title: Expression data from human  melanoma cell lines with or without GNAQ/11 mutation

status: Public on Jul 01 2017

city: San Francisco

first: Xu

last: Chen

state: CA

address: 1450 3rd street, HD200

department: Dermatology

institute: UCSF

summary: We used microarray to compare global gene expression profiles between 5 GNAQ/11 mutant uveal melanoma cell lines (GNAQ mutant: 92-1, omm1.3, mel270; GNA11 mutant: omm-gn11 and upmd-1) and 5 GNAQ/11 wild type melanoma cell lines(sk-mel-2, mm415, mm485, sk-mel-5 and mum2c). Uveal melanoma is the most common intraocular tumor that mainly metastasizes to the liver in about 50% patients. Over 80% of UMs harbor GNAQ or GNA11 activating mutation. Currently there is no effective treatment available for UM patients. Results provide insights into downstream signaling of oncogenic GNAQ/11 and identification of therapeutic targets in UM.

overall_design: We extracted total RNAs from human melanoma cell lines with or without GNAQ/11 mutation. Purified RNAs were performed for amplification, fragmentation and biotin-labeling. The labeled cDNA was hybridized to Affymetrix microarrays.


title: Analysis of splicing pattern and gene expression level of Matrin3 knockdown.

status: Public on Jul 12 2017

city: Suita

first: Yukio

last: Kawahara

state: Osaka

address: 2-2 Yamada-oka

department: Graduate School of Medicine

country: Japan

institute: Osaka University

summary: We identified RNA targets of Matrin3 using SH-SY5Y by PAR-CLIP analysis.  Because Matrin3 mainly bound to intron of pre-mRNA,  in order to find the effect of Matrin3 on splicing pattern and expression, we knocked down Matrin3 using SH-SY5Y cells by electroporation and extracted total RNAs from those cells.  The total RNAs were subjected to whole transcripts microarray GeneChip® Affymetrix Human Transcriptome array 2.0.

overall_design: SH-SY5Y cells were electroporated with Matrin3-siRNA or negative control siRNA. Forty eight hours after electroporation, total RNA was extracted and subjected to microarray analysis.

first: Munetaka

last: Yamamoto

first: Yuri

last: Uemura


title: Expression data from human primary skeletal muscle myotubes treated with aldosterone alone or in combination

status: Public on May 05 2017

city: Columbus

first: Jill

last: Rafael-Fortney

state: OH

address: 460 W. 12th Ave

department: Physiology & Cell Biology

country: USA

institute: The Ohio State University

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

overall_design: Refer to individual Series


title: Expression data from human primary skeletal muscle myotubes treated with aldosterone alone or co-incubated with aldosterone plus spironolactone, eplerenone, or mifepristone

summary: To uncover whether aldosterone induces gene expression changes through mineralocorticoid or glucocorticoid receptors and determine if eplerenone and spironolactone could block aldosterone induced gene expression to the same extent

overall_design: 12 total samples were analyzed.  3 biological replicates for each of the following treatment groups were included: 1) aldosterone; 2) spironolactone plus aldosterone; 3) eplerenone plus aldosterone; 4) mifepristone plus aldosterone.  Pairwise comparison between groups were carried out and a fold-change ≥2 were selected.

middle: A

first: Jessica

last: Chadwick


title: Expression data from human primary skeletal muscle myotubes treated with aldosterone, spironolactone, eplerenone, mifepristone, prednisolone or vehicle

summary: To define the direct gene expression changes in normal human skeletal muscle with mineralocorticoid and glucocorticoid receptor agonist and antagonist treatment.

overall_design: 18 total samples were analyzed.  3 biological replicates for each of the following treatment groups were included: 1) aldosterone; 2) spironolactone; 3) vehicle (DMSO); 4) eplerenone; 5) mifepristone; 6) prednisolone.  Pairwise comparison between groups were carried out and a fold-change ≥2 were selected.


title: Gene expression data of parental and ibrutinib-resistant TMD8 cells.

status: Public on Apr 30 2017

city: Sunnyvale

first: Hsu-Ping

last: Kuo

address: 995 E Arques Ave

institute: Pharmacyclics

summary: Diffuse large B-cell lymphoma (DLBCL) and follicular lymphoma (FL) are the most prevalent B-lymphocyte neoplasms in which abnormal activation of the Bruton’s tyrosine kinase (BTK)–mediated B-cell receptor (BCR) signaling pathway contributes to pathogenesis. Ibrutinib is an oral covalent BTK inhibitor that has shown some efficacy in both indications. To improve ibrutinib efficacy through combination therapy, we first investigated differential gene expression in parental and ibrutinib-resistant cell lines to better understand the mechanisms of resistance. Ibrutinib-resistant TMD8 cells had higher BCL2 gene expression and increased sensitivity to ABT-199, a BCL-2 inhibitor. Consistently, clinical samples from ABC-DLBCL patients who experienced poorer response to ibrutinib had higher BCL2 gene expression. We further demonstrated synergistic growth suppression by ibrutinib and ABT-199 in multiple ABC-DLBCL, GCB-DLBCL, and FL lymphoma cell lines. The combination of both drugs also reduced colony formation, increased apoptosis, and inhibited tumor growth in a TMD8 xenograft model. A synergistic combination effect was also found in ibrutinib-resistant cells generated by either genetic mutation or drug treatment. Together, these findings suggest a potential clinical benefit from ibrutinib and ABT-199 combination therapy.

overall_design: Gene expression in parental or ibrutinib-resistant TMD8 cells was detected by HTA2.0 arrays and the level of BCL2 expression was compared between these two groups.

first: Scott

last: Ezell

first: Karl

middle: J

last: Schweighofer

first: Leo

middle: W

last: Cheung

first: Sidney

last: Hsieh

first: Mutiah

last: Apatira

first: Mint

last: Sirisawad

last: Eckert

first: Jeff

last: Hsu

first: Chun-Te

first: Darrin

last: Beaupre

first: Matthias

last: Versele

first: Betty

middle: Y

last: Chang


title: Gene expression profiling from MCF7

status: Public on Apr 10 2017

city: Stockholm

first: Johan

last: Hartman

state: Sweden

address: Karolinska Vägen

department: Department of Clinical Pathology and Cytology

country: Sweden

institute: Karolinska University Hospital

summary: proliferative effect in MCF7 cells.

overall_design: We use different treatments to study the effect on MCF7 proliferation.


title: Analysis of BRD4-regulated genes in human glioma U251 cells

status: Public on Apr 15 2017

city: Shanghai,

first: Feng

middle: jun

last: lin

state: xvhuiqv

address: 2Institute of Health Sciences

department: Department of Pathophysiology

country: China

institute: 1Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education

summary:
BRD4 is a member of the bromodomain and extra-terminal (BET) family, which has become a promising drug target for numerous cancers. It has been reported that BRD4 is deregulated in gliomas; however, the precise molecular pathways regulated by BRD4 are still elusive.
In this study, we knocked down BRD4 expression in glioma cell line U251 by lentivirus-mediated short hairpin RNA (shRNA) approach. BRD4 downregulation attenuated cell proliferation and promoted cell apoptosis. Genome-wide analysis of BRD4-regulated transcripts in U251 cells was performed using microarray to reveal the possible molecular mechanism

overall_design: To knock down BRD4 expression in U251 cells, lentivirus that expressed shRNA against human BRD4 were transfected U251 cells. Scrambled shRNA (Scr-shRNA) that targeted a non-specific sequence was used as the normal control. The efficiency of BRD4 knockdown were demonstrated by real-time PCR and western blot assays. BRD4-shRNA- transfected and Scr-shRNA-transfected U251 cells were collected for RNA extraction and hybridization on Affymetrix microarrays.

first: Zhanhui

last: Du

first: Shangming

last: Liu

first: Yuxia

last: Zhao


title: Characterizing the global changes in miRNA expression in human atrial appendages with persistent atrial fibrillation.

status: Public on Apr 25 2017

city: Yufu

first: Masaki

last: Morishima

state: Oita

address: 1-1 Idaigaoka Hasama

department: Pathophysiology

institute: Oita University School of Medicine

summary: Atrial fibrillation (AF), the most common cardiac rhythm disorder, is a major cause of cardiovascular morbidity and mortality. AF is characterized by the rapid and irregular activation of the atrium with diverse abnormalities, including electrical, structural, metabolic, neurohormonal, or molecular alterations.3 Although the pathophysiology of AF is complex, it has traditionally been treated with antiarrhythmic drugs that control the rhythm by altering cardiac electrical properties, principally by modulating ion channel function. However, treatments of AF with antiarrhythmic drugs have mostly failed to control the heart rhythm, because the electrical characteristics of atrial cardiomyocytes are eventually altered or remodeled during the course of AF. The aims of this study were to characterize the global changes in miRNA expression in human atrial appendages and to identify the target ion channel(s) responsible for electrical remodeling in AF. In this study, we performed a comprehensive analysis of miRNA microarrays, using a strict selection for human samples.

overall_design: Human atrial right appendages were collected from patients who had received open-heart surgery at Oita University Hospital; 10 samples were from patients with persistent AF (AF group) and 11 samples from patients with normal sinus rhythm (NSR group). The samples were only from male (60–79 years old) patients, and excluded those with chronic heart failure, diabetes, inflammatory diseases, endocrine diseases, metabolic diseases, kidney diseases requiring hemodialysis, history of steroid treatment, and paroxysmal AF. The AF group included patients with a documented record of sustained AF for 6 months or longer. The NSR group included patients with no documented history of AF.

first: K

last: Ono

first: C

last: Nakada

first: Y

last: Tsukamoto

first: M

last: Moriyama


title: miRNA Expression data from the uterus of ovariectomized young adult rats treated for three days with E2

status: Public on Mar 08 2017

city: Rensselaer

first: Sridar

middle: V

last: Chittur

state: NY

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

summary:
Examination of crosstalk between Aryl hydrocarbonreceptor (AHR) and Estrogen receptor (ER) in tha rat uterus on the level of miRNA transcriptome
The study was designed to see the overall ncRNA-expression change in the uterus induced by E2

overall_design: ovariectomized young adult rats were treated with vehicle control (DMSO)or 4µg/kg/d 17β-Estradiol (E2) for three consecutive days. Uteri were obtained 24 h after the last treatment. Biological samples from three rats were analyzed for each treatment group.

first: Helle

last: Janina

first: Kretzschmar

last: Georg

first: Chittur

last: Sridar


title: Gene expression profiling of the prostate cancer cell line PC3.

status: Public on Mar 10 2017

city: Oslo

first: Anita

last: Sveen

address: P.O.Box 4953, Nydalen

department: Department of Molecular Oncology

country: Norway

institute: Institute for Cancer Research, Oslo University Hospital

summary: To study the effect of miR-130a in prostate cancer, PC3 cells overexpressing miR-130a were analyzed for global gene expression.

overall_design: PC3 cells were transfected with miR-130a or negative control in three independent experiments.

first: Ina

last: Eilertsen

first: Carmen

last: Jerónimo

first: Ragnhild

last: Lothe


title: Re-activating pRB via PD 0332991 treatment in NSCLC H1299 Cells

status: Public on Mar 07 2017

city: Philadelphia

first: Thangavel

last: Chellappagounder

state: Pennsylvania

address: 10 th  South Locust, BLSB, ROOM 1006

department: Medicine

institute: Thomas Jefferson University

summary: CDk4/6 inhibitor activates RB and represses RB/E2F target genes

overall_design: H1299 parental cells were treated with DMSO or DMSO containing  PD 0332991 ( 500 nM)  for 14 days

first: Yi

last: Lu

first: Sankar

last: Addya

first: Robert

middle: B

last: Den


title: Re-activating pRB via PD 0332991 treatment in Prostate Cancer Cell PC3-ML

overall_design: PC3-ML parental cells were treated with DMSO or DMSO containing  PD 0332991( 500 nM)  for 24 hours


title: Genome-wide profiling of gene expression/splicing patterns in iAs-transformed cells

