title: Blood transcription profiling of infections of humans with Leishmania infantum.

city: Ribeirao Preto

first: Luiz Gustavo

middle: Araujo

last: Gardinassi

state: Sao Paulo

address: Av. dos Bandeirantes, 3900

country: Brazil

institute: Ribeirao Preto Nursing School/ University of São Paulo

summary: Gene expression profiling to address the effects of infection with Leishmania infantum during distinct clinical outcomes as active visceral leishmaniasis (VL), remission of disease and asymptomatic infection.

overall_design: Total RNA was extracted from whole-blood lysates obtained from VL patients, treated VL patients, asymptomatic individuals and uninfected controls. The aim was to evaluate  gene expression signatures associated with protective and pathological responses.

first: L

first: I

last: de Miranda Santos


title: Transcriptome profiles of Huh7.5.1-NTCP cells treated with HBV preS1 peptide

status: Public on Oct 25 2016

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

country: USA

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 acid-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 acid uptake and HBV infection, inhibits HCV entry by enhancing the expression of ISGs. Our study highlights NTCP as a novel player linking bile acid 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 Huh7.5.1 cells transduced to express NTCP.

first: Eloi

middle: R

last: Verrier

first: Mirjam

middle: B

last: Zeisel

first: Thomas

middle: F

last: Baumert


title: Expression data from human placental derived mesenchymal stem cells (PDMSCs).

status: Public on Oct 19 2016

city: Hangzhou

first: Chenxia

last: Hu

state: Zhejiang

address: School of Medicine; First Affiliated Hospital; Zhejiang University

country: China

institute: Zhejiang University

summary:
Inductive environments and extracelluar mediums will leads to the alteration of gene expression pattern.
We used microarrays to detail the global programme of gene expression underlying adipogenic differentition, immediately osteogenic differentiation and deletion of stimulations for 21 days, we intend to identify distinct classes of differentiated genes during these processes.

overall_design: Human PDMSCs were incubated in adipogenic medium for 14 days, then the inductive medium was replaced by osteogenic medium for 7 days, finally the medium was removed and the manipulated cells were cultured in general medium for 21 days. These adherent cells were selected for RNA extraction and hybridization on Affymetrix microarrays. To that end, we hand-selected cells at four time-points: before  induction (P), adipogenic PDMSCs at 14 days (A), osteogenic adipocyte like cells for 7 days (AO) and MSC-like cells in general medium for 21 days(TAO).

first: Yuchao

last: Yu


title: Promiscuous targeting of bromodomains by Bromosporine identifies BET proteins as master regulators of primary transcription response in leukemia [set2]

city: Oxford

first: Panagis

last: Filippakopoulos

state: Oxfordshire

address: ORCRB - Roosevelt Drive

department: Nuffield Department of Medicine

country: United Kingdom

institute: Oxford University

summary: Bromodomains (BRDs) have emerged as compelling targets for cancer therapy. The development of selective and potent BET inhibitors and their significant activity in diverse tumor models has rapidly translated into clinical studies and has motivated drug development efforts targeting non-BET BRDs. However, the complex multidomain/subunit architecture of bromodomain protein complexes complicates predictions of consequences of their pharmacological targeting. To address this issue we developed a promiscuous bromodomain inhibitor (bromosporine, BSP) that broadly targets BRDs (including BETs) with nanomolar affinity, creating a tool for the identification of cellular processes and diseases where BRDs have a regulatory function. As a proof of principle we studied the effect of BSP in leukemic cell-lines known to be sensitive to BET inhibition and found as expected strong anti-proliferative activity. Comparison of the modulation of transcriptional profiles by BSP at short inhibitor exposure resulted in a BET inhibitor signature but no significant additional changes in transcription that could account for inhibition of other BRDs.  Thus, non-selective targeting of BRDs identified BETs, but not other BRDs, as master regulators of a context dependent primary transcription response.

overall_design: Cells were seeded the day prior to treatment at 2x10^5 per ml. Treatments were performed so that a final concentration of 0.1 % DMSO (Cat.#D1435; Sigma) was achieved and cells were incubated with DMSO or 500 nM test compound (BSP, JQ1, LP99, GSK2801, iCBP112 or OF1) for 6 h prior to isolation of RNA. Total RNA was isolated using a standard TRIzol (Invitrogen) protocol and prepared using RNeasy columns (Cat.#74106 plus; Qiagen). RNA was quantified using a Nanodrop spectrophotometer (model ND1000; Thermo Fisher) and integrity assessed on a BioAnalyzer (2100; Agilent Laboratories, USA). All samples had a RNA Integrity Number (RIN) ≥ 9. Biological triplicates were performed for each condition tested.

first: Christine

last: Blancher


title: The role of thyroid hormone receptors (TRs) in human adipose derived stem cells (hADSC), isolated from human adipose tissue collected during liposuction procedures

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 transcriptional networking and disection of the  TRalpha and TRbeta roles in hADSC, and during differentiation of hADSC towadrd different lineages.

overall_design: Total RNA was obtained from hADSC, and adipocytes, chondrocytes and osteoblasts differentiated from hADSC treated with triiodothytonine (T3)  for 0 and 18 h. T3 response in each cell line was analyzed.

first: Doug

last: Sieglaff

first: Aleksandra

last: Cvoro


title: The transcriptional profile of human CD8+ lung resident memory T-cells

status: Public on Oct 23 2016

city: Amsterdam

first: Perry

middle: D

last: Moerland

address: Meibergdreef 9

department: Epidemiology and Data Science

country: Netherlands

institute: Amsterdam UMC

summary: A specialized population of memory CD8+ T-cells resides in the epithelium of the respiratory tract to maintain protection against recurring infections. These cells express CD69 and the integrin αβ7 (CD103) and correspond to tissue resident memory T-cells (TRM) also described in intestine, liver and brain. A less well characterized population of CD103- CD8+ T-cells also resides in lungs and expresses markers characteristic of effector memory T-cells (TEM). We determined the transcriptional profiles of these memory CD8+ T-cell subsets retrieved from human lung resection samples and compared these with corresponding T-cell populations from peripheral blood of the same individuals. Our results demonstrate that each of the populations exhibits a distinct transcriptional identity. We found that the lung environment has a major impact on gene expression profiles. Thus, transcriptomes from CD103+ and CD103- subsets from lungs are much more resemblant to one another than to those from CD103+ or CD103- memory CD8+ T-cells from blood. TRM express specific sets of chemokine receptors, in accordance with their unique migratory properties. Furthermore, these cells constitutively express cytokine and cytotoxic genes for immediate effector function and chemokines to attract auxiliary immune cells. At the same time, multiple genes encoding inhibitory regulators are also expressed. This suggests that rapid ability to unleash effector functions is counterbalanced by programmed restraint, a combination that may be critical in the exposed but delicate tissue of the lung. Comprehensive sets of transcription factors were identified that characterize the memory CD8+ populations in the lungs. Prominent among these were components of the Notch pathway. Using mice genetically lacking expression of the NOTCH1 and NOTCH2 receptors in T-cells, we demonstrated that Notch controls both the number of lung TRM as well as the function of lung TEM. Our data illustrate the adaptation of lung resident T-cells to the requirements of the respiratory epithelial environment. Defining the molecular imprinting of these cells is important for rational vaccine design and may help to improve the properties of T-cells for adoptive cellular therapy.

overall_design: Material was collected from a total of 6 subjects. Three patients underwent a lobectomy for a peripheral primary lung tumor and three received lung transplantation because of end-stage pulmonary disease (COPD). Lung mononuclear cells where isolated after digestion of the partial or complete human lung resection material. Paired peripheral blood mononuclear cells were also isolated. CD8+CD16-CD56- T-cells were sorted for expression of CD103 (ITGAE). Lung and blood derived CD103+ and CD103- T-cell fractions were directly lysed after FACS sorting or stimulated overnight with antiCD3/28 beads. Due to the low frequency of resting (non-stimulated) CD103+ T-cells in peripheral blood this subset was obtained from five non-related buffy coat donors. RNA was isolated from 36 sorted cell samples and hybridized on Illumina HumanHT-12 V4.0 microarrays. Eight microarray samples (including two samples from the buffy coat donors) were excluded after hybridization since their average signal was too low.

first: Pleun

last: Hombrink

first: Aldo

last: Jongejan

first: René

middle: A

last: van Lier


title: Gene expression profiles of OSCC cells and the metastatic sublines

status: Public on Oct 13 2016

city: Miaoli County

first: Ya-Wen

last: Chen

address: 35, Keyan Rd, Zhunan Town

department: National Institute of Cancer Research

country: Taiwan

institute: National Health Research Institutes

summary:
The orthotopic transplantation of human OEC-M1 cells in immune-compromised mice was established to feasibly study tumorigenesis and lymph node metastasis of OSCC.
Through in vivo selection, two sublines, designated as LN1-1 and LN1-2 were successfully isolated from cervical lymph nodes and identified to originate from OEC-M1 cells.

overall_design: Two sublines, LN1-1 and LN1-2 were established from lymph nodes of orthotopic transplantation of human OEC-M1 cells in immune-compromised mice.

first: Y

middle: C

last: Yen

middle: W


title: Transcriptome profiles of liver cells treated with HBV preS1 peptide

first: Yujin

last: Hoshida

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

overall_design: Refer to individual Series


title: Spatial transcriptome analysis reveals Notch pathway-associated prognostic markers in IDH1 wild-type glioblastoma involving the subventricular zone

city: Heidelberg

first: Christel

last: Herold-Mende

address: Im Neuenheimer Feld 400

department: Department of Neurosurgery

country: Germany

institute: Heidelberg University Hospital

summary:
Background: The spatial relationship of glioblastoma (GBM) to the subventricular zone (SVZ) is associated with inferior patient survival. However, the underlying molecular phenotype is largely unknown. We interrogated an SVZ-dependent transcriptome and potential location-specific prognostic markers.

Methods: mRNA microarray data of a discovery set (n = 36 GBMs) were analyzed for SVZ-dependent gene expression and process networks using the MetaCoreTM workflow. Differential gene expression was confirmed by qPCR in a validation set of 142 IDH1 wild-type GBMs that was also used for survival analysis.

Results: Microarray analysis revealed a transcriptome distinctive of SVZ+ GBM that was enriched for genes associated with Notch signaling. No overlap was found to The Cancer Genome Atlas’s molecular subtypes. Independent validation of SVZ-dependent expression confirmed four genes with simultaneous prognostic impact: overexpression of HES4
(p = 0.034; HR 1.55) and DLL3 (p = 0.017; HR 1.61) predicted inferior, and overexpression of NTRK2 (p = 0.049; HR 0.66) and PIR (p = 0.025; HR 0.62) superior overall survival (OS). Additionally, overexpression of DLL3 was predictive of shorter progression-free survival (PFS) (p = 0.043; HR 1.64). Multivariate analysis revealed overexpression of HES4 to be independently associated with inferior OS (p = 0.033; HR 2.03), and overexpression of DLL3 with inferior PFS (p = 0.046; HR 1.65).

