title: Patterns of transcriptional response to 1,25-dihydroxyvitamin D3 and bacterial lipopolysaccharide in primary human monocytes

first: Silvia

last: Kariuki

state: IL

summary: This study examines patterns of genome-wide transcriptional response to the active form of vitamin D, 1,25-dihyroxyvitamin D3 (1,25D), and the bacterial lipopolysaccharide (LPS) in primary human monocytes, to better understand pathways underlying the immunomodulatory role of 1,25D.

overall_design: Total RNA extraced from monocytes from 20 healthy individuals of African-African and European-American ancestry treated with 1,25D alone or in the presence of LPS for 24 hours.

first: John

last: Blischak

first: Shigeki

last: Nakagome

middle: B

last: Witonsky

first: Anna

last: Di Rienzo


title: Derivation, characterization, and neuronal differentiation of integration-free induced pluripotent stem cell lines from Parkinsons disease patients carrying SNCA, LRRK2, PARK2, and GBA mutations

status: Public on Feb 23 2016

city: novato

first: Ying

last: Pei

state: ca

address: 8001 redwood blvd

country: USA

institute: Buck Institute

summary: Analysis of whole genome expression in control and patients with Parkinsons disease iPSC lines. The hypothesis tested in present study was that deficient GBA, SNCA, LRRK2 and PARKIN expression can be used for disease modeling by their affects on multiple pathways. These results provide information on relationship between PD genes and mitochondria related gene expression.

overall_design: Total RNA obtained from patient iPSC line compare to control iPSC line

first: Xianmin

last: Zeng


title: Investigating the DNA damage response of different cell types in the normal human breast

status: Public on Feb 07 2016

city: Herston

first: Rebecca

last: Johnston

state: QLD

address: Building 71/918, Royal Brisbane & Women's Hospital Campus

department: Molecular and Cellular Pathology

country: Australia

institute: University of Queensland Centre for Clinical Research

summary: Growing interest in the cellular origins of different breast cancer subtypes has prompted investigations into the subpopulations of the normal breast epithelia and their differentiation hierarchy. Several groups have demonstrated a likely luminal-progenitor cell origin for basal-like breast cancer. However, the molecular and cellular mechanisms underlying why one breast cell type might be more susceptible to transformation are yet to be elucidated. To observe the molecular differences in the different cell subpopulation response to ionizing radiation (IR), we performed gene expression profiling of MUC1+-sorted and CD10+-sorted primary human mammary epithelial cell cultures. Transcriptional response was measured at 2 and 24 hr after treatment with 2 and 5 Gy IR using Illumina HumanHT-12 v4 Expression Beadchips. The complete sample cohort included time-point matched untreated (0 Gy) controls in a total of 5 individual patients. Our analyses indicated several cell-type specific differences in response to IR.

overall_design: RNA was extracted from MUC1+-sorted and CD10+-sorted primary human mammary epithelial cell cultures at 2 and 24 hr after treatment with 0, 2, and 5 Gy ionizing radiation  (12 samples per patient), in a total of 5 individual patients.

middle: L

first: Leesa

last: Wockner

first: Amy

middle: E

last: McCart Reed

first: Adrian

last: Wiegmans

first: Georgia

last: Chenevix-Trench

first: K

last: Khanna

first: Sunil

middle: R

last: Lakhani

first: Chanel

last: Smart


title: HOXA5 depletion in MCF10A cells

status: Public on Feb 01 2016

city: Baltimore

first: Saraswati

last: Sukumar

state: MD

address: 1650 Orleans St, CRB 1, Rm 132

department: Breast Cancer Program

institute: Johns Hopkins School of Medicine

summary: Microarray analysis of gene expression in MCF10A cells following HOXA5 depletion.

overall_design: Total RNA was isolated using RNeasy mini kit (#74104, Qiagen) after stable transduction with either scramble or target shRNA.

first: Wei

middle: W

last: Teo

first: Soonweng

last: Cho


title: Identification of JMJD3 target genes

status: Public on Feb 03 2016

city: DaeJeon

first: Mi Young

last: Kim

address: Biological science

country: South Korea

institute: KAIST

summary:
Purpose:To indentify downtream effectors of JMJD3, we performed microarray profiling in vector- or JMJD3-expressing A375-LM3 and those in freshly isolated melanoma cells from tumors formed by aforementioned cell lines
Results: we identifed 31 genes whose expression increased in WT JMJD3 expression cells  at least by over 1.5-fold.

overall_design: RNA profiling of JMJD3 expressing A375-LM3 and dissociated cells was analyzed by genome-wide microarray using Illuminabread chip TotalPrep RNA amplification Kit. Biotin labeled cDNA are hybridized with Illumina HumanHT-12 V4.0 Beadchips using Illumina standard protocol. The beadchips are scanned using Illumina HiScan scanner. The data is analyzed using Illumina GenomeStudio software (Framwork version: v2011.1, Gene Expression module version: 1.9.0).

first: Woo-Yong

last: Park

first: Mi-Young


title: Gene expression data from induced Pluripotent Stem cells from Parkinson's Disease patients harbouring G2019S mutations in the LRRK2 gene

status: Public on Feb 09 2016

city: Oxford

first: Sally

middle: A

last: Cowley

address: South Parks Road

department: Sir William Dunn School of Pathology

country: United Kingdom

institute: University of Oxford

summary:
We have generated human induced Pluripotent Stem cells (hiPSc) using Retroviral virus-mediated delivery of reprogramming factors. hiPSc lines have been screened using SNP array to assess chromosomal stability (alongside the fibroblast lines from which they derived), and validation of the pluripotency of the hiPSc lines is provided by Pluritest assessment of transcriptome datasets, prior to differentiation and downstream assays.
Gene expression profiling in patient-derived dopamine neurons identifies candidate therapeutic molecules in Parkinson’s disease.

overall_design: human iPSc lines were derived from human dermal fibroblasts from 3 PD LRRK2 G2019S patients and 3 control donors. SNP and gene expression datasets were generated from patient and control lines. Note that iPS OX1-19 and iPS-NHDF-1, also used in the current study, have been published previously so datasets are not given here [GSE45472 PMID:23951090 ;  GSE43904 PMID:24586273]

first: Cynthia

last: Sandor

first: Paul

last: Robertson

first: Charmaine

last: Lang

first: Andreas

last: Heger

first: Heather

last: Booth

first: Jane

last: Vowles

first: Lorna

last: Witty

first: Rory

last: Bowden

first: Michele

last: Hu

first: Richard

last: Wade-Martins

first: Caleb

last: Webber


title: Expression data from IMQ-induced psoriasis-like skin inflammation in miR-146a-/- and C57BL6J mice

status: Public on Feb 19 2016

city: Stockholm

first: Ankit

last: Srivastava

state: - Select a State -

address: CMM L8:02

department: Department of Medicine

country: Sweden

institute: Karolinska Institutet

summary:
miR-146a acts as a negative feedback regulator of inflammation. To investigate the role of miR-146a  in psoriasis  psoriasiform skin inflammation was indeuced in Mir-146a-/- and  wild type mice (C57BL6J) by topical applciation of imiquimod (IMQ)-cream (Aldara).
Gene expression profiling (Affymetrix) was used to identify transcriptomic changes associated with psoriasis-like skin inflammation in wild type vs. miR-146a -/-mice.

overall_design: A daily topical dose of 31.25 mg of Aldara cream (5% IMQ) was applied on the right ear of miR-146a -/- and C57BL/6 mice on three consecutive days to induce psorisis-like skin inflammation. Mice were sacrificed at day 4. Ear flaps were collected for total RNA extraction and hybridization on Affymatrix GeneTitan plate format Gene ST 2.1 (mouse).

first: Enikö

last: Sonkoly

first: Andor

last: Pivarcsi


title: Expression data from glioblastoma stem cells

city: duarte

first: LU

last: YANG

address: 1500 duarte rd

institute: city of hope

summary:
TLX (NR2E1), as an orphan nuclear receptor, plays a critical role in growth, self-renewal, and tumorigenesis of glioblastoma stem cells.
We used microarrays to investigate the global gene expression regulated by TLX and identified downstream targets of TLX in glioblastoma stem cells. We further investigated the global gene expression regulated by TET3, a downstream target of TLX, to identified downstream targets of TLX-TET3 axis in glioblastoma stem cells.

overall_design: Glioblastoma stem cells were treated with lentivurs expressing constrol shRNA or target (TLX or TET3) shRNA to knockdown the expression of TLX or TET3. RNAs were extracted and hybridized on Affymetrix microarrays.

first: Q

last: Cui

first: S

last: Yang

first: Y

last: Shi

first: L

first: C

last: Warden

first: X

last: Wu


title: Regulation of gene expression by the TSPO ligand PK 11195

status: Public on Feb 18 2016

city: Haifa

first: nasra

middle: mohamed

last: yasin

address: Bat Galim haifa- rappaport

department: neuropharmacology

country: Israel

institute: technion

summary: We hypothesized that the potential ability of the 18 kDa mitochondrial translocator protein (TSPO) to regulate gene expression may underlie its numerous reported functions, ranging from mitochondrial activity till mental disorders. Therefore, we applied microarray analysis of gene expression to U118MG glioblastoma cells. Within 1 hr the TSPO ligand PK 11195 induced changes in expression of immediate early genes and transcription factors. After 24 hrs primarily gene expression for enzymes and other proteins is changed.  The associated gene products are known to affect various cellular functions: programmed cell death, cell cycle, viability, proliferation, migration, differentiation, development, tumorigenesis, and inflammatory / immune responses. Our microscopic studies showed intense TSPO mitochondrial labeling but no TSPO signal in the cell nuclei. Thus, it appears that the TSPO is part of the retrograde mitochondrial-nuclear signaling pathway for modulation of gene expression and thereby may exert its numerous effects on cell function, phenotype, and disease.

overall_design: U118MG cells (1.255 × 106) were seeded in Petri dishes (i.e. 28.5 × 103 cells / cm2) and allowed to proliferate for 3 days in full medium. Experiments for gene expression assayed with microarray typically consisted of three experimental groups and a vehicle control group (n = 3 for each group). Serum deprived medium was applied for 24 hrs, in the experimental groups ending with the inclusion a choice of various PK 11195 exposures i.e. either 1 hr, 3 hrs, or 24 hrs. Exposure to PK 11195 implies serum deprived medium with 1% alcohol (vehicle) and PK 11195 (25 µM final concentration) for the required time period. 25 µM of PK 11195 is the optimal concentration for these types of experiments with U118MG cells (Kugler et al., 2008). The cells were collected by trypsinization, washed by centrifugation in phosphate buffered saline (PBS) (400 × g, 5 min), and lysed [RLT lysis buffer provided with the RNeasy Mini Kit diluted with β-mercaptoethanol (1 : 100)], according to the manufacturer's instructions. Lysates were stored at -70oC.

first: N

last: Yasin

last: Veenman

first: M

last: Gavish


title: Derivation of Human Naïve Pluripotent Stem Cells by Activation of YAP

city: London

first: Michelle

last: Percharde

address: Du Cane Road

department: Imperial College London

institute: MRC Laboratory of Medical Sciences

summary:
Expression profiling of Naïve and Primed hESCs using Illumina HT-12 v.4 expression BeadChip
We report that over-expression of the transcription factor YAP in male and female human ESCs and iPSCs promotes the generation of naïve PSCs. YAP-induced naïve PSCs have a naïve-specific dome-like colony morphology, rapid clonal growth rate for more than 70 passages, normal karyotype, expression of pluripotency markers and ability to form teratomas. Lysophosphatidic acid (LPA) can substitute for YAP to generated transgene-free human naïve PSCs. We performed microarray analyses on hESCs and hIPSCs in primed and naïve ESC media and show that YAP overexpressing cells in naïve media (Ying et al 2008, Ludwig et al 2006, Theunnissen 2014) display a distinct naïve-like transcriptional profile and other hallmarks of the naïve state. These results uncover an unexpected role for YAP in the transition to the human naïve state, and provide a platform in which to further dissect this transition and probe early human embryology.

