copy number changes especially on 1q, 8q, and 16q in DCIS regulated the expression of a subset of genes in a very similar way to that recently described in invasive ductal carcinomas.
Conclusions: These combined approaches show that the molecular heterogeneity of breast ductal carcinomas exists already in in situ lesions and further indicate that DCIS and invasive ductal carcinomas share genomic alterations with a similar effect on  gene expression profile.

overall_design:
Experimental Design: We did a combined phenotypic and genomic analysis of a series of 57 DCIS integrated with gene expression profile analysis for 26 of the 57 cases.
vince-00013
Assay Type: Gene Expression
Provider: Affymetrix
Array Designs: HG-U133A
Organism: Homo sapiens (ncbitax)
Tissue Sites: Breast, Breast
Material Types: cDNA, genomic_DNA, total_RNA
Cell Types: Ductal carcinoma in situ
Disease States: Breast Carcinoma


title: Expression data from MCF7 and HCC1937 cells long-term treated with everolimus

status: Public on Dec 22 2016

city: Barcelona

first: Miguel Angel

last: Pujana

address: Gran Via 199

country: Spain

institute: Institut Catala d'Oncologia IDIBELL

summary: Inhibitors of the mechanistic target of rapamycin (mTOR) are currently used to treat advanced metastatic breast cancer. However, whether an aggressive phenotype is sustained through adaptation or resistance to mTOR inhibition remains unknown. Here, complementary studies in human tumors, cancer models and cell lines reveal transcriptional reprogramming that supports metastasis in response to mTOR inhibition. This cancer feature is driven by EVI1 and SOX9. EVI1 functionally cooperates with and positively regulates SOX9, and promotes the transcriptional upregulation of key mTOR pathway components (REHB and RAPTOR) and of lung metastasis mediators (FSCN1 and SPARC). The expression of EVI1 and SOX9 is associated with stem cell-like and metastasis signatures, and their depletion impairs the metastatic potential of breast cancer cells. These results establish the mechanistic link between resistance to mTOR inhibition and cancer metastatic potential, thus enhancing our understanding of mTOR targeting failure.

overall_design: MCF7 and HCC1937 cell cultures were treated with everolimus for approximately 120 days and subsequently RNA extracted, processed and hybridized on Affymetrix microarrays.

first: Helena

last: Aguilar

first: Francesca

last: Mateo

first: Miguel

middle: A


title: Expression data from BT-474 cells long-term treated with everolimus

overall_design: BT-474  cell cultures were treated with 150 nM everolimus for approximately 100 days and subsequently RNA extracted, processed and hybridized on Affymetrix microarrays

first: Miquel


title: MSI2 gene expression profile in breast cancer cell

status: Public on Dec 21 2016

city: Seoul

first: YUNYONG

last: PARK

address: 84 Heukseok-ro

country: South Korea

institute: ChuangAng University

summary: MSI2 is one of RNA Binding protein. To investigate the role of MSI2 in breast cancer cell (MCF7), we carried out microarray.

overall_design: MSI2 was silenced in MCF-7 cell (siCon=3, siMSI2=3)

first: Myoung-Hee

last: Kang

first: Yun-Yong

last: Park


title: Transcriptome profiles of human hepatic stellate cells (LX2 and TWNT4) with overexpression of unspliced or spliced XBP1 gene

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

country: USA

institute: University of Texas Southwestern Medical Center

summary:
BACKGROUND AND AIM: We previously established that endoplasmic reticulum stress leads to unfolded protein response (UPR) that promotes liver fibrosis by activating hepatic stellate cell (HSC). We aimed to determine the role of X-box binding protein 1 (XBP1), one of three UPR effector pathways, in the fibrogenic HSC activation.

METHODS: XBP1 expression was measured by qPCR in tunicamycin-treated human HSC lines (TWNT4 and LX2) and culture-activated human primary HSCs. XBP1 was overexpressed in primary human HSCs and the HSC lines, and fibrogenic genes (COL1A1, ACTA2, PDGFRB, MMP2, TIMP1) and encoded proteins were assessed by qPCR and Western blotting, respectively. Autophagy was inhibited by knockdown of ATG7. Genome-wide transcriptome profiling was performed to determine modulated molecular pathway by XBP1. In vivo XBP1 activation was assessed in transcriptome datasets of fibrotic mouse models and immunohistochemistry of human liver tissues.

RESULTS: XBP1 overexpression accompanied both tunicamycin- and culture-based HSC activation. Ectopic overexpression of XBP1 induced fibrogenic gene expression in the HSC lines, which was inhibited by knockdown of ATG7. UPR pathway together with PDGFRB pathway, a hallmark of HSC activation, were induced in transcriptome profiles of XBP1-transduced HSC lines. Some known fibrogenic pathways such as transforming growth factor (TGF)-beta pathway were not induced, suggesting partial contribution of XBP1 to the entire fibrogenic HSC activation machinery. XBP1 target gene signature defined in our XBP1-overexpressing HSC lines was significantly induced in liver tissue transcriptome profiles of carbon tetrachloride-treated or bile duct-ligated mouse models, and XBP1 and alpha-smooth muscle actin (encoded by ACTA2, another hallmark of HSC activation) were co-localized in human fibrotic liver tissues, collectively supporting involvement of XBP1 in HSC activation and fibrogesis in vivo.

CONCLUSIONS: XBP1-mediated UPR is at least partially responsible for fibrogenic HSC activation via autophagy.

overall_design: Human hepatic stellate cell lines (LX2 and TWNT4) were lentivirally transduced by either unspliced or spliced XBP1 gene and cultured for 96h.

first: Rosa

middle: S

last: Kim

first: Scott

middle: L

last: Friedman


title: The Gfi1-Foxo1 axis controls the fidelity of effector gene expression and developmental maturation of thymocytes

status: Public on Dec 19 2016

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

summary: Double-positive (DP) thymocytes respond to intrathymic TCR signals by undergoing positive selection and lineage differentiation into single-positive (SP) mature cells. Concomitant with these wellcharacterized events is the acquisition of a mature T cell gene expression program characterized by the induction of effector molecules IL-7Ra, S1P1 and CCR7, but the underlying mechanism remains elusive. We report here that transcription repressor Gfi1 orchestrates the fidelity of DP gene expression program and developmental maturation into SP cells. Loss of Gfi1 resulted in premature induction of effector genes and transcription factors Foxo1 and Klf2 in DP thymocytes, and accumulation of post-selection intermediate populations and accelerated transition into SP cells. Strikingly, partial loss of Foxo1 function, but not restored survival fitness, rectified the dysregulated gene expression and thymocyte maturation in Gfi1-deficient mice. Our results establish Gfi1-Foxo1 axis and the transcriptional circuitry that actively maintain DP identity and shape the proper generation of mature T cells

overall_design: We used microarrays to compare the global transcription profiles of CD4+CD8+ double-positive (DP) thymocytes isolated from wild-type mice, and thymocytes from hCD2-iCre x Gfi1fl/fl mice

first: Lewis

last: Shi

first: Jordy

last: Saravia

first: Clifford

last: Guy

first: Hongbo

last: Chi


title: Gene array analysis of human adult skin and spleen antigen presenting cells.

city: Singapore

first: Kaibo

last: Duan

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

country: Singapore

institute: Singapore Immunology Network

summary: Antigen presenting cells (APC) are a heterogenous population, comprised of macrophages/monocytes (CD14+ cells), classical dendritic cells (CD141+DC and CD1c+ DC) and pDC. Upon stimulation, APC migrate from peripheral organs to lymph nodes, where they drive T cell specific lineage fate, that is towards immune activation or suppression.  APC in human tissues remain poorly defined. Through our previous published data we have charactised APC within adult skin and blood. Here we extend these findings, by increasing the sample for skin CD14+ DC and CD1c+ DC and performing gene array analysis of adult spleen CD14+ DC, CD141+DC and CD1c+ DC. Once, we were confident we could clearly distinguish our populations (CD14+ cell, CD141+ DC and CD1c+ DC) of interest from other cells, we sorted FACS purified the cells and prepared them for gene array analysis. Through generating subset specific gene signatures and comparing CMAP scores we confirmed we had identified equivalent APC subsets across human adult skin and spleen.

overall_design: APC were isolated from adult skin that was collagenase digeseted overnight by FACS.  Adult spleen was collagenase digested for 1hr and the APC isolated 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

first: Michael

last: Poidinger


title: Gene array analysis of human adult lung antigen presenting cells.

summary: Antigen presenting cells (APC) are a heterogenous population, comprised of macrophages/monocytes (CD14+ cells), classical dendritic cells (CD141+DC and CD1c+ DC) and pDC. Upon stimulation, APC migrate from peripheral organs to lymph nodes, where they drive T cell specific lineage fate, that is towards immune activation or suppression.   APC in human tissues remain poorly defined. Through our previous published data we have charactised APC within adult skin and blood. Here we extend these findings, by performing microarray analysis of adult lung CD14+ DC, CD141+ DC and CD1c+ DC.  Once, we were confident we could clearly distinguish the populations of interest (CD14+ cell, CD141+ DC and CD1c+ DC)  from other cells, we sorted FACS purified the cells and prepared them for gene array analysis.

overall_design: APC were isolated by FACS from adult lung that was collagenase digeseted for 1hr.  Gene expression analysis using total RNA from specific human APC subsets purified by FACS was performed.

last: McGovern


title: Functional Subclone Profiling for Prediction of Treatment-Induced Intratumor Population Shifts and Discovery of Rational Drug Combinations in Human Glioblastoma [expression]

city: Bonn

first: Roman

last: Reinartz

address: Sigmund Freud Strasse 25

department: Institute of Reconstructive Neurobiology

country: Germany

institute: University of Bonn

summary:
Purpose: Investigation of clonal heterogeneity may be key to understanding mechanisms of therapeutic failure in human cancer. However, little is known on the consequences of therapeutic intervention on the clonal composition of solid tumors.
Experimental Design: Here, we used 33 single cell–derived subclones generated from five clinical glioblastoma specimens for exploring intra- and interindividual spectra of drug resistance profiles in vitro. In a personalized setting, we explored whether differences in pharmacologic sensitivity among subclones could be employed to predict drug-dependent changes to the clonal composition of tumors.
Results: Subclones from individual tumors exhibited a remarkable heterogeneity of drug resistance to a library of potential antiglioblastoma compounds. A more comprehensive intratumoral analysis revealed that stable genetic and phenotypic characteristics of coexisting subclones could be correlated with distinct drug sensitivity profiles. The data obtained from differential drug response analysis could be employed to predict clonal population shifts within the naïve parental tumor in vitro and in orthotopic xenografts. Furthermore, the value of pharmacologic profiles could be shown for establishing rational strategies for individualized secondary lines of treatment.
Conclusions: Our data provide a previously unrecognized strategy for revealing functional consequences of intratumor heterogeneity by enabling predictive modeling of treatment-related subclone dynamics in human glioblastoma

overall_design: Gene expression analysis of 7 cultured glioblastoma-samples from one surgical specimen and U-87, fibroblasts and embryonic stem cell derived neural progenitors. 5 subclones (GNV019_CL1/2/3/6/7) were derived from a parental culture (GNV019; in an early (5) and late (10) passage).