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

summary: Chronic low dose inorganic arsenic (iAs) exposure leads to changes in gene expression and epithelial-to-mesenchymal transformation. During this transformation, cells adopt a fibroblast-like phenotype accompanied by profound gene expression changes. While many mechanisms have been implicated in this transformation, studies that focus on the role of epigenetic alterations in this process are just emerging. DNA methylation controls gene expression in physiologic and pathologic states. Several studies show alterations in DNA methylation patterns in iAs-mediated pathogenesis, but these studies focused on single genes. We present a comprehensive genome-wide DNA methylation analysis using methyl-sequencing to measure changes between normal and iAs-transformed cells. Additionally, these differential methylation changes correlated positively with changes in gene expression and alternative splicing. Interestingly, most of these differentially methylated genes function in cell adhesion and communication pathways. To gain insight into how genomic DNA methylation patterns are regulated iAs-mediated carcinogenesis, we show that iAs probably targets CTCF binding at the promoter of DNA methyltransferases, regulating their expression. These findings reveal how transcription factor binding regulates DNA methyltransferase to reprogram the methylome in response to an environmental toxin.

overall_design: To examine the global impact of  iAs on gene expression and splicing patterns, RNA was extracted from 2 replicates of normal (NT) BEAS-2B cells and 2 replicates of inorganic arsenic-transformed (iAs-T) BEAS-2B cells and analyzed using Affymetrix Human Transcriptome 2.0 arrays.

first: Matthew

last: Rea

first: Meredith

last: Eckstein

first: Rebekah

last: Eleazer

first: Caroline

last: Smith

middle: C

first: Yvonne

last: Fondufe-Mittendorf


title: Gene expression data of human hepatocellular carcinoma (HCC) and Cholangiocarcinoma (CCA) from Thailand Initiative in Genomics and Expression Research for Liver Cancer (TIGER-LC)

status: Public on Jun 27 2017

city: Bethesda

first: Xin

middle: Wei

last: Wang

state: MD

address: 37 Convent Drive

department: Laboratory of Human Carcinogenesis

institute: National Cancer Institute

summary:
We used Affymetrix HTA2.0 microarray profiling to analyze gene expression patterns in tumor and paired non-tumor tissue of HCC and CCA patients.
We used microarrays data to identified molecular subgroup of HCC and CCA patients from Thailand

overall_design: For gene expression profiling, tumors and paired non-tumor tissues were profiled separately using Affymetrix Human Transcriptome Array 2.0 according to the manufacturer's protocol. Raw gene expression data were normalized using the Robust Multi-array Average (RMA) method and sketch-quantile normalization method on Affymetrix Expression Console Software Build 1.3.1.187.

first: Wang

last: Xin Wei


title: Rapid and efficient generation of myelinating oligodendrocytes from human induced pluripotent stem cells using a combination of three transcription factors [hiPSC]

status: Public on Mar 06 2017

city: Münster

first: Marc

last: Ehrlich

address: Röntgenstraße 20

country: Germany

institute: Max Planck Institute for Molecular Biomedicine

summary: We demonstrate that the induction of three transcription factors (SOX10, OLIG2, NKX6.2) in hiPSC-derived neural progenitor cells (hiPSC-NPC) is sufficient to rapidly generate O4+ oligodendrocytes with an efficiency of 60 to 70% within 28 days.

overall_design: Neural progenitor cells and transduced induced oligodendrocytes from 4 independent human induced pluripotent stem cell lines

first: Michael

last: Glatza


title: Gene Expression in Human Vastus Lateralis after PrimaVie Shilajit Supplementation

status: Public on Mar 01 2017

first: Sashwati

last: Roy

department: Surgery

institute: Ohio State University

summary:
Changes in Gene exporession after 8 weeks of PrimaVie Shilajit Supplementation were measured in vastus lateralis
GeneChip® Human Transcriptome Array 2.0  was used to study the gene expression in human vastus lateralis after supplementation of PrimaVie Shilajit and identified distinct classes of up-regulated genes during this process.

overall_design: Gene expression was studied in 3 subjects prior to and post-supplementation of PrimaVie Shilajit for 8 weeks; so total 6 samples

first: Roy

last: Sashwati


title: Expression data from HIF1A WT vs KD Madin-Darby canine kidney epithelial cells (MDCK strain II cells (ATCC:CCL-34)) under normoxic and hypoxic conditions

status: Public on Feb 11 2017

city: Oulu

first: Irina

last: Raykhel

address: Aapistie 5

department: FBMM

country: Finland

institute: University of Oulu

summary:
The expression of TGFbeta pathway genes were downregulated in HIF1A KD Madin-Darby canine kidney epithelial cells (MDCKII) in hypoxic condition.
We used microarray to study the differential expression of genes in HIF1A knockdown versus WT Madin-Darby canine kidney epithelial cells (MDCKII)

overall_design: Madin-Darby canine kidney epithelial cells (MDCKII) were incubated 24h in normoxic condition then additionally were incubated 24h in normoxic or hypoxic conditions and total RNA was extracted for microarray analysis.

first: Johanna

last: Myllyharju


title: Expression data from colon cancer cell HCT116 mouse xenograft - Control vs. traditional Chinese medicine Astragalus membranaceus-treated conditions

status: Public on Feb 13 2017

city: Taoyuan

first: Ailun

last: Tseng

address: 300 Jhong Da Rd.

country: Taiwan

institute: National Central University

summary:
To identify biomarkers regulated by traditional Chinese medicine Astragalus membranaceus Fischer Bge. var. mongolicus Bge. Hsiao in colorectal cancer. We have identified several differentially expressed genes including microRNAs using Affymetrix HTA-2.0 array.
In this dataset, we include the expression data obtained from colon cancer cell line HCT116 grafted into nude mice. The mice was treated either water or traditional Chinese medicine Astragalus membranaceus for 28 days. These data are used to obtain 1425 genes that are differentially expressed in response to Astragalus membranaceus treatment.

overall_design: 16 total samples were analyzed. The data was RMA-normalized and differentially expressed genes were selected using GeneSpring. Genes with a p < 0.05 and a fold-change > 1.5 were selected.

first: Li-Jen

last: Su


title: Expression data from human myocardial cells, AC16

first: Feng

last: lin

summary:
This study aimed to provide new compelling clues in the PM2.5-induced toxicity and mechanism which order the meaningful bioinformatics evidences for further study on human cardiovascular system.
We used microarrays to detail the global program of gene expression underlying cellularisation and identified distinct classes of up-regulated genes after treated with chemical substance.

overall_design: Human myocardial cells AC16 were exposed to PM2.5 for 24h, and collected for RNA extraction and hybridization on Affymetrix microarrays. After that, we tested the expression data of human myocardial cells.

first: Junchao

last: Duan

first: Zhiwei

last: Sun


title: Role of the PhoP-PhoQ Gene Regulatory System in Adaptation of Yersinia  pestis to Environmental Stress in the Flea Digestive Tract

status: Public on Feb 09 2017

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

summary: The Yersinia pestis PhoPQ gene regulatory system is induced during infection of the flea digestive tract and is required to produce adherent biofilm in the foregut, which greatly enhances bacterial transmission during a flea bite. To understand the in vivo context of PhoPQ induction and to determine PhoP-regulated targets in the flea, we undertook whole genome comparative transcriptional profiling of Y. pestis wild-type and ΔphoP strains isolated from infected fleas and from temperature-matched in vitro planktonic and flowcell biofilm cultures. In the absence of PhoP regulation, the gene expression program indicated that the bacteria experience diverse physiological stresses and are in a metabolically less active state. Multiple stress response genes, including several toxin-antitoxin loci and YhcN family genes responsible for increased acid tolerance, were upregulated in the phoP mutant during flea infection. The data imply that PhoPQ is induced by low pH in the flea gut, and that PhoP modulates physiologic adaptation to acid and other stresses encountered during infection of the flea. This adaptive response, together with PhoP-dependent modification of the bacterial outer surface that includes repression of pH 6 antigen fimbriae, supports stable biofilm development in the flea foregut.

platform_organism:
Borreliella burgdorferi
Yersinia pestis
Coxiella burnetii
Chlamydia trachomatis
Staphylococcus aureus
Streptococcus pyogenes

overall_design: Yersinia pestis wild type vs. phoP mutant at various growth conditions

first: Viveka

last: Vadyvaloo

first: Austin

last: Viall

first: Clayton

last: Jarrett

first: Angela

last: Hinz

first: Daniel

first: Joseph

last: Hinnebusch


title: Comparison of gene expression profiles between myxoid and round cell component in myxoid liposarcoma

city: Tokyo

first: Yutaka

last: Nezu

address: Tsukiji 5-1-1, Chuo-ku

department: Molecular and Cellular Medicine

institute: National Cancer Center, Research Institute

summary: Round cell component is a resk factor associated with metastasis and poor prognosis in myxoid liposarcoma. To identify microRNAs which play a role in the malignancy of round cell component, we performed microRNA microarray analysis and compared the miRNA expression profilings between myxoid and round cell component.

overall_design: microRNA expression profiles were measured in myxoid component and round cell component. Eight sample pairs from clinical myxoid liposarcoma FFPE were included. All enrolled patients did not receive any chemotherapy and radiotherapy.


title: Wnt5a Drives The State Transition To An Invasive Phenotype In Human Glioblastoma Cancer Stem Cells

city: S. Giovanni Rotondo (FG)

first: Tommaso

last: Mazza

address: Viale Cappuccini, 1

department: Bioinformatics

country: Italy

institute: IRCCS Casa Sollievo della Sofferenza

summary: Numerous pathways underlie brain invasion by tumors, a critical element underpinning recurrence and lethality in human glioblastomas (hGBMs). The identification of the master factors that elicit these pathways globally, driving invasion altogether, eludes us. We report that high expression levels of non-canonical Wnt5a characterize the most invasive gliomas, epitomize dismal prognosis and discriminate the most infiltrating mesenchymal hGBMs from proneural and classical ones. Exacerbated Wnt5a defines mesenchymal hGBM cells (Wnt5aHigh) possessing prototypical invasiveness and tumor-promoting stem-like characteristics (TPCs), but not their Wnt5aLow siblings. While inhibition of Wnt5a suppresses infiltration in mesenchymal hGBM TPCs, administration or over-expression of Wnt5a elicits the opposite effects, turning on infiltrative “mesenchymal-like” molecular programs in poorly motile, classical hGBM TPCs and Wnt5aLow mesenchymal TPCs, ex vivo and intracranially. Anti-Wnt5a antibodies or antagonist Wnt5a peptides block invasion, increasing survival in clinically relevant intracranial hGBM models. Wnt5a emerges as a master regulator in gliomatous invasion, endowing hGBM TPCs with archetypal, infiltratory transcriptional and functional profiles, providing a unique target to tackle brain invasion by hGBM cancer stem cells.

overall_design: A total of 12 samples were analyzed. Each experimental group was made of two biological replicates. Each biological replicate had two technical replicates. Sorted hGBM specimens were compared with unsorted hGBM specimens.