overall_design: Six primed and six naïve human ESCs (hESCs) were profiled in microarray experiments. Primed samples consist of H1 and H9 hESCs and IMR-90 iPSCs with or without overexpression of YAP where indicated, in standard primed hESC conditions. Naïve samples consist of YAP overexpressing cell lines that were profiled after conversion to the naïve state (mTeSR or N2B27 medium where indicated). Two cell lines, H9 ESCs, and WIBR ESCs (Theunissen et al 2014) were also generated in mTeSR naïve conditions without YAP overexpression, when using the YAP activator, Lysophosphatidic acid (LPA) - (“H9 mTeSR+2iFL+LPA naïve” and “WIBR3 mTeSR+2iFL+LPA naïve”). RNA samples were taken from the described cell lines and used in microarray experiments.

first: Han

last: Qin

first: Miguel

last: Ramalho-Santos


title: Impact of influenza A on human plasmacytoid dendritic cells (pDC) gene expression

city: Dallas

middle: Ann

last: Gill

address: 5323 Harry Hines Blvd

department: Pediatrics

institute: University of Texas Southwestern Medical Center

summary: Over 2600 genes were differentially expressed in pDCs exposed to influenza A compared with the controls (no virus). Multiple functional group clusters of genes were impacted, including those involving antiviral responses and also metabolism, such as the glycolysis, oxidative phosphorylation, glucose metabolic process, and positive regulation of macromolecule biosynthesis clusters.

overall_design: Blood pDCs were purified from 5 human donors, exposed ex vivo for 8 h to either influenza A or no virus, harvested, and RNA was extracted for subsequent DNA microarray analysis.

first: Gagan

last: Bajwa


title: Inhibition of class I histone deacetylases 1 and 2 promotes urothelial carcinoma cell death by various mechanisms (HDAC siRNA knockdown)

status: Public on Jan 31 2016

city: Duesseldorf

first: Karl

last: Koehrer

address: Universitaetsstr. 1

department: BMFZ

country: Germany

institute: University of Duesseldorf

summary: Class I histone deacetylases HDAC1 and HDAC2 contribute to cell proliferation and are commonly upregulated in urothelial carcinoma (UC). To evaluate whether specific inhibition of HDAC1 and HDAC2 might serve as an appropriate therapy of UC we applied specific siRNA mediated double knockdown of HDAC1 and HDAC2 in the UCCs VM-CUB1 and UM-UC-3. HDAC1/2 double knockdown  significantly reduced proliferation and clonogenicity of UC cells.

overall_design: For differential gene expression analyses independently replicated high quality RNA preparations from VM-CUB1 and UM-UC-3 cells, transfected with HDAC1 and HDAC2 siRNA (72 h), were compared to irrelevant (non-targeting) siRNA control cells.

last: Pinkerneil

middle: J

last: Hoffmann

first: R

last: Deenen

first: K

last: Köhrer

first: T

last: Arent

first: W

last: Schulz

first: G

last: Niegisch


title: miR-126 governs human leukemia stem cell quiescence and therapeutic resistance [Illumina]

status: Public on Feb 02 2016

city: Toronto

first: John

last: Dick

address: 101 College St. Toronto

country: Canada

institute: Ontario Cancer Institute

summary: In acute myeloid leukemia (AML), leukemia stem cells (LSCs) play a central role in disease progression and recurrence due to their intrinsic capacity for self-renewal and chemotherapy resistance. Whereas epigenetic regulation balances normal blood stem cell self-renewal and fate decisions, mutation and dysregulation of epigenetic modifiers are now considered fundamental to leukemia initiation and progression. Alterations in miRNA function represent a non-canonical epigenetic mechanism influencing malignant hematopoiesis; however, the function of miRNA in LSC remains undetermined. Here we show that miRNA profiling of fractionated AML populations defines an LSC-specific signature that is highly predictive of patient survival. Gain-of-function genetic analysis demonstrated that miR-126 restrained cell cycle progression, prevented LSC differentiation, and increased LSC self-renewal. miR-126 promoted chemo-resistance, preserving LSC quiescence in part through suppression of the G0-to-G1 gatekeeper, CDK3. Thus, in AML, miRNAs influence patient outcome through post-transcriptional regulation of stemness programs in LSC.

overall_design: Total RNA was extracted from 8227 cells and treated with miR-126 sponge or miR-126-containing viral particles (and corresponding controls).

first: Eric

last: Lechman

first: Peter

last: van Galen

first: Veronique

last: Voisin


title: Developing a Gene Expression Signature For T Cells Resident in Human Skin

status: Public on Jan 29 2016

city: Melbourne

first: Jane

last: Li

state: Victoria

address: The Peter Doherty Institute of Infection and Immunity

department: Department of Microbiology and Immunology

institute: The University of Melbourne

summary: Human skin contains various populations of memory T cells in permanent residence and in transit. The most well characterized subset of resident memory T cell is the CD8+ CD103+ T cell. In order to investigate the remaining subsets, we isolated skin-tropic helper T cells, T regulatory cells, and CD8+ CD103- T cells from skin and from blood by fluorescence activated cell sorting. We extracted RNA and performed a microarray analysis to compare the transcriptional profile of these groups. We found that despite expressing the same marker for skin tropism, the T cells of skin origin were significantly different from those from blood.

overall_design: Total RNA obtained from CLA+ Tregulatory cells, CLA+ helper T cells, and CLA+ CD8+ CD103- T cells isolated from human skin compared to CLA+ Tregulatory cells, CLA+ memory helper T cells, and CLA+ memory CD8+ T cells from human blood. 5 replicates of each; each replicate contains pooled cells from 3 subjects; total 15 subjects.

first: Moshe

last: Olshansky

first: Joel

middle: Z

last: Ma

first: Francis

last: Carbone


title: Modeling the combined effect of RNA-binding proteins and microRNAs in post-transcriptional regulation

status: Public on Jan 30 2016

city: Ankara

first: Saber

last: HafezQorani

state: Ankara

address: Bioinformatics Lab, Informatics Institute, Middle East Technical University, Üniversiteler Mah. Dumlupınar Blv. No:1, 06800 Çankaya Ankara/TURKEY

department: Health Informatics

country: Turkey

institute: Middle East Technical University

summary: Recent studies show that RNA-binding proteins (RBPs) and microRNAs (miRNAs) function in coordination with each other to control post-transcriptional regulation (PTR). Despite this, the majority of research to date has focused on the regulatory effect of individual RBPs or miRNAs. Here, we mapped both RBP- and miRNA-binding sites on human 3'UTRs and utilized this collection to better understand PTR. We show that the transcripts that lack competition for HuR binding are destabilized more after HuR depletion. We also confirm this finding for PUM1(2) by measuring genome-wide expression changes following the knockdown of PUM1(2) in HEK293 cells. Next, to find potential cooperative interactions, we identified the pairs of factors whose sites co-localize more often than expected by random chance. Upon examining these results for PUM1(2), we found that transcripts where the sites of PUM1(2) and its interacting miRNA form a stem-loop are more stabilized upon PUM1(2) depletion. Finally, using dinucleotide frequency and counts of regulatory sites as features in a regression model, we achieved an AU-ROC of 0.86 in predicting mRNA half-life in BEAS-2B cells. Altogether, our results suggest that future studies of PTR must consider the combined effects of RBPs and miRNAs, as well as their interactions.

overall_design: HEK293T cells were maintained at 37⁰C at 5% CO2 in Dulbecco's Modified Eagle's Medium (DMEM), high glucose (4500mg/L), supplemented with Penicillin (100units/ml), Streptomycin (100μg/ml), Glutamine (2mM) and 10% heat-inactivated fetal calf serum. Trypsin-EDTA solution was used to dissociate the cells to subcultivate the cells in a 1:8 ratio, every 3-4 days (all materials were purchased from Gibco, Life Technologies). siRNA pools for Pumilio 1 and Pumilio 2 (siRNAs from Dharmacon/GE) were mixed and diluted to a final concentration of 50nM and transfected overnight in a 24-wells culture plate. Cells were incubated for 48 hours, thereafter lysed in Trizol Reagent (Life Technologies). RNA was isolated using the RNeasy Mini Kit (Qiagen, cat no: 74104) according to the manufacturer's instructions. An on-column DNA digestion was also performed to eliminate any genomic DNA contamination (Qiagen cat no: 79254). RNA concentration and purity were assessed using a NanoDrop1000 (NanoDrop Products). RNA integrity number (RIN) was assessed using a BioAnalyzer (Agilent Technologies), all RNA's used had a RIN value of 10. Arrays were performed by AROS Applied Biotechnology A/S (Aarhus, Denmark) according to the manufacturer's instructions. Arrays were scanned using the iScan system (Illumina, Inc.), and the fluorescence intensities were analyzed and annotated using GenomeStudio software (Illumina, Inc.)

first: Atefeh

last: Lafzi

first: Ruben

middle: G

last: Bruin

middle: P

last: Veer

first: Anton

last: Zonneveld

first: Yeşim

last: Aydın Son

first: Hilal

last: Kazan


title: Genome-wide analysis of gene expression in Normal Cervical mucosa, Cervical intraepithelial neoplasia and Cervical squamous cell carcinoma

city: Kharagpur

first: Jyotirmoy

last: Chatterjee

state: West Bengal

address: Near Vikramshila complex

department: School of Medical Science and Technology

country: India

institute: Indian Institute of Technology Kharagpur

summary:
Analysis of various of up-regulated and down-regulated genes in Normal Cervical mucosa, Cervical intraepithelial neoplasia and Cervical squamous cell carcinoma. The report provides a data analysis methodology for identification of co-expressed gene patterns, as emerging clusters, in global transcriptome of cervical mucosal pre-malignant and malignant conditions in comparison to their normal counterparts.
Microarray based study of global gene expression is often used to extract molecular signatures underlying cancer progression. Such endeavors endorse self organizing map, a type of artificial neural network to analyze high dimensional pre-processed transcriptome data to segregate hotspot genes in component plane for disease subtypes. This report provides a data analysis methodology for identification of coexpressed gene patterns, as emerging clusters, in global transcriptome of oral and cervical mucosal premalignant and malignant conditions in comparison to their normal counterparts. Four exclusive cluster patterns, each involving 100 − 300 genes, were identified from component planes for oral study groups. Gene expression associated with each pattern belonged to 32 biological processes. Analysis on cervical biopsies, where cancer was compared to cervical interepithelial neoplasia and normal counterpart, it revealed three non-overlapping patterns for each condition. In cervical interepithelial neoplasia an intermediate pattern with nine different dominant functional processes was identified, whereas, in cervical squamous cell carcinoma pattern showed dominance for seven different functions. This analysis demonstrated utility of self organizing map to capture dominant enriched patterns as visual plots and revealed six common biological processes like transcription and RNA processing, cytoskeleton reorganization, angiogenesis, immunity, neuron signalling, and connective tissue remodelling in the pathogenesis of oral and cervical cancers. In fact it could provide an intuitive understanding of molecular course in carcinogenesis and may contribute for combinatorial biomarker discovery.