first: Björn

last: Scheffler


title: VEGF blockade enhances the antitumor effect of BRAFV600E inhibition (human)

city: Candiolo

first: Davide

last: Cora'

state: TO

department: Dept. of Oncology

country: Italy

institute: Piemonte Orientale University and IRCCS Candiolo Cancer Institute

summary: In this work we investigated the combined effects  of the BRAF inhibition and of the VEGF blockade in a preclinical model of melanoma. The purpose of this dataset was to examine the transcriptional responses of a A375 xenograft model to PLX472 and bevacizumab, either as single agents or as combination therapy. We performed species-specific analysis of gene expression to discriminate the effects of the different therapeutic regimens on tumor cells (human) and stromal microenvironment (mouse). Here, Illumina Human BeadChips were used to profile the transcriptome after 12 days treatment. We reported that dispensing the dual treatment is more efficient than the single compounds and the occurrence of resistance by modifying the tumor genetic programs regulating myeloid cells recruitment and extracellular matrix remodeling.

overall_design: A375 melanoma cell line xenografts treated with vehicle, PLX4720, bevacizumab or COMBO for 12 days

first: V

last: Comunanza

first: D

last: Corà


title: Targeting metastasis stem cells through the fatty acid receptor CD36 (II)

status: Public on Dec 16 2016

city: Sabadell

first: Antoni

last: Berenguer-LLergo

state: Barcelona

address: Parc del Taulí, 1

department: A8G2 Group - Rheumatology Service

institute: Parc Taulí Research and Innovation Institute (I3PT)

summary: Metastasis is the leading cause of cancer-related deaths. For most human cancers, the identity of the cells that initiate and promote metastasis is still unknown, hampering our ability to develop therapies to prevent or inhibit the spread of tumour cells to distant sites. Using an orthotopic model of human oral squamous cell carcinoma (OSCC), we have now identified a subpopulation of CD44bright cells within the primary lesion with the highest potential to develop lymph node and lung metastasis. This population is slow-cycling, expresses high levels of the receptor CD36 at the cell membrane and relies on fatty acid metabolism to thrive in lymph nodes and bronchoalveolar environments. Importantly, inhibition of CD36 by either shRNA or neutralizing monoclonal antibodies severely impairs metastatic spread of primary OSCC patient samples and established cell lines. Further underscoring its importance, CD36 overexpression in poorly disseminating tumours confers an aggressive metastatic behaviour. Analyses of public gene expression data indicate that the presence of the signature-defining CD36+ cells also strongly correlates with a poor prognosis in patients with lung SCC, ovarian cancer, bladder cancer, or luminal breast cancer. By identifying metastasis-promoting cells and then targeting them with CD36 inhibition, novel anti-metastatic therapies could be developed for patients with these types of tumours.

overall_design: 3 biological replicates from Detroit-562 (Detroit #1,#2, #3) cell line and 2 biological replicates from patient derived cell line VDH-02 (hpSCC/VDH02 #2, #4) were included. From each biological replicate, 2 independent populations were sorted (CD36+ and CD36- respectively).

first: Salvador

last: Aznar-Benitah

first: Gloria

last: Pascual Angulo

first: Camille

last: Stephan-Otto Attolini


title: Whole-genome DNA methylation and expression profiles of CD4+ CD28+ and CD4+ CD28null T lymphocytes

status: Public on Dec 15 2016

city: Oviedo

first: Beatriz

last: Suarez-Alvarez

state: Oviedo

address: Celestino Villamil s/n

institute: Hospital Universitario Central de Asturias

type:
Methylation profiling by array
Expression profiling by array

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

overall_design: Refer to individual Series


title: Whole-genome expression profiles of CD4+ CD28+ and CD4+ CD28null T lymphocytes.

summary: The loss of the CD28 co-stimulatory molecule by CD4+ lymphocytes (CD28null T cells) is accompanied by the acquisition of new biological and functional properties that lead to an impaired immune response. The regulatory mechanisms that govern the appearance and function of this cell subset in several inflammatory disorders and in healthy individuals, mainly in aging, are yet a controversial point. Here, we provide the whole-genome DNA methylation and gene expression profiles of CD28null T cells and its CD28+ counterpart. A comparative analysis reveals that 296 genes are differentially methylated between both cell subsets. One hundred sixty (160 genes) associated with the cytotoxicy ability (e.g., GRZB, TYROBP, and RUNX3) and cytokine/chemokine signaling (e.g., CX3CR1, CD27, and IL1R) are demetylated in CD28null T cells, whilst 136 de-novo methylated genes matched with defects in the TCR signaling pathway (e.g., ITK, TXK, CD3G, and LCK). Moreover, we show that genes related inflammasome activation are differentially expressed between CD28null and CD28+ T cells, highlight the contribution of this pathways to the pro-inflammatory profile of CD28null T cells. Overall, our results reveal that CD28null T cells have a unique DNA methylation landscape, which is associated with alteration in gene expression and contributes to the functionality of these cells. Understanding these epigenetic regulatory mechanisms could provide novel therapeutic strategies to prevent the accumulation and activation of these cells in aging and inflammatory disorders.

overall_design: Peripheral blood mononuclear cells (PBMCs) were isolated by density gradient centrifugation from 24 healthy donors. Further, CD4+CD28null and CD4+CD28+ T lymphocytes were purified using CD4 Multisort kit and CD28 MicroBead kit (Miltenyi Biotec) following the manufacturer´s instructions or sorted with a BD FACSARIA II cytometer (BD Bioscience) after staining with CD4-APC and CD28-FITC monoclonal antibodies (mAbs) (BioLegend). Purity was always higher than 95% for all samples. Datasets were generated from two biological replicates per each cell type (CD28null and CD28+) obtained from a pool of twelve healthy donors each one. Samples were pooled using the same RNA quantity by donor. For expression data, a gene was considered to be differentially expressed if had a value of FDR-adjusted p < 0.05 and at least an expression of >1.5 fold-change (FC).

first: Ramón

middle: M

last: Rodriguez

first: Karin

last: Schlangen

first: Aroa

middle: B

last: Raneros

first: Leonardo

last: Márquez

first: Agustín

middle: F

last: Fernandez

first: Carmen

last: Díaz-Corte

first: Ana

last: Aransay

first: Carlos

last: López-Larrea


title: Targeting metastasis stem cells through the fatty acid receptor CD36


title: Expression data from MCF-7 breast cancer cells treated with CNTs, ginsenosides (Rb1 and Rg1) and  conjugates (Rb-CNTs and Rg-CNTs)

city: Little Rock

first: Mariya

last: Khodakovskaya

state: AR

address: 2801 S. University Avenue

department: Biology

institute: University of Arkansas at Little Rock

summary:
To investigate the effects of ginsenosides-CNTs conjugtaes on total expression profile of MCF-7 breast cancer cells, we conjugated ginsenoides Rb1 and Rg1 with multi-walled carbon nanotubes in a 5:1 ratio.
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 ginsenoside-CNTs conjugates and compare it to the ginsenosides alone (Rb1 and Rg1)

overall_design:
MCF-7 breast cancer cells were incubated with CNTs (8 ug/ml), Rb1 (2 ug/ml), Rg1 (2 ug/ml), Rb-CNTs (10 ug/ml) and Rg-CNTs (10 ug/ml) for 24 hours  and selected for RNA extraction and hybridization on Affymetrix microarrays.
type: cell death responses


title: Oncostatin M promotes cancer cell plasticity through cooperative STAT3-SMAD3 signaling

status: Public on Dec 13 2016

city: Cleveland

first: Mark

last: Jackson

state: OH

address: 10900 Euclid Ave

department: Pathology

institute: Case Western Reserve University

summary: Increasing evidence supports the idea that cancer cell plasticity promotes metastasis and tumor recurrence, resulting in patient mortality. While it is clear that the tumor microenvironment (TME) contributes to cancer cell plasticity, the specific TME factors most actively controlling plasticity remain largely unknown. Here, we performed a screen to identify TME cytokines and growth factors that promote epithelial-mesenchymal plasticity, and acquisition of cancer stem-cell (CSC) properties. Of 28 TME cytokines and growth factors tested, we identified Oncostatin M (OSM) as the most potent inducer of mesenchymal/CSC properties. OSM-induced plasticity was Signal Transducer and Activator of Transcription 3 (STAT3)-dependent, and also required a novel intersection with Transforming Growth Factor-β (TGF-β)/SMAD signaling. OSM/STAT3 activation promoted SMAD3 nuclear accumulation, DNA-binding, and induced SMAD3-dependent transcriptional activity. Suppression of TGF-β receptor activity or ablation of SMAD3 or SMAD4, but not SMAD2, strongly suppressed OSM/STAT3-mediated plasticity. Moreover, removal of OSM or inhibition of STAT3 or SMAD3 resulted in a marked reversion to a non-invasive, epithelial phenotype. We propose that, targeted blockade of the STAT3/SMAD3 axis in tumor cells may represent a novel therapeutic approach to prevent the plasticity required for metastatic progression and tumor recurrence.

overall_design: Total RNA was isolated from sorted CD24+ 48R-shp16-shp53-MYC-RAS which were cultured under normal conditions (CD24+ NT) or in the presence of human recombinant OSM 10ng/mL (CD24+ OSM) or human recombinant TGF-b 10ng/mL (CD24+ TGF-b) for three weeks. Cells were treated at every medium change.

middle: W


title: caArray_stegm-00394: Broad: Identification of AML1-ETO modulators by chemical genomics

status: Public on Dec 08 2016

city: Rockville

first: Mervi

last: Heiskanen

state: MD

address: 9609 Medical Center Drive, 1W378

department: CBIIT

institute: NCI

summary: Somatic rearrangements of transcription factors are common abnormalities in the acute leukemias. With rare exception, however, the resultant protein products have remained largely intractable as pharmacologic targets. One example is AML1-ETO, the most common translocation reported in acute myeloid leukemia (AML). To identify AML1-ETO modulators, we screened a small molecule library using a chemical genomic approach. Gene expression signatures were used as surrogates for the expression versus loss of the translocation in AML1-ETO-expressing cells. The top classes of compounds that scored in this screen were corticosteroids and dihydrofolate reductase (DHFR) inhibitors. In addition to modulating the AML1-ETO signature, both classes induced evidence of differentiation, dramatically inhibited cell viability, and ultimately induced apoptosis via on-target activity. Furthermore, AML1-ETO-expressing cell lines were exquisitely sensitive to the effects of corticosteroids on cellular viability compared with nonexpressers. The corticosteroids diminished AML1-ETO protein in AML cells in a proteasome- and glucocorticoid receptor-dependent manner. Moreover, these molecule classes demonstrated synergy in combination with standard AML chemotherapy agents and activity in an orthotopic model of AML1-ETO-positive AML. This work suggests a role for DHFR inhibitors and corticosteroids in treating patients with AML1-ETO-positive disease.

