title: Clinical Utility of Patient Derived Xenografts to Determine Biomarkers of Prognosis and Map Resistance Pathways in EGFR-Mutant Lung Adenocarcinoma

status: Public on Mar 28 2017

first: Ming

last: Tsao

state: Ontario

address: 610 University Avenue

department: Ontario Cancer Institute

summary:
PURPOSE: Although epidermal growth factor receptor (EGFR) mutated adenocarcinomas initially have very high response rates to EGFR tyrosine kinase inhibitors (TKIs), most atients eventually develop resistance. Patient derived xenografts (PDXs) are considered preferred preclinical models to study the biology of patient tumors. EGFR-mutant PDX models may be valuable tools to study the biology of these tumors and to elucidate mechanisms  of resistance to EGFR-targeted therapies.
METHODS: Surgically resected early stage non-small cell lung carcinoma (NSCLC) tumors were implanted into non-obese diabetic severe combined immune deficient (NODSCID) mice.  EGFR TKI treatment was initiated at tumor volumes of 150 mm3. Gene expression analysis was performed using microarray platform.
RESULTS: Of 33 lung adenocarcinomas with EGFR activating mutations, only 6 engrafted  18%)  and could be propagated beyond passage one. Engraftment was associated with upregulation of genes involved in mitotic checkpoint and cell proliferation. A differentially expressed gene set between engrafting and non-engrafting patients could identify EGFRmutant patients with significantly different prognoses in The Cancer Genome Atlas (TCGA) Lung Adenocarcinoma datasets. The PDXs included models with variable sensitivity to first- and second-generation EGFR TKIs and the monoclonal antibody cetuximab. All EGFR-mutant NSCLC PDXs studied closely recapitulated their corresponding patient tumor phenotype and clinical course, including response pattern to EGFR TKIs.
CONCLUSIONS: PDX models closely recapitulate primary tumor biology and clinical outcome. They may serve as important laboratory models to investigate mechanisms of resistance to targeted therapies, and for preclinical testing of novel treatment strategies.

overall_design: Total RNAs from primary EGFR mutant tumor were amplified by DASL kit and hybridized to Illumina HT12v4 chip

first: Ming-Sound

first: Chang-Qi

last: Zhu


title: Effect of PI3K-gamma inhinition of human Langerhans cells

status: Public on Mar 30 2017

city: Southampton

first: Marta

middle: Ewa

last: Polak

state: Hampshire

address: Southampton General Hospital, Mailpoint 813, LE59,

department: Clinical and Experimental Sciences

country: United Kingdom

institute: University of Southampton

summary: The potential involvement of PI3Kγ in immune-related diseases has been recently investigated leading to efforts in developing specific inhibitors of this isoform as therapeutic strategies. (Takeda et al 2010, Rommel et al 2007). Of particular significance to cutaneous disease, murine studies have indicated the importance of PI3Kγ in Langerhans cell (LC) function. Recently, it has been postulated, PI3Kγ is a molecular switch that controls immune suppression in macrophages, a cell type closely related to LCs. [Nature letter 2016]. In our analysis PIK3CG, encoding PI3Kγ was highly expressed by LC, in contrast to dermal dendritic cells (Polak et al 2014). Here we sought to examine the effect of PI3Kg inhibition on the function of human epidermal LCs.

overall_design: Human epidermal biopsies (n=2 biological donors) were treated with AS605240, a potent, cell-permeable and ATP-competitive inhibitor of PI3Kγ at the non-toxic dose 0.1uM for 48h.Migratory cells (>80% LCs) were processed for transcriptomic analysis

middle: E


title: A global transcriptome analysis of human epidermal keratinocytes upon overexpression of microRNA-19a or microRNA-19b or microRNA-20a

status: Public on Feb 15 2017

city: Stockholm

first: Ning

last: Xu

address: CMM L8:02

country: Sweden

institute: Karolinska Institutet

summary:
Several members from microRNA 17-92 cluster, i.e. miR-19a, miR-19b and miR-20a, were found up-regulated in human epidermal keratinocytes at wound-edges compared to the intact skin; however their biological role in keratinocytes during wound repair has not been studied.
To study the genes regulated by miR-19a, miR-19b and miR-20a, we transfected miRNA specific mimics, i.e. pre-miR-19a, pre-miR-19b or pre-miR-20a into human primary epidermal keratinocytes to overexpress them.
We performed a global transcriptome analysis of keratinocytes upon overexpression of miR-19a or miR-19b or miR-20a using Affymetrix arrays.

overall_design: Expression profiling of primary human epidermal keratinocytes transfected with 20nM miR-19a mimics (pre-miR-19a) or 20nM miR-19b mimics (pre-miR-19b) or 20nM miR-20a mimics (pre-miR-20a) or 20nM control oligos (pre-miR-Ctrl) for 24 hours (biological triplicates in each group) was performed using Affymetrix GeneTitan system.


title: Expression data from root tips of  Wildtype and Osaim1 mutant rice treated with or without salicylic acid (SA)

status: Public on Mar 22 2017

city: Hangzhou

first: Xu

last: Lei

state: Zhejiang province

address: 198, Shiqiao Rd.

department: The Institute of Virology and Biotechnology

country: China

institute: zhejiang Academy of Agricultural sciences

summary:
To determine the possible role of SA in root meristem activity, we compared the gene expression profiles of the root tip of Osaim1 and WT under control condition and SA treatment.
We used microarrays to detail the global programme of gene expression underlying control condition and SA treatment between WT and Osaim1 mutant.

overall_design: Root tips of four days old plants treated with SA(500µM) or without SA from 2 biological repeats were sampled for Affymetrix microarray analysis.

first: Yi

last: Keke


title: Gene expression profiling of prostate cancer (PCa) and normal prostatic samples

status: Public on Mar 08 2017

city: Biella

first: Paola

last: Ostano

address: via Malta 3

country: Italy

institute: Fondazione Edo ed Elvo Tempia

summary:
Prostate cancer tissue samples containing at least 70% of neoplastic cells were obtained from patients (age range: 50–75 years) who had undergone radical prostatectomy at the Hospital of Biella (Italy) and prostate biopsies were obtained from healthy patients of the same age range, without any diagnosis of prostate tumor or BPH.
Gene expression profiling was performed using Human Gene Expression 8 × 60K Microarray, Agilent Technologies.

overall_design: 14 samples from normal prostate and  54 from prostate cancer from Caucasian men were analyzed for gene expression profiling

first: Giovanna

last: Chiorino

first: Maurizia

last: Mello-Grand

first: Karine

last: Lefort

first: Antonella

last: Farsetti

first: Gian-Paolo

last: Dotto


title: Differential gene expression of T-cell lymphomas (TCL) upon engagement of T-cell receptor (TCR) signaling

status: Public on Feb 10 2017

city: Ann Arbor

first: Ryan

middle: A

last: Wilcox

state: MI

address: 4310 Cancer Center, 1500 E Medical Center Dr.

department: Internal Medicine

country: USA

institute: University of Michigan

summary:
This SuperSeries is composed of the SubSeries listed below.
GSE77875;
GSE77876;
GSE77877;

overall_design:
To study differential gene expression of TCLs upon TCR signaling, three TCL primary cells and one TCL cell line T8ML1 were chosen for this study. The prmiary TCL cells consist of TCL1 and TCL2 (sezary patients) and TCL3 (PTCL, NOS patient). The TCR signaling was engaged by anti-CD3/CD28 treatment in vitro. The TCL cells were treated without/with anti-CD3/CD28 for different time periods in vitro in cell culture. The total RNA was isolated from the TCLs and subjected to affimetry microarray (GPL17692) analysis. The differential gene expression of individual TCL was identified as well as a set of common genes invloved in TCR signaling in TCLs.
The subject for this study includes pirmary cells isolated from three TCL patients [two sezary patients (TCL1 & TCL2) and one PTCL, NOS patient (TCL3)] and cells from a TCL cell line (T8ML1). The purity of isolated primary cells is >93% as idnetified by flow cytometry. The TCLs were treated with/without anti-CD3/CD28 for different time points, with 2-3 replicates for each time point. Gene expression value was presented as Log2 transformed. Differntial expressed genes were identified by ∆log2x>1 in comparison to no anti-CD3/CD28 treatment.


title: DNA methylation analysis of bull semen according to peripubertal age (12vs16 mo)

status: Public on Apr 08 2017

city: Québec City

first: Marc-André

last: Sirard

state: Quebec

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

country: Canada

institute: Université Laval

type: Methylation profiling by genome tiling array

summary: The DNA methylation pattern in spermatozoa of bulls at different age was investigated. Spermatozoa collected from 4 different bulls at 12 and 16 month each. Genome-wide DNA methylation analysis was performed by micro array using EDMA platform.

overall_design: Two condition experiment,  4 bulls, all collected at 12 and 16 months old

first: Simon

last: Lambert

first: Patrick

last: Blondin

first: Christian

last: Vigneault

first: Rémi

last: Labrecque


title: Oncogene-induced senescence in primary mouse keratinocytes

status: Public on Jan 13 2017

city: Barcelona

first: William

middle: M

last: Keyes

address: Carrer del Dr. Aiguader, 88

department: Gene Regulation, Stem Cells and Cancer

country: Spain

institute: Centre for Genomic Regulation (CRG)

summary: Analysis of growing or oncogene-induced senescent primary mouse keratinocytes 6 days post infection.

overall_design: Primary mouse keratinocytes were infected with retrovirus containing empty vector (MSCV) or HRasV12.

first: Bill

first: Mekayla

last: Storer


title: Efficient immune responses in immunocompetent individuals developing symptomatic CMV infection

status: Public on Jan 03 2017

city: Nantes

first: Christelle

last: Retière

address: 34 boulevard jean Monnet

country: France

institute: Blood Transfusion Center

summary: Primary human cytomegalovirus (HCMV) infection usually goes unnoticed, causing mild or no symptoms in immunocompetent individuals. Some rare severe clinical cases have however been reported without investigation of host immune responses or viral virulence. In this present study, we investigate, for the first time, phenotypic and functional features together with gene expression profiles in immunocompetent adults experiencing a severe primary HCMV infection. Twenty PHIP were enrolled as well as 26 HCMV-seronegative and 39 HCMV-seropositive healthy controls. PHIP had a huge lymphocytosis marked by massive expansion of NK and T cell compartments. Interestingly, PHIP mounted efficient innate and adaptive immune responses with a deep HCMV imprint, revealed mainly by the expansion of NKG2C+ NK cells, CD16+ V2-  T cells and conventional HCMV-specific CD8+ T cells.  The main effector lymphocytes were activated and displayed an early immune phenotype that developed toward a more mature differentiated status. We suggest that both huge lymphocytosis and excessive lymphocyte activation could contribute to a massive cytokine production known to mediate tissue damage observed in PHIP. Taken together, these findings bring new insights into the comprehensive understanding of immune mechanisms involved during primary HCMV-infection in immunocompetent individuals.

overall_design: Gene expression profile were performed from PBMCs from HCMV-seronegative (n=12) or HCMV-seropositive (n=25) healthy donors or from immunocompetent adults undergoing a symptomatic primary HCMV-infection (n=11). Healthy-seropositive healthy sudjects were discriminated according to the presence (n=13) or not (n=12) of the NKG2C+ NK cell expansion.


status: Public on Feb 14 2017

city: Baltimore

first: Alan

middle: E.

last: Berger

state: MD

address: 5501 Hopkins Bayview Circle Room 3B.74C

department: School of Medicine

institute: Johns Hopkins University

summary: Gene expression in 10 skin metastases from a patient with melanoma who had been treated with anti-PD-1 (Nivolumab) therapy was measured. Differences in gene expression between the lesions which responded to the treatment (n = 6) and the lesions which progressed (n = 4) were analyzed. Expression of certain genes associated with the extracellular matrix and with neutrophil function was found to be higher in the metastases which progressed. Insight into the biology governing response to immunotherapy may lead to improved rationally designed therapies, and to biomarkers for selecting patients who are more likely to benefit from these treatments.

overall_design:
Gene expression profiling was performed on total RNA extracted from 10 formalin-fixed paraffin-embedded (FFPE) separate skin metastasis specimens taken from one patient, postmortem. 6 of these metastases had regressed after anti-PD-1 therapy, and 4 had progressed. Gene expression levels were compared between these two groups of samples.