first: Elena

last: Binda

first: Angelo

middle: L

last: Vescovi


title: Transcription factor TWIST-1 overexpression in acute myeloid leukemia cell line U937

city: TianJin

first: Xiao Tong

last: Ma

state: TianJin

address: Blood hospital, 288 Nanjing Road

department: Institute of Hematology & Blood Diseases Hospital

institute: Chinese Academy of Medical Sciences

summary:
Alterations of TWIST-1 expression are often seen in solid tumors and contribute to tumorigenesis and cancer progression. However, studies concerning its pathogenic role in leukemia are scarce. Here we show that TWIST-1 is a new candidate gene contributing to leukemogenesis of myeloid leukemia.
We used array as one tool to determine gene expression profiles of control and TWIST-1-overexpressing U937 cells.

overall_design: U937 cell line was transduced with TWIST-1 or empty vector. GFP+ cells were sorted. Microarray was performed at GMINIX in Shanghai. Total RNA was isolated with TRIzol reagent (Invitrogen, Canada) and purified using RNeasy Mini Kit (Qiagen, German), including a DNase digestion treatment. RNA concentrations were determined by NanoDrop 2000 (Thermo, America). RNA was labeled using the GeneChip® WT Terminal Labeling and Controls Kit combined with the Ambion® WT Expression Kit. Labeled cRNA was hybridized to GeneChip® Human Transcriptome Array 2.0 arrays (Affymetrix, America).

first: XiaoTong

last: Wang


title: Functional role and therapeutic targeting of p21-associated kinase 4 (PAK4) in Multiple Myeloma

status: Public on Jan 19 2017

city: Boston

first: Mehmet

middle: Kemal

last: Samur

state: MA

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute

summary: Dysregulated oncogenic serine/threonine kinases play a pathological role in diverse forms of malignancies, including multiple myeloma (MM), and thus represent potential therapeutic targets. Here, we evaluated the biological and functional role of p21-activated kinase 4 (PAK4), and its potential as a new target in MM for clinical applications. PAK4 promoted MM cell growth and survival via activation of MM survival signaling pathways, including the MEK-ERK pathway. Furthermore, treatment with orally bioavailable PAK4 allosteric modulator (KPT-9274) significantly impacted MM cell growth and survival in a large panel of MM cell lines and primary MM cells alone and in the presence of bone marrow microenvironment. Intriguingly, we have identified FGFR3 as a novel binding partner of PAK4 and observed significant activity of KPT-9274 against t(4;14)-positive MM cells. These data support PAK4 as an oncogene in myeloma, and provide the rationale for the clinical evaluation of PAK4 modulator in myeloma.

overall_design: Control and 48 hours treated samples from 2 multiple myeloma cell lines

first: Mariateresa

last: Fulciniti

middle: K

first: Nikhil

last: Munshi


title: EGFR-mediated FASN signaling promotes TKI resistant Non-Small Cell Lung Cancer tumor cell survival

status: Public on Jan 31 2017

city: Singapore

first: Henry

last: Yang

address: 28 Medical Drive

country: Singapore

institute: Cancer Science Institute of Singapore

summary: Metabolic reprogramming is widely known as a hallmark of cancer cells to allow adaptation of cells to sustain survival signals. In the past decade, altered lipid metabolism has been recognized to be a property of malignant cells. In this report, we describe a novel oncogenic signaling pathway exclusively in tyrosine kinase inhibitor (TKI)-resistant epidermal growth factor receptor (EGFR) mutant non-small cell lung cancer (NSCLC). EGFR mediates TKI-resistance through regulation of the fatty acid synthase (FASN), and inhibition of this pathway using the FASN inhibitor Orlistat, triggers cell death and reduces tumor sizes both in culture systems and in vivo. Together, data shown here provide compelling evidence that the fatty acid metabolism pathway is a candidate target for TKI-resistant NSCLC treatment.

overall_design: Total RNA prepared from parental and gefitinib-resistant PC-9 cells was used to probe Illumina HT-12v4 chip.

first: Azhar

last: Ali

last: Levantini

first: Jun

middle: T

last: Teo

first: Julian

last: Goggi

first: John

last: Clohessy

first: Chan-shuo

last: Wu

first: Polly

last: Chen

first: Olivier

last: Kocher

first: Junyan

last: Zhang

first: Kishore

last: Bhakoo

first: Tan

middle: M

last: Chin

last: Tenen


title: A machine learning classifier trained on cancer transcriptomes detects NF1 inactivation signal in glioblastoma

status: Public on Feb 01 2017

city: Hanover

first: Robert

last: Allaway

state: New Hampshire

address: Vail 501A, 72 College St

department: Department of Molecular and Systems Biology

institute: Geisel School of Medicine

summary: Analysis of gene expression in pathologically confirmed glioblastoma (GBM) samples. These data were used to test a classifier that was generated to distinguish GBM tumor samples with loss of neurofibromin 1 (NF1) function

overall_design: Microarray analysis was performed on total RNA isolated from flash frozen GBM samples.

first: Gregory

middle: P

last: Way

first: Rebecca

last: Barnard

first: Stephanie

last: Bouley

first: Brian

last: O'Roak

first: Camilo

last: Fadul

first: Yolanda

last: Sanchez

first: Casey

middle: S

last: Greene


title: Human expression data from Glioblastoma cell malignancy and drug sensitivity are affected by the cell of origin.

status: Public on Jan 23 2017

city: Uppsala

first: Sven

last: Nelander

address: Dag Hammarskjölds v. 20

department: Department of Immunology, Genetics and Pathology

institute: Uppsala University

summary:
The cell of origin in glioblastoma is not formally proven but generally accepted to be a neural stem cell or glial precursor cell. In addition, there is also limited knowledge about the functional consequences of the cell of origin for glioblastoma development and response to therapy.
We have investigated the role of cell of origin in glioblastoma by inducing glioblastomas of defined cell of origin using PDGFB in the brains of adult mice. Gene expression was analysed from cultured mouse glioblastoma cells and a mouse cell origin gene signature was extracted that we used in a cluster analysis on gene expression data from patient-derived glioblastoma cell lines.

overall_design: Gene expression was analyzed on a panel of 61 patient-derived glioblastoma cell lines. All cells were cultured adherently under stem cell conditions.

first: S

first: L

last: Uhrbom


title: Gene expression changes in early phase of venom immunotherapy

status: Public on Jan 21 2017

city: Wroclaw

first: Pawel

last: Karpinski

address: Marcinkowskiego 1

department: Department of Genetics

country: Poland

institute: Wroclaw Medical University

summary: Towards a better understanding of molecular processes underlying the acquisition of immune-tolerance during VIT (venom immunotherapy), we analysed genome-wide gene expression profiles of  patients with severe hymenoptera venom allergy (HVA), who were analyzed prior to VIT and 12 months after the beginning of a VIT. The study also includes individuals withhout signs of HVA (as revealed by skin tests); beekepers and HVA patients sampled between 1st and 2nd month of VIT.

overall_design:
Study includes 11 HVA patients sampled prior VIT; 12 HVA patients sampled after 12months of VIT; 12 patients sampled between 1st and 2nd month of VIT; 12 individuals with negative skin  tests for HVA; 12 beekepers. For computation, imputation and testing of deconvolution-based cell-specific differential expression we used blood counts available for 24 samples. Blood used for measurements of blood counts has been sampled in parallel to blood sample for microarray experiment.
The after1MonthVIT patients are unrelated to the priorVIT/after12monthsVIT paired patients.

first: Maria

last: Sasiadek


title: Identification of microRNA profile specific to Cancer Stem-Like Cells directly isolated from Human Larynx Cancer Specimens

status: Public on Jan 16 2017

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

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

overall_design: Refer to individual Series


title: Expression data from BEAS-2B cells

status: Public on Jan 10 2017

city: Beijing

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

summary:
BEAS-2B cells are human bronchial epithelial cells, and often used as a in vitro model for the detection of potential pulmonary toxicity of chemicals.
We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes after treated with chemical substance

overall_design: BEAS-2B cells were selected for RNA extraction and hybridization on Affymetrix microarrays. We tested the expression data of BEAB-2B cells treated with PM2.5 suspended in DMEM or DMEM only as normal control.

first: Yang

last: Li

first: Zhiwei

last: Sun


title: Global Gene Expression Fails to Discriminate Thin Melanomas with Poor Outcomes

status: Public on Jan 15 2017

city: Royal Oak

first: Bryan

last: Thibodeau

state: MI

address: 3811 West 13 Mile Road

department: BioBank

institute: Beaumont Research Institute

summary:
Melanoma is the fifth-most common cancer diagnosed in the United States with a dramatic increase in incidence among both men and women. Most melanomas present as thin lesions (≤1.0mm) and have a good prognosis. However a small percentage of patients (5-10%) with thin lesions recur or metastasize. The aim of our study was to elucidate which thin melanomas (< 1.0 mm thickness) have the propensity to metastasize to regional lymph nodes or distant sites. Our focus was analyzing gene expression as a whole. We sought to identify a distinct pattern of gene expression within thin melanomas that were known to have eventually metastasized to regional lymph nodes or distant sites, from those that followed the typical course with good response to wide local excision alone.
While gene expression differences were observed between nine thin melanoma patients with poor clinical outcome compared to ten patients with a good clinical outcome, neither the number of genes nor the magnitude of the fold difference was very substantial or significant. Although cluster analysis was able to use this subset of genes to definitively separate a subset of the poor responders from the good responders, there remained a mixed group of tumors which could not be predicted from gene expression alone.  Pathway analysis did identify cellular processes that were regulated based upon response, including categories commonly associated with melanoma progression
The goal of this pilot study was to identify gene expression changes within the tumor cells of thin melanomas that have a poor outcome that would discriminate them  from thin melanomas that do not recur or metastasize . Our results conclude that there were very few differences between these groups.  Future research will be required and investigation of the mutational landscape of these different tumor sub-types may be another strategy to uncover genomic changes that drive recurrence and metastasis.

overall_design: Formalin-fixed paraffin-embedded tissue from patients with thin melanoma were used to compare gene expression from patients with a good response to wide local excision alone (>10 years with no recurrence) to those that eventually metastasized either to regional lymph nodes or distantly.

first: Zachary

last: Hothem

first: Andrew

last: Bayci

first: Billie

middle: E

last: Ketelsen

first: Laura

last: Fortier

first: Alison

middle: F

last: Uzieblo

first: Diane

last: Cosner

first: Kristin

last: Totoraitis

first: Richard

middle: D

last: Keidan

first: George

last: Wilson


title: Transcript expression analysis of the NETotic neutrphils

status: Public on Dec 31 2016

city: New Delhi

first: Meraj

middle: Alam

last: Khan

state: Delhi

address: Room No.2029

department: Physiology

country: India

institute: All India Institute of Medical Sciences

summary: Neutrophils are short-lived innate immune cells. Upon encountering appropriate stimuli, neutrophils generate and release neutrophil extracellular traps (NETs), primarily via NADPH oxidase (Nox)-dependent (~2 hours) or Nox-independent NETosis (~15-60 minutes). Ironically, DNA transcription in dying neutrophils remains an enigma. We hypothesized that transcriptional activation, regulated by NETosis-specific kinases, is important to drive the chromatin decondensation necessary for NETosis. For the first time, we show here that (i) the degree of NETosis corresponds to the degree of genome-wide transcription; (ii) kinase-specific transcriptional activation reflects transcriptional firing during different types of NETosis; and (iii) Transcriptomics suggests that NETosis could differentially regulate inflammation. Therefore, we propose that the initial steps of transcriptional firing, but neither transcription per se help to drive NETosis.

overall_design: To determine the transcriptional activity during NETosis in the same time period, we extracted total RNA from unstimulated and NETotic neutrophils at 30- and 60-min time points (3 conditions: unstimulated controls, PMA-activated cells, A23187-activated cells; 3 independent donors for each condition; each time point had its own control; a total of 18 samples). Using these samples we conducted transcriptome analysis by using Affymetrix platform (HTA2) gene chips.

