title: Pale-green durum wheat mutant under terminal drought stress condition

status: Public on May 09 2016

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

department: Virtual Reality Application Center

institute: Iowa State University

summary: Two durum wheat (Triticum turgidum L. var. durum) genotypes, the variety Borgia (derived from the cross IRTA-1004 x Bidi 17) and a pale-green mutant (MD-597) derived from it, were used for the measurement of physiological traits and gene expression. Mutant plants used for this study were the stable eight generation (M8) derived from the isolated original mutant plant. Terminal water stress: irrigation was drastically reduced from the booting stage until maturity by watering the pots with the amount of water necessary to maintain the pots at 1/3 of field capacity. The drought treatment was started by withholding water at the anthesis stage.  ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Alessio Aprile. The equivalent experiment is TA48 at PLEXdb.]

overall_design: genotype: WT - drought: CTRL(3-replications); genotype: WT - drought: Drought(3-replications); genotype: M - drought: CTRL(3-replications); genotype: M - drought: Drought(3-replications)

first: Alessio

last: Aprile

first: Luigi

last: De Bellis


title: caArray_lavar-00111: SPECIFIC GENE EXPRESSION PROFILES ASSOCIATED WITH INFANT DISSEMINATED NEUROBLASTOMA

status: Public on May 26 2016

city: Rockville

first: Mervi

last: Heiskanen

state: MD

address: 9609 Medical Center Drive, 1W378

department: CBIIT

country: USA

institute: NCI

summary: Neuroblastoma (NB) tumours have the highest incidence of spontaneous remission, especially among the stage 4s NB subgroup affecting infants. Clinical distinction of stage 4s from lethal stage 4 can be difficult, but critical for therapeutic decisions. The aim of this study was to investigate differential gene expression amongst infant disseminated NB subgroups. Thirty-five NB tumours from patients diagnosed at < 18 months (25 stage 4 and 10 stage 4s), were evaluated gene expression analyses. Initial comparison analyses between stage 4s and 4 < 12 months tumours revealed distinct gene expression profiles. A significant portion of genes mapped to chromosome 1 (p<0.0001), 90% with higher expression in stage 4s, and chromosome 11 (p=0.0054), 91% with higher expression in stage 4. Less definite expression profiles were observed between stage 4s and 4 < 18m, yet, association with chromosomes 1 (p<0.0001) and 11 (p=0.005) was maintained. Distinct gene expression profiles but no significant association with specific chromosomal region localization was observed between stage 4s and stage 4 < 18 months without MYCN amplification. Distinct gene expression profiles characterize spontaneously regressing or aggressive infant NB, providing the biological basis for the distinct clinical behaviour.

overall_design:
lavar-00111
Assay Type: Gene Expression
Provider: Affymetrix
Array Designs: HG_U95Av2
Organism: Homo sapiens (ncbitax)
Tissue Sites: Adrenal Gland
Material Types: synthetic_RNA, total_RNA
Cell Types: primary tumor
Disease States: Neuroblastoma


title: Expression data for EGFR TKI resistant EGFR-mutated Cells

status: Public on Jun 04 2016

city: Maywood

first: Takeshi

last: Shimamura

state: IL

address: 2160 S. 1st Ave LUHS Cancer  Center Rm205

department: Molecular Pharmacology and Therapeutics

institute: Loyola University Chicago

summary:
Intratumoral heterogeneity in EGFR mutant NSCLC results in divergent resistance mechanisms in response to EGFR tyrosine kinase inhibition
We used microarrays to investigate the  gene expression underlying EGFR TKI resistance with a mesenchymal phenotype.

overall_design: Total 4 samples in triplicates were analyzed.


title: caArray_lavar-00109: Differential expression of genes characterize neuroblastic tumours with distinct ploidy status

summary: Neuroblastic tumours (NBTs) represent a heterogeneous spectrum of neoplastic diseases associated with multiple genetic alterations. Structural and numerical chromosomal changes are frequent and are predictive parameters of NBTs outcome. We performed a comparative analysis of the biological entities constituted by NBTs with different ploidy status. Gene expression profiling of 49 diagnostic primary near-triploid (n= 22) and near-diploid/tetraploid (n=27) NBTs performed using Affymetrix U95Av2 arrays, revealed distinct expression profiles associated with each NBT subgroup. A statistically significant portion of genes mapped to 1p36 (P=0.01) and 17p13-q21 (P<0.0001). Specific chromosomal abnormalities observed in NBTs, 1p loss, 17q and whole chromosome 17 gains, were reflected in the gene expression profiles. This study demonstrates that NBTs with different cellular DNA content display distinct transcriptional profiles with a significant portion of differentially expressed genes mapping to specific chromosomal regions known to be associated with outcome. Furthermore, our results suggest that NBTs with different ploidy status may result from different mechanisms of aneuploidy driving tumourigenesis.

overall_design:
lavar-00109
Assay Type: Gene Expression
Provider: Affymetrix
Array Designs: HG_U95Av2
Organism: Homo sapiens (ncbitax)
Tissue Sites: Adrenal Gland
Material Types: total_RNA
Cell Types: primary tumor
Disease States: Neuroblastoma


title: Synthetic cystine addiction via programmed necrosis in VHL-deficient renal cell carcinoma

status: Public on Jul 01 2016

city: Durham

first: Xiaohu

last: Tang

state: NC

address: CIEMAS Rm 2133, 101 Science Dr.

department: Department of Molecular Genetics and Microbiology

institute: Duke University

summary: Altered metabolism is an important part of malignant transformation of tumor cells. Oncogenic transformation may reprogram tumor metabolism and render tumor cells addicted to extracellular nutrients. Such nutrient addictions associated with oncogenic mutations may offer therapeutic opportunities; however, it remains difficult to predict these nutrient addictions. Here, we performed a nutrigenetic screen to determine the phenotypes of isogenic pairs of clear-cell renal cancer cells (ccRCC) with or without VHL upon the deprivation of individual amino acids. We identified that cystine deprivation triggered rapid programmed necrosis in VHL-deficient RCC, but not in their VHL-restored counterparts. Similar cystine addiction was also observed in VHL-deficient primary RCC tumors cells. Blockage of cystine uptake significantly delayed xenograft growth of ccRCC. Importantly, cystine deprivation triggered similar metabolic changes regardless of VHL status. Therefore, metabolic differences due to cystine deprivation are not different enough to readily explain the distinct fate of life vs. death in VHL-deficient and restored cell.. Instead, we found that increased levels of TNFα associated with VHL loss in the VHL-deficient RCC force them to rely on intact RIPK1 to inhibit apoptosis. However, this pre-existing elevated TNFα in the VHL-deficient ccRCC renders these cells susceptible to the necrosis signaling triggered by cystine deprivation. In addition, we identified that cystine-deprived necrosis in VHL-deficient RCC depends on reciprocal amplification of the Src-p38-Noxa signaling and TNFα-RIP1/3-MLKL necrosis pathways that culminate in MLKL oligomerization and programmed necrosis. Together, our data reveal that the contextual cystine-addictions in VHL-deficient ccRCC is dependent on activating pre-existing oncogenic pathways to trigger programmed necrosis.

overall_design: RNA was extracted by RNAeasy kits (Qiagen) from the RCC4 Vec and VHL-reconstituted cells which were exposed to the control full DMEM or cystine deprived DMEM media for 6 hours (three replicates in each condition).

first: Jen-Tsan

last: Chi


title: MicroRNA profile in Castleman disease

status: Public on Apr 15 2016

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

summary: To elucidate the aetiology of Castleman disease, especially with regard to microRNA (miRNA) profiles, samples obtained from three different parts of both normal and tumour tissues were analysed. The details of RNA extraction have been described in our previous reports. Interestingly, 3 miRNAs were significantly up-regulated and 31 miRNAs were down-regulated in the tumour tissues compared to the normal tissues (Student’s t-test, p<0.01). In addition, unsupervised hierarchical clustering analysis using a Pearson’s correlation showed that the tumour tissues clustered separately from the normal tissues.

overall_design: microRNA samples obtained from three different parts of both normal and tumour tissues were analysed.

first: Asahiro

last: Morishita

first: Hisakazu

last: Iwama


title: Study of microRNA associated with the anti-tumor effect of gemcitabine

status: Public on Apr 01 2016

summary: The miRNAs expression was markedly altered with the treatment of gemcitabine on human CCC cells in vitro.  And various miRNAs induced by gemcitabine may contribute to tumor regression in vitro.

overall_design: Using a custom microarray platform, we analyzed the expression levels of 2555 human miRNA probes in the cell lines in vitro that were treated with and without gemcitabine.

first: Yuka

last: Toyota

first: Tsutomu

last: Masaki


title: caArray_louis-00379: Gene Expression-based Classification of Malignant Gliomas Correlates Better with Survival than Histological Classification

status: Public on May 28 2016

summary: Microarray analysis was used to determine the expression of 12,000 genes in a set of 50 gliomas, 28 glioblastomas and 22 anaplastic oligodendrogliomas. Supervised learning approaches were used to build a two-class prediction model based on a subset of 14 glioblastomas and 7 anaplastic oligodendrogliomas with classic histology. A 20-feature k-nearest neighbor model correctly classified 18 of the 21 classic cases in leave-one-out cross-validation when compared with pathological diagnoses. This model was then used to predict the classification of clinically common, histologically nonclassic samples. When tumors were classified according to pathology, the survival of patients with nonclassic glioblastoma and nonclassic anaplastic oligodendroglioma was not significantly different (P = 0.19). However, class distinctions according to the model were significantly associated with survival outcome (P = 0.05). This class prediction model was capable of classifying high-grade, nonclassic glial tumors objectively and reproducibly. Moreover, the model provided a more accurate predictor of prognosis in these nonclassic lesions than did pathological classification. These data suggest that class prediction models, based on defined molecular profiles, classify diagnostically challenging malignant gliomas in a manner that better correlates with clinical outcome than does standard pathology.

overall_design:
louis-00379
Assay Type: Gene Expression
Provider: Affymetrix
Array Designs: HG_U95Av2
Organism: Homo sapiens (ncbitax)
Material Types: total_RNA, synthetic_RNA, organism_part, whole_organism
Disease States: Classic anaplastic oligodendroglioma, Non-classic glioblastoma, Classic glioblastoma, Non-classic anaplastic oligodendroglioma


title: Differentially expressed miRNAs in xenografts and organoids derived from human cholangiocarcinoma [miRNA]

summary:
We established xenografts and organoids derived from human cholangiocarcinoma.
To investigate the signature of cancer stem cells, miRNA expression profiles were analyzed in cholangiocarcinoma xenografts and organoids (passage 7).

overall_design: Microarray analyses were conducted in cholangiocarcioma xenografts and organoids (passage 7).

first: Yoshimasa

last: Saito


title: Differentially expressed genes in xenografts and organoids derived from human cholangiocarcinoma

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

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

overall_design: Refer to individual Series


title: Gene expression data from MCF7 breast adenocarcinoma cells treated with prolactin and/or bufexamac

status: Public on May 07 2016

city: Richmond

first: Justin

middle: Michael

last: Craig

state: Virginia

address: 1201 E Marshall St

department: Massey Cancer Center

institute: Virginia Commonwealth University

summary:
The hormone prolactin is implicated in the pathogenesis of breast cancer, and a subset of prolactin-induced gene expression is mediated by HDAC6 activity.
The NSAID, bufexamac, is a fairly specific inhibitor of HDAC6 and HDAC10. We used bufexamac in combination with prolactin treatment in MCF7 cells to determine differential expression under these conditions.

