title: Transcriptome analysis of tumors from Olfactory neuroblastoma patients

status: Public on Aug 05 2017

city: los angeles

first: anatole

last: ghazalpour

state: CA

address: 675 charles young dr south

institute: UCLA

summary: The RNA from tumors of four olfactory neuroblastoma patients were studied to understand the molecular pathways perturbed in such tumors. The resulting up and down regulated genes were used to look for novel cellular pathways that are commonly perturbed in plfactory neuroblastoma

overall_design: Total RNA obtained from four FFPE olfactory neuroblastoma tumor was compared to commercially purchased healthy control RNA sample comprised of pooled RNA from three healthy tissues.

first: Ghazalpour

last: Anatole

first: Vranic

last: Semir


title: A recombinant lentiviral PDGF-driven mouse model of proneural GBM

status: Public on Jul 12 2017

city: Boston

first: Gilbert

middle: Joseph

last: Rahme

state: MA

address: 365 Longwood Ave.

department: Cancer Biology

country: USA

institute: Dana-Farber Cancer Institute

summary: Informed by the genetic alterations observed in human GBM, we engineered a novel, lentiviral injection mediated, mouse model of proneural GBM.

overall_design: Total RNA obtained from PDGF-driven primary GBM tumors arising in the ShCdkn2a-PDGFB-T2A-CreERT2 mouse model developed in our study was analysed to determine to which transcriptomic subtype of GBM these specimens belonged.

middle: J

first: Mark

middle: A

last: Israel


title: Therapeutic antibodies to ganglioside GD2 evolved from highly selective germline antibodies VI

status: Public on Aug 25 2017

city: Frederick

first: Jeff

last: Gildersleeve

state: MD

address: 376 Boyles St.

institute: National Cancer Institute

summary:
Purpose:  This study uses a high-throughput glycan microarray to evaluate the immunological evolution of antibodies to the glyco-antigen GD2.  The goal is to determine germline and affinity mature antibody specificity and affinities/
Results:  Affinity mature anti-GD2 antibodies 3F8 and ch14.18 had high affinity and were highly specific for the target GD2.  Germline antibodies were also hihgly specific and had surprisingly high affinity.
Conclusion: Antibodies to GD2 evolved from highly specific germlines.  Highly specific germlines may be critical in evading autoimmunity issues.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Quercus alba
Gossypium hirsutum
Rhodotorula
Trypanosoma cruzi
Pandalus borealis
Oncorhynchus nerka
Gallus gallus
Homo sapiens
Sus scrofa domesticus
Bos taurus
Ovis aries
Oryctolagus cuniculus
Mus musculus
Human immunodeficiency virus 1
Ceratonia siliqua
Megathura crenulata
Bothrops moojeni
Frangula alnus
Senegalia senegal
Pachymenia carnosa
Dermestes lardarius

overall_design: Germline variable regions of 3F8 and ch14.18 were determined.  Germline and affinity mature antibody DNA were synthesized and transfected into HEK293 cell lines.  Secreted antibodies were purified from supernatant using affinity chromatography.  Antibodies were evaluated on multiple assay platforms, including glycan microarrays, protein microarrays, and cell binding assays.

first: Eric

last: Sterner

first: Megan

middle: L

last: Peach

first: Marc

middle: C

last: Nicklaus

first: Jeffrey


title: microRNA profiles of CD4 T cells after cognate antigen specfic stimulation

status: Public on Aug 15 2017

city: Madrid

first: Fatima

last: Sanchez-Cabo

address: Melchor Fernandez Almagro

country: Spain

institute: CNIC

summary: Microarray analysis of miRNAs from CD4 T cells after their encounter with DCs in the presence of the antigen vs the absence

overall_design: To determine the changes on miRNA repertoires CD4 T cells upon antigen specfic activation, CD4 T cells were cocultuered for 18 h with dendric cells in the absense or presence of the specific antigen OVA. Subsecuently, CD4 T cells where sorted by flow cytometry and their RNA isolated for the microarray analysis.

first: Cristina

last: Gutiérrez-Vázquez

first: Ana

last: Rodríguez-Galán

first: Marcos

last: Fernandez-Alfara

first: María

last: Mittelbrunn

first: Fátima

last: Sánchez-Cabo

first: Dannys

last: Martínez-Herrera

first: Marta

last: Ramírez-Huesca

first: Alberto

last: Pascual-Montano

first: Francisco

last: Sánchez-Madrid


title: Therapeutic antibodies to ganglioside GD2 evolved from highly selective germline antibodies V


title: Development of gene expression signatures of ascending aorta of the patients with bicuspid aortic valve compared to tricuspid aortic valve.

status: Public on Jun 30 2017

city: Kurume

first: Yuuichirou

last: Hirata

address: 67 Asahimachi

department: Department of Surgery

country: Japan

institute: Kurume University School of Medicine

summary: Bicuspid aortic valve is well known as a risk factor of dilation of ascending aorta. But the mechanisms of dialation are unknown. Morever, patients with bicuspid aortic valve tend to be aortic valve disease at younger age. After aortic valve surgery, if ascending aorta is dilated, the patient must be performed re-operation. For that reason, surgery for aortic root or ascending aorta is recommended to patient with bicuspid aortic valve with dilated ascending aorta.  We thought that abnormality of cell cycle of the structure protein participated in ascending aorta dilation of patient with bicuspid aortic valve. We resected the wall of the ascending aota from patient undergoing aortic valve replacement for aortic valve stenosis during operation, and performed immunohistochemical staining for akt. Anti Akt antibodys were stained much on aortic media with bicuspoed aortic valve. Akt is a protein that is involved in mTOR / PI3K, and modulate the cell differenciation and proliferation. Further, the same samples were analyzed using a microarray method. On bicuspid aortic valve patients, the expression of TSC2 is reduced, and GβL is increased. TSC2 inhibit this pathway, and MLST8 activate this pathway. In the ascending aorta of BAV patients, PI3K / mTOR system is considered to be activated. When this pathway is activated, cell proliferation and cytodifferentiation are promoted abnormally,

overall_design: The aortic valve replacement surgery, excised the ascending aorta wall of aortotomy site, was used as a sample. We divided into 2 groups(bicuspid aortic valve vs tricuspid aortic valve) and analysed.

first: Yuichiro

first: Hiroki

last: Aoki


title: Therapeutic antibodies to ganglioside GD2 evolved from highly selective germline antibodies IV

first: Jeff

first: Eric


title: Therapeutic antibodies to ganglioside GD2 evolved from highly selective germline antibodies III

first: Megan

first: Marc


title: Mediator subunit MED23 links pigmentation and DNA repair through the transcription factor MITF (RNA-Seq)

status: Public on Aug 22 2017

city: Shanghai

first: Min

last: Xia

address: 320 YueYang Road

country: China

institute: SIBCB

type: Expression profiling by high throughput sequencing

summary: mRNA profile of wild type (WT) and Med23 knockdown in B16F10 melanoma cell line

overall_design: Med23 knockdown vs. WT

first: Gang

last: Wang


title: Therapeutic antibodies to ganglioside GD2 evolved from highly selective germline antibodies II

last: Gildersleeve

last: Sterner

first: Jeffrey


title: RNA-microarray analyses and protein profiles from affected and clinically non-affected scalp in male androgenetic alopecia patients

city: Berlin

first: Annika

last: Vogt

address: Charitéplatz 1

department: Department of Dermatology and Allergy

country: Germany

institute: Charité – Universitätsmedizin Berlin

summary: The aim of this pilot study was to combine standard clinical diagnostics with RNA and protein analyses from non-invasively obtained material. In 6 male volunteers with AGA, Norwood-Hamilton stage IIIv-IV, we performed global photography, phototrichogram, pH and sebum measurements, as well as skin surface cytokine measurements on AGA-affected frontal and vertex scalp skin compared to clinically unaffected occiput.

overall_design: Six male volunteers with AGA, aged 18-45, with Hamilton-Norwood stage IIIv-IV, were included in the study. Institutional review board (Charité-Universitaetsmedizin Berlin) approval and written informed consent were obtained. The study was performed in adherence with the Declaration of Helsinki Principles. After a screening visit and obtaining a written informed consent, subjects came for a first visit (day 0) where global photography, shaving, mini-zone CSSS (to collect scalp surface protein material), ultrasound, pH and scalp and hair sebum levels were determined. Until the second visit (V2, day 3) subjects were not allowed to wash their hairs or apply any product on scalp or hair. On visit 2, pH and sebum measurements were repeated, together with OCT, phototrichogram and hair root plucking for RNA extraction and analysis.

first: Sabine

last: Fimmel

first: Eva Katharina

last: Barbosa Pfannes

first: Sabrina

last: Hadam

first: Annette

last: Andruck

first: Jan

last: Kottner

first: Ulrike

last: Blume-Peytavi


title: Gene expression profiling of human gastric tissues at different pathological stages

status: Public on Aug 21 2017

city: Beijing

first: li

middle: cheng

last: Zhang

state: Beijing

address: No. 17 Panjiayuan Nanli, Chaoyang District

institute: National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College

summary: Gastric cancer is characterized by prolonged, well-defined precancerous stages. In our study, we performed the whole genome gene expression mircroarray of 22 gastric tissues at different pathological stages. We aim to find genes that closely related to the changes of TCR repertoire during gastric carcinogenesis. By integrative analysis of the microarray data and TCR variation degrees, we identified a 11-gene module that can predict the overall survival of gastric cancer patients.

overall_design: A total of 22 gastroscopic biopsy tissue samples from 19 patients were profiled by Agilent SurePrint G3 Human GE  8x60K Microarray .

first: Li

first: Chao

middle: M

last: Kuang

first: Lin

last: Feng

first: Jun

middle: S

last: Cheng

first: Tai

middle: K

first: Ming

last: Yang


title: Gene expression analysis of sickle cell disease patients

city: Raipur

first: Ipsita

last: Das

state: Chhattisgarh

address: Jail Road

department: Biochemistry

country: India

institute: Pt. Jawaharlal Nehru memorial Medical College

summary: Sickle cell disease (SCD) is a devastating hemoglobinopathy prevalent in Chhattisgarh and other states of central India. Clinical features in SCD arise mainly due to anemia and vaso-occlusion and inflammation leading to gradual multiple organ failure. Vaso-occlusive crisis (VOC) is a common cause of sudden death among SCD patients. Aim of the study was to evaluate gene expression in patients of SCD in a quest to search up-regulated genes in VOC.

overall_design: 20 subjects were enrolled in the study, 7 each from sickle cell steady (HbSS SS) and crisis state (HbSS CS) and 6 healthy controls (HbAA). Whole blood transcriptome was compared between the study groups.

first: Hrishikesh

last: Mishra

first: Prafulla

last: Khodiar

first: Pradeep

last: Patra


title: Regulation of autophagy, NF-kB signaling and cell viability by miR-124 in KRAS mutant mesenchymal-like NSCLC cells

status: Public on Aug 08 2017

first: Anurag

last: Singh

address: 72 E. Concord St.

department: Pharmacology and Experimental Therapeutics

institute: Boston University School of Medicine

summary: Comparison of microRNA expression profiles in human KRAS mutant non-small cell lung cancer (NSCLC) derived cell lines based on differential KRAS dependency and epithelial or mesenchymal differentiation characteristics.

overall_design: TLDA qPCR assays were performed on reverse-transcribed total RNA from 3 KRAS independent cell lines (mesenchymal/KM) and 3 KRAS dependent (epithelial/KE) cell lines.