overall_design: Cervical cancer is among top ten cancers worldwide with mortality rate of 52 % . It goes through a series of pre-malignant stages - Cervical Intraepithelial Neoplasia CIN 1, 2 and 3. However, some CIN2 lesions may develop soon after HPV infection, suggesting that there could be alternate pathways involved. Incisional biopsies from Cervical interepithelial neoplasia (CIN) and Cervical squamous cell carcinoma (OSCC) were collected. All the collected biopsies were divided into two and one half was processed for the purpose of light microscopy evaluation. After histopathological confirmation of disease condition by onco-pathologist, the other half of the tissue was used for microarray analysis. In the inclusion of histopathologically normal cervical biopsies were done from patients undergoing hysterectomy due to prolapsed uterus or uterine polyp or fibroid. The aim of the study is to investigate the differential transcrptomics modulations that are responsible for the transition of normal cervical mucosa to CIN and later its malignant transformation to cancer.

first: Raunak

middle: K

last: Das

first: Anji

last: Anura

first: Swarnendu

last: Bag

first: Lopamudra

last: DasGhosh

first: Probhas

last: Banerjee

first: Kunjuraman

last: Sujathan


title: Genome-wide analysis of gene expression in Normal oral mucosa and different stages of oral submucous fibrosis

summary:
Analysis of various of up-regulated and down-regulated genes in normal oral mucosa and different stages of OSF. The report provides a data analysis methodology for identification of co-expressed gene patterns, as emerging clusters, in global transcriptome of oral mucosal pre-malignant and malignant conditions in comparison to their normal counterparts.
Microarray based study of global gene expression is often used to extract molecular signatures underlying cancer progression. Such endeavors endorse self organizing map, a type of artificial neural network to analyze high dimensional pre-processed transcriptome data to segregate hotspot genes in component plane for disease subtypes. This report provides a data analysis methodology for identification of co-expressed gene patterns, as emerging clusters, in global transcriptome of oral mucosal pre-malignant and malignant conditions in comparison to their normal counterparts. Four exclusive cluster patterns, each involving 100 − 300 genes, were identified from component planes for oral study groups. Gene expression associated with each pattern belonged to 32 biological processes. The transcription and RNA processing, and angiogenesis were dominant in normal oral condition, while immunity, cellular differentiation and migration, neuron signalling, connective tissue organization, tumor suppression, and enzyme regulation showed predominance in oral squamous cell carcinoma. In dysplasia skeletal and ligament development processes were dominant while in non-dysplastic sub-mucous fibrosis cytoskeleton reorganization and neuron signalling were pre-dominant. In dysplasia an intermediate pattern with nine different dominant functional processes was identified. This analysis demonstrated utility of self organizing map to capture dominant enriched patterns as visual plots and revealed six common biological processes like transcription and RNA processing, cytoskeleton reorganization, angiogenesis, immunity, neuron signalling, and connective tissue remodeling in the pathogenesis of oral cancer. In fact it could provide an intuitive understanding of molecular course in carcinogenesis and may contribute for combinatorial biomarker discovery.

overall_design: Oral submucous fibrosis (OSF) is one of the potential premalignant condition with high prevalence (0.3 − 3.2%) in South-Asian population . Clinically, OSF patient exhibit marked rigidity of oral mucosa and trismus. OSF is frequently accompanied by different grades of epithelial dysplasia which contributes to the high rate of malignant transformation (7 − 13%). Incisional biopsies from Oral submucous Fibrosis (OSF) and OSF associated squamous cell carcinoma (OSCC) were collected. All the collected biopsies were divided into two and one half was processed for the purpose of light microscopy evaluation. After histopathological confirmation of disease condition by onco-pathologist, the other half of the tissue was used for microarray analysis. The normal oral mucosa (NOM) samples were used as control. NOM samples were collected from individuals suffering from impacted mandibular third molar teeth and were in need of trans-alveolar extraction. The excess amount of muco-periosteal buccal flaps that has been left after trans alveolar surgeries have been excised and used as normal sample. The aim of the study is to investigate the differential transcrptomics modulations that  are responsible for the transition of normal oral mucosa to premalinant disorders and later its malignant transformation to cancer.

first: Satarupa

first: Monika

last: Rajput

first: Mousumi

last: Mandal

last: Pal

first: Ranjan

last: Pau


title: miR-126 Governs Human Leukemia Stem Cell Quiescence and Therapeutic Resistance

first: John

last: Dick

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

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

overall_design: Refer to individual Series


title: Expression data in MDA-MB-231 breast cancer cell lines with Histone deacetylase SAHA treatment

status: Public on Jan 26 2016

city: Shanghai

first: Hanlin

last: Zeng

address: 555 Zuchongzhi Road

country: China

institute: Shanghai Institute of Materia Medica, Chinese Academy of scineces

summary: Analysis of gene expression change after 8hr's treatment with 5μM SAHA, which is a histone deacetylase inhibitor, in MDA-MB-231 cell lines.

overall_design: two sample, one is control, one is SAHA treatment. Each sample is triplicated.

first: Meiyu

last: Geng

first: Jian

last: Ding

first: Min

last: Huang


title: Genome-wide gene expression analysis of FAF1 silencing in HeLa cells

city: Seoul

first: Soonhwa

last: SONG

address: Ewha Womans University-gil 52

department: College of Pharmacy

institute: Ewha Womans Univiersity

summary: This study is designed to examine the cellular functions of human Fas-associated factor 1 (FAF1) containing multiple ubiquitin-related domains. Microarray analyses revealed that interferon stimulated genes related to antiviral response are significantly increased in FAF1 knocked down HeLa cells. Silencing FAF1 enhanced the poly I:C and respiratory syncytial virus (RSV) induced productions of type I interferons (IFNs), the target gene of interferon regulator factor 3 (IRF3). IRF3 is a key transcription factor in IFNβ signaling responsible for host innate immune response. This study also found that FAF1 and IRF3 physically associate with IPO5/importin-β3 and that overexpression of FAF1 reduces the interaction between IRF3 and IPO5/importin-β3. These findings suggest that FAF1 negatively regulates IRF3-mediated IFNβ production and antiviral innate immune response via regulating nuclear translocation of IRF3. We conclude that FAF1 plays a novel role negatively regulating virus-induced IFNβ production and antiviral response by inhibiting the translocation of active phosphorylated IRF3 from cytosol to nucleus.

overall_design: HeLa cells were transfected with control siRNA or FAF1 siRNA. After 48 h, cells were harvested and total RNA were purified. Biotin labeled cRNA were hybridized to each Huamn HT12 expression v.4 bead array. Data analysis was performed using manufacturer's software.

first: Kong-Joo

last: Lee

last: Song


title: Liver Expression Profiling In HMDP (Atherosclerosis F1 study)

status: Public on Jan 25 2016

city: Los Angeles

first: Calvin

last: Pan

address: 675 Charles Young Dr South

institute: UCLA

summary: Identify genes in the liver whose expression is under genetic regulation in the Hybrid Mouse Diversity Panel (HMDP).  The HMDP comprises classical inbred and recombinant inbred wild type mice.  104 of these strains were bred onto a C57BL/6J background carrying transgenes for both ApoE-Leiden and cholesteryl ester transfer protein (CETP). The RMA values of genes were used for genome wide association as described in Davis et al PLOS Genetics 2015.  These data are used to identify candidate genes at loci associated with atherosclerotic lesion size.

overall_design: GWAS for expression in livers of F1 offspring of inbred strains crossed with C57BL/6J carrying ApoE-Leiden and CETP transgenes fed chow diet for 8 weeks followed by Western diet for 16 weeks

first: Aldons

last: Lusis

first: Brian

last: Bennett

first: Richard

last: Davis


title: Differential expression of genes after alterations in cellular levels of hsa-miR-195

city: New Delhi

first: Richa

last: Singh

state: Delhi

address: Mall Road

department: Functional Genomics Unit

institute: Institute of Genomics and Integrative Biology

summary:
The experiment was designed to identify the genes which get altered after over-expression and depletion of hsa-miR-195 levels in MCF7 and HEK 293T cells.
Recent research has established that microRNAs (miRNAs) are key regulators of many cell processes including those often deregulated in cancer such as apoptosis. In our previous work we have shown that hsa-miR-195 targets the key anti-apoptotic molecule BCL2 and its over-expression induces apoptosis and augments sensitivity of cancer cells towards chemotherapeutic drug. These results suggested a possible anticancer role of miR-195 and therefore oblige its complete functional characterization. In this study global effect of alterations in cellular miR-195 levels on transcriptome was analysed in order to identify the regulatory functions of miR-195. Together our findings highlight a novel and important role of hsa-miR-195 potentially opening new avenues for the treatment of various diseases.

overall_design: Biological duplicates of six samples were used viz. MCF7 cells depleted of endogenous miR-195 using 100nM antimiR-195 (MCF7-AntimiR), MCF7 cells with overexpressed miR-195 using 3 µg p195 (MCF7-195), MCF7 untransfected (MCF7-Control) ; HEK 293T cells depleted of endogenous miR-195 using 100nM antimiR-195 (HEK 293T-AntimiR), HEK 293T cells with overexpressed miR-195 using 3µg p195 (HEK 293T-195) and untransfected HEK 293T cells (HEK 293T control)

first: Neeru

last: Saini


title: RUNX1 and RUNX2 responsiveness in MCF7 breast cancer cells: relationship to estrogen signaling

first: Nyam-Osor

last: Chimge

state: CA

address: 2250 Alcazar street

department: IGM

institute: USC

summary: Comparative analysis of RUNX1 and RUNX2 responsiveness in the presence or absence of E2

overall_design: RUNX1 was constitutively silenced in MCF7 cells, and kept in charcoal stripped serum for 48h prior to dox inducible re-expression of RUNX1 in MCF7/Rx1dox, or expression of RUNX2 in MCF7/Rx2dox cells. Global gene expression was profiled to define genes regulated by estradiol, RUNX1 (or RUNX2) or both.


title: Perivascular Progenitor Cells Derived from Human Embryonic Stem Cells Exhibit Functional Characteristics of Pericytes, and Improve the Retinal Vasculature in a Rodent Model of Diabetic Retinopathy

status: Public on Jan 22 2016

first: Hyung-Min

last: Chung

address: 120 Neungdong-ro, Gwangjin-gu

institute: Konkuk university school of medicine

summary: Diabetic retinopathy (DR) is the leading cause of blindness in working-age people. Pericyte loss is one of the pathologic cellular events in DR, which weakens the retinal microvessels. Damages to the microvascular networks are irreversible and permanent, thus further progression of DR is inevitable. In this study, we hypothesize that multipotent perivascular progenitor cells derived from human ESCs (hESC-PVPCs) improve the damaged retinal vasculature in the streptozotocin (STZ)-induced diabetic rodent models. We describe a highly efficient and feasible protocol to derive such cells using a natural selection method without cell sorting processes. As a cellular model of pericytes, hESC-PVPCs exhibited marker expressions such as CD140B, CD146, NG2, and functional characteristics of pericytes. Following a single intravitreal injection into diabetic Brown Norway (BN) rats, we demonstrate that the cells localized alongside typical perivascular regions of the retinal vasculature, and stabilized blood-retinal barrier (BRB) breakdown. Findings in this study highlight a therapeutic potential of hESC-PVPCs in DR by mimicking the role of pericytes in vascular stabilization.

overall_design: The molecular profiling analysis of ontological selected gene sets demonstrated that the transcripts associated with stemness markers, neural crest, neuro-ectoderm, and endoderm gene expressions.