Conclusions: We identified four genes with SVZ-dependent expression and prognostic significance, among those HES4 and DLL3 as part of Notch signaling, suggesting further evaluation of location-tailored targeted therapies.

overall_design: Comparative transcriptomic analysis of 36 glioblastomas in different locations of the brain.

first: Andreas

last: Mock

last: Jungk


title: TRANSCRIPTIONAL PROFILING OF EGG ALLERGY AND RELATIONSHIP TO DISEASE PHENOTYPE

status: Public on Oct 18 2016

city: New York

first: Roman

last: Kosoy

state: New York

address: 1468 Madison Avenue, 18-88

department: Genetics and Genomic Sciences

institute: Mount Sinai School of Medicine

summary: The transcriptional response to egg differed between PBMCs from egg allergic and clinically tolerant subjects. Differentially expressed genes included IL-9 and TNFg. Enrichment analysis of differentially expressed gene signatures and associated co-expressed gene modules revealed an association of egg allergy with unique immune pathways. In addition to showing a positive association of egg-induced gene transcription in allergic individuals with Th2 CD4+ T cells and a novel negative association with induced Tregs, this approach identified a highly significant overlap with genes induced by TLR4 stimulation of myeloid cells.

overall_design: PBMCs were obtained from egg allergic children, some of whom are baked egg responsive (BER) and some are baked egg tolerant (BET), as well as food allergic controls (AC) who were clinically tolerant to egg. PBMCs were stimulated with egg antigen, gene transcription measured by microarray after 24 hours, and cytokine secretion by multiplex assay after 5 day incubation.

first: Cecilia

last: Berin


title: Expression array of early postnatal Mt1-mmp-targeted mammary glands

status: Public on Oct 05 2016

city: Ann Arbor

first: Stephen

middle: J.

last: Weiss

state: MI

address: 210 Washtenaw Avenue

department: Life Sciences Institute

institute: University of Michigan

summary:
Mammary gland branching morphogenesis is thought to depend on the mobilization of the membrane-anchored matrix metalloproteinases, MT1-MMP and MT2-MMP, that drive epithelial cell invasion by remodeling the extracellular matrix and triggering associated signaling cascades. However, the roles that these proteinases play during mammary gland development in vivo remains undefined.  A mammary gland branching program that occurs during the first 10 days of early postnatal development was used to characterize the impact of global Mt1-mmp or Mt2-mmp targeting on mammary gland morphogenesis.
Transcriptome profiling of ductal networks and associated stroma was used to investigate the functional roles of MT1-MMP in the early postnatal mammary gland in an unbiased fashion.

overall_design: Intact mammary gland tissue was harvested from global knockout [Mt1-mmp(-/-)] mice and wild-type [Mt1-mmp(+/+)] littermates on an outbred Swiss Black background at postnatal day 10 for RNA extraction and hybridization on Affymetrix microarrays.

first: Tamar

middle: Y

last: Feinberg

middle: J


title: MBNL1-dependent modulation of transcript stability

status: Public on Oct 14 2016

city: San Francisco

first: Hani

last: Goodarzi

state: CA

department: Biochemistry and Biophysics

institute: UCSF

summary:
In order to identify MBNL1-dependent changes in MBNL1 target transcript stability, MBNL1 levels in MDA-MB-231 breast cancer cells were stably knocked-down using short-hairpin RNAs.
The cells were then treated with alpha-amanitin to inhibit transcription, RNA was isolated at 0 and 9 hours post-alpha-amanitin treatment, and the samples were transcriptomically profiled.

overall_design: shRNAs targeting either MBNL1 or a control shRNA were stably expressed in MDA-MB-231 breast cancer cells. These cells were treated with 10ug/mL alpha-amanitin to inhibit transcription, and total RNA was isolated at 0 and 9 hours post-alpha-amanitin treatment.

first: Lisa

last: Fish

first: Nora

last: Pencheva

first: Hien

last: Tran

first: Mitsukuni

last: Yoshida

first: Sohail

last: Tavazoie


title: Affymetrix microarrays of early postnatal Mt1-mmp-targeted and Mt2-mmp-targeted mammary glands


title: Transcriptomic profiling of miR10a inhibitor transfection for 24 hours in primary human mesangial cells

status: Public on Oct 31 2016

city: Bangkok

first: Pattarin

last: TANGTANATAKUL

state: กรุงเทพมหานคร

address: Thoethai Road

country: Thailand

institute: Chulalongkorn University

summary: Analysis genes which are elevated after miR10a inhibitor transfection for 24 hours with transfection efficiency more than 95 %inhibition in mesangial cells.  The hypothesis is genes which up-regulated significantly can be potential targets for miR-10a in primary human mesangial cells.

overall_design: Total RNA were obtained from human mesangial cells (1x106 cells) transcient transfected with miR-10a inhibitor (assay ID MH10787) for 24 hours.  Transfection efficiency were determined by stem-loop RT PCR and Real-Time PCR against miR-10a.  The result showed more than 95% inhibition.

last: Tangtanatakul


title: Effect of dopamine covered iron oxide core - titanium dioxide shell nanoparticles on HeLa cells

status: Public on Oct 15 2016

city: Chicago

first: Gayle

middle: E

last: Woloschak

state: IL

address: 300 E Superior St, Tarry 4-713

department: Radiation Oncology

institute: Northwestern University

summary:
Gene expression analysis of HeLa cell samples treated with nanoparticles for 2 or 4 hours, with matching non-treated samples as controls - exact cell culture growing conditions were replicated, same cell numbers plated in matching pairs of flasks
Dopamine covered Fe3O4@TiO2 nanoparticles were added to cells grown for 16h and incubated fror 2 or 4 hours

overall_design: Total RNA was isolated from cells after different treatments; four independent experiments were done (labeled as A,B,C and D), three sample sets were run on one array once, one sample was run once each on two arrays

first: Ruben

middle: O

last: Lastra


title: Transcriptomic profiling of purified polyclonal anti-dsDNA antibodies stimulated human mesangial cells

status: Public on Oct 01 2016

state: กรุงเทพมหานคร

summary: Analysis genes which alter after anti-dsDNA antibodies stimulation in human mesangial cells.  The hypothesis is anti-dsDNA antibodies might affected a pro-inflammatory cytokine gene or genes in cell proliferation and apoptosis pathways

overall_design: Total RNA were obtained from human mesangial cells (1x10^6 cells) stimulated with anti-dsDNA antibodies (100 µg/mL) and normal serum 1:100 for 3 hours compared to non specific polyclonal IgG stimulation as control.


title: Gene expression profile for BL2 and BL2 AID-/- cell lines

city: New Haven

first: Yang

last: Xi

address: 300 George St

department: Cancer Center

institute: Yale University

summary: AID (activation-induced cytidine deaminase) is expressed at low levels in many tissue types but is most highly expressed in germinal center B cells where it deaminates cytidine to uracil during somatic hypermutation and class switch recombination of the immunoglobulin genes. In addition to this critical role in immune diversification, aberrant targeting of AID contributes to oncogenic point mutations and chromosome translocations associated with B cell malignancies. Thus, to explore a role for AID in DNA demethylation in B cell lymphoma, we performed genome-wide gene expression profiling in BL2 and AID-deficient (AID-/-) BL2 cell lines (Burkitt lymphoma that can be induced to express high levels of AID).

overall_design: The Human4$4 targets more than 47,000 probes derived from the National Center for Biotechnology Information Reference Sequence (NCBI) RefSeq Release 38 (November 7, 2009) and other sources. We did it in two samples BL2 and BL2 AID-/- cell lines.

first: Velizar

last: Shivarov

first: Matthew

last: Strout


title: Expression array of early postnatal Mt2-mmp-targeted mammary glands

summary:
Mammary gland branching morphogenesis is thought to depend on the mobilization of the membrane-anchored matrix metalloproteinases, MT1-MMP and MT2-MMP, that drive epithelial cell invasion by remodeling the extracellular matrix and triggering associated signaling cascades. However, the roles that these proteinases play during mammary gland development in vivo remains undefined.  A mammary gland branching program that occurs during the first 10 days of early postnatal development was used to characterize the impact of global Mt1-mmp or Mt2-mmp targeting on mammary gland morphogenesis.
Transcriptome profiling of ductal networks and associated stroma was used to investigate the functional roles of MT2-MMP in the early postnatal mammary gland in an unbiased fashion.

overall_design: Intact mammary gland tissue was harvested from global knockout [Mt2-mmp(-/-)] mice and wild-type [Mt2-mmp(+/+)] littermates on a congenic C57Bl/6J background at postnatal day 10 for RNA extraction and hybridization on Affymetrix microarrays.


title: Expression data from human nucleus accumbens in heroin users and controls

status: Public on Oct 12 2016

first: Yasmin

last: Hurd

state: NY

address: 1470 Madison Avenue

institute: Icahn School of Medicine at Mount Sinai

summary:
The nucleus accumbens plays a central role in ther regulation of reward, emotion, motivation and goal-directed behavior. Gene expression impairments in this brain region are of crucial interest to understand the neurobiological underpinnings of heroin use disorder.
We used the Affymetrix HG-U133A microarray to assess gene expression in the post-mortem nucleus accumbens of human heroin users and control subjects and identified differentially expressed genes.

overall_design: Human brains from apparent heroin overdose and normal control Caucasian subjects without head trauma were collected at autopsy with 24 hours of death. Cause of death was determined by forensic pathologist

middle: L


title: The TNF family member TL1A induces IL-22 secretion in committed human TH17 cells via IL-9 induction

city: Los Angeles

first: Kathrin

last: Michelsen

address: 110 George Burns Rd

department: Medicine/GI

institute: Cedars-Sinai Medical Center

summary: TL1A contributes to the pathogenesis of several chronic inflammatory diseases, including Inflammatory Bowel Diseases by enhancing TH1, TH17, and TH2 responses.  TL1A mediates a strong co-stimulation of these TH subsets particularly of mucosal CCR9+ T cells. However, the signaling pathways that TL1A induces in different TH subsets are incompletely understood. Here, we investigated the function of TL1A on human TH17 cells. TL1A together with TGF- IL-6, and IL-23 enhanced the secretion of IL-17 and IFN- from human CD4+ memory T cells. TL1A induced the expression of the transcription factors BATF and T-bet that correlated with the secretion of IL-17 and IFN-. In contrast, TL1A alone induced high levels of IL-22 in memory CD4+ T cells and committed TH17 cells. However, TL1A did not enhance expression of IL-17A in TH17 cells. Expression of the transcription factor aryl hydrocarbon receptor that regulates expression of IL-22 was not affected by TL1A. We performed transcriptome analysis of TH17 cells to determine genes that are transcriptionally regulated by TL1A. transcriptome analysis revealed increased expression of IL-9 in response to TL1A.

overall_design: Total RNA was obtained from human TH17 cells (sorted by flow cytometry for CD4+ CD45RO+ CCR6+) that were untreated (control) or treated with TL1A (TL1A) for 24, 48, or 72 h. Total RNA was extracted from 5 healthy donors (5 independent experiments).

middle: S

last: Thomas

first: Emebet

last: Mengesha


title: Promiscuous targeting of bromodomains by Bromosporine identifies BET proteins as master regulators of primary transcription response in leukemia [set 1]

first: Panagis

last: Filippakopoulos

overall_design: Cells were seeded the day prior to treatment at 2x10^5 per ml. Treatments were performed so that a final concentration of 0.1 % DMSO (Cat.#D1435; Sigma) was achieved and cells were incubated with DMSO or 500 nM test compound (BSP or JQ1) for 6 h prior to isolation of RNA. Total RNA was isolated using a standard TRIzol (Invitrogen) protocol and prepared using RNeasy columns (Cat.#74106 plus; Qiagen). RNA was quantified using a Nanodrop spectrophotometer (model ND1000; Thermo Fisher) and integrity assessed on a BioAnalyzer (2100; Agilent Laboratories, USA). All samples had a RNA Integrity Number (RIN) ≥ 9. Biological triplicates were performed for each condition tested.