overall_design:
stegm-00394
Assay Type: Gene Expression
Provider: Affymetrix
Array Designs: HG-U133A, HG_U95A
Organism: Homo sapiens (ncbitax)
Tissue Sites: Bone marrow
Disease States: Lymphoma, Acute Myeloid Leukemia


title: Transcriptome profiles of differentiated hepatoma cells infected with oncogenic hepatitis C virus

status: Public on Dec 11 2016

first: Yujin

last: Hoshida

summary:
BACKGROUND & AIMS: Although patients infected by genotype 1b hepatitis C virus (HCV) with Q(70) and/or M(91)core gene mutations have an almost five-fold increased risk of developing hepatocellular carcinoma (HCC) and increased insulin resistance, the absence of a suitable experimental system has precluded direct experimentation on the effects of these mutations on cellular gene expression.
METHODS: HuH7 cells were treated long-term with human serum to induce differentiation and to produce a model system for testing high-risk and control HCV. For clinical validation, profiles of infected cells were compared to each other and to those of liver biopsies of patients with early-stage HCV-related cirrhosis followed prospectively for up to 23 years (n=216).
RESULTS: Long-term culture in human serum produced growth-arrested, hepatocyte-like cells whose gene profile overlapped significantly with that of primary human hepatocytes. High-risk (Q(70)/M(91)) and control (R(70)/L(91)) viruses had dramatically different effects on gene expression of these cells. The high-risk virus enhanced expression of pathways associated with cancer and type II diabetes, while the control virus enhanced pathways associated with oxidative phosphorylation. Of special clinical relevance, the transcriptome of cells replicating the high-risk virus correlated significantly with an HCC high-risk profile in patients (Bonferroni-corrected p=0.03), whereas no such association was observed for non-HCC-related clinical outcomes.
CONCLUSIONS: The cell-based system allowed direct head-to-head comparison of HCV variants, and provided experimental support for previous clinical data indicating an oncogenic effect of core gene mutations. This simple experimental system distinguished HCV variants and will enable future mechanistic analysis and exploration of interventional approaches.

overall_design: Huh-7 cells were cultured with either fetal bovine serum (FBS) or human serum (HS) and infected with hepatitis C virus (HCV) clones with or without oncogenic mutations.

first: Ahmed

last: Elshamy

first: Xiaochen

last: Sun

first: Andrea

last: Branch


title: Microarray-based Gene Expression Analysis of WA09 hESC  After Manipulation of Intracellular Potassium Content

status: Public on Dec 03 2016

city: Fort Worth

first: Yu-Chieh

last: Wang

address: 3500 Camp Bowie Blvd

department: Pharmaceutical Sciences

institute: University of North Texas Health Science Center

summary: Analysis of intracellular inorganic element alterations to human pluripotent stem cells at gene expression level. The hypothesis tested in the present study was that changes in intracellular inorganic elements, like potassium, would change the pluripotent signaling network and influence differentiation cues. Results provide important information on the response of human pluripotent stem cells to tetraethylammonium-  and salinomycin-based changes to intracellular potassium, such as specific  up- or down-regulated genes governing cell proliferation, cell growth, differentiation, and development of specific cell lineages.

overall_design: Total RNA obtained from 48hr treatment with and without tetraethylammonium (TEA) and salinomycin (SAL), with and without changes in media by the addition of potassium chloride or sodium chloride. Study included 6 samples, repeated twice, for a total of 12 samples. Untreated samples in E8 TeSR media served as controls.

first: Victor

middle: J

last: Lin

first: Yu-chieh


title: Hypoxia-independent gene expression signature associated with radiosensitisation of prostate cancer cell lines by histone deacetylase inhibition

city: Oslo

first: Heidi

last: Lyng

address: Montebello

department: Department of Radiation Biology

country: Norway

institute: Oslo University Hospital

summary:
We aimed to investigate gene expression associated with radiosensitisation of normoxic and hypoxic prostate cancer cells by the class I/II histone deacetylase inhibitor (HDACi) vorinostat.
A pronounced deregulation of DNA repair and chromatin organization genes by vorinostat in DU 145 than in PC-3 or 22Rv1 was found and was a likly mechanism underlying radiosensitisation of DU 145. Expression of these genes was generally not affected by hypoxia and was altered by vorinostat in DU 145 towards the baseline levels of PC-3 and 22Rv1. A 56-gene expression signature associated with radiosensitisation under normoxia and hypoxia, including 8 genes with baseline expression characteristic of the radiosensitising effect was generated.  These findings propose a hypoxia independent expression signature to predict the radiosensitising effect of vorinostat.

overall_design: DU 145, PC-3 and 22Rv1 cell lines, for which differences in intrinsic radiosensitivity have been demonstrated in previous work,  were exposed to vorinostat (1µM, 24h) and hypoxia (0.2% O2, 24h), subjected to gene expression profiling and irradiated at 2 and 5 Gy. Samples collected for gene expression analysis were taken prior to irradiation. Vorinostat mediated radiosensitisation occurred under normoxia and hypoxia in the intrinsically radioresistant DU 145, but not in the radiosensitive PC-3 and 22Rv1. To identify a gene expression signature most likely playing a major role in the vorinostat mediated radiosensitisation, a supervised analysis of global gene expression data were performed.

first: Marte

last: Jonsson

first: Harald

last: Ragnum

first: Cathinka

middle: H

last: Julin

first: Andree

last: Yeramian

first: Trevor

last: Clancy

first: Kari-Anne

last: Frikstad

first: Trond

last: Stokke

first: Xavier

last: Matias-Guiu

first: Anne

last: Ree

first: Kjersti

last: Flatmark


title: Level of FACT defines the transcriptional landscape and aggressive phenotype of breast cancer cells

city: BUFFALO

first: Eduardo

last: Cortes

state: NY

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

institute: ROSWELL PARK CANCER INSTITUTE

summary: FACT inhibition, via small molecule or shRNA, lead to reduced growth and viability of all BrCa cells tested. Phenotypic changes were more severe in high FACT cells (death or growth arrest) than in low FACT cells (decreased proliferation). Though inhibition had no effect on the rate of general transcription, expression of individual genes was changed in a cell-specific manner. Initially distinct transcriptional profiles of BrCa cells became almost identical via equalizing FACT expression. We found that in “high-FACT” cells FACT supports expression of genes involved in the regulation of cell cycle, DNA replication, maintenance of undifferentiated cell state and regulated by the activity of proto-oncogenes, such as Hras, cMyc, E2F family ets.  In “low-FACT” cells presence of FACT reduces expression of genes coding enzymes of steroid metabolism characteristic for the differentiated mammary epithelia. Inhibition of FACT leads to the shift from more aggressive transcriptional program to more benign, accompanied with similar type of phenotypical changes.   Thus we propose FACT as a marker to predict aggressiveness of BrCa and as a target to either kill aggressive BrCa cells or to convert them to a less aggressive phenotype.

overall_design: MCF7, MCF7v.1 and T47D cells were transduced with lentiviral vectors encoding control shRNA or two shRNAs to SSRP1 subunit of FACT. RNA was isolated from cells at 72 hrs post-transduction and used for microarray hybridization.

first: Katerina

last: Gurova


title: Partially exhausted CD8+ T cells are associated with clinically beneficial response to Teplizumab in new onset type I diabetes (microarray)

status: Public on Dec 06 2016

city: Seattle

first: Scott

last: Presnell

state: WA

address: 1201 Ninth Avenue

institute: Benaroya Research Institute

summary: Biologic agents active in other autoimmune settings have had variable effectiveness in newly diagnosed type 1 diabetes (T1D) where treatment across therapeutic targets is accompanied by transient stabilization of C-peptide levels in some patients, followed by progression at the same rate as in control groups. Why disparate treatments lead to similar clinical courses is currently unknown. Here, we use integrated systems biology and flow cytometry approaches to elucidate immunologic mechanisms associated with C-peptide stabilization in T1D subjects treated with the anti-CD3 monoclonal antibody, teplizumab.

overall_design: We used unbiased whole blood transcriptomic approaches to identify cellular and molecular markers that accompany successful treatment with a non-Fc binding anti-CD3 antibody (teplizumab)

first: S

last: Long

first: Jerill

last: Thorpe

first: Hannah

last: DeBerg

first: Vivian

last: Gersuk

first: James

last: Eddy

first: Kristina

last: Harris

first: Mario

last: Ehlers

first: Kevan

last: Herold

first: Jerry

last: Nepom

first: Peter

last: Linsley


title: Bioengineered tumoral microtissues recapitulate desmoplastic reaction of pancreatic cancer

status: Public on Dec 14 2016

first: Davide

last: Cora'

summary: In this work, we reported a strategy to produce 3D in vitro microtissues of pancreatic ductal adenocarcinoma (PDAC) for studying the desmoplastic reaction activated by the stroma-cancer crosstalk. The purpose of this dataset was to examine the transcriptional expression changes of normal fibroblasts (NF), cancer-associated fibroblasts (CAF) and pancreatic adenocarcinoma cell line (PT45) in 3D versus 2D culture and in mono-culture versus co-culture. Illumina Human BeadChips were used to profile the transcriptome after 12 days of culture. We reported that human PDAC microtissues, obtained by co-culturing PT45 with NF or CAF within biodegradable microcarriers in spinner flask bioreactor, closely recapitulate key PDAC microenvironment characteristics.

overall_design: Normal fibroblasts (NF), cancer-associated fibroblasts (CAF) and pancreatic adenocarcinoma cell line (PT45) cultured in 2D or 3D conditions for 12 days, in mono- or co-cultures.

first: V

last: Comunanza

first: D

last: Corà


title: A 17-Gene Stemness Score for Rapid Identification of High-Risk AML Patients [Illumina]

status: Public on Dec 02 2016

city: Toronto

first: Stanley

last: Ng

state: Ontario

address: 160 College Street

country: Canada

institute: Univerity of Toronto

summary: In AML, most patients are initiated on standard chemotherapy and afterwards assigned to a post-remission strategy based on genetically-defined risk categories. However, outcomes remain heterogeneous, indicating the need for novel biomarker tests that can rapidly and accurately identify high-risk patients, allowing better stratification of both induction and post-remission therapy. As patient outcomes are linked to leukemia stem cell (LSC) properties that confer therapy resistance and drive relapse, LSC-based biomarkers may be highly informative. We tested 227 CD34/CD38 cell fractions from 78 AML patients for LSC activity in xenotransplantation assays. Comparison of microarray-based gene expression (GE) profiles between 138 LSC+ and 89 LSC? fractions identified 104 differentially-expressed LSC-specific genes. To obtain prognostic signatures, we performed statistical regression analysis of LSC GE against patient outcome using a training cohort of 495 AML patients treated with curative intent. A score calculated as the weighted sum of expression of 17 LSC signature genes (LSC17) was strongly associated with survival in 4 independent datasets (716 AML cases) spanning all risk categories in multi-variate analysis; an optimized 3-gene sub-score (LSC3) was prognostic in favorable risk subsets. These scores were robust across GE technology platforms, including the clinically serviceable NanoString system (LSC17: HR=2.73, P<0.0001; LSC3: HR=6.3, P<0.02). The LSC17 and LSC3 scores provide rapid and accurate identification of high-risk patients for whom conventional chemotherapy is non-curative. These scores will enable evaluation in clinical trials of whether such patients may benefit from novel and/or more intensified therapies during induction or in the post-remission setting.