Details of the design, and the gene signatures found are given in the paper associated with this GEO Series:
Maria L. Ascierto, Alvin Makohon-Moore, Evan J. Lipson, Janis M. Taube, Tracee L. McMiller, Alan E. Berger, Jinshui Fan, Genevieve J. Kaunitz, Tricia R. Cottrell, Zachary A. Kohutek, Alexander Favarov, Vladimir Makarov, Nadeem Riaz, Timothy A. Chan, Leslie Cope, Ralph H. Hruban, Drew M. Pardoll, Barry S. Taylor, David B. Solit, Christine A. Iacobuzio-Donahue, and Suzanne L. Topalian, "Transcriptional mechanisms of resistance to anti-PD-1 therapy," Clinical Cancer Research, Published OnlineFirst February 13, 2017, doi: 10.1158/1078-0432.CCR-17-0270

first: Maria

middle: L

last: Ascierto

first: Alvin

last: Makohon-Moore

first: Evan

middle: J

last: Lipson

first: Janis

last: Taube

first: Tracee

last: McMiller

first: Jinshui

last: Fan

first: Genevieve

last: Kaunitz

first: Tricia

middle: R

last: Cottrell

first: Zachary

last: Kohutek

first: Alexander

last: Favarov

first: Vladimir

last: Makarov

first: Nadeem

last: Riaz

first: Timothy

last: Chan

first: Leslie

last: Cope

first: Ralph

middle: H

last: Hruban

first: Drew

last: Pardoll

first: Barry

middle: S

last: Taylor

first: David

middle: B

last: Solit

first: Christine

last: Iacobuzio-Donahue

first: Suzanne

last: Topalian


title: Differential gene expression of T-cell lymphomas (TCL) upon engagement of T-cell receptor (TCR) signaling [TCL2]

first: Ryan

last: Wilcox

summary: To study differential gene expression of TCLs upon TCR signaling, three TCL primary cells and one TCL cell line T8ML1 were chosen for this study. The prmiary TCL cells consist of TCL1 and TCL2 (sezary patients) and TCL3 (PTCL, NOS patient). The TCR signaling was engaged by anti-CD3/CD28 treatment in vitro. The TCL cells were treated without/with anti-CD3/CD28 for different time periods in vitro in cell culture. The total RNA was isolated from the TCLs and subjected to affimetry microarray (GPL17692) analysis. The differential gene expression of individual TCL was identified as well as a set of common genes invloved in TCR signaling in TCLs.

overall_design: The subject for this study includes pirmary cells isolated from three TCL patients [ two sezary patients (TCL1 & TCL2) and one PTCL, NOS patient (TCL3)] and cells from a TCL cell line (T8ML1). The purity of isolated primary cells is >93% as idnetified by flow cytometry. The TCLs were treated with/without anti-CD3/CD28 for different time points, with 2-3 replicates for each time point. Gene expression value was presented as Log2 transformed. Differntial expressed genes were identified by ∆log2x>1 in comparison to no anti-CD3/CD28 treatment.

first: Tianjiao

last: Wang


title: Differential gene expression of T-cell lymphomas (TCL) upon engagement of T-cell receptor (TCR) signaling [TCL3]


title: Expression data from different stages of erythropoiesis from cord derived CD34+ haematopoietic stem cells and human induced pluripotent stem cells

status: Public on Dec 13 2016

city: Oxford

first: Stephen

address: Headington

institute: CBRG

summary:
Erythropoiesis from pluripotent stem cells is very complex, and mirrors that observed in developmental erythropoiesis, with primitive and definitive waves. For a better understanding of their potential for their use in blood transfusion, they were compared to erythropoiesis from cord derived CD34 haematopoietic stem cells.
We used microarrays to detail the global programme of gene expression underlying different stages of erythropoiesis from each source, pluripotent or haematopoietic stem cells.

overall_design: We isolated mRNA (as well as conducting phenotypic and  functional studies) at each stage of erythropoiesis from pluripotent and haematopoietic stem cells, that includes pro-erythroblast, erythroblast, and the orthochromatic erythroblast. Also included in tis study is the primitive erythroblast stage from pluripotent sources.

first: Lee

last: Carpenter


title: Differential gene expression of T-cell lymphomas (TCL) upon engagement of T-cell receptor (TCR) signaling [TCL1; T8ML1]

summary:
To study differential gene expression of TCLs upon TCR signaling, three TCL primary cells and one TCL cell line T8ML1 were chosen for this study. The prmiary TCL cells consist of TCL1 and TCL2 (sezary patients) and TCL3 (PTCL, NOS patient). The TCR signaling was engaged by anti-CD3/CD28 treatment in vitro. The TCL cells were treated without/with anti-CD3/CD28 for different time periods in vitro in cell culture. The total RNA was isolated from the TCLs and subjected to affimetry microarray (GPL17692) analysis. The differential gene expression of individual TCL was identified as well as a set of common genes invloved in TCR signaling in TCLs.
The subject for this study includes pirmary cells isolated from three TCL patients [two sezary patients (TCL1 & TCL2) and one PTCL, NOS patient (TCL3)] and cells from a TCL cell line (T8ML1). The purity of isolated primary cells is >93% as idnetified by flow cytometry. The TCLs were treated with/without anti-CD3/CD28 for different time points, with 2-3 replicates for each time point. Gene expression value was presented as Log2 transformed. Differntial expressed genes were identified by ∆log2x>1 in comparison to no anti-CD3/CD28 treatment.

overall_design: TCR signaling of TCLs was stimulated by anti-CD3/CD28 for vairous time points, with triplicates for each time points. The total RNAs were extracted and converted to cDNA for microarray analysis.


title: Genotype data from induced Pluripotent Stem cells from OPA1 Haploinsufficiency patients

status: Public on Feb 03 2017

first: Sally

last: Cowley

address: South Parks Road

department: Sir William Dunn School of Pathology

institute: University of Oxford

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

summary:
We have generated human induced Pluripotent Stem cells (hiPSc) from two individuals with OPA1 haploinsufficiency, and one control donor, using Sendai virus-mediated delivery of reprogramming factors. hiPSc lines have been screened using SNP array to assess chromosomal stability (alongside the fibroblast lines from which they derived), and validation of the pluripotency of the hiPSc lines is provided by Pluritest assessment of transcriptome datasets, prior to differentiation to dopaminergic neuronal clutures and downstream functional assays.
Mitochondrial fragmentation in iPSC-derived dopaminergic neurons with OPA1 haploinsufficiency underpins increased apoptosis  and syndromic Parkinsonism.

overall_design: human iPSc lines were derived from human dermal fibroblasts from 2 related individuals with heterozygous OPA1 mutations, one of whom had syndromic Parkinsonism, and 1 control donor.

first: M

last: Jonikas

first: T

last: Zekoll

first: S

last: Wigfield

first: A

last: Mathy

last: Kurzawa-Akanbi

first: C

last: Browne

first: D

last: Sims

first: P

middle: F

last: Chinnery

first: G

middle: K

last: Tofaris


title: Chip data of OsMYB30 overexpression and mutant plants under cold stress

status: Public on Jan 20 2017

city: Wuhan

first: Hanyan

last: Ye

state: Hubei

address: No. 5, Shizishan street

institute: HuaZhong Agricultural University

summary:
It is important to reveal the regulatory mechanism of OsMYB30 gene which participated in cold response.
We used microarrays to find differentially expressed genes that might be regulated by OsMYB30 and resolve its regulation mechanism.
The rice gene OsMYB30 was overexpressed in the two OsMYB30 overexpression plants (OE2 and OE28) compared to the control plant (CK, ZH11). The rice gene OsMYB30 was knocked out in the two osmyb30 homozygous mutants (mutant1 and mutant2) compared to the wild type (WT, Huayang).OE2-C0h and OE28-C0h are two repititions of OsMYB30 overexpression plants under normal conditions with CK-C0h used as control plant. OE2-C6h and OE28-C6h are two repititions of OsMYB30 overexpression plants under cold stress conditions with CK-C6h used as control plant. mutant1-C0h and mutant2-C0h are two repititions of osmyb30 homozygous mutant plants under normal conditions with WT-C0h used as control plant. mutant1-C6h and mutant2-C6h are two repititions of osmyb30 homozygous mutant plants under cold stress conditions with WT-C6h used as control plant.

overall_design: In order to find differentially expressed genes in the OsMYB30-OE (comparing two independent OE plants with ZH11) and osmyb30 mutant (comparing two independent homozygous mutant plants with Huayang) under normal conditions and cold treatment for 6 hours.

first: Mei

last: Yang

first: Yan

last: Lv

first: Lizhong

last: Xiong


title: Expression data from rice roots treated with Glu

status: Public on Dec 31 2016

city: Taipei

first: Ming-Hsiun

last: Hsieh

address: 128 Academia Road, Section 2

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica

summary:
We used GeneChip Rice Genome Array (Affymetrix, Santa Clara, CA, USA) to identify genes that were rapidly induced by glutamate in rice roots.
Transcriptomic analysis of rice roots revealed that the expression of at least 122 genes involved in metabolism, transport, signal transduction, defense, and stress responses was rapidly induced by glutamate within 30 minutes.

overall_design: Total RNA from –N and Glu-treated roots (2.5 mM Glu, 30 min) was extracted using a phenol extraction protocol. RNA samples from two biological repeats were sent to the Affymetrix Gene Expression Service Lab at Academia Sinica, Taipei, Taiwan (http://ipmb.sinica.edu.tw/affy/) for target preparation, and hybridization to the GeneChip Rice Genome Array.

first: Tsui-Yun

last: Chung

first: Chia-Cheng

last: Kan


title: The gene expression data of OsNPR1 overexpression and its wild type Taipei 309 plants.

status: Public on Nov 22 2016

city: Shanghai

first: Zuhua

last: He

state: Shanghai

address: 300 Fenglin Road

department: shanghai institute of plant physiology and ecology

institute: Chinese Academy of Science

summary:
We have found that overexpression of OsNPR1, a master gene for SAR in rice, greatly enhanced disease resistance. However, the growth and development of the OsNPR1 overexpression (OsNPR1-OX) lines were restrained and the mechanism remained elusive.
In this study, we used microarray to identify the differential expression genes to explain the OsNPR1-induced growth inhibition.

overall_design: We used the uppermost two  internodes of Taipei309 and OsNPR1-OX to isolate total RNA.