overall_design: MCF7 cells were serum starved for 24 hours prior to treatment with bufexamac and/or prolactin, and subsequent RNA extraction.

middle: M

first: Charles

middle: V

last: Clevenger


title: caArray_meyer-00191: Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses

status: Public on Jun 11 2016

summary: We have generated a molecular taxonomy of lung carcinoma, the leading cause of cancer death in the United States and worldwide. Using oligonucleotide microarrays, we analyzed mRNA expression levels corresponding to 12,600 transcript sequences in 186 lung tumor samples, including 139 adenocarcinomas resected from the lung. Hierarchical and probabilistic clustering of expression data defined distinct subclasses of lung adenocarcinoma. Among these were tumors with high relative expression of neuroendocrine genes and of type II pneumocyte genes, respectively. Retrospective analysis revealed a less favorable outcome for the adenocarcinomas with neuroendocrine gene expression. The diagnostic potential of expression profiling is emphasized by its ability to discriminate primary lung adenocarcinomas from metastases of extra-pulmonary origin. These results suggest that integration of expression profile data with clinical parameters could aid in diagnosis of lung cancer patients.

overall_design:
meyer-00191
Assay Type:  Gene Expression
Provider: Affymetrix
Array Designs: HG_U95Av2
Organism: Homo sapiens (ncbitax)
Material Types: total RNA, synthetic_RNA, organism_part, whole_organism
Disease States: lung cancer, Normal


title: Drought, heat and combined stress in durum wheat

status: Public on Mar 22 2016

summary: Durum wheat is an important cereal crop grown mainly in semi-arid environments (e.g. Mediterranean regions) characterized by water scarcity and high temperatures often occurring at the same time. This work reports on a transcriptomic analysis carried out on two durum wheat cultivars (Cappelli and Ofanto) characterized by different water use efficiency (WUE), grown to booting stage and subjected to a combination of drought and heat stresses, a situation similar to the experience of a crop grown in Mediterranean environments and exposed to a terminal heat/drought stress.   ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  alessio.  The equivalent experiment is TA47 at PLEXdb.]

overall_design: treatment: CTRL - genotype: Ofanto(3-replications);  treatment: CTRL - genotype: Cappelli(3-replications);  treatment: Drought - genotype: Ofanto(3-replications);  treatment: Drought - genotype: Cappelli(3-replications);  treatment: Heat - genotype: Ofanto(3-replications);  treatment: Heat - genotype: Cappelli(3-replications);  treatment: Mixed - genotype: Ofanto(3-replications);  treatment: Mixed - genotype: Cappelli(3-replications)

first: alessio

last: aprile


title: Transdifferentiation of Human Endothelial Progenitors into Smooth Muscle Cells

status: Public on Mar 21 2016

first: Nicolas

last: Christoforou

address: 136 Hudson Hall, Box 90281

department: Biomedical Engineering

summary:
Derivation of induced smooth muscle cells (iSMC) through direct transdifferentiation of a convenient and expandable primary cell source would open a wide range of prospects for their use in tissue engineering, drug testing, and disease modeling. Hypothesizing that MYOCD as a master regulator of smooth muscle gene expression would facilitate the generation of iSMC, we studied the conversion of human endothelial progenitor cells (EPC) into iSMC through the induced expression of by over-expression of MYOCD. A significant cytoskeletal rearrangement of the EPC resembling that of mesenchymal cells occurred within 3 days post initiation of MYOCD expression. This transition was associated with a downregulation of endothelial cell surface markers (CD31, CD105) as determined by flow cytometry. By day 7, iSMC derivation was evident with a significant upregulation of smooth muscle markers ACTA2, MYH11, TAGLN, and downregulation of CD31 and CDH5 as determined by gene expression analysis. Immunofluorescence revealed expression of MYH11 and ACTA2 and absence of endothelial markers VWF and CD31. By two weeks, microarray gene expression analysis demonstrated a significant similarity between iSMC and umbilical artery SMC (UASMC). The iSMC continued to develop toward the SMC lineage after four weeks of MYOCD induced expression. Microarray gene expression analysis showed an upregulation of molecular pathways associated with smooth muscle contraction and cytoskeletal reorganization in iSMC. Calcium transients were detected in iSMC when stimulated with phenylephrine but not in EPC. Contractility of iSMC was also higher than that of EPC as determined by traction force microscopy. Tissue-engineered blood vessels constructed using iSMC showed functionality with respect to flow- and drug- mediated vasodilation and vasoconstriction.
We used microarrays to detail the global programme of gene expression underlying the transdifferentiation of endothelial progenitor cells into smooth muscle cells via the transient induced expression of the transcriptional co factor MYOCD

overall_design: To further ascertain the overall effect that the induction of MYOCD expression had on cells undergoing transdifferentiation we performed microarray gene expression analysis on iSMC following 2 weeks of continuous MYOCD expression (iSMC-2w) or 2 weeks of continuous MYOCD expression followed by 2 weeks of culture under standard conditions (iSMC-4w). Control cells included non-transduced EPC and primary human smooth muscle cells isolated from the umbilical artery (UASMC).


title: MicroRNA profile in hepatic epithelioid hemangioendothelioma

status: Public on Mar 15 2016

summary: To elucidate the aetiology of HEH, especially with regard to microRNA (miRNA) profiles, samples obtained from three different parts of both normal and tumour tissues were analysed . The details of RNA extraction have been described in our previous reports. Interestingly, 16 miRNAs were significantly up-regulated and 51 miRNAs were down-regulated in the tumour tissues compared to the normal tissues (Student’s t-test, p<0.01). In addition, unsupervised hierarchical clustering analysis using a Pearson’s correlation showed that the tumour tissues clustered separately from the normal tissues.

overall_design: microRNA samples obtained from three different parts of both normal and tumour tissues were analysed


title: caArray_merco-00121: In silico dissection of cell-type-associated patterns of gene expression in prostate cancer

status: Public on Jun 02 2016

summary: Prostate tumors are complex entities composed of malignant cells mixed and interacting with nonmalignant cells. However, molecular analyses by standard gene expression profiling are limited because spatial information and nontumor cell types are lost in sample preparation. We scored 88 prostate specimens for relative content of tumor, benign hyperplastic epithelium, stroma, and dilated cystic glands. The proportions of these cell types were then linked in silico to gene expression levels determined by microarray analysis, revealing unique cell-specific profiles. Gene expression differences for malignant and nonmalignant epithelial cells (tumor versus benign hyperplastic epithelium) could be identified without being confounded by contributions from stroma that dominate many samples or sacrificing possible paracrine influences. Cell-specific expression of selected genes was validated by immunohistochemistry and quantitative PCR. The results provide patterns of gene expression for these three lineages with relevance to pathogenetic, diagnostic, and therapeutic considerations.

overall_design:
merco-00121
Assay Type: Gene Expression
Provider: Affymetrix
Array Designs: HG_U95Av2
Organism: Homo sapiens (ncbitax)
Material Types: whole_orrganism, synthetic_RNA, organism_part, total_RNA
Disease States: Normal, Prostate Cancer


title: Cell type influences metastasis tropism

status: Public on Feb 13 2016

first: David

last: Hsu

address: Rm 2167 CIEMAS Bldg, 101 Science Dr.

department: Institute for Genome Sciences and Policy

summary:
We report that the cell of origin plays an important role in this metastatic tropism. Following injection into the arterial circulation of mice, each of the identically transformed cell types gave rise to different metastatic patterns.
Using gene expression analysis, we identified the chemokine receptor CXCR4 as being instrumental in determining the distinct metastatic patterns between skeletal muscle precursor cells and skeletal myoblasts.

overall_design:
3 independent cell lines of primary human skeletal myoblasts, primary skeletal muscle cell precursors, and each of these cell lines transformed with hTERT, the early region of SV40 encoding T-Ag and t-Ag, and RasG12V
analysis of primary human skeletal myoblasts, primary skeletal muscle cell precursors, and each of these cell lines transformed with hTERT, the early region of SV40 encoding T-Ag and t-Ag, and RasG12V

first: Kendall

last: DiSean

middle: S

first: Christopher

last: Counter


title: HER2 and EGFR dependent activation of RalA in breast cancer

summary: Activated HER2 and EGFR stimulate the Ras small GTPases, which in turn primarily activate the MAPK, PI3K-Akt and RalGEF-Ral pathways.  While activation of the MAPK and PI3K-Akt pathways downstream of HER2 and EGFR promote mammary tumorigenesis, little is known regarding the role of the RalGEF-Ral pathway.  RalGEFs convert the small GTPases RalA and RalB to an active GTP-bound state.  Of the two proteins, only activated RalA is transforming, while RalB is more important for cell motility, and hence we investigated the role of RalA in HER2-overexpressing and EGFR-positive breast cancer.  We now report that shRNA-mediated knockdown of RalA reduced the in vitro transformed growth and in vivo tumorigenic growth of MDA-MB-231 human breast cancer cells, while knockdown of RalB reduced migration and invasion.  Lastly, we demonstrate that expression of activated HER2 increases RalA-GTP levels, and that a number of genes associated with activated RalA are elevated in tumor compared to normal mammary tissue.  Taken together, these results suggest a possible role for RalA in mammary tumorigenesis.

overall_design:
Four independent cultures of HEK-HT cells stably infected with a retrovirus confirmed to expressed RalAQ72L and four independent cultures of HEK-HT cells stably infected with a control retrovirus
RalA activation expression analysis

first: Sameer

middle: H

last: Issaq

first: Donita

middle: C

last: Brady

first: Mickey

middle: K

last: Kim

first: Thomas

last: Ribar

first: Neil

middle: L

last: Spector


title: Heat priming induces transgeneration thermo-tolerance

status: Public on Mar 17 2016

city: Nanjing

first: Xiao

last: Wang

address: NO.1 Weigang Road

country: China

institute: Nanjing Agricultural University

summary:
Effects of heat priming applied to the first generation on tolerance of the successive generation to post-anthesis high temperature stress were investigated.
Compared with the progeny of non-heat primed plants (NH), the progeny of heat-primed plants (PH) presented higher grain yield, leaf photosynthesis and activities of antioxidant enzymes and lower cell membrane damage under high temperature stress. In the transcriptome profile, 1430 probes showed obvious difference in expression between PH and NH. These genes were those of signal transduction, transcription, energy, defense, and protein destination and storage, respectively.