first: Jung

last: Kim

first: Ki-Sung

last: Hong

first: Won

first: Daekyeong

last: Bae


title: Stimulation of endogenous FGFR2 signalling in MCF-7 cells following knock-down of FGFR2

city: Cambridge

first: Kerstin

last: Meyer

address: Robinson Way

department: Cancer Research UK Cambridge Institute

institute: University of Cambridge

summary: Genome-wide association studies have identified a locus within the second intron of the FGFR2 gene that is consistently the most strongly associated with estrogen receptor-poisive breast cancer risk. However, we know little about the mechanisms by which the FGFR2 locus mediates risk or the pathways in which multiple risk loci may combine to cause disease. Previously, a systems biology approach was adopted to elucidate the regulatory networks operating in MCF-7 breast cancer cells in order to examine the role of FGFR2 in mediating risk. Here, the same approach has been employed using MCF-7 cells that have been treated with siRNA directed against FGFR2, in order to knock-down FGFR2 expression, to confirm that the differential gene expression that we see when FGF10 signalling is perturbed, on a background of estrogen signalling, is mediated via FGFR2 stimulation.

overall_design: The data consists of 24 microarray samples from MCF-7 cells treated under different conditions at a time point of 6 h in order to perturb FGFR2 signalling. The data have been pre-processed in R using the beadarray package, and are presented in the form of log2 expression values. The experiment was carried out on 2 Humanv4 arrays using 12 samples per array.

first: Tom

last: Campbell


title: Expression Profiling In HMDP (Atherosclerosis F1 study)


title: Gene expression signature from tumor initiating population predicts clinical outcome in undifferentiated pleomorphic sarcoma (UPS)

first: qingxia

last: wei

state: Ontario - ON

address: 4 jardin hill court

institute: The hospital for sick children

summary: Undifferentiated pleomorphic sarcomas (UPS) are thought to harbor a small population of cells with unique capability of tumor initiation and maintenance. These tumor initiating cells (TICs) are regarded as the drivers of cancer progression. However, the evidence for this tumor initiating cell (TIC) concept is based on the xenotransplantation assays in mice and the clinical relevance of the TIC concept remains unclear in UPS. We hypothesized that the distinct properties of the TICs would be reflected in the clinical outcome if the TIC concept is relevant in UPS. Here we performed global gene expression profiling of TIC-enriched side population (SP) fractions and non-SP fractions sorted from 15 UPS primary samples. Ninety-three genes were differentially expressed in between SP fractions and non-SP fractions. The UPS TIC gene expression signature score summarizing expression of these genes was calculated for a gene expression data and was correlated with clinical outcome. In the 15 samples used to generate the signature, patients with high scores in the SP fractions were associated with worse survival. We then tested the two independent published datasets with gene expression data on bulk unsorted samples, assuming that the TIC gene expression would persist in the non-TICs. Patients with high scores had significantly worse metastasis-free survival in both datasets. The significance of the score remained significant even considering for the known prognostic factor of UPS. Thus, gene expression signature derived from UPS TICs predicts clinical outcome, suggesting the clinical relevance of the TIC concept in UPS.

overall_design: Fifteen human UPS samples were obtained at the Mount Sinai Hospital between February of 2008 and January of 2011, according to an approved protocol of the institutional review board.

first: Ilkyu

last: Han

first: Qingxia

last: Wei


title: Expression changes following combined treatment with RG7388 + GSK2830371

status: Public on Jan 20 2016

city: Newcastle Upon Tyne

first: Olaf

last: Heidenreich

address: Brewery Lane

department: Wolfson Childhood Cancer Research Centre

institute: Newcastle University

summary: Microarray-based gene expression analysis showed that combination treatment with RG7388 and GSK2830371 increases the subset of early RG7388 induced p53-transcriptional target genes.   These findings demonstrate that potent and selective WIP1 inhibition potentiates the response to MDM2 inhibitors in TP53 wild-type cells.

overall_design: NGP cells were treated for 4 hours with 0.5% DMSO (solvent control), RG7388 (75nM) + GSK2830371 (2.5µM) before cell harvesting and total RNA extraction. Four independent biological repeats were performed.

first: Arman

last: Esfandiari

first: Sirintra

last: Nakjang

first: John

last: Lunec


title: Honokiol Bis-Dichloroacetate (Honokiol DCA) Demonstrates Activity in Vemurafenib-Resistant Melanoma in Vivo.

city: Atlanta

first: Jack

last: Arbiser

state: GA

address: 101 Woodruff Circle WMB 5309

department: Dermatology

institute: Emory School of Medicine

summary: The majority of human melanomas bears BRAF mutations and thus is treated with inhibitors of BRAF, such as vemurafenib. While patients with BRAF mutations often demonstrate an initial dramatic response to vemurafenib, relapse is extremely common. Thus, novel agents are needed for the treatment of these aggressive melanomas. Honokiol is a small molecule compound derived from Magnolia grandiflora that has activity against solid tumors and hematopoietic neoplasms. In order to increase the lipophilicity of honokiol, we have synthesized honokiol DCA, the dichloroacetate ester of honokiol. In addition, we synthesized a novel fluorinated honokiol analog, bis-trifluoromethyl-bis-(4-hydroxy-3-allylphenyl) methane (hexafluoro).  Both compounds exhibited activity against A375 melanoma in vivo, but honokiol DCA was more active. Gene arrays comparing treated with vehicle control tumors demonstrated induction of the respiratory enzyme succinate dehydrogenase B (SDHB) by treatment, suggesting that our honokiol analogs induce respiration in vivo.  We then examined its effect against a pair of melanomas, LM36 and LM36R, in which LM36R differs from LM36 in that LM36R has acquired vemurafenib resistance. Honokiol DCA demonstrated in vivo activity against LM36R (vemurafenib resistant) but not against parental LM36. Honokiol DCA and hexafluoro inhibited the phosphorylation of DRP1, thus stimulating a phenotype suggestive of respiration through mitochondrial normalization. Honokiol DCA may act in vemurafenib resistant melanomas to increase both respiration and reactive oxygen generation, leading to activity against aggressive melanoma in vivo.

overall_design: Tumors from animals treated with control vehicle, honokiol DCA, and hexafluoro were harvested and snapped-frozen in liquid nitrogen until RNA Extraction. RNA extraction was performed according to the Qiagen RNeasy kit. RNA samples were then submitted to Emory University’s Intergrated Genomics Core for RNA quality analysis and gene expression assay. Gene expression analysis was performed using an Illumina HumanHT-12 v3 Expression Bead Chip and Gene Expression Module of Illumina’s GenomeStudio Software package (v2011.1, Illumina).

first: Michael

middle: Y

last: Bonner


title: HSPA6 is an ulcerative colitis susceptibility factor that is induced by cigarette smoke and protects intestinal epithelial cells by stabilizing anti-apoptotic Bcl-XL

city: Groningen

first: vincent

last: bloks

country: Netherlands

institute: UMCG

summary:
Objective: Cigarette smoking ameliorates ulcerative colitis (UC) and aggravates Crohn’s disease (CD). Cigarette smoke suppresses inflammation-induced apoptosis in intestinal epithelial cells (DLD-1), which may explain its protective effect in UC. Here, we performed transcriptome profiling of cigarette smoke extract (CSE)-exposed DLD-1 and Jurkat cells (T-lymphocytes) and related this to UC susceptibility genes with protective functions in the intestinal epithelium.
Design: CSE-regulated genes in DLD-1 and Jurkat cells were identified by Illumina microarrays and compared to genes in UC susceptibility loci. Colon biopsies were analyzed by immunohistochemistry for cell-specific expression of HSPA6. CSE-induced gene expression was analyzed by Q-PCR, Western blotting and immunofluorescence microscopy. Protein (HSPA6/Bcl-XL) interactions were analyzed by immunoprecipitation.
Results: CSE changed the expression of 536 and 2,560 genes in DLD-1 and Jurkat cells, respectively. The “response to unfolded protein” was one of the most significantly affected gene sets with prominent induction (20.3-fold) of heat shock protein A6 (HSPA6). Six CSE-induced genes in DLD-1 cells were located in UC-susceptibility loci, including HSPA6 (rs1801274). HSPA6 is highly expressed in the human colonic epithelium. CSE caused a dose-dependent strong (>100-fold at 30% CSE for 6 hours), but transient induction of HSPA6 mRNA and protein in DLD-1 cells. HSPA6 co-immune precipitated with anti-apoptotic Bcl-XL, protein levels of which were increased while mRNA levels were unchanged.
Conclusion: HSPA6 is a cigarette smoke-induced UC-susceptibility gene. The HSPA6 risk locus is associated with decreased HSPA6 expression. HSPA6 provides epithelial protection by stabilizing anti-apoptotic Bcl-XL, thereby contributing to the beneficial effect of cigarette smoking in UC.

overall_design: 12 controls and 6 smoke in each cell line

first: A

last: Regeling

first: F

last: Imhann

first: H

middle: H

last: Volders

first: T

last: Blokzijl

first: V

last: Bloks

first: R

last: Weersma

first: G

last: Dijkstra

first: K

middle: N

last: Faber


title: Haploinsufficiency of BAZ1B contributes to Williams syndrome through transcriptional dysregulation of neurodevelopmental pathways

status: Public on Jan 19 2016

city: New York

first: Matthew

last: Lalli

state: NY

address: 1 Gustave L. Levy Pl

department: Psychiatry

institute: Icahn School of Medicine at Mount Sinai

summary: Williams syndrome (WS) is a neurodevelopmental disorder caused by a genomic deletion of ~28 genes that results in a cognitive and behavioral profile marked by overall intellectual impairment with relative strength in expressive language and hypersocial behavior. Advancements in protocols for neuron differentiation from induced pluripotent stem cells allowed us to elucidate the molecular circuitry underpinning the ontogeny of Williams syndrome. In patient-derived stem cells and neurons, we determined the expression profile of the Williams-Beuren Syndrome Critical Region deleted genes and the genome-wide transcriptional consequences of the hemizygous genomic microdeletion at 7q11.23. Derived neurons displayed disease-relevant hallmarks and indicated novel aberrant pathways in WS neurons including over-activated Wnt signaling accompanying an incomplete neurogenic commitment. We show that haploinsufficiency of the ATP-dependent chromatin remodeler, BAZ1B, which is deleted in WS, significantly contributes to this differentiation defect. Chromatin-immunoprecipitation (ChIP-seq) revealed BAZ1B target gene functions are enriched for neurogenesis, neuron differentiation, and disease-relevant phenotypes. BAZ1B haploinsufficiency caused widespread gene expression changes in neural progenitor cells, and together with BAZ1B ChIP-seq target genes, explained 42% of the transcriptional dysregulation in WS neurons. BAZ1B contributes to regulating the balance between neural precursor self-renewal and differentiation and the differentiation defect caused by BAZ1B haploinsufficiency can be rescued by mitigating over-active Wnt signaling in neural stem cells. Altogether, these results reveal a pivotal role for BAZ1B in neurodevelopment and implicate its haploinsufficiency as a likely contributor to the neurological phenotypes in WS.