first: Dong-Lei


title: mRNA expression profiles of colorectal liver metastases as a novel biomarker for early recurrence after partial hepatectomy

status: Public on Jan 01 2017

city: Rotterdam

first: Marcel

last: Smid

address: Dr. Molewaterplein 50

department: Medical Oncology

country: Netherlands

institute: Erasmus MC

summary: Identification of specific risk groups for recurrence after surgery for colorectal liver metastases (CRLM) remains challenging due to the heterogeneity of the disease. Classical clinicopathologic parameters have limited prognostic and predictive value. The aim of this study was to identify a gene expression signature measured in CRLM discriminating early from late recurrence after surgery for CRLM. Methods: Tumour samples of CRLM from two patient groups were collected: I) patients with recurrent disease within 12 months after surgery (N=33), and II) patients without recurrences and disease free for at least 36 months (N=30). The included patients were clinically homogeneous; all patients had a low risk profile (clinical risk score 0-2) and did not receive (neo-) adjuvant chemotherapy. Extracted total RNA from both groups was hybridized to Illumina arrays, and processed for analysis. A leave-one-out cross validation (LOOCV) analysis was performed to identify a potentially prognostic gene expression signature.  Results: The LOOCV yielded an 11-gene profile with prognostic value in relation to recurrent disease within 12 months after partial hepatectomy. This gene expression profile had a sensitivity of 81.8%, with a specificity of 66.7% for predicting early recurrences (within 12 months) versus no recurrences for at least 36 months after surgery (X2 P<0.0001). Conclusion: The current study yielded an 11-gene signature at mRNA level in CRLM discriminating early from late or no relapse after partial hepatectomy.

overall_design: Total RNA isolated from FFPE-material was used to generate gene-expression data; from these, a signature was identied in CRC patients  distinguishing early or late relapse after partial hepatectomy.

first: Eric

middle: P

last: van der Stok

first: Anieta

last: Sieuwerts

first: John

middle: W

last: Martens

first: Cees

last: Verhoef


title: Genome-wide monitoring of gene expression in Saccharomyces cerevisiae upon KP1019 treatment

status: Public on Dec 01 2016

city: Bhopal

first: Raghuvir

middle: singh

last: Tomar

state: MP

address: ITI (Gas Rahat) Building Govindpura - Bhopal

department: Department of Biological Sciences

country: India

institute: Indian Institute of Science Education & Research

summary:
KP1019 (trans-[tetrachlorobis(1H-indazole) ruthenate(III)]) is a ruthenium complex that exhibited anti-cancer activity in several in vitro and in vivo studies. KP1019 was even efficient against cancer cells that were resistant to other chemotherapeutic agents and thus emerged as a promising anti-cancer drug without dose-limiting cytotoxicity. However, the molecular mechanisms of its action are elusive.
So, the present study was designed to understand the cellular processes that were affected by KP1019 treatment using budding yeast as a model organism through the transcriptomics approach. The genome-wide transcriptome was analyzed in wild-type yeast cells upon treatment with a sub-lethal dose of KP1019 (50µg/ml). The functional enrichment analysis of KP1019 transcriptome revealed many of cellular processes that were compromised and thus probable mechanisms of action.

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: Wild-type yeast (W1588-4c) cells were grown to exponential phase and then treated with either DMSO (Untreated Control) or a sub-lethal dose of 50µg/ml KP1019 for 3h. Two independent repeats were performed for each experiment (Control or KP1019). Total RNAs were extracted and hybridized on Affymetrix microarrays.

first: Upendarrao

last: Golla


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

status: Public on Nov 16 2016

first: Sally

last: Cowley

summary:
We have generated human induced Pluripotent Stem cells (hiPSc) using Sendai virus-mediated delivery of reprogramming factors. hiPSc lines have been screened using SNP array to assess chromosomal stability (alongside the fibroblast lines from which they derived), and validation of the pluripotency of the hiPSc lines is provided by Pluritest assessment of transcriptome datasets, prior to differentiation and downstream assays.
Excess α-synuclein compromises phagocytosis in iPSC-derived macrophages.

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

first: Walther

last: Haenseler

first: Federico

last: Zambon

first: Heyne

last: Lee

first: Jane

last: Vowles

first: Federica

last: Rinaldi

first: Galbha

last: Duggal

first: Henry

last: Houlden

first: Katrina

last: Gwinn

first: Selina

last: Wray

first: Kelvin

middle: C

last: Luk

first: Richard

last: Wade-Martins

first: William

last: James


title: Gene Expression Profiling of Ex-vivo expanded Hematopoietic Stem and Progenitor Cells using SCF+TPO+FLT3L and homing factor SDF1

status: Public on Dec 11 2016

city: Navi Mumbai

first: Jyoti

middle: Anand

last: Kode

state: Maharashtra

address: Kharghar

department: Kode Lab

institute: Advanced Centre for Treatment, Research & Education in Cancer (ACTREC), Tata Memorial Centre

summary: Efficient bone marrow homing is a prerequisite for successful engraftment of transplanted HSPC. This study aims at determining factors important in homing of these cells from the blood to the marrow and their re-engraftment.  We have isolated nucleated cells from mobilized peripheral blood stem cell harvests (PBSC). CD34+ hematopoietic stem and progenitor cells (HSPC) were enriched from PBSC harvests by immunomagnetic  separation  using negative selection method. Enriched cells were cultured in vitro for expansion in presence or absence of cytokine (GF: SCF+TPO+FLT3L) and/or chemokine (homing factor SDF1) mixture for 8 days at 370C in humidified atmosphere of 5% CO2 in air. GF+SDF1 –stimulated HSPC showed significantly increased total nucleated ells as well as CD34+ cells as compared to GF-stimulated HSPC as well s unstimulated cultured HSPC. On transplantation of these cells in vivo in mice model who were previously irradiated at sublethal dose of 375cGy, it was observed that GF+SDF1-stimulated HSPC exhibited significantly better engraftment in terms of presence of human CD45+ cells in mouse blood at 6 week post –transplantation. We have compared gene expression profiles of mobilized PBSC harvest cells, enriched CD34+ HSPC population and HSPC cultured in plain media, in presence with GF and in presence of GF+SDF1  derived from mobilized PBSC harvests with respect to genes involved in homing and engraftment capacities.

overall_design: SDF1 induced gene expression was measured in CD34-enriched HSPC expanded for 8-day in ex-vivo culture. This Gene expression profiles were compared with that of freshly mobilized PBSC harvests, CD34-enriched HSPC and HSPC cultured in absence of any stimulus and in presence of GF mixture. Five independent experiments were performed at each time using different transplantation donors. Agilent one-color experiment,Organism: Human ,Agilent-Custom Whole Genome Human 8x60k designed by Genotypic Technology Pvt. Ltd. (AMADID: 027114)  , Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)

first: Navin

last: Khattry

first: Rohini

last: Karandikar

first: Vasanti

last: Amrutkar

first: Shubhada

middle: V

last: Chiplunkar


title: Neuroblastoma response to C2 ceramide and PARP inhibitor (PJ34)

status: Public on Nov 29 2016

city: Warsaw

first: Krzysztof

last: Gogolewski

address: Banacha 2a

department: Intitute of Informatics

country: Poland

institute: University of Warsaw

summary: Analysis of Neuroblastoma SH-SY5Y cell line treated with C2 ceramide, or combination of C2 ceramide and PJ34. Samples were collected in three time points: 3 hours, 6 hours and 24 hours. Results provide insight into the mechanism of cramide induced cell death and role of poly (ADP-ribose) polymerase in these proces.

overall_design: Neuroblastoma SH-SY5Y 27 in 2 experimental conditions (cells treated with C2 ceramide or C2 ceramide and PJ34) and the contol sample (pure medium).  For each experimental condition and the control 3 time points (3, 6 and 24 hours) were analysed.  For each variant 3 biological replications were collected.

first: Weronika

last: Wronowska

first: Robert

last: Strosznajder

first: Przemysław

last: Wencel

first: Bogdan

last: Lesyng

first: Anna

last: Gambin


title: Dissimilar manifestation of heterosis in super hybrid rice at early-tillering stage under nutrient-deficient and nutrient-sufficient condition

status: Public on Nov 07 2016

city: Hefei

first: Longjiang

last: Gu

state: Anhui Province

address: 130 Changjiang West Avenue

department: School of Life Sciences

institute: Anhui Agricultural University

summary:
Heterosis has long been exploited for crop breeding; however, the genetic mechanisms, particularly the initial establishment of heterosis during the early vegetative growth phase, remain elusive. The biggest challenge for that is to exclude noise genes from the identified heterosis-related candidates. Herein, we use nutrient-deficient hybrid with no measurable growth heterosis as control to filter potential background noise differentially expressed genes
In this dataset, we compared the differentially expressed genes in both heterotic  and non-heterotic hybrid. After filtering these irrelevant genes, only 336 differentially expressed genes (DEGs), which is significantly lower than those of previous reports, were identified as heterosis-related genes in a super hybrid rice of Liang-You-Pei-Jiu (LYP9) at early-tillering stage

overall_design: Major object was aimed to eliminate the potential background DEGs in hybrid, and therefore to identify possibly geninue DEGs, which were directly responsible for the initial establishment of heterosis during early vegetative growth phase.

first: Ying

last: Wu

first: Mengmeng

last: Jiang

first: Weina

last: Si

first: Xiaohui

last: Zhang

first: Sihai

last: Yang

first: Dacheng

last: Tian


title: Expression data from BPH resistant and susceptible rice varieties

status: Public on Oct 17 2016

first: Rongzhi

last: Chen

address: 16, Luojia Mountain

institute: Wuhan University

summary:
BPH9 is a gene that confers rice strong resistance to its devastating pest BPH. Understanding the molecular responses of the resistant and susceptible varieties would pave the way to controlling the pest more effectively.
To better understand the molecular mechanism underlying resistance to BPH mediated by BPH9, we conducted a genome-wide microarray analysis of NIL-BPH9 and 9311 at the early stage of BPH infestation.

overall_design: Leaf shealth of resistant and susceptible rice plants were collected at 0(without BPH infestation), 3, 6h post BPH infestation for RNA extraction and hybridization on Affymetrix microarrays.


title: MicroRNA Expression Profiling of Saliva in Tongue Squamous Cell Carcinoma Patients

status: Public on Oct 20 2016

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary: 41% of all oral carcinomas have been found to localize at tongue, where they were characterized as being aggressive and having capacity to locally invade and relapse frequently. Despite considerable enhancements in the cancer diagnosis and treatment techniques, tongue squamous cell carcinoma (TSCC) still remains to be one of the most common and lethal cancer types in the head and neck region. In this study, we aimed to identify a signature of saliva-specific microRNAs (miRNAs) expression in TSCC patients. To explore putative diagnostic biomarkers, we compared the miRNA profiles of saliva samples obtained from 3 TSCC patients and 4 healthy control individual using Agilent miRNA microarray (V19). Three of the differentially expressed miRNAs were selected for further validation with quantitative reverse-transcription PCR (qRT-PCR) using saliva samples of 25 TSCC patients and 25 healthy control individuals. Microarray analysis demonstrated that 428 miRNA probes were deregulated in TSCC patients when compared to control group and qRT-PCR results validated the reduced expression of miR-139-5p in TSCC saliva. Further analysis of post-operative saliva samples of TSCC patients revealed that miR-139-5p level elevated to normal level after surgery, pointing its diagnostic and prognostic power. As a conclusion, we propose saliva as a feasible source in routine patient examination for early diagnosis of TSCC patients, and our results suggest saliva miR-139-5p as a novel potential diagnostic marker.