title: Expression data from early stage CRC patients' tumors [Agilent]

status: Public on Aug 02 2017

city: Singapore

first: Steve

last: Rozen

address: 8 College Road

country: Singapore

institute: Duke-NUS

summary: This study was conducted in order to identify biomarkers for a prognostic gene expression signature for metastases in early stage CRC.

overall_design: Expression profiles from 99 metastasis negative and 49 metastasis positive early stage CRC tumors were obtained.

first: Yee-Syuen

last: Low

first: Christopher

last: Blöcker

first: Iain

middle: B

last: Tan

first: Steven

middle: G

first: Peh-Yean

last: Cheah


title: Real-time quantitative PCR analysis of primary human dermal fibroblasts_comparing young (5 month old) and old (78 years old) samples treated with GC4419

status: Public on Jul 08 2017

city: Iowa City

first: Kranti

last: Mapuskar

state: Iowa

address: 500 Newton Road

department: Radiation Oncology

institute: University of Iowa

summary: To analyze the age-associated changes in the nuclear encoded genes of the mitochondrial ETC following treatment with a Superoxide dismutase mimetic GC4419 using the mitochondrial energy metabolism profiler array from Qiagen.

overall_design: qPCR gene expression profiler array.  Both samples were treated with 0.25 uM of GC4419. 48 hours following the treatment with GC4419, equal amount total RNA from each donor was isolated prior to making the cDNA and analyzing the changes in nuclear-encoded genes.


title: Whole-genome DNA methylation profiling of 152 pediatric AML patients

status: Public on Jun 22 2017

city: Rotterdam

first: Nicole

last: Larmonie

address: Wytemaweg

country: Netherlands

institute: ErasmusMC

type: Methylation profiling by genome tiling array

summary: Genome-wide CpG-island methylation profiling on pediatric AML samples was performed to identify specific methylation patterns discriminating particular AML subgroups from the rest of AML samples based on the methylation profile.

overall_design:
Genomic DNA from pediatric AML material representing different cytogenetic subgroups was used: inv(16)(p13;q22) (CBFB-MYH11), MLL-rearrangement, t(8;21)(q22;q22) (RUNX1-RUNX1T1), t(15;17)(q24;q21) (PML-RARA), t(8;16)(p11;p13) (KAT6A-CREBBP), t(5;11)(q35;p15.5) (NUP98-NSD1) or C/EPBα (double mutation) and NPM1 mutations and CN AMLs.
AML samples were enriched for  ≥80% leukemic cells.

first: N

first: T

last: Arentsen-Peters

first: A

last: Obulkasim

first: D

last: Valerio

last: Danen-van Oorschot

first: M

last: van den Heuvel-Eibrink

first: C

last: Zwaan

last: Fornerod


title: Reduction of the tumorigenic potential of human retinoblastoma cell lines by TFF1 overexpression involves p53/caspase signaling and miR-18a regulation

city: Essen

first: Maike

last: Busch

address: Hufelandstr. 55

institute: University Hospital Essen

summary:
TFF1 overexpression in retinoblastoma cell line Y79
Differentially expressed genes and pathways involved in cancer progression were identified after TFF1 overexpression in Y79 cells by gene expression array analysis, underlining the effects on reduced tumorigenicity.

overall_design: Retinoblastoma cell line: Y79 overexpressing TFF1 versus Y79; 2 biological replicates

first: Jan

last: Große-Kreul

first: Janina

last: Wirtz

first: Manfred

last: Beier

first: Harald

last: Stephan

first: Brigitte

last: Royer-Pokora

first: Klaus

last: Metz

last: Dünker


title: Single cell QRT-PCR analysis of PND7 mice endometrial epithelial cells

city: HangZhou

first: Bingbing

last: Wu

state: Zhejiang

address: 866 Yuhangtang Rd

department: School of Medcine

institute: Zhejiang University

summary:
96 CD326+ single cells from post-natal day7 mice endometrial epithelial cells were isolated by FACS
single cell pre-amplification and Q-PCR were then conducted

overall_design: 96 CD326+ epithelia single cells from post-natal day7 mice uterus

first: Xiaohui

last: Zou

first: Hongwei

last: Ouyang


title: Expression anaysis of mouse aortic vascular smooth muscle cells

status: Public on Jun 23 2017

city: Heidelberg

first: Stephanie

middle: Sarah

last: Kapel

state: Baden-Württemberg

address: Im Neuenheimer Feld 280

department: Division of Vascular Oncology and Metastasis

institute: German Cancer Research Center (DKFZ)

summary:
Analysis of differential gene expression of aortic vascular smooth muscle cells isolated from Tie2floxed:SM22α Cre- (WT) and Tie2floxed:SM22α Cre+ (KO) mice
Looking for candidates, that could potentialy be upregulated or downregulated

overall_design: Total RNA was isolated from whole lysates of cultured aortic vascular smooth muscle cells isolated from Tie2floxed:SM22α Cre- (WT) and Tie2floxed:SM22α Cre+ (KO) mice

first: Hellmut

last: Augustin


title: ATM signalling and autophagy cooperate in the regulation of breast cancer stem-like phenotype: a transcriptional profile

status: Public on Jun 12 2017

city: Roma

first: Ivan

last: Arisi

address: viale Regina Elena 295

department: Bioinformatics Facility

country: Italy

institute: European Brain Research Institute

summary: In the last past decades, it has been focused the attention on a new emerging concept in the field of cancer research, such as the involvement of a small fraction of cells within many solid tumours that seem to be responsible for tumour initiation, maintenance and, more importantly, for drug resistance, called cancer stem cells (CSCs). According to this hypothesis, this pool of cells could be distinguished from all the other tumour cells, not only because they have different properties, such as the ability to self-renew or to differentiate into different tumour types, but also because they grow in a specific microenvironment, suggesting a different metabolic requirement; understanding this concept and the signalling pathways involved could be be extremely important for the development of new specific therapeutic drugs. Recent studies have underlined the role of the DNA damage response (DDR) as an important mechanism that promotes radio resistance in CSCs, but some aspects need to be clarified. Indeed, the DDR and its major player ATM show a duality in cancer; ATM could act as tumor suppressor, according to its canonical role in response to a DNA damage, or as tumor promoter in specific cancer contexts. Recently, our group identified a new tumorigenic role of ATM in HER2-positive breast cancer (BC), but currently, very little is known about the role of ATM in the regulation of CSCs. Based on literature data and our results, the aim of this study is to identify new possible crosslinks between ATM and other signalling pathways involved in the maintenance of the stem-like phenotype in BC. We characterized cells with stem-like features from BC cell lines as MCF-7 and MCF-7HER2, by using mammosphere assay. We performed a transcriptomic study using Agilent 8x60K whole human genome microarray. Our data show an increase in ATM protein and mRNA levels in cells grown in 3D, and interestingly, the downregulation of ATM expression significantly reduces spheres formation and the activity of ALDH-1, a well-known marker of breast cancer stem cells (BCSCs) features. We analysed different gene expression profiles obtained by microarray analysis in mammospheres with or without ATM and we found a strong correlation with some important pathways for breast cancer stem cells maintenance.

overall_design: Transcriptional profiles of MCF7 and MCF7-HER2 cell lines infected with ATM silencing vectors were compared to the corresponding samples infected with control vectors.

first: Martina

last: Antonelli

first: Flavie

last: Strappazzon

first: Rossella

last: Brandi

first: Mara

last: D'Onofrio

first: Manolo

last: Sambucci

first: Daniela

last: Barilà

first: Venturina

last: Stagni


title: TTF-1-regulated miR-532-5p targets KRAS and MKL2 oncogenes and induces apoptosis in lung adenocarcinoma [pts]

status: Public on Jun 21 2017

city: Nagoya

first: Takashi

last: Takahashi

state: Aichi

address: 1-1 Kanokoden, Chikusa-ku

institute: Aichi Cancer Center

summary: Thyroid transcription factor-1 (TTF-1), also known as NKX2-1, plays a role as a lineage-survival oncogene in lung adenocarcinoma with double-edged sword characteristics. Although previous studies steadily accumulated evidence for roles of TTF-1 in the transcriptional regulation of protein-coding genes, very little is known about its regulatory relationship with miRNAs. In this study, we have identified miR-532-5p as a novel transcriptional target of TTF-1 by an integrative approach, which was designed to extract maximal information from expression profiles of both patient tumors in vivo and TTF-1-inducible cell lines in vitro. Consequently, we have found that miR-532-5p is directly regulated by TTF-1 through its binding to a genomic region 8 kb upstream of miR-532-5p, which appeared to impose transcriptional regulation independent of that of CLCN5, a protein-coding gene harboring miR-532-5p in its intron 3. Further, we have also identified KRAS and MKL2 as novel direct targets of miR-532-5p. Introduction of miR-532-5p mimics markedly induced apoptosis in KRAS-mutant as well as KRAS wildtype lung adenocarcinoma cell lines. Interestingly, miR-532-5p affected the MEK-ERK pathway signaling specifically in cell lines sensitive to siKRAS treatment, while the miR-532-5p-mediated effects were clearly phenocopied by repressing expression or inhibiting function of MKL2 regardless of KRAS mutation status. In summary, our findings demonstrate that miR-532-5p is as novel transcriptional target of TTF-1 and plays a tumor suppressive role by targeting KRAS and MKL2 in lung adenocarcinoma. Novel therapeutic strategies using miR-532-5p or an MKL2 inhibitor may prove effective against this hard-to-cure cancer irrespective of the dependence on KRAS-mediated signaling.

overall_design:
Microarray analysis using a SurePrint G3 Human GE 8 x 60K ver 2 Microarray G4851B (Agilent) was conducted.
Tumors of 75 lung adenocarcinoma patients which successfully underwent potential curative resection at Aichi Cancer Center, Nagoya, Japan, were investigated.

first: Sebastian

last: Griesing

first: Taisuke

last: Kajino

first: Mei

last: Tai

first: Zhuoran

last: Liu

first: Masahiro

last: Nakatochi

first: Yukako

last: Shimada

first: Motoshi

last: Suzuki


title: Gene expression profile perturbed by ATRA

city: Buffalo

first: AC

last: CHANG

address: Elm and Carlton

institute: RPCI

summary: Global gene expression profiling compared between T47D cells that treated with ATRA or vehicle

overall_design: Whole human genome 4x44K array analysis was performed following the manufacturers protocol (Agilent, 3 triplicates each sample)

first: C

last: Chang


title: Gene expression  in amniotic menbrane-derived cells (mesenchymal stromal cells and epithelial cells) and expression  signatures of these two types of cells after IL-10 stimulation

city: Setagaya-ku

first: Akihiro

last: Umezawa

state: Tokyo

department: Center for Regenerative Medicine

institute: National Center for Child Health and Development

summary: To further cell therapy, we have investigated gene expression profile of amniotic membrane-derived, two types of cells: mesenchymal stromal cells and epithelial cells. We previously reported that amniotic membrane derived cells are immunologically privileged and produced only minimal immune reactivity and that these cells, when stimulated by immunosuppressive agent IL-10, had higher differential potential for cardiomyocyte and more immunotolerance. To analysis these phenomenons, we performed gene expression profile of two types of cells after IL10 stimulation.

overall_design: To investigate characterization of amniotic membrane-derived mesenchymal stem cells, we have separated these cells into two types, stromal cells and epithelial cells by enzyme reaction. IL10 induced gene expression was measured at 48 hours after exposure to doses of 10ng/ml.