overall_design: We profiled the transcriptomes from 2 WS individuals and 2 controls in iPS cells and neurons, all in biological triplicate. We profiled neural progenitor cells, neural progenitors cells with BAZ1B knockdown, and differentiated NPCs

first: Jiwon

last: Jang

first: Kenneth

middle: S

last: Kosik


title: Comparison kPSCs versus bmMSCs

status: Public on Jan 27 2016

city: Leiden

first: Danielle

last: Leuning

address: Albinusdreef 2

department: Nephrology

institute: LUMC

summary:
Expression profiles kPSCs versus bmMSCs
Here we characterized human kidney derived perivascular stromal cells  (hkPSCs) and compared them to human bmMSCs in expression profile

overall_design: hkPSCs were isolated from human kidneys based on plastic adherence and NG2 expression and compared to human bmMSCs

first: D

last: Rabelink


title: Monocyte Transcriptional Networks are Associated with Tuberculin Skin Test Status in Uganda

status: Public on Jan 15 2016

city: Seattle

first: Chetan

last: Seshadri

state: WA

address: 750 Republican Street

department: Medicine

institute: University of Washington

summary: Understanding mechanisms of resistance to M. tuberculosis (M.tb) infection in humans could identify novel therapeutic strategies as it has for other infectious diseases.  We hypothesized that monocytes from household contacts of pulmonary tuberculosis patients that failed to convert their tuberculin skin tests (TSTNEG) would respond differently to M.tb infection when compared to matched tuberculin skin test positive controls (TSTPOS).    We obtained genome-wide transcriptional profiles of M.tb-infected peripheral blood monocytes from 10 TSTNEG and 18 TSTPOS Ugandans.  We used Gene Set Enrichment Analysis and interaction networks to identify cellular processes associated with TST status. We discovered gene sets associated with histone deacetylases that were differentially expressed when comparing TSTPOS and TSTNEG subjects.  We used small molecule inhibitors to demonstrate that histone deacetylase function is important for the pro-inflammatory response to M.tb infection in monocytes.  Monocytes from individuals who appear to resist M.tb infection differentially activate pathways controlled by histone deacetylase in response to M.tb infection when compared to those who are susceptible to infection.  These data identify a potential cellular mechanism underlying the clinical phenomenon of persistently negative tuberculin skin tests despite known exposure to an infectious contact.

overall_design: CD14+ monocytes from 18 TSTPOS and 10 TSTNEG subjects were isolated by positive selection.  Depending on the yield, between 5E5 and 1E6 monocytes were plated in duplicate in a 24-well tissue culture plate and rested overnight at 37oC, 5% CO2.  The next day, cells were mock-infected or infected with virulent M. tuberculosis strain H37Rv at a multiplicity of infection (MOI) 10:1.  After a six hour incubation at 37C, 5% CO2, the mycobacteria were killed and total RNA harvested using TRIzol-LS (Invitrogen).  TRIzol samples were stored at -80oC until all infections were completed.  To minimize batch effects, equal numbers of TSTPOS and TSTNEG subjects were processed on each of six days and frozen aliquots of M.tb were used for infections.  RNA was extracted using the RNeasy Mini Kit with on-column DNAse digestion.  RNA was transcribed into complementary DNA, labeled, and hybridized onto Illumina HT-12 microarrays according to the manufacturer’s instructions. Probe intensities were quantified using Illumina iScan platform and processed using BeadArray without performing normalization or background correction.


title: Aorta Expression Profiling In HMDP (Atherosclerosis F1 study)

first: Calvin

last: Pan

summary: Identify genes in the aorta whose expression is under genetic regulation in the Hybrid Mouse Diversity Panel (HMDP).  The HMDP comprises classical inbred and recombinant inbred wild type mice.  104 of these strains were bred onto a C57BL/6J background carrying transgenes for both ApoE-Leiden and cholesteryl ester transfer protein (CETP). The RMA values of genes were used for genome wide association as described in Davis et al PLOS Genetics 2015.  These data are used to identify candidate genes at loci associated with atherosclerotic lesion size.

overall_design: GWAS for expression in aortas of F1 offspring of inbred strains crossed with C57BL/6J carrying ApoE-Leiden and CETP transgenes fed chow diet for 8 weeks followed by Western diet for 16 weeks

first: Aldons

last: Lusis

first: Brian

last: Bennett

first: Richard

last: Davis


title: Expression data from MCF7 cells depleted of the cohesin subunit RAD21 and treated with estrogen or vehicle

city: Dunedin

first: Julia

last: Horsfield

state: Otago

address: Corner of Great King and Hannover Streets

department: Pathology

country: New Zealand

institute: University of Otago

summary:
RAD21 is a subunit of cohesin. Cohesin is maninly known for its role in holding sister chromatids together during cell-division but it also plays a role in gene regulation. Genome wide study in MCF7 cells have shown that cohesin co-binds with estrogen receptor alpha at numerous sites. To identify estrogen sensitive genes that are influenced by cohesin, a microarray expression analysis was conducted in MCF7 cells lacking the cohesin subunit RAD21.
Global changes in gene expression were identified in cells treated with Control/RAD21 siRNA and stimulated with estrogen/vehicle thereafter.

overall_design: MCF7 cells growing in hormone depleted conditions for 24 hours were transfected with RAD21 or control siRNA and cultured in hormone-depleted conditions for a further 48 hours. Cells were subsequently treated with 100 nM 17-β estradiol or vehicle for 3 and 6 hours. Cells were harvested for RNA and protein at both time points. Knockdown of RAD21 message and protein were verified by quantitative PCR and western blotting respectively. For each time point, RNA from three independent biological experiments were used for analyses

last: Dasgupta

first: J

last: Antony

last: Horsfiled


title: Infusion of CCR5-edited T cells Allows Immune Reconstitution and HIV Reservoir Decay

city: Cleveland

first: Peter

last: Wilkinson

state: Ohio

address: 2103 Cornell Road

department: Pathology / Systems Biology & Bioinformatics

institute: Case Western Reserve University

summary: Hematopoietic stem cell transplantation from a donor whose T cells did not express CCR5—a co-receptor for HIV—resulted in an apparent cure of an HIV-infected adult1. Herein, we have exploited this strategy by adoptive transfer of autologous CCR5 gene disrupted CD4+ T cells (SB-728-T) in 9 HIV+ participants. A single infusion of SB-728-T, a minimally invasive intervention, led to sustained increases in CD4+ T cell counts through 3.5 years (33-44 months) compared to baseline (median increase of +193 cells/µl, P = 0.02). The degree of long-term immune reconstitution was associated with expansion of a polyclonal stem cell-like CCR5-depleted CD4+ T cell population. SB-728-T therapy was also associated with expansion of polyfunctional HIV-specific CD8+ T cells (P = 0.03) and decline in size of the HIV reservoir (-0.23 to -3.6 log decrease). Collectively, these data suggest that generation and protection of CD4 memory cells will improve T cell homeostasis, enhance HIV-specific immunity, and accelerate the decline of the host HIV reservoir.

overall_design: We studied nine HIV-infected adults on long-term cART who had a CD4+ T cell count between 200 and 500 cells/µL.  Transcriptional analysis of CD4+ T cell memory subsets was performed at month 33-44 (at plateau) to determine if CD4 CD45RAintROint cells represented a memory subset distinct from CD45RA+RO- CD95+, TCM, and TEM subsets.

last: Zeidan

last: Lee

last: Lalezari

first: A

last: Giedlin

last: Fromentin

first: C

last: Benne

first: M

last: Aid

first: S

last: Fourati

last: Joo

first: T

last: Winson

last: Wang

last: Mitsuyasu

first: Y

last: Zhang

last: Cartwright

last: Balderas

last: Cameron

first: N

last: Chomont

last: Deeks

last: Ando

last: Sekaly

first: P

last: Stafova


title: Expression profiling of the TC32 Ewing sarcoma cell line following silencing of SUPT6H, SF3B1 or HNRNPH1

city: Bethesda

first: Suntae

last: Kim

address: Bldg 37, room 6128

department: Genetics Branch

institute: CCR, NCI, NIH

summary: The investigation of the function of SUPT6H, SF3B1 and HNRNPH1 in Ewing sarcoma

overall_design: The expression profiles of TC32 Ewing sarcoma cells were determine 48 hours post siRNA-transfected. Groups consisted of untreated cells (three samples), and negative control (siNeg) transfected-TC32 cells (six samples), and TC32 cells in which either SUPT6H, SF3B1 or HNRNPH1 were silenced; three different siRNAs corresponding to each gene were assessed separately.

first: Natasha

last: Caplen


title: The novel atypical retinoid ST5589 down-regulates Aurora Kinase A and has anti-tumour activity in lymphoma pre-clinical models

status: Public on Jan 08 2016

city: Bellinzona

first: Francesco

last: Bertoni

state: Ticino

address: Via V. Vela 6

department: Lymphoma & Genomics Research Program

country: Switzerland

institute: IOR

summary: we report characterized the preclinical activity of a new member of this class, the ST1926-derivative ST5589, in lymphomas

overall_design: GEP analysis of 2 lymphoma cell lines with and without treatment

first: Elena

last: Bernasconi

first: Ivo

last: Kwee

first: Eugenio

last: Gaudio

first: Andrea

last: Rinaldi


title: Expression profiling of Ewing sarcoma cell lines exposed to 5nM Pladienolide B (PlaB) for 24 hours

summary: Identification of genes and pathways altered by PlaB, a bacterial natural product that acts as a spliceosome modulator by targeting the SF3b subunit of the spliceosome

overall_design: SKNMC, TC32, TC71, and RD-ES Ewing sarcoma cell lines were treated with 0.1% (v/v) DMSO vehicle or 5nM PlaB for 24 hours. Three samples in each group were analyzed.


title: Profiling of normal human colonic epithelial cells according to their PTK7 surface abundance

status: Public on Jan 12 2016

city: Sabadell

first: Antoni

last: Berenguer-LLergo

state: Barcelona

address: Parc del Taulí, 1

department: A8G2 Group - Rheumatology Service

country: Spain

institute: Parc Taulí Research and Innovation Institute (I3PT)

summary: Human mucosa was collected from two different individuals undergoing colectomy. After treatment with EDTA, colonic crypts were isolated and further dis-aggregated using Dispase. Next, cells were stained using antibodies directed against the extracellular domain of EpCAM, PTK7, CD11, CD31, and CD45. Cells were analyzed and sorted via flow cytometry (BD Aria). After excluding non-epithelial cells (Epcam. CD11, CD31, and CD45 negative), the EpCAM positive fraction was divided into fractions expressing either high, medium, low, or negative levels of PTK7. Sorted cells were transferred to Trizol for RNA extraction and RNA was purified using the Qiagen RNA Mini Kit.

overall_design: Colonic crypts were isolated from normal human mucosa derived from individuals undergoing colectomy. Single cell fractions from these crypts were sorted and isolated RNA processed and hybridized to Affymetrix PrimeView Arrays

last: Jung


title: c-MET inhibitor inducing KSHV+ primary effusion lymphoma apoptosis

status: Public on Jan 05 2016

city: New Orleans

first: Zhiqiang

last: Qin

state: LA

address: 1700 Tulane Ave

institute: LSUHSC-NO

summary: KSHV is a principal causative agent of primary effusion lymphoma (PEL). Despite this knowledge about the close relationship between HGF/c-MET network and solid tumors development, the role of HGF/c-MET in KSHV-related malignancies remains mostly unclear. We report that HGF/c-MET pathway is highly active within KSHV+ PEL cells and plays important role in tumor cell survival/growth. Targeting HGF/c-MET by a selective inhibitor, PF-2341066, significantly induces PEL apoptosis through a complex of underlying mechanisms, including cell-cycle arrest and DNA damage. By using microarray analysis, we have identified the global gene profile controlled by HGF/c-MET pathway within KSHV+ PEL cell-lines and several novel “druggable” candidates closely related to cancer cell survival/growth. Finally, we found that targeting HGF/c-MET pathway by PF-2341066 effectively prevents PEL tumor expansion and/or reduce established lymphoma progression in vivo.