middle: A

first: Nades

last: Palaniyar


title: Identification of microRNA profile specific to Cancer Stem-Like Cells directly isolated from Human Larynx Cancer Specimens (Agilent-031181)

summary: Our results showed that certain miRNAs in CD133high cells could be used as cancer stem cell markers. Based on these results, we propose that this panel of miRNAs might carry crucial roles in LCa initiation, progression, metastasis, chemoresistance and recurrence through regulating stem cell properties of tumor cells.

overall_design: In this study, we investigated genome-wide miRNA expression profile of laryngeal CSLCs enriched for CD133 surface marker to identify a CSLCs specific miRNA signature.  Two group comparison.

first: Michael

last: Ittmann

first: Mustafa

last: Ozen

first: Yiqun

last: Zhang


title: Expression data from human clear-cell renal cell carcinoma cell line 769-P after overexpression of FOXK2

status: Public on Dec 23 2016

city: beijing

first: zhang

last: fan

address: beijing china

department: Department of Urology

institute: 301 hospital

summary:
Clear-cell renal cell carcinoma (ccRCC) is one of the most common urological malignant neoplasms. In addition, ccRCC is a highly aggressive cancer with a concomitant poor prognosis. Forkhead box K2 (FOXK2) has been reported to involve in many molecular mechanisms.However, little is known about the role FOXK2 plays in clear-cell renal cell carcinoma. Our previous study showed that FOXK2 mRNA and protein expression were decreased in human ccRCC tissues and suppressed the proliferation of ccRCC cells both in vitro and in vivo.
We used microarrays (Affymetrix HTA2.0 Array) to detail the differentially expressed genes after overexpression of FOXK2, and aim to find potential one or more target gene/genes of FOXK2

overall_design: We conducted the genome-wide transcriptome profiling of human ccRCC cell line 769-P after transfection with pLV-EGFP-FOXK2 (overexpression of FOXK2) and plv-EGFP empty vector (control)

first: Fan


title: Transcriptional profiling on leaves overexpressing Pha13 or Pha21 in Phalaenopsis aphrodite

status: Public on Jan 07 2017

city: Taipei

first: Hsin-Hung

last: Yeh

address: No. 128, Sec. 2, Academia Road, Nankang,

department: ABRC

institute: Academia Sinica


title: Genome-wide Expression Profiling in Irritable Bowel Syndrome

city: Los Angeles

first: Chang

last: Lin

state: CA

address: 10833 Le Conte Avenue, CHS 47-122

department: Medicine

institute: University of California, Los Angeles

summary: Differential gene expression profiling in peripheral blood mononuclear cells (PBMCs) was performed using Human Transcriptome Array 2 (HTA2)

overall_design: Expression profiles of peripheral blood mononuclear cell (PBMCs) from 35 IBS samples and 32 healthy control was assessed.

first: Lin

last: Chang

first: Emeran

last: Mayer


title: Transcriptional profiling on leaves of Pha13 (PATC148746) overexpressed Phalaenopsis aphrodite

summary: To identify genes affected by Pha13, Pha13 was transiently overexpressed in leaves of P. aphrodite by agroinfiltration.  The leaves of P. aphrodite infiltrated with agrobacterium carrying empty vector (without Pha13) was used as a control. Transcriptional profiling was analyzed using a customized oligonucleotide array with RNA extracted from Pha13 and empty vector overexpressed leaves of P. aphrodite.  The sequences used for probe design were collected from the Orchidstra 2.0 database (http://orchidstra2.abrc.sinica.edu.tw/orchidstra2/index.php). Totally, 42,973 probes were designed on this oligonucleotide array.

overall_design: Two-condition experiment, Empty vector (EV) vs. Pha13 transient overexpression (Pha13-OE). Biological replicates: 3 control replicates, 3 transient overexpression replicates.


title: Expression data from colorectal cancer and liver metastasis

status: Public on Dec 02 2016

city: Montreal

first: Qin

last: Shao

state: Quebec

address: 1001 Décarie Boulevard

department: Pathology

country: Canada

institute: McGil University Health Centre Research Institute

summary:
To identify the driver factors in liver metastasis of colorectal cancer, and seek for possible biomarkers, we applied array trascriptome detection using approaches tailored to FFPE derived RNA
Integrated analysis identified metastasis related genes with potentially high clinical significance.

overall_design: We used matched primary cancer tissue, liver metastasis samples from same patient and primary control with no liver metastasis in order to compare their genomic and transcriptomic profile.

first: Hani

last: Choudhry

first: Peter

last: Metrakos

first: Victoria

last: Marcus

first: Kung

last: Dong

first: Iioannis

last: Ragoussis

first: Zu-hua

last: Gao


title: Expression data from 2 cohorts of human pancreatic ductal adenocarcinoma (PDAC) tumors

status: Public on Nov 18 2016

city: New York

first: Julia

middle: Nanyi

last: Zhao

address: 408 68th Streer

institute: Memorial Sloan Kettering Cancer Center

summary:
In this dataset, we included expression data obtained from 30 resected human PDAC tumors, to examine what genes are differentially expressed in different cohorts that might lead to various outcomes
The two cohorts we have are defined as short term survivors (STS) with median survival of >3 month and <1 year postsurgery, and long term survivors (LTS) with overall survival of >3 years postsurgery.

overall_design: 30 total samples were analyzed

middle: N

first: Vinod

last: Balachandran


title: Transcriptional profiling on leaves of Pha21 (PATC144963) overexpressed Phalaenopsis aphrodite

summary: To identify genes affected by Pha21, Pha21 was transiently overexpressed in leaves of P. aphrodite by agroinfiltration.  The leaves of P. aphrodite infiltrated with agrobacterium carrying empty vector (without Pha21) was used as a control. Transcriptional profiling was analyzed using a customized oligonucleotide array with RNA extracted from Pha21 and empty vector overexpressed leaves of P. aphrodite.  The sequences used for probe design were collected from the Orchidstra 2.0 database (http://orchidstra2.abrc.sinica.edu.tw/orchidstra2/index.php). Totally, 42,973 probes were designed on this oligonucleotide array.

overall_design: Two-condition experiment, Empty vector (EV) vs. Pha21 transient overexpression (Pha21-OE). Biological replicates: 3 control replicates, 3 transient overexpression replicates.


title: Clonal variation in drug and radiation response among glioma-initiating cells is linked to  proneural-mesenchymal transition (HTA 2.0)

status: Public on Dec 13 2016

first: Bo

last: Segerman

address: Dag Hammarskjolds v 20

summary: Intra-tumor heterogeneity is a hallmark of glioblastoma multiforme, and thought to negatively affect treatment efficacy. Here we establish libraries of glioma-initiating cell (GIC) clones from patient samples and find extensive molecular and phenotypic variability between clones, including a wide range of responses to radiation and drugs. This widespread variability was observed as a continuum of multitherapy resistance phenotypes linked to a proneural-to-mesenchymal shift in the transcriptome.

overall_design: Affymetrix HTA 2.0 array analyses were performed according to the manufacturer's directions on total RNA extracted from 115 clonal malignant glioma cultures and 6 bulk cultures representing the parental material used to derive clones. 25 bilogical replicates were also included.

first: Bengt

last: Westermark


title: Nanostring nCounter expression analysis of sea lamprey embryos and adult testes (Petromyzon marinus)

status: Public on Oct 21 2016

city: Lexington

first: Mark

last: Evers

address: 800 Rose Street

department: College of Medicine

institute: University of Kentucky

summary: This project is designed to measure changes in gene expression during sea lamprey development and in the adult germline

overall_design: RNA was extracted in biological triplicate from sea lamprey embryos at 1, 2, 2.5, 3, 4, and 5 days post-fertilization and in technical replicates from adult testes using trizol extraction. RNA was analyzed on the Nanostring nCounter gene expression assay to measure changes in gene expression across developmental time points and in adult testes

first: Jeramiah

last: Smith

first: Stephanie

last: Bryant


title: Distinct gene expression programs during erythropoiesis from adult and cord blood progenitor cells compared to hiPSCs

status: Public on Oct 05 2016

city: Oxford

first: Alison

last: Merryweather-Clarke

address: John Radcliffe Hospital, Headley Way, Headington

country: United Kingdom

institute: NHSBT Oxford

summary:
Erythropoiesis in mammals replenishes the circulating red blood cell (RBC) pool from hematopoietic stem/progenitor cells (HSPCs). Two distinct erythropoietic programs have been described. In the first trimester, hematopoietic precursors in the fetal yolk sac follow a primitive pattern of erythropoiesis. However, in the second trimester, hematopoietic stem cells (HSCs) from the fetal liver and later from the bone marrow differentiate by a definitive program of erythropoiesis to yield enucleated erythrocytes. RBCs can also be derived from human induced pluripotent stem cells (hiPSCs) and can express many of the red cell proteins required for normal erythrocyte function, presaging in vitro RBC production for clinical use. However, expansion and enucleation from hiPSCs is less efficient than with erythroblasts (EBs) derived from adult or cord blood progenitors. We hypothesized that substantial differential gene expression during erythroid development from hiPSCs compared to that from adult blood or cord blood precursors could account for these hitherto unexplained differences in proliferation and enucleation. We have therefore grown EBs from human adult and cord blood progenitors and from hiPSCs. Gene expression during erythroid culture from each erythroblast source was analyzed using algorithms designed to cluster co-expressed genes in an unsupervised manner and the function of differentially expressed genes explored by gene ontology. Using these methods we identify specific patterns of gene regulation for adult- and cord- derived EBs, regardless of the medium used, that are substantially distinct from those observed during the differentiation of EBs from hiPSC progenitors which largely follows a pattern of primitive erythropoiesis.
A total of 74 samples were analyzed. Our primary goal was to compare erythropoiesis from hiPSC-derived EBs with that from adult or cord blood PBMC-derieved EBs. We wanted to provide a high resolution atlas for investigators dissecting the programs of erythroid development and highlight the disparities between erythropoiesis in vitro from diverse stem/progenitor cell origins. Erythroblasts were grown in vitro from CD34+ erythroid progenitors isolated from Human Adult PBMCs (51 AB-EB samples), Human Cord PBMCs (10 CB-EB samples) or human induced pluripotent stem cells (13 hiPSC-EB samples). Three culture media were used for AB-EBs: Standard Erythroid Medium (SEM) containing 2% FBS (SEM-F), SEM in which FBS was replaced with 1% BSA (SEM-B) and SEM optimized for culture of EBs from hiPSCs (SEM-i). After culturing for 4,7,10,12, or 14 days in SEM-F, AB-EBs media were harvested in triplicate and sorted using flow cytometry (FACS) into enriched homogeneous erythroblast populations based on cell surface expression of CD36 (used for days 4-7), CD71 and CD235a. Magnetic beads specific for CD34 were used to isolate CD34+ day 0 progenitors. Magnetic beads were also used to isolate AB-EBs grown in SEM-F and SEM-i after 7 days (CD71+) and 14 days (CD235a beads). AB-EBs were also cultured in SEM-B for 4,7, or 14 days and sorted by FACS. CB-EBs were cultured in SEM-F for 7 or 14 days, and sorted by FACS as for AB-EBs. HiPSC-EBs were cultured in SEM-i for 7 or 14 days, and isolated using magnetic beads as fof AB-EBs. Total RNA was isolated from all these populations in triplicate (with a few exceptions), and also at day zero from CD34+ AB-EB progenitors, CB-EB progenitors and hiPSCs using magnetic beads. Additionally, CD31+ day zero hiPSCs were isolated using magnetic beads. RNA was extracted using MiRVana (Life Technologies) and DNA removed using Turbo DNA-Free (Life Technologies). The microarray target was prepared from 100ng total RNA for hybridization to Affymetrix GeneChip Human Transcriptome 2.0 ST microarrays (HTA2) using the Ambion WT protocol (Life Technologies) and Affymetrix labelling and hybridization kits (Affymetrix). Labelled DNA mean yield was 13.5 μg (minimum: 8.5 μg; maximum: 20.5 μg). HTA2 arrays were hybridized with 5 μg of labelled DNA.   The Affymetrix GeneChip Fluidics Station 450 was used to wash and stain the arrays with streptavidin–phycoerythrin, according to the standard protocol for eukaryotic targets (IHC kit, Affymetrix). Arrays were scanned with an Affymetrix GeneChip scanner 3000 at 570nm. Intensity values were determined using GeneChip Operating Software (Affymetrix)and normalized by the Robust Multiarray Average algorithm using Affymetrix Expression Console software. Statistical analysis of differential expression was conducted using the Linear Models for Microarray Data package from the Bioconductor suite in R (www.bioconductor.org). The B values, p-values, and fold changes were used to select differentially expressed (DE) genes reaching a minimum linear expression value of 100 in all replicates of at least one sample group (p ≤ 0.01, fold change (FC) ≥ 2, B > 2.945). Principal component analysis (PCA) was conducted and displayed using Python packages. Hierarchical clustering (HC) analysis was performed using Python SciPy. Heat maps were generated using Python matplotlib. More advanced consensus clustering was conducted using SMART and Bi-CoPaM algorithms in MATLAB, using Biclustering from the biclust package in R. Biopython to fetch 1kb of genomic DNA sequence upstream of the transcriptional start sites (TSS) of each gene in the cluster. MEME suite was used for transcription factor binding site (TFBS) analysis, seeking homology with motifs in the Jolma database. Differentially-expressed genes were examined for enriched functional ontologies using GeneCoDis. Expression profiles of selected genes were validated by QPCR. Gene expression profiles (GEPs) of AB-EBs in SEM-F were as expected for erythroid genes and similar to those observed for CB-EBs in SEM-F. The media used had little effect on AB-EB GEPs. However, substantial robust and specific GEPs were observed in hiPSC-EBs which may, at least in part, underlie reduced proliferation and enucleation of erythroid cells from hiPSCs.  These include genes involved in autophagy and cell cycle.