first: Christine

last: Blancher


title: MSX1-induced neural crest-like phenotype in human melanocytes

status: Public on Sep 30 2016

city: Philadelphia

first: Mizuho

last: Fukunaga-Kalabis

address: 3601 Spruce Street

institute: The Wistar Institute

summary: Msh homeobox 1 (MSX1) is a transcription factor implicated in neural crest specification. Ectopic expression of MSX1 reprograms mature melanocytes into a neural crest-like state as a single factor. MSX1-reprogrammed melanocytes lose pigmentation and become multipotent. To identify immediate targets of MSX1, we generated a tetracycline-inducible system (Tet-ON) in order to express MSX1 in primary melanocytes (iMSX1) in a clean and rapid way starting at defined time points and perform a global gene expression analysis.

overall_design: The analysis was done in melanocytes derived from two different donors. iMsx1-expressing melanocytes before (0 h) and after short-term induction of MSX1 (6 h)

last: Kalabis


title: Promiscuous targeting of bromodomains by Bromosporine identifies BET proteins as master regulators of primary transcription response in leukemia


title: The histone deacetylase HDAC7 represses lineage-inappropriate genes and is essential for proper B cell generation

status: Public on Sep 26 2016

city: Barcelona

first: Maribel

last: Parra

state: Barcelona

address: Avda. Gran Via 199-203, L'Hospitalet de Llobregat

department: Cancer Epigenetics and Biology Programme (PEBC)

country: Spain

institute: Bellvitge Biomedical Research Institute (IDIBELL)

summary: B lymphocyte development is a complex process tightly controlled at the transcriptional level by the action of networks of transcription factors. The repression of genes from alternative lineages is necessary to ensure the acquisition of the correct B cell identity. However, the mechanisms of transcriptional repression during B cell generation are largely unknown. Here, using a conditional knockout mouse model, we show that the histone deacetylase HDAC7 is essential for B cell development. Early deletion of HDAC7 dramatically blocked B cell development at the pro-B cell stage and gave rise to a severe lymphopenia in peripheral organs. HDAC7-deficient pro-B cells exhibit cell lineage promiscuity, expressing myeloid and T lymphocyte genes. In wild-type B cells HDAC7 is recruited to myocyte enhancer factor 2C (MEFC2) binding sites located at the promoters of macrophage and T lymphocyte genes. Our results demonstrate that HDAC7 is a bona fide transcriptional repressor essential for B cell development.

overall_design: Biological triplicates of pro-B cells purified from wild-type and HDAC7 conditional mice. Total RNA from purified pro-B cells was extracted by Trizol. PCR amplified RNAs were hybridized against Affymetrix mouse arrays chip (Mouse Genome 430 PM strip)

first: Abul

middle: K

last: Islam


title: Comparative study of the transcriptome of HUVECs from infants born to mothers diagnosed with GDM and controls.

status: Public on Sep 24 2016

city: Singapore

first: Walter

last: Stunkel

address: 30 Medical Drive, Brenner Centre Lvl 4

country: Singapore

institute: Singapore Institute for Clinical Sciences

summary: The prevalence of metabolic syndrome comprising obesity, type 2 diabetes mellitus and cardiovascular disease has been on the rise world-wide in recent years. As non-communicable diseases such as type 2 diabetes mellitus have their roots in prenatal development and conditions such as maternal gestational diabetes (GDM), we aimed to test this hypothesis in primary cells derived from the offspring of GDM mothers compared to control subjects. Methods We have assessed primary umbilical cord derived cells such as human vascular endothelial cells (HUVECs) and Wharton’s jelly derived mesenchymal stem cells (WJMSCs) from both, the offspring of GDM and healthy mothers. We have compared the primary isolates in cell based assays measuring proliferation, mitochondrial oxygen consumption, as well as the ability to support blood vessel growth. We conducted gene expression microarray studies with subsequent pathway analysis and candidate gene validation. Results We observed striking differences between the two groups such as lower metabolic rates and impairment of tube formation in cells with GDM background. HUVECs from subjects with maternal GDM have lower expression of the anti-apoptotic protein BCL-Xl suggesting compromised angiogenic capabilities. Comparative gene expression analysis revealed blood vessel formation as a major pathway enriched in the GDM derived HUVECs with the surface marker CD44 as a significant gene under-expressed in the GDM group. Functional validation of CD44 revealed that it regulates tube formation in HUVECs thereby providing new insights into a novel pathway imprinted in primary umbilical cord derived cells from GDM offspring. Conclusions/interpretation Our data demonstrate that primary cells isolated from the umbilical cord of offspring born to GDM mothers maintain metabolic and molecular imprints of maternal hyperglycemia, which occurred during prenatal development reflecting an enhanced risk for cardiovascular disease later in life.

overall_design: 5 HUVECs samples from GDM background and 5 HUVECs samples from controls (mothers with no GDM) were used to conduct transcriptomic comparisons at the basal level.

first: I

last: Ajith

first: Jun

middle: H

last: Tan

first: Cheng

last: Chang

last: Stünkel


title: Tail and Kinase Modules Differently Regulate Core Mediator Recruitment and Function In Vivo

city: Montreal

first: Francois

last: Robert

state: QC

address: 110 av des Pins Ouest

country: Canada

institute: IRCM

type: Genome binding/occupancy profiling by genome tiling array

summary: Mediator is a highly conserved transcriptional coactivator organized into four modules, namely Tail, Middle, Head and Kinase (CKM). Previous work suggests regulatory roles for Tail and CKM, but an integrated model for these activities is lacking. Here, we analyzed the genome-wide distribution of Mediator subunits in wild-type and mutant yeast cells in which RNA polymerase II promoter escape is blocked allowing detection of transient Mediator forms.  We found that while all modules are recruited to upstream activated regions (UAS), assembly of Mediator within the pre-initiation complex is accompanied by the release of CKM. Interestingly, our data show that CKM regulates Mediator-UAS interaction rather than Mediator-promoter association. In addition, while Tail is required for Mediator recruitment to UAS, Tail-less Mediator nevertheless interacts with core promoters. Collectively, our data suggest that the essential function of Mediator is mediated by Head and Middle at core promoters, while Tail and CKM play regulatory roles.

overall_design: We took a systematic approach to examine the genome-wide distribution (using ChIP-chip) of various Mediator subunits in WT, kin28as, med13Δ, med3Δ/med15Δ,  med13Δ/kin28as and med3Δ/med15Δ/kin28as cells.  Mediator ChIPs were performed with Myc/FLAG/HA-tagged subunits. ChIPs (in Cy5) were hybridyzed against a control ChIP sample from an isogenic non-tagged strain (in Cy3). In addition to Mediator ChIPs, the project includes TFIIB ChIP-chip datasets in WT, med3Δ/med15Δ and med18(srb5)-AA cells. All ChIP-chip experiments were done in duplicates. Each microarray was normalized using the Lima Loess and replicates were combined using a weighted average method as previously described (Pokholok et al., 2005).

first: Célia

last: Jeronimo

first: Marie-France

last: Langelier

first: Alain

last: Bataille

first: John

middle: M

last: Pascal

first: B

last: Pugh

first: François


title: Maternal BCG scar is associated with enhanced infant proinflammatory responses

city: Cleveland

first: Ali

last: Filali

address: 10900  Euclid Avenue

department: Pathology

institute: CWRU

summary: Prenatal exposures such as infections and immunisation may influence infant responses. We had an opportunity to undertake an analysis of responses in infants within the context of a study investigating the effects of maternal mycobacterial exposures and infection on bacille Calmette-Guerin (BCG) vaccine-induced responses in Ugandan infants. Gene expression profiles for pathways associated with maternal LTBI and with maternal BCG scar were examined using samples collected at one (n=42) and six (n=51) weeks after BCG immunisation using microarray. Interferon and inflammation response pathways were up-regulated in infants of mothers with LTBI at six weeks, and in infants of mothers with a BCG scar at one and six weeks after BCG immunisation.  Maternal BCG scar had a stronger association with infant responses than maternal LTBI, with an increased proinflammatory immune profile.

first: P

last: Mawa

first: E

last: Webb

first: A

last: Filali-Mouhim

first: G

last: Nkurunungi

first: R

middle: P

last: Sekaly

first: S

last: Lule

last: Prentice

last: Nash

first: H

last: Dockrell

first: M

last: Elliott

last: Cose


title: Genome-wide expression microarray analysis of romidpesin treated GCC cell lines, fibroblasts and Sertoli cells.

status: Public on Sep 23 2016

city: Düsseldorf

first: Daniel

last: Nettersheim

state: NRW

address: Universitätsstr. 1

department: Urology

institute: University Hospital Düsseldorf

summary: Illumina expression microarray analysis of TCam-2, 2102EP, NCCIT, JAR, MPAF, ARZ and FS1 cells 8 and 16 h after 10 nanomolar romidepsin application. DMSO treated cells were used as controls. These data are part of the article 'A signaling cascade including ARID1A, GADD45B and DUSP1 induces apoptosis and affects the cell cycle of germ cell cancers after romidepsin treatment' (Nettersheim et al., 2016).

overall_design: Total RNA was isolated from TCam-2, 2102EP, NCCIT, JAR, MPAF, ARZ and FS1 cells 8 and 16h after Romidepsin treatement. DMSO treated cells served as control.

first: Hubert

last: Schorle


title: Genome variation profiling of A204 parental and acquired-resistance cells treated with Pazopanib, Dasatinib and Sunitinib

city: Salt Lake City

first: Aik Choon

last: Tan

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

institute: Huntsman Cancer Institute

summary:
Malignant rhadboid tumors (MRTs) are lethal paediatric cancers characterised by a deficiency in the SWI/SNF subunit SMARCB1. Here we employ an integrated molecular profiling and chemical biology approach to demonstrate that the receptor tyrosine kinases (RTKs) PDGFRα and FGFR1 are coactivated in MRT cells and that dual blockade of these receptors has synergistic efficacy.
Genome variation profiling of A204 parental and acquired resistance cell line

overall_design: Genome variation profiling of 4 cell lines, parental A204, A204 Dasatinib resistant, A204 Pazopanib resistant and A204 Sunitinib resistant

first: Aik

first: Paul

last: Huang


title: Knockdown of the schizophrenia susceptibility gene TCF4 alters gene expression and proliferation of progenitor cells from the developing human neocortex.

city: Cardiff

first: Matthew

middle: James

last: Hill

address: Maindy Road

institute: Cardiff University

summary:
BACKGROUND: Common variants in the TCF4 gene are among the most robustly supported genetic risk factors for schizophrenia. Rare TCF4 deletions and loss-of-function point mutations cause Pitt-Hopkins syndrome, a developmental disorder associated with severe intellectual disability.
METHODS: In order to explore molecular and cellular mechanisms by which TCF4 perturbation could interfere with human cortical development, we experimentally reduced the endogenous expression of TCF4 in a neural progenitor cell line derived from the developing human cerebral cortex using RNA interference. Effects on genome-wide gene expression were assessed by microarray, followed by Gene Ontology and pathway analysis of differentially expressed genes. Effects on cell proliferation were assessed using high content imaging.
RESULTS: Genes that were differentially expressed following TCF4 knockdown were highly enriched for involvement in the cell cycle. Consistent with the gene expression data, TCF4 knockdown was associated with reduced proliferation of cortical progenitor cells in vitro.
CONCLUSIONS: Our data indicate effects of TCF4 perturbation on human cortical progenitor cell proliferation, a process that could contribute to cognitive deficits in Pitt-Hopkins Syndrome and risk for schizophrenia.