overall_design: PEL cells were treated with vehicle control or c-MET inhibitor PF-2341066 (0.8 µM) for 24 h, and the gene expression signature was compared to respective vehicle controls

first: Lu

last: Dai

first: Jimena

last: Trillo-Tinoco

first: Yueyu

last: Cao

first: Karlie

last: Bonstaff

first: Luis

last: Del Valle

first: Denise

last: Whitby

first: Chris

last: Parsons

first: Jovanny

last: Zabaleta


title: Myc and N-myc induce distinct medulloblastoma subgroups via Miz1

status: Public on Jan 21 2016

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

summary: Medulloblastomas (MBs) are cerebellar tumors that can be classified into molecularly distinct subgroups that differ in pathology and prognosis. The mechanisms that underlie subgroup specification are largely unknown. While human SHH MBs express MYCN, Group3 (G3) MBs are associated with c-MYC (MYC) overexpression and often show metastasis that confers a poor prognosis. Although MYC proteins are thought to be functionally exchangeable, ectopic expression of Myc or N-myc in Trp53-/-;Cdkn2c-/- cerebellar granule neuron progenitors (GNPs) induces G3 and SHH MBs, respectively, demonstrating that each Myc protein has distinct biological properties. We now show that Myc and N-myc differ in their affinity to Miz1 and that Myc, but not N-myc, effectively recruits Miz1 to its target sites on chromatin. The interaction of Myc with Miz1 is required for the genesis of G3 MB.  Myc suppresses ciliogenesis and “reprograms” the transcriptome of SHH-dependent GNPs to stem-like cells by repressing genes highly expressed in SHH MB via Miz1. Consistently, target genes of Myc/Miz1 are repressed in human G3 MBs but not in other MB subgroups.  Collectively, the data show that the interaction of Myc with Miz1 is a defining hallmark of G3 MB development.

overall_design: In this study, we show that Myc and N-myc differ in their affinity for Miz1, and Myc/Miz1 interaction is required for Group3 medulloblastoma (MB). The gene expression profiles of these tumors were compared to our previously published Group3 MB model as well as SHH model of MB (Kawachi et al., 2012, Cancer Cell). Cerebellar granule neuron progenitors (GNPs) [dka220-222] from postnatal (P) 6 Math1-GFP;Trp53-/-;Cdkn2c-/-. For SHH medulloblastomas, [dka204-206] and [blm015-017 or dka050-dka051], spontaneous medulloblastomas from Cdkn2c-/-;Trp53Fl/Fl;Nestin-Cre (Kawachi et al., 2012, Cancer Cell) and Ptch1+/-;Cdkn2c-/- (Uziel et al., 2005, Genes Dev) were used, respectively. Myc- [dka201-203] and MycV394D (termed MycVD thereafter)- [bvo017-bvo023] tumors were from Trp53-/-;Cdkn2c-/- cerebella of P6-P7 pups. Myc/ΔPOZ tumors [bvo002-bvo006] were obtained from Trp5Fl/Fl;Miz1ΔPOZ/POZ;Nestin-Cre cerebella of P6-P7 pups.

first: BaoHan

middle: T

last: Vo

first: Elmar

last: Wolf

first: Daisuke

last: Kawauchi

first: Anneli

last: Gebhardt

first: Jerold

last: Rehg

first: Susanne

last: Walz

first: Brian

last: Murphy

first: Young

last: Youn

first: Young-Goo

last: Han

first: Martin

last: Eilers

first: Martine

middle: F

last: Roussel


title: Reconstructing human kidney microvasculature for the study of kidney injury

first: James

middle: William

last: MacDonald

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

summary: Kidney peritubular capillaries are particularly susceptible to rarefaction and regeneration-limited after exposure to toxins or injuries. Studying these kidney microvessels remain challenging, primarily resulting from difficulties imaging in vivo, as well as isolating and culturing kidney microvascular cells in vitro, in particular in a three-dimensional (3D) microenvironment with proper hemodynamics. Here, we developed methods to isolate, purify, and characterize human kidney peritubular microvascular endothelial cells (hKMECs), and reconstituted a 3D kidney microvasculature in collagen matrix. Compared to other endothelial cells, isolated hKMECs are very sensitive to VEGF for survival and growth, and have a high vasculogenic but low angiogenic potential. Under flow, they formed a fenestrated endothelium with a comprehensive permeability barrier. When exposed to calcineurin inhibitors, hKMECs formed microvessels displayed cell retraction, broken fenestrae, and swollen endothelium, which led to a thrombogenic luminal wall and erythrocytes extravasations into the subendothelial space. Our study recapitulated the human kidney microvascular structure and function, and shed lights on potential mechanistic studies of kidney specific injuries and diseases.

overall_design: Expression levels for human kidney microvascular cells (n=3) were compared to human umbilical vein endothelial cells (n=3)

first: Giovanni

last: Ligresti

first: Ryan

last: Nagao

first: June

last: Xue

first: Yoon-Jung

last: Choi

first: Jin

last: Xu

first: Takahide

last: Aburatani

first: Theo

last: Bammler

first: Stephen

last: Schwartz

first: Kim

last: Muczynski

first: Jeremy

last: Duffield

first: Jonathan

last: Himmelfarb

first: Ying

last: Zheng


title: Transcriptomic profiling of urine extracellular vesicles reveals alterations of CDH3 in prostate cancer

status: Public on Jan 13 2016

city: Derio

first: Verónica

last: Torrano Moya

address: 801 Building. Technology Park of Vizcaya

institute: CICbioGUNE

summary: One of the challenges of current research in prostate cancer is to improve the differential non-invasive diagnosis of prostate cancer (PCa) and benign prostate hyperplasia (BPH). Extracellular vesicles (EV) are emerging structures with promising properties for intercellular communication. In addition, the characterization of EV in biofluids is an attractive source of non-invasive diagnostic, prognostic and predictive biomarkers. Here we show that urinary EV (uEV) from prostate cancer patients exhibit genuine and differential physical and biological properties. Importantly, transcriptomics characterization of uEVs led us to define the decreased abundance of Cadherin 3, type 1 (CDH3) transcript in uEV from PCa patients. Tissue and cell line analysis strongly suggested that the status of CDH3 in uEVs is a distal reflection of changes in the expression of this cadherin in the prostate tumor. Our results reveal that uEVs could represent a non-invasive tool to inform about the molecular alterations in prostate cancer.

overall_design: RNA extraction was performed in 10 ultracentrifuge-isolated-uEVs samples (4 BPH, 6 Pca)

first: F

last: Royo

first: V

last: Torrano


title: Integrative network analysis reveals different pathophysiological mechanisms of insulin resistance among Caucasians and African Americans

first: Yongzhong

last: Zhao

state: New York

address: 1470 Madison Avenue btw. 101st and 102nd Streets

department: Genetics

institute: Mount Sinai Medical Center

summary: Background: African Americans (AA) have more pronounced insulin resistance and higher insulin secretion than European Americans (Caucasians or CA) when matched for age, gender, and body mass index (BMI). We hypothesize that physiological differences (including insulin sensitivity [SI]) between CAs and AAs can be explained by co-regulated gene networks in tissues involved in glucose homeostasis.   Methods: We performed integrative gene network analyses of transcriptomic data in subcutaneous adipose tissue of 99 CA and 37 AA subjects metabolically characterized as non-diabetic, with a range of SI and BMI values.   Results: Transcripts negatively correlated with SI in only the CA or AA subjects were enriched for inflammatory response genes and integrin-signaling genes, respectively. A sub-network (module) with TYROBP as a hub enriched for genes involved in inflammatory response (corrected p= 1.7E-26) was negatively correlated with SI (r= -0.426, p= 4.95E-04) in CA subjects. SI was positively correlated with transcript modules enriched for mitochondrial metabolism in both groups. Several SI-associated co-expressed modules were enriched for genes differentially expressed between groups. Two modules involved in immune response to viral infections and function of adherens junction, are significantly correlated with SI only in CAs. Five modules involved in drug/intracellular transport and oxidoreductase activity, among other activities, are correlated with SI only in AAs. Furthermore, we identified driver genes of these race-specific SI-associated modules.   Conclusions: SI-associated transcriptional networks that were deranged predominantly in one ethnic group may explain the distinctive physiological features of glucose homeostasis among AA subjects.

first: Swapan

last: Das

first: Neeraj

last: Sharma

first: Bin

last: Zhang


title: Low-power photodynamic therapy induces survival signaling in cultured  hilar cholangiocarcinoma cells

status: Public on Jan 04 2016

city: Amsterdam

first: Perry

middle: D

last: Moerland

address: Meibergdreef 9

department: Epidemiology and Data Science

institute: Amsterdam UMC

summary: Photodynamic therapy (PDT) of solid cancers comprises the administration of a photosensitizer followed by illumination of the photosensitizerreplete tumor with laser light. This induces a state of local oxidative stress, culminating in the destruction of tumor tissue and microvasculature and induction of an anti-tumor immune response. However, some tumor types, including perihilar cholangiocarcinoma, are relatively refractory to PDT, which may be attributable to the activation of survival pathways in tumor cells following PDT (i.e., activator protein 1 (AP-1)-, nuclear factor of kappa light polypeptide gene enhancer in B-cells (NF-κB)-, hypoxia-inducible factor 1-alpha (HIF-1α)-, nuclear factor (erythroid-derived 2)-like 2 (NFE2L2), and unfolded protein response-mediated pathways).  To assess the activation of survival pathways after PDT, human perihilar cholangiocarcinoma (SK-ChA-1) cells were subjected to PDT with zinc phthalocyanine (ZnPC)-encapsulating liposomes. Following a 30-minute incubation with liposomes, the cells were either left untreated or treated at low (50 mW) or high (500 mW) laser power (cumulative light dose of 15 J/cm2). Cells were harvested 90 minutes post-PDT and whole genome expression analysis was performed using Illumina HumanHT-12 v4 expression beadchips.

overall_design: Hilar cholangiocarcinoma (SK-ChA-1) cells were incubated with PBS (control group) or 500 μM zinc phthalocyanine (ZnPC)-encapsulating liposomes (ZnPC-ITLs, final lipid concentration). After 30 minutes, cells that were incubated with ZnPC-ITLs were either kept in the dark (ITL group) or were treated with 500-mW (ITL 500) or 50-mW (ITL 50) laser light (n = 3 per group, cumulative light dose of 15 J/cm2). Ninety minutes after photodynamic therapy, total cellular RNA was isolated and gene expression levels were analyzed by using the Illumina HumanHT-12 v4 platform. The data was analyzed in the context of survival signalling and comparisons were made with the control group.

first: Ruud

last: Weijer

first: Michal

last: Heger


title: Comprehensive gene expression analysis of a MESP1-progenitor derived cardiac lineage

status: Public on Jan 01 2016

first: Sabine

last: Den Hartogh

state: Zuid-Holland

address: Einthovenweg 20

department: Anatomy and Embryology

summary: A hESC MESP1 reporter line was used to isolate MESP1 expressing pre-cardiac progenitors. These progenitor were replated and fulter differentiated in culture. At four sequential timepoints upon further differentiation, samples were isolated for gene expression analysis, in order to identify key cardiac transcription factors and molecules.

overall_design: hESCs were differentiated towards the cardiac lineage. MESP1-mCherry expressing progenitors were isolated at day 3 of differentiation and replated as aggregates, in presence of Wnt-inhibitor Xav939. Two days after replating (D5), four days (D7), seven days (D10), ad 11 days (D14), total RNA of each sample was isolated for gene expression analysis. MESP1-mCherry positive derivatives were compared to MESP1-mCherry negative derivatives, in order to identify cardiac-specific regulators and cell surface markers.