overall_design: Pot experiments (25 cm in diameter and 22 cm in depth) were conducted at the Experimental Station of Nanjing Agricultural University, Nanjing, China (32˚30ʹN and 118˚42ʹE). During the first generation, wheat plants were divided into two groups: one group were not primed (N) while the other were heat-primed (P) at pre-anthesis (at a day/night temperature of 32/28˚C for two days at the seven-leaf stage and the nine-leaf stage) and post-anthesis (34/30˚C for seven days at the 10th day after anthesis). At maturity, seeds from both groups were harvested. Seedlings (the progeny generation) from each group seed were further divided two sub-groups: one was subjected to high temperature stress at a day/night temperature of 34/30˚C, while the other was set at 26/22˚C for six days from the 10th day after anthesis (DAA). During both priming and high-temperature stress, plants under different treatments were moved into sepatarate growth chambers at preset temperatures. Thereafter, four treatments were established: NC, progeny of non-primed plants without post-anthesis high temperature stress; NH, progeny of non-primed plants with post-anthesis high temperature stress; PC, progeny of primed plants  without post-anthesis high temperature stress; and PH, progeny of primed plants with post-anthesis high temperature stress.

first: Caiyun

last: Xin

first: Jian

last: Cai

first: Qin

last: Zhou

first: Tingbo

last: Dai

first: Weixing

last: Cao

first: Dong

last: Jiang


title: NC2 has a role in determining the transcription start site in Saccharomyces cerevisiae

status: Public on Mar 01 2016

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

country: Spain

institute: Universitat de Valencia

type: Expression profiling by genome tiling array

summary: In this study we show that disruption of NC2 function by shutting off either of its two protein subunits in yeast provokes an immediate increase in cryptic transcription around and inside any kind of RNA pol II genes.

overall_design: 9 samples total; 3 strains (2 mutants and 1 WT, 3 biological replicates each).

first: Natalia

last: Gómez-Navarro

first: Antonio

last: Jordán-Pla

first: Francisco

last: Estruch

first: José

middle: E

last: Pérez-Ortín


title: Exosomal microRNA released from primary normal BM and AML CD34+ cells.

status: Public on Feb 01 2016

first: Satoshi

last: Kondo

summary:
In an attempt to clarify the diferrence of exosomal microRNA derived from Normal BM and primary AML CD34+ cells. Primary cells  were cultured in serum free medium and supernatant was harvested.
After extract microRNAs, the difference of exosomal microRNAs between normal BM and leukemia was analyzed by array.

overall_design: Normal BM CD34+ cells was used as control (n=1). CD34+ fraction of leukemic cells (AML M1 [n=1], AML M4 [n=1]) was used as experimental samples.

first: Masayoshi

last: Kobune

first: Hiroto

last: Horiguchi


title: Early microbial colonisation affects transcriptome of pig jejunum perfused with E. coli F4, F4 fimbria or Lact. amylovorus

status: Public on Feb 11 2016

city: bologna

first: PAOLO

middle: o

last: BOSI

state: BOLOGNA

address: Viale Fanin, 46

department: DISTAL

country: Italy

institute: UNIVERSITY OF BOLOGNA

summary:
An early settlement of a complex gut microbiota can protect against gastro-intestinal dysbiosis, but the effects of neonatal microbiota colonization on the gut barrier upon the further encounter of favorable bacteria or not, are largely unknown.
The jejunal transcriptome of differently perfused intestinal loops of 12 caesarian-derived pigs previously associated with microbiota of different complexity was studied.
Pigs received pasteurized sow colostrum at birth (d0), 2 mL of starter microbiota (10^7 CFU of each Lactob. Amylovorus (LAM), Clostr. glycolicum, and Parabacteroides spp.) on d1-d3 of age and either a placebo inoculant (simple association, SA) or an inoculant consisting of diluted feces of an adult sow (complex association, CA) on d3-d4 of age. On days 26-37 of age, jejunal loops were perfused for 8 h with either enterotoxigenic E. coli F4 (ETEC), F4 fimbriae (F4), LAM or saline (CTRL) and jejunal samples were obtained from each piglet immediately afterwards.

overall_design: The analysis of whole mRNA transcript expression was done by Affymetrix©Porcine Gene 1.1 ST array strips, a Robust Multichip Analysis was performed on the CEL files, and Transcripts ID’s were associated to 13,406 Human gene names, based on Sus scrofa Ensemble

first: Paolo

last: Trevisi

first: Davide

last: Priori

first: Alfons

middle: J

last: Jansman

first: Sietse-Jan

last: Koopmans

first: Jan

last: van der  Meulen

last: Bosi


title: Transcriptome Shock Invokes Disruption of Parental Expression-Conserved Genes in Tetraploid Wheat

status: Public on Feb 12 2016

city: Changchun

first: Huakun

last: Zhang

state: Jilin

address: Renmin Street

institute: Northeast Normal University

summary: Allopolyploidy, entailing whole genome duplication (WGD) of merged divergent genomes of different species, often instigates transcriptome shock, whereby both total gene expression level and homeolog expression partitioning can be disrupted and remodeled. Little is known about the extent to which the parental expression-conserved genes will be disrupted/remodeled by allopolyploidization, nor the evolutionary relevancy of shock-induced expression repatterning. Here, by microarray-based gene expression profiling and gene-specific cDNA-pyrosequencing, we assessed transgenerational transcriptome shock in a synthetic allotetraploid wheat (AT2) with karyotype and basic morphology mimicking those of natural tetraploid wheat, Triticum turgidum. We show that the transcriptome shock in AT2 is exceptionally strong that it disrupted intrinsically conserved parental gene expression, and resulted in extensive expression nonadditivity in the newly formed allotetraploid plants. At total expression level, a substantial proportion of shock-induced novel expression, especially over-transgressive expression, was rapidly stabilized already in early generations of AT2. Extensive remodeling of homeolog expression occurred in AT2, including those genes that showed additive total expression, and which generated subgenome expression dominance, a pattern that mirrors T. turgidum. Thus, the shock-induced new patterns of gene expression at both the total expression level and subgenome homeolog partitioning showed evidence of evolutionary persistence. Complex relationships between homeolog expression remodeling and nonadditive total expression were observed in a tissue-specific manner.

overall_design: We have 9 samples including two tissues, leaf and young-inflorescence, respectively. Each sample has three replicates. So we overall have 54 samples.

first: Xiaowan

last: Gou

first: Ai

first: Xutong

last: Wang

first: Yuzhu

last: Dong

first: Bao

last: Liu


title: Effect of obesity on molecular characteristics of invasive breast tumors: gene expression analysis of 405 tumors by BMI

status: Public on Mar 08 2016

city: Windber

first: Rachel

last: Ellsworth

state: PA

address: 620 Seventh Street

department: Clinical Breast Care Project

institute: Windber Research Institute

summary:
Background: Obesity is a risk factor for breast cancer in postmenopausal women and is associated with decreased survival and less favorable clinical characteristics such as greater tumor burden, higher grade, and poor prognosis, regardless of menopausal status. Despite the negative impact of obesity on clinical outcome, molecular mechanisms through which excess adiposity influences breast cancer etiology are not well-defined.

Methods: Affymetrix U133 2.0 gene expression data were generated for 405 primary breast tumors using RNA isolated from laser microdissected tissues.  Patients were classified as normal-weight (BMI<25), overweight (BMI 25-29.9) or obese (BMI>30). Statistical analysis was performed by ANOVA using Partek Genomics Suite version 6.6 using a false discovery rate <0.05 to define significance.

Results: Obese patients were significantly more likely to be diagnosed >50 years or with African American ancestry compared to lean or overweight women. Pathological characteristics, including tumor stage, size or grade, lymph node status, intrinsic subtype, and breast cancer mortality did not differ significantly between groups. No significant gene expression differences were detected by BMI In a non-stratified analysis which included all subtypes or within luminal B, HER2-enriched or basal-like subtypes. Within luminal A tumors, however, 84 probes representing 77 genes from pathways such as cell cycle, p53 and mTOR signaling, tight junctions and a number of cancer associated pathways were differentially expressed.

Conclusions: Identification of transcriptome differences in luminal A tumors from normal-weight compared to obese women suggests that obesity alters gene expression within ER+ tumor epithelial cells.  Alterations of pathways involved in cell cycle control, tumorigenesis and metabolism may promote cellular proliferation and provide a molecular explanation for less favorable outcome of obese women with breast cancer.  Targeted treatments, such as mTOR inhibitors, may allow for improved treatment and survival of obese women, especially African American women, who are more likely to be obese and suffer outcome disparities.

overall_design:
Two to five serial sections (8 um thick) were cut, mounted on glass PEN foil slides (Leica Microsystems, Wetzlar, Germany), stained using the LCM staining kit (Applied Biosystems, Foster City, CA) and laser microdissected on an ASLMD laser microdissection system (Leica Microsystems, Wetzlar, Germany).  Slide preparation, staining and cutting were performed within a 15 minute period to preserve RNA integrity. RNA was then isolated using the RNAqueous-Micro kit (Applied Biosystems, Foster City, CA) and treated with DNase I to remove any contaminating genomic DNA.  RNA integrity was assessed using the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA), converted to biotin-labeled aRNA using two rounds of amplification with the MessageAmpII aRNA Amplification kit (Applied Biosystems, Foster City, CA), and the concentration and quality of the samples was measured with the NanoDrop 1000 (NanoDrop Products, Wilmington, DE) and 2100 Bioanalyzer.  Hybridization, washing, staining and scanning of HG U133A 2.0 arrays (Affymetrix, Santa Clara, CA) were conducted according to manufacturer’s protocols. The gene expression data were analyzed with Partek® Genomics Suite v 6.6 (Partek Incorporated). Probe set intensities were obtained by robust multi-array average background correction, quantile normalization, median polish summarization, and log2 transformation. Data integrity was then assessed by standard GeneChip® quality control parameters.

Please note that some of the patients (19 out of 424) did not have a BMI available from the diagnosis date and so they were coded Unknown for BMI and not used in downstream analysis.


title: Does Type of Dietary Fat Matter?  Prostate Cancer Xenograft Progression in a SCID Mouse Model with Varying Dietary Fat Sources

status: Public on Jan 01 2016

first: Jen-Tsan

last: Chi

address: 101 Science Drive, DUMC 3382

department: Molecular Genetics and Microbiology

summary:
PURPOSE:  Previous mouse studies using corn oil (ω-6) as the dietary fat source suggest that decreasing dietary fat content can slow prostate cancer (PCa) growth.  However, other studies, in which the diet was composed around saturated fat, showed no difference in outcomes between high-fat and low-fat diets.  The relative effects of other fats, such as fish oil and olive oil, also remain unexplored.  To our knowledge, no trial has yet compared the effect of various fats on prostate cancer progression.  Therefore, we sought to systematically study the effect of fish oil, olive oil, corn oil, and saturated fat on prostate cancer progression.  METHODS:  A total of 96 male SCID mice were injected with LAPC-4 human PCa cells.  Two weeks following injection, mice were singly-housed and randomized to either a fish oil, olive oil, corn oil, or saturated fat based diet.  Animals were euthanized when tumors reached 1,000 mm3.  Serum was collected at sacrifice and assayed for PSA, insulin, IGF-1, IGFBP-3, and PGE-2 levels.  Tumors were also assayed for PGE-2, and COX-2 levels, and gene array analysis was performed.  RESULTS:  Mice weights and tumor volumes were equivalent across groups at randomization.  Overall, fish-oil consumption was associated with improved survival, relative to all other dietary groups (Log-rank, all p<0.05).  We did not detect any significant difference in serum PSA, insulin, IGF-1, IGFBP-3, and PGE-2 levels.  Glucose at the time of sacrifice was statistically different between groups, with the fish-oil fed mice having the highest levels of serum glucose (Kruskal-Wallis, p=0.03).
CONCLUSIONS:  In this prostate cancer xenograft model, we found that consuming a diet in which fish-oil was the only fat source slowed tumor growth in improved survival, compared to mice consuming diets composed of olive oil, corn oil, or saturated fat sources.  These results suggest that type of dietary fat consumed may be as important as amount of dietary fat consumed in the setting of prostate cancer.