first: Masashi

last: Toyoda

first: Naoko

last: Hida

first: Hiroyuki

last: Morishita


title: Gene and microRNA modulation upon ET-743 treatment in a human intrahepatic cholangiocarcinoma paired patient derived xenograft and cell line [gene expression]

status: Public on Jun 10 2017

city: Biella

first: giovanna

last: chiorino

address: via malta 3

department: Cancer Genomics

institute: Fondo Edo Tempia

summary:
Transcriptional profiling and microRNA profiling of paired PDX and derived cell line MT-CHC01 upon ET-743 treatement
Intrahepatic cholangiocarcinoma (ICC) is an aggressive and lethal malignancy with limited therapeutic options.  ET-743 has a high antitumor activity in preclinical models of biliary tract carcinoma (BTC), being a promising alternative treatment. Here, we studied the effect of ET-743 at transcriptomic level on an ICC patient derived xenograft (PDX) and on the derived cell line, MT-CHC01. Further, putative targets of ET-743 were explored in the in vitro model. In vitro, ET-743 inhibited genes involved in protein modification, neurogenesis, migration, and motility; it induced the expression of genes involved in keratinization, tissues development, and apoptotic processes. In the PDX model, ET-743 affected ECM-receptor interaction, focal adhesion, complement and coagulation cascades, Hedgehog, MAPK, EGFR signaling via PIP3 pathway, and apoptosis. In MT-CHC01, 24 microRNAs were deregulated upon drug treatment. Only 5 microRNAs were perturbed by ET-743 in PDX; 2 up and 3 down-regulated. Among down- regulated genes, we selected SYK and LGALS1; their silencing caused a significantly reduction of migration, but did not affect proliferation in MT-CHC01 and WITT cells. In conclusion, we described that ET-743 affected genes and microRNAs involved in tumor progression and metastatic processes, reflecting data previously obtained at macroscopically level; in particular, we identified SYK and LGALS1 as new putative targets of ET-743.

overall_design: MT-CHC01 cell line treated with ET-743 at the dose of 5 nM for 24 hours vs MT-CHC01 cell line untreated;ICC PDX treated with ET-743 at the dose of 0.15 mg/Kg/weekly for three weeks vs ICC PDX untreated

first: Caterina

middle: P

last: Neia

first: Giuliana

last: Cavalloni

first: Giovanna

last: Chiorino

first: Paola

last: Ostano

first: Francesco

last: Leone

first: Massimo

last: Aglietta


title: Deciphering the genetic control of gene expression following Mycobacterium leprae antigens stimulation

status: Public on Jul 07 2017

city: Montreal

first: Erwin

last: Schurr

address: 1001 boulevard Decarie

country: Canada

institute: McGill University Health Centre

summary: Leprosy is a human infectious disease caused by Mycobacterium leprae. A strong host genetic contribution to leprosy susceptibility is well established. However, the modulation of the transcriptional response to infection and the mechanism(s) of disease control are poorly understood. To address this gap in knowledge of leprosy pathogenicity, we conducted a genome-wide search for expression quantitative trait loci (eQTL) that are associated with transcript variation –– before and after stimulation with M. leprae sonicate in whole blood cells. We show that M. leprae antigen stimulation mainly triggered the upregulation of immune related genes and that a substantial proportion of the differential gene expression is genetically controlled. Indeed, using stringent criteria, we identified 318 genes displaying cis-eQTL at an FDR of 0.01, including 66 genes displaying response-eQTL (reQTL), i.e. cis-eQTL that showed significant evidence for interaction with the M. leprae stimulus. Such reQTL correspond to regulatory variations that affect the interaction between human whole blood cells and M. leprae sonicate, and thus likely between the human host and M. leprae bacilli. We found that reQTL are significantly enriched among binding sites of transcription factors that are activated in response to infection, and that they were enriched among single nucleotide polymorphisms (SNPs) associated with susceptibility to leprosy per se and Type-I Reaction, as well as SNPs targeted by recent positive selection. Our study suggests that natural selection shaped our genomic diversity to face pathogen exposure including M. leprae infection.

overall_design: 51 unrelated individuals from Vietnam diagnosed with borderline leprosy were recruited. Whole blood was obtained from each subject in two aliquots of 10mL, one was stimulated with Mycobacterium leprae sonicate, the other remained untreated for 26-32 hours. Total RNA were extracted.

first: Jeremy

last: Manry


title: Newborn Sex-specific Transcriptome Signatures and Gestational Exposure to Fine Particles: Findings from the ENVIRONAGE Birth Cohort

city: Diepenbeek

first: Tim

last: Nawrot

address: Campus Diepenbeek Agoralaan Gebouw D

department: Centre for Environmental Sciences

country: Belgium

institute: Hasselt University

summary: We investigated sex-specific transcriptomic responses to gestational long- and short-term exposure to particulate matter with a diameter < 2.5 µm (PM2.5) in order to elucidate potential underlying mechanisms of action. Whole genome gene expression was investigated in cord blood of 142 mother-newborn pairs that were enrolled in the ENVIRONAGE birth cohort. Daily PM2.5 exposure levels were calculated for each mother’s home address using a spatial-temporal interpolation model in combination with a dispersion model to estimate both long- (annual average before delivery) and short- (last month of pregnancy) term exposure. We explored the association between gene expression levels and PM2.5 exposure, and identified modulated pathways by overrepresentation analysis and gene set enrichment analysis.

overall_design: Epidemiological study

first: Ellen

last: Winckelmans

first: Karen

last: Vrijens

first: Maria

last: Tsamou

first: Bram

last: Janssen

first: Nelly

middle: D

last: Saenen

first: Harry

last: Roels

first: Jos

last: Kleinjans

first: Wouter

last: Lefebvre

first: Charlotte

last: Vanpoucke

first: Theo

last: de Kok


title: Real-time quantitative PCR analysis of primary human dermal fibroblasts_comparing two young samples (fibroblasts isolated from a 5 month old vs. those from a 1 year old)

first: Kranti

last: Mapuskar

summary: Endogenous changes in the nuclear encoded genes of the mitochondrial ETC were analyzed using the mitochondrial energy metabolism profiler array from Qiagen to compare nuclear-encoded gene expression changes between fibroblasts isolated from two young patients.

overall_design: qPCR gene expression profiler array.  Equal amount total RNA from each donor was isolated prior to making the cDNA and analyzing the changes in nuclear-encoded gene expression.


title: TTF-1-regulated miR-532-5p targets KRAS and MKL2 oncogenes and induces apoptosis in lung adenocarcinoma

first: Takashi

last: Takahashi

type:
Expression profiling by array
Expression profiling by RT-PCR

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

overall_design: Refer to individual Series


title: Effectes of temperatures on meiotic recombination in S. cerevisiae

status: Public on Jun 06 2017

city: Hangzhou

first: Daoqiong

last: Zheng

address: 866 Yuhangtang Road

department: Institute of Microbiology

institute: College of Life Sciences, Zhejiang University

type: Genome variation profiling by genome tiling array

summary: Temperature is key for biological activities, but its role in meiotic recombination processes is less known. Here, we uncovered the patterns of meiotic recombination by monitoring the genotypes of diploid strain JSC22-1-derived spores formed at 14ºC, 30ºC, and 37ºC. These spores were analyzed by whole genome SNP microarray that can examine about 13,000 SNPs distinguishing W303-1A and YJM789 sequences throughout the genome.

overall_design: Using whole genome SNP microarray, we examined crosssovers and non-crossover gene conversion from all four products of 21 S. cerevisiae meioses at different temperatures. 11 were from 30-degree, 5 were from 14-degree, and the other 5 were from 37-degree.

first: Ke

last: Zhang

first: Tom

last: Petes


title: SNP genotype data from induced Pluripotent Stem cells from Parkinson's Disease patients harboring mutations in the GBA1 gene, and from healthy control donors

status: Public on Jun 01 2017

city: Oxford

first: Sally

last: Cowley

address: South Parks Road

department: Sir William Dunn School of Pathology

country: United Kingdom

institute: University of Oxford

type:
SNP genotyping by SNP array
Genome variation profiling by SNP array

summary:
We have generated human induced Pluripotent Stem cells (hiPSc) using Retroviral and Sendai virus-mediated delivery of reprogramming factors. hiPSc lines have been screened using SNP array to assess chromosomal stability (alongside the fibroblast lines from which they were derived), and validation of the pluripotency of the hiPSc lines is provided by Pluritest assessment of transcriptome datasets, prior to differentiation and downstream assays.
Proteomic analysis of GBA1 patient-derived dopaminergic neurons reveal impeded neurite outgrowth.

overall_design: human iPSc lines were derived from human dermal fibroblasts from PD patients harboring the mutation N370S in GBA1, and control donors. SNP datasets were generated from 7 previously unpublished iPSC clones and the fibroblasts from which they were derived

first: Helle

last: Bogetofte

first: Brent

last: Ryan

first: Pia

last: Jensen

first: Dana

last: Vergoossen

first: Tara

last: Caffrey

first: Lisa

last: Kiani

first: Hugo

last: Fernandez

first: Jane

last: Vowles

first: Morten

last: Meyer

first: Martin

last: Røssel-Larsen

first: Richard

last: Wade-Martins


title: Three TF Gene Co-expression Modules are involved in Pressure-Overload Cardiac Hypertrophy in Male Mice (mRNA)

status: Public on May 31 2017

city: Taipei city

first: Yao-Ming

last: CHANG

address: No.128, Academia Rd. Nangang Dist.

country: Taiwan

institute: Academia Sinica

summary: Pathological cardiac hypertrophy, a dynamic remodeling process, is a major risk factor for heart failure. Although a number of key regulators and related genes have been identified, how the transcription factors (TFs) dynamically regulate the associated genes and control the morphological and electrophysiological changes during the hypertrophic process are still largely unknown. In this study, we obtained the time-course transcriptomes at five time points in four weeks from male murine hearts subjected to transverse aorta banding surgery. From a series of computational analyses, we identified three major co-expression modules of TF genes that may regulate the gene expression changes during the development of cardiac hypertrophy in mice. After pressure overload, the TF genes in Module 1 were up-regulated before the occurrence of significant morphological changes and one week later were down-regulated gradually, while those in Modules 2 and 3 took over the regulation as the heart size increased. Our analyses revealed that the TF genes up-regulated at the early stages likely initiated the cascading regulation and most of the well-known cardiac miRNAs were up-regulated at later stages for suppression. In addition, the constructed time-dependent regulatory network reveals some TFs including Egr2 as new candidate key regulators of cardiovascular-associated (CV) genes.

overall_design: In this study, we obtained the time-course transcriptomes at five time points in four weeks from male murine hearts subjected to transverse aorta banding surgery. Eight-week-old adult male mice (C57BL/6J) were anaesthetized and subjected to pressure overload by transverse aortic banding (TAB). The RNAs of cardiac tissues were taken from Sham- and TAB-operated mice at 3, 5, 7, 14, and 28 days after surgery. Then, the expression changes of mRNAs and miRNAs were estimated by cDNA and miRNA microarrays, respectively.

first: Chien-Chang

last: Chen


title: Three TF Gene Co-expression Modules are involved in Pressure-Overload Cardiac Hypertrophy in Male Mice (microRNA)


title: Pho4 binding to JokerCAKE 8-mer library

status: Public on Jun 16 2017

city: Stanford

first: Polly

middle: Morrell

last: Fordyce

address: 443 Via Ortega

department: Genetics, Bioengineering

institute: Stanford University

summary: MITOMI 2.0 fluorescence intensity data for C-terminally 6xHis-tagged S. cerevisae Pho4 protein interacting with a JokerCAKE 8mer library containing joker characters.

overall_design: Microfluidic affinity assay for BODIPY-labeled S. cerevisiae Pho4 protein produced via in vitro transcription-translation in rabbit reticulocyte extract interacting with a library of Alexa-647-labeled dsDNA sequences.