overall_design:
We compared the miRNA profiles of saliva samples obtained from 3 TSCC patients and 4 healthy control individual using Agilent miRNA microarray (V19).
Two group comparison

first: Mustafa

last: Ozen

first: Yiqun


title: Intermittent hypoxia confers pro-metastatic gene expression selectively through NF-kB in inflammatory breast cancer cells

status: Public on Oct 06 2016

city: Zurich

first: Katrin

last: Gutsche

address: Winterthurerstrasse 190

country: Switzerland

institute: University of Zurich

summary: Inflammatory breast cancer (IBC) is the most aggressive form of breast cancer. Treatment options are limited and the mechanisms underlying its aggressiveness are poorly understood. Intermittent hypoxia (IH) causes oxidative stress and is emerging as important regulator of tumor metastasis. Vessels in IBC tumors were shown to be immature, which is a primary cause of IH. We therefore investigated the relevance of IH for the modulation of gene expression in IBC cells in order to assess IH as potential regulator of IBC aggressiveness. Gene array analysis of IBC cells following chronic IH (45-60 days) demonstrated increased expression of pro-metastatic genes of the extracellular matrix, such as tenascin-C (TNC; an essential factor of the metastatic niche) and matrix metalloproteinase 9 (MMP9), and of pro-inflammatory processes, such as cyclooxygenase-2 (COX-2). Investigating the oxidative stress-dependent regulation of TNC, we found a gradual sensitivity on mRNA and protein levels. Oxidative stress activated NF-E2-related factor 2 (Nrf2), c-Jun N-terminal kinase (JNK), c-Jun and nuclear factor κB (NF-κB), but TNC upregulation was only dependent on NF-κB activation. Pharmacological inhibition of inhibitor of NF-κB α (IκBα) phosphorylation as well as overexpression of IκBα prevented TNC, MMP9 and COX-2 induction, whereas the pro-inflammatory cytokine interleukin-1β (IL-1β) increased their expression levels. Analysis of the gene array data showed NF-κB binding sites for 64% of all upregulated genes, linking NF-κB and IH-dependent regulation of pro-metastatic gene expression in IBC cells. Our results provide a first link between intermittent hypoxia and pro-metastatic gene expression in IBC cells, revealing a putative novel mechanism for the high metastatic potential of IBC.

overall_design: SUM149PT cells were seeded. Following 24 h one part was harvested for analysis of gene expression of untreated cells (0 h). The other part was cultured for 45 days in intermittent hypoxia conditions (24 h 0.2% O2 alternated with 48 h 21% O2). RNA extraction and hybridization on Affymetrix microarrays was performed to compare gene expression after 45 days in IH conditions with the gene expression of untreated cells at the timepoint 0 h. One biological replicate was analyzed.

first: Cornelia

last: Leo


title: The small molecule ID8 increases Aldefluor+ breast cancer stem cells

status: Public on Nov 01 2016

first: Sean

middle: Patrick

last: McDermott

address: 2800 Plymouth Rd

department: Internal Medicine - Hem/Onc

institute: University of Michigan

summary: The cancer stem cell (CSC) hypothesis postulates that tumors are maintained by a self-renewing CSC population that is also capable of differentiating into non-self renewing cell populations that constitute the bulk of the tumor. Targeting breast CSC (BCSC) self-renewal represents an avenue for developing therapeutics; however, the molecular mechanisms that govern self-renewal of BCSCs are poorly understood. Our data show the small molecule ID8 decreases overall cell growth, but increases the self-renewal of Aldefluor+ BCSCs and increases functional metastatic BCSCs in a xenograft model. Microarray analysis showed that ID8 is a pleotropic molecule by increasing numerous pathways, including cytokines and chemokines. However, inhibition of those pathways does not abrogate the ID8-induced increase in Aldefluor+ BCSCs. Rather, ID8 is able to activate MAPK pathway through upregulation of the scaffold protein LAMTOR3 and inhibition of MEK prevented the increase in Aldefluor+ BCSCs. By using ID8 as a molecular tool, we identified a new function of the MAPK pathway in regulating BCSC growth and self-renewal.

overall_design: In three separate experiments per cell line, SUM159 and T47D breast cancer cells were treated with DMSO or 5uM (micromolar) ID8 for 3 days. DMSO and ID8 treated cells were trypsinized, processed, and stained for intracellular aldehyde dehydrogenase (ALDH) activity using the Aldefluor assay to identify cancer stem cells (Aldefluor+). CSCs and non-CSCs (Aldefluor-) were collected by flow cytometry from both groups.     Total RNA was collected from each fraction (Aldefluor+, Aldefluor-), treatment (DMSO, ID8), and experiment (#2-7). A total of 24 samples were analyzed on an Affymetrix Human Gene ST 2.1 plate. Differential gene expression was determined with R/Bioconductor with Robust Multiarray Average (RMA) and fitting the data to linear models (limma). Experimental and processing batch effects were accounted for using ComBat. Eight sets of univariate comparisons were made: 1) SUM159 ID8 Aldefluor+ vs SUM159 DMSO Aldefluor+; 2) SUM159 ID8 Aldefluor+ vs SUM159 ID8 Aldefluor-; 3) SUM159 DMSO Aldefluor+ vs SUM159 DMSO Aldefluor-; 4) SUM159 ID8 Aldefluor- vs SUM159 DMSO Aldefluor-; 5) T47D ID8 Aldefluor+ vs T47D DMSO Aldefluor+; 6) T47D ID8 Aldefluor+ vs T47D ID8 Aldefluor-; 7) T47D DMSO Aldefluor+ vs T47D DMSO Aldefluor-; 8) T47D ID8 Aldefluor- vs T47D DMSO Aldefluor-. Multiple testing comparisons were adjusted using Benjamini and Hochberg (aka FDR). Probes with an adjusted p-value <0.05 were considered statistically significant.

first: Max

last: Wicha


title: Expression data in human renal cell carcinoma samples from patients who did or did not respond to anti-PD-1 (Nivolumab) immunotherapy

status: Public on Aug 04 2016

first: Alan

last: Berger

summary: Pre-treatment tumor expression of PD-L1 has been shown to correlate with favorable clinical outcomes following PD-1 blocking therapies. However, the majority of patients with PD-L1+ tumors do not respond to treatment. With the goal of obtaining insights into the mechanisms underlying the response to anti-PD-1 targeted therapies in patients with renal cell carcinoma (RCC) with positive tumor expression of PD-L1, microarray expression data was obtained for pre-treatment tumors from patients with RCC who did or did not have a positive response to anti-PD-1 (nivolumab) therapy. Insight into these mechanisms may lead to improved rationally designed therapies, and biomarkers for selecting patients who are more likely to benefit from these treatments.

overall_design:
Gene expression profiling was performed on total RNA extracted from 11 formalin-fixed paraffin-embedded (FFPE) RCC specimens, 4 of which were from patients who had a positive response (objective tumor regression) to the anti-PD-1 (nivolumab) immunotherapy, and 7 of which were from patients who did not have a response. Details of the design, and the gene signatures found are given in the paper associated with this GEO Series: Maria Libera Ascierto, Tracee L. McMiller, Alan E. Berger, Ludmila Danilova, Robert A. Anders, George J. Netto, Haiying Xu, Theresa S. Pritchard, Jinshui Fan, Chris Cheadle, Leslie Cope, Charles G. Drake, Drew M. Pardoll, Janis M. Taube, and Suzanne L. Topalian, The Intratumoral Balance between Metabolic and
Immunologic Gene Expression Is Associated with
Anti–PD-1 Response in Patients with Renal Cell
Carcinoma, published online in Cancer Immunology Research on 4 August 2016, doi: 10.1158/2326-6066.CIR-16-0072

first: Maria

last: Ascierto

first: Tracee

last: McMiller

middle: E

first: Ludmila

last: Danilova

first: Robert

middle: A

last: Anders

first: George

last: Netto

first: Haiying

last: Xu

first: Theresa

last: Pritchard

first: Jinshui

last: Fan

first: Chris

last: Cheadle

first: Leslie

last: Cope

first: Charles

middle: G

last: Drake

first: Drew

middle: M

last: Pardoll

first: Janis

last: Taube

first: Suzanne

last: Topalian


title: A five-gene expression signature to predict progression in T1G3 bladder cancer

status: Public on Jul 29 2016

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

institute: CIBEREHD

summary: To analyze the gene expression profiles of progressive and non-progressive T1G3 bladder cancer (BCa) patients in order to develop a gene expression signature to predict tumour progression. Multicenter, retrospective study of formalin-fixed paraffin embedded (FFPE) tissue samples from 96 T1G3 BCa patients who underwent a transurethral resection. Patients with concomitant CIS were excluded. Global gene expression patterns were analyzed in 21 selected samples from progressive and non-progressive T1G3 BCa patients using microarrays. Expression levels of 94 key genes selected from microarrays and from the literature were studied by quantitative PCR in an independent cohort of 75 samples from progressive and non-progressive T1G3 BCa patients.  Univariate logistic regression was used to identify individual predictors. Progressive and non-progressive T1G3 BCa patients show different gene expression patterns. Identification of new genes associated with a high probability of tumour progression in combination with a robust, easy-to-use and reliable algorithm may contribute to tailor treatment and surveillance strategies in these patients.

overall_design: Transcriptomic profile from nine non-progressive and twelve progressive T1G3 bladder cancer FFPE samples

first: J

middle: J

first: A

last: Alcaraz

first: L

last: Mengual


title: Brain Metastasis Prediction by DASL Transcriptomic Profiling in Triple Negative Breast Cancer based on FFPE samples

status: Public on Sep 13 2016

city: Gliwice

first: Aleksandra

last: Pfeifer

address: Wybrzeze Armii Krajowej 15

institute: MSC Memorial Cancer Center and Institute of Oncology

summary:
Triple negative breast cancer (TNBC) lacks expression of steroid hormone receptors (estrogen alpha and progesterone) and epidermal growth factor receptor type 2. This phenotype shows high metastatic potential, with particular predilection to lungs and brain. Determination of transcriptomic profiles specific for brain metastasis (BM)-prone TNBC might identify high-risk patients requiring the use of alternative, more aggressive or specific preventive and therapeutic approaches.
The aim of the study was to compare the gene expression profile in the primary tumor of patients who developed brain metastases in comparison to these who were metastatic to other organs (excluding central nervous system) in an attempt to verify, whether there exist a significant difference in the transcriptome of these two subgroups.

overall_design: Gene expression profiles of primary tumors  in 71 TNBC patients (23 patients with BM and 48 patients without BM, discovery cohort), derived from a consecutive series of 324 advanced TNBC treated in 17 oncology centers in Poland and Italy between 1997 and 2013. Analysis was carried out in mRNA samples isolated from formalin-fixed paraffin embedded (FFPE) specimens, using Illumina cDNA-mediated Annealing, Selection, Extension and Ligation (DASL) method and Illumina HumanHT-12 oligonucleotide microarrays. The expression of 29,369 gene transcripts was compared between patients with and without BM, no reliable differences were identified. The results were validated in independent cohort of 48 samples, the top transcripts selected in discovery cohort showed no significant differences in the test set.