overall_design: DESIGN:  A total of 96 male SCID mice were injected with LAPC-4 human prostate cancer cells.  After 2 weeks of tumor growth, the mice were randomized to one of four diets:  corn oil, fish oil, olive oil, and saturated fat source diets.  Animals were euthanized when tumor volumes exceeded 1000 mm^3.  Sera and tissues from the median 6 surviving animals from each of the four dietary groups were analyzed.

first: Jessica

last: Lloyd

first: Elizabeth

last: Masko

first: Chen

last: Wu

first: Kirpatrick

last: Melissa

first: William

last: Aronson

middle: A

first: Stephen

last: Freedland


title: A pilot study of integrative genomics analysis of genes with biallelic loss and its relation to the expression of mRNA and micro-RNA in esophageal squamous cell cancer

status: Public on Dec 30 2015

city: Bethesda

first: Howard

last: Yang

address: 37 CONVENT DR, Room 5120

department: CCR

summary: In the current study we focused on biallelic loss and its relation to expression of mRNA and miRNA in ESCC using arrays of 500K SNP, mRNA, and miRNA in 30 cases from a high-risk region of China.  Our main results are the followings: 1) 77 genes had biallelic loss in at least 10% of ESCC samples, and most of them are located on chromosome 3p (gene number, n=42), 9p (n=14), 5q (n=10) and 4p (n=7); 2) 52 of 77 genes had signals in both tumor and matched normal on Affymetrix Hu 133 array whereas  79% of them (n=41) showed lower expression levels in patients with biallelic loss (group 1) than that without biallelic loss (group 2) and 19% (n=10) of genes showed higher expression levels in group1 than in group2; 3) 70 miRNAs targeting 35 genes were analyzed, and expression levels of 50 miRNAs (71%) were high while expression levels of their targets  were low, and 20 miRNA (29%) showed low expression while their target genes showed high expression; 4) 60 miRNAs target 32 affected genes showed that  43% of (n=26) miRNA expression level were low in group 1 than in group 2 and 57% (n=34) miRNA showed higher expression levels in group 1 than in group 2; and the expression patterns of miRNA and genes affected are complex when comparison the two groups of patients.

overall_design: 30 tumors and adjacent normal tissue (60 samples in total)

last: Hu

first: Maxwell

middle: P

last: Lee

first: Philip

middle: R

last: Taylor


title: Functional abnormalities and changes in gene expression in fibroblasts and macrophages from the bone marrow of patients with acute myeloid leukemia

status: Public on Dec 21 2015

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

country: Germany

institute: Institut fuer Zellbiologie

summary: In leukemias and other malignancies of the bone marrow, little is known about the fate of fibroblasts and resident macrophages after normal hematopoietic cells are replaced by neoplastic cells. In the present investigation we used two-stage long-term bone marrow cultures to detect functional stromal cell abnormalities in acute myeloid leukemia, myelodysplastic syndromes and multiple myeloma. While fibroblasts from multiple myeloma and macrophages from multiple myeloma and myelodysplastic syndromes were functionally indistinguishable from the respective cell types from normal bone marrow, fibroblasts from patients with acute myeloid leukemia or myelodysplastic syndromes possessed a significantly lower ability to support hematopoiesis originating from co-cultured normal CD34-positive cells than fibroblasts from healthy marrow. Conversely, macrophages from acute myeloid leukemia marrow significantly enhanced the production of blood cells compared with control macrophages. Aberrant function in fibroblasts and macrophages was associated with consistent changes in the expression of genes whose products are involved in hematopoietic stem cell control, such as cytokines and regulators of the Wnt and Notch signalling pathways.

overall_design: Analysis of gene expression in fibroblast and macrophage populations isolated from primary long-term bone marrow cultures (LTBMC). Adherent layers of LTBMCs were trypsinized, fibroblasts and macrophages were purified using anti-Fibroblast or CD14 MicroBeads (Miltenyi Biotec, Begisch-Gladbach, Germany), and total RNA was extracted by using the RNeasy kit from Qiagen (Hilden, Germany), as specified by the manufacturer. Global gene expression was analyzed in 4 samples each of fibroblasts and macrophages from AML patients and control subjects.

first: Yu

last: Li

first: Ulrich

last: Dührsen

first: Dürig

last: Jan


title: Genomic Run On (GRO): determination of the nascent transcriptional rates and mRNA levels in several yeast mutants (SAC3, SUS1, SRC1)

status: Public on Dec 31 2015

first: Jose

last: Perez-Ortin

summary: We analyzed the effect of SAC3, SUS1 and SRC1 on the transcription rates, mRNA stabilities and mRNA levels by doing GRO experiments in a deletion mutants and the partial C-truncated version of Sac3 comparing with a wild type. Some data for mRNA amounts (sus1 ans src1 mutants) are not included because were already in GEO database: GSE920 and GSE6370 accession numbers.

overall_design: This study focus on the transcriptional activity of RNA pol II in yeast genes. S. cerevisiae cells grown in YPD to exponential phase were subjected to Genomic Run On.  Data were normalized by the ArrayStat software. Home-made macroarrays containing entire ORFs were used.

first: José

last: Pérez-Ortín

first: Daniel

last: Medina

first: Priyanka

last: Palit

first: Oreto

last: Antunez

last: García-Martínez


title: mRNA and miRNA expression profile of MCF7 cells with retroviral inducible expression of ΔNp63α

status: Public on Dec 28 2015

first: Satoshi

last: Kondo

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

overall_design: Refer to individual Series


title: Profiling of naïve and memory Tregs

status: Public on Jan 19 2016

city: Vancouver

first: Megan

last: Levings

address: 950 West 28th Ave

country: Canada

institute: University of British Columbia

summary:
Changes in Treg function are difficult to quantify due to the lack of Treg-exclusive markers in humans and the complexity of functional experiments. We sorted naive and memory human Tregs and conventional T cells, and identified genes that identify human Tregs regardless of their state of activation. We developed this Treg signature using Affymetrix human genome U133A 2.0 microarrays.
To generate Tregs and Tconvs in multiple states of activation, naïve (CD4+CD25hiCD45RA+) and memory (CD4+CD25hiCD45RA-) Tregs, and naïve (CD4+CD25-CD45RA+) and memory (CD4+CD25-CD45RA-) Tconvs were sorted from blood of 7 healthy adults and RNA was isolated ex vivo or after stimulation for 40h, promoting activation-induced FOXP3 in Tconvs. The gene-expression profile of the eight cell subsets was analyzed.

overall_design: 7 adult healthy control samples were sorted into 4 subsets: naïve (CD4+CD25hiCD45RA+) and memory (CD4+CD25hiCD45RA-) Tregs, and naïve (CD4+CD25-CD45RA+) and memory (CD4+CD25-CD45RA-) Tconvs. These were used for RNA ex vivo and after 40h stimulation with anti-CD3/CD28 beads to induce an activation phenotype.

first: Anne

last: Pesenacker

first: Adele

middle: Y

last: Wang

first: Amrit

last: Singh

first: Jana

last: Gillies

first: YoungWoong

last: Kim

first: Ciriaco

last: Piccirillo

first: Duc

last: Nguyen

first: W

middle: N

last: Haining

first: Scott

last: Tebbutt

first: Constadina

last: Panagiotopoulos


title: microRNA expression profile of MCF7 cells with retroviral inducible expression of ΔNp63α [miRNA]

summary: MCF7 is a breast adenocarcinoma cell line which exhibits properties of differentiated luminal epithelial cells. ΔNp63α, an N-terminally truncated isoform of p51/p63 protein, plays a critical role in mammary gland development. Here, we inducibly express ΔNp63α in MCF7 cells and studied its role in stemness of breast cancer cells.

overall_design: Expression of ΔNp63α was induced in MCF7 cells with Doxycycline (Dox) for 48 hours. Total RNA containing microRNAs was isolated. microRNA microarray analysis was performed in Dox- (MCF7-PTO-ΔNp63α-Dox-) and Dox+ (MCF7-PTO-ΔNp63α-Dox+) samples.

first: Ruhul

last: Amin

first: Yuiko-Morita

last: Fujimura

first: Shuntaro

last: Ikawa


title: ACLY and ACC1 Regulate Hypoxia-Induced Apoptosis by Modulating ETV4 via α-ketoglutarate

status: Public on Dec 10 2015

first: Jen-Tsan

last: Chi

summary: In order to propagate a solid tumor, cancer cells must adapt to and survive under various tumor microenvironment (TME) stresses, such as hypoxia or lactic acidosis. To systematically identify genes that modulate cancer cell survival under stresses, we performed genome-wide shRNA screens under hypoxia or lactic acidosis. We discovered that genetic depletion of acetyl-CoA carboxylase (ACACA or ACC1) or ATP citrate lyase (ACLY) protected cancer cells from hypoxia-induced apoptosis. Additionally, loss of ACLY or ACC1 reduced levels and activities of the oncogenic transcription factor ETV4. Silencing ETV4 also protected cells from hypoxia-induced apoptosis and led to remarkably similar transcriptional responses as with silenced ACLY or ACC1, including an anti-apoptotic program. Metabolomic analysis found that while α-ketoglutarate levels decrease under hypoxia in control cells, α-ketoglutarate is paradoxically increased by hypoxia when ACC1 or ACLY are depleted. Supplementation with α-ketoglutarate rescued the hypoxia-induced apoptosis and recapitulated the decreased expression and activity of ETV4 via an epigenetic mechanism. Therefore, ACC1 and ACLY regulate the levels of ETV4 under hypoxia via increased α-ketoglutarate. These results reveal that ACC1/ACLY- α-ketoglutarate-ETV4 is a novel means by which metabolic states regulate transcriptional output for life vs. death decisions under hypoxia. Since many lipogenic inhibitors are under investigation as cancer therapeutics, our findings suggest that the use of these inhibitors will need to be carefully considered with respect to oncogenic drivers, tumor hypoxia, progression and dormancy. More broadly, our screen provides a framework for studying additional tumor cell stress-adaption mechanisms in the future.

overall_design: DESIGN: H1975 lung cancer cells transduced with a scramble shRNA hairpin or two different shRNAs against ACLY, ACC1, or ETV4 under hypoxia.

first: Melissa

last: Keenan


title: Differences of miRNA expression profiling between GIST and leiomyoma tissue samples acquired by Tunneling Bloc Biopsy

status: Public on Jan 04 2016

first: Satoshi

last: Kondo

summary: miRNA expression profiling between GIST and leiomyoma specimens taken by Tunneling Bloc Biopsy

overall_design: Nine GIST patients and seven gastric leiomyoma patients underwent endoscopic biopsy called Tunnel Block Biopsy. MiRNAs were extracted from the tissues, then.