first: Robert

last: Puccinelli


title: TTF-1-regulated miR-532-5p targets KRAS and MKL2 oncogenes and induces apoptosis in lung adenocarcinoma [cell line]

first: Takashi

last: Takahashi

overall_design:
Microarray analysis using a SurePrint G3 Human GE 8 x 60K v2 Microarray G4851B (Agilent) was conducted
BEAS-2B, NCI-H23, NCI-H1299 and PC-9 CTRL and TTF-1 cell lines were treated with 1 ug/ml Doxycycline for 24 h before RNA was harvested; NCI-H23 and NCI-H1299 cells were transfected with miR-532-5p mimics or a negative control and incubated for 48h before harvest

first: Sebastian

last: Griesing

first: Taisuke

last: Kajino

first: Mei

last: Tai

first: Zhuoran

last: Liu

first: Masahiro

last: Nakatochi

first: Yukako

last: Shimada

first: Motoshi

last: Suzuki


title: Population structure and ancestry of Qinchuan cattle by GeneSeek HD Bovine 77k Genotyping BeadChip

status: Public on Jun 15 2017

city: Yangli

first: Chuzhao

last: Lei

state: Shannxi

address: Xinong Road

institute: Northwest Agriculture and Forestry University

summary: GeneSeek HD Bovine 77k Genotyping array is used to estimate population structure and ancestry of bovine and evaluate loci responsible for complex traits. Further, copy number variation of bovine can be estimated by GeneSeek HD Bovine 77k Genotyping array. Here, we estimate population structure and ancestry of Qinchuan cattle.

overall_design: A total of 288 Qinchuan cattle were conducted by GeneSeek HD Bovine 77k Genotyping Beadchip.

first: Jieping

last: Huang


title: Treatment of extracellular vesicles change gene expression in mesothelial cells

city: Tokyo

first: Akira

last: Yokoi

state: Tokyo-to

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

department: Group for Research of Molecular Functions and Targets

institute: National Cancer Center　Research Institute

summary: To investigate whether the EVs from cancer cell lines could change gene expression in mesothelial cells, the EVs from five types of cells (ES-2 cells, A2780 cells, SKOV3 cells, HOSE1 cells and HOSE2 cells) were added to MeT-5A cells (Fig. 2a). All three selected cancer cell lines expressed metastatic phenotypes in mouse model (Fig. 1c), and EVs from HOSE2 cell line, established together with HOSE1 cell line, was also set as control. Total mRNAs were extracted by MeT-5A cells treated with EVs, and then microarray analysis was performed.

overall_design: Treatment of extracellular vesicles from ES-2, SKOV3, A2780, HOSE1 and HOSE2 cells induced gene expression in human mesothelial cell lines was measured at 12 and 48 hours after exposure to doses of 10 and 30 mg

first: Yusuke

last: Yoshioka


title: Gene and microRNA modulation upon ET-743 treatment in a human intrahepatic cholangiocarcinoma paired patient derived xenograft and cell line

first: giovanna

last: chiorino

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


title: Micro RNA array analysis in OLETF, a type 2 diabetic rats, and LETO, a non-diabetic control rats

city: Sapporo

first: Masaya

last: Tanno

department: Department of Cardiovascular, Renal and Metabolic Medicine

institute: Sapporo Medical University

summary: AMP deaminase (AMPD) plays a crucial role in adenine nucleotide metabolism, and its upregulated activity contributes to diastolic dysfunction of the heart caused by type 2 diabetes mellitus (T2DM) via reduction of the adenine nucleotide pool. Here we examined the mechanism of AMPD upregulation by T2DM. The protein level of 90-kDa full-length AMPD3 was increased in whole myocardial lysates and in the sarcoplasmic reticulum (SR) fraction by 55% and 123%, respectively, in OLETF, a rat model of T2DM, compared to those in LETO, a non-diabetic control, though AMPD mRNA level was unchanged in OLETF. MicroRNA array analysis revealed downregulation (>50%) of 57 microRNAs in OLETF compared to those in LETO, among which miR-301b was predicted to interact with the 3’UTR of AMPD3 mRNA. The 90-kDa AMPD3 level was significantly increased by miR-301b inhibitor, but decreased by a miR-301b mimetic in H9c2 cells. A luciferase reporter assay indicated binding of miR-301b to the 3’UTR of AMPD3 mRNA.  The results indicate that translational regulation by miR-301b mediates AMPD3 upregulation in the diabetic heart.  Since ATP generated by SR-associated glycolytic enzymes contributes to Ca2+ uptake by SERCA2a, upregulated AMPD3 in the vicinity of the SR may be a therapeutic target for diabetic cardiomyopathy.

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: Rats were anesthetized and ventilated as in in vivo hemodynamic experiments. Hearts of the rats were excised, rapidly frozen in liquid nitrogen, and stored at -80°C until further use. The expression of a set of 595 miRNAs in rat heart samples was examined using a Taqman® Rodent MiRNA Array v2.0 (Applied Biosystems, Foster City, CA).

first: Yuki

last: Tatekoshi

first: Takayuki

last: Miki

first: Atsushi

last: Kuno

first: Toshiyuki

last: Yano

first: Satoko

last: Ishikawa

first: Tetsuji

last: Miura


title: NanoString DNA data for CNV Analysis

status: Public on May 27 2017

city: Toronto

first: Dorota

last: Sendorek

state: ON

address: 661 University Ave, Suite 510

institute: Ontario Institute for Cancer Research

summary: Quantification of DNA obtained from prostate cancer tissues and matched blood normals using the NanoString Cancer CN Panel Assay

overall_design: A total of 96 genes/genomic regions from the NanoString Cancer CN Panel were profiled from 65 DNA samples using nCounter. Tumour (35 + 6 replicates) and matched blood normal (n = 12 + 12 replicates) samples were obtained from radical prostatectomy-treated, intermediate-risk (NCCN definition) prostate cancer patients. Tumour tissues are either fresh frozen (n = 30) or FFPE-preserved (n = 5) and were evaluated for Gleason Score (3+3 or 3+4 or 4+3) and cellularity (>= 70%). Prior to nCounter processing, each sample underwent DNA fragmentation by one of two methods: sonication or AluI digestion.

middle: H

first: Emilie

last: Lalonde

first: Paul

last: Boutros


title: Th17 polarization under hypoxia

city: Oslo

first: Bjørn

last: Skålhegg

address: Sognsvannsveien 9

department: Institute of Basic Medical Sciences

country: Norway

institute: University of Oslo

summary: Analysis of Th17 polarization under different oxygen concentrations and environmental toxin exposure at gene expression level. Results provide important information of the response of CD4+ T cells  to low oxygen , such as genes involved in metabolism, transcriptional factor, up- or down-regulated specific cellular functions.

overall_design: Total RNA obtained from isolated CD4 cells subjected to polarization into Th17 cells and treated with environmental toxins (cigarette smoke extract) and different oxygen concentrations.

first: Roman

last: Volchenkov

first: Vegard

last: Nygaard

first: Zenep

last: Sener


title: LASSIM -a network inference toolbox for genome-wide mechanistic modeling [MAF, MYB & GATA3 siRNA]

city: Linköping

first: Danuta

last: Gawel

address: Garnisonsvägen

country: Sweden

institute: Linköping University

summary: We present LASSIM, which is a toolbox built to build and infer parameters within mechanistic models on a genomic scale. This is made possible due to a property shared across biological systems, namely the existence of a subset of master regulators, here denoted the core system. The introduction of a core system of genes simplifies the inference into small solvable sub-problems, and implies that all main regulatory actions on peripheral genes come from a small set of regulator genes. This separation allows substantial parts of computations to be solved in parallel, i.e. permitting the use of a computer cluster, which substantially reduces the time for the computation to finish.

overall_design: Human Naïve CD4+ T cells were isolated from fresh buffy coats with Miltenyis Naïve CD4+ T Cell Isolation Kit II, according to the manufacturer’s instructions. Cells were either transfected in a cuvette with 600nM human on target plus SMART pool against MAF,MYB and GATA3 (ThermoFisherScientific Inc, USA), non-targeting siRNA (ThermoFisherScientific Inc) or with transfection buffer using the Amaxa transfection program U-014. Five hours after the nucleofection cells were washed, activated and polarized towards TH2 for or 24h. The cells were activated with platebound anti-CD3 (500 ng/ml), 500 ng/ml soluble anti-CD28, 5 µg/ml anti-IL-12, 10 ng/ml IL-4 and 17 ng/ml IL-2 (R&D Systems). For microarray experiments the cells were harvested at 24h of polarization and lysed in 600 ll Qiazol. The expression profiling 200 ng of total RNA from each sample was labeled with Cy3 and transcribed to cRNA using the Agilent Quick Amp Labeling Kit, one color. The labeled cRNA was purified with the RNEasy Mini Kit from Qiagen. The labeling efficiency was assessed using the NanoDrop ND-1000 UV-Vis Spectrophotometer. 1.65 µg Cy3 labeled cRNA from each sample was hybridized to Agilent SurePrint G3 Human GE v2 8x60K slides. The microarray slides were hybridized for 17 hours at 65°C in a rotating oven. After washing according to the manufacturer’s instructions, the slides were analyzed using the Agilent Microarray scanner 2505C with default settings for all parameters. Gene expression data was obtained with Agilent`s feature extraction software (version 10.7.3.1)

first: Mattias

last: Köpsén

first: William

last: Lövfors

middle: R

first: Colm

middle: E

last: Nestor

first: Sören

last: Bruhn

first: Gunnar

last: Cedersund

first: Mikael

last: Benson

first: Mika

last: Gustafsson


title: Interleukin-7 induced transcriptome differences of CD4+ T cells with or w/o additional T cell activation (TCA)

status: Public on May 26 2017

city: Duesseldorf

first: Karl

last: Koehrer

address: Universitaetsstr. 1

department: BMFZ

institute: University of Duesseldorf

summary: Gene expression analyses of CD4+ T cells from three healthy donors cultured in the presence or absence of IL-7 for 6h and (for samples 6 to 12) after additional 16h TCA by CD3/CD28 stimulation.

overall_design: CD4+ T cells were purified of PBMC from three healthy volunteers by magnetic cell sorting (IMag, BD Bioscience) following manufacturer’s instructions. An enrichment purity > 95% was confirmed by flow cytometry and 1 x 106 CD4+ T cells were then cultured in 96-well round bottom plates (2x105/well) in the presence or absence of IL-7 for 6 h. TCA was induced after pre-culture with IL-7 or w/o for 6 h by adding CD3/CD28 beads for additional 16 h of culture.

first: Marc

last: Jacobsen

first: René

last: Deenen


title: Gene expression profile of peri-implantation uteri treated with LPA3 receptor agonist

city: Bunkyo-ku

first: Shizu

last: Aikawa

address: 7-3-1 Hongo

institute: The University of Tokyo

summary: To investigate gene expression changes induced by Lysophosphatidic acid receptor 3 (LPA3) activation in peri-implantation uteri,  we performed microarray analysis in LPA3 agonist (T13)-injected pseudopregnant uteri. On 3.5 dpc, pseudopregnant mice were subjected with intrautero-injection of vehicle (0.01% BSA-PBS) or T13 and then uteri were dissected 24-36 hr after the injection. We found that several thousand genes were up- or down-regulated by T13 injection.  Interestingly, well-known decidual markers such as Bmp2 and Wnt4 were dramatically induced by T13, which we certificated in quantitive RT-PCR.