first: Renata

last: Duchnowska

first: Michał

last: Jarząb

first: Jadwiga

last: Żebracka

first: Rafał

last: Matkowski

first: Anna

last: Kowalczyk

first: Barbara

last: Radecka

first: Małgorzata

last: Kowalska

last: Foszczyńska-Kłoda

first: Antonio

last: Musolino

first: Bogumiła

last: Czartoryska-Arłukowicz

first: Maria

last: Litwiniuk

last: Surus-Hyla

first: Sylwia

last: Szabłowska-Siwik

first: Bożenna

last: Karczmarek-Borowska

last: Dębska-Szmich

first: Beata

last: Głodek-Sutek

first: Katarzyna

last: Sosińska-Mielcarek

first: Ewa

last: Chmielowska

last: Kalinka-Warzocha

first: Wojciech

last: Olszewski

first: Janusz

last: Patera

first: Anton

last: Żawrocki

first: Tomasz

last: Tyszkiewicz

first: Dagmara

last: Rusinek

last: Oczko-Wojciechowska

first: Jacek

last: Jassem

last: Biernat


title: MICRORNA EXPRESSİON PATTERNS OF CD8+ T CELLS IN ACUTE AND CHRONIC BRUCELLOSIS

status: Public on Oct 01 2016

city: Bursa

first: Ferah

last: Budak

address: Gorukle

department: Medical Faculty

country: Turkey

institute: Uludag University

overall_design: Using miRNA microarray, more than 2000 miRNAs were screened in CD8 + T cells of patients with acute or chronic brucellosis and healthy controls that were sorted from peripheral blood with flow cytometry and validated through qRT-PCR.  Findings were evaluated using GeneSpring GX (Agilent) 13.0 software and KEGG pathway analysis.

first: Budak

last: Ferah

first: Bal

last: Haldun

first: Tezcan

last: Gulcin

first: Guvenc

last: Furkan

first: Akalın

last: Halis

first: Goral

last: Guher

first: Deniz

last: Gunnur

first: Oral

middle: H

last: Barbaros


status: Public on Sep 03 2016

first: Jianping

last: Guo

address: Wuhan University

department: College of Life Sciences

institute: National Key Laboratory of Hybrid Rice

summary:
Bph6 is a gene that confers rice high resistance to its devastating pest BPH. Understanding the molecular responses of the resistant and susceptible varieties would pave the way to controlling the pest more effectively.
To better understand the molecular mechanism underlying resistance to BPH mediated by Bph6, we conducted a genome-wide microarray analysis of NIL-BPH9 and 9311 at the early stage of BPH infestation.

overall_design: Leaf shealth of resistant and susceptible rice plants were collected at 0(without BPH infestation),6, 48h by BPH infestation for RNA extraction and hybridization on Affymetrix microarrays.

first: Guangcun

last: He


title: Genomic Similarity between Gastroesophageal Junction and Esophageal Barrett's Adenocarcinomas

city: Ann Arbor

first: Derek

middle: John

last: Nancarrow

address: 1500 E. Medical Center Dr.

department: Department of Surgery

summary: Specimens were collected from esophageal adenocarcinoma patients undergoing esophagectomy for adenocarcinoma at the University of Michigan Health System between 1991 and 2012. Written consent was obtained from each patient according to the approval and guidelines of the University of Michigan institutional review board. Patients receiving treatment with chemotherapy and/or radiotherapy prior to surgery were excluded. Tissue samples were fresh-frozen in liquid nitrogen and stored at -80 °C until use.

overall_design: Cellularity of tumor samples were assured to be greater than 70% before sample RNA was isolated. RNA was extracted from histological confirmed adenocarcinomas arising at the gastroesophageal junction (GEJAC: n=70) or within the tubular esophagus (tEAC: n=52), along with histologically normal esophageal squamous (NE: n=8) and gastric mucosa (NG: n=5) sections collected at the time of tumor resection and processed for hybridization on Affymetrix Human Gene 2.1 ST Array.

first: Daysha

last: Ferrer-Torres

first: Rork

last: Kuick

first: Andrew

last: Chang

first: David

last: Beer


title: Effect of serum extracellular vesicle depletion protocols on miRNA expression of cultured cells

status: Public on Oct 18 2016

first: Kenneth

last: Witwer

address: 733 N Broadway, BRB Rm 820

department: Molecular and Comparative Pathobiology

institute: Johns Hopkins University School of Medicine

summary: This study examined microRNA expression of cells maintained in media prepared with replete serum (EVR) or with serum depleted of extracellular vesicles (EVs) by either of two methods: standard overnight ultracentrifugation (UC-EVD) or a proprietary method used by Thermo Fisher (TF-EVD).

overall_design: Human donor monocyte-derived macrophages, T-lymphocytic ACH-2 cells (HIV latency model), and promonocytic U1 cells (HIV-latency model) were maintained in the respective media, with the harvested media conditioned for 48 hours before harvesting. Total RNA was extracted, and miRNA profiles were generated for each sample by custom TaqMan low-density array (TLDA, Thermo Fisher).

first: Zhaohao

last: Liao


title: Expression data from shoots of rice seedlings after inoculation by Sinorhizobium meliloti 1021

status: Public on Sep 01 2016

city: Beijing

first: Shihua

last: Shen

address: No.20 Nanxincun, Xiangshan South Rd

department: Institute of Botany,

institute: the Chinese Academy of Sciences

summary:
Comparative transcriptome was profiled of rice seedling shoots in responding to live S. meliloti1021(LS) and dead S. meliloti1021 (DS) inoculation. The shoots with LS and DS were collected at 1, 2, 5 and 8 DAI respectively for microarry analysis. A total of 2413 differentially expressed genes (DEGs) were detected (q ≤ 0.05 and 1.5-fold change used as a cutoff), showing significantly differences between LS and DS. Enriched gene ontology terms and pathways analysis indicated that functions of these DEGs were observably involved in biotic stress, cellular regulation, plant hormone transduction, cell cycle and cell division. Among the classes of transcription factors, some key regulatory gene families such as WRKYs, NAC, bZIP, MYB and ZIM were involved in responding to defense. Others such as AUX, E2F/DP, BES1 and GASR were growth related.
We used microarrays to profile the global view of gene expression underlying S. meliloti 1021 inoculation and identified regulated plant genes and pathway that likely key events in endophytic colonization and molecular promotion mechanism.

overall_design: Surface sterilized seeds were germinated in petri plates with distilled water in the dark for 3 days at 28°C. And  then transferred aseptically into sterilized glass bottle, which containing 175 cm3 of sterile vermiculite and 100 mL of 1/4 Kimura B solution. After 2 days transferred to sterilized glass bottle, the seedling were inoculation with live S. meliloti1021 (LS) as treatment and dead S. meliloti1021 (DS) as control. Shoots from inoculated by live S. meliloti1021 (LS) and dead bacteria as control (DS) were collected at 1, 2, 5 and 8 DAI respectively. Every RNA sample was derived from 5 independent seedlings. In sum, four time points were selected and three biological replicates were performed, totally 24 rice genome arrays were used.

first: Qingqing

last: Wu


title: A global transcriptome analysis of human dermal fibroblasts upon overexpression of microRNA-132

city: Stockholm

first: Ning

last: Xu

address: CMM L8:02

institute: Karolinska Institutet

summary:
MiR-132 is one of the most upregulated miRNAs in human skin wounds at the inflammatory phase of healing; however its biological role in dermal fibroblasts during wound repair has not been studied.
To study the genes regulated by miR-132, we transfected miR-132 mimics (pre-miR-132) into primary human dermal fibroblasts to overexpress miR-132.
We performed a global transcriptome analysis of fibroblasts upon overexpression of miR-132 using Affymetrix arrays.

overall_design: Expression profiling of primary human dermal fibroblasts transfected with 20nM miR-132 mimics (pre-miR-132) or control oligos (pre-miR-Ctrl) for 48 hours (biological triplicates in each group) was performed using Affymetrix GeneTitan system.

middle: X

last: Landén


title: Gene expression profiling of Nodular fasciitis

status: Public on Jun 30 2016

city: Jacksonville

first: Yan

middle: W.

last: Asmann

state: FL

address: 4500 San Pablo Road South

institute: Mayo Clinic

summary: Analyses of gene expression profiling in Nodular fasciitis tumors harboring USP6 fusions

overall_design: Total RNA was obtained from FFPE tissues tumors and profiled using Illumina expression arrays

first: Andre

last: Oliveira

first: Xiaoke

last: Wang


title: Transcriptomic response of rice leaves to 30% CO2 concentration

status: Public on Jul 01 2016

city: Girona

first: Maria

last: Pla

address: Campus Montilivi

institute: University of Girona

summary:
Analysis of rice leaves (V2 stage) in response to a short treatment with very high CO2 concentration in the dark, using standard atmosphere as control.
Results provide insight into molecular mechanisms occurring in response to these extreme conditions, which are often used in the food industry.

overall_design: V2 rice plants were either treated with 30%  [CO2] or kept under normal atmosphere (control) for 6 h at 27ºC in the dark. Two biological replicates per treatment (30% [CO2] and control), each encompassing the leaves of ten plants, were analyzed.

first: Cristina

last: Ruiz

first: Nuri

last: Company

first: Jordi

last: Riudavets

first: Anna

last: Nadal


title: SNP array of AML and MDS specimens with dic(20;22)

city: Fitzroy

first: Ruth

middle: N

last: MacKinnon

state: Vic

address: PO Box 2900

department: Victorian Cancer Cytogenetics Service

country: Australia

institute: St Vincent's Hospital (Melbourne)

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

summary: This study describes a recurrent dicentric chromosome formed by telomere fusion between chromosome 20 and chromosome 22 in myelodysplastic syndromes (MDS) and acute myeloid leukaemia (AML). This is the first description of a recurrent telomere fusion event in myeloid malignancy. The derivative chromosome is further characterised by the presence of nucleolus organiser region material from the chromosome 22 short arm, loss of the putative tumour suppressor gene at 20q12 and secondary rearrangements including gain or amplification of 20q material adjacent to the deletion encompassing 20q12. The presence of residual telomere sequence at the site of translocation in three of the four cases is compelling support for telomere fusion, and supports previous evidence that over half of dicentric chromosomes involving 20q are produced by telomere fusion events. We propose that the sequence of events producing this chromosome abnormality is initial formation of an unstable dicentric chromosome by 20q and 22p telomere fusion, followed by breakage-fusion-bridge cycles causing 20q12 deletion and 20q11.2 gain which provide a growth advantage to the cell. Selection of these clones contributes to leukaemogenesis. Finding recurrent patterns in the complex genome reorganisation events which characterise poor prognosis, complex karyotype AML and MDS will help us understand the mechanisms and oncogenic driver mutations in these poorly understood malignancies.

overall_design: The sample consists of leukaemia specimens from three different cases of AML and MDS. The consistent feature was the presence of a dicentric chromosome formed from chromosomes 20 and 22.


title: Transcriptomic study of hepatocarcinoma cells exposed to sorafenib

city: Amiens

first: Antoine

last: Galmiche

address: avenue Laennec

institute: Centre Hospitalier Universitaire Amiens

summary:
sorafenib is the treatment of reference for hepatocellular carcinoma (HCC). We applied sorafenib on the human HCC cell line Huh7 and the subclone shRb, carrying a stable knock-down of the expression of the RB1 gene, a key regulator of liver carcinogenesis. Our aim was to better understand the physiologic and metabolic consequences of the exposure of HCC cells to sorafenib.
We used microarrays to detail the global programme of gene expression at an early time point (9h) after exposure to sorafenib

overall_design: Whole-genome microarrays were used to study the transcriptome of Huh7 cells exposed to Sorafenib

first: Aline

last: Houessinon

first: Catherine

last: François

first: Christophe

last: Louandre

first: Gaëlle

last: Mongelard

first: Corinne

last: Godin

first: Sandra

last: Bodeau

first: Chloé

last: Sauzay

first: Shinichiro

last: Takahashi

first: Zuzanna

last: Saidak

first: Laurent

last: Gutierrez

first: Jean-marc

last: Régimbeau

first: Nathalie

last: Barget

last: Ganne

first: Bruno

last: Chauffert


title: Gene expression profile in relapsed or metastatic HNSCC patients treated with cetuximab and platinum therapy

status: Public on Aug 01 2016

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

institute: IRCSS Istituto Nazionale Tumori

summary: First line chemotherapy with  platinum and cetuximab is usually offered to RM-HNSCC pts. In the Extreme trial a median progression free survival (PFS) time of 5.6 months was reported. However, a small fraction of pts achieves a prolonged PFS (> than 12 months). Till now, no recognized predictive biological factor has been identified.

overall_design:
A group of 14 cases treated with a first line platinum and cetuximab with a PFS exceeding 12 months (long PFS) and a group of 26 pts with a PFS less than 5.6 months (short PFS) were selected. The 2 groups were well balanced in regard to recognized prognostic factors (performance status, weight loss, prior radiotherapy, tumor grade, site of primary tumor, residual disease at primary tumor site).  Tumor specimens of the recurrence or, if not available, of the primary tumor were collected. In order to identify molecular profiles deregulated between the 2 groups, a gene expression microarray analysis was performed using the Whole-Genome DASL assay and HumanHT-12_v4 BeadArray chips (lllumina).