overall_design: Microarray GE profiling was performed on funcationally validated 138 LSC+ and 89 LSC– cell fractions sorted from 83 primary AML patient samples based on the expression of CD34 and CD38

first: Amanda

last: Mitchell

last: Kennedy

first: Claire

last: Chen

first: Jessica

last: McLeod

first: Narmin

last: Ibrahimova

first: Andrea

last: Arruda

first: Andreea

last: Popescu

first: Vikas

last: Gupta

first: Aaron

middle: D

last: Schimmer

first: Andre

middle: C

last: Schuh

first: Karen

last: Yee

first: Lars

last: Bullinger

first: Klaus

last: Metzeler

first: Tobias

first: Christian

last: Buske

first: Bob

last: Löwenberg

last: Valk

last: Zandstra

first: Mark

last: Minden

first: John

middle: E

last: Dick

first: Jean

last: Wang


title: Androgen-dependent repression of estrogen-related receptor γ expression mediates metabolic reprogramming in prostate cancer

city: Québec City

first: Etienne

last: Audet-Walsh

state: QC

address: 2705 boulevard Laurier

department: Molecular Medicine

institute: Université Laval

summary:
Androgens are central to prostate cancer (PCa) development and targeting this pathway is currently the main therapeutic axis in the clinic, but the mechanism by which androgen signaling contributes to the oncometabolic state of PCa cells remains to be fully elucidated. The intersection of gene expression, binding-events and motif finding analyses following androgen exposure identified a metabolic gene signature associated with the action of estrogen-related receptors (ERRs). Unexpectedly, we show that ERRγ acts as a negative regulator of mitochondrial respiration in the context of PCa, and that AR-dependent direct repression of ERRγ promotes the reactivation of a functional TCA cycle. This metabolic state, which parallels the loss of ERRγ expression, was observed in both androgen-dependent and castration-resistant PCa and was associated with cell proliferation. Interrogation of several clinical studies revealed a strong inverse relationship between ERRγ expression and the severity of the disease. Our study uncovers a novel mechanism by which AR-dependent repression of ERRγ contributes to the reprogramming of PCa cell metabolism to favor mitochondrial activity and cell proliferation.
We used microarrays to investigate the transcriptional regulation of metabolic genes by 72h treatment with R1881, a synthetic androgens, with or without repression of the estrogen-related receptor gamma, in LNCaP prostate cancer cells.

overall_design: Cells were seeded in media containing 2% serum deprived from steroids  and transfected with siRNA controls or against estrogen-related receptor gamma. 48h later, cell were trypsinized and seeded in 6-well plates for treatment with 10nM R1881 or vehicle (EtOH) for 72h, with fresh medium and treatment added after 48h. Triplicate samples were sent for each conditions.

first: Étienne

first: Vincent

last: Giguère


title: Genome-wide analysis of 22Rv1 and its metastatic derivatives

status: Public on Dec 20 2016

city: Taipei

first: Pei-Wen

last: Hsiao

state: Taiwan

address: 128 Academia Road, Section 2, Nankang

department: ABRC

country: Taiwan

institute: Academia Sinica

summary: Metastasis of prostate cancer lacks effective curatives and results in significant mortality in men worldwide. Here, we developed highly metastatic cells from 22 Rv1 cell line and characterized these sublines as exhibiting high invasion capacity, epithelial-mesenchymal transition, and stem cell-like properties. To understand the molecular signature causally related to these phenotypes, cDNA microarray was applied to compare 22Rv1 with the metastatic sublines for differential gene expression.

overall_design: 22Rv1 cells were subjected to in vivo propagation to develop their metastases. Total RNA obtained from 22Rv1 and 22Rv1-derived metastases were analyzed compared.

first: Sheue-Fen

last: Tzeng

first: Chin-Hsien

last: Tsai

first: Mong-Hsun


title: caArray_strue-00134: Identification of BRCA1 mutation carriers using oligonucleotide arrays

first: Mervi

last: Heiskanen

summary: To determine if oligonucleotide arrays can be used to identify BRCA1 positive mutation carriers and to gain further insight into the role of BRCA1.

overall_design:
strue-00134
Assay Type: Gene Expression
Provider: Affymetrix
Array Designs: HG-U133A, HG-U133B
Organism: Homo sapiens (ncbitax)


title: System Analysis: Respiratory Syncytial Virus induces a decrease expression of HLA-DR at both the cell surface and transcriptional level in Infants with Severe Bronchiolitis.

status: Public on Dec 01 2016

city: Columbus

first: Santiago

last: Lopez

address: 700 Children's dr.

department: Center for Vaccines & Immunity

institute: The Research Institute at the Nationwide Children's Hospital

summary: The objective of this study was to better understand the immune response to RSV at the port of entry, in the upper respiratory tract mucosa of children naturally infected with RSV.

overall_design: For the present study, we collected Nasal wash samples from a total of 76 naturally infected RSV infants within 48 hours of hospital admission and 10 healthy controls. After sample collected, samples were process and RNA was extracted for further microarray hybridization.

first: Emilio

last: Flano

first: Maria

last: Suarez-Arrabal

first: Sara

last: Mertz

first: Cesar

last: Mella

first: Blerta

last: Dimo

first: Gail

last: Arthur

first: Octavio

last: Ramilo

first: Asuncion

last: Mejias


title: Gene expression signature baesd screening identifies ribonucleotide reductase as a candidate therapeutic target in Ewing sarcoma

city: Iowa City

first: David

middle: Jon

last: Gordon

state: Iowa

address: 25 S Grand Ave

department: Pediatric Hematology/Oncology

institute: University of Iowa

summary: There is a critical need in cancer therapeutics to identify targeted therapies that will improve outcomes and decrease toxicities compared to conventional, cytotoxic chemotherapy. Ewing sarcoma is a highly aggressive bone and soft tissue cancer that is caused by the EWS-FLI1 fusion protein. Although EWS-FLI1 is specific for cancer cells, and required for tumorigenesis, directly targeting this transcription factor has proven challenging. Consequently, targeting unique dependencies or key downstream mediators of EWS-FLI1 represent important alternative strategies. We used gene expression data derived from a genetically defined model of Ewing sarcoma to interrogate the Connectivity Map and identify a class of drugs, iron chelators, that downregulate a significant number of EWS-FLI1 target genes. We then identified ribonucleotide reductase M2 (RRM2), the iron-dependent subunit of ribonucleotide reductase (RNR), as one mediator of iron chelator toxicity in Ewing sarcoma cells. Inhibition of RNR in Ewing sarcoma cells led to apoptosis and cell death in vitro and attenuated tumor growth in vivo in a xenograft model. Additionally, we discovered that the sensitivity of Ewing sarcoma cells to inhibition or suppression of RNR is mediated, in part, by high levels of SLFN11, a protein that sensitizes cells to DNA damage. This work demonstrates a unique dependency of Ewing sarcoma cells on RNR and supports further exploration of clinically used inhibitors of RNR as a therapeutic approach in treating this cancer.

overall_design:
We used microarrays to detail the effects of ciclopirox and RRM2 siRNA on gene expression in Ewing sarcoma cell lines.
Triplicate biological replicates were collected and analyzed

first: Kelli

last: Goss


title: T cell responses to H1N1v and a longitudinal study of seasonal influenza vaccination - 2011

city: palo alto

first: weiqi

last: wang

state: ca

address: 1291 welch road

institute: stanford

summary: Systems biology approach to examine effects of seasonal flu vaccination in adults of different ages on gene expression, cytokine stimulation and serum cytokines with parameters such as immune senescence to uncover new markers and mechanisms behind failure of immune function in many older people.

overall_design: 1. Combinatorial tetramer analysis by FACS and/or CyTOF; Phosphoflow. 2. Luminex; Gene expression profiling (Affymetrix microarray). 3. Luminex; Gene expression profiling (Affymetrix microarray); Microneutralization assays. 4. Gene expression profiling (Affymetrix microarray); Immune phenotyping by CyTOF. 5. Gene expression profiling (Affymetrix microarray). 6. Immune phenotyping by CyTOF; Luminex. 7. ELISA

first: Mark

last: Davis


title: Gene microarray of human adipocytes exposed to medium conditioned by inflamed adipose tissue

city: Roseworthy

first: Ruijie

last: Liu

state: South Australia

address: Mudla Wirra Rd

country: Australia

institute: the university of Adelaide

summary: Omental adipose tissue explants were cultured for 24h in serum-free medium in the presence of vehicle (control medium) or macrophage (LPS) and T-cell (anti-CD3/28) stimulants (active medium). SGBS human preadipocytes were differentiated into adipocytes and then exposed to 25% v/v control or active medium.

overall_design: Total RNA was extracted from SGBS adipocytes that had been cultured for 24 hours or 48 hours in the presence of 25%v/v. Each active sample (Om) and control sample (StimOm) are from three repeat expreiments.


title: 1-day styrene inhalation dose response in C57BL/6 mice (liver)

status: Public on Nov 30 2016

city: Research Triangle Park

first: Michael

middle: B.

last: Black

state: North Carolina

address: 100 Capitola Dr., Suite 106

institute: Scitovation, LLC.

summary: This data set is #3 of three generated as part of a coordinated series of experiments to examine potential modes of action of Styrene inhalation on lung and liver in male C57Bl/6 mice.  Styrene causes increased lung tumors in mice, but not in rats.  Mouse lung tumors were found mostly at the conclusion of a life-time (104 weeks for males) exposure study and most were benign.  Styrene is largely negative in genotoxicity assays.  Styrene metabolism by CYP2F2 produced a different metabolite pattern in mouse lung than in liver or in rats or humans.  The purpose of this study was to use genomic analyses to further investigate potential modes of action (MoA) of styrene in mice, using a total of three genomic data sets.  Dataset #1 exposed C57BL/6 wild-type (WT), CYP2F2 knockout (-/-; KO) and CYP2F21 humanized (2F2-KO + 2F1,2A13,2B6-transgenic, TG) male mice to 0, 40 or 120 ppm styrene at 6 hr/day 5 days/wk for 1 or 4 wk.  Lungs were analyzed by whole genome microarrays for each strain at each dose.  The second part of the study examined a broader dose response and short term exposure.  Male wild type C57Bl/6 mice were exposed to 6 inhalation concentrations of styrene: 0, 1, 5, 10, 20, 40, and 120 ppm for a single 6 hour exposure. This was intended to gain dose-response data at low-observed-adverse-effect-levels (LOAELs) of styrene (≥ 20 ppm) and at no-observed-adverse-effect-levels (NOAELs) of styrene (< 20 ppm). Dataset #2 examined lung gene expression, while dataset #3 examined liver gene expression data from the same animals.

overall_design: Liver gene expression was evaluated in male C57Bl/6 (WT) mice following a single 6-hr inhalation exposure of styrene at 0, 1, 5, 10, 20, 40, and 120ppm

first: Melvin

last: Andersen


title: 1-day styrene inhalation dose response in C57BL/6 mice (lung)

summary: This data set is #2 of three generated as part of a coordinated series of experiments to examine potential modes of action of Styrene inhalation on lung and liver in male C57Bl/6 mice.  Styrene causes increased lung tumors in mice, but not in rats.  Mouse lung tumors were found mostly at the conclusion of a life-time (104 weeks for males) exposure study and most were benign.  Styrene is largely negative in genotoxicity assays.  Styrene metabolism by CYP2F2 produced a different metabolite pattern in mouse lung than in liver or in rats or humans.  The purpose of this study was to use genomic analyses to further investigate potential modes of action (MoA) of styrene in mice, using a total of three genomic data sets.  Dataset #1 exposed C57BL/6 wild-type (WT), CYP2F2 knockout (-/-; KO) and CYP2F21 humanized (2F2-KO + 2F1,2A13,2B6-transgenic, TG) male mice to 0, 40 or 120 ppm styrene at 6 hr/day 5 days/wk for 1 or 4 wk.  Lungs were analyzed by whole genome microarrays for each strain at each dose.  The second part of the study examined a broader dose response and short term exposure.  Male wild type C57Bl/6 mice were exposed to 6 inhalation concentrations of styrene: 0, 1, 5, 10, 20, 40, and 120 ppm for a single 6 hour exposure. This was intended to gain dose-response data at low-observed-adverse-effect-levels (LOAELs) of styrene (≥ 20 ppm) and at no-observed-adverse-effect-levels (NOAELs) of styrene (< 20 ppm). Dataset #2 examined lung gene expression, while dataset #3 examined liver gene expression data from the same animals.