overall_design: Total RNA extracted from human neural progenitor cells manipulated with three siRNAs: control siRNA , siRNA_TCF4 1 (Cat #s13863) and siRNA TCF4 2 (Cat #s13864). 4 replicates per group. Genome wide transcript levels were then measured using gene expression microarrays.

first: Richard

last: Killick

first: Katherinne

last: Navarrete

first: Aleksandra

last: Maruszak

first: Gemma

last: McLaughlin

first: Brenda

last: Williams

first: Nicholas

last: Bray


title: Cell type-specific chromatin states differentially prime squamous cell carcinoma tumor-initiating cells for epithelial to mesenchymal transition [expression 2]

city: Brussels

first: Cédric

last: Blanpain

address: Route de Lennik 808

country: Belgium

institute: ULB

summary: Epithelial to mesenchymal transition (EMT) in cancer cells has been associated with metastasis, stemness and resistance to therapy. The reason why some tumors undergo EMT and other not might reflect intrinsic properties of their cell of origin, although this possibility is largely unexplored. By targeting the same oncogenic mutations to discrete skin compartments, we show cell type-specific chromatin and transcriptional states differentially prime tumors to EMT.  Squamous cell carcinomas (SCCs) derived from intrafollicular epidermis (IFE) are generally well-differentiated, while hair follicle (HF) stem cell-derived SCCs frequently exhibit EMT, efficiently form secondary tumors, and possess increased metastatic potential.  Transcriptional and epigenomic profiling revealed IFE and HF tumor-initiating cells possess distinct chromatin landscapes and gene regulatory networks associated with tumorigenesis and EMT that correlate with accessibility of key epithelial and EMT transcription factor binding sites.  These findings highlight the importance of chromatin states and transcriptional priming in dictating tumor phenotypes and EMT.

overall_design: KrasG12D expression combined with deletion of p53 and overexpression of DeltaNp63 were induced in Hair Follicle Stem cells (SCs) and their progeny using Lgr5CREER/KRasG12D/p53fl/fl/DeltaNp53-IRES-GFP mice by intraperitoneal tamoxifen injection. Epcam+ tumors epithelial Cells and Epcam- mesenchymal tumor cells were FACS cells sorted and compared  from fully grown tumours.

last: Latil

first: D

last: Nassar

first: B

last: Beck

last: Boumhadi

first: A

last: Brisebarre

first: C


title: Generation of kisspeptin-responsive GnRH-expressing  neurons from human pluripotent stem cells

status: Public on Sep 17 2016

city: London

first: Ariel

last: Poliandri

state: London

address: Cranmer Terrace

department: Core Support

institute: St George's University

summary: GnRH neurons are fundamental for reproduction in all vertebrates ultimately integrating all reproductive inputs. The inaccessibility of human GnRH-neurons has been a major impediment to studying the central control of reproduction and its disorders. Here, we report the efficient generation of kisspeptin responsive GnRH-secreting neurons by directed differentiation of human Pluripotent Stem Cells. The protocol involves the generation of intermediate Neural Progenitor Cells (NPCs) through long-term Bone morphogenetic protein 4 inhibition followed by terminal specification of these NPCs in a media containing FGF8 and a NOTCH inhibition. The resulting GnRH expressing and secreting neurons display a neuroendocrine gene expression pattern and present spontaneous calcium transients that can be stimulated by kisspeptin. These in vitro generated GnRH expressing cells provide a new resource for studying the molecular mechanisms underlying the development and function of GnRH neurons.

overall_design: Hues7 embryonic stem cells (ESCs) where differentiated into Neural Progenitor Cells (NPCs). NPCs were expanded for 4 passages and finally differentiated into neurons for 21 (GnRH-EC 21) or 35 (GnRH-EC 35) days. Total RNA was extracted from ESCs, NPCs, GnRH-EC 21, and GnRH-EC 35, hybridized to an Illumina genome wide gene expression array (HT12v4) and data processed  using Illumina's Genome Studio software.

first: Duncan

last: Miller

first: Sasha

last: Howard

first: Muriel

last: Nobles

first: Steven

last: Harmer

first: Andy

last: Tinker

first: Tristan

last: McKay

first: Leonardo

last: Guasti

first: Leo

last: Dunkel


title: Gene expression profile of calcified bicuspid, tricuspid and normal human aortic valves

status: Public on Sep 22 2016

city: Quebec

first: Yohan

last: Bossé

state: Quebec

address: 2725, chemin Sainte-Foy

institute: Laval University

summary: The objective of this study was to identify genes differentially expressed between calcified bicuspid aortic valves (BAV) and tricuspid valves with (TAVc) and without (TAVn)  aortic valve stenosis. Ten human BAV and nine TAVc were collected from male who underwent primary aortic valve replacement. Eight TAVn were obtained from male who underwent heart transplantation. mRNA levels were measured using Illumina HumanHT-12 v4 Expression BeadChip and compared between valve groups.

overall_design: Gene expression was performed in three groups of human aortic valves including 10 calcified bicuspid aortic valves, 9 stenotic tricuspid valves and 8 tricuspid normal valves. A total of 27 samples are included in this dataset.


title: Patient derived melanoma xenografts

status: Public on Oct 04 2016

city: Dallas

first: Zhiyu

last: Zhao

state: Texas

address: 5323 Harry Hines Blvd.

department: Children's Medical Center Research Institute

institute: University of Texas Southwestern Medical Center

summary: New therapies are required for melanoma. Here we report that multiple cardiac glycosides, including digitoxin and digoxin, are significantly more toxic to human melanoma cells than normal human cells. This reflects on-target inhibition of the ATP1A1 Na+/K+ pump, which is highly expressed by melanoma. MEK inhibitor and/or BRAF inhibitor additively or synergistically combine with digitoxin to induce cell death, inhibiting growth of patient-derived melanomas in NSG mice and synergistically extending survival. MEK inhibitor and digitoxin do not induce cell death in human melanocytes or hematopoietic cells in NSG mice. In melanoma, MEK inhibitor reduces ERK phosphorylation while digitoxin disrupts ion gradients, altering plasma membrane and mitochondrial membrane potentials. MEK inhibitor and digitoxin together cause intracellular acidification, mitochondrial calcium dysregulation, and ATP depletion in melanoma cells but not in normal cells. The disruption of ion homeostasis in cancer cells can thus synergize with targeted agents to promote tumor regression in vivo. In this study the microarray analysis was based on melanomas obtained from 32 patients and melanocytes from 3 donors. Results provide insight into molecular mechanisms underlying melanoma progression.

overall_design: Total of 84 samples including 2-4 biological replicate for each of the 32 melanomas and three melanocytes isolated from different donors.

first: Ugur

last: Eskiocak

first: Vijayashree

last: Ramesh

first: Jennifer

middle: G

last: Gill

first: Stacy

last: Yuan

first: Meng

last: Wang

first: Travis

last: Vandergriff

first: Mark

last: Shackleton

first: Elsa

last: Quintana

first: Timothy

last: Johnson

first: Ralph

last: DeBerardinis

first: Sean

last: Morrison


title: Inactivation of the putative ubiquitin-E3 ligase PDLIM2 in classical Hodgkin and anaplastic large cell lymphoma

status: Public on Sep 13 2016

city: Berlin

first: Stephan

last: Mathas

address: Robert-Rössle-Straße 10

institute: MDC Berlin

summary: Apart from its unique histopathological appearance with rare tumor cells embedded in an inflammatory background of bystander cells, classical Hodgkin lymphoma (cHL) is characterized by an unusual activation of a broad range of signaling pathways involved in cellular activation. This includes constitutive high-level activity of nuclear factor-κB (NF-κB), Janus kinase/signal transducer and activator of transcription (JAK/STAT), activator protein-1 (AP-1) and interferon regulatory factor (IRF) transcription factors (TFs) that are physiologically only transiently activated. Here, we demonstrate that inactivation of the putative ubiquitin E3-ligase PDLIM2 contributes to this TF activation. PDLIM2 expression is lost at the mRNA and protein levels in the majority of cHL cell lines and Hodgkin and Reed–Sternberg (HRS) cells of nearly all cHL primary samples. This loss is associated with PDLIM2 genomic alterations, promoter methylation and altered splicing. Reconstitution of PDLIM2 in HRS cell lines inhibits proliferation, blocks NF-κB transcriptional activity and contributes to cHL-specific gene expression. In non-Hodgkin B-cell lines, small interfering RNA-mediated PDLIM2 knockdown results in superactivation of TFs NF-κB and AP-1 following phorbyl myristate acetate stimulation. Furthermore, expression of PDLIM2 is lost in anaplastic large cell lymphoma (ALCL) that shares key biological aspects with cHL. We conclude that inactivation of PDLIM2 is a recurrent finding in cHL and ALCL, promotes activation of inflammatory signaling pathways and thereby contributes to their pathogenesis

overall_design: L591 cells were transfected with 40 μg  of a pcDNA3-PDLIM2 transcript variant 2 (tv 2)  or mock pcDNA3 construct along with 10 μg  pEGFP-N3. GFP+ cells were enriched by fluorescence-activated cell sorting.

first: Kathrin

last: Wurster

first: Martin

last: Janz

first: Karl

last: Koechert


title: Telomerase promotes cell survival by suppression of long noncoding RNAs

city: Seattle

first: Shibani

last: Mukherjee

state: WA

address: 1100 Fairview Ave N.,  A3-020

department: Division of Basic Sciences

institute: Fred Hutchinson Cancer Research Center

summary: Human telomerase, hTERT, catalyzes telomere elongation using the hTR long noncoding RNA (lncRNA) template and confers replicative immortality, a hallmark of cancer. hTERT is reactivated in nearly 90% of cancers and telomere elongation was considered its sole role in tumorigenesis. However, evidence for telomere-independent hTERT cell phenotypes, which surprisingly require hTERT catalytic activity, is mounting. These phenotypes could profoundly impact our understanding and clinical exploitation of hTERT’s role in cancer, but their underlying mechanisms remain unclear. One mechanism was suggested by the demonstration of hTERT’s ability to bind an alternative lncRNA, RMRP, and synthesize double-stranded RNAs that are processed into Argonaute2-bound small interfering RNAs that suppress the lncRNA itself. Here we performed systematic lncRNA profiling to determine whether this is a general mode of hTERT action involving novel lncRNAs, and investigated the implications of hTERT-mediated lncRNA suppression for tumorigenesis. We found that hTERT’s telomere-independent catalytic activity increased cell survival resulting in luminal hyperplasia in a human breast acinar morphogenesis model. Using next-generation sequencing of Argonaute2-associated small RNAs, we discovered novel hTERT-downregulated lncRNAs. One such lncRNA, MEG3, could bind hTERT and was significantly downregulated in human breast carcinoma cell lines and tissues. MEG3 knockdown promoted survival and hyperplasia, consistent with early tumorigenesis, and ectopic MEG3 expression caused cell death and inhibited breast cancer cell proliferation. Microarray analysis identified Bcl2-interacting proteins, BEX1 and BNIPL, as MEG3 targets. BEX1 mediates cell death by decreasing phospho-Bcl2, and MEG3 or hTERT modulated phospho-Bcl2 levels. This pathway could, in part, underlie the observed phenotypes. Collectively, our findings show that hTERT can suppress multiple lncRNAs, including MEG3, and establish a novel mechanism of hTERT-mediated proliferative control that could facilitate tumorigenesis. Our mechanistic insights suggest that small RNA-directed diagnostic and therapeutic strategies will be relevant for targeting hTERT.