Gender: male=0; female=1.
Age: years at diagnosis
Site of primary: oral cavity=0; oropharynx=1; hypopharynx=2; larynx=3.
Stage of T at first diagnosis according to AJCC 8th edition
Grading  according to WHO: well differentiated=1; moderately differentiated=2; scarcely differentiated=3.
Radiotherapy (RT) prior to recurrence: No=0; Yes=1.
Progression Free Survival (PFS): Long (>12 months); Short(<5 months).


title: Expression data from fibroblasts BjhTERT-RhoA-KO and PC3 tumor cells after cocultivation and before

first: Tatiana

last: Pavlova

address: Nobelsvag 16

department: MTC

summary:
Gene expression analysis of BJhTERT RhoA-KO and PC3 mRFP was performed before and after six days confrontation in co-cultivation. Analyses of original and control fibroblasts was also performed.
To identify molecules that may mediate the tumor promoting effect of RhoA knock out fibroblasts, we performed gene expression analysis of BJhTERT RhoA-KO and PC3 mRFP cells before the confrontation and then after six days after it, using  Affymetrix Whole Transcript Assay platform.

overall_design: Four days old fibroblast monolayer was confronted with PC3 mRFP tumor cells, plated in ratio 1:30 to number of plated fibroblasts. After six days of confrontation cells were sorted by FACS (Fluorescence-activated cell sorting). Total RNA was isolated from each confronted and non-confronted cells with kit. Then 150 ng of total RNA were used for transcriptomic analysis.for RNA extraction and hybridization on Affymetrix microarrays

first: Marika

last: Rönnholm


title: Sebaceous gland atrophy in psoriasis: An explanation for psoriatic alopecia?

status: Public on Jun 02 2016

first: William

middle: R

last: Swindell

address: 1500 E. Medical Center Drive

department: Dermatology

summary: In a transcriptome study of psoriatic (PP) vs. normal (NN) skin, we found a co-expressed gene module (N5) enriched 11.5-fold for lipid biosynthetic genes. We also observed fewer visible hairs in PP skin, compared to uninvolved (PN) or NN skin (p<0.0001). To ask whether these findings might be due to abnormalities of the pilosebaceous unit, we carried out 3D morphometric analysis of paired PP and PN biopsies. Sebaceous glands (SG) were markedly atrophic in PP vs. PN skin (91% average reduction in volume, p=0.031). Module N5 genes were strongly downregulated in PP vs. NN skin (fold-change [FC] < 0.25, 44.4-fold), and strongly up-regulated in sebaceous hyperplasia (SH, FC > 4, 54.1-fold). The intersection of PP-downregulated and SH-upregulated gene lists generated a gene expression signature consisting solely of module N5 genes, whose expression in PP vs. NN skin was inversely correlated with the signature of IL17-stimuated keratinocytes. Despite loss of visible hairs, morphometry identified elongated follicles in PP vs. PN skin (average 1.7 vs. 1.2 Jm, p=0.020). These results document SG atrophy in non-scalp psoriasis, identify a cytokine-regulated set of SG signature genes, and suggest that loss of visible hair in PP skin may result from abnormal SG function.

overall_design: Gene expression was compared between sebaceous hyperplasia lesions (n = 5) and normal skin (n = 3) from control subjects.

first: Laure

last: Rittié

first: James

middle: T

last: Elder


title: Estrogen receptor α promotes breast cancer by reprogramming cell metabolism [gene expression]

status: Public on Oct 12 2016

city: Huddinge

first: Karin

last: Dahlman-Wright

address: Blickagången 16

department: Department of Biosciences and Nutrition

summary: Estrogen receptor α (ERα) is a key regulator of breast growth and breast cancer development. However, the role of ERα in metabolic reprogramming, a hallmark of cancer, is not well documented. In this study, using an integrated approach combining genome-wide mapping of chromatin bound ERα with estrogen induced transcript and metabolic profiling, we demonstrate that ERα reprograms metabolism upon estrogen stimulation, including changes in aerobic glycolysis, nucleotide and amino acid synthesis, and choline metabolism. We show, for the first time, that the ERα target gene choline phosphotransferase 1 (CHPT1) plays an essential role in estrogen induced increases in phosphatidylcholine (PtdCho) levels and that CHPT1 promotes tumorigenesis and proliferation. Furthermore, we show that CHPT1 is overexpressed in tumors compared to normal breast. We also demonstrate that ERα promotes aerobic glycolysis through increased expression of glycolytic genes. In conclusion, this study highlights the importance of ERα for metabolic alterations in breast cancer cells. Furthermore, overexpression of the ERα target CHPT1 in breast cancer supports its potential as a therapeutic target.

overall_design: Examination of E2 induced gene expression changes in T47D cells

first: Min

last: Jia

first: Trygve

last: Andreassen

first: Siver

last: Moestue

first: Indranil

last: Sinha

first: Hui

last: Gao

first: Tone

middle: F

last: Bathen

first: Chunyan

last: Zao


title: 6S RNA plays a role in recovery from nitrogen depletion in Synechocystis sp. PCC 6803

status: Public on Jun 16 2016

city: Freiburg

first: Jens

last: Georg

address: Schänzlestr. 1

country: Germany

institute: University of Freiburg

summary:
Background: The 6S RNA is a global transcriptional riboregulator, which is exceptionally widespread among most bacterial phyla. While its role is well-characterized in some heterotrophic bacteria, we subjected a cyanobacterial homolog to functional analysis, thereby extending the scope of 6S RNA action to the special challenges of photoautotrophic lifestyles. Results: Physiological characterization of a 6S RNA deletion strain (ΔssaA) demonstrates a delay in the recovery from nitrogen starvation. Significantly decelerated phycobilisome reassembly and glycogen degradation are accompanied with reduced photosynthetic activity compared to the wild type. Transcriptome profiling further revealed that predominantly genes encoding photosystem components, ATP synthase, phycobilisomes and ribosomal proteins were negatively affected in ΔssaA. In vivo pull-down studies of the RNA polymerase complex indicated that the presence of 6S RNA promotes the recruitment of the cyanobacterial housekeeping σ factor SigA, concurrently supporting dissociation of group 2 σ factors during recovery from nitrogen starvation.
Conclusions: The combination of genetic, physiological and biochemical studies reveals the homologue of 6S RNA as an integral part of the cellular response of Synechocystis sp. PCC 6803 to changing nitrogen availability. According to these results, 6S RNA supports a rapid acclimation to changing nitrogen supply by accelerating the switch from group 2 σ factors SigB, SigC and SigE to SigA-dependent transcription. We therefore introduce the cyanobacterial 6S RNA as a novel candidate regulator of RNA polymerase sigma factor recruitment in Synechocystis sp. PCC 6803. Further studies on mechanistic features of the postulated interaction should shed additional light on the complexity of transcriptional regulation in cyanobacteria.

overall_design: We performed microarray analysis of total RNA from wild-type and ∆ssaA cultures that were starved for nitrogen for seven days and recovered over a period of 48 hours. Sampling time points were t1 = 0h, 1h +N, t2 = 4h +N and t3 = 22h +N after nitrogen recovery. Samples were taken in biological replicates.

first: Beate

last: Heilmann

first: Kaisa

last: Hakkila

first: Taina

last: Tyystjärvi

first: Wolfgang

last: Hess

first: Ilka

last: Axmann

first: Dennis

last: Dienst


title: Pathway based integrative analysis reveals a key role for the hexosamine biosynthetic pathway in prostate cancer progression with therapeutic implications

status: Public on Sep 20 2016

first: Akash

middle: Kumar

last: Kaushik

state: Texas

address: One Baylor Plaza

department: Molecular and Cellular Biology

summary: To better understand the biochemical changes associated with castrate resistant prostate cancer (CRPC), we developed a pathway-based integrated analytical method to examine prostate cancer (PCa) gene expression and metabolomic datasets and found distinct alterations in the Hexosamine Biosynthetic Pathway (HBP) between androgen dependent (AD) PCa and CRPC, with elevated expression of HBP genes in primary PCa associated with poor clinical outcome. Expression of the HBP enzyme glucosamine-phosphate N-acetyltransferase 1 (GNPNAT1) was regulated by androgens and elevated in AD PCa while relatively diminished in CRPC.Genetic loss of function experiments for GNPNAT1 in CRPC-like cells led to increased aggressiveness, while GNPNAT1 knockdown decreased proliferation in AD PCa cells. Each scenario was accompanied by specific bio-energetic and molecular alterations. Strikingly, addition of HBP metabolite UDP-N-acetylglucosamine significantly enhanced efficacy of the anti-androgen enzalutamide in CRPC cells by repressing NF-Y driven cell cycle regulators. Our study demonstrates the therapeutic value of targeting altered metabolic pathways in lethal PCa.

overall_design:
1. Metabolic therapy approach was used where C4-2 cells were treated with PBS, UDP-N-acetylglucosamine (UDP-GlcNAc), MDV3100, UDP-GlcNAc+MDV3100. The expression of these cells were generated using Human Affymetrix Gene ST 2.1
2. Affimatrix platform based microarray was also done on GNPNAT1 Knockdow C42 cells.