overall_design: Lung gene expression was evaluated in male C57Bl/6 (WT) mice following a single 6-hr inhalation exposure of styrene at 0, 1, 5, 10, 20, 40, and 120ppm


title: Examining potential modes of action of Styrene inhalation on lung and liver in male C57Bl/6 mice

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

overall_design: Refer to individual Series


title: Effects of maggot excretions and secretions (ES) on human cultured cells in vitro

city: Auckland

first: Cherie

last: Blenkiron

address: Private bag 92019

department: Surgery

country: New Zealand

institute: University of Auckland

summary:
Maggot ES is known to induce wound healing in vivo to improve chronic wound repair. The effects have been studies at the protein and molecular level but never before at the transcriptional level.
Affymetrix microarrays were used to identify the genes modulated by maggot ES and link these to gene pathways to understand the molecular effects on cells.

overall_design: Cells were plated in 6 well plates overnight before treating with 8µg/mL ES or an equal volume of carrier buffer PBS for 48 hours. Treatments were performed in three biological replicate. After the treatment time total RNA was isolated.

first: Priscila

last: Singorenko

first: Roseanne

last: Rosario

first: John

last: Windsor

first: Anthony

middle: R

last: Phillips


title: A 17-Gene Stemness Score for Rapid Identification of High-Risk AML Patients

first: Stanley

last: Ng

first: Amanda

last: Mitchell

first: James

last: Kennedy

first: Weihsu

last: Chen

first: Jessica

last: McLeod

first: Narmin

last: Ibrahimova

first: Andrea

last: Arruda

first: Andreea

last: Popescu

first: Vikas

last: Gupta

first: Aaron

last: Schimmer

first: Andre

last: Schuh

first: Karen

last: Yee

first: Lars

last: Bullinger

first: Tobias

last: Herold

first: Dennis

last: Görlich

first: Thomas

last: Büchner

first: Wolfgang

last: Hiddemann

last: Berdel

first: Bernhard

last: Wörmann

first: Meyling

last: Cheok

first: Claude

last: Preudhomme

first: Hervé

last: Dombret

first: Klaus

last: Metzeler

first: Christian

last: Buske

first: Bob

last: Löwenberg

first: Peter

last: Valk

last: Zandstra

last: Minden

last: Dick

first: Jean

last: Wang


title: Impairment of host liver repopulation by transplanted hepatocytes in aged rats and the release by short-term growth hormone treatment

city: Leipzig

first: Bruno

last: Christ

state: Saxony

address: Liebigstraße 21

department: Department of Surgery

institute: University of Leipzig

summary:
By using high-density DNA microarrays, we analyzed the gene-expression profile of liver biopsies from young and aged donors
Stock et al., accepted

overall_design: RNA was extracted from liver biopsies and analyzed with Affymetrix HG_U133A microarrays.

first: Peggy

last: Stock

first: Maximilian

last: Bielohuby

first: Martin

last: Staege

first: Mei-Ju

last: Hsu

last: Bidlingmaier


title: Gene expression data from induced Pluripotent Stem cells from Parkinson's Disease patients harbouring amplification of, or mutations in the SNCA gene, and from healthy control donors

status: Public on Nov 16 2016

city: Oxford

first: Sally

last: Cowley

address: South Parks Road

department: Sir William Dunn School of Pathology

country: United Kingdom

institute: University of Oxford

type:
Expression profiling by array
SNP genotyping by SNP array


title: Expression data from nine (9) pancreatic cancer cell lines incubated under normoxic or hypoxic conditions

city: New York

first: Christine

last: Iacobuzio-Donahue

state: New York

address: 417 East 68th Street

institute: Memorial Sloan Kettering

summary: We used microarrays to detail the hypoxic gene expression profile in human pancreatic cancer cells

overall_design: Pancreatic cancer cells were cultured for 24 hours under normoxic or hypoxic (1% oxygen) conditions. RNA from two independent experiments was collected and pooled for microarray hybridization.

first: Salvador

last: Naranjo-Suarez


title: Effect of IL12 on clonal CD8+ CD45RA+ population

status: Public on Nov 21 2016

city: Würzburg

first: Claus

middle: Juergen

last: Scholz

address: Josef-Schneider-Str. 2

department: Core Unit SysMed

institute: University Hospital Würzburg

summary: Effector memory T-cell clones against well known tumor antigens (STEAP1, PRAME; CD8+, CD45RA+) were or were not  treated with 10ng/ml IL12 and analyzed after 12 and 48 hours

overall_design: Global expression profiling of two T-cell clones upon interleukin 12 stimulation.

first: Matthias

last: Braun

last: Wölfl


title: Epigenetic regulation of the transcriptional program in memory and terminally differentiated CD8+ T cells [HCAFIS_12_Gene_Expression]

status: Public on Nov 15 2016

city: Derio

first: Jose

middle: Luis

last: Lavin

state: Bizkaia

address: Parque Tecnológico de Bizkaia Building 502, Floor 0

institute: CIC bioGUNE

summary: Epigenetic mechanisms play a critical role during differentiation of T cells by contributing to the formation of stable and heritable transcriptional patterns. To further study the mechanisms of memory maintenance in CD8+ T cells, we performed genome-wide analysis of DNA methylation, histone marking (H3K9Ac and H3K9me3) and gene expression profiles in naive, effector memory (EM) and terminally differentiated memory (TEMRA) cells. Our results indicate that DNA demethylation and histone acetylation are coordinated to generate the transcriptional program associated with memory cells. Conversely, EM and TEMRA cells share a very similar epigenetic landscape. Nonetheless, the TEMRA transcriptional program predicts an innate immunity phenotype associated with genes never reported in these cells, including several mediators of NK cell activation (VAV3 and LYN) and a large array of NK receptors (KIR2DL3, KIR2DL4, KIR2DL1, KIR3DL1, KIR2DS5, etc.). In addition, we identified up to 161 genes that encode transcriptional regulators, some of unknown function in CD8+ T cells, that were differentially expressed in the course of differentiation. Overall, these results provide new insights into the regulatory networks involved in memory CD8+ T cell maintenance and T cell terminal differentiation.

overall_design: Genome-wide changes in gene Expression in naive CD8+ T cells control and after LEF1 knockdown were generated by Human HT12 v4 BeadChips (Illumina Inc.).

first: Ramón

last: Rodriguez

first: Carlos

last: Lopez Larrea

first: José

last: Luis Lavín


title: Microarray analysis of mRNA expression in human microvascular endothelial cells exposed to colorectal cancer cell derived stimuli

city: Vienna

first: Markus

last: Jeitler

address: Lazarettgasse 14

country: Austria

institute: Medical University Vienna

overall_design: Human microvascular endothelial cells (HMECs) were seeded at 3x10˄5 cells  in complete EGM2-MV growth medium on PET transwells of 1 µm pore size to form a confluent layer within 24 h and were then cultured for another 24 h in EGM2-MV medium including 5% FCS but no additional growth factor supplements. HT-29 colon carcinoma cells were seeded in the same growth medium at 4x10˄6 per 30 mm well and conditioned supernatant was collected from 24 to 48 h after cell seeding. HMEC cultures in transwells were left untreated or were stimulated by tumor-conditioned medium from the basal (experiment 1) or apical (experiment 2) side for 4 hours prior to isolation of total RNA.

last: Brostjan

first: Elisabeth

last: Buchberger

first: Anita

last: Bayer

last: Bilban


title: Differential expression signature of EpiCAM/CD45 positive cells in ascitic fluid from serous ovarian cancer patients

status: Public on Nov 13 2016

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

summary:
Differential transcriptome signature of FACS purified cell population (EpiCAM/CD45 dual positive cells vs EpiCAM only) from the ascites of human serous ovarian cancer.
Primary objective: To characterize the phenotypic expression of stem cells markers, elucidation of differential gene expression and oncogenic functions in EpiCAM/CD45 dual positive vs EpiCAM cells.
Methods: Cell Sorting (FACS) from ascites of human serous ovarian cancer patients, apoptotic assay, Drug sensitivity assay, tumor spheroid assay, Cell invasion and cell migration assay.

overall_design:
Expression profiling of EpiCAM/CD45 dual positive and EpiCAM cells
Platform: GPL10558; Catalog number : BD-103-0204; Array Content: HumanHT-12 v4 Expression BeadChip Kit; No. of Probes on Array: 47323; No.of Annotated Genes: 31000; No.of Control : 887; Label: Biotin; Molecule: RNA; No.of Sample sections on chip: 12

first: Asok

last: Mukhopadhyay

first: Surender

last: Kumar Sharawat

first: Zahid

last: Akhter

first: Vikas

last: Kumar


title: 1 week & 4 week styrene inhalation exposure at 2 concentrations (40ppm & 120ppm) in three strains of C57BL/6 mice (lung): wild-type (WT), CYP2F2 knockout (KO), and CYP2F1 humanized (TG) mice

first: Michael

last: Black

summary: This data set is #1 of three generated as part of a coordinated series of experiments to examine potential modes of action of Styrene inhalation on lung and liver in male C57Bl/6 mice.  Styrene causes increased lung tumors in mice, but not in rats.  Mouse lung tumors were found mostly at the conclusion of a life-time (104 weeks for males) exposure study and most were benign.  Styrene is largely negative in genotoxicity assays.  Styrene metabolism by CYP2F2 produced a different metabolite pattern in mouse lung than in liver or in rats or humans.  The purpose of this study was to use genomic analyses to further investigate potential modes of action (MoA) of styrene in mice, using a total of three genomic data sets.  Dataset #1 exposed C57BL/6 wild-type (WT), CYP2F2 knockout (-/-; KO) and CYP2F21 humanized (2F2-KO + 2F1,2A13,2B6-transgenic, TG) male mice to 0, 40 or 120 ppm styrene at 6 hr/day 5 days/wk for 1 or 4 wk.  Lungs were analyzed by whole genome microarrays for each strain at each dose.  The second part of the study examined a broader dose response and short term exposure.  Male wild type C57Bl/6 mice were exposed to 6 inhalation concentrations of styrene: 0, 1, 5, 10, 20, 40, and 120 ppm for a single 6 hour exposure. This was intended to gain dose-response data at low-observed-adverse-effect-levels (LOAELs) of styrene (≥ 20 ppm) and at no-observed-adverse-effect-levels (NOAELs) of styrene (< 20 ppm). Dataset #2 examined lung gene expression, while dataset #3 examined liver gene expression data from the same animals.

overall_design: A total of 90 male C57BL/6 mice were exposed to two inhalation doses of styrene (40ppm and 120ppm) for 1 week and 4 weeks.  For each treatment a total of 5 biological replicates were used, from 3 strains of mice; wild type (WT), CYP2F2(-/-) knock-out (KO) and  CYP2F2(-/-),2F1,SA13,2B6 transgenic (TG), with strain specific controls included (0ppm).