overall_design: The study comprised 74 samples in: 16 adult sample groups, in triplicate unless otherwise stated (day (d) 0_CD34+;  d4_SEM-B_CD36+,CD71+,CD235a- (2 replicates); d4_SEM-F_CD36+,CD71+,CD235a-; d4_SEM-i_CD36+,CD71+,CD235a-; d7_SEM-B_CD36+,CD71+,CD235a-; d7_SEM-F_CD36+,CD71+,CD235a-; d7_SEM-B_CD36+,CD71+,CD235a+; d7_SEM-F_CD36+,CD71+,CD235a+; d7_SEM-F_CD71+ (5 replicates); d7_SEM-i_CD71+ (5 replicates); d10_SEM-F_CD71+,CD235a+; d12_SEM-F_CD71+,CD235a+; d14_SEM-F_CD71+,CD235a+; d14_SEM-B_CD71+,CD235a+; d14_SEM-F_CD235a+; d14_SEM-i_CD235a+); 4 Cord Blood sample groups (d0_CD34+;  d7_SEM-F_CD36+,CD71+,CD235a-; d7_SEM-F_CD36+,CD71+,CD235a+ (in duplicate); d14_SEM-F_CD71+,CD235a+ (in duplicate)); and 4 hiPSC sample groups (d0_CD31+; d0_CD34+, d7_SEM-i_CD71+ (4 replicates); d14_SEM-i_CD235a+). The reference samples used were d0_CD34+ AB-EBs, CB-EBs or hiPSC-EBs as appropriate.

first: Alex

middle: J

last: Tipping

first: Abigail

last: Lamikanra

first: Rui

last: Fa

first: Basel

last: Abu-Jamous

first: H

last: Tsang

first: Lee

last: Carpenter

first: Kathryn

last: Robson

first: Asoke

last: Nandi

first: David

last: Roberts


title: Expression data of human lymphoid progenitors

status: Public on Dec 07 2016

city: PARIS

first: Bruno

last: CANQUE

address: 1 avenue Claude VELLEFAUX

department: INSERM U1126

country: France

institute: INSTITUT UNIVERSITAIRE D'HEMATOLOGIE

summary: We used whole genome transcriptome as gene discovery to dissect the developmental organization of human lymphopoiesis.

overall_design: Gene expression of human CD127-CD7-/+ (CD34++CD45RA+ITGB7++CD127-CD2-CD115-CD116-CD123-CD10-CD19-CD24-) or CD127+CD7-/+ (CD34++CD45RA+ITGB7++CD127+CD2-CD115-CD116-CD123-CD10-CD19-CD24-) Early Lymphoid Progenitors (ELPs) as compared to Lymphoid-Mono-Dendritic Progenitors (LMDPs: CD34++ CD45RA+CD7-ITGB7-CD127-CD2-CD115-CD116-CD123-CD10-CD19-CD24-). Cells were extracted from the bone marrow of NSG mice engrafted with neonatal UCB CD34+ HPCs (NSG) or from of 21-week-old fetal donor (PRIM).

last: Canque


title: Transplant tissue specfic exosome platform for noninvasive monitoring of immunologic rejection [mRNA]

status: Public on Oct 18 2016

city: Philadelphia

first: Prashanth

last: Vallabhajosyula

state: PA

address: 3400 Spruce Street

department: Surgery

institute: University of Pennsylvania

summary: In transplantation, there is a critical need for non-invasive biomarker platforms for monitoring immunologic rejection. We hypothesized that transplanted tissues release donor specific exosomes into recipient circulation/ bodily fluids, and that the quantitation and profiling of their intra-exosomal cargoes would constitute a novel biomarker platform for monitoring rejection.  We tested this hypothesis in a human into mouse xenogeneic islet transplant model, and validated the concept in clinical settings of islet and renal transplantation.  In the xenogeneic model, islet transplant exosomes in recipient blood were quantified over long-term follow-up using anti-human leukocyte antigen (HLA) antibody that is only expressed on human islets (p=1.6x10-14).  Transplant islet exosomes were purified using anti-HLA antibody conjugated beads and their cargoes contained bona fide islet endocrine hormone markers insulin, glucagon, and somatostatin.  Rejection led to significant decrease in transplant islet exosome signal (p=4x10-15), along with distinct changes in its microRNA and proteomic profiles prior to appearance of hyperglycemia.  In the clinical settings of islet (n=5) and renal (n=5) transplantation, donor exosomes with respective tissue specificity for islet β cells and renal epithelial cells were reliably characterized in recipient plasma over follow-up (up to 5 years; p=0.0001).  Collectively, these findings demonstrate the biomarker potential of transplant exosome characterization for providing a non-invasive window into the conditional state of the transplant tissue.

overall_design: We assessed an in vivo read-out of TISE cargo as compared to its transplanted human islet tissue counterpart. Transplant islet exosomes from two independent experiments were analyzed.  Long RNA microarray profiling of islet exosomes and islet graft tissue was performed.

first: Laxminarayana

last: Korutla

first: Andreas

last: Habertheuer

first: Ming

last: Yu

first: Susan

last: Rostami

first: Chao-Xing

last: Yuan

first: Sanjana

last: Reddy

first: Chengyang

last: Liu

first: Varun

first: Brigitte

last: Koeberlein

first: Jennifer

last: Trofe-Clark

first: Michael

middle: R

last: Rickels

first: Ali

last: Naji


title: Transplant tissue specfic exosome platform for noninvasive monitoring of immunologic rejection

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

platform_organism:
Homo sapiens
synthetic construct


title: Expression data from HCT116 cells following H19 knockdown

status: Public on Sep 29 2016

first: HUI

last: LING

address: 1901 east road

department: Experimental Therapeutics

institute: The University of Texas MD Anderson Cancer Center

summary:
Knockdown of H19 leads to cell cycle arrest, reduced cell proliferation, and reduced cell migration in HCT116 cells.
We used microarrays to detail the global programme of gene expression following H19 knockdown in HCT116 cells

overall_design: We used two different siRNAs to knockdown H19 expression for 48 hr in HCT116 cells, and collected RNAs for gene expression profiling.

first: George

last: Calin

first: Hui

last: Ling


title: Expression data from HCT116 cells following CTNNB1 knockdown

summary: We used microarrays to detail the global programme of gene expression following CTNNB1 knockdown in HCT116 cells

overall_design: We treated HCT116 cells with CTNNB1 siRNA for 48 hr, and collected RNAs for gene expression profiling.


title: Expression data from HCT116 cells following CDK8 knockdown

summary: We used microarrays to detail the global programme of gene expression following CDK8 knockdown in HCT116 cells

overall_design: We treated HCT116 cells with CDK8 siRNA for 48 hr, and collected RNAs for gene expression profiling.


title: H19 Noncoding RNA, an independent prognostic factor, regulates essential Rb-E2F and CDK8/ß-catenin signaling in colorectal cancer

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

overall_design: Refer to individual Series


title: Expression data from DLD1 cells following H19 knockdown

summary:
Knockdown of H19 leads to cell cycle arrest, reduced cell proliferation, and reduced cell migration in DLD1 cells.
We used microarrays to detail the global programme of gene expression following H19 knockdown in DLD1 cells

overall_design: We used two different siRNAs to knockdown H19 expression for 24 hr in DLD1 cells, and collected RNAs for gene expression profiling.


title: Gene expression profiles (GEP) from melanocyte cell line (HeMa), and from two melanoma cell lines (M6 and A375)

status: Public on Sep 02 2016

city: Florence

first: Anna

last: Laurenzana

address: Viale Morgagni 50

department: Department of Experimental and Clinical Biomedical Sciences

institute: University of Florence

summary:
In most solid tumors, the Warburg effect, also known as aerobic glycolysis, represents a major biochemical alteration associated with malignant transformation. Although the exact molecular mechanisms underlying this metabolic change remain to be clarified, the biochemical alteration in cancer cell energy metabolism opens novel avenues for the development of therapeutic strategies to preferentially kill cancer cells by targeting the glycolytic pathway.
We used microarrays to focus on differences among A375, M6 melanoma cells and normal melanocytes (HeMa cells) in terms of glucose metabolism- and invasion-related properties. The transcript analysis showed that melanoma cells  exhibit typical transcriptional features of a glycolytic phenotype, matched with high invasive markers (including increased expression of several matrix metallo-proteinases)

overall_design: Primary Human Epidermal Melanocytes (HeMa) isolated from adult skin were purchased from GIBCO Life Technologies Corporation (California, USA) and were grown in Medium 254CF with calcium plus Human Melanocytes Growth Supplement, obtained from the same company, were used as control . The melanoma cell line A375 (MITF wild type, BRAF V600E, NRAS wild type) was obtained from American Type Culture Collection and grown in Dulbecco’s modified Eagle’s medium  containing 2 mM glutamine, 100 UI/ml penicillin, 100 μg/ml streptomycin and supplemented with 10 % FBS (Euroclone, Milano, Italy). cDNA samples have been generated and labeled from three independent RNA samples of each cellular line. Principal Component Analysis confirmed no batch effect among samples, i.e. no technical sources of variation that have been added to the samples during handling   A375-M6 melanoma cells (M6) were isolated in our laboratory from lung metastasis of SCID bg/bg mice i.v. injected with A375 human melanoma cell line.   A375 cell line was independently validated by STR profiling by the DNA diagnostic centre BMR Genomics (Padova, Italy). The cellular samples for array studies were amplified and kept in culture as mentioned above. Three chips for each experimental group (normal melanocytes, A375 cells and A375-M6 cells) were used in the microarray experiments.