overall_design: 6 different samples (1-6) mixed with uteri from 3 mice, respectively; vehicle-injected pseudopregnant uteri (psp; 1,3,5) and lysophosphatidic acid receptor 3 agonist injected pseudopregnant uteri (T13; 2,4,6); 24 hr after the injection (E4.5; 1,2), 30 hr after the injection (E4.8; 3,4) and 36 hr after the injection (E5.0; 5,6); A comparison between psp vs T13 in each timepoint

first: Kuniyuki

last: Kano

first: Junken

last: Aoki

first: Yasumasa

last: Nishito

first: Yoshitaka

last: Taketomi

first: Makoto

last: Murakami


title: Gene expression signature of MYB-GATA overexpression plus GATA1 down regulation in undifferentiated or differentiated UT7 cells

city: BORDEAUX

first: Bruno

last: CARDINAUD

address: 146 rue Leo Saignat

department: INSERM U1035

country: France

institute: Bordeaux University

summary: Acute basophilic leukemia is a rare subtype of acute myeloblastic leukemia. We recently described a recurrent t(X;6)(p11;q23) translocation occurring in male infants with acute basophilic leukemia, generating a MYB-GATA1 fusion gene. To better understand the role of MYB-GATA1 in the leukemogenesis of acute basophilic leukemias, we expressed this chimeric transcription factor in the UT-7 cell line under normal or differentiating conditions. A gene expression analysis revealed 9 genes deregulated by both MYB-GATA1 and the basophilic differentiation. Three of these genes (CCL23, IL1RL1 and NTRK1) were also increased by MYB-GATA1 in CD34-positive cells, as indicated by quantitative RT-PCR.

overall_design: Two independant experiments (A and S) were performed. For each experiment, UT7 cells were transduced with two lentivirus: a lentivirus carrying the MYB-GATA1 (or a control) coding sequence, and a lentivirus carrying a GATA1 (or control) shRNA. Cells transduced with both lentiviruses were selected, and kept in culture under standard or differentiating conditions for 7 days before RNA extraction.

last: Cardinaud

first: Stephane

last: Ducassou


title: Development of chemically modified peptide targeting BIG3-PHB2 interaction on estrogen-dependent breast cancer

status: Public on Jun 09 2017

city: Tokushima

first: Tetsuro

last: Yoshimaru

address: 3-18-15 Kuramoto-cho

department: Institute for Genome Research

institute: Tokushima University

summary: Our previous studies demonstrated that specific inhibition of the BIG3-PHB2 complex, which is indispensable for estrogen (E2)-signaling activation, using ERAP, a dominant-negative peptide inhibitor, leads to the suppression of E2-dependent breast cancer cell growth in vitro and in vivo. However, duration of its effect is very short for clinical use. Here, we developed the chemically modified ERAP using stapling methods (stERAP; stapled ERAP) to improve duration of their antitumor effects. Tumor bearing mice treated with every 4 and 7 days with stERAP (1 mg/kg body weight) treatment effectively prevented the BIG3-PHB2 interaction, thereby releasing PHB2 to directly bind to both nuclear- and cytoplasmic ERalpha. This event led to the complete suppression of the E2-signalling pathways and ERalpha-positive breast cancer cell growth both in vitro and in vivo, but did not suppress the growth of normal mammary epithelial cells. Our findings suggest that the chemically modified stERAP may be a promising anti-tumor drug to suppress the growth of luminal-type breast cancer in clinical use.

overall_design: Up- and down-regulated genes by treatment of stapled-peptide or unspecific stapled-peptide at 24 and 48 hours was measured.

first: Toyomasa

last: Katagiri

first: Yosuke

last: Matsushita


title: Transcriptional comparisons of stem cell-derived hepatocytes (hiPS-Hep), HepaRG cells and 3D human hepatocyte spheroids as predictive in vitro systems for drug-induced liver injury

status: Public on May 22 2017

city: Stockholm

first: Magnus

last: Ingelman-Sundberg

address: Nanna Svartz väg 2

institute: Karolinska Institutet

summary: Three current hepatic in vitro cell systems were compared at the gene expression level in order to determine their suitability for investigations of hepatotoxicity. For mechanistic investigations we focussed on the PHH spheroid system, treating them with IC10 concentrations of either aflatoxin B1, amiodarone or chlorpromazine for up to 2 weeks and investigating the transcriptional changes induced by each of the compounds. We observed significant alterations in genes regulating carcinogenic, steatotic and cholestatic pathologies respectively.

overall_design: At 48h, 7 days (3 treatments) and 14 days (6 treatments) cells were harvested and RNA isolated. For each treatment three technical replicates were analysed.

first: Catherine

last: Bell

first: Volker

last: Lauschke


title: SNP genotype data from induced Pluripotent Stem cells from healthy control donors

first: Sally

last: Cowley

summary:
We have generated human induced Pluripotent Stem cells (hiPSc) using Retroviral or Sendai virus-mediated delivery of reprogramming factors. hiPSc lines have been screened using SNP array to assess chromosomal stability (alongside the fibroblast lines from which they derived), and validation of the pluripotency of the hiPSc lines is provided by Pluritest assessment of transcriptome datasets, prior to differentiation and downstream assays.
MAPT genetic variation and neuronal maturity alter isoform expression affecting axonal transport in iPSC-derived dopamine neurons. Joel E Beevers, Mang-Ching Lai, Heather A Booth, Federico Zambon, Laura Parkkinen, Jane Vowles, Sally A Cowley, Richard Wade-Martins, Tara M Caffrey. Stem Cell Reports 2017

overall_design: human iPSc lines were derived from human dermal fibroblasts from 3 control donors (newly-derived lines are reported here; for lines that have been previously described and for fibroblasts from which lines have been derived, refer to current manuscript for relevant references). SNP and gene expression datasets were generated.

first: Joel

last: Beevers

first: Mang-Ching

last: Lai

first: Heather

last: Booth

first: Federico

last: Zambon

first: Laura

last: Parkkinen

first: Jane

last: Vowles

first: Richard

last: Wade-Martins

first: Tara

last: Caffrey


title: Long noncoding RNA expression profiles in sub-lethal heat treated hepatoma carcinoma cells. (SMMC-7721 cells: sub-lethal heat treated vs. untreated)

city: Chongqing

first: qingsong

last: deng

state: Chongqing

address: Gaotanyan, NO.30

department: hepatobiliary surgery

institute: Southwest Hospital, Third Military Medical University

summary: Transcriptional profiling of SMMC-7721 cells comparing control untreated with sub-lethal heat treated cells (50°C for 10 min). Differentially expressed lncRNA and mRNA were measured with an Agilent Human lncRNA+mRNA Array V4.0 (4 × 180 K format) containing 41,000 lncRNAs and 34,000 mRNAs. Goal was to determine the effects of sub-lethal heat treatment on global hepatoma carcinoma cells gene expression.

overall_design:
Two-condition experiment, sub-lethal heat treated vs. untreated cells. Biological replicates: 3 control replicates, 3 experimental replicates.
Please note that experiments were carried out technically as dual channel (eg, Cy3 and Cy5-labeled samples hybridized to the same array) but the data was processed as though they are single channel (Cy3 and Cy5 signals are calculated insted of Cy3/Cy5 ratios).  Therefore three raw data files (for total 6 samples) are linked as Series supplementary files and the corresponding raw data file is indicated in the sample description field.

first: Qingsong

last: Deng

first: Kuansheng

last: Ma


title: Human monocyte-derived macrophages polarized by GM-CSF (M1) or M-CSF (M2) in the presence or absence of 50 nanomolar Methotrexate

status: Public on May 08 2017

city: Madrid

first: Amaya

last: Puig

state: Madrid

address: Dr. Esquerdo 46

department: Immunology

institute: Hospital Gregorio Marañón

summary: Identification of genes differentially expressed between human monocyte-macrophages generated in the presence of either GM-CSF (termed M1) or M-CSF (termed M2) and in the presence (+MTX) or absence (-) of Methotrexate

overall_design: Human peripheral blood monocytes from three independent healthy donors (1, 2 and 3) were isolated by anti-CD14-labeled magnetic microbeads. CD14+ monocytes were exposed to 50 nanomolar methotrexate (MTX) and cultured for 7 days in RPMI 10% FCS containing either GM-CSF (M1) or M-CSF (M2). Total RNA from each condition was extracted and purified using the RNeasy kit (Qiagen). Labelled RNA was used as hybridization probes on human Agilent human whole genome array (G4845A). All experimental procedures were performed following manufacturer instructions. Microarrays were scanned with a GenePix 4000B (Axon Instruments) scanner. Scanned images and raw data were pre-processed with GeneSpring v12 (Agilent).

last: Kröger

first: Lizbeth

last: Capetillo


title: Real-time quantitative PCR analysis of gene expression in mechanical stimulated invasion assay [cell motility]

status: Public on May 15 2017

city: Detroit

first: Karen

last: Beningo

state: Michigan

address: 5047 Gullen Mall

department: Biological Sciences

institute: Wayne State University

summary: HT1080 human fibrosarcoma cells were seeded onto a 3D collagen-fibronectin matrix and mechanical stimulation in the form of tugging forces was applied to the matrix. Cells not stimulated were used as the control group. The aim of this study was to examine which genes related to ECM and adhesion were deferentially expressed when the mechanical stimulation was applied to the matrix compared to unstimulated, control cells.

overall_design: Two samples were analyzed: unstimulated and stimulated

first: Snehal

last: Ozarkar


title: Real-time quantitative PCR analysis of gene expression in mechanical stimulated invasion assay [tumor metastasis]

summary: HT1080 human fibrosarcoma cells were seeded onto a 3D collagen-fibronectin matrix and mechanical stimulation in the form of tugging forces was applied to the matrix. Cells not stimulated were used as the control group. The aim of this study was to examine which genes related to ECM and adhesion were differentially expressed when the mechanical stimulation was applied to the matrix compared to unstimulated, control cells.


title: Gene expression signatures for entecavir treated HepG2.2.15 cells compared to entecavir untreated HepG2.2.15 cells

status: Public on May 24 2017

city: Beijing

first: dongping

last: xu

address: #100 Xisihuan Middle Road, Beijing

institute: Research Center for Clinical and Translational Medicine, Beijing 302 Hospital, Beijing

summary: To further analyze the gene expression profile regulated by entecavir, we employed whole genome microarray expression profiling as a discovery platform to identify the differentially expressed genes. Human hepatocellular carcinoma cell lines HepG2.2.15 cells were treated for 48 hr with 10 μmol/L entecavir or 0μmol/L entecavir(control samples) in vitro. The differentially expressed genes including all detected and normalized signal more than 8 were selected and 30 upregulated- and downregulated- genes  were identified between 10μmol/L dose and control samples.Afterwards, the differentially-expressed genes were analyzed using KEGG database (http://www.genome.jp/kegg/) and none of 30 genes were related to HBV infection-related molecular interaction network were identified.

overall_design: Entecavir-regulated genes in HepG2.2.15 cells was measured at 48 hours after exposure to doses of 0 μmol/L, 10 μmol/L.

first: Yan

last: Liu

first: Weiming

last: Yao

first: Dongping

last: Xu


title: Targeting MDM4/MDM2 binding interface for reactivation of p53 in cancer therapy

status: Public on Apr 18 2017

city: Roma

first: Ivan

last: Arisi

address: viale Regina Elena 295

institute: European Brain Research Institute

summary: The aim of this experiment has been to investigate the transcriptional profile of HCT116 cells treated with Peptide-3 (Pep3) compared to untreated (NT), treated with solvent (DMSO) or with a mutated peptide (Pep3M) cells. Peptide-3 is a dodecapeptide able to interact with MDM2 at the levels of the interaction region of the MDM4 and MDM2 proteins, thereby interfering with the coopeartivy function of the proteins in the regulation of p53.  This peptide is indeed able to specifically activate p53 and to cause apoptotis in different cancer cell lines and tumor growth inhibition in xenograft models.