overall_design: Primary human mammary epithelial cells (HMECs), derived from two human donors, were first stably retrovirally transduced with hTERT and then stably transfected with either empty vector control (Vector) or with MEG3. Cells were cultured in mitogen-limited conditions, and total RNA extracted on day 5.  Statistical analyses were carried out between donor-paired samples (hTERT+Vector versus hTERT+MEG3).

first: James

last: Roberts


title: Expression profiles of the G protein-coupled estrogen receptor (GPER)-knockout versus intact cardiomyocytes

city: Winston-Salem

first: Hao

state: NC

address: Medical Center Boulevard

department: Anesthesiology

institute: Wake Forest School of Medicine

summary: To determine if there are differences in the gene expression profile of cardiomyocytes with GPER deletion when compared to intact cardiomyocytes in both sexes. None of the gene expression profiles have been previously published. Here we provide the original DNA microarray data with the hope that other investigators will be able to utilize this data in their own research.

overall_design: Cardiomyocytes were isolated from adult male and female GPER knockout and wild type mice. Total RNA was isolated from cardiomyocytes and gene expression levels were profiled on the Affymetrix GeneAtlas Mouse MG-430 PM Array Strips.

first: Xuming

last: Sun

first: Jeff

last: Chou

first: Marina

last: Lin

first: Leanne

last: Groban


title: Gene expression assay for ALCAM depleted endometrial cancer cell lines

status: Public on Sep 08 2016

first: Eva

last: Colas

address: Pg. Vall Hebron 119-129

institute: Vall Hebron Research Institute

summary: Endometrial cancer is the most common gynaecological cancer in western countries, being the endometrioid tumours the most common subtype. Most patients are diagnosed at an early stage and present an excellent prognosis. However, a consistent number of those continue to suffer recurrence, without means to be identified by risk classification systems. Thus, finding a reliable marker to predict recurrence becomes an important unmet clinical issue. ALCAM is a cell–cell adhesion molecule, member of the Immunoglobulin superfamily, which has been associated to the carcinogenesis of many cancers. In here, we first determined the value of ALCAM as marker of recurrence in endometrioid endometrial cancer by conducting a retrospective multicenter study in 174 primary tumours. In early stage patients (N=134), recurrence-free survival was poorer in patients with ALCAM-positive compared to ALCAM-negative tumours (HR 4.237; 95%CI 1.01-17.76). This difference was more significant in patients with early stage moderately-poorly differentiated tumours (HR 9,259; 95%CI 2.12-53.47). In multivariate analysis, ALCAM-positivity was an independent prognostic factor in early stage disease (HR 6.027, 95% CI 1.41-25.74). Then, we demonstrated in vitro a role for ALCAM in cell migration and invasion by using a loss-of-function model in two endometrial cancer cell lines. Moreover, ALCAM depletion resulted in a reduced primary tumour size and reduced metastatic local spread in an orthotopic murine model. Gene expression analysis of ALCAM-depleted cell lines supported that motility, invasiveness, cellular assembly and organization were the most deregulated functions associated to ALCAM. Finally, we evidenced some of the downstream effector genes that are involved in ALCAM mediated cell migration; specifically FLNB, TXNRD1 and LAMC2 were validated. In conclusion, our results highlight the potential of ALCAM as a recurrent biomarker in early stage endometrioid endometrial cancer and point to ALCAM as an important molecule in endometrial cancer dissemination by regulating cell migration, invasion and metastasis.

overall_design: Total RNA from two endometrial cancer cells, Ishikawa and Hec1a, with shALCAM and ShControl stably transfected vectors was analyzed in triplicates.

first: Laura

last: Devis

first: Antonio

last: Gil

first: Jaume

last: Reventos


title: Gene expression of A204 parental and acquired resistant cells treated with Pazopanib, Dasatinib, and Sunitinib.

city: Aurora

first: Karen

last: Ryall

state: Colorado

address: Mail Stop 8117, 12801 East 17th Avenue

department: Medical Oncology

institute: University of Colorado Denver

summary:
Malignant rhadboid tumours (MRTs) are lethal paediatric cancers characterised by a deficiency in the SWI/SNF subunit SMARCB1. Here we employ an integrated molecular profiling and chemical biology approach to demonstrate that the receptor tyrosine kinases (RTKs) PDGFRα and FGFR1 are coactivated in MRT cells and that dual blockade of these receptors has synergistic efficacy.
Gene expression analysis of the four cell lines in the presence of TKI showed that the resistant sublines clustered together with the untreated parental cells and confirmed that PDGFRA was among the most highly downregulated genes in the resistant cells.

overall_design: Microarray on parental and acquired resistant A204 cells treated with Pazopanib, Dasatinib, and Sunitinib.

first: Jocelyn

last: Wong

first: Jason

middle: R

last: Todd

first: Martina

last: Finetti

first: Frank

last: McCarthy

first: Malgorzata

last: Broncel

first: Simon

last: Vyse

first: Maciej

middle: T

last: Luczynski

first: Stephen

last: Crosier

first: Kate

last: Holmes

first: Leo

last: Payne

first: Frances

last: Daley

first: Patty

last: Wai

first: Andrew

last: Jenks

first: Barbara

last: Tanos

first: Aik-Choon

last: Tan

first: Rachael

last: Natrajan

first: Daniel

last: Williamson

first: Paul

last: Huang


title: Expression profiling of cutaneous squamous cell carcinoma with perineural invasion implicates the p53 pathway in the process

city: Brisbane

first: Glen

last: Boyle

state: Queensland

address: 300 Herston Road Herston

department: Department of Cell and Molecular Biology, Cancer Program

country: Australia

institute: QIMR Berghofer Medical Research Insitute

summary: Squamous cell carcinoma (SCC) is the second most common cancer worldwide and accounts for approximately 30% of all keratinocyte cancers.  The vast majority of cutaneous SCCs of the head and neck (cSCCHN) are readily curable with surgery and/or radiotherapy unless high-risk features are present.  Perineural invasion (PNI) is recognized as one of these high-risk features.  The molecular changes during clinical PNI in cSCCHN have not been previously investigated.  In this study, we assessed the global gene expression differences between cSCCHN with or without incidental or clinical PNI.  The results of the analysis showed signatures of gene expression representative of activation of p53 in tumors with PNI compared to tumors without, amongst other alterations.  Immunohistochemical staining of p53 showed cSCCHN with clinical PNI to be more likely to exhibit a diffuse over-expression pattern, with no tumors showing normal p53 staining.  DNA sequencing of cSCCHN samples with clinical PNI showed no difference in mutation number or position with samples without PNI, however a significant difference was observed in regulators of p53 degradation, stability and activity.  Our results therefore suggest that cSCCHN with clinical PNI may be more likely to contain alterations in the p53 pathway, compared to cSCCHN without PNI.

overall_design: In this study, we assessed the global gene expression differences between cSCCHN with or without incidental or clinical PNI.  Single color, Illumina Human HT12v4 Beadarrays.

first: Timothy

middle: A

last: Warren

first: Natasa

last: Broit

first: Jacinta

last: Simmons

first: Carly

last: Pierce

first: Sharad

last: Chawla

first: Duncan

last: Lambie

first: Gary

last: Quagliotto

first: Ian

last: Brown

first: Peter

last: Parsons

first: Benedict

last: Panizza


title: Microbes associate with host innate immune response in idiopathic pulmonary fibrosis

status: Public on Sep 15 2016

city: Charlottesville

first: Yong

state: VA

address: 1340 Jefferson Park Ave

department: Medicine

institute: University of Viginia

summary: The goal of this study is to explore molecular mechanisms underpinning the progression-associated host-microbial interactions in IPF. Multi-omics analysis revealed that the majority (8/11) of the progression-associated pathways were involved in inflammatory response and pattern recognition receptors (PRRs), including NOD-, TOLL- and RIG-I-like receptor pathways. Microbial community richness was correlated with all of the three PRRs (Pearson's p<0.007). The known IPF-progression marker Streptococcus (OTU1345) was correlated with NOD like receptor signaling pathway (p=0.047). Up-regulated genes in PBMCs of CpG-ODN responsive patients were over-represented in 22 canonical pathways (FDR<0.01). Network modeling revealed that 14/22 pathways were significantly correlated with community diversity (Shannon's index) and three genera (Otu1341 Prevotella, OTU1348 Staphylococcus, and OTU1302 Pseuodomonadacea), as well as 10/11 host gene co-expression modules. Toll-like receptor signaling pathway was mutually linked by CpG-response, Otu1341 and microbial Shannon's index. Notably, OTU1341 and IPF-progression marker OTU1348 were also correlated with TLR9 (r=0.48, p=3x10-5; r=0.38, p=0.002, respectively). These findings suggest that PRR and immune response signaling pathways play a central  role in PFS-associated host-microbial interactions and the probifbrotic differentiation induced by CpG-ODN upon TLR9 stimulation.

overall_design:
Sixty-eight COMET-IPF participants with matched PBMC microarray data and 16s rRNA sequencing data are included in this study. In addition, 32/68 patients have matched leukocyte phenotypes by flow cytometry. Lung fibroblasts derived from transbronchial biopsy of COMET-IPF patients (n=27) were cultured in vitro with growth media. Fibroblasts were treated for 24 hours with or without CpG-ODN (hypomethylated DNA; 10 M). A > 2 fold change in alpha smooth muscle actin expression (i.e. treated vs. untreated) was deemed CpG-ODN “responsive”. Therefore,  27/68 patients have CpG-ODN reponsive data.
This series contains the gene expression data for the 68 PBMC samples from COMET-IPF participants.

first: Shwu-Fan

last: Ma

first: MeiLan

last: Han

first: Naftali

last: Kaminski

first: G

middle: N

last: Garcia

first: Cory

last: Hogaboam

first: Fernando

last: Martinez

first: Imre

last: Noth


title: Regulators of NRAS-mediated transformation and melanoma tumor maintenance

city: Birmingham

first: Narendra

last: Wajapeyee

state: AL

address: 720 20th Street South, Kaul 540A

department: Department of Biochemistry and Molecular Genetics

institute: University of Alabama at Birmingham

summary: Mutations in the NRAS oncogene are present in up to 20% of melanoma. Here, we show that interferon alpha-inducible protein 6 (IFI6) is necessary for NRASQ61K-induced transformation and melanoma growth. IFI6 was transcriptionally upregulated by NRASQ61K, and knockdown of IFI6 resulted in DNA replication stress due to dysregulated DNA replication via E2F2. This stress consequentially inhibited cellular transformation and melanoma growth via senescence or apoptosis induction depending on the RB and p53 pathway status of the cells. NRAS-mutant melanoma were significantly more resistant to the cytotoxic effects of DNA replication stress-inducing drugs, and knockdown of IFI6 increased sensitivity to these drugs. Pharmacological inhibition of IFI6 expression by the MEK inhibitor trametinib, when combined with DNA replication stress-inducing drugs, blocked NRAS-mutant melanoma growth. Collectively, we demonstrate that IFI6, via E2F2 regulates DNA replication and melanoma development and growth, and this pathway can be pharmacologically targeted to inhibit NRAS-mutant melanoma.