first: Melvin

last: Andersen


title: Exploring Regulatory Mechanisms of Atrial Myocyte Hypertrophy of Mitral Regurgitation through Gene Expression Profiling Analysis: Role of NFAT in Cardiac Hypertrophy

status: Public on Nov 07 2016

first: Tzu-Hao

last: Chang

address: 250 Wu-Xin Street

department: Graduate Institute of Biomedical Informatics

institute: Taipei Medical University

summary: Regulatory Mechanisms of Atrial Remodeling of Human Mitral Regurgitation

overall_design: This study enrolled 10 human subjects and divided into two groups: mitral regurgitation patients (MR) (n = 7; 7 females), and normal control subjects (NC) (n= 3).We sought to systemically elucidate critical differences in the alteration of RNA expression pattern between the atrial myocardium of MR patients and normal subjects using high-density oligonucleotide microarrays and functional network enrichment analysis.

first: Mien-Cheng

last: Chen

first: Jen-Ping

first: Hsien-Da

last: Huang

first: Wan-Chun

last: Ho

first: Wen-Hao

last: Liu

first: Yu-Sheng

last: Lin

first: Kuo-Li

last: Pan


title: Differentially regulated genes on days 0, 12 and 17 of pancreatic differentiation of control and MODY5 hiPSCs

status: Public on Nov 10 2016

city: Singapore

first: Adrian

middle: Kee Keong

last: Teo

address: 61 Biopolis Drive, Proteos, #06-07

institute: Institute of Molecular and Cell Biology

summary: To determine the differentially expressed genes between control and MODY5 after 0, 12 and 17 days of pancreatic differentiation of hiPSCs

overall_design: One sample from iAG16102, iN805-6, iN805-1 and iN805-2 each on days 0, 12 and 17 were analysed via DNA microarray


title: Analysis of BAFF-mediated gene expression in primary CLL cells

status: Public on Nov 03 2016

city: Portland

first: Alexey

last: Danilov

state: OR

address: 3181 SW Sam Jackson Pk Rd

institute: Oregon Health and Science Univeristy

summary: BAFF ligand induces NF-kappaB activation in CLL cells

overall_design: Primary CLL cells were cultured on BAFF-expressing stroma for 18 hours. Cells were lysed. RNA was prepared using standard techniques and submitted for gene expression profiling


title: Genome-wide analysis of gene expression in pancreatic adenocarcinoma associated fibroblast cells.

status: Public on Nov 23 2016

city: Hangzhou

first: Donger

last: Zhou

address: Jiefang Road 88#

country: China

institute: Zhejiang University

summary: Analysis of cancer associated fibroblasts at gene expression level. The hypothesis tested in the present study was that tumor induced DNA methylation in cancer associated fibroblasts and thus regulated the gene expression in cancer associated fibroblasts. Results showed gene expression level in cancer associated fibroblasts changed  after coculture with pancreatic cancer cells.

overall_design: Mesenchymal stem cells and 09.05CAFs which was primary cultured fibroblasts either cultured alone or co-cultured with pancreatic tumor cells then purified by anti-FAP antibody coupled Dynabeads. Total RNA were abtained and gene expression were compared between cultured alone and cocultured.

first: Lei

last: Zheng


title: Early Developmental Perturbations in a Human Stem Cell Model of MODY5/HNF1B Pancreatic Hypoplasia


title: Unliganded estrogen receptor alpha regulates vascular cell function and gene expression

status: Public on Nov 22 2016

city: Boston

first: Gavin

middle: R.

last: Schnitzler

state: MA

address: 800 Washington St. Box 80

department: Molecular Cardiology Research Institute

institute: Tufts Medical Center

summary: Estrogen receptor alpha (ERa) has generally been thought to be transcriptionally inactive until it binds estrogen. Here we show that unliganded ERa, far from being transcriptionally inert, regulates a large number of genes both in vascular endothelial cells (ECs) and in mouse aorta. The genes regulated by unliganded ERa in the aorta (largely composed of smooth muscle cells) differ from those in ECs, and aorta- and EC-regulated promoters show enrichment in binding sites for distinct sets of transcription factors. In vitro, the presence of unliganded ERa decreases the migration and proliferation of ECs, and also increases proliferation of SMCs. Consistent with these effects on individual cells in vitro, mice lacking ERa, in the absence of estrogen, show significantly less SMC proliferation and medial thickening after carotid artery wire injury than ER intact mice. The effects of unliganded ERa on vascular gene expression, cell function in vitro and vascular injury responses in vivo are all reversed by the addition of estrogen. Taken together, these results indicate that unliganded ERa regulates vascular gene expression, vascular cell function, and vascular injury responses, and that the cardiovascular protective effects of estrogen may largely be due to the reversal of these effects of unliganded ERa. These results have important implications for the vascular health of men and post-menopausal women with vascular ERa and low circulating levels of estrogen. This study also raises the possibility that the steroid receptor family could have substantial hormone-independent functions in the vasculature and in other tissues.

overall_design: Eahy 926 stable cell lines carrying a human estrogen receptor alpha (ERa) expression vector (ERa ECs) or a control empty vector (Ctrl ECs) were treated with or without 17-b-estradiol (E2) for 16 hrs. RNA from 3 bioligical replicates per condition was harvested and used to probe Illumina bead arrays.

first: Qing

last: Lu

first: Caroline

middle: S

last: Vallaster

first: Kazutaka

last: Ueda

first: Stephanie

last: Erdkamp

first: Christine

last: Briggs

first: Lakshmanan

middle: K

last: Iyer

first: Iris

middle: Z

last: Jaffe

first: Richard

last: Karas


title: Trancriptional changes upon JMJD3 and PI3K inhibition in MCF-7 cells

first: Keng Gat

last: Lim

address: 60 Biopolis St, #02-01,

institute: Genome Institute of Singapore

summary: This study examines the effects of GSK-J4, GDC0941 and MK2206 on transcriptional changes of MCF-7 cells. The hypothesis tested was that genes that are co-downregulated by each inhibitor might be required for the induction of combination therapy-induced apoptosis. Results provided important information of the mechanisms of action of these inhibitors and revealed potential biomarkers to monitor drug response and development of drug resistance.

overall_design: MCF-7 cells were treated with 5µM GSK-J4 in combination with 1µM GDC0941 or 2µM MK2206 for 3 days. Total RNA was isolated and quantified before being amplified for microarray analysis.

first: Keng

middle: G

first: Qiang

last: Yu


title: Topoisomerase I dependent gene expression in human primary astrocytes

status: Public on Nov 19 2016

city: SYDNEY

first: Irina

last: VOINEAGU

address: High ST

institute: UNSW

summary: Gene expression measurements were carried out in human primary astrocytes treated with either 0.1% DMSO (Control) or 300nM Topotecan for 24h and 48h, to assess the effect of topoisomerase I inhibition on the transcription of long genes.

overall_design: Treatment was carried out in triplicate wells of a 6-well plate.

last: Voineagu

first: Akira

last: Gokoolparsadh


title: Gene expression data from induced Pluripotent Stem cells from Parkinson's Disease patients harbouring amplification of, or mutations in the SNCA gene, and from healthy control donors [gene expression]

first: Sally

middle: A

last: Cowley

summary:
We have generated human induced Pluripotent Stem cells (hiPSc) using Sendai virus-mediated delivery of reprogramming factors. hiPSc lines have been screened using SNP array to assess chromosomal stability (alongside the fibroblast lines from which they derived), and validation of the pluripotency of the hiPSc lines is provided by Pluritest assessment of transcriptome datasets, prior to differentiation and downstream assays.
Excess α-synuclein compromises phagocytosis in iPSC-derived macrophages. Walther Haenseler, Federico Zambon, Heyne Lee, Jane Vowles, Federica Rinaldi,   Galbha Duggal, Henry Houlden, Katrina Gwinn, Selina Wray, Kelvin C. Luk, Richard Wade-Martins,  William S. James and Sally A. Cowley

overall_design: human iPSc lines were derived from human dermal fibroblasts from 3 PD patients harbouring SNCA A53T mutations, 1 patient harbouring SNCA triplication, and 5 control donors (newly-derived lines are reported here; for control lines that have been previously described, see GSE53426, GSE64582, GSE77664, and refer to Table S1 of current manuscript). SNP and gene expression datasets were generated from patient and control lines.

first: Walther

last: Haenseler

first: Federico

last: Zambon

first: Heyne

last: Lee

first: Jane

last: Vowles

first: Federica

last: Rinaldi

first: Galbha

last: Duggal

first: Henry

last: Houlden

first: Katrina

last: Gwinn

first: Selina

last: Wray

first: Kelvi

last: Luk

last: Wade-Martins

first: William

last: James


title: Epigenetic regulation of the transcriptional program in memory and terminally differentiated CD8+ T cells [HCAFIS_07_Gene_Expression]

first: Jose

last: Lavin

overall_design: Genome-wide changes in gene expression in human CD8+ T cell subsets isolated from peripheral blood were generated by Human HT12 v4 BeadChips (Illumina Inc.)

first: Ramón

middle: M

last: Rodriguez

first: Carlos

last: Lopez Larrea

first: José

last: Luis Lavín


title: Differentially regulated genes on day 10 of pancreatic differentiation of hiPSCs

first: Adrian

last: Teo

summary: To determine the pancreatic genes which are upregulated after 10 days of pancreatic differentiation of hiPSCs

overall_design: Two undifferentiated control hiPSCs and two day10-differentiated hiPSCs were analysed via DNA microarray


title: The transcriptional signature of active tuberculosis reflects symptom status in extra-pulmonary and pulmonary tuberculosis

status: Public on Nov 04 2016

city: London

first: Krzysztof

last: Potempa

address: The Ridgeway

institute: National Institute for Medical Research (NIMR)

summary:
Background:   Mycobacterium tuberculosis infection is a leading cause of infectious death worldwide. Gene-expression microarray studies profiling the blood transcriptional response of tuberculosis (TB) patients have been undertaken in order to better understand the host immune response as well as to identify potential biomarkers of disease. To date most of these studies have focused on pulmonary TB patients with gene-expression profiles of extra-pulmonary TB patients yet to be compared to those of patients with pulmonary TB or sarcoidosis.
Methods  A novel cohort of patients with extra-pulmonary TB and sarcoidosis was recruited and the transcriptional response of these patients compared to those with pulmonary TB using a variety of transcriptomic approaches including testing a previously defined 380 gene meta-signature of active TB.
Results  The 380 meta-signature broadly differentiated active TB from healthy controls in this new dataset consisting of pulmonary and extra-pulmonary TB. The top 15 genes from this meta-signature had a lower sensitivity for differentiating extra-pulmonary TB from healthy controls as compared to pulmonary TB. We found the blood transcriptional responses in pulmonary and extra-pulmonary TB to be heterogeneous and to reflect the extent of symptoms of disease.
Conclusions  The transcriptional signature in extra-pulmonary TB demonstrated heterogeneity of gene expression reflective of symptom status, while the signature of pulmonary TB was distinct, based on a higher proportion of symptomatic individuals. These findings are of importance for the rational design and implementation of mRNA based TB diagnostics.