first: Koji

last: Fujita

first: Hideki

last: Kobara


title: MDA-9/Syntenin regulates differentiation and angiogenesis programs in Head and Neck Squamous Cell Carcinoma

status: Public on Nov 23 2015

city: Jacksonville

first: Catherine

last: Dumur

state: FL

address: 5008 Mustang Rd

department: Anatomic Pathology

institute: Sonic Healthcare USA

summary:
We identified MDA-9/Syntenin (8q12) as a key component of HNSCC differentiation and angiogenesis.
Robust reduction in the expression of cyclinD1, CDK4, CTNNB1, STAT3 and PI3K were evident in MDA- 9/Syntenein depleted cells, which was reversed following MDA-9/Syntenin overexpression in immortalized oral epithelial cells.

overall_design: To further elucidate the role of MDA-9/Syntenin in tumor growth and epithelial cell differentiation in vitro and in vivo by sielnicng its expression.

first: Santanu

last: Dasgupta

middle: I


title: Transcriptome analysis reveals key differentially expressed genes involved in wheat grain development.

status: Public on Dec 02 2015

city: Beijing

first: Yonglong

last: Yu

address: 105 Xisanhuan North Road

institute: College of Life Science, Capital Normal University

summary:
Wheat seed development is a very important stage in the cereal crops seed life cycle. The accumulation reserves of wheat mature seeds provide not only the food for human and livestock feed, but also the energy for the seed germination.However, due to the large genome size, many studies related to wheat seed are very complex and uncompleted. Transcriptome analysis of elite Chinses bread wheat cultivar Jimai 20 may provides a comprehensive understanding of wheat seed development.
Seed development involves in the regulation of large number of genes, whether these genes are normal activated  or not is very important to seed development. We performed microarray analysis using the Affymetrix Gene Chip to reveal the gene expression profiles in the phases of wheat cultivar Jimai 20 grain filling. Our results provide a new insights into the thoroughly metabolic changes of seed development as well as the key differentially expressed genes involved in wheat grain development.

overall_design: The three groups including development seeds were harvest at three successive phases, which were 11 (P1), 15 (P2), 20 (P3) days post-anthesis (DPA) respectively. Three independent experiments were performed for each group.

first: Chaoying

last: Ma

first: Dong

last: Zhu

first: Yaping

last: Wang


title: Genome-wide analysis of MCF-7 cells expressing or not MMP-14 (MT1-MMP) growing in monolayer cell culture conditions

status: Public on Dec 11 2015

city: Liège

first: Erik

last: Maquoi

address: Tour de Pathologie, B23 Sart-Tilman

country: Belgium

institute: University of Liège

summary: In order to investigate the impact of MMP-14 (MT1-MMP) on the transcriptomes of a human breast adenocarcinoma cell line, we performed a microarray analysis from RNAs isolated from MCF-7 cells expressing either an empty vector (VEC) or human MMP-14 cDNA (MT1) in monolayer growth conditions.

overall_design: MCF-7 cells were stably transfected with either an empty vector (pcDNA3.1/Zeo) or human MMP-14 cDNA (pcDNA3.1-MMP-14/Zeo). Cells were grown for 48 hours in monolayer culture. Cells were then lysed in TRIzol and total RNA was isolated. For each experimental condition, total RNAs isolated from 3 independant biological replicates were pooled.

first: Agnès

last: Noël


title: Secreted frizzled related protein 3 (SFRP3) is required for tumorigenesis of PAX3-FOXO1-positive alveolar rhabdomyosarcoma

status: Public on Dec 09 2015

summary:
Alveolar rhabdomyosarcoma (aRMS) is a soft tissue sarcoma associated with the skeletal muscle lineage.  The majority of aRMS tumors express the fusion protein PAX3-FOXO1 (PF), which has proven chemically intractable.  As such, we identified proteins downstream from or cooperate with PF to support tumorigenesis, including SFRP3 (FRZB).  Suppression of SFRP3 using lentivirally transduced shRNAs inhibits cell growth in vitro and tumor growth in vivo.  This study aims to identify the genetic changes that underlie the SFRP3 suppression-mediated decreased cell growth.  We analyzed changes using Gene Ontology (GO) enrichment and found the induced genes were enriched in striated muscle development/differentiation. In contrast, the repressed genes were enriched in response to stimulus and cell cycle/mitosis genes. We also observed as expected downregulation of SFRP3 (FRZB) but also downregulation of Wnt pathway-repressing genes such as CTBP2 (a transcriptional repressor of TCF, similar to CTBP1 ) and NAV2 (which is downstream from APC).  Conversely, we noted upregulation of genes including CCND1 (cyclin D1) and SNAI2 (SLUG), both Wnt signaling target genes and WNT6, which is known to inhibit myoblast proliferation but induce myoblast elongation.
A human aRMS cell line (Rh28) was lentivirally transduced with an empty vector (V) or doxycycline-inducible SFRP3 shRNAs (sh3, sh5) and selected for on puromycin.  Population doubling 18 (PD18) cells were plated at the same confluence and treated for 5 days with either growth media (No) or growth media supplemented with 4 ug/ul doxycycline (Dox) prior to harvesting.  Only empty vector cells treated with growth media (VNo) were included in the array as a control.

overall_design: The gene expression affected by the introduction of doxycyline-inducible SFRP3 shRNAs.

first: Julie

middle: G

last: Kephart

first: Po-Han

last: Chen

first: Corinne

middle: M

last: Linardic


title: Molecular and cellular profilling of scalp psoriasis reveals differences and similarities compared to skin psoriasis

status: Public on Nov 25 2015

city: New York

first: Juan

last: Ruano

state: NY

address: 1230 York ave

institute: Rockefeller University

summary: Scalp psoriasis shows a variable clinical spectrum and in many cases poses a great therapeutic challenge. However, it remains unknown whether the immune response of scalp psoriasis differs from understood pathomechanisms of psoriasis on other skin areas. We sought to determine the cellular and mollecular phenotype of scalp psoriasis by performing a comparative analysis of scalp vs skin using lesional and nonlesional samples from 20 Caucasian subjects with untreated moderate to severe psoriasis and significant scalp involvement, and 10 control subjects without psoriasis. Our results suggest that even in the scalp psoriasis is a disease of the inter-follicular skin. The immune mechanisms that mediate scalp psoriasis were found to be similar to those involved in skin psoriasis. However, the magnitude of dysregulation, number of differentially expressed genes, and enrichment of the psoriatic genomic fingerprinting were more prominent in skin lesions. Furthermore, the scalp transcriptome showed increased modulation of several gene-sets, particularly those induced by interferon-gamma, compared with skin psoriasis which was mainly associated with activation of TNF↵/L-17/IL-22-induced keratinocyte response genes. We also detected differences in expression of gene-sets involving negative regulation, epigenetic regulation, epidermal differentiation, and dendritic cell or Th1/Th17/Th22-related T-cell processes.

overall_design: To define the transcriptomic profile of scalp skin, punch biopsies (6 mm diameter) were obtained from 20 Caucasian patients with untreated moderate to severe psoriasis with significative scalp involvement and 10  control subjects without psoriasis (N). Lesional (LS) samples were isolated from the infiltrated border of a plaque of psoriasis. Non lesional (NL) samples were taken from  scalp areas with no visible psoriasis between the infiltrated plaques.

first: Mayte

last: Suarez-Farinas

first: James

last: Krueger


title: Expression data from CD34+ HSPCs from patients with Multiple Myeloma before and after lenaldomide consolidation therapy.

status: Public on Nov 18 2015

first: Christian Matthias

last: Wilk

address: 1470 Madison Ave

department: Precision Immunology Institute

institute: Icahn School of Medicine at Mount Sinai

summary:
Little is known about the effects of lenalidomide therapy on Bone Marrow HSPCs in patients with Multiple Myeloma. In this experiment, we examined the gene expression changes associated with a six months
lenalidomide consolidation therapy in patients who underwent induction therapy and HDCT with ASCT and who all achieved a remission.

overall_design: Paired Bone Marrow samples from patients with Multiple Myeloma before and after lenalidomide consolidation therapy.

first: Fenk

last: Roland

first: Wilk

last: Christian Matthias


title: Profiling of bacterial respiratory infection, viral respiratory infection, and non-infectious illness

status: Public on Jan 20 2016

first: Ephraim

last: Tsalik

address: 315 Trent Dr., Hanes House Rm 157, Box 102359

department: Center for Applied Genomics and Precision Medicine

summary:
A pressing clinical challenge is identifying the etiologic basis of acute respiratory illness. Without reliable diagnostics, the uncertainty associated with this clinical entity leads to a significant, inappropriate use of antibacterials. Use of host peripheral blood gene expression data to classify individuals with bacterial infection, viral infection, or non-infection represents a complementary diagnostic approach.
Patients with respiratory tract infection along with ill, non-infected controls were enrolled through the emergency department or undergraduate student health services. Whole blood was obtained to generate gene expression profiles. These profiles were then used to generate signatures of bacterial acute respiratory infection, viral acute respiratory infection, and non-infectious illness.

overall_design: 273 subjects were ascertained for this analysis. This included 88 patients with non-infectious illness, 115 with viral acute respiratory infection, and 70 with bacterial acute respiratory infection.  Samples were obtained at the time of enrollment, which was at initial clinical presentation. Total RNA was extracted from human blood using the PAXgene Blood RNA Kit. Microarray data were generated using the GeneChip Human Genome U133A 2.0 Array.   Microarrays were generated in two microarray batches with seven overlapping samples giving rise to 280 total microarray experiments.

first: Ricardo

last: Henao

first: Marshall

last: Nichols


title: Therapy-induced self-renewal of CD133hi cells regulates escape from tumor dormancy and endocrine-resistant metastatic luminal breast cancer

status: Public on Feb 09 2016

first: Jeffrey

last: Zhao

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

summary:
HT induces an OXPHOS metabolic editing of ER+ breast cancers, paradoxically establishing HT-driven self-renewal of dormant CD133hi/ERlo cells mediating metastatic progression, which is sensitive to dual targeted therapy
In this study, we demonstrated that CD133hi cells can mediate HT resistance and metastatic progression. Using human luminal breast cancer cell lines we have developed an in vivo model of spontaneous metastatic disease recapitulating what is observed in patients. Combining in vivo and in vitro studies we identified a de-novo cancer stem cell population (CSCs) “CD133hi/ERlo/Notch3hi/IL6hi”, which are generated from non-CSCs via the sustained suppression of ER activity. We provide evidence that an ER-IL6-IL6R-CD133 loop is a mechanism mediating HT-resistance.

overall_design: Cancer cells were isolated from primary tumor and metastases, labeled with anti-CD133/CD44 conjugated antibodies and FACS sorted (gated on GFP, cancer cells).For microarray gene expression profiling and real time PCR (QPCR), we extracted RNA using Trizol (Invitrogen) from FACS sorted tumour derived cells. RNA concentration was determined with a NanoDrop 2000. The samples were prepared according to standard protocols and hybridized them on Affymetrix HG-U133 A 2.0 microarrays. We normalized the data using Microarray Suite 5.0. Differentially expressed genes between groups were identified with fold-change and t-test cut-offs.