overall_design: Three different experimental conditions have been analysed compared to untreated cells at time 0 (NT cells, the starting point of the treatment): cells treated with DMSO solvent (DMSO); treated with peptide-3 (Pep3) and with control peptide (Pep3M). The analysis has been performed at 24 and 48 hours after treatment. In addition, untreated cells after 24 hours of growth have been analysed as further control. All analyses have been performed in triplicates.

first: Marsha

last: Pellegrino

first: Francesca

last: Mancini

first: Rossella

last: Lucà

first: Isabella

last: Manni

first: Fulvio

last: Florenzano

first: Marianna

last: Buttarelli

first: Emanuela

last: Teveroni

first: Alice

last: Coletti

first: Nicola

last: Giacchè

last: Brandi

first: Mara

last: D'Onofrio

first: Roberto

last: Pellicciari

first: Giulia

last: Piaggio

first: Alfredo

last: Pontecorvi

first: Antonio

last: Macchiarulo

first: Fabiola

last: Moretti


title: Validation of the Personalized Gene Therapy by stably transfection of UBALD1 in the papillary (BCPAP) and anaplastic (8505C) thyroid cancer cell lines

status: Public on Apr 06 2017

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

summary: An ideal cancer gene therapy would selectively destroy the cancer cells without affecting much the healthy tissue. This would be possible if and only if the cancer and normal cells of the tumor are governed by distinct gene master regulators (GMRs). Logic dictates that, while being strongly protected by the homeostatic mechanisms, expression of a GMR governs the phenotype by modulating major functional pathways through controlling the expression of the involved genes.  We determined the GMRs of the standard papillary (BCPAP) and anaplastic (8505C) thyroid cancer cell lines. The hierarchy of the known biomarkers was established based on their gene commanding height (GCH), an original measure combining the expression control and coordination with expression of other genes. We found that the sets of the GMRs are largely different in the two thyroid cancer cell lines, indicatibg that each type of thyroid cancer needs a different gene-targeting therapy. In this experiment, we determined the transcriptomic effects of the stable transfection of UBALD1 gene in the BCPAP and 8505C thyroid cancer cell lines. UBALD1 was selected because it has significantly different GCHs in the two cell lines:  10.31 in 8505C and 1.12 in BCPAP.  The significantly more up- and down-regulated genes in the transfected 8505C cells than in the transfected BCPAP cells compared to their untransfected counterparts validated the theory and indicated the usefulness of our personalized gene therapy approach.

overall_design: Two-conditions (AU=BCPAP cells stably transfected with UBALD1, BU=8505C cells stably transfected with UBALD1), 4 replicas of each condition

first: Sanda

first: Neha

last: Tuli

first: Jan

last: Geliebter

first: Raj

last: Tiwari


title: The effect of EPO on gene expression signatures of hepatocellular carcinoma cells

status: Public on May 01 2017

city: shanghai

first: shizhong

last: ke

address: Xietu Road No. 25 Lane 2200

department: Shanghai Cancer Institute

institute: Shanghai Jiao Tong University School of Medicine

summary: To gain further insight into the downstream effects of EPO signaling on HCC cells, we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to illustrate EPO-induced the proliferation of HCC cells. 1×10e6 7721-EPOR cells were plated in 6 cm dishes and starved for 8 hours and then treated with either NS or EPO (10 IU/ml) for 16 hours. Total RNA was extracted and profiled using oligo microarrays. Differentially expressed genes were then identified through fold change as well as P value calculated with t-test. The threshold set for up- and down-regulated genes was a fold change>= 2.0 and a P value<= 0.05. Afterwards, GO analysis and KEGG analysis were applied to determine the roles of these differentially expressed mRNAs. EPO treated HCC cells up-regulated 14 genes expression and down-regulated 29 gene expression compared to control cells.

overall_design: 1×10e6 7721-EPOR cells were plated in 6 cm dishes and starved for 8 hours and then treated with either NS or EPO (10 IU/ml) for 16 hours. Total RNA was extracted from 2 independent experiments.

first: Shizhong

last: Ke


title: Validation of the Personalized Gene Therapy by stably transfection of DDX19B in the papillary (BCPAP) and anaplastic (8505C) thyroid cancer cell lines

status: Public on Mar 25 2017

summary: An ideal cancer gene therapy would selectively destroy the cancer cells without affecting much the healthy tissue. This would be possible if and only if the cancer and normal cells of the tumor are governed by distinct gene master regulators (GMRs). Logic dictates that, while being strongly protected by the homeostatic mechanisms, expression of a GMR governs the phenotype by modulating major functional pathways through controlling the expression of the involved genes.  We determined the GMRs of the standard papillary (BCPAP) and anaplastic (8505C) thyroid cancer cell lines. The hierarchy of the known biomarkers was established based on their gene commanding height (GCH), an original measure combining the expression control and coordination with expression of other genes. We found that the sets of the GMRs are largely different in the two thyroid cancer cell lines, indicatibg that each type of thyroid cancer needs a different gene-targeting therapy. In this experiment, we determined the transcriptomic effects of the stable transfection of DDX19B gene In the papillary (BCPAP) and anaplastic (8505C) thyroid cancer cell lines. DDX19B was selected because it has significantly different GCHs in the two cell lines: 1.64 in BCPAP and 6.03 in 8505C.  The significantly more up- and down-regulated genes in the transfected 8505C than in the transfected BCPAP cells compared to their untransfected counterparts validated the theory and indicated the usefulness of our personalized gene therapy approach.

overall_design: Two-conditions (AD = BCPAP cells stably transfected with DDX19B, BD=8505C cells stably transfected with DDX19B), 4 replicas of each condition

middle: A

middle: Y


title: Validation of the Personalized Gene Therapy by stably transfection of NEMP1 (TMEM194A) in the papillary (BCPAP) and anaplastic (8505C) thyroid cancer cell lines

summary: An ideal cancer gene therapy would selectively destroy the cancer cells without affecting much the healthy tissue. This would be possible if and only if the cancer and normal cells of the tumor are governed by distinct gene master regulators (GMRs). Logic dictates that, while being strongly protected by the homeostatic mechanisms, expression of a GMR governs the phenotype by modulating major functional pathways through controlling the expression of the involved genes.  We determined the GMRs of the standard papillary (BCPAP) and anaplastic (8505C) thyroid cancer cell lines. The hierarchy of the known biomarkers was established based on their gene commanding height (GCH), an original measure combining the expression control and coordination with expression of other genes. We found that the sets of the GMRs are largely different in the two thyroid cancer cell lines, indicatibg that each type of thyroid cancer needs a different gene-targeting therapy. In this experiment, we determined the transcriptomic effects of the stable transfection of NEMP1 (TMEM194A) gene encoding a nuclear envelope protein in the papillary (BCPAP) and anaplastic (8505C) thyroid cancer cell lines. NEMP1 was selected because it has significantly different GCHs in the two cell lines: 5.95 in BCPAP and 0.40 in 8505C.  The significantly more up- and down-regulated genes in the transfected BCPAP than in the transfected 8505C cells compared to their untransfected counterparts validated the theory and indicated the usefulness of our personalized gene therapy approach.

overall_design: Two-conditions (AT=BCPAP cells stably transfected with TMEM194A, BT=8505C cells stably transfected with TMEM194A), 4 replicas of each condition


title: Profiling of microRNAs in tumor interstitial fluid of breast cancer patients - a novel resource to identify biomarkers for prognostic classification and detection of cancer

first: Ann Rita

last: Halvorsen

address: Montebello

institute: OUS- The Norwegian Radium Hospital

summary: The purpose of this study was to identify biomarkers and to elucidate the crosstalk between stromal cells.

overall_design: Compare the level of microRNA in tumor interstitial fluid (TIF) and breast tumor tissue of breast cancer patients.

first: Ann

first: Vilde

last: Haakensen


title: Hierarchal gene master regulators of one case of papillary thyroid cancer

summary: The incidence of thyroid cancer (TC) has doubled in recent years but the molecular mechanisms responsible for various TC forms are largely unknown. We hypothesize that, in a thyroid tumor, cancer nodules and surrounding benign tissue are governed by different gene master regulators (GMRs). GMRs are defined as coding/non-coding RNAs whose strongly protected (by the homeostatic mechanisms) abundance modulates most functional pathways by coordinating the expression of their composing genes. GMRs are the most legitimate targets for TC gene therapy. However, because of strong expression control, GMRs are not selectable among TC biomarkers whose frequent regulation in large cancer patient populations indicates low protection as for minor players. We tested the hypothesis by profiling the transcriptomes of the papillary cancer and benign tissue from a surgically removed TC. The hierarchy of the known biomarkers was established for both cancer and benign regions of the tumor based on their gene commanding height (GCH), an original measure combining the expression control and coordination with expression of other genes. We found that 1/3 of the 544 known biomarkers had higher GCH in the malignant region, 1/3 in the benign region, while the rest did not discriminate between the two, raising the question of the biomarkers’ utility.

overall_design: Two-conditions (N=normal/benign region of the tumor, T=papllary thyroid cancer region of the tumor), 4 replicas of each condition


title: Mechanism of Kindlin-2 regulating invasion and metastasis of human Hepatocellular carcinoma

status: Public on Apr 19 2017

city: Fuzhou City

first: Lin

last: Jie

state: Fujian Province

address: No.134, Dong Street

department: Pathology

institute: Fujian Provincial Hospital

summary: To explore the mechanism of Kindlin-2 regulating invasion and metastasis of human Hepatocellular carcinoma, we performed gene expression microarray analysis on Kindlin-2 knockdown LM3 cells and the control cells to compare the gene expression levels between the two groups.

overall_design: Short hairpin RNAs (shRNA) targeting Kindlin-2 and negative control (NC) were synthesized and cloned into the lentiviral vector. Lentivirus expressing shRNA was generated and used to infect LM3 cells. After 72h of infection, the infected cell lines were cultured in the medium containing 2ug/ml puromycin to select Kindlin-2 stable knockdown cell line.

last: Wansong


title: Cellular Senescence RT2 Profiler PCR Array of replicative senescent and hyperglycemia treated HUVECs

status: Public on May 18 2017

city: Barcelona

first: Francesco

last: Prattichizzo

address: Carrer del Rossellò 149

institute: IDIBAPS

summary: Young endothelial cells (CPD >25 and <30; SA-Beta Gal positivity <10%) were exposed to one week of hyperglycemia (25 mmol/L) or sub-cultured until complete growth arrest (CPD > 50).  Using real-time PCR, we analyzed the expression of a focused panel of genes involved in cellular senescence.The array includes genes involved in the primary senescence program and known stresses that cause premature senescence.

overall_design: qPCR gene expression profiling.  Equal amount total RNA from three conditions (NG= normal glucose, HG= high glucose, RS= replicative senescence) was used to gene expression analysis. Three differential batches of HUVECs were used. One of single donor and two pooled.