first: Katrin

last: Panzitt

first: Ali

last: Shojaie

middle: K

first: Nagireddy

last: Putluri

first: Rajni

last: Sonavane

first: Harene

last: Venghatakrishnane

first: Vasanta

first: Vadiraja

middle: B

last: Bhat

first: Kimal

last: Rajapakshe

first: Yiquing

last: Zhang

first: Xuhong

last: Cao

first: Hangwen

last: Li

first: Efi

last: Tsouko

first: Stacy

last: Lloyd

first: Alexander

last: Zaslavsky

first: Susmita

last: Samanta

first: Shixia

last: Huang

first: Qianxing

last: Mo

first: Cristian

last: Coarfa

first: Dean

middle: P

last: Edwards

first: Nicholas

last: Erho

first: Ismael

last: Vergara

first: Elai

last: Davicioni

first: Robert

last: Jenkins

first: Daniel

last: Frido

first: Qi

last: Mitsiades

first: Nancy

middle: L

last: Weigel

first: Michael

last: Ittmann

first: Arul

last: Chinnaiyan

first: Ganesh

middle: S

last: Palapattu

first: George

last: Michailidis

first: Arun

last: Sreekumar


title: Expression data of young panicles from microspore mother cell to meiosis of rice

city: Guangzhou

first: Hai

last: Zhou

state: Guangdong

address: Wushan

institute: South China Agricultural University

summary: Male sterility is an important trait in hybrid crop breeding. Thermo-sensitive genic male sterility (TGMS) lines, which are male-sterile at restrictive (high) temperatures but convert to male-fertile at permissive (low) temperatures, have been widely utilized in two-line hybrid rice breeding. However, the molecular mechanism underlying TGMS remains unclear. Here we show that the rice (Oryza sativa L.) thermo-sensitive genic male sterile gene 5 (tms5) locus, which in 2010 was present in cultivars occupying more than 71% (2.3 million hectares) of two-line hybrid rice-growing land in China, confers the TGMS trait through a loss-of-function mutation of RNase ZS1, resulting in failure to mediate mRNA decay of three temperature-responsive ubiquitin fusion ribosomal protein L40 genes (UbL40) genes. RNase ZS1, a member of the evolutionarily conserved endonuclease, processed tRNAs in vitro, but does not do so in vivo due to its localization in the cytoplasm. Defective RNase ZS1 in tms5 plants leads to over-accumulation of UbL401, UbL402 and UbL404 mRNAs at restrictive but not permissive temperatures. Over-expression of UbL401 and UbL404 in wild-type plants caused male sterility, whereas knockdown of UbL401 and UbL404 in tms5 plants partially restored the male fertility at restrictive temperatures. Our results uncover a novel mechanism of RNase ZS1-mediated UbL40 mRNA decay which controls TGMS in rice and has potential applications not only of rice but also of other crops.

sample_organism:
Oryza sativa Indica Group
Oryza sativa Japonica Group

overall_design: To address whether RNase ZS1 involves in mRNA metabolism, whole-genome microarray was performed using RNA from young panicles of wild type (AnN and ZH11) and tms5 (AnS-1 and Os02g12290iL1) plants grown at permissive and restrictive temperatures.

first: Chuxiong

last: Zhuang

first: Yaoguang

last: Liu

first: Liya

last: Zhu


title: CNA profiling using high-density DNA methylation arrays (SNP array)

status: Public on May 31 2016

city: Toronto

first: Paul

last: Guilhamon

state: ON

address: 686 Bay Street

institute: SickKids

summary: The integration of genomic and epigenomic data is becoming increasingly popular as we try to gain better understanding of the complex mechanisms driving the development and progression of cancer. However, this results in increased cost and sample depletion, the latter being particularly important when considering intra-tumour heterogeneity. We therefore sought to investigate the possible utility of high-density DNA methylation arrays to assess both aberrant methylation as well as changes in gene copy number. Comparing CN (Copy Number) data derived from the Infinium Human Methylation 450K arrays with that generated on SNP arrays, we demonstrate the utility of the Infinium arrays to detect single copy alterations as well as homozygous deletions and high level amplification with the reliability of current gold standard platforms. Furthermore, we show that the gene centric design of the Infinium methylation arrays allows identification of small single gene alterations, which would not be detected using standard SNP array analysis. These results show that Infinium 450K methylation arrays provide a robust and economic platform for detecting copy number and methylation changes in a single experiment. The ability to integrate such data from the same sample is critical for cancer research and will improve our understanding of how complex genomic and epigenomic interactions are driving the development and progression of a malignant phenotype.

overall_design: Extracted DNA from each sample was hybridised to Illumina CytoSNP12 v2.1 BeadChips.

first: Andrew

last: Feber


title: Comparison of the in vivo transcriptome of the myometrium to the transcriptome of myometrial explants, primary cultured myometrial cells and the hTert myometrial cell line

status: Public on May 30 2016

city: Nottingham

first: Marios

last: Georgiou

address: Queen's Medical Centre

institute: University of Nottingham

summary:
Circulating progesterone (P4) levels decline before the onset of parturition in most animals, but not in humans. This has led to the suggestion that there is functional withdrawal of P4 action at the myometrial level prior to labor onset. Mifepristone is widely used to induce human labour
In this study, we aimed to establish and validate a model of human myometrial explants for the study of P4 action. Myometrial biopsies obtained at Caesearean section at term were dissected into explants after a portion was immediately snap-frozen (t=0). Transcriptomic comparison of paired explants and primary myometrial cells as well as the hTert immortalized myometrial cell line demonstrated that explants more closely resemble t=0.

overall_design: Biopsies obtained from non-laboring women at elective Caesarean section at term were divided into 3: (i) dissected and immediately snap-frozen (t=0), (ii) dissected into 3x3x3mm3myometrial explants and (iii) processed for primary cell culture. Explants, primary cells at passage 4 (the typical passage our group uses for experiments) and hTERT cells were cultured for a period of 30 hours without treatment. Total RNA was extracted and microarray analysis performed. 6  replicates were used for this study.

first: Ektoras

first: Kaiyu

last: Lei

first: Mark

last: Johnson

first: Marcos

middle: C

last: Uribe


title: Muscle Transcriptome Profile of Resistance Exercise is Augmented by Aerobic Exercise

status: Public on May 24 2016

first: Eric

last: Rullman

address: C1:82 Karolinska University Hospital, Huddinge

department: Laboratory Medicine

summary:
10 male subjects performed ~45 min one-legged cycling and 4 x 7 maximal concentric-eccentric knee extensions for each leg 15 min later. Thus, one limb performed aerobic and resistance exercise (AE+RE), while the opposing leg did resistance exercise only (RE). Biopsies were obtained from m. vastus lateralis of each leg 3 h after the resistance exercise bout.
Gene expression analysis was carried out on the Affymetrix HuGene-2.1-st platform.

overall_design: Skeletal muscle gene expression after a single bout of one-legged resistance type exercise only or one bout of one-legged resistance type exercise combined with one bout of aerobic exercise

first: Thomas

last: Gustafsson


title: Segmental chromosomal imbalances arise at high frequency in human fibroblasts (SB_sc_2)

status: Public on May 01 2016

city: Leuven

first: Eftychia

last: Dimitriadou

address: Herestraat 49, ON1, bus 602

country: Belgium

institute: KU Leuven

summary: Preservation of chromosome integrity is key for the survival of any organism. To assure segregation of intact chromosomes, cell division is presumed to be under strict control of cell-cycle checkpoints. Estimates of chromosomal mutation rates per generation based on cytogenetic analyses of newborns and products of conception, range between 4.57x10-5 and 3.42x10-4. In contrast, the high incidence of segmental imbalances detected by single-cell genome-wide copy number profiling indicates that the error rate per cell division might be more than an order of magnitude higher. To directly measure the de novo incidence of segmental chromosomal imbalances, we plated a single fibroblast and analyzed the genomes of the two sister cells following a single cell division. Analysis of 89 pairs of sister cells (178 single cells in total) from 5 different cell lines revealed megabase-sized chromosomal imbalances in 21 fibroblasts, 14 of which derived from 7 mitoses with complementary segmental aneuploidies in the two daughter cells. The mutation rate of segmental imbalances is thus at least 7.9%, indicating that compared to the per generation chromosome stability is at least 100 times lower in vitro and likely underestimated in vivo.

overall_design: Here we provide a sample set including a series of MDA whole genome amplified fibroblasts 'SB' isolated from a fresh skin biopsy of a phenotypically normal individual and genomic DNA samples isolated from peripheral blood of a sibling 'SB_Sibling', the mother 'SB_Mother' and father 'SB_Father'. Single cells were amplified using GenomiphiV2 (GE Healthcare).

first: Masoud

last: ZamaniEsteki

first: Thierry

last: Voet

first: Joris

last: Vermeesch


title: Segmental chromosomal imbalances arise at high frequency in human fibroblasts

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

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

overall_design: Refer to individual Series


title: Segmental chromosomal imbalances arise at high frequency in human fibroblasts (S1_S2)

summary: Preservation of a balanced chromosomal content is regarded to be a key point for the success of multicellular organisms. Chromosomal segregation takes place under the strict control of well-orchestrated cell-cycle checkpoints, consequently leading to accurate transmission of intact chromosomes. Estimates of the whole chromosomal error rates per cell division based on cytogenetic analyses of newborns and products of conception, range between 4.57x10-5 and 3.42x10-4. Recent sporadic studies of single cell genome wide CNV analysis suggested that the error rate might be higher than currently estimated. To obtain accurate measures of chromosomal error rates, we plated single fibroblast and analyzed the two daughter sister cells following a single cell division. In total 14 single fibroblasts derived from 7 mitoses carried segmental aneuploidies in a total of 178 cells from 5 different cell lines that were analyzed after a single cell division, indicating a mean frequency of 7.9% in vitro. In conclusion, the chromosomal stability is hundreds times lower than the current dogma, showing that chromosomal instability is a common place and putting the efficacy of the DNA-repair mechanisms and control checkpoints in question.

overall_design: Here we provide a sample set including a series of MDA whole genome amplified in vitro cultured single primary fibroblasts of two siblings, 'S1' and 'S2', and genomic DNA samples isolated from peripheral blood of two siblings 'S2' and 'S3' (identical tween of S1), the mother and father of these siblings. Single cells WGAed by two different kits [GenomiphiV2 (GE Healthcare) and RepliG-sc (Qiagen)] are available.

middle: Z

last: Esteki


title: Segmental chromosomal imbalances arise at high frequency in human fibroblasts (S2)


title: Segmental chromosomal imbalances arise at high frequency in human fibroblasts (SB)


title: Expression data from rice calli cultured with 2,4-D

status: Public on Mar 03 2016

city: Shanghai

first: Jin

last: Jing

address: No. 300 Fenglin Road

institute: Shanghai Insitute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

summary:
Four days old rice calli were selected to grow 324h under spaceflight controls, 1g-flight controls and 1g-ground controls.
We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes during this process.

overall_design: Rice calli were selected at different treatment for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain the diff-genes that caused by the microgravity.

first: Jing

last: Jin

first: Weiming

last: Cai


title: Gene expression profiling of primary HER2-positive breast cancers treated with neoadjuvant trastuzumab

status: Public on Mar 31 2016

first: Loris

last: De Cecco

summary: Trastuzumab, a humanized monoclonal antibody directed to the HER2 protein, is the standard-of-care treatment for patients with HER2 positive breast cancer, reducing the risk of relapse and death in patients. Nonetheless, some patients do not benefit from this treatment, underscoring the need to identify patients for whom chemotherapy + trastuzumab is adequate versus patients requiring additional drugs. The series comprised 24 incisional biopsies of breast carcinomas derived from patients that received neoadjuvant trastuzumab based therapy.

overall_design: Gene expression profiling was performed using RNA from frozen core biopsies from 24 patients with primary HER2-positive (HER2+) tumors treated with neoadjuvant chemotherapy and trastuzumab.