title: Genome-wide profiling of total RNA from mutants that affect chromatin dynamics: RTT109, SWR1, and the nuclear RNA exosome RRP6

status: Public on Nov 12 2015

city: Worcester

first: Craig

last: Peterson

state: MASSACHUSETTS

address: 373 Plantation Street

department: Program in Molecular Medicine

institute: University of Massachusetts Medical School

summary: The histone variant H2A.Z is a hallmark of nucleosomes flanking the promoters of protein coding genes, and is often found in nucleosomes that also carry lysine 56- acetylated histone H3 (H3-K56Ac), a mark which promotes rapid replication- independent turnover of nucleosomes. Although H2A.Z and H3-K56Ac have been generally implicated in transcriptional activation, their exact contributions have remained elusive. Here we find that H3-K56Ac promotes RNA polymerase II occupancy at a large number of protein coding and noncoding loci, yet neither H3- K56Ac nor H2A.Z has a significant impact on steady state mRNA levels in yeast. Instead, broad effects of H3-K56Ac or H2A.Z on levels of both coding and noncoding RNAs (ncRNAs) are only revealed in the absence of the nuclear RNA exosome. H2A.Z is also necessary for expression of divergent, promoter-proximal ncRNAs in mouse embryonic stem cells, suggesting a conserved role for H2A.Z across eukaryotes. Finally, we show that H2A.Z functions with H3-K56Ac in chromosome folding, facilitating formation of chromosome interaction domains (CIDs). Our study suggests that H2A.Z and H3-K56Ac work in concert with the RNA exosome to control mRNA and ncRNA expression, perhaps in part by regulating higher order chromatin structures.

overall_design: Total RNA isolated from 27 samples with replicates of each strain ranging from 2 to 5. 12 samples from the Proudfoot lab [deposited in  ArrayExpress, accession number E-TABM-936] were downloaded as .CEL files and analyzed alongside samples generated in this study. The identical processing for used for both sets of samples. For details refer to supplementary methods in the paper.

first: Lars

last: Steinmetz


title: Isolation and Characterisation of a Novel Trophoblast Hoescht Side-Population with Stem Cell Properties from First Trimester Placentae

status: Public on Nov 03 2015

city: Melbourne

first: Daniel

middle: Glyn

last: Hurley

address: Level 4, Bldg 193, EEE

department: Systems Biology Laboratory

country: Australia

institute: The University of Melbourne

summary: In this work, we have isolated a Hoescht side-population of trophoblasts from first trimester human placentae that cluster separately from more differentiated trophoblast populations, and have a transcriptomic profile indicative of a stem cell population.

overall_design: Hoescht side-population cells were compared in quintuplicate with extravillous trophoblasts and cytotrophoblasts extracted from the same placentae, giving a total of 15 samples.

first: J

last: James

first: D

first: T

last: Zhang

first: R

last: Vather

first: P

last: Pantham

last: Murthi

first: L

middle: W

last: Chamley


title: Transcriptome modification to the BBAA subgenomes of common wheat since allohexaploidization is largely irreversible

status: Public on Nov 01 2015

city: changchun

first: bao

last: qi

state: jilin province

address: 5268, renmindajie

institute: northeast normal university

summary: The three subgenomes (B, A and D) of common wheat (2n=6x=42) are largely intact, which makes extraction of the BBAA subgenomes as organismally independent genomes possible. Availability of such novel extracted tetraploid wheat (Extracted-tetra) provides a unique opportunity to study whether and to what extent the BBAA subgenomes of common wheat have been irreversibly modified, as well as its attendant biological consequences, during their evolutionary trajectory as allohexaploidy. We report here that the extracted-tetra is stable in karyotype but with severely deteriorated phenotypes. Microarray-based transcriptome analysis revealed a substantial portion of differentially expressed genes (down- or up-regulation) between extracted and natural tetraploid wheat, Triticum turgidum, which exceeded the transcriptome divergence at tetraploid level, implying reinforced effects of allopolyploidization and domestication at the allohexaploid level. Great majority of the differentially expressed genes showed additive expression in a resynthesized allohexaploid wheat (parented by Extracted-tetra), indicating transcriptome modifications to the BBAA subgenomes are largely irreversible. Analysis of a newly synthesized allohexaploid wheat (parented by T. turgidum) suggests that whereas most of the modified genes are accrued evolutionary changes, some showed immediate regulation post-allohexaploidization and evolutionary perseverance. Homeologue-specific pyrosequencing of 44 genes revealed either concordant or independent expression changes to the B and A homeologues. The Extracted-tetra vs.T. turgidum down-regulated genes showed enrichment for distinct GO categories.

sample_organism:
Triticum aestivum
Triticum turgidum subsp. durum
Triticum turgidum
Aegilops tauschii
Triticum dicoccoides
Triticum carthlicum

overall_design: Structurally, the three constituent subgenomes of common wheat, BB, AA and DD, are largely intact with only a few inter-subgenomic translocations. Because of these unique attributes, it is feasible to extract the BBAA subgenomes from the common wheat BBAADD genome by hybridization to a durum line and repeated back-crossing to the hexaploid parent, restituting a novel type of extracted tetraploid wheat, namely Extracted-tetr, with a genome constitution BBAA, virtually identical to the subgenomes BBAA of its common wheat donor. Availability of the extracted-tetra, the resynthesized allohexaploid wheat parented by the extracted-tetra, and newly synthesized allohexaploid wheat parented by natural tetraploid wheat, T. turgidum, provides an excellent system to address the issues of whether and to what extent transcriptome modifications to the BBAA subgenomes of common wheat have occurred since its formation ca. 10,000 years ago, timing of the modifications, and their biological consequences. Here, we have addressed these issues by microarray-based transcriptome analysis.

first: Bao

last: Liu

last: Qi

first: Huankun

first: Bo

last: Zhu


title: Gene expression profiling in response to radiation treatment in breast cancer

status: Public on Nov 02 2015

city: Durham

first: Wei

last: Chen

address: 101 Science Drive

department: Center for Genomic and Computational Biology

institute: Duke University


title: Gene expression profiling in response to radiation treatment in breast cancer [cell lines]

status: Public on Oct 31 2015

summary: Introduction: Breast radiotherapy is currently “one size fits all” regardless of breast cancer subtype (eg. luminal, basal). However, recent clinical data suggests that radiation response may vary significantly among subtypes.  Therefore, current practice leads to over- or under-treatment of women whose tumors are more or less radiation responsive.  We hypothesized that this clinical variability may be due, in part, to differences in cellular radiation response. Methods: We exposed 16 biologically-diverse breast tumor cell lines to 0 or 5GY radiation. Microarray analysis was performed on RNA harvested from those cell lines.  Samples were run in triplicate. Following quality assessment, differential gene expression analysis was performed using a two-way multiplicative linear mixed-effects model.  A candidate radiation response biomarkers with  biologically plausible role in radiation response, were identified and confirmed at the RNA and protein level with qPCR and Western blotting assays.  Induction in human breast tumors was confirmed in 32 patients with paired pre- and post-radiation tumor samples using IHC and microarray analysis.  Quantification of  protein was performed in a blinded manner and included positive and negative controls.

overall_design: The objective of our study was to identify genomic determinants of radiation sensitivity using clinical samples as well as breast tumor cell lines. In order to identify differences in the radiation response gene expression profiles of specific breast cancer subtypes, we exposed 16 biologically-diverse breast tumor cell lines to 0 or 5GY radiation. Microarray analysis was performed on RNA harvested from those cell lines.  Samples were run in triplicate. Following quality assessment, differential gene expression analysis was performed using a two-way multiplicative linear mixed-effects model.  Candidate radiation response biomarker with a biologically plausible role in radiation response, were identified and confirmed at the RNA and protein level with qPCR and Western blotting assays.  Induction of the genes of interest were further evaluated and confirmed in human breast tumors in 32 breast cancer patients with paired pre- and post-radiation tumor samples using IHC and microarray analysis assays.

first: Janet

last: Horton

first: Mark

last: Dewhirst

first: Joseph

last: Geradts

first: Diane

last: Fels

first: Yingchun

last: Zhou

first: Chenting

last: Lee

first: Sharareh

last: Siamakpour-Reihani

first: Kathleen

last: Ashcraft

first: Jeff

last: Groth

first: Hsiu-Ni

last: Kung

first: Ashley

last: Chi


title: Expression data from NSC11, 0923, and GBMJ1 polysome-bound RNA and total RNA

status: Public on Oct 16 2015

first: Philip

last: Tofilon

state: Maryland

address: 10 Center Drive-MSC 1002

department: Radiation Oncology

institute: NCI

summary:
Defining radioresponse using the translatome and the transcriptome to identify functional consequences of radiation.
We used microarrays to detail the changes in glioblastoma stem-like cells (GSCs) in both the translatome and transcriptome after irradiation.

overall_design: GBM stem-like cells were grown in monolayer and irradiated with 2Gy. Cells were collected 1h or 6h after irradiation (IR).

first: Kevin

last: Camphausen

first: Amy

last: Wahba


title: Depletion of the Chromatin Remodeler CHD4 Sensitizes AML Blasts to Genotoxic Agents and Reduces Tumor Formation

status: Public on Oct 01 2015

first: Catherine

last: Dumur

summary:
Depletion of CHD4 sensitizes AML cells but not normal CD34+ progenitors to genotoxic agents by relaxing chromatin and impairing DSB repair.
Depletion of CHD4 modulates expression of AML cell genes that regulate tumor formation in vivo and colony formation in vitro.

overall_design: To investigate the effect of CHD4 depletion on the overall chromatin structure and transcriptome of AML cells by integration of a CHD4-targeting shRNA into U937 and MV4-11 cells, compared to scramble shRNA integration. Biological triplicates for each cell line, including scramble shRNA controls, were run on microarrays.

first: Gordon

last: Ginder

first: Justin

last: Sperlazza


title: Blood transcriptomics of drug-naïve sporadic Parkinson’s disease patients

status: Public on Oct 29 2015

city: Trieste

first: Paola

last: Roncaglia

state: TS

address: via Bonomea 265

department: Neurobiology

institute: SISSA/ISAS (International School for Advanced Studies)

summary: Parkinson's disease (PD) is a chronic progressive neurodegenerative disorder that is clinically defined in terms of motor symptoms. These are preceded by prodromal non-motor manifestations that prove the systemic nature of the disease. Identifying genes and pathways altered in living patients provide new information on the diagnosis and pathogenesis of sporadic PD. We study changes in gene expression in the blood of 40 sporadic PD patients and 20 healthy controls (“Discovery set”) by taking advantage of the Affymetrix platform. Patients were at the onset of motor symptoms and before initiating any pharmacological treatment. By applying Ranking-Principal Component Analysis, PUMA and Significance Analysis of Microarrays, gene expression profiling discriminates patients from healthy controls and identifies differentially expressed genes in blood. The majority of these are also present in dopaminergic neurons of the Substantia Nigra, the key site of neurodegeneration. Together with neuronal apoptosis, lymphocyte activation and mitochondrial dysfunction, already found in previous analysis of PD blood and post-mortem brains, we unveiled transcriptome changes enriched in biological terms related to epigenetic modifications including chromatin remodeling and methylation. Candidate transcripts were validated by RT-qPCR in an independent cohort of 12 patients and controls (“Validation set”). Our data support the use of blood transcriptomics to study neurodegenerative diseases. It identifies changes in crucial components of chromatin remodeling and methylation machineries as early events in sporadic PD suggesting epigenetics as target for therapeutic intervention.

overall_design:
Analyzed samples include blood samples from 40 PD patients and 20 healthy controls.