first: Anastasia

last: Chillà

first: Cristina

last: Luciani

first: Silvia

last: Peppicelli

first: Alessio

last: Biagioni

first: Gabriella

last: Fibbi

first: Francesca

last: Bianchini

first: Elena

last: Tenedini

first: Eugenio

last: Torre

first: Lido

last: Calorini

last: Margheri

first: Mario

last: Del Rosso


title: Splicing in gliomas

status: Public on Sep 01 2016

city: Pleasanton

first: Juan

middle: Pablo

last: Romero

address: 6230 Stoneridge Mall Rd

department: Computational Biology

institute: 10x Genomics

summary: The objective of our study was to determine whether aberrant alternative splicing could play a role in the malignant phenotype of GBM.   Patients with GBM were operated with 5-aminolevulinic fluorescence guided surgery. The fluorescent was used to take biopsies from the tumor center, and from adjacent normal-looking tissue. Three paired normal/GBM samples were analyzed in a HJAY J array. We validated our results with conventional PCR and qRT-PCR in those tumor samples and in ten additional GBMs. We performed functional studies using MTT assays (proliferation) and IF qRT-PCR (differentiation).  We generated a list of seven genes with differential alternative splicing between central tumor samples and the adjacent normal-looking tissue. DPF-2(BAF45d) was one of our top candidates. Interestingly, DPF-2 is known as a tumor suppressor gene in the context of the SWI/SNF complex and plays a key role in the development of the central nervous system. The inhibition of our DPF-2 isoform resulted in a significative reduction in proliferation and in a morphology changes towards a more differentiated phenotype in GBM cell lines. Interestingly, our DPF2 tumoral isoform was the predominant transcript in early postnatal murine neural precursors and its expression disappeared as these cells were instructed towards neurons. Our results suggest that the alternative splicing of DPF-2 in GBM could participate in the maintenance of an undifferentiated cellular state. In addition, our data suggest that alternative splicing is a mechanism that could be central to GBM development

overall_design: We compared three paired samples of tumor (glioma)/normal like and 1 sample of pooled brain RNA from healthy donors

first: Guillermo

last: Aldave

first: Marisol

last: Gonzalez-Huarriz

first: Angel

last: Rubio

first: Datta

last: Ravi

last: Valcárcel

first: Belén

last: Miñana

first: Mar

last: Cuadrado-Tejedor

first: Ana

last: García-Osta

first: Roeland

last: Verhaak

first: Enric

last: Xipell

first: Naiara

last: Martínez-Vélez

first: Arlet

last: Acanda de la Rocha

first: Miguel

last: Marigil

first: Jaime

last: Gállego

first: Oskar

last: Marín-Béjar

first: María

last: Carro

first: Roberto

last: Ferrarese

first: Cristobal

last: Belda

last: Ayudos

first: Fernando

last: Pastor

first: Ricardo

last: Díez-Valle

first: Sonia

last: Tejada

first: Marta

last: Alonso


title: Gene expression breast cancer

status: Public on Sep 18 2016

city: Subang Jaya

first: Wei Xiong

last: Wen

state: Selangor

address: No. 1, Jalan SS12/1A

department: Breast Cancer Team

country: Malaysia

institute: Cancer Research Malaysia

summary:
There exists a common deletion polymorphism on the genetic loci of APOBEC3B and this polymorphism exist in ~37% of East Asians and ~7% of Europeans. Germline APOBEC3B deletion has bee27233495n shown to confer modest risk to breast cancer in both East Asian women and women of European descent
We performed expression profiling by array to investigate the significantly differentially expressed genes and enriched gene sets in APOBEC3B-null vs. APOBEC3B breast cancers

overall_design: This series represents RNA isolated from 28 primary breast cancer patients and 3 normal breast tissues. We aim to investigate the distinguish features between APOBEC3B-null and APOBEC3B breast cancers to identify significantly differentially expressed genes and enriched gene sets

first: Wei

middle: X

first: Sian

last: Soo


title: Developmental Vitamin D availability impacts hematopoietic stem cell production

status: Public on Aug 27 2016

city: Boston

first: Trista

last: North

state: Massachusetts

address: 3 Blackfan Circle

institute: Beth Israel Deaconess Medical Center, Harvard Medical School

summary: Vitamin D insufficiency is a global epidemic and despite its high incidence the impact of Vitamin D signaling beyond calcium-bone regulation is not fully understood. To expand our analysis of the impact of 1,25(OH)D3 on hematopoietic stem and progenitor cell (HSPC) production and function in zebrafish and human umbilical cord blood (hUCB), we performed a microarray study to indentify signaling pathways downstream of 1,25(OH)D3 stimulation in hUCB CD34+ cells.

overall_design: Microarray analysis was performed to identify downstream targets of Vitamin D signaling in human umbilical cord blood  (hUCB) CD34+ cells. We compared the expression profile of hUCB HSCs, split and treated ex vivo for 4 hrs with 1,25(OH)D3 at 1mM, with matched vehicle (DMSO) controls. This treatment lead to the identification of 407 differentially expressed genes.

first: M

last: Cortes

first: T

first: S

last: Ho

last: Mistry


title: Global expression profile difference of  hiPSCs between hESCs and human Urine-Derived Cells

status: Public on Aug 23 2016

city: GuangZhou

first: Linli

last: Wang

state: GuangDong

address: Science city Juquan road no. 3

institute: Guangzhou Biocare Cancer Institude

summary: Compare difference Global expression profile of hiPSCs between hESCs and human Somatic cells, showing that hiPSCs and hESCs is consistent in lineages and indicated that the induce method is safe and reliable.

overall_design: There are three groups of samples, each group has two repeated samples, hiPSCs respectively compared with hESCs and human Urine-Derived Cells.

first: Jun

last: Li

first: Yuehua

last: Chen

first: Chunyan

last: Guan

first: Zhiju

last: Zhao

first: Qiang

first: Jianguo

last: Yang

first: Bin

last: Wu

first: Xiaohui


title: HI-LNC RNA knockdown in EndoC-betaH1 cell using lentiviral ami-aRNAs

city: birmingham

first: ildem

last: akerman

address: BR Tower, 3rd Floor, Room 333, Edgbaston,

department: IMSR

institute: University of Birmingham

summary:
We have previously identified hundreds of human islet lncRNAs. Here we functionally characterise 12 such lncRNAs in EndoC-betaH1 cells through loss of function studies.
Our results suggest that a number of them display transcriptional phenotypes.

overall_design: We have used lentiviral based ami-RNAs to knockdown 12 human islet expressed lncRNAs (HI-LNCs) in the beta cell line EndoC-betaH1. EndoC-betaH1cells were transduced with virus for 80 hrs prior to RNA-harvest followed by hybridisation to HTA-2.0 affymetrix microarrays. Each experiment was done in replicates and 5 non targetinf (NT) controls were used.

first: Ildem

last: Akerman

first: Philippe

last: Ravassard

first: Marion

last: Benzara

first: Claire

last: Sauty-Colace

first: Jorge

last: Ferrer


title: APOL1 renal-risk variants induce mitochondrial dysfunction (Affymetrix 1)

city: Winston Salem

first: Lijun

last: Ma

state: NC

address: 1 Medical Center Blvd

department: Nephrology

institute: Wake Forest School of Medicine

summary: To elucidate pathways whereby apolipoprotein L1 gene (APOL1) G1 and G2 variants facilitate kidney disease in African Americans, human embryonic kidney cells (HEK293) were used to establish doxycycline-inducible (Tet-on) cell lines stably expressing reference APOL1 G0 and its G1 and G2 renal-risk variants. Illumina human HT-12-v4 arrays and Affymetrix HTA 2.0 arrays were employed to generate global gene expression data with doxycycline induction. Significantly altered pathways identified through bioinformatics involved mitochondrial function; results were validated using immunoblotting, immunofluorescence and functional assays.

overall_design: Global gene expression profiles were performed on HEK293 Tet-on G0, G1, G2 and empty vector cells with and without Dox induction using Illumina human HT-12 v4 arrays. Another independent gene expression array system, Affymetrix HTA 2.0, was used to verify the results of Illumina arrays. Pair-wise and pattern-based analyses were applied to detect the mostly impacted pathways due to overexpression and by APOL1 genotypes.

first: Jeff

middle: W

last: Chou

first: James

last: Snipes

first: Manish

last: Bharadwaj

first: Ann

middle: L

last: Craddock

first: Dongmei

last: Cheng

first: Allison

last: Weckerle

first: Snezana

last: Petrovic

first: Pamela

last: Hicks

first: Ashok

last: Hemal

first: Gregory

last: Hawkins

first: Lance

last: Miller

first: Anthony

last: Molina

first: Carl

last: Langefeld

first: Mariana

last: Murea

first: John

last: Parks

first: Barry

middle: I

last: Freedman


title: APOL1 renal-risk variants induce mitochondrial dysfunction

first: Lijun

last: Ma


title: Expression data from Human Umbilical Vein Endothelial Cells

status: Public on Aug 11 2016

city: Beijing

first: Hejing

last: Hu

state: Beijing

address: No.10 of XiToutiao street ouside YouAnmen, Fengtai district

department: Department of Toxicology and Sanitary Chemistry

institute: School of Public Health, Capital Medical University

summary:
Examine the toxic effect and molecular mechanisms of PM2.5 in primary human umbilical vein endothelial cells (HUVECs) .
We used microarrays to detail the global programme of gene expression in HUVECs exposed to PM2.5 and identified distinct classes of up-regulated genes.

overall_design: Cultured HUVECs which were treated with PM2.5 at the concentrations of 50 μg/mL or DMEM for 24 h were collected for RNA  extraction and hybridization on Affymetrix microarrays.

first: Junchao

last: Duan

first: Zhiwei

last: Sun


title: Gene expression data from yerba mate treated and non-treated cultured PBMCs activated with phytohemagglutinin

status: Public on Aug 15 2016

city: San Sebastian

first: Maider

last: Muñoz-Culla

address: Paseo Dr.Begiristain s/n

country: Spain

institute: Biodonostia Institute

summary: Yerba mate (YM) has been shown to have anti-inflammatory properties in several studies. However, this effect has been found mainly in obesity-related in inflammation. The aim of this work was to study the effect of YM in cultured peripheral blood mononuclear cells to see whether it has anti-inflammatory properties.  We stimulated peripheral blood mononuclear cells in vitro with phitohemaglutinin in the presence of yerba mate and determined their activation measuring the the expression of CD25 by flow cytometry. We observed that YM treatment produced a dose-dependent reduction in PBMC activation (CD25 positive cells) when they were stimulated with PHA. This effect was also observed in T cells (CD3 positive) subpopulation. Microarray analysis revealed the differential expression of 128 genes in YM-treated cells. According to a protein-protein interaction database, these genes were highly connected and they are involved in inflammatory response.  In summary, it was demonstrated that YM produces a reduction in the amount of activated cells under the stimulation of PHA. Therefore, it might be used in diseases with an inflammatory component.

overall_design: PBMC samples from a healthy individual were cultured and stimulated with phytohemagglutinin. Gene expression of yerba mate treated and non-treated cells was analyzed in duplicates, having in total four microarrays.