first: Raffaella

last: Lazzarini


title: Hierarchal gene master regulators of papillary (BCPAP) and anaplastic (8505C) thyroid cancer cell lines

summary: The incidence of thyroid cancer (TC) has doubled in recent years but the molecular mechanisms responsible for various TC forms are largely unknown. We hypothesize that, in a thyroid tumor, cancer nodules and surrounding benign tissue are governed by different gene master regulators (GMRs). GMRs are defined as coding/non-coding RNAs whose strongly protected (by the homeostatic mechanisms) abundance modulates most functional pathways by coordinating the expression of their composing genes. GMRs are the most legitimate targets for TC gene therapy. However, because of strong expression control, GMRs are not selectable among TC biomarkers whose frequent regulation in large cancer patient populations indicates low protection as for minor players. We determined the GMRs of the standard papillary (BCPAP) and anaplastic (8505C) thyroid cancer cell lines. The hierarchy of the known biomarkers was established based on their gene commanding height (GCH), an original measure combining the expression control and coordination with expression of other genes. We found that the sets of the GMRs are largely different in the two thyroid cancer cell lines, indicatibg that each type of thyroid cancer needs a different gene-targeting therapy.

overall_design: Two-conditions (A0 = BCPAP cells, B0 = 8505C cells), 4 replicas of each condition


title: Validation of the Personalized Gene Therapy by stably transfection of PANK2 in the papillary (BCPAP) and anaplastic (8505C) thyroid cancer cell lines

summary: An ideal cancer gene therapy would selectively destroy the cancer cells without affecting much the healthy tissue. This would be possible if and only if the cancer and normal cells of the tumor are governed by distinct gene master regulators (GMRs). Logic dictates that, while being strongly protected by the homeostatic mechanisms, expression of a GMR governs the phenotype by modulating major functional pathways through controlling the expression of the involved genes.  We determined the GMRs of the standard papillary (BCPAP) and anaplastic (8505C) thyroid cancer cell lines. The hierarchy of the known biomarkers was established based on their gene commanding height (GCH), an original measure combining the expression control and coordination with expression of other genes. We found that the sets of the GMRs are largely different in the two thyroid cancer cell lines, indicatibg that each type of thyroid cancer needs a different gene-targeting therapy. In this experiment, we determined the transcriptomic effects of the stable transfection of PANK2 gene In the papillary (BCPAP) and anaplastic (8505C) thyroid cancer cell lines. PANK2 was selected because it has significantly different GCHs in the two cell lines:  44.64 in BCPAP and 3.61 in 8505C.  The significantly more up- and down-regulated genes in the transfected BCPAP than in the transfected 8505C cells compared to their untransfected counterparts validated the theory and indicated the usefulness of our personalized gene therapy approach.

overall_design: Two-conditions (AP=BCPAP cells stably transfected with PANK2, BP=8505C cells stably transfected with PANK2), 4 replicas of each condition


title: MiRNA expression variation in primary NK cells treated with TGF-β1

status: Public on May 11 2017

city: Genova

first: Stefano

last: Regis

address: Via G. Gaslini 5

institute: Istituto G. Gaslini

summary: Human NK cells activity against cancer cells is deeply suppressed by TGF-β1, an immunomodulatory cytokine that is released and activated in the tumor microenvironment. Moreover, our previous data showed that TGF-β1 modifies the chemokine receptor repertoire of NK cells. In particular, it decreases the expression of CX3CR1 that drives these effectors toward peripheral tissues, including tumor sites. In order to identify possible mechanisms mediating chemokine receptors modulation, we analyzed the miRNA profile of TGF-β1-treated primary NK cells. The analysis pointed out miR-27a-5p as a possible modulator of CX3CR1. We demonstrated the functional interaction of miR-27a-5p with the 3’ untranslated region (3’UTR) of CX3CR1 mRNA by two different experimental approaches: by the use of a luciferase assay based on a reporter construct containing the CX3CR1 3’UTR and by transfection of primary NK cells with a miR-27a-5p inhibitor. We also showed that the TGF-β1-mediated increase of miR-27a-5p expression is a consequence of miR-23a-27a-24-2 cluster induction. Moreover, we demonstrated that miR-27a-5p down-regulates the surface expression of CX3CR1. Finally we showed that Neuroblastoma cells induced in resting NK cells a downregulation of the CX3CR1 expression that was paralleled by a significant increase of miR-27a-5p expression. Therefore, the present study highlights miR-27a-5p as a pivotal TGF-β1-induced regulator of CX3CR1 expression.

overall_design: Real-time PCR-based miRNA expression profiling. Primary resting NK cells from three donors were treated for 24h with 5 or 40 ng/ml TGF-β1 or were left untreated.

first: Cristina

last: Bottino


title: Dido as a switchboard that regulates self-renewal and differentiation in embryonic stem cells (vsmutCT)

status: Public on Mar 16 2017

first: Carlos

last: Martinez

address: C/Darwin 3

department: Inmunology and Oncology

institute: Centro Nacional de Biotecnologia

summary:
Transition from symmetric to asymmetric cell division requires precise coordination of differential gene expression. Embryonic stem cells (ESC) strongly express Dido3, whose C-terminal truncation impedes ESC differentiation while retaining self-renewal. We show that Dido3 binds to its gene locus via H3K4me3 and RNA pol II and, at differentiation onset, induces expression of its splice variant Dido1, which then leads to Dido3 degradation and downregulation of stemness genes. We propose that Dido isoforms act as a switchboard to regulate genetic programs for ESC transition from pluripotency maintenance to promotion of differentiation.
We used microarrays to determine how the deletion of exon 16 (C-terminal truncation) of the Dido3 affects gene expression that results in the suppression of ESC differentiation.

overall_design: Mouse embryoid bodies from 2 conditions, wild type and truncated C-terminal Dido3 protein mutant overexpressing the missing terminal CT region (exon 16), were cultured in pararell and equal conditions. After 10 days development, RNA was extracted and processed for hybridization on Agilent microarrays (Agilent Mouse GE 4x44K v2 Microarray). Three biological replicates for each condition were processed simultaneously.

first: Agnes

last: Futterer

first: Jesus

last: De-Celis


title: Gene expression of sorted Eomes+ and Eomes‒ γδ T cells from spleen of Eomes-IRES-GFP mice.

status: Public on Apr 10 2017

city: Hannover

first: Ciro

last: Novaes Rosa Lino

address: Carl-Neuberg-Str. 1

institute: Hannover Medical School

summary: Eomesodermin (Eomes) is a transcription factor with a crucial role regulating cytotoxic function, development and survival of immune cells. Although it is known that γδ T cells can express Eomes, its function on those cells is still largely unknown. Using Eomes-IRES-GFP mice we were able to sort for Eomes+ and Eomes‒ γδ T cells populations and get their gene expression profiles, bringing light to the role of Eomes on γδ T cells.

overall_design: Eomes+ and Eomes‒ γδ T cells samples were obtained from three completely independent flow cytometric sorts.  As a source, cells from spleen from 4 to 6 Eomes-IRES-GFP were prepared for each sort.

first: Immo

last: Prinz

middle: N

last: Lino


title: Dido as a switchboard that regulates self-renewal and differentiation in embryonic stem cells (vsmut)

overall_design: Mouse embryoid bodies from 2 conditions, wild type and truncated C-terminal Dido3 protein mutant, were cultured in pararell and equal conditions. After 10 days development, RNA was extracted and processed for hybridization on Agilent microarrays (Agilent Mouse GE 4x44K v2 Microarray). Three biological replicates for each condition were processed simultaneously.


title: Peripheral blood lymphocytes with different levels of gH2AX foci and micronuclei

city: Tomsk

first: Aleksei

last: Sleptcov

state: Tomskaya oblasty

address: 10 Naberejnaya Ushaiki

country: Russia

institute: Research Institute of Medical Genetics

summary: Transcriptional profiling of peripheral blood lymphocytes with different levels of gH2AX foci and micronuclei after 0 and 2 Gy of gamma-rays. The aim was to identify differentially expressed genes, associated with level of gH2AX and micronuclei.

overall_design: Radiation induced gene expression in human lymphocytes was measured at 24 hours after exposure to doses of 0 and 2 Gy g-rays. Six independent experiments were performed using different donors for each experiment. Donors were diveded in two groups: 1) with low level of endogenous gH2AX foci and high radiation-induced micronucleus frequency (n=3); 2) with high level of endogenous gH2AX foci and low radiation-induced  micronucleus frequency

first: Stanislav

last: Vasilyev

first: Andrey

last: Belenko

first: Alena

middle: I

last: Velichevskaya

first: Tatiana

middle: V

last: Vishnevskaya

first: Nikolay

last: Skryabin

last: Sleptsov

first: Olga

last: Gribova

first: Zhanna

last: Startseva

first: Igor

last: Lebedev


title: Dido as a switchboard that regulates self-renewal and differentiation in embryonic stem cells (vsmutNT)

overall_design: Mouse embryoid bodies from 2 conditions, wild type and truncated C-terminal Dido3 protein mutant overexpressing the N-terminal common region containing the PHD domain of the Dido gene, were cultured in pararell and equal conditions. After 10 days development, RNA was extracted and processed for hybridization on Agilent microarrays (Agilent Mouse GE 4x44K v2 Microarray). Three biological replicates for each condition were processed simultaneously.


title: Whole Human Genome Oligo Microarray

status: Public on Mar 02 2017

city: Shanghai

first: Lin

last: Fan

address: Zhengmin Road 507#

department: Tuberculosis

institute: Shanghai Pulmonary hospital

summary:
Human expression microarray analysis of the 11 samples that you submitted. Total RNA from each sample was quantified using the NanoDrop ND-1000 and the RNA integrity was assessed using standard denaturing agarose gel electrophoresis. For microarray analysis, Agilent Array platform was employed. The sample preparation and microarray hybridization were performed according to the manufacturer’s standard protocols. Briefly, total RNA from each sample was amplified and transcribed into fluorescent cRNA with using the manufacturer’s Agilent’s Quick Amp Labeling protocol (version 5.7, Agilent Technologies). The labeled cRNAs were hybridized onto the Whole Human Genome Oligo Microarray (4x44K, Agilent Technologies). After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5 software package (Agilent Technologies). After quantile normalization of the raw data, genes that at least 7 out of 11 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis.

overall_design: 11 blood samples were collected and divided into A group (4 samples), B group (4 samples) and heathy controls (3 samples), Blood samples were abstracted RNA, and go through RNA quality testing, transcribed into fluorescent cDNA, tested by microarray of Aligent, finally get the gene expression image and raw data through hybridization of whole human genome oligo microarray. through the pathway and GO analysis, we got the elementary results through the comparison of these samples


title: Analysis of gene expression changes in mature colonic macrophages due to TGFβR1 deficiency

status: Public on Feb 28 2017

city: Edinburgh

first: Anika

last: Schridde

address: 47 Little France Crescent

institute: University of Edinburgh

summary: We have analysed transcriptomic changes of colonic macrophages due to TGFβR1 deficiency.

overall_design: Macrophages (Lin-CD45+CD11b+CD64+Ly6C-MHCII+) were FACS purified from colonic cell isolates from CD11cCrexTgfbr1fl/flxRag1-/- mice. Microarray data were generated using a refined version of the Whole Mouse Genome Oligo Microarray 4x44 K v2 from Agilent Technologies. Three replicates deriving from Cre+ mice (that lack the receptor) and Cre- controls were analysed.

first: Calum

middle: C

last: Bain

first: Oliver

last: Pabst

first: Allan

middle: M

last: Mowat


title: Gene Expresion Analysis of A-498 cells after treatment with Englerin A

status: Public on Feb 24 2017

city: Columbia

first: Diego

last: Altomare

state: SC

address: 715 Sumter Street, Room 617

department: Department of Drug Discovery and Biomedical Sciences

country: USA

institute: University of South Carolina

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

overall_design: Refer to individual Series


title: Gene expression analysis of renal cell carcinoma cell line A-498 after 20-hour treatment with englerin A.