Of the original 60 samples, one (a control sample) did not pass the microarray hybridization quality controls and was excluded from further analyses. All results of bioinformatics analyses shown in this study refer to this set of 59 samples (reported here).


title: Identification of selective lead compounds for treatment of high-ploidy breast cancer

status: Public on Oct 03 2015

city: Madison

first: Mark

last: Burkard

state: WI

address: 1111 Highland Ave.

department: Medicine

institute: UW-Madison

summary: Increased ploidy is common in tumors but treatments for tumors with excess chromosome sets are not available.  Here, we characterize high-ploidy breast cancers and identify potential anticancer compounds selective for the high-ploidy state.  Among 354 human breast cancers, 10% have mean chromosome copy number exceeding 3, and this is most common in triple negative and HER2-positive types.  Women with high-ploidy breast cancers have higher risk of recurrence and death in two patient cohorts, demonstrating that it represents an important group for improved treatment.  Because high-ploidy cancers are aneuploid, rather than triploid or tetraploid, we devised a two-step screen to identify selective compounds.  The screen was designed to assure both external validity on diverse karyotypic backgrounds and specificity for high-ploidy cell types.  This screen identified novel therapies specific to high-ploidy cells.  First, we discovered 8-azaguanine, an antimetabolite that is activated by hypoxanthine phosphoribosyltransferase (HPRT), suggesting an elevated gene-dosage of HPRT in high-ploidy tumors can control sensitivity to this drug.  Second, we discovered a novel compound, 2,3-Diphenylbenzo[g]quinoxaline-5,10-dione (DPBQ).  DPBQ activates p53 and triggers apoptosis in a polyploid-specific manner, but does not inhibit topoisomerase or bind DNA.  Mechanistic analysis demonstrates that DPBQ elicits a hypoxia gene signature and its effect is replicated, in part, by enhancing oxidative stress.  Structure-function analysis defines the core benzo[g]quinoxaline-5,10 dione as being necessary for the polyploid-specific effects of DPBQ.  We conclude that polyploid breast cancers represent a high-risk subgroup and that DPBQ provides a functional core to develop polyploid-selective therapy.

overall_design:
Expression data from MCF7s +/- DPBQ
We used microarrays to evaluate the effect of DPBQ on gene expression
MCF7 cells were treated with or without DPBQ for 6 hours for RNA extraction and hybridization on Affymetrix microarrays

first: Amber

last: Lasek


title: Early seed development in wheat under control and drought stress

status: Public on Sep 15 2015

city: Gainesville

last: Begcy

state: Florida

address: 1535 Fifield Hall

institute: University of Florida

summary:
To better undersand the effects of drought stress on wheat developing seeds, the transcription profile of early developing wheat seeds under control and drought stress conditions were comparatively analyzed by using the Affymetrix wheat geneChip.
Drought stress is a major yield-limiting factor for wheat. Wheat yields are particularly sensitive to drought stress during reproductive development. Early seed development stage is an important determinant of seed size, one of the yield components. We specifically examined the impact of drought stress imposed during postzygotic early seed development in wheat. We imposed a short-term drought stress on plants with day-old seeds and observed that even a short-duration drought stress significantly reduced the size of developing seeds as well as mature seeds. Drought stress delayed the developmental transition from syncytial to cellularized stage of endosperm. Coincident with reduced seed size and delayed endosperm development, a subset of genes associated with cytoskeleton organization was misregulated in developing seeds under drought-stressed. Several genes linked to hormone pathways were also differentially regulated in response to drought stress in early seeds. Notably, drought stress strongly repressed the expression of wheat storage protein genes such as gliadins, glutenins and avenins as early as 3 days after pollination. Our results provide new insights on how some of the early seed developmental events are impacted by water stress, and the underlying molecular pathways that can possibly impact both grain size and quality in wheat.

overall_design:
Winter wheat cultivar Redland, PI 502907 (Triticum aestivum L.) was used for this study. Seedlings were vernalized at 4°C for 6 weeks and then transplanted to a one gallon pot of soil-sand mixture (3:1, v/v) and grown in a growth chamber under the following conditions: relative humidity, 50–70%; 16-h light/8-h dark photoperiod; 21°C daytime temperature and 18°C nights. Plants were watered regularly twice daily at the rate of 100ml/ per pot. Because, wheat has an asynchronous fertilization pattern for ovlues in the inflorescence, each floret needs to be specifically marked for timing the fertilization and stress induction. After spikes developed, unfertilized ovules were monitored and observed for the fertilization process. Closed wheat spikes with anthers outside were marked as fertilized. Drought stress was imposed 24h after the fertilization (HAF). Drought stress treatment was initiated by discontinuing watering on the drought treatment plants while control plants were regularly watered twice daily. Stress treatment was applied at 48 HAF and relieved at 96 HAF.
The microarray study focuses on 24 HAF to 72 HAF in control and drought stress conditions.  We started to impose drought stress 24HAF.

first: Harkamal

last: Walia


title: Expression data from glucocorticoid-treated acute lymphoblastic leukemia cell line, RS4;11

city: Boston

first: Jennifer

middle: Nan-Wah

last: Wu

state: MA

address: 450 Brookline Ave.

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

summary:
Precise nucleosome positioning is an increasingly recognized feature of promoters and enhancers, reflecting complex contributions of DNA sequence, nucleosome positioning, histone modification and transcription factor binding to enhancer activity and regulation of gene expression. Changes in nucleosome position and occupancy, histone variants and modifications, and chromatin remodeling are also critical elements of dynamic transcriptional regulation, but poorly understood at enhancers. We investigated glucocorticoid receptor-associated (GR) nucleosome dynamics at enhancers in acute lymphoblastic leukemia. For the first time, we demonstrate functionally distinct modes of nucleosome remodeling upon chromatin binding by GR, which we term central, non-central, phased, and minimal. Central and non-central remodeling reflect nucleosome eviction by GR and cofactors, respectively. Phased remodeling involves nucleosome repositioning and is associated with rapidly activated enhancers and induction of gene expression. Minimal remodeling sites initially have low levels of enhancerassociated histone modification, but the majority of these regions gain H3K4me2 or H3K27Ac to become de novo enhancers. Minimal remodeling regions are associated with gene ontologies specific to decreased B cell number and mTOR inhibition and may make unique contributions to glucocorticoid-induced leukemia cell death. Our findings form a novel framework for understanding the dynamic interplay between transcription factor binding, nucleosome remodeling, enhancer function, and gene expression in the leukemia response to glucocorticoids.
We used microarrays to measure changes in gene expression following treatment of cells with dexamethasone for 0, 8, or 24 hours.

overall_design: RS4;11 acute lymphoblastic leukemia cells were first starved of hormone exposure for 48 hours, then treated with 10 nM dexamethasone for 0, 8, or 24 hours.  RNA was extracted and hybridized on Affymetrix microarrays.

first: Luca

last: Pinello

first: Elinor

last: Yissachar

first: Jonathan

last: Wischhusen

first: Guo-Cheng

last: Yuan

first: Charles

last: Roberts


title: CD39 expression identifies terminally exhausted CD8+ T cells

status: Public on Sep 08 2015

first: Jernej

last: Godec

address: 44 Binney Street

summary: Exhausted T cells express multiple co-inhibitory molecules that impair their function and limit immunity to chronic viral infection. Defining novel markers of exhaustion is important both for identifying and potentially reversing T cell exhaustion. Herein, we show that the ectonucleotidse CD39 is a marker of exhausted CD8+ T cells. CD8+ T cells specific for HCV or HIV express high levels of CD39, but those specific for EBV and CMV do not. CD39 expressed by CD8+ T cells in chronic infection is enzymatically active, co-expressed with PD-1, marks cells with a transcriptional signature of T cell exhaustion and correlates with viral load in HIV and HCV. In the mouse model of chronic Lymphocytic Choriomeningitis Virus infection, virus-specific CD8+ T cells contain a population of CD39high CD8+ T cells that is absent in functional memory cells elicited by acute infection. This CD39high CD8+ T cell population is enriched for cells with the phenotypic and functional profile of terminal exhaustion. These findings provide a new marker of T cell exhaustion, and implicate the purinergic pathway in the regulation of T cell exhaustion.

overall_design: CD8+ T cells from subjects with HCV infection were sorted and pelleted and re-suspended in TRIzol (Invitrogen). RNA extraction was performed using the RNAdvance Tissue Isolation kit (Agencourt). Concentrations of total RNA were determined with a Nanodrop spectrophotometer or Ribogreen RNA quantification kits (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies). Total RNA was amplified with the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer's instructions. After fragmentation and biotinylation, cDNA was hybridized to HG-U133A 2.0 microarrays (Affymetrix).

first: Prakash

middle: K

last: Gupta

first: W

last: Haining


title: Transcriptomic analysis of Clostridium acetobutylicum biofilm cells in repeated-batch fermentation

status: Public on Sep 09 2015

city: Nanjing

first: Dong

last: Liu

state: Jiangsu

address: No. 30, Puzhu South Road

department: National Engineering Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering

institute: Nanjing Tech University

summary: Previously, we performed DNA array-based transcriptomic analysis of Clostridium acetobutylicum biofilm adsorbed onto fibrous matrix in batch fermentation. Here, to further shed light on the transcriptomic modulation of maturing Clostridium acetobutylicum biofilm, we performed the DNA array-based transcriptomic analysis in repeated-batch fermentation. Significant time course changes in expression levels were observed for the genes involved in amino acid metabolism, oligopeptide ABC transporter, nitrogen fixation, and various other processes.

platform_organism:
Arthrobacter sp.
Clostridium acetobutylicum DSM 1731

overall_design: Repeated-batch fermentation was carried out in 2-L stainless steel columns packed with 40 g of cotton towel （cut into pieces，approximately 3 cm × 5 cm)  containing 1.5 L of P2 medium. Medium circulation rate was maintained at 35 mL/min via a peristaltic pump and the temperature was controlled at 37°C.  Fermentation broth was replaced with fresh P2 medium every 12 h. Samples were withdrawn at 6 h after the medium replacement at predetermined interval, except for the last 3 samples. The last 3 samples were withdrawn at 12 h, 15 h, and 17 h after the medium replacement, respectively, to study the transcriptomic response to the adverse condition at the end of fermentation. A total of 8 samples were withdrawn over a period of 7 days, and time course gene expression profiles were studied.

first: Jiahui

last: Xu

first: Yanyan

last: Wang

first: Yong

last: Chen

first: Hanjie

last: Ying


title: Expression data from Vulvar, Cervical, Endometrial Carcinoma tissue

status: Public on Jul 26 2015

first: Prokopios Alexandros

last: Polyzos

address: 413 E 69th St

institute: Weill Cornell Medicine

summary:
A growing number of studies on gynecological cancers (GCs) have revealed potential gene markers associated either with the pathogenesis and progression of the disease on representing putative targets for therapy and treatment of cervical (CC), endometrial (EC) and vulvar cancer (VC). However, quite a little overlap is found between these data. In this study we combined data from the three GCs integrating gene expression profile analysis.
The meta-analysis including our results and data emerge from other available studies on gynecological malignancies and other cancer types, revealed common properties among them including deregulation of cell cycle, immune response, antiviral response and apoptosis.