first: Matías

last: Sáenz-Cuesta

first: Maier

last: Guereca-Barandiaran

first: Marcelo

last: Ribeiro

first: David

last: Otaegui


title: Expression profiling of Early Stage Lung Squamous Cell Carcinomas

status: Public on Sep 14 2016

city: Bethesda

first: Ana

last: Robles

address: 37 Convent Dr 37/3060D

institute: National Cancer Institute/NIH

summary: One hundred and seven lung Squamous Cell Carcinomas collected from early stage (stage I+II; AJCC 7th edition) patients at the National Cancer Center Hospital (Tokyo, Japan) between 1997 and 2008 were hybridized to the Human Transcriptome (HT) Array 2.0

overall_design: Fresh frozen tissues collected from 107 lung SCC were analyzed with the Affymetrix Human Transcriptome (HT) Array 2.0

first: Rintaro

last: Noro

first: Curtis

middle: C

last: Harris


title: Expression and alternative splicing data of cartilage endplate-derived stem cells (CESCs) under hypoxia or normoxia

status: Public on Jul 18 2016

city: Chongqing

first: Yuan

last: Yao

address: 83 Xinqiao Street, District of Shapingba

institute: Xinqiao Hospital, Third Military Medical University

summary:
Cartilage endplate-derived stem cells (CESCs) with chondro-osteogenic differentiation capacity may be responsible for the balance of chondrification and ossification in cartilage endplate (CEP). CEP is an avascular and hypoxic tissue, and hypoxia could influence the fate of CESCs.
We used high-throughput scanning to identify differentially expressed genes (DEGs) and alternatively spliced genes (ASGs) of CESCs under hypoxia compared to those under normoxia.

overall_design: Human cartilage endplate-derived stem cells (CESCs) were cultured under normoxia and hypoxia for 21 days respectively.


title: miRNAs as Common Regulators of the Transforming Growth Factor (TGF)-β Pathway in the Preeclamptic Placenta and Cadmium-treated Trophoblasts: Links between the Environment, the Epigenome and Preeclampsia

status: Public on Jul 12 2016

city: Chapel Hill

first: Rebecca

middle: Catherine

last: Fry

address: 1213 MHRC

department: Environmental Sciences and Engineering

institute: UNC-Chapel Hill

summary: Preeclampsia (PE) is a pregnancy disorder characterized by high blood pressure and proteinuria that can cause adverse health effects in both mother and fetus. There is no current cure for PE other than delivery of the fetus. While the etiology is unknown, poor placentation of the placenta due to aberrant signaling of growth and angiogenic factors has been postulated as causal factors of PE. In addition, environmental contaminants, such as the metal cadmium (Cd), have been linked to placental toxicity and increased risk of developing PE. Here, we use a translational study design to investigate genomic and epigenomic alterations in both placentas and placental trophoblasts, focused on the angiogenesis-associated transforming growth factor-beta (TGF-β) pathway. Genes within the TGF-β pathway displayed increased expression in both the preeclamptic placenta and Cd-treated trophoblasts. In addition, miRNAs that target the TGF-β pathway were also significantly altered within the preeclamptic placenta and Cd-treated trophoblasts. Integrative analysis resulted in the identification of a subset of Cd-responsive miRNAs, including miR-26a and miR-155, common to preeclamptic placentas and Cd-treated trophoblasts. These miRNAs have previously been linked to PE and are predicted to regulate members of the TGF-β pathway. Results from this study provide future targets for PE treatment.

overall_design:
Placental Tissue Samples from 32 women (16 normotensive women, denoted with a P, and 16 preeclamptic women, denoted with a Q) were analyzed for differenital miRNA expression controling for age, race and gestational age
JEG3 cells were exposed and not exposed to cadmium and were analyzed for differential miRNA expression
JEG3 cell changes were compared to preelcampsia associated changes to determine overlaps

first: Samira

last: Brookes

first: Elizabeth

last: Martin

first: Lisa

last: Smeester

first: Kim

last: Boggess

first: Matthew

last: Grace


title: Comparison of gene expression in xenograft tissue stably expressing ShRNA KDM1A

status: Public on Jul 27 2016

city: Shanghai

first: FAN

last: ZHANG

state: Shanghai

address: 507 Zhengmin Road

institute: Clinical Translational Research Center, Shanghai Pulmonary Hospital, Tongji University School of Medicine

summary:
The purpose of this study was to chacterise the effect of KDM1A knocking down on genome-wide gene expression in human NSCLC cells in vivo. Affymetrix human transcriptome array 2.0 was used to profile the transcriptome of xenograft tumors derived from PC9 cells stably expressing either ShRNA KDM1A or ShRNA control. These cells were subcutanously injected into the right axillary of the mouse, and allowd to grow for 5 weeks to form xenograft tumors. Although KDM1A is up-regulated in NSCLC, but key genes and pathways regulated by KDM1A was not well-understood in NSCLC. Using this approach, we have shown that KDM1A repressed or activated a distinctive set of pathways and key target genes in vivo.
This first comprehesive study of transciptome profile upon KDM1A koncking-down in vivo highlights the distinctive pathways regulated by KDM1A during NSCLC tumorigenesis, and it will help to identify new therapeutic targets for NSCLC treatment.

overall_design: Xenograft tumors derived from two cell lines: PC9 cells stably expressing ShRNA KDM1A or ShRNA control. We extracted total RNA from 3 independent xenograft tumors per cell line.

first: Fan

last: Zhang


title: microRNA expression signatures for colon cancer initiating cell in CRC

status: Public on Aug 10 2016

city: TAIPEI

first: SHIH-TING

last: CHA

address: 6F., No.2, Syu-jhou Road,

institute: National Taiwan University

summary: In CCICs, G9a expression significantly increases K-RAS protein expression but has no effect on mRNA level. This raises the question of whether microRNA (miRNA) is involved in regulation. A heat map of a miRNA array in G9a versus shG9a transfectants ranked the Let-7 family first, with only Let-7b consistently up-regulated in G9a-knockdown CCICs and down-regulated in G9a-overexpressed non-CCICs

overall_design: microRNA array  in CRC clinical patient–derived cell line transfected with shRNA against G9a (CCICs/shG9a) or DN-G9a (CCICs/DN-G9a), or in non-CCICs transfected with G9a-expression vector (non-CCICs/G9a).

first: S

last: Cha


title: APOL1 renal-risk variants induce mitochondrial dysfunction (Affymetrix 2)

first: Lijun

last: Ma

summary: To assess differential gene expression by APOL1 renal-risk (2 risk alleles) vs. non-risk (G0G0) genotypes in primary proximal tubule cells (PTCs), global gene expression (mRNA) levels were examined on Affymetrix HTA 2.0 arrays in primary PTCs cultured from non-diseased kidney in African Americans without CKD who underwent nephrectomy for localized renal cell carcinoma.

overall_design: To detect differentially expressed gene profiles attributable to APOL1 renal-risk genotypes, African American primary proximal tubule cells with two APOL1 renal-risk alleles (N=5) and  lacking renal-risk alleles (N=25) were included in comparisons of global gene expression.

first: Jeff

last: Chou

first: James

last: Snipes

first: Manish

middle: S

last: Bharadwaj

first: Ann

last: Craddock

first: Dongmei

last: Cheng

first: Allison

last: Weckerle

first: Snezana

last: Petrovic

first: Pamela

last: Hicks

first: Ashok

middle: K

last: Hemal

first: Gregory

last: Hawkins

first: Lance

last: Miller

first: Anthony

last: Molina

first: Carl

last: Langefeld

first: Mariana

last: Murea

first: John

last: Parks

first: Barry

last: Freedman


title: L1CAM knockdown significantly reduces metastasis in a xenograft model of human melanoma

city: Moscow

first: Maxim

last: Shkurnikov

address: 2 bld. 85, Ugreshkaya st.

country: Russia

institute: SRC Bioclinicum

summary: As L1CAM expression is associated with metastasis in melanoma patients, it could be a target for the combination therapies. We investigated the functional role of L1CAM  in melanoma metastasis by the use of a xenograft model of human melanoma in mice using RNAi mediated L1CAM knockdown melanoma cells.

overall_design: Human melanoma cells (cell lines MeWo and MV3) with (L1CAM) and without (luc) shRNA mediated L1CAM knockdown were transplanted subcutaneously into scid mice. Total RNA was prepared from subcutaneous tumors.

first: Ann-Kathrin

last: Ernst

first: Annika

last: Putscher

first: Udo

last: Schumacher

first: Daniel

last: Wicklein

first: Timur

last: Samatov

first: Vladimir

middle: V

last: Galatenko

first: Alexey

middle: Y

first: Evgeniy

last: Knyazev

first: Alexander

middle: G

last: Tonevitsky


title: Effect of Cathepsin L exposure on endothelial cell transcriptomics

status: Public on Jun 20 2016

city: Utrecht

first: Maria

middle: Belen

last: Rabaglino

address: Yalelaan 7

department: Population Health Science

country: Netherlands

institute: Utrecht University

summary: Cathepsin L is a lysosomal protease that is secreted by several cancer cells. Cathepsin L upregulation has been widely associated with poor clinical outcome and increased metastatic incidence. However, whether Cathepsin L participates in tumor angiogenesis remains less studied. Our study showed a significant activation of angiogenic capacity of endothelial cells in presence of purified or tumor derived Cathepsin L. In addition, Cathepsin L exposure led to a significant increase in the proliferative capacity of endothelial cells. While the ability of Cathepsin L to promote endothelial cell sprouting, migration, invasion and tube formation can be attributed to its proteolytic effects on extracellular matrix, how it promotes endothelial cell proliferation remains obscure. The objective of this study was to test if Cathepsin L exposure can activate signaling cascades and gene expression leading to proliferation of endothelial cells.

overall_design: Human microvascular endothelial cells were exposed to 10 ng/ml of purified human Cathepsin L. 4hr later, cells were lysed and gene expression was measured using Affymetrix HTA 2.0 Transcriptome Array.

first: Dhivya

last: Sudhan

first: Dietmar

last: Siemann

first: Belen

middle: M

first: Charles

middle: E

last: Wood


title: Thalicthuberine: A Novel Mitotic Inhibitor in Prostate Cancer Cells

status: Public on Jun 17 2016

city: Brisbane

first: Colleen

last: Nelson

state: Queensland

address: 199 Ipswich Road

department: Institute of Health and Biomedical Innovation; Vancouver Prostate Centre

country: Australia

institute: Queensland University of Technology; University of British Columbia

summary: Bioassay-guided fractionation of a cytotoxic extract derived from the Australian endemic plant Hernandia albiflora (twigs) resulted in the isolation of the two known compounds: deoxypodophyllotoxin and thalicthuberine. Both compounds were tested for their inhibition of LNCaP cell viability. Thalicthuberine (TH, IC50=2.0 µM) was selected for mechanism of action studies. Ongoing investigations have shown that TH induced a strong accumulation of LNCaP cells in mitosis, severe mitotic spindle defects and asymmetric cell divisions, ultimately leading to mitotic catastrophe accompanied by cell death through apoptosis. However, unlike microtubule-targeting drugs (vinblastine, paclitaxel and nocodazole), TH did not affect tubulin polymerization in a cell-free system, while it reduced cellular microtubule polymer mass, suggesting that TH indirectly targets microtubule dynamics through inhibition of critical regulators or tubulin-associated proteins. Based on phenotypic comparisons, we excluded the mitotic regulators Aurora kinase A and Polo-like kinase 1 as potential targets of TH. TH did not directly interact with DNA (cell-free assay) or induce DNA damage in cells. Further experiments will attempt to address the molecular target(s) and inhibition mechanism of TH. This is the first report of a mechanism of action study for this natural product. Based on these results, TH has great promise for further development into a potent non-tubulin-targeting mitotic inhibitor.

overall_design: The dataset was derived from three biological repeats of each of the treatment groups DMSO, vinblastine and TH.