first: S

first: R

last: Passier


title: Interaction of CDCP1 with HER2 enhances HER2-driven tumorigenesis and promotes trastuzumab resistance in breast cancer

first: Francesco

last: Bertoni

summary: Our findings demonstrate that CDCP1 is a novel modulator of HER2 signalling, and a biomarker for the stratification of breast cancer patients with poor prognosis

overall_design: GEP analysis of human breast cancer cell lines SKBR3 overexpressing CDCP1 and control.

first: Abdullah

last: Alajati

first: Ilaria

last: Guccini

first: Sandra

last: Pinton

first: Andrea

last: Rinaldi

last: Alimonti


title: T Cell Receptor-Induced NF-kB Signaling and Transcriptional Activation Are Regulated by STIM1- and Orai1-Mediated Calcium Entry

status: Public on Jan 14 2016

city: Philadelphia

first: daniel

last: beiting

state: PA

address: 380 S. University Ave

department: Pathobiology

institute: University of Pennsylvania

summary: T cell activation following antigen binding to the T cell receptor (TCR) involves the mobilization of intracellular calcium (Ca2+) to activate the key transcription factors NFAT and NF-κB. The mechanism of NFAT activation by Ca2+ has been determined; however, the role of Ca2+ in controlling NF-κB signaling is poorly understood and the source of Ca2+ required for NF-κB activation is unknown. We demonstrate that TCR- but not TNF- induced NF-κB signaling upstream of IκB kinase (IKK) activation absolutely requires the influx of extracellular Ca2+ via STIM1-dependent CRAC/Orai channels. We further show that Ca2+ influx controls phosphorylation of the NF-κB protein p65 on Ser536 and that this post- translational modification controls its nuclear localization and transcriptional activation. Notably our data reveal that this role for Ca2+ is entirely separate from its upstream control of IκBα degradation, thereby identifying a novel Ca2+- dependent distal step in TCR-induced NF-κB activation. Finally, we demonstrate that this control of distal signaling occurs via Ca2+-dependent PKCk-mediated phosphorylation of p65. Thus, we establish the source of Ca2+ required for TCR induced NF-kB activation and we define a new distal Ca2+-dependent checkpoint in TCR-induced NF-kB signaling that has broad implications for the control of immune cell development and T cell functional specificity.

overall_design: 3 treatments were analyzed, with biological replicates for each treatment. In addition, three timepoints (1 hour, 4 hour, and 8 hour) were examined for each treatment, as well as an untreated control.  In total 19 samples were analyzed

first: Daniel

last: Beiting

first: Corbett

last: Berry

first: Bruce

last: Freedman


title: Gene expression response to HBV infection in PHH

city: Bron

first: Hector

last: Hernandez-Vargas

state: Rhone

address: 36 bis Rue de la Batterie

country: France

institute: Genomics Consulting

summary:
Hepatitis B virus (HBV) is known for its ability to interact with the host cell DNA methylation machinery. In HBV-infected hepatocytes, this interaction leads to chronic liver diseases, including hepatocellular carcinoma (HCC). We studied the extent of genomic changes induced by natural HBV infection in human primary hepatocytes.
Transcriptome and methylome profiles were obtained at different time points post-infection to identify HBV-specific alterations. Although gene expression and DNA methylation do not directly correlate, they both seem to reflect the effect of cell culture and viral infection at different levels.These changes in the hepatocyte cellular program shed light on the initial events leading to HBV-associated liver diseases.

overall_design: Primary human hepatocytes (PHH) were prepared from adult patients undergoing lobectomy or segmental liver resection. HBV was concentrated from the supernatant of HepG2.2.15 cells using centrifugal filter devices and tittered by HBV-DNA dot blot analysis after sedimentation into a CsCl density-gradient to determine enveloped DNA-containing viral particles. PHH were isolated from surgical liver resections, cultured, and infected with HBV. Infected PHH and corresponding controls were kept for 4 hours, 8 hours, and 1, 6, and 12 days. Supernatants were obtained to validate the efficiency of infection by ELISA and qRT-PCR, and nucleic acids were extracted for expression and DNA methylation analyses.

first: H


title: We performed gene expression profiles of human bronchoalveolar epithelial cells (HBEC) transduced with GFP labeled murine focal adhesion kinase (PMX-Purom-GFP-mFAK) or GFP control empty vector counterpart (PMX-Purom-GFP-empty)

city: Dallas

first: Jerfiz

last: Constanzo

state: Texas

address: 6001 Forest Park Road

department: Hematology Oncology

institute: University of Texas Southwestern Medical Center

summary:
The goal if this project was to determine the cellular pathways affected by FAK protein overexpression downstream of oncogenic KRAS and RHOA in normal lung epithelium. In addition, we aim to characterize the potential downstream modulators of cell growth and migration upon FAK hyperactivation.
We identified pathways in DNA damage, cell growth, apoptosis and cytoskeleton remodeling pertaining to tissue differentiation and carcinogenesis signature respectively.

overall_design: For this study, two duplicate samples were analyzed in triplicate arrays for a total of 6 data poinst per condition. The groups compared were PMX-Purom-GFP-mFAK against PMX-Purom-GFP-emty.

first: Pier

last: Scaglioni


title: Selective coregulator function for different steroid receptors and restriction of steroid receptor chromatin occupancy by Hic-5 (ER)

city: Los Angeles

first: Dai-Ying

last: Wu

address: 1441 Eastlake Ave, NOR 6314

department: Biochemistry

institute: University of Southern California

summary:
The estrogen receptor (ER) recruits many coregulators but not as well as GR?
We investigate the relationship between ER and Hic5 and identify classes of genes that respond differently when cells are induced with hormone and when Hic5 is knocked down

overall_design: We knock down Hic-5 (TGFB1I1) in U2OS cells using siRNA (siHic5) along with nonspecific siRNA (shNS) and assay gene expression changes at 3 different time points of hormone treatment.

first: Rajas

last: Chodankar

first: Michael

middle: R

last: Stallcup


title: Selective coregulator function for different steroid receptors and restriction of steroid receptor chromatin occupancy by Hic-5 (GRγ)

summary:
The glucocorticoid receptor (GR) recruits many coregulators via the well characterized AF2 interaction surface in the GR ligand binding domain, but LIM domain coregulator Hic-5 binds to the relatively uncharacterized tau2 activation domain in the hinge region of GR. Requirement of Hic-5 for glucocorticoid-regulated gene expression in U2OS osteosarcoma cells was defined by Hic-5 depletion and global gene expression analysis. Hic-5 depletion had selective and dramatic effects, positive and negative, on both activation and repression of GR target genes. For some hormone-induced genes, Hic-5 facilitated recruitment of the Mediator complex and RNA polymerase II. In contrast, many genes were not regulated by hormone until Hic-5 was depleted. On these genes Hic-5 acted at a very early step of the regulatory process, preventing efficient GR binding on enhancers, chromatin remodeling, and thus preventing glucocorticoid-driven transcriptional regulation. Overall, Hic-5 has selective and diverse roles on GR target genes, functioning as coactivator on some genes and corepressor on others, and either facilitating or opposing the glucocorticoid-driven actions of GR. Hic-5 exhibits multiple mechanisms of action, either regulating GR binding to DNA and chromatin remodeling, or facilitating later steps in transcription complex assembly.
We investigate the relationship between GR and Hic5 and identify classes of genes that respond differently when cells are induced with hormone and when Hic5 is knocked down

overall_design: We knock down Hic-5 (TGFB1I1) in U2OS cells using two different siRNA (siHic5_2 and siHic5_5) along with nonspecific siRNA (shNS) and assay gene expression changes at 4 different time points of hormone treatment. We also include non-infected control (NI) as a second control at each time point.


title: Phenotypic plasticity determines cancer stem cell therapeutic resistance in oral squamous cell carcinoma I

city: London

first: Adrian

last: Biddle

address: 4 Newark Street

department: Blizard Institute

institute: Queen Mary, University of London

summary: Cancer stem cells (CSCs) drive tumour spread and therapeutic resistance, and can undergo epithelial-to-mesenchymal transition (EMT) and mesenchymal-to-epithelial transition (MET) to switch between epithelial and post-EMT sub-populations. Examining oral squamous cell carcinoma (OSCC), we now show that increased phenotypic plasticity, the ability to undergo EMT/MET, underlies increased CSC therapeutic resistance within both the epithelial and post-EMT sub-populations. The post-EMT CSCs that possess plasticity exhibit particularly enhanced therapeutic resistance and are defined by a CD44highEpCAMlow/-CD24+ cell surface marker profile. Treatment with TGFβ and retinoic acid (RA) enabled enrichment of this sub-population for therapeutic testing, through which the endoplasmic reticulum (ER) stressor and autophagy inhibitor Thapsigargin was shown to selectively target these cells. Demonstration of the link between phenotypic plasticity and therapeutic resistance, and development of an in vitro method for enrichment of a highly resistant CSC sub-population, provides an opportunity for the development of improved chemotherapeutic agents that can eliminate CSCs.

overall_design: The CA1 OSCC cell line was sub-cloned to derive 4 clonal sub-lines, termed pEMT-P, pEMT-S, Epi-S and Epi-P (here 18, 23, 7 and 4 respectively).

first: Ian

middle: C

last: Mackenzie


title: Phenotypic plasticity determines cancer stem cell therapeutic resistance in oral squamous cell carcinoma II

overall_design: The clonal derivative of the CA1 OSCC cell line termed 18 here (otherwise termed pEMT-P) was treated with 0.5ng/ml TGFbeta and/or 5uM RA for eight days, with media changed every second day. The LM OSCC cell line was FACS sorted to recover the CD44highEpCAMlowCD24+ sub-population, which was then treated with 0.5ng/ml TGFbeta and/or 5uM RA for eight days, with media changed every second day. The parental CA1 and LM cell lines are included as reference samples.


title: Gene expression profiling of SHSY5Y cells exposed to Endosulfan

city: Nagpur

first: Dr. saravana

last: devi

state: Maharashtra

department: Environmental Health Division

institute: CSIR-National Environmental Engineering Research Institute

summary:
SHSY5Y cells grown in MEM:F12 media (1:1) were treated with Endosulfan and total RNA was isolated from cells after 24 hour exposure
Three replicate were used for the experiment

overall_design: Cells grown in  75mm2 flask. three replicates for each sample

first: Deepa

last: Gandhi

first: S

last: Devi

first: K

last: Krishnamurthi


title: A Patient-derived In Vitro - In Vivo Preclinical Model of Renal Cell Carcinoma

city: Stanford

first: Hongjuan

last: Zhao

state: CA

address: 300 Pasteur Dr

department: Urology

institute: Stanford

summary:
Purpose: Authentic preclinical models of renal cell carcinoma (RCC) are lacking.  We aimed to establish and characterize primary RCC cultures and demonstrate the feasibility of evaluating drug responses in vitro and in vivo.
Materials and Methods: Previously published methodology, with minor modifications, was used to establish, cryopreserve, and serially passage RCC cells from nephrectomy and tumorgraft specimens.  Cells were characterized for immuno- and molecular phenotype by immunochemistry, DNA sequencing and gene expression profiling.  Tumorigenic potential was evaluated by implanting cells under the renal capsule of immunocompromised mice.  The ability to monitor xenograft growth by magnetic resonance imaging (MRI) was investigated.  Responses to a tyrosine kinase inhibitor (TKI) and an mTOR inhibitor were measured.
Results: Primary cultures were successfully established from 11 clear cell and 1 chromophobe RCC, cryopreserved and serially passaged.  Retention of immuno- and molecular phenotypes was demonstrated.  Cultured cells formed xenografts in mice that could be measured by MRI.  Patient-specific responses to drugs were observed in vitro and response to an TKI was confirmed in vivo.
Conclusions: Our study is the first to show the derivation of primary cultures from RCC tumorgrafts, and to demonstrate the ability of primary RCC cultures to generate xenografts in mice. Our results suggest the feasibility of establishing large, well-annotated banks of RCC primary cultures for high-throughput drug screening in vitro and validation in vivo, providing a versatile platform together with xenografts and patient-derived precision-cut tissue slice tumorgrafts we developed previously for precilinical studies of RCC.