overall_design: YUGASP cells stably expressing a non-silencing shRNA or two individual shRNAs against IFI6 were used to prepare the total RNA, which was then used to analyze for gene expression using Illumina expression array.

first: Romi

last: Gupta

first: Matteo

last: Forloni

first: Shaillay

last: Dogra


title: Regulation of GLI underlies a role for BET bromodomains in pancreatic cancer growth and the tumor microenvironment

city: Boston

first: Andrew

last: Liss

state: MA

address: 55 Blossom St

department: Surgery

institute: Massachusetts General Hospital

summary: Pancreatic ductal adenocarcinoma (PDAC) is extraordinarily chemoresistant and the abundant stromal content of these tumors contributes to the ineffective treatment of this disease.  While the genetic alterations of PDAC have been well characterized, the epigenetic pathways regulating PDAC remain, for the most part, elusive.  Employing an in vivo shRNA screen targeting epigenetic regulators, we identified members of the BET family of chromatin adaptors as key regulators of PDAC cell growth and maintenance of the tumor stroma.  BET family members contribute to PDAC cell growth by modulating the activity of two key transcriptional programs, MYC and GLI.  Within the cancer cells, BET inhibition also results in down-regulation of a key mediator of the tumor microenvironment, SHH, corresponding to a decrease in the stromal content of tumors.  Taken together, these results suggest that therapeutic inhibition of BET proteins offers a novel mechanism to target both the neoplastic and stromal components of PDAC.

overall_design: Total RNA was isolated from 4 untreated PDAC cell lines or those exposedto the BET bromodomain inhibibitor CPI203 (1.6 uM) or control DMSO for 5 and 10 hours

first: Yinshi

last: Huang

first: Sabikun

last: Nahar

first: Jennifer

last: Mertz

first: Barbara

last: Bryant

first: Charlie

last: Hatton

first: Robert

last: Sims

first: Keith

middle: D

last: Lillemoe

first: Carlos

last: Fernandez-del Castillo

last: Warshaw

first: Sarah

last: Thayer


title: IL-1β-induced modulation of gene expression profile in human dermal fibroblasts: the effects of Thai herbal Sahatsatara formula (AVS023), piperine and gallic acid possessing antioxidant properties

status: Public on Sep 11 2016

city: Bangkok

first: Onusa

last: Thamsermsang

address: Prannok Road.

department: Pharmacology

institute: Faculty of Medicine Siriraj Hospital, Mahidol University

summary:
Analysis of the effects of AVS023 and its active compounds (gallic acid and piperine) on human gene expression in primary human dermal fibroblasts induced by IL-1β.
The results provided up- and down- regulated genes resulting from IL-1β and IL-1β plus with each test compound in primary human dermal fibroblasts

overall_design: Human dermal fibroblasts were cultured with test compounds for 30 minutes and stimulated with IL-1β for 4 h. All results  were compared to control or  IL-1β treated only. Total samples were 11 samples with duplicate experiments


title: Gene expression signatures in whole blood to predict vaccine responses

status: Public on Sep 12 2016

city: Palo Alto

first: Jorg

last: Goronzy

state: CA

address: Rm E4201, Bldg100, 3801 Miranda Ave

institute: Stanford University

summary: To identify host factors that influence the immunogenicity of the attenuated VZV pOka vaccine strain and the efficacy of VZV vaccination, we immunized 39 individuals aged 50 to 75 years, including 9 monozygotic twin pairs. We measured VZV-specific T cell frequencies by IFN-γ–specific ELISpot, and VZV-specific antibody titers by ELISA. Whole gene expression arrays were performed on vaccinees before (n=28) and one (n=18) or three days (n=10) after vaccination. Cell-specific gene expression profiles were generated by deconvolution using previously described algorithms. Only very few neutrophil- and lymphocyte-related genes changed in expression from day 0 to 1. Significant changes for monocyte-related genes were found, but even here the number of probes with a significant change was low after adjusting for false discovery. When expression changes in monocyte-derived genes were analyzed for their correlation with T cell responses, we identified 493 probes corresponding to 479 genes that correlated with generation of VZV-specific effector T cells and 641 probes corresponding to 621 genes that correlated with the subsequent contraction phase with p<0.05. Interestingly, these two sets of genes were significantly overlapping, i.e., the same changes that were positively or negatively correlated with expansion inversely predicted contraction; their effects therefore cancelled out in determining net benefit in memory cell generation.

overall_design: We immunized 39 individuals aged 50 to 75 years with the life zoster vaccine Zostava, including 9 monozygotic twin pairs. We measured VZV-specific T cell frequencies by IFN-γ–specific ELISpot, and VZV-specific antibody titers by ELISA. Gene expression arrays were performed on whole blood of vaccinees before (n=28) and one (n=18) or three days (n=10) after vaccination.  Gene expression was correlated with vaccination-induced changes in the frequencies of VZV-specific T cells.

first: Qian

last: Qi

first: Sabine

last: Le Saux

first: Mary

last: Cavanagh


title: Gene expression signatures to predict T cell responses to zoster vaccination

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

overall_design: Refer to individual Series


title: Effect of anti-IL-15 administration on T cell and NK cell homeostasis in rhesus macaques (TEM)

status: Public on Sep 07 2016

city: Cleveland

first: AARTHI

last: TALLA

state: OH

address: 2103 Cornell Rd

institute: Case Western Reserve University School of Medicine

summary: Analysis of the effect of anti-IL-15 monoclonal antibody treatment on T cell and NK cell homeostasis in rhesus macaques. The hypothesis tested in the present study was that repeated administrations of a rhesusized anti-IL-15 monoclonal antibody would block IL-15 activity in vivo and result in changes to T and/or NK cell population dynamics that would reflect physiologic IL-15 function. The results provide important information on the specific role IL-15 plays in effector memory T cell and NK cell homeostasis, noting that effector memory T cells but not NK cells can be maintained in the absence of IL-15 signaling by the activity of other cytokines.

overall_design: Sort-purified CD8+ TEM  from PBMC, before and after treatment with IgG1 Ab and anti-IL15 Ab

first: Maren

middle: Q

last: DeGottardi

first: Afam

last: Okoye

first: Mukta

last: Vaidya

first: Aarthi

last: Talla

first: Rafick-Pierre

last: Sekaly

first: Louis

last: Picker


title: Effect of anti-IL-15 administration on T cell and NK cell homeostasis in rhesus macaques (TCM)

overall_design: Sort-purified CD8+ and CD4+ TCM from PBMC, before and after treatment with IgG1 Ab and anti-IL15 Ab

middle: J


title: Gene expression induced in HEK293 by treatment with the differentiating agents all-trans retinoic acid (tRA) and N6,2'-O-dibutyryl-cAMP (cAMP)

status: Public on Sep 06 2016

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

summary: This gene array analysis shows that the transcriptome of HEK293, representing low-differentiated human embryonic kidney cells, cultured in presence of tRA and cAMP differentiating agents, is consistent with a genetic program relevant to kidney development

overall_design: Comparison of HEK293 cells grown in standard contitions or in presence of differentiating agents. Cells were seeded in 10 cm dishes, cultured for 3 days either in complete medium or in medium supplemented with tRA and cAMP, harvested, and spun down before RNA isolation. Comparative analysis allowed us to identify genes transcriptionally by tRA/cAMP.

first: Antonio

last: Fiorino


title: Effect of anti-IL-15 administration on T cell and NK cell homeostasis in rhesus macaques

type: Expression profiling by high throughput sequencing


title: Gene expression profile for L1CAM knockdown in esophageal squamous carcinoma cell

status: Public on Sep 01 2016

city: Shantou

first: Jincheng

last: Guo

address: Xinling Road

department: Medical collage

institute: Shantou University

summary: The protein encoded by this gene is an axonal glycoprotein belonging to the immunoglobulin supergene family. The ectodomain, consisting of several immunoglobulin-like domains and fibronectin-like repeats (type III), is linked via a single transmembrane sequence to a conserved cytoplasmic domain. This cell adhesion molecule plays an important role in nervous system development, including neuronal migration and differentiation. Mutations in the gene cause X-linked neurological syndromes known as CRASH (corpus callosum hypoplasia, retardation, aphasia, spastic paraplegia and hydrocephalus). Alternative splicing of this gene results in multiple transcript variants, some of which include an alternate exon that is considered to be specific to neurons.

overall_design: shRNA sequences targeting L1CAM was ligated into the pGLV3/H1/GFP/+Puro Vector and transfected into ESCC cell line KYSE150 with an empty plasmid as a control. The mRNA expression profiles of L1CAM knockdown was analyzed by GeneChip® PrimeView™ Human Gene Expression Array (Affymetrix, USA). The knockdown of L1CAM was confirmed by QRT-PCR and Western blot. Total RNAs from L1CAM knockdown cells and control cells were extracted for GeneChip® PrimeView™ Human Gene Expression Array.

first: JIncheng

last: GUO

first: Enmin

last: Li

first: Liyan

last: Xu

first: Jianjun

last: Xie


title: Expression data of human cumulus cells treated with follicle stimulating hormone in the presence of absence of an insulin-like growth factor 1 inhibitor

city: Chicago

first: Carlos

middle: Oscar

last: Stocco

state: IL

address: 835 S Wolcot Ave

department: Physiology and Biophysics

institute: Univ Of Illinois at Chicago

summary:
Ovulatory dysfunction affects nearly 40% of women of reproductive age that are struggling with infertility. Ovulation is the culmination of a complex and long process during which most follicles undergo atresia instead of developing into preovulatory follicles. The rescue of follicles from atresia and their maturation towards ovulatory competence requires “a pas de deux” between endocrine and locally-produced factors. Unequivocally, the most crucial endocrine factor is follicle-stimulating hormone (FSH). Insulin-like growth factors (IGFs) are among the most important local factors and are an irreplaceable partner of FSH. Therefore, understanding the mechanisms involved in the regulation of granulosa cell (GC) differentiation by FSH and IGF in humans will contribute to improve infertility treatments. In this report, we characterize a novel experimental approach to study human GC differentiation using cumulus cells from patients undergoing in vitro fertilization (IVF). Our findings demonstrate that human cumulus cells from IVF patients respond to FSH with the expression of genes that are known to be markers of granulosa cell differentiation during follicle maturation from the preantral to the large antral stage. Moreover, these results demonstrate that a large number of FSH-regulated genes require IGF1R activity and suggest that several aspects of follicle growth are coordinately regulated by FSH and the IGF system in humans.
We used microarrays to detail the global effects of FSH on gene expression and to determine the effect that IGF1R inhibition has on FSH-induced stimulation.

overall_design: Human cumulus cells were plates in serum free media and treated with FSH in the presence of absence of AEW for 48h, before total RNA isolation.