first: Claire

last: Levrier

first: Martin

last: Sadowski

first: Anja

last: Rockstroh

first: Melanie

last: Lehman

first: Rohan

middle: A

last: Davis


title: Expression Profiling:  Guanylate Cyclase Soluble Subunit Beta-3 (GUCY1B3) overexpression U87 MG cells

status: Public on Jun 15 2016

city: washington

first: haijie

last: xiao

state: DC

address: 2300 eye street

department: Biochemistry

country: USA

institute: george washington University

summary:
Total RNA were extracted from Guanylate Cyclase Soluble Subunit Beta-3 (GUCY1B3) overexpression U87 MG stable cell lines and U87 MG cells. Three RNA samples of each of the two cell lines were used for
microarray analysis to compare gene expression profile

overall_design: Guanylate Cyclase Soluble Subunit Beta-3 (GUCY1B3) was cloned into pCDNA3.1D/V5-His-TOPO plasmid (Invitrgen) and then transfected into U87 MG (ATCC HTB-1) cells to generate stable overexpression cells. RNA from the stable cell lines and U87 MG were used for microarray

first: Haijie

last: Xiao

first: Haifeng

last: zhu

first: Ka

last: bian

first: Ferid

last: Murad


title: Clinical and biological characterization of children with FLT3-ITD-mutated acute myeloid leukemia

city: Padova

first: Matteo

last: Zampini

state: PD

address: corso stati uniti 4

institute: Istituto di Ricerca Pediatrica (IRP)  Città della Speranza

summary: We examined if the minimal residual disease (MRD) and the Allelic Ratio (AR) of FLT3 internal tandem duplication (ITD) mutated patients may be prognostic factors.  We correlated these parameters both with event free survival (EFS), with incidence of relapse and with gene expression profile (GEP).  GEP showed that patients with high-ITD-AR or persistent MRD had different expression profiles.  Results indicated that the ITD-AR levels and the MRD after I induction course are associated with transcriptional oncogenic profiles, which highlight differences in epigenetic control that may explain the variability in outcome among FLT3-ITD patients

overall_design: 100 ng of bone marrow RNA from 14 patients with de novo AML harboring FLT3-ITD mutation at diagnosis were hybridized on the GeneChip® Human Transcriptome Array 2.0. Class comparisons between different patient subgroups (high vs low Allelic Ratio, good vs poor responders) were performed.

first: Elena

last: Manara

first: Martina

last: Pigazzi


title: Expression data of osteogenic differentiated cartilage endplate-derived stem cells (CESCs) under hypoxia or normoxia

status: Public on Jun 14 2016

first: Yuan

last: Yao

country: China

summary:
Cartilage endplate-derived stem cells (CESCs) with chondro-osteogenic differentiation capacity may be responsible for the balance of chondrification and ossification in cartilage endplate (CEP). CEP is an avascular and hypoxic tissue, and hypoxia could inhibit the osteogenic differentiation of CESCs.
We used high-throughput scanning to identify differentially expressed genes (DEGs) and alternatively spliced genes (ASGs) during osteogenic differentiation of CESCs under hypoxia compared to those induced under normoxia.

overall_design: Human cartilage endplate-derived stem cells (CESCs) were treated with osteogenic differentiation medium under normoxia and hypoxia for 21 days respectively.


title: Isolation and comparative analysis of mesenchymal stem cells from human umbilical cord

status: Public on Jun 08 2016

city: Royal Oak

first: Bryan

last: Thibodeau

address: 3811 West 13 Mile Road

department: BioBank

institute: Beaumont Research Institute

summary:
A non-controversial and non-invasive source of adult stem cells (ASCs), particularly hematopoietic stem cells (HSCs) and mesenchymal stem cells (MSCs) is human umbilical cord blood.  HSCs derived from cord blood have been used for treating leukemia and other blood disorders for the last 30 years.  While the presence of MSCs in cord blood is limited, umbilical cord has been found to be promising source of MSCs.  However, the cord is an anatomically complex organ and potential isolation of MSCs from its various parts has not been fully explored.
In this study we dissected the cord into cord placenta junction (CPJ), cord tissue (CT), and Wharton’s jelly (WJ) and isolated stem cells.  These cells exhibited fibroid morphology, expressed MSC-specific markers including CD90, CD73, CD105, CD44, and CD29 and differentiated into chondrogenic, osteogenic, myogenic and neurogenic lineages.   In addition, they all expressed pluripotency genes, OCT4, Nanog, Sox2 and KLF4 but expression of these markers was highest in CPJ followed by WJ and CT.
CPJ-MSCs also had higher rate of proliferation compared to WJ- and CT-MSCs.  Proliferation of WJ- and CT-MSCs was markedly decreased upon passaging with concomitant decrease in expression of MSC and pluripotency markers.  Based on their greater self-renewal potential, CPJ-MSCs could be superior to WJ- and CT-MSCs for the applications in therapeutic and regenerative medicine.

overall_design: Human umbilical cord derived MSCs were cultured in vitro. Gene expression of cells originating from each of cord-placenta junction and Wharton's jelly were compared to cells originating from cord tissue.

first: Naimisha

last: Beeravolu

first: Irfan

last: Khan

first: Christina

last: McKee

middle: J

first: George

middle: D

last: Wilson

first: Miguelangelo

last: Perez-Cruet

first: Rasul

last: Chaudhry


title: Isolation and comparative analysis of mesenchymal stem cells from human umbilical cord II

summary:
A non-controversial and non-invasive source of adult stem cells (ASCs), particularly hematopoietic stem cells (HSCs) and mesenchymal stem cells (MSCs) is human umbilical cord blood.  HSCs derived from cord blood have been used for treating leukemia and other blood disorders for the last 30 years.  While the presence of MSCs in cord blood is limited, umbilical cord has been found to be promising source of MSCs.  However, the cord is an anatomically complex organ and potential isolation of MSCs from its various parts has not been fully explored.
In this study we dissected the cord into cord placenta junction (CPJ), cord tissue (CT), and Wharton’s jelly (WJ) and isolated stem cells.  These cells exhibited fibroid morphology, expressed MSC-specific markers including CD90, CD73, CD105, CD44, and CD29 and differentiated into chondrogenic, osteogenic, and adipogenic lineages.   In addition, they all expressed pluripotency genes, OCT4, Nanog, Sox2 and KLF4 but expression of these markers was highest in CPJ followed by WJ and CT.
CPJ-MSCs also had higher rate of proliferation compared to WJ- and CT-MSCs.  Proliferation of WJ- and CT-MSCs was markedly decreased upon passaging with concomitant decrease in expression of MSC and pluripotency markers.  Based on their greater self-renewal potential, CPJ-MSCs could be superior to WJ- and CT-MSCs for the applications in therapeutic and regenerative medicine.

overall_design: Human umbilical cord derived MSCs were isolated from different anatomical segments and cultured in vitro. Gene expression of cells originating from each of cord-placenta junction and Wharton's jelly were compared to cells originating from cord tissue.


title: Expression data from human lung epithelial cells after amorphous silica nanoparticle exposure for 40 passages

status: Public on Jun 01 2016

first: Caixia

last: Guo

address: No.10 Xitoutiao, You An Men

institute: Capital Medical University

summary:
Amorphous silica nanoparticles induce malignant transformation and tumorigenesis of human lung epithelial cells.
We used microarrays to detail the global programme of gene expression underlying the cellular malignant transformation induced by amorphous silica nanoparticles and identified distinct classes of up-regulated and down-regulated genes during this process.

overall_design: The human lung epithelial cells, Beas-2B were continuously exposed to 5 μg/mL amorphous silica nanoparticles for 40 passages, and named as BeasSiNPs-P40 (shortly as P40-5 during the further microarray detection). Meanwhile, the passage-matched control Beas-2B cells, named as Beas-P40 (shortly as NC during the further microarray detection).

first: Yanbo

last: Li


title: Combined epigallocatechin-3-gallate and resveratrol supplementation for 12 wk increases mitochondrial capacity and fat oxidation, but not insulin sensitivity, in obese humans: a randomized controlled trial

status: Public on Aug 03 2016

city: Maastricht

first: Ellen

middle: E.

last: Blaak

address: PO Box 616

department: Dept. of Human Biology

institute: Maastricht University Medical Center+

summary:
The obese, insulin resistant state is characterized by impairments in lipid metabolism. Dietary polyphenols might improve these deteriorations. We have previously shown that 3-days supplementation of combined Epigallocatechin-gallate and Resveratrol (E+R) increased energy expenditure, which was accompanied by improved metabolic flexibility after a high-fat mixed-meal (HFMM) in men. The present study aimed to investigate whether these short-term effects translate into longer-term improvement of insulin sensitivity and lipid metabolism.  In this randomized, double-blind study, 42 overweight subjects (21 male, 38±2 yrs, BMI 29.7±0.5 kg/m2, HOMA-IR 2.1±0.2) received either E+R (300 and 80 mg/d, respectively) or placebo (PLA) for 12 weeks (3 months). Before (t0) and after (t3) intervention, tissue-specific insulin sensitivity was assessed by a hyperinsulinemic-euglycemic clamp with stable isotope infusion. Fasting and postprandial (HFMM) lipid metabolism was assessed using indirect calorimetry and blood sampling. Adipose tissue and skeletal muscle lipolysis was measured using microdialysis in men and skeletal muscle biopsies were collected to assess mitochondrial function and gene expression alterations via microarray analysis.  E+R supplementation increased fasting (P=0.06) and postprandial (P=0.03) fat oxidation but did not alter energy expenditure compared to PLA. This was accompanied by an E+R-induced increase in oxidative capacity in permeabilized muscle fibers (p<0.05). Moreover, E+R supplementation attenuated the increase in plasma triacylglycerol concentration that was observed in the PLA group (AUC, p<0.05), and tended to decrease visceral fat mass (P=0.09). Finally, insulin-stimulated glucose disposal and suppression of endogenous glucose production were not affected by E+R supplementation.  12 weeks E+R supplementation increased whole-body fat oxidation and skeletal muscle oxidative capacity, but this did not translate into increased tissue-specific insulin sensitivity in overweight and obese subjects.
To identify pathways that may underlie the E+R-induced improvement of skeletal muscle mitochondrial capacity, we performed microarray analysis on skeletal muscle biopsies (vastus lateralis muscle), collected before and after 12-weeks E+R or PLA treatment. Gene Set Enrichment Analysis (GSEA) indicated that the most upregulated pathways after E+R supplementation were related to the citric acid cycle and respiratory electron transport chain, while pathways related to carbohydrate metabolism were upregulated in the PLA group.

overall_design: In this randomized, double-blind placebo-controlled, parallel intervention trial, subjects received either a combination of E+R supplements (INTV, 282 mg/d and 80 mg/d, respectively) or placebo (PLA, partly hydrolyzed microcrystalline cellulose-filled capsules) for a period of 12 weeks (3 months) to assess effects of E+R supplementation on tissue-specific insulin sensitivity (primary outcomes) and fasting and postprandial substrate metabolism (secondary outcomes). Skeletal muscle (m. vastus lateralis) biopsies were taken under local anesthesia during fasting conditions before (t0) and after the 12-weeks (t3) intervention period. Extraxted RNA was hybridized on HTA 2.0 Affymetrix arrays and microarray analysis was performed on paired sample sets for 27 subjects (p, PLA n = 14; E+R n = 13).

first: Mark

last: Boekschoten

first: Jasper

last: Most

first: Ines

last: Warnke

first: Igor

last: Bendik


title: Inhibition of Histone Deacetylase induces miR-320-mediated Androgen Receptor Suppression in Prostate Cancer

city: Nagoya

first: Keisuke

last: Katsushima

address: 1 Kawasumi, Mizuho-cho, Mizuho-ku

department: Department of Epigenomics

country: Japan

institute: Nagoya City University Graduate School of Medical Sciences

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

overall_design: Refer to individual Series