overall_design: Total RNA was extracted from physiological and cancer patients from cervix, endometrium and vulvar tissue and was hybridized on Affymetrix HG133_A_2.0 microarray chips corresponding to more than 12.000 uniquely represented genes. A total of 35 samples were used to identify potential biomarkers and signatures in each type of cancer.

first: Alexander

first: Nicholas

last: Anagnou

first: Kaliopi

last: Pappa


title: Expression data from wheat cultivar TAM 107 flag leaf

status: Public on Aug 13 2015

first: zhenshan

last: liu

address: NO.2 Yuanmingyuan Xi Road,Haidian District

institute: China Agricultural University

summary: We used microarray to study the transcriptome response of wheat flag leaves to heat stress (40℃)

overall_design: In order to study the transcriptome response of wheat flag leaf to heat stress, wheat cultivar ‘TAM 107’ plants were subjected to heat stress (40℃). After 1 hour of stress, flag leaves were sampled from both stressed and control plants and were used for microarray analysis.

first: Zhenshan

first: Huiru

last: Peng

first: Mingming

last: Xin


title: Expression data from HepG2 (liver hepatocellular cells)

status: Public on Jul 31 2015

city: Napoli

first: Giancarlo

last: Chesi

address: via Castellino 111

institute: Tigem

summary:
In order to identify the effects of ATP7B H1069Q overexpression on the liver transcriptome, we performed Affymetrix GeneChip hybridization experiments.
Transcriptome analysis of the hepatocytes overexpressing ATP7B H1069Q, compared with hepatocytes overexpressing ATP7B WT.

overall_design: For the analysis on the hepatocytes overexpressing ATP7B H1069Q, total RNA was extracted from HepG2 cells; RNA extracted from hepatocytes overexpressing ATP7B WT was used as control.

first: Simona

last: Iacobacci

first: Roman

last: Polishchuk


title: RNA expression in MDA-MB-231 cells treated for 24h with SAHA, Pargyline, or both [HG-U133A_2]

status: Public on Sep 04 2015

city: Pittsburgh

first: Yi

last: Huang

state: Pennsylvania

address: 204 Craft Ave

department: Pharmacology & Chemical Biology

institute: University of Pittsburgh Cancer Institute

summary: Abnormal activities of histone lysine demethylases (KDMs) and lysine deacetylases (HDACs) are associated with aberrant gene expression in breast cancer development. However, the precise molecular mechanisms underlying the crosstalk between KDMs and HDACs in chromatin remodeling and regulation of gene transcription are still elusive. In this study, we showed that treatment of human breast cancer cells with inhibitors targeting the zinc cofactor dependent class I/II HDACs, but not NAD+ dependent class III HDACs, led to significant increase of H3K4me2 which is a specific substrate of histone lysine-specific demethylase 1 (LSD1) and a key chromatin mark promoting transcriptional activation. We also demonstrated that inhibition of LSD1 activity by a pharmacological inhibitor, pargyline, or siRNA resulted in increased acetylation of H3K9 (AcH3K9). However, siRNA knockdown of LSD2, a homolog of LSD1, failed to alter the level of AcH3K9, suggesting that LSD2 activity may not be functionally connected with HDAC activity. Combined treatment with LSD1 and HDAC inhibitors resulted in enhanced levels of H3K4me2 and AcH3K9, and exhibited synergistic growth inhibition of breast cancer cells. Finally, microarray screening identified a unique subset of genes whose expression was significantly changed by combination treatment with inhibitors of LSD1 and HDAC. Our  study suggests that LSD1 intimately interacts with histone deacetylases in human breast cancer cells. Inhibition of histone demethylation and deacetylation exhibits cooperation and synergy in regulating gene expression and growth inhibition, and may represent a promising and novel approach for epigenetic therapy of breast cancer.

overall_design: Twelve samples were subject to microarray anaylsis:  3 biological replicates were treated for 24h with 1)DMSO, 2) 5uM SAHA (suberanilohydroxamic acid), 3) 2.5mM Pargyline or 4) 5uM SAHA + 2.5mM Pargyline.

first: Shauna

last: Vasilatos


title: Mcl-1 is a key determinant of breast cancer cell survival [expression]

status: Public on Aug 07 2015

city: North Chicago

first: Xin

last: Lu

state: IL

address: 1 North Waukegan Rd

department: Oncology Discovery

institute: Abbvie

summary: mRNA expression profile of cultured Breast Cancer cell line measured by Affymetrix microarrays

overall_design: Whole genome expression profile of 32 breast cancer cell lines were analyzed with 3 biological replicates.

first: Yu

last: Xiao

first: Darren

middle: C

last: Phillips


title: Expression data from cyclohexamide treated Human Foreskin Fibroblasts (HFFs) infected with type I Toxoplasma gondii and stimulated with interferon gamma.

status: Public on Aug 01 2015

city: Cambridge

first: Emily

last: Rosowski

address: 77 Massachusetts Ave, 68-258d

department: Biology

institute: MIT

summary:
Pre-infection with Toxoplasma parasites inhibits induction of an interferon gamma responsive gene expression program.  In this study we aimed to determine what role host negative regulatory proteins that are induced by Toxoplasma infection, such as SOCS-1, have in this inhibition.
We used Affymetrix microarrays to analyze host cell transcription after pre-treatment with the protein synthesis inhibitor cyclohexamide (CHX), Toxoplasma infection, and subsequent interferon-gamma stimulation.

overall_design: Human foreskin fibroblasts (HFFs) were left untreated or treated with CHX for 40min.  Cells were infected, or not, with type I (RH) Toxoplasma parasites, for one hour, and subsequently stimulated with human IFN-γ for one hour.  Total RNA was isolated and hybridized to Affymetrix Human U133A 2.0 gene chips.

first: Jeroen

last: Saeij


title: The Nlrp12 inflammasome negatively regulates NOD2-mediated adjuvanticity, endotoxic shock and host defence afforded by an immunomodulatory muropeptide.

status: Public on Jul 25 2015

city: Lille

first: Mathias

last: Chamaillard

address: 1, rue Prof A. Calmette

department: Center for Infection and Immunity of Lille

country: France

institute: Inserm

summary: Transcriptional profiling of intestinal response to Citrobacter rodentium in wild-type and Nlrp12-deficient mice

overall_design: Four-conditions experiment, Nlrp12-deficient mouse infected by Citrobacter rodentium at day 7 versus non-infected Nlrp12-deficient mice with two biologicals replicates , Wild-type mouse infected by Citrobacter rodentium at day 7 versus non-infected Wild-type mice with two biologicals replicates and Nlrp12-deficient mouse infected by Citrobacter rodentium versus Control mouse infected by Citrobacter rodentium at 2 differents times ( day 0 and post infection at day 7 )  with three biologicals replicates

first: Myriam

last: Delacre

first: Nadine

last: Waldschmitt

first: Sylvain

last: Normand

first: Ludovic

last: Huot

first: David

last: Hot


title: Gene expression profiles of induced pluripotent stem cells (iPSCs) and skin fibroblasts from orangutans

status: Public on Jun 10 2015

city: Los Angeles

first: Joseph

middle: Gerard

last: Hacia

state: CA

address: 2250 Alcazar Street, IGM 261

department: Biochemistry and Molecular Biology

institute: University of Southern California

summary:
Orangutans are an endangered species whose natural habitats are restricted to the Southeast Asian islands of Borneo and Sumatra. For potential species conservation and functional genomics studies, we derived induced pluripotent stem cells (iPSCs) from cryopreserved skin fibroblasts obtained from captive orangutans.
We report the gene expression profiles of iPSCs and skin fibroblasts derived from orangtuans.

overall_design: The overall goal was to evaluate gene expression biomarkers of pluripotency in iPSCs and skin fibroblasts  derived from PBD-ZSD patients and healthy controls. Dermal fibroblast cultures from 2 orangutans were reprogrammed into iPSCs by transfection with retroviruses designed to express the human OCT4, SOX2, KLF4 and c-MYC cDNA.  Fibroblasts and iPSCs were cultured in 1:1 ratio of DMEM:F12 medium supplemented with 20% KOSR (knock-out serum replacement) at 37°C with 5% CO2 until confluence for RNA extraction. The overall goal was to evaluate gene expression biomarkers of pluripotency in iPSCs and original fibroblast cultures.

first: Xiao-Ming

last: Wang


title: Mcl-1 is a key determinant of breast cancer cell survival

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

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

overall_design: Refer to individual Series


title: Gene based expression changes in glioblastoma cells after downregulation of MPS1 kinase

status: Public on Jun 15 2015

city: Bethesda

first: Uma

middle: T

last: Shankavaram

state: MD

address: 9000 Rockville Pike

department: NCI

institute: NIH

summary: Gene expression changes were analyzed in U251 GBM cells after downregulation of MPS1 by RNA interference technology at different time points

overall_design: Microarray analysis was used to compare the mRNA expression profile of siMPS1 silenced U251 cells compared to siNegative (siNeg) and untransfected (Control) cells at 6, 24 and 48 hours post tranfection

first: A

last: Tandle

first: U


title: Secondary siRNAs from Medicago NB-LRRs modulated via miRNA-target interactions and their abundances

status: Public on Jun 20 2015

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

type: Non-coding RNA profiling by high throughput sequencing

type: Expression profiling by high throughput sequencing

summary: Small RNAs are a class of noncoding RNAs which are of great importance in gene expression regulatory networks. Different families of small RNAs are generated via distinct biogenesis pathways. One such family specific to plants is that of phased, secondary siRNAs (phasiRNAs); these require RDR6, DCL4, and microRNA (miRNA) trigger for their biogenesis. Protein-encoding genes are an important source of phasiRNAs. The model legume Medicago truncatula generates phasiRNAs from many PHAS loci, and we aimed to investigate their biogenesis and mechanism by which miRNAs trigger these molecules. We modulated miRNA abundances in transgenic tissues showing that the abundance of phasiRNAs correlates with the levels of both miRNA triggers and the target, precursor transcripts. We identified sets of phasiRNAs or PHAS loci that predominantly and substantially increase in response to miRNA overexpression. In the process of validating targets from miRNA overexpression tissues, we found that in the miRNA-mRNA target pairing, the 3’ terminal nucleotide (the 22nd position), but not the 10th position, is important for phasiRNA production. Mutating the single 3’ terminal nucleotide dramatically diminishes phasiRNA production. Ectopic expression of Medicago NB-LRR-targeting miRNAs in Arabidopsis showed that only a few NB-LRRs are capable of phasiRNA production; our data indicate that this is due to target inaccessibility determined by sequences flanking target sites. We propose that target accessibility is an important component of miRNA-target interactions that could be utilized in target prediction, and the evolution of mRNA sequences flanking miRNA target sites may be impacted.

sample_organism:
Arabidopsis thaliana
Medicago truncatula

overall_design: Genome-wide small RNA profiling was done by Illumina TruSeq sample preparation followed by high-throughput sequencing with an Illumina HiSeq 2000 instrument.

first: Qili

last: Fei