overall_design: Novel cohort comprising 61 healthy human controls, 47 human with EPTB, 45 human with PTB, 49 human with Sarcoid was recruited

first: Simon

last: Blankley

first: Christine

last: Graham

first: Jacob

last: Turner

first: Matthew

middle: P

last: Berry

first: Chloe

middle: I

last: Bloom

first: Zhaohui

last: Xu

first: Virginia

last: Pascual

first: Jacques

last: Banchereau

first: Damien

last: Chaussabel

first: Ronan

last: Breen

first: George

last: Santis

first: Derek

last: Blankenship

first: Marc

last: Lipman

first: Anne

last: O'Garra


title: Integrative Epigenome-Wide Analysis Shows That DNA Methylation May Mediate Genetic Risk In Inflammatory Bowel Disease [Expression profiling]

city: Edinburgh

first: Nichols

last: Ventham

address: Western General Hospital

department: CGEM

institute: Univerisity of Edinburgh

summary:
Epigenetic alterations may provide important insights into gene-environment interaction in inflammatory bowel disease (IBD). Here we observe  epigenome-wide DNA methylation differences in 240 newly-diagnosed IBD cases and 190 controls. These include 439 differentially methylated positions (DMPs) and 5 differentially methylated regions (DMRs), which we study in detail using whole genome bisulphite sequencing. We replicate the top DMP (RPS6KA2) and DMRs (VMP1, ITGB2, TXK) in an independent cohort.
Using paired genetic and epigenetic data, we delineate methylation quantitative trait loci; VMP1/microRNA-21 methylation associates with two genetic polymorphisms in linkage disequilibrium with a known IBD susceptibility variant. Separated cell data highlight the cell type of origin of epigenetic signals seen in whole blood; IBD-associated hypermethylation within the TXK gene transcription start-sitepromoter region negatively correlates with gene expression in whole blood and CD8+ T-cells, but not other cell types. Thus, site-specific DNA methylation changes in IBD are relatedrelate to underlying genotype and associate with cell-specific alteration in gene expression.

overall_design:
RNA expression profiling in globin depleted whole blood and separated cells (WB=whole blood, CD8 = CD8+ T cells, CD4=CD4+ T cells, CD14 = CD14+ monocytes, n4=naive CD4 T-cells) in inflammatory bowel disease cases and controls
Outlying samples or incorrectly labelled samples removed based on sex or cell-type mismatch (Sample 247).

first: Nicholas

first: Jack

last: Satsangi


title: ERN1 and ALPK1 inhibit differentiation of bi-potential tumor-initiating cells in human breast cancer

status: Public on Oct 27 2016

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

institute: University of Lübeck

summary: Cancers are heterogeneous by nature. While traditional oncology screens commonly use a single endpoint of cell viability, altering the phenotype of tumor-initiating cells may reveal alternative targets that regulate cellular growth by processes other than apoptosis or cell division. We evaluated the impact of knocking down expression of 420 kinases in bi-lineage triple-negative breast cancer (TNBC) cells that express characteristics of both myoepithelial and luminal cells. Knockdown of ERN1 or ALPK1 induces bi-lineage MDA-MB-468 cells to lose the myoepithelial marker keratin 5 but not the luminal markers keratin 8 and GATA3. In addition, these cells exhibit increased β-casein production. These changes are associated with decreased proliferation and clonogenicity in spheroid cultures and anchorage-independent growth assays. Confirmation of these assays was completed in vivo, where ERN1- or ALPK1-deficient TNBC cells are less tumorigenic. Finally, treatment with K252a, a kinase inhibitor active on ERN1, similarly impairs anchorage-independent growth of multiple breast cancer cell lines. This study supports the strategy to identify new molecular targets for types of cancer driven by cells that retain some capacity for normal differentiation to a non-tumorigenic phenotype. ERN1 and ALPK1 are potential targets for therapeutic development.

overall_design: AKPK1 and ERN1 gene expression was knocked down in the MDA-MB-468 breast cancer cell line in duplicate by either siRNA or shRNA  and tested in vitro for proliferation and differentiation.

first: Melanie

last: Boerries

first: Jochen

last: Maurer

first: Corinne

last: Vannier

first: Juliane

last: Strietz

first: Stella

last: Stepputtis


title: Transcriptomic, (phospho)proteomic, and metabolomic analysis of tumor-comprising cells treated by photodynamic therapy [human]

status: Public on Nov 25 2016

city: Amsterdam

first: Perry

middle: D

last: Moerland

address: Meibergdreef 9

department: Epidemiology and Data Science

country: Netherlands

institute: Amsterdam UMC

summary: Photodynamic therapy (PDT) is a tumor treatment strategy that relies on the production of reactive oxygen species (ROS) in the tumor following local illumination. Although PDT has shown promising results in the treatment of non-resectable perihilar cholangiocarcinoma, it is still employed palliatively. In this study, tumor-comprising cells (i.e., cancer cells, endothelial cells, macrophages) were treated with the photosensitizer zinc phthalocyanine that was encapsulated in cationic liposomes (ZPCLs). Post-PDT survival pathways were studied following sublethal (50% lethal concentration (LC50)) and supralethal (LC90) PDT using a multi-omics approach.     ZPCLs did not exhibit toxicity in any of the cells as assessed by toxicogenomics. Sublethal PDT induced survival signaling in perihilar cholangiocarcinoma (SK-ChA-1) cells via mainly hypoxia-inducible factor 1 (HIF-1)-, nuclear factor of kappa light polypeptide gene enhancer in B cells (NF-кB)-, activator protein 1 (AP-1)-, and heat shock factor (HSF)-mediated pathways. In contrast, supralethal PDT damage was associated with a dampened survival response. (Phospho)proteomic and metabolomic analysis showed that PDT-subjected SK-ChA-1 cells downregulated proteins associated with epidermal growth factor receptor (EGFR) signaling, particularly at LC50. PDT also affected various components of glycolysis and the tricarboxylic acid cycle as well as metabolites involved in redox signaling.  In conclusion, sublethal PDT activates multiple pathways in tumor parenchymal and non-parenchymal cells that, in tumor cells, transcriptionally regulate cell survival, proliferation, energy metabolism, detoxification, inflammation/angiogenesis, and metastasis. Accordingly, sublethally afflicted tumor cells are a major therapeutic culprit. Our multi-omics analysis unveiled multiple druggable targets for pharmacological intervention.

overall_design: Common cell types that comprise a tumor environment were analyzed by whole genome expression analysis following photodynamic therapy (PDT). The cells that were employed are human umbilical vein endothelial cells (HUVECs) as a model for tumor endothelium; human biliary adenocarcinoma (SK-ChA-1) cells as model for PDT-recalcitrant perihilar cholangiocarcinomas; and EGFR-overexpressing human epidermoid carcinoma (A431) cells. Cells were incubated with buffer (control group) or received a sublethal (vehicle group, 50% lethal concentration (LC50) group) or superlethal concentration (LC90 group) of zinc phthalocyanine (ZnPC)-encapsulating cationic liposomes (ZPCLs). After 60 minutes, cells were either maintained in the dark (control group, vehicle (dark toxicity (DT)) group) or were treated with 500-mW laser light (LC50 and LC90 groups) using a cumulative light dose of 15 J/cm2 (n = 3 per group). Ninety minutes after photodynamic therapy, total cellular RNA was isolated and gene expression levels were analyzed by using the Illumina HumanHT-12 v4 platform. The data was analyzed in the context of survival signalling and comparisons were made with the control group.

first: Ruud

last: Weijer

first: Michal

last: Heger


title: EphA3 as a Target for Antibody Immunotherapy in Acute Lymphoblastic Leukemia

city: Herston

first: Fares

last: Al-Ejeh

state: QLD

address: 300 Herston Road

department: Cancer

institute: QIMR Berghofer

summary: The human EphA3 gene was discovered in a pre-B acute lymphoblastic leukemia (pre-B-ALL) using the EphA3-specific monoclonal antibody (mAb), IIIA4, which binds and activates both human and mouse EphA3. We use two models of human pre-B-ALL to examine EphA3 function, demonstrating effects on pre-B-cell receptor signaling. In therapeutic targeting studies, we demonstrated antitumor effects of the IIIA4 mAb in EphA3-expressing leukemic xenografts and no antitumor effect in the xenografts with no EphA3 expression providing evidence that EphA3 is a functional therapeutic target in pre-B-ALL. Here we show that the therapeutic effect of the anti-EphA3 antibody was greatly enhanced by adding an α-particle-emitting 213Bismuth payload.

overall_design: We analysed the gene expression profiles of Reh cells (duplicate), LK63 cells (duplicate) and LK63 cells with stable knockdown of EphA3 (duplicate) using the Illumina HumanHT-12 V4.0 expression beadchip.

first: Sara

last: Charmsaz

first: Andrew

last: Boyd


title: Epipolymorphisms associated with the clinical outcome of autoimmune arthritis affect CD4+ T cell activation pathways (expression)

status: Public on Oct 28 2016

city: Los Angeles

first: Maura

last: Rossetti

address: 1000 Veteran Avenue

institute: UCLA

summary: Multifactorial diseases, including autoimmune juvenile idiopathic arthritis (JIA), result from a complex interplay between genetics and environment. Epigenetic mechanisms are believed to integrate such gene-environment interactions, fine-tuning gene expression and possibly contributing to immune system dysregulation. Although anti-TNF therapy has strongly increased JIA remission rates, it is not curative and up to 80% of patients flare upon treatment withdrawal. Thus, a crucial unmet medical and scientific need is to understand the immunological mechanisms associated with remission or flare to inform clinical decisions. Here, we explored the CD4+ T cell DNA methylome of 68 poly-articular and extended oligo-articular JIA patients, before and after anti-TNF therapy withdrawal, to identify features associated with maintenance of inactive disease (ID). Individual CpG sites were clustered in coherent modules without a priori knowledge of their function through network analysis. The methylation level of several CpG modules, specifically those enriched in CpG sites belonging to genes that mediate T cell activation, uniquely correlated with clinical activity. Differences in DNA methylation were already detectable at the time of therapy discontinuation, suggesting epigenetic predisposition. RNA profiling also detected differences in T cell activation markers, including HLA-DR, but, overall, its sensitivity was lower than epigenetic profiling. Changes to the T cell activation signature at the protein level were detectable by flow cytometry, confirming the biological relevance of the observed alterations in methylation. Our work proposes, for the first time, epigenetic discrimination between clinical activity states, and reveals T cell-related biological functions tied to, and possibly predicting and/or causing, clinical outcome.

overall_design: We measured gene expression (single replicates) in 125 CD4+ T cell samples form 68 randomly selected patients recruited in the trial “Determining Predictors of Safe Discontinuation of Anti-TNF Treatment in JIA” (ID: NCT00792233). At baseline (T0), patients were in clinical remission on medication, i.e., they maintained ID, for at least 6 months under treatment (anti-TNF). Therapy was withdrawn for eight months, after which (Tend) patients were stratified by clinical activity in patients maintaining ID or not (NO ID). Flares were tested at the time of flare (Tend), and therapy was then reintroduced.

first: Roberto

last: Spreafico

first: John

middle: W

last: Whitaker

first: Wei

last: Wang

first: Daniel

middle: J

last: Lovell

first: Salvatore

last: Albani


title: The role of unliganded thyroid hormone receptors (TRs) in human adipose derived stem cells (hADSC)

status: Public on Oct 26 2016

city: Houston

first: Paul

last: Webb

address: 6670 Bertner Ave

department: Genomic Medicine

institute: Houston Methodist Research Institute

summary:
Analysis of change in transcriptosome after TRα or TRβ knockdown in hADSC.
Analysis of effects of siRNA transfection (siCtrl, siTRα, siTRβ or siETV5) in hADSC at gene expression level.The hypothesis tested in the present study was that unliganded TRα and TRβ have distinctive roles in these cells.

overall_design: Total RNA was obtained from hADSC, transfected with siCtrl,  siTRα, siTRβ or ETV5. siTRα, siTRβ or siETV5 samples were compared to  siCtrl samples.