first: L


title: Segmental chromosomal imbalances arise at high frequency in human fibroblasts (S1)


title: Expression data from non-small cell lung cancer cell line DV90 after Bromodomain and extra terminal domain (BET) inhibitor JQ1 treatment

city: Berlin

first: Ralf

last: Lesche

address: Muellerstr 178

institute: Bayer Pharma AG

summary:
Bromodomain and extra terminal domain (BET) inhibition reduces occupancy of BET-family proteins at promoter and enhancer sites resulting in changes in the transcription of specific genes.
We used microarray profiling to investigate the transcriptional changes induced by BET inhibitor JQ1 treatment in DV90 cells to identify the underlying changes of gene regulation that lead to JQ1 sensitivity.

overall_design: DV90 cells (JQ1 sensitive non-small cell lung cancer cell line) were treated with 135 nM (IC50) or 785 nM (IC90) of JQ1 for 4h and 24h. DMSO treated controls served as reference and at least four replicates per condition were collected. RNA was extracted and hybridized to Affymetrix HuGene-2.1ST microarrays to identify treatment induced transcriptional changes.

first: Olaf

last: Klingbeil


title: Classification of fibroadenomas and phyllodes tumors

status: Public on Apr 29 2016

city: Singapore

first: Wai Jin

last: Tan

address: 31 Biopolis Way, The Nanos, #04-01

department: Biodevices and Diagnostics

country: Singapore

institute: Institute of Bioengineering and Nanotechnology

summary:
WG-DASL expression of breast fibroepithelial lesions
Breast fibroepithelial lesions are biphasic tumors and include fibroadenomas and phyllodes tumors. Fibroadenomas are clinically benign while phyllodes tumors are more unpredictable in biological behavior, with potential for recurrence. Differentiating the tumors may be challeneging when they have overlapping clinical and histological features especially on the core biopsies

overall_design: The transcriptome of a training set of 48 formalin-fixed, paraffin embedded fibraodenomas and phyllodes tumors. Differential gene expression between fibroadenomas and phyllodes tumors was investigated

first: Wai-Jin

first: Min-Han


title: Distinct molecular signatures of mild extrinsic and intrinsic atopic dermatitis

status: Public on Mar 08 2016

city: Copenhagen N

last: Litman

state: Outside the US or Canada

address: Blegdamsvej 3C

department: ISIM

country: Denmark

institute: University of Copenhagen

summary: Atopic dermatitis (AD) is a common inflammatory skin disease with underlying defects in epidermal function and immune responses. The goal of this study was to investigate differences in gene expression in lesional skin from patients with mild extrinsic or intrinsic AD compared to skin from healthy controls and from lesional psoriasis skin. The aim was to identify differentially expressed genes involved in skin barrier formation and inflammation, and to compare our results with those reported for patients with moderate and severe AD.

overall_design: A total of 31 samples were analyzed: 8 healthy skin, 9 psoriatic plaques, 4 extrinsic AD lesional skin, 10 intrinsic AD lesional skin.

first: Britta

last: Martell


title: CaSR modulator in neuroblastoma model [human]

status: Public on Mar 30 2016

city: Esplugues

first: Carmen

last: de Torres

state: Barcelona

address: Santa Rosa 39

department: Oncology

institute: Hospital Sant Joan de Deu

summary: CaSR modulation inhibits neuroblastoma growth

overall_design: 8 control and 7 samples treated with CaSR allosteric activator


title: KRAS mutation (G12V) expression by pBABE-Puro vector in NCI-H1703 cells

status: Public on Mar 23 2016

city: Boston

first: Meng

last: Wang

state: MA

address: CNY149-4406 13th st Charlestown

department: Radiation Oncology

institute: Mass. General Hospital

summary:
The goal of this study was to determine genes affected by expressing KRAS mutation (G12V) in NCI-H1703 cells
This data was used in Meng Wang et. al. Cancer Research 2016 to determine the alterations of gene expression profiling associated with expression of KRAS mutation (G12V).

overall_design: The experiment uses a pBABE-Puro vector encoding KRAS G12V and a corresponding empty vector control.

last: Han

first: Henning

last: Willers


title: mRNA expression in SIDS

status: Public on Mar 01 2016

city: Oslo

first: Linda

last: Ferrante

address: Gaustadalle 30

country: Norway

institute: Norwegian institute of public health

summary: The purpose of this study was to investigate gene expression in SIDS cases and controls, in order to uncover genes that are differentially expressed in the two groups. Tissue from brain, heart and liver from 15 SIDS cases and 15 controls were included in this study, and mRNA expression was determined using the Illumina whole genome gene expression DASL HT assay

overall_design: WGDASL_HT ASSAY 15018210_D

first: Torleiv

last: Rognum

first: Ståle

last: Nygård


title: Segmental chromosomal imbalances arise at high frequency in human fibroblasts (SB_sc_1)

first: Eftychia

last: Dimitriadou

first: Masoud

last: ZamaniEsteki

first: Thierry

last: Voet

first: Joris

last: Vermeesch


title: Expression data from plant tissues during incompatible interaction between the rice host and its major pest, the Asian rice gall midge

status: Public on Feb 23 2016

city: New Delhi

first: Suresh

last: Nair

address: Aruna Asaf Ali Marg

department: Plant Molecular Biology Group

institute: International Centre for Genetic Engineering and Biotechnology (ICGEB)

summary:
During an incompatible or compatible interaction between rice (Oryza sativa) and the Asian rice gall midge (Orseolia oryzae), a lot of genetic reprogamming occurs in the plant host
We used microarray to know the changes occuring in the resistant host (indica rice variety RP2068-18-3-5) when challenged by avirulent biotype of gall midge (GMB 1).  During this incompatible interaction the resistance in the host is manifested by a hypersenstive response. Using microarray data, we identified distinct classes of up- and down-regulated genes during this process.

overall_design: Tissues from the stem region (feeding site of insect larvae) of the plants that were exposed to gall midge, were taken for RNA extraction and hybridization on Affymetric microarrays. For control, tissues were taken from the corresponding region of plants that were not exposed to gall midge.

first: Ruchi

last: Agarrwal

first: J

last: Bentur


title: Gene-level expression data from Oryza sativa.indica (mock-treated or blast pathogen treated resistant rice line and susceptible rice line )

status: Public on Jan 01 2016

first: Jingxin

last: Zhang

country: China

institute: Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, P.R.China

summary:
In this dataset, we include the expression data obtained from untreated and blast pathogen treated rice seedlings using a variety of blast resistant rice line H4, as well as the susceptible rice line Zhonger-Ruanzhan. These data are used to obtain 4087 genes that are differentially expressed in response to blast pathogen in both of rice lines,as well as 717 genes that are differentially expressed between different lines both in the moch-treated and the blast treated.
We used microarrays to detail the global gene expression in leaf from blast resistant rice line and susceptible rice line

overall_design: Four total samples were analyzed, The untreated rice line Zhonger-Ruanzhan: Zhonger-0;the untreated rice line H4:H4-0;Zhonger-Ruanzhan inoclutated with blast pathogen after 24h:Zhonger-24;H4 inoculated with blast pathogen after 24h: H4-24. We generated the following pairwise comparisons : H4-0 VS H4-24; Zhonger-0 vs Zhonger-24; H4-0 vs H4-0; Zhonger-24 vs H4-24.


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

status: Public on Feb 09 2016

city: Oxford

first: Sally

middle: A

last: Cowley

address: South Parks Road

department: Sir William Dunn School of Pathology

country: United Kingdom

institute: University of Oxford

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

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

first: Cynthia

last: Sandor

first: Paul

last: Robertson

first: Charmaine

last: Lang

first: Andreas

last: Heger

first: Heather

last: Booth

first: Jane

last: Vowles

first: Lorna

last: Witty

first: Rory

last: Bowden

first: Michele

last: Hu

first: Richard

last: Wade-Martins

first: Caleb

last: Webber


title: The Marrow Niche Controls The Cancer Stem Cell Phenotype Of Disseminated Prostate Cancer

status: Public on Jan 30 2016

city: Winston-Salem

first: Yusuke

last: Shiozawa

state: NC

address: 1 Medical Center Blvd

department: Cancer Biology

country: USA

institute: Wake Forest School of Medicine

summary:
Dissemination of cancer stem cells (CSCs) serves as the basis of metastasis. Recently, we demonstrated that circulating prostate cancer (PCa) targets the hematopoietic stem cell  (HSCs) ‘niche’ in marrow during dissemination.  Once in the niche, disseminated tumor cells (DTCs) may remain dormant for extended periods. As the major function of the HSC niche is to maintain stem cell functions, we hypothesized that the niche regulates CSC activities of DTCs. We show that DTCs recovered from marrow were significantly enriched for a CSC phenotype.  Critically, the conversion of DTCs to CSCs is regulated by niche. The data demonstrate that the niche plays a significant role in maintaining tumor-initiating PCa in marrow and suggests a functional relationship between CSCs and dormancy. Understanding how the marrow niche regulates the conversion of DTCs to CSCs is critical for the development of therapeutics specifically targeting skeletal bone metastasis and dormancy.
We used microarrays to determine the global changes in gene expression underlying the significant roles of the marrow niche in activating cancer stem-like cell programs of prostate caner.

overall_design: The CD133+/CD44+ fraction and CD133-/CD44- fraction were sorted with a FACSAria II Cell Sorter from in vitro cultured prostate cancer cells (PC3, C4-2B) and in vivo disseminated PCa cells obtained from bone marrow of SCID mice innoculated with PCa cells (24 h) by intracadiac injection. Experimental groups were duplicated ((i) PC3, CD133+/CD44+, in vitro; (ii) PC3, CD133-/CD44-, in vitro; (iii) PC3, CD133+/CD44+, in vivo; (iv) PC3, CD133-/CD44-, in vivo; (v) C4-2B, CD133+/CD44+, in vitro; (vi) C4-2B, CD133-/CD44-, in vitro; (vii) C4-2B, CD133+/CD44+, in vivo; (viii) C4-2B, CD133-/CD44-, in vivo). Cells were obtained from 5 animals / group.

first: Russell

last: Taichman


title: Molecular analysis identifies a specific role for memory effector T cells in kidney chronic T-cell mediated rejection

status: Public on Dec 30 2015

city: Bari

first: Fabio

last: Sallustio

state: Bari

address: Piazza G. Cesare N°11

country: Italy

institute: University of Bari

summary: Chronic T-cell mediated rejection (TCMR) is characterized by the reduction of vessel lumen with marked intimal thickening, fibrous hyperplasia and a strong component of leukocyte infiltrate. Aim of our work was the study of gene expression profile in renal TCMR biopsies. We performed transcriptomics study using RNA extracted from archival formalin-fixed and paraffin-embedded (FFPE) renal biopsies obtained from patients with chronic and acute TCMR. Using a FC≥1.5 and a FDR<0.05, we identified 191 genes differentially expressed in patients with chronic and acute TCMR compared to cadaveric donor (CDs). The study of gene pathways showed the up-regulation of OX40 signaling, that is involved in the generation of memory effector T cell, and the up-regulation of KLRG-1, BLIMP-1 and CD25 that characterized CD8+ memory effector T cells. However, OX40 signaling was specific only for chronic TCMR. These results suggested the involvement of memory effector T cells in chronic TCMR. The identified genes may be used as a target for specific treatment of chronic TCMR.

overall_design: FFPE renal biopsies from 14 patients with chronic TCMR, 10 patients with acute TCMR and 52 cadaveric donors.

first: Claudia

last: Curci

first: Francesco

last: Schena