title: Expression data from human normal liver cell line HL7702 treated with tributyltin

city: Ningbo

first: Jin

address: 818 Fenghua Road

institute: Ningbo University

summary:
Tributyltin (TBT) accumulates at higher levels in the liver than in any other organ, and it acts as a hepatotoxic agent. Most of the available studies on TBT have focused on observations at the cellular level, and studies at the level of genes and proteins have been limited; therefore, the information concerning possible mechanisms of TBT-induced adverse health effects remains scarce and inconclusive.
In the present study, we applied a toxicogenomic approach to investigate the effects of TBT on gene expression in the human normal liver cell line HL7702.

overall_design: The HL7702 cells were treated with 0 μM (C0), 2 μM(C1), 6 μM (C2) and 10 μM (C3) TBT for 2 h, and three biological replicates for each concentration.

first: Mi

last: Zhou

first: Mei

last: Feng


title: Expression data from hMSC-TERT4 cells after during osteoblast differentiation

city: Sydney

first: Natalie

last: Twine

address: High Street, Kensington

institute: University of New South Wales

summary: Differentiation of human skeletal stem cells (hMSC) into osteoblasts is regulated by a few well described transcription factors. Our study used clustering and gene expression data to identify a novel transcription factor. ZNF25, which we showed is involved in osteoblast differentiation.

overall_design: We used microarrays to study gene expression of hMSC-TERT4 cells after induction of osteoblast differentiation. Samples were taken at 0, 1, 7 and 13 days post induction of osteoblast differentiation.

first: Marc

last: Wilkins

first: Linda

last: Harkness

first: Moustapha

last: Kassem


title: Gene expression analysis of T cell subsets infiltrating lacrimal glands from the NOD mouse model of Sjögren's

city: Cambridge

first: MICHAEL

last: MINGUENEAU

address: 115 Broadway

department: Immunology

institute: Biogen

summary:
Despite being one of the most common rheumatologic diseases, there is still no disease-modifying drug for primary Sjögren’s syndrome (pSS). Advancing our knowledge of the target tissue has been limited by the low dimensionality of histology techniques and the small size of human salivary gland biopsies.
The goal of this study was to characterize CD4+ T cell subsets infiltrating the target tissue of the disease. We took advantage of a molecularly-validated mouse model of pSS (the NOD mouse model) and used cytometry techniques (flow and mass cytometry) in combination with transcriptional analyses. We identified three novel CD4+ T cell subsets that were not previously described in pSS pathogenesis and this GEO dataset reports the transcriptomic analysis of each of these three subsets: (1) effector Tregs (eTregs) expressing high levels of PD1 and ICOS as well as many immunoregulatory factors such as Il10, Areg, Fgl2, Itgb8; (2) Il21+ Th1 cells that also expressed high levels of PD1 and ICOS as well as osteopontin and shared striking transcriptional similarities with a pathogenic T follicular subset described in several lupus mouse models; (3) naïve PD1neg ICOSneg CD4+ T cells.

overall_design: All three T-cell subsets were purified from lacrimal gland (LG) cell suspensions of 16-week old male NOD mice by FACS cell sorting (>99% purity) using the following surface markers: TCRbeta, CD4, PD1, ICOS, CD73, CD200, and the DAPI as live/dead dye. The PD1negICOSneg population (naive) was isolated as DAPI-CD4+TCRb+PD1-ICOS-; the effector Treg (eTreg) population was isolated as DAPI-CD4+TCRb+PD1highICOShighCD73lowCD200low; the effector Tconv (eTconv) population was isolated as DAPI-CD4+TCRb+PD1highICOShighCD73lowCD200low;RNA was purified and QC’d before processing for gene expression analysis. Total CD4+ and CD8+ T cells from the spleen of the same mice as controls.

first: Scott

last: Haskett

first: Jian

last: Ding

first: Wei

last: Zhang

first: Alice

last: Thai

first: Patrick

last: Cullen

first: Shanqin

first: Britta

last: Petersen

first: Luke

last: Jandreski

first: Stefan

last: Hamann

first: Taylor

last: Reynolds

first: Norm

last: Allaire

first: Timothy

first: Michael

last: Mingueneau


title: GSK8814: a chemical probe fort he ATAD2 bromodomain

first: KA HING

last: CHE

state: Cambridgeshire

address: Tennis Court Road

department: Gurdon Institute

institute: University of Cambridge

summary: Differential gene expression analysis of LNCaP cells treated with GSK8814 and GSK8815

overall_design: Total RNA obtained from cells treated with GSK8814 and GSK8815 for 24 hours

first: Ka

last: Che

first: Paul

last: Bamborough

first: Rab

last: Prinjha

first: Samual

last: Robson

first: Chun-wa

last: Chung

first: Robert

last: Sheppard

first: Andrew

last: Bannister

first: Emmanuel

last: Demont

first: Richard

last: Upton

first: Tony

last: Kouzarides

first: Rebecca

middle: C

last: Furze

last: Watson

first: Hawa

last: Diallo

first: Clement

last: Douault

first: Paola

last: Grandi

first: Anne-Marie

last: Michon

first: Darren

last: Mitchell


title: The identified enhancer RNAs across human cell and tissue types

status: Public on May 31 2017

city: Beijing

first: Wenjie

last: Shu

address: Taiping Road 27

institute: Beijing Institute of Radiation Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: In order to identity enhancer RNA across human cell and tissue types, histone modifications and RNA-Seq data were used to calculate candidate enhancers and classify enhancer RNA

overall_design:
Identity enhancer regions based on H3k27ac, H3k4me3,H3k4me1 ChIP-Seq data across 50 different human tissues and cell lines, corresponding RNA-Seq data were used to detect enhancer RNA

This series includes data from 281 re-analyzed samples from GSE16256 (127), GSE16368 (69),  GSE17312 (44), GSE18927 (15) and GSE19465 (26).

first: W

first: F

last: Liu

first: C

last: Ren


title: Gene expression analysis of total B, CD4+ T and epithelial cells in lacrimal glands from the NOD mouse model of Sjogren's syndrome

first: MICHAEL

last: MINGUENEAU

summary:
Despite being one of the most common rheumatologic diseases, there is still no disease-modifying drug for primary Sjögren’s syndrome (pSS). Advancing our knowledge of the target tissue has been limited by the low dimensionality of histology techniques and the small size of human salivary gland biopsies.
The goal of this study was to characterize the gene expression profile of total B cells, CD4+ T cells and epithelial cells in the target tissue of the most commonly-used model of pSS (the NOD model of pSS characterized by severe dacryoadenitis developing in males between 8 and 16 weeks of age).

overall_design: All immune subsets were purified from lacrimal gland (LG) cell suspensions of 16-week old male NOD mice by FACS cell sorting (>99% purity) using the following surface markers: CD326, CD45, NKp46, CD11b, CD11c, B220, CD3, CD4 and DAPI as live/dead marker. Epithelial cells were isolated as CD45-CD326+ cells; CD4+ T cells were isolated as CD45+NKp46-CD11b-CD11c-B22-CD3+CD4+ cells; B cells were isolated as CD45+NKp46-CD11b-CD11c-B220+CD3- cells. RNA was purified and QC’d before processing for gene expression analysis. Splenic subsets were purified from 4-week old NOD mice as steady-state control immune cells to be compared with tissue-infiltrating subsets.

first: Jian

last: Ding

first: Wei

last: Zhang

first: Scott

last: Haskett

first: Alex

last: Pellerin

first: Shanqin

last: Xu

first: Britta

last: Petersen

first: Luke

last: Jandreski

first: Stefan

last: Hamann

first: Taylor

middle: L

last: Reynolds

first: Timothy

last: Zheng

first: Michael

last: Mingueneau


title: Gene expression profile of human fibroblasts stimulated by breast cancer cell lines secretome

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

institute: IRCCS Ospedale San Raffaele

summary: Normal human dermal fibroblasts (NHDF) were treated under serum-free conditions with cell culture media conditioned by breast cancer cell lines (SkBr3, MDA-MB-468, T47D) for 72 hours and subjected to gene expression profiling with Illumina platform.

overall_design: NHDF treatments with c.m. was performed on independent biological triplicates and RNA derived from each replicate was separately extracted. Three hundred ng of total RNA were used for gene expression profiling by microarray using Illumina HumanHT-12 v4 Expression BeadChips.

first: Giuseppe

last: Merlino


title: Gene expression array analysis of tumor-propagating cell populations in human osteosarcoma

city: Toronto

first: Yuning

middle: Jackie

last: Tang

state: Ontario

address: 686 Bay Street

department: Program in Developmental Biology

institute: Hospital for Sick Children

summary: Gene expression profiling of side population cells (SP) and CD146+ cells from primary human osteosarcoma.  We aimed to identify genes that differentially regulated between the tumor propagating cells and the bulk tumor cells.

overall_design: Total RNA was isolated from SP, Non-SP(NSP), CD146+ and CD146- cells.  The RNA is converted to cDNA using Nugen Ovation Kit (Nugen, CA, USA) and subjected to Illumina HT-12 array.

first: Qingixa

last: Wei


title: PKCδ regulates the transformed growth of K-ras dependent lung cancer cells through regulation of integrin αVβ3 expression

city: Salt Lake City

first: Aik Choon

last: Tan

address: 2000 Circle of Hope

department: Oncological Sciences

institute: Huntsman Cancer Institute

summary: To explore how PKCδ regulates tumorigenesis, we performed mRNA expression analysis of four KRAS mutant NSCLC cell lines that stably express scrambled shRNA or PKCδ targeted shRNA

overall_design: Four human lung cancer cell lines (A549, H441, H460 and H2009) with scrambled and PKC-delta knock down (shRNA), in triplicate.

first: Aik

first: Mary

last: Reyland


title: HIP1 mediates prostate carcinogenesis and progression through STAT3 signalling

first: Roslin

last: Russell

address: Robinson Way

institute: Cambridge Research Institute, Cancer Research UK

summary: Overexpression of HIP1 has been associated with fibroblast transformation, increasing grades of prostate cancer (CaP), and biochemical relapse. Here we demonstrate cellular transformation and phenotypic effects of HIP1 overexpression in a benign prostate epithelial cell line to be dependent on STAT3 signalling. In vivo xenografts confirmed the cellular transformation phenotype and revealed serum GDF15 to be a marker of CaP in our model. STAT3 signalling was in part, dependent on HIP1 expression, in a highly invasive, metastatic and androgen receptor (AR) negative DU145 cell line, Immunohistochemistry of a large prostate tissue microarray (TMA) revealed increased HIP1 and reciprocal GDF15 expression to adversely affect outcome warranting further studies to assess HIP1 and GDF15 as biomarkers for detection and prognostication of CaP.

overall_design: Gene expression of PNT1a cells stably overexpressing HIP1 protein and LNCaP cells transiently overexpressing HIP1 protein were compared with their respective empty vector control cell lines using the illumina expression array platform. There were six biological replicates for each of the four different groups.

first: Roheet

last: Rao

first: Ian

last: Mills

first: David

last: Neal


title: Multi-scale genomic, transcriptomic and proteomic analysis of colorectal cancer cell lines to identify novel biomarkers (BeadChip)

status: Public on Aug 31 2016

city: Edinburgh

first: Romina

last: Briffa

state: Lothian

address: Crewe Road South

department: Division of Pathology

institute: University of Edinburgh

summary: Selecting colorectal cancer (CRC) patients likely to respond to therapy remains a clinical challenge. The objectives of this study were to establish which genes were differentially expressed with respect to treatment sensitivity and relate this to copy number in a panel of 15 CRC cell lines. Copy number variations of the identified genes were assessed in a cohort of colorectal cancers. IC50’s were measured for 5-fluorouracil, oxaliplatin, and BEZ-235, a PI3K/mTOR inhibitor. Cell lines were profiled using array comparative genomic hybridisation, Illumina gene expression analysis, reverse phase protein arrays, and targeted sequencing of KRAS hotspot mutations.