summary: Natural products possess enormous structural and chemical diversity and are a rich source of drugs or drug-like leads. Although the final products may not necessarily represent the active ingredients of the natural source, the majority of all drugs in the market have their origin in nature. Englerin A is guaiane sesquiterpene that was isolated from the Tanzanian plant Phyllanthus engleri and has attracted much attention because of its unique structure and cytotoxicity profile in cancer cells. Englerin A was documented to have potent cytotoxicity preferentially against renal cancer cells when tested against the NCI60 cell panel. Very recently, however, a study which screened englerin A against 524 cancer cell lines from the cancer cell line encyclopedia reported that englerin A was also cytotoxic to a small subset of cancer cells in addition to renal cancer cells.[19]. In addition to its unique structure and cytotoxicity profile, englerin A is distinctive because it can cause cell death by multiple death mechanisms including necrosis and apoptosis, with apoptosis occurring in the absence of caspase activation. The distinctive features of englerin A suggest that it has a unique mechanism of action and recent reports, though lacking consensus, support this notion. Englerin A has been shown to activate protein kinase C theta (PKCθ) and was proposed to affect cell viability by promoting glucose dependence while simultaneously starving cells of glucose. Englerin A has also been shown to increase cytosolic calcium levels which may play a role in the decreased phosphorylation and activity of the oncoprotein, EWS-FLI1, in Ewing’s sarcoma. Two other groups have reported that englerin A inhibits tumor cell growth by activating the transient receptor potential cation channel, subfamily C, member 4 (TRPC4) ion channel, while a third group reported that englerin A antagonized L-type calcium channels. However, in at least two of these studies, the concentration of englerin A that was required to modulate these calcium channels was much higher than that required to kill renal carcinoma cells and other cells sensitive to the cytotoxic effects of englerin A. For instance, the most recent study reported that englerin A displaced a radiolabeled tool compound bound to an L-type calcium channel in a concentration-dependent manner with a Ki of 5.7 M. In contrast, the EC50 of englerin A in reducing the viability or growth of most renal cancer cell lines in the NCI60 cell panel is less than 60 nM, suggesting that modulation of L-type or TRPC calcium channels is not required for englerin A to induce toxic effects in these cells. It is still not clear what mechanisms account for the cytotoxicity of englerin A at nanomolar levels in these cells. We anticipate that there may be other mechanisms and targets of englerin A as natural products generally have multiple targets. In the current study, we chose microarray as well as other technologies to explore the mechanism(s) of action of englerin A at a more global level.

overall_design: Gene expression analysis was performed on A-498 cells treated with 100 nM englerin A during 20 hours.  Four replicates of vehicle control and englerin A treated A-498 cells were used in the experiment.

first: Ayse

last: Batova

first: Kim

last: Creek


title: Prominent oncogenic roles of EVI1 in breast carcinoma

city: Basel

first: Hui

last: Wang

address: Hebelstr. 20

country: Switzerland

institute: University Hospital Basel

summary: Overexpression of the Ecotropic viral integration site 1 (EVI1) gene typically associates with aggressive forms of leukemia. Aberrant EVI1 expression is also detected in breast carcinoma but its role in this tumor type is largely unknown. In order to analyze its effects in breast cancer, shRNA knockdown was performed on MDA-MB-231 cells and gene expression compared in EVI1 knockdown versus corresponding control shRNA treated cells.

overall_design: MDA-MB-231 cells were lentivirally transduced with two independent shRNA construct targeting EVI1 expression and respectively two corresponding non-coding shRNA constructs as control. Cells were transduced and analyzed independently in three biological experiments.

first: Claudia

last: Lengerke


title: Gene expression analysis of renal cell carcinoma cell line A-498 after 8-hour treatment with englerin A.

overall_design: Gene expression analysis was performed on A-498 cells treated with 100 nM englerin A during 8 hours.  Four replicates of vehicle control and englerin A treated A-498 cells were used in the experiment.


title: Gene expression profile changes after ANLN knockdown in J82 cells

first: Shuxiong

last: Zeng

state: shanghai

address: 168 changhai road

institute: Changhai Hospital

summary: To investigate gene expression profile changes after ANLN knockdown, we have employed whole genome microarray expression profiling as a discovery platform to identify genes that altered after ANLN knockdown, so as to explore the potential function of ANLN. Bladder cancer cell line J82 was knocked down by using small interfering RNA (siRNA) or control siRNA 24, 48 and 72 hours, respectively.

overall_design: J82 cells were transfected with siRNA against ANLN or control siRNA for 24, 48 and 72 hours. Each time point had one sample. As a result, we have 3 samples with ANLN knock down at 24, 48 and 72 hours in the treatment group, 3 corresponding control samples in the control group.

first: Chuanliang

last: Xu


title: Gene expression analysis of renal cell carcinoma cell line A-498 after 3-hour treatment with englerin A.

overall_design: Gene expression analysis was performed on A-498 cells treated with 100 nM englerin A during 3 hours.  Four replicates of vehicle control and englerin A treated A-498 cells were used in the experiment.


title: Gene expression in hepatocytes isolated from diet-induced obesity mice treated with anti-VLA-4 blocking antibody.

status: Public on Feb 15 2017

city: Bunko-ku

first: Yasutaka

last: Miyachi

address: 1-5-45 Yushima

department: Molecular Endocrinology and Metabolism

country: Japan

institute: Tokyo Medical and Dental University

summary: We compared gene expression pattern of hepatocytes isolated from lean and diet-induced obesity (DIO) mice. Genes increased >2-fold in DIO mice were further filtered based on >2-fold change between hepatic gene expression from DIO mice treated with anti-VLA-4 and those with IgG

overall_design: Six-week-old male wild-type C57BL/6 mice were fed a standard or high-fat diet for 16 weeks. After 10 weeks of high-fat diet feeding, mice were treated intraperitoneally with anti-VLA-4 blocking antibody or control IgG twice a week for 6 weeks. After 6 weeks of treatment, Hepatcoytes were isolated by collagenage digestion of livers from overnight fasted mice.

first: Y

first: K

last: Tsuchiya

last: Ogawa


title: Time series messenger RNA analysis of immature T-cells and reMAIT cells by microarrays

status: Public on Mar 14 2017

city: Koto-ku

first: Toutai

last: MITUYAMA

department: Artificial Intelligence Research Team

institute: National Institute of Advanced Industrial Science and Technology (AIST)

summary: To explore the molecular mechanisms underlying selective differentiation of MAIT-derived iPSCs into reMAITs, we conducted mRNAs profiling based on microarrays. We sampled reMAITs during the time course of differentiation from iPSCs as well as mature MAITs isolated from cord blood (CB MAITs). As control, we used immature T cells differentiated from hematopoietic stem cells (HSCs). For each of reMAITs and the immature T cells, we selected four time points: Start, Early, Middle, and Late.

overall_design: MAITs isolated from CB were reprogrammed to iPSCs (PMID:23523177). The MAIT-derived iPSCs were cultured on OP9, and CD34+ CD43+ cells were isolated. These CD34+ CD43+ precursor cells were furthered cultured on OP9/DL1 for re-differentiation into MAITs. Based on the observation of the reported surface antigen profiles (PMID:23523177), reMAITs were harvested at four different time points: day 0 (Start), day 4 (Early), day 7-10 (Middle), and after day 30 (Late). For the immature T cells, CD34+ cells were isolated from CB using CD34 MicroBead Kit (Miltenyi Biotech). These CD34+ HSCs were cultured on OP9/DL1 for differentiation into T cell lineage as previously described (PMID:15494433). Based on the surface antigen profiles, the immature T cells were harvested at four different time points: CD34+ cells at day 0 (Start), CD4- CD8- double negative cells at day 21 (Early) and day 40 (Midlle), and CD4+ CD8+ double positive cells after day 50 (Late). Total RNA was extracted from each sample using RNeasy Kit (Quiagen). For mRNA analysis, RNA was labeled with reverse transcription by incorporating Cy3, and subjected to analysis using Human Gene Expression v2 4x44K Microarray Kit (Agilent).

first: Yutaka

last: Saito

first: Chie

last: Sugimoto

last: Mituyama

first: Hiroshi

last: Wakao


title: Gene expression response in human peripheral blood exposed to x-rays or neutrons ex vivo

status: Public on Feb 22 2017

city: New York

first: Sally

last: Amundson

state: NY

department: Center for Radiological Research

institute: Columbia University

summary: The detonation of an improvised nuclear device would produce prompt radiation consisting of both photons (gamma-rays) and neutrons.  While much effort in recent years has gone into the development of radiation biodosimetry methods suitable for mass triage, the possible effect of neutrons on the endpoints studied has remained largely uninvestigated.  We have used a novel neutron irradiator with an energy spectrum based on that 1-1.5 km from the epicenter of the Hiroshima blast to begin examining the effect of neutrons on global gene expression, and the impact this may have on the development of gene expression signatures for radiation biodosimetry.  We have exposed peripheral blood from healthy human donors to 0, 0.1, 0.3, 0.5, or 1 Gy of neutrons ex vivo using our neutron irradiator, and compared the transcriptomic response 24 h later to that resulting from exposure to 0.1, 0.3, 0.5, 1, 2 or 4 Gy of photons (x-rays).

overall_design: Initially, aliquots of blood were exposed to doses of 0.25, 0.5 or 1 Gy neutrons or 1, 2, or 4 Gy x-rays, or treated as a mock-irradiated control, and RNA was harvested 24 hours later. Six different donors were used in this part of the study.  Later, six additional donors were recruited, and their blood was exposed to a lower range of doses: control, 0.1, 0.3, 0.5, or 1 Gy x-rays or neutrons.  One each of the 0.5 Gy neutron, 1 Gy x-ra,y and control samples were lost in processing, resulting in a total of 92 samples in the overall study

first: Constantinos

last: Broustas


title: Gene expression profiling of the human HepaRG hepatocellular carcinoma cell line under WNT3A stimulation.

status: Public on Feb 11 2017

city: Rennes

first: Cedric

last: Coulouarn

address: CLCC Eugène Marquis, Rue de la Bataille Flandres Dunkerque, Bat D, 1er étage

institute: INSERM

summary:
The aim of the study was to characterize at a molecular level (changes in mRNA level) the effects of WNT3A on the human HepaRG hepatocellular carcinoma cell line.
This was adressed by culturing HepaRG cells in presence or absence of Wnt3a.

overall_design: HepaRG cells were treated with 200 ng/ml Wnt3a for 72hrs. To dissect the gene networks involved, experiments were also performed to silence β-catenin expression with a specific siRNA and to inhibit Wnt3a in the extracellular space with FZD8_CRD, a soluble Wnt-binding domain with SFRP-like functions. HepaRG cells were plated three days before siRNA transfection and treated with 200 ng/ml Wnt3a alone and/or 300 ng/ml FZD8_CRD from day one through day three after transfection. Independent culture experiments were performed in triplicate.


title: Real-time quantitative PCR analysis of gene expression in mechanical stimulated invasion assay [extracellular and adhesion]

status: Public on May 15 2017

city: Detroit

first: Karen

last: Beningo

address: 5047 Gullen Mall

institute: Wayne State University

summary: HT1080 human fibrosarcoma cells were seeded onto a 3D collagen-fibronectin matrix and mechanical stimulation in the form of tugging forces was applied to the matrix. Cells not stimulated were used as the control group. The aim of this study was to examine which genes related to ECM and adhesion were deferentially expressed when the mechanical stimulation was applied to the matrix compared to unstimulated, control cells.

overall_design: Two samples were analyzed: unstimulated and stimulated

first: Snehal

last: Ozarkar