first: Aleksandra

last: Cvoro


title: The gene expression profiles of P4N treated THP-1 cells

status: Public on Nov 09 2016

city: Hsinchu City

first: Yu-Ling

last: Lin

address: Po-Ai street

department: Department of Biological Science and Technology

institute: National Chiao Tung University

summary: Analysis of P4N treated THP-1 cells at gene expression level. The hypothesis in the present study was that low dose P4N influence the activation of monocyte. Results provide important information of the response of monocyte activation, such as cytokine genes and growth factors genes.

overall_design: Total RNA isolated  from THP-1 cells treated w/o P4N for 12h.

first: Kuang-Wen

last: Liao

first: Ru-Chih

middle: C

last: Huang


title: Genomic profiling of patient-derived xenografts identify high level “passenger” gene aberrations associated with better prognosis in non-small cell lung cancer

city: Toronto

first: Ming

last: Tsao

address: 610 University Avenue

department: Ontario Cancer Institute

institute: University of Toronto

summary: Patient-derived tumor xenografts (PDXs) increasingly are being used as preclinical models to study human cancers and to evaluate novel therapeutics, as they reflect clinical cancers more closely than established tumor cell lines. With >100 PDXs established from resected non-small cell lung carcinomas (NSCLC), we reported previously that xenograftability correlates significantly with poorer patient prognosis. In this study, genomic, transcriptomic, and proteomic profiling of 36 PDXs showed greater similarity in somatic alterations between PDX and primary tumors than with cell lines, using publicly available data on the latter. A higher number of somatic alterations among 865 frequently altered genes in the PDX tumors was associated with better overall patient survival (HR=0.15, p=0.00015) compared to patients with corresponding PDXs characterized by a lower number of alterations; this was validated with the TCGA lung cancer patient dataset (HR=0.28, p=0.000022). These passenger-like alterations, identified in PDXs, link cell-cell signaling and adhesion to patient prognosis.

overall_design: Total RNAs from xenograftswere amplified by DASL kit and hybridized to Illumina HT12v4 chip

first: Ming-Sound

first: Chang-Qi

last: Zhu


title: Early whole blood transcriptional signatures are associated with severity of lung inflammation in cynomolgus macaques with Mycobacterium tuberculosis infection

city: Dallas

first: Jason

last: Skinner

state: TX

address: 3434 Live Oak

institute: Baylor Institute for Immunology Research

summary: This longitudinal dataset was generated to assess changes in whole blood gene expression following low dose Mycobacterium tuberculosis infection of Cynomolgus macaques.  In addition to changes in mRNA transcript abundance, changes in circulating immune cell populations were also assessed using both complete blood counts (CBC) and using flow cytometry.  Disease severity was determined using both clinical diagnosis (active vs. latent)  and 18F-flurodeoxyglucose (FDG avidity) by 6 months post-infection. The greatest change in transcriptional activity occurred 20-56 days after infection, when the maximum activity of immune related transcripts was observed.  After stratifying macaques based on clinical diagnosis, those macaques with active disease exhibited a similar signature to that observed in humans with active TB.  However, only modest transcriptional differences between active TB and latently infected macaques were observed. As an alternative stratification approach, the severity of lung inflammation measured by lung FDG avidity was used to separate macaques into high and low FDG groups.  Blood transcript activity was highly correlated with lung inflammation at early time points post-infection. The differential expression signatures between animals stratified with high and low lung FDG were stronger than those observed with groups defined by clinical outcome.. Furthermore, gene level analysis of of pre-infection signatures suggest that interferon and inflammation signatures may distinguish eventual clinical outcomes and lung FDG avidity prior infection.  In conclusion, this study demonstrates that  transcriptional changes in the macaque model recapitulate those observed in human Mtb infection while providing additional insight into the early and pre-infection events associated with disease severity and outcome.

overall_design: In total, the responses of 38 Cynomolgus macaques to low dose Mtb infection (Erdman ~25CFU) were assessed in this study.  Blood draws for the assessment of gene expression and cellular composition were assessed at two time points prior to infection (Pre1 and Pre2) and at days: 3,7,10,20,30,42,56,90,120,150,180 post-infection. Binary clinical diagnosis (active v. latent) and lung inflamation (FDG avidity) were both used used to stratify the severity of infection outcome.  Those samples that were taken at the time of clinical diagnosis along with the pre-infection control are denoted by Yes in the SynchroSet column.

first: Hannah

last: Gideon

first: Nicole

last: Baldwin

first: JoAnne

middle: L

last: Flynn

first: Philana


title: S100A6 Regulates Endothelial Cell Cycle Progression by Attenuating Antiproliferative Signal Transducers and Activators of Transcription 1 Signaling

first: Hauke

last: Busch

summary:
S100A6, a member of the S100 protein family, has been described as relevant for cell cycle entry and progression in endothelial cells. The molecular mechanism conferring S100A6's proliferative actions, however, remained elusive. Originating from the clinically relevant observation of enhanced S100A6 protein expression in proliferating endothelial cells in remodeling coronary and carotid arteries, our study unveiled S100A6 as a suppressor of antiproliferative signal transducers and activators of transcription 1 signaling. Discovery of the molecular liaison was enabled by combining gene expression time series analysis with bioinformatic pathway modeling in S100A6-silenced human endothelial cells stimulated with vascular endothelial growth factor A. This unbiased approach led to successful identification and experimental validation of interferon-inducible transmembrane protein 1 and protein inhibitors of activated signal transducers and activators of transcription as key components of the link between S100A6 and signal transducers and activators of transcription 1.
Given the important role of coordinated endothelial cell cycle activity for integrity and reconstitution of the inner lining of arterial blood vessels in health and disease, signal transducers and activators of transcription 1 suppression by S100A6 may represent a promising therapeutic target to facilitate reendothelialization in damaged vessels.

overall_design: To eludicate the transcriptome response of endothelial cells to S100A6 under VEGFA stimulation, RNA was isolated from S100A6 siRNA silenced and normal control Human Umbilical Vein Endothelial Cells (HUVEC) in a timecourse at 0h, 1h, 2h, 4h, 6h, 8h, 12h, 18h, 24h for S100A6 knockdown and at  0h, 1h, 4h, 8h, 12h, 24h for siRNA control using a scrambled vector.

first: Melanie

last: Boerries

first: Caroline

last: Lerchenmüller

first: Patrick

last: Most


title: Transcriptome profiles of primary human hepatocytes treated with HBV preS1 peptide with or without bile acids

status: Public on Oct 25 2016

first: Yujin

last: Hoshida

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

summary: Chronic hepatitis B, C and D virus (HBV, HCV, HDV) infections are leading causes of liver disease and cancer worldwide. Although these viruses differ markedly in their life cycle and genomic organization, they exclusively infect hepatocytes. Recently, the sodium taurocholate cotransporting polypeptide (NTCP) was identified as the first functional receptor for HBV and HDV. Here, we report that NTCP also facilitates HCV entry into human hepatocytes, by augmenting the bile acids-mediated repression of IFN-stimulated genes (ISGs), including IFITM2 and IFITM3, to increase the susceptibility of cells to HCV entry. Furthermore, an HBV-derived preS1 peptide, known to bind NTCP and to inhibit bile acids uptake and HBV infection, inhibits HCV entry by enhancing the expression of ISGs. Our study highlights NTCP as a novel player linking bile acids metabolism to the interferon response in hepatocytes and establishes a role for NTCP in the entry process of multiple hepatotropic viruses, via distinct mechanisms. Collectively, these findings enhance our understanding of hepatitis virus-host interactions and suggest NTCP as an attractive antiviral target for HBV/HCV co-infection.

overall_design: Transcriptome profiling by DNA microarray of primary human hepatocytes.

first: Eloi

middle: R

last: Verrier

first: Mirjam

middle: B

last: Zeisel

first: Thomas

middle: F

last: Baumert


title: Helper T cell response to low amino acid environments

status: Public on Nov 02 2016

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

summary: Recent observations about how cells sense amino acids have argued for preeminent roles of mTOR and the stress kinase GCN2 in allowing cells to estimate their amino acid needs. Here we used models of programmed immune microenvironments where helper T cells have to sense how much amino acids are available to engage in antigen-fueled proliferation. Contrary to current models, T cells activate mTOR in the competency phase of the cell cycle regardless of amino acid amounts, GCN2 or surface TCR. Instead, we found T cells use an amino acid sensing system to target IL-2-induced STAT5 phosphorylation at the restriction point of cell cycle commitment. mTOR activity is subsequently reduced and specifically connected to SREBP activation. T cells can be pushed into cycle by increasing IL-2 even when no amino acids are available. Collectively, our studies reveal helper T cells use sequential and distinct pathways to measure local amino acid concentrations.

overall_design: We used microarrays to measure the T cell transcriptional response to low leucine, arginine or lysine environments (with macrophages present, with or without cognate antigen stimulation).

first: Lee

last: Van de Velde

first: Amber

last: Smith

first: Jessica

last: Haverkamp

first: Peter

last: Murray


title: Overcoming acquired resistance to BIBW2992 in HCC827, a non-small cell lung cancer cell line by dasatinib

status: Public on Oct 22 2016

city: Miaoli County

first: Shih Sheng

last: Jiang

address: No. 35 Keyan Road, Zhunan County

department: National Institute of Cancer Research

institute: National Health Research Institutes

summary: EGFR tyrosine kinase inhibitors (TKIs) have demonstrated tremendous clinical benefits in non-small cell lung cancer (NSCLC) patients. However, resistance emerges rapidly due to a variety of mechanisms including a secondary mutation of T790M in EGFR that abrogates the binding of the drugs. It has been postulated that EGFR TKIs, such as afatinib (BIBW2992), with activity against the T790M mutant EGFR kinase might overcome the drug resistance problem or, when used as the first-line treatment, delay or suppress the emergence of resistance in EGFR. In this study, we generated BIBW2992-resistant cells, HCC827-BR1 and HCC827-BR2, from the parental HCC827 cells. In HCC827-BR cells, EGFR, MET, and Erb2 were down-regulated and no secondary mutation was found to be present in the coding region of EGFR. Gene set enrichment analysis (GSEA) revealed an obvious signature of epithelial to mesenchymal transition (EMT) in the drug resistant cells. Subsequently, the HCC827-BR cells were shown to be more invasive. Most importantly, we strived to seek if alternative medicine might be applied alone or in combination to treat the BIBW2992-resistant cells or to, under BIBW2992 treatment, diminish the emergence of resistant cells. Compared to the parental cells, the HCC827-BR cells were more sensitive to dasatinib, an FDA-approved kinase inhibitor. Furthermore, as revealed in the clonogenicity assay, the reduction of tumor-colony-forming cells after exposure to BIBW2992 was substantially potentiated by low concentration of dasatinib. Thus, prospective clinical investigations may be needed to evaluate if dasatinib can be beneficial to patients receiving second-generation EGFR TKIs for the treatment of NSCLC.

overall_design: Over a period of 3-4 months, BIBW2992-resistant cells were isolated in cell culture by maintenance of HCC827 cells in the presence of escalating concentrations of BIBW2992 up to 2 μM. Two cell lines, HCC827-BR1 and HCC827-BR2, were established based on individual clones. Total RNA of these HCC827, HCC827-BR1 and HCC827-BR2, were extracted for gene expression microarray analysis using Illumina HumanHT12 v3 BeadChip.

first: W

last: Lin

first: J-T

last: Hsu

first: S