overall_design: Microarray analyses were performed to compare the gene expression profile of one of the primary cultures (case 7) to its parental tumor and tissue slice tumorgrafts in the study. Tissue slice grafts and parent tumors were preserved in Allprotect tissue reagent (Qiagen, Valencia, CA) at -20°C prior to RNA extraction using an AllPrep DNA/RNA/Protein Mini Kit (Qiagen, Valencia, CA).  The quality of RNA was determined using an Agilent 2100 Bioanalyzer (Agilent Biotechnologies, Santa Clara, CA).  Microarray hybridization was performed using Illumina Human HT-12 v4 Beadchips (Illumina Inc., San Diego, CA) according to the manufacturer’s directions.  Expression data was rank invariant normalized using BeadStudio software (Illumina Inc.).

first: Matthias

last: Saar

first: Alan

middle: E

last: Thong

first: Alexandre

last: Ingels

first: Maija

last: Valta

first: Sarah

last: Young

first: Rosalie

last: Nolley

first: Jennifer

last: Santos

first: Donna

middle: M

last: Peehl


title: Dissecting the immunogenicity of RD1-recombinant live tuberculosis vaccine candidates studying host-pathogen interaction in human primary dendritic cells

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

summary:
New tuberculosis vaccines are highly desirable and urgently needed since the attenuated Mycobacterium bovis Bacillus Calmette-Guerin (BCG) provides only variable efficacy against the pulmonary form of the disease. The region of difference 1 (RD1), which is deleted in BCG and strongly impacts on Mycobacterium tuberculosis (Mtb) virulence and immunogenicity, represents a crucial locus to be engineered for either the improvement of the current BCG vaccine, or the attenuation of Mtb. Therefore, mutants secreting or not wild-type or mutated variants of the RD1-encoded 6 kDa early secreted antigenic target (ESAT-6) were generated. Comparative analysis of the transcriptome, phenotype, cytokine production profiles and the capacity to promote T cell responses were conducted in human primary dendritic cells (DCs), as they represent critical regulators of vaccine-induced immunity, unveiling a distinct immunogenic potential for BCG or Mtb mutants.
In contrast to Mtb, BCG induced a poor DC maturation, and to our surprise, a BCG strain complemented with the RD1 region only partially restored DC maturation and expansion of interferon (IFN)-γ producing T cells. In contrast, infection with a recombinant attenuated Mtb strain, secreting a truncated version of ESAT-6 lacking 11 amino acids at the C-terminus portion, drove full maturation in infected DC and maintained their capacity to promote polarization of T helper (Th) 1 cells, as observed upon infection with the virulent Mtb.

overall_design: We performed a comparative microarray analysis of dendritic cells (DCs), infected with Mtb and BCG strains, expressing/complemented (MtbΔRD1::RD1 and BCG::RD1) or not (MtbΔRD1::B412 and BCG::B412) the/with the RD1 region. DCs were challenged with different BCG and Mtb recombinant strains for 8h.

first: Marilena

last: Etna

first: Elena

last: Giacomini

first: Manuela

last: Pardini

first: Martina

last: Severa

first: Daria

last: Bottai

first: Fabiana

last: Rizzo

first: Roland

last: Brosch

first: Eliana

last: Coccia


title: Genome-wide microarray analysis of normal human keratinocytes in response to genistein

city: Gdańsk

first: Magdalena

last: Gabig-Cimińska

address: Wita Stwosza 59

department: of Medical Biology and Genetics

country: Poland

institute: University of Gdańsk

summary: Establishment of a transcriptomic profile of human cells treated with genistein with particular emphasis on the assessment of the role of this isoflavone in regulation of expression of psoriasis-related genes stands for the present study. The hypothesis tested was that genistein modulates activity of psoriasis-related genes, by reducing the expression efficiency of genes revealing enhanced activity in psoriatic cells, and by stimulating the expression efficiency of genes revealing decreased activity in psoriatic cells. Results provide important information concerning the extent of action of genistein at the molecular level in terms of modulation of gene expression by this substance.

overall_design: Total RNA obtained from human immortalized keratinocyte (HaCaT) subjected to 24 or 48 hours in vitro exposure to 30, 60 or 100 µM genistein, or 0.05%DMSO (K).


title: Cancer stem cell features shift during skin squamous cell carcinoma progression

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

institute: IDIBELL

summary: Cancer stem cells (CSCs) play a key role in tumour growth and metastasis. Although an expansion of CSC population was previously described in advanced cutaneous squamous cell carcinoma (SCC), it remains unknown whether CSC regulatory mechanisms also change through tumour progression to promote malignancy. Here, we generate mouse models of skin SCCs to study alterations in CSC regulation over progression. We found that features of CSCs change at late stage of progression, correlating with a switch from epithelial to mesenchymal tumour shape. beta-catenin and EGFR signalling are down-regulated, whereas autocrine FGFR1 and PDGFR alpha pathways are up-regulated in CSCs of advanced tumours. Inhibition of FGFR and PDGFR signalling repress malignant SCCs growth and metastasis, respectively. An enhanced epithelial-to-mesenchymal transition (EMT) program and over-expression of PDGFR alpha and FGFR1 are observed in malignant human skin SCCs, suggesting that these pathways are also induced over human SCC progression. Therefore, uncover signalling pathways controlling CSCs at specific stage of progression may improve the selection of more accurate targeted therapeutic strategies according to tumour stage, blocking SCC relapse and metastasis.

overall_design: Mouse models of skin SCCs progression were first generated. For that, individual samples of spontaneous or DMBA-TPA induced skin SCCs generated in K14-HPV16 mice were orthotopically engrafted in immunodeficient mice and then serially transplanted, generating lineages in which the progression from WD-SCCs to PD-SCCs was observed. Then, tumour cells expressing CD34 and alpha 6-integrin, previously identified as cutaneous cancer stem cells, were isolated by flow cytometry-sorter from WD-SCCs and PD-SCCs of different tumour lineages. RNA extraction and hybridization on Affymetrix microarrays was carried out to compare whole gene profiling of these populations of CSCs.

first: Victoria

last: da Silva-Diz

first: Purificación

last: Muñoz


title: Tissue Slice Grafts of Human Renal Cell Carcinoma: an Authentic Preclinical Model with High Engraftment Rate and Metastatic Potential

first: Hongjuan

last: Zhao

country: USA

summary: Purpose: Discovery of curative therapies for renal cell carcinoma (RCC) is hampered by lack of authentic preclinical models.  Tumorgrafts, generated by direct implantation of patient-derived tissues into mice, have demonstrated superior ability to predict therapeutic response.  We evaluated “tissue slice grafts” (TSGs) as an improved tumorgraft model of RCC.       Experimental Design: Cores of fresh RCC were precision-cut at 300-μm and implanted under the renal capsule of RAG2-/-γC-/- mice.  Engraftment rate, histology, biomarker expression, genetic fidelity and metastatic potential were evaluated.  Magnetic resonance imaging (MRI) was tested as a non-invasive method to measure tumor volume, and response to a targeted therapy was determined.       Results: All 13 cases of RCC engrafted and displayed characteristic histology and biomarkers.  TSG volume quantified non-invasively by MRI highly correlated with graft weights, providing a unique tool for monitoring orthotopic growth.  Moreover, in 2 cases, cancer cells from TSGs metastasized to clinically relevant sites, including bone.  Microarray analysis and DNA sequencing demonstrated a high degree of correlation of global gene expression and VHL status between TSGs and parental tumors.  Treatment of TSGs with sunitinib significantly decreased graft weight and mean vessel density compared to controls.       Conclusions: The TSG model of RCC faithfully recapitulates tumor pathology, gene expression, genetic mutation and drug response.  The high engraftment rate and metastatic potential of this authentic model, in conjunction with the ability to generate large first-generation animal cohorts and to quantitate tumor volume at the orthotopic site by MRI, proffer significant advantages compared to other preclinical platforms.

overall_design: Three pairs of tissue slice graftes and parent tumors were included in the study. Tissue slice grafts and parent tumors were preserved in Allprotect tissue reagent (Qiagen, Valencia, CA) at -20°C prior to RNA extraction using an AllPrep DNA/RNA/Protein Mini Kit (Qiagen, Valencia, CA).  The quality of RNA was determined using an Agilent 2100 Bioanalyzer (Agilent Biotechnologies, Santa Clara, CA).  Microarray hybridization was performed using Illumina Human HT-12 v4 Beadchips (Illumina Inc., San Diego, CA) according to the manufacturer’s directions.  Expression data was rank invariant normalized using BeadStudio software (Illumina Inc.).

first: Alan

last: Thong

first: Alexandre

last: Ingels

first: Maija

last: Valta

first: Sarah

last: Young


title: miR-203, a microRNA of multilayered epithelia, inhibits metastatic fitness in human squamous cell carcinoma

first: Nathan

last: Benaich

address: Great Maze Pond

department: Centre for Stem Cells and Regenerative Medicine

institute: King's College London

summary: The colonization of distant organs by metastatic carcinoma cells underpins most human cancer-related deaths, including those from head and neck squamous cell carcinoma (HNSCC). We report that miR-203, a miRNA that promotes keratinocyte differentiation, is necessary and sufficient to inhibit multiple post-extravasation events during HNSCC lung metastasis, including initial survival/engraftment, escape from metastatic dormancy, and overt colonization in vivo. Restoration of miR-203 expression in established lung metastases reduces overall metastatic burden. Instead of promoting differentiation, miR-203 controls lung metastasis through direct targeting of genes involved in cytoskeletal dynamics (LASP1), ECM remodeling (SPARC), and cell metabolism (NUAK1). Expression of miR-203 and its downstream targets correlates with HNSCC overall survival outcomes, suggesting the therapeutic potential of targeting this signaling axis.

overall_design: Total RNA (including small RNAs) was isolated from cultured cells stably infected in biological duplicate with either a scrambled control hairpin or miR-203. Samples were harvested in technical duplicate.

first: Suraj

last: Menon

first: Fiona

last: Watt


title: mTORC inhibition of neuroblastoma SK-N-BE(2)c cells cultured under hypoxic conditions

city: Lund

first: Kristoffer

last: von Stedingk

address: Scheelevägen 2

institute: Lund University

summary: Differential expression of the oxygen sensitive hypoxia-inducible transcription factor (HIF) subunits HIF-1a and HIF-2a occurs in many tumor types, but the underlying regulatory mechanisms remain poorly understood. Here we investigate the role of mTOR complex in the regulation of HIF expression in cells cultured under hypoxic conditions.

overall_design: Neuroblastoma SK-N-BE(2)c cells were treated with DMSO or the mTORC complex inhibitor PP242 and cultured at hypoxia for 24, 48 or 72 hours.

first: Sofie

last: Mohlin

first: Arash

last: Hamidian

first: Sven

last: Påhlman