overall_design: Three sets of RNA samples were prepared for Illumina® Whole Genome Gene Expression Profiling, where 48,804 transcripts per sample were generated.  The three sets consisted of two sets of biological replicates and one set of technical replicates.  All the RNA samples were diluted to a concentration of 500ng/11µl.  The Illumina® TotalPrepTM RNA Amplification Kit (Ambion®, cat. no. AMIL1791) was used to generate biotinylated, amplified RNA for hybridization with the Illumina® Human HT-12 v4.0 BeadChip.

first: Louise

last: Evenden

first: Lee

last: Murphy

first: Arran

last: Turnbull


title: Elucidating the molecular mechanisms for CAT-SKL drug effects on breast cancer cells

city: Detroit

first: Aliccia

last: Bollig-Fischer

address: 4100 John R

department: Oncology

institute: Karmanos Cancer Institute & Wayne State University

summary:
Time-course analysis was done to measure antioxidant CAT-SKL drug treatment effects on whole genome expression in a breast cancer cell line.
total RNA was isolated from parallel cell cultures, starting at the 0 hour (immediately before 1uM CAT-SKL treatment) and every 6 hours after treatment up to 30 hours

overall_design: The MDA-MB-468 breast cancer cell line model was used in this study of logitudinal whole genome mRNA expression data. Expression data were collected by microarray analysis using Illumina HT12v3 arrays.


title: Defining the role of ZEB1 in the pathogenesis of lung cancer

city: Dallas

first: Luc

last: Girard

state: TX

address: 5323 Harry Hines Blvd

department: Hamon Center for Therapeutic Oncology Research

institute: UT Southwestern Medical Center

summary: Using an in vitro model for malignant transformation of human bronchial epithelial cells (HBECs) we have found epithelial-to-mesenchymal transition (EMT) and expression of the EMT-transcription factor ZEB1 are early and critical events.  Specifically, we found preexisting oncogenic mutations in TP53 and KRAS were required for HBECs to engage EMT machinery in response to microenvironmental (serum/TGFβ) or specific oncogenetic (MYC) EMT-inducing factors, which induce EMT through distinct TGFβ-dependent and vitamin D receptor (VDR)-dependent pathways, respectively, with both requiring ZEB1.  Functional studies demonstrated ZEB1 causally promotes the malignant progression of HBECs and tumorigenicity of NSCLC and small cell lung cancer (SCLC) lines.  Mechanistically ZEB1 directly represses ESRP1 leading to increased mesenchymal splicing of CD44, which drives a switch to CD44hi status and defines a highly transformed subpopulation.  This was supported by finding ZEB1 is expressed in early-stage primary non-small cell lung cancers (NSCLC), as early as stage IB tumors, and its expression correlates with TNM stage.  We conclude that: ZEB1-induced EMT and associated ESRP1 and CD44 molecular changes are important biomarkers for lung cancer pathogenesis; TGFβ and VDR are EMT chemoprevention targets; and as such, ZEB1 represents an important therapeutic target in NSCLC and SCLC.

overall_design: Human bronchial epithelial cells (HBECs) immortalized with cdk4 and hTERT and subsequently transformed with various oncogenetic manipulations (p53 knockdown, KrasV12, cMYC and ZEB1 over-expression) and/or growth conditions (10%FBS) were profiled on Illumina HumanHT-12 V4.0 expression beadchips. All cell lines were grown in KSFM (defined, serum-free medium) except HBEC3-KTRL53(R10), which was grown in RPMI1640 with 10% FBS.

first: Jill

middle: E

last: Larsen

first: John

last: Minna


title: Diagnosis of childhood bacterial and viral infection using host RNA expression [validation set]

status: Public on Aug 29 2016

city: London

first: Michael

last: Levin

address: South Kensington Campus

department: Paediatrics

institute: Imperial College London

summary: Genome-wide analysis of transcriptional profiles in children <17 years of age with bacterial or viral infections or with clinical features suggestive of infection.

overall_design: Patients were recruited at or after presentation to hospital. Main inclusion criteria were presence of illness of sufficient severity to warrant blood tests for clinical reasons, in child aged <17 years. Blood was collected into PAX gene tubes (PreAnalytiX). Total RNA integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA). Labeled cRNA was hybridized to Illumina Human HT-12 V3 Beadchips (Validation set). Numbers of arrays analysed in the validation set were as follows: Definite Bacterial infection (n=23), Definite Viral infection (n=28), Probable Bacterial infection (n=17), Probable Viral infection (n=7), infections of uncertain bacterial or viral aetiology (n=55), Healthy controls (n=16).


title: Aurora kinase inhibition triggers senescence in human melanoma cells

city: Philadelphia

first: Xiaowei

last: Xu

state: PA

address: 3400 Spruce st

institute: University of Pennsylvania

summary: Phenotypically, there is a heterogeneous response of cancer cells to chemotherapy or targeted therapy. While therapeutically much attention is focused on cell death, there is growing evidence suggesting that a subpopulation of cancer cells undergo therapy-induced senescence. Depending on the therapy, dose and timing, senescence may be a dominant phenotype over cell death. An integrated FACS approach identified two types of therapy-induced senescence in human melanoma cells, irreversible senescence induced by Aurora kinase inhibition vs. transient senescence induced by B-RAF kinase inhibition. Autophagy and ER stress response precede and are required for therapy-induced senescence in cancer cells, mirroring their functions in normal cells undergoing oncogene-induced senescence. Importantly, autophagy serves a survival pathway for senescent cancer cells. Antagonizing autophagy converts therapy-induced senescence into cell death but paradoxically promotes cell proliferation or quiescence. Our work calls for a rationale-based design of combination therapy for cancer treatment that should lead to a greater synergy.

overall_design: There are three or four replicates per treatment per time point.

first: Gao

last: Zhang

first: Wei

last: Zhi


title: Normal stroma suppresses cancer cell proliferation via mechanosensitive regulation of JMJD1a-mediated transcription [array]

city: Turku

first: Johanna

last: Ivaska

address: Tykistökatu 6

country: Finland

institute: University of Turku

summary:
Matrix induced effects on gene expression in HeLa and MDA-MB-231 cells
Tissue homeostasis is dependent on the spatially controlled localization of specific cell types and the correct composition of the extracellular stroma. While the role of the cancer stroma in tumor progression has been well characterized, the specific contribution of the matrix itself is unknown. Furthermore, the mechanisms enabling normal – not cancer – stroma to provide tumor suppressive signals and act as an anti-tumorigenic barrier are poorly understood. Here, we show that extracellular matrix (ECM) generated by normal fibroblasts (NFs) is softer than CAF-matrix and it is the physical and structural features of NF-generated matrix that regulate cancer cell proliferation . We find that normal stromal ECM triggers downregulation and nuclear exit of the histone demethylase JMJD1a resulting in the epigenetic growth restriction of carcinoma cells. Interestingly, JMJD1a positively regulates transcription of many target genes, including YAP/TAZ, and thus therefore gene expression in stiffness-dependent manner. Thus normal stromal restricts cancer cell proliferation through JMJD1a-dependent modulation of gene expression.

overall_design: gene expression profiles of HeLa or MDA-MB-231 cells grown on plastic, or cell derived matrix (ECM)

first: Riina

last: Kaukonen


title: Diagnosis of childhood bacterial and viral infection using host RNA expression - Inflammatory validation cohort

overall_design: Patients were recruited at or after presentation to hospital. Main inclusion criteria were presence of illness of sufficient severity to warrant blood tests for clinical reasons, in child aged <17 years. Blood was collected into PAX gene tubes (PreAnalytiX). Total RNA integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA). Labeled cRNA was hybridized to Illumina Human HT-12 v4 Beadchips. Numbers of arrays analysed were as follows: HSP (n=18), JIA (n=30)


title: Diagnosis of childhood bacterial and viral infection using host RNA expression [Discovery set]

overall_design: Patients were recruited at or after presentation to hospital. Main inclusion criteria were presence of illness of sufficient severity to warrant blood tests for clinical reasons, in child aged <17 years. Blood was collected into PAX gene tubes (PreAnalytiX). Total RNA integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA). Labeled cRNA was hybridized to Illumina Human HT-12 v4 Beadchips (Discovery set) or Illumina Human HT-12 V3 Beadchips (Validation set). Numbers of arrays analysed were as follows: Definite Bacterial infection (n=52), Definite Viral infection (n=92), Probable Bacterial infection (n=42), Probable Viral infection (n=5), infections of uncertain bacterial or viral aetiology (n=49), Healthy controls (n=52).


title: Implication of Long noncoding RNAs in the endothelial cell response to hypoxia II.

status: Public on Aug 25 2016

first: Fabio

last: Martelli

address: via morandi 30

institute: IRCCS-Policlinico San Donato

summary:
Long noncoding RNAs (lncRNAs) are non-protein coding RNAs regulating gene expression. Although for some lncRNAs a relevant role in hypoxic endothelium has been shown, the regulation and function of lncRNAs is still largely unknown in the vascular physio-pathology.
Taking advantage of next-generation sequencing techniques, transcriptomic changes induced by endothelial cell exposure to hypoxia were investigated. Paired-end sequencing of polyadenylated RNA derived from human umbilical vein endothelial cells (HUVECs) exposed to 1% O2 or normoxia was performed. Bioinformatics analysis identified ≈ 2000 differentially expressed genes, including 122 lncRNAs. Extensive validation was performed by both microarray and qPCR. Among the validated lncRNAs, H19, MIR210HG, MEG9, MALAT1 and MIR22HG were also induced in a mouse model of hindlimb ischemia. To test the functional relevance of lncRNAs in endothelial cells, knockdown of H19 expression was performed. H19 inhibition decreased HUVEC growth, inducing their accumulation in G1 phase of the cell cycle; accordingly, p21 (CDKN1A) expression was increased. Additionally, H19 knockdown also diminished HUVEC ability to form capillary like structures when plated on matrigel.
In conclusion, a high-confidence signature of lncRNAs modulated by hypoxia in HUVEC was identified and a significant impact of H19 lncRNA was shown.

overall_design: HUVEC were exposed to normoxia or 24 and 48 hours of hypoxia (1% oxygen). For each time point and condition was performed in duplicate was produced Total RNAs of six samples were extracted and analysed.

first: Christine

last: Voellenkle

first: Pasquale

last: Fasanaro


title: Implication of Long noncoding RNAs in the endothelial cell response to hypoxia I.

overall_design: For H19 knock-down, 50 nM of antisense LNA™ GapmeRs customer-designed for H19 or Negative control A (Exiqon) were transfected by siRNA transfection reagent (Santa Cruz Biotechnology) in 40% confluent HAOEC according to the manufacturer’s manual.

first: Simona

last: Greco

first: Jose

last: Garcia-Manteiga


title: Diagnosis of childhood bacterial and viral infection using host RNA expression

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

overall_design: Refer to individual Series