title: KCa3.1 depletion effect on hepatocellular carcinoma cell line Huh7

status: Public on Jun 23 2018

city: Hangzhou

first: Yehui

last: Du

state: Zhejiang

address: 79# Qinchun Road

institute: Zhejiang University

summary:
Analysis of Huh7 hepatocellular carcinoma (HCC) cells depleted for potassium channel KCa3.1, the intermediate conductance calcium-activated potassium channel. Result provide insight into the role of KCa3.1 in the carcinogenesis of HCC.
We used microarrays to detail the gene expression differences between KCa3.1 knockdown and negative control in Huh7 HCC cells.

overall_design: A human gene expression chip was applied to assess the gene transcriptional profiles of KCa3.1 silenced Huh7 cells and Huh7 control cells.

first: Penghong

last: Song


title: Molecular profiling of ovarian carcinoma platinum-sensitive and -resistant cell lines (gene expression)

status: Public on Jun 26 2018

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

summary: Resistance to platinum compounds represents a major obstacle to the cure of ovarian carcinoma. The molecular profiling of drug-sensitive and drug-resistant cells may be helpful to clarify if altered gene expression can contribute to the drug-resistant phenotype. The expression pattern of three ovarian carcinoma cell lines was examined. The analysis revealed the modulation of several genes in the two platinum-resistant cell lines as compared to parental platinum-sensitive cells. The integration of the information obtained through gene expression analysis may be useful to clarify the specific molecular alterations of factors and pathway favouring survival of tumor cells.

overall_design: To examine gene expression changes in platinum-sensitive cells versus platinum-resistant cells, we used three ovarian carcinoma cell lines: the parental cisplatin-sensitive IGROV-1 cell line, the platinum-resistant variants IGROV-1/Pt1, generated by exposure of parental cells to cisplatin and IGROV-1/OHP, obtained by exposure of parental cells to cisplatin. Three independent samples for each cell line were prepared. Exponentially growing cells were harvested using trypsin and counted. Cells were centrifuged and pellets (10 million cells/sample) were immediately frozen in liquid nitrogen. RNA was isolates and microarrays were run. Overall, nine samples were analysed consisting of three biological replicates for each cell line.

first: Laura

last: Gatti

first: Noemi

last: Arrighetti

first: Giacomo

last: Cossa

first: Paola

last: Perego


title: The influence of the Chelidonium majus extract NSC-631570 on gene expression in the head and neck carcinoma cell line FaDu

status: Public on Jun 16 2018

city: Wuerzburg

first: Marianne

last: Schmidt

state: Outside U.S. & Canada

country: Germany

institute: University of Wuerzburg, Dept. of Otorhinolaryngology

summary: It has been shown that the Chelidonium majus extract NSC-631570 has growth and invasion inhibiting properties on head and neck carcinoma cell lines. The Affymetrix PrimeView array was used to gain a first view on the influence of NSC-631570 on gene expression of head and neck cancer cells.

overall_design: FaDu cells were grown for 48 hrs with or without the EC50 dose of NSC-631570.

first: Ruth

last: Herrmann


title: gene-expression profiling between UBE2S knock down A375 cells and control A375 cells

status: Public on Jun 19 2018

first: Ping

last: Wang

address: 38 West Lake Avenue

country: China

institute: Affiliated 3rd Hospital of Hangzhou

summary: investigate the gene expression change between UBE2S konck down A375 cells mediated by Lentivirus and control A375 cells.

overall_design: In the study, melanoma A375 cell line was selected and transfected UBE2S shRNA mediated by Lentivirus. UBE2S knock down A375 cells and control A375 cells both in triplicate were assayed to acquire the expression profiles of a total of 49,395 probes.

first: Yong

last: Li


title: Prior activity of olfactory receptor neurons is required for proper sensory processing and behavior in Drosophila larvae

status: Public on Jun 21 2018

city: Seattle

first: Jay

last: Parrish

state: Washington

department: Department of Biology

country: USA

institute: University of Washington

type: Expression profiling by high throughput sequencing

summary: Animal responses to their environment rely on activation of sensory neurons by external stimuli. In many sensory systems, however, neurons display basal activity prior to the external stimuli. This prior activity is thought to modulate neural functions, yet its impact on animal behavior remains elusive. Here, we reveal a potential role for prior activity in olfactory receptor neurons (ORNs) in shaping larval olfactory behavior. We show that prior activity in larval ORNs is mediated by the olfactory receptor complex (OR complex). Mutations of Orco, an odorant co-receptor required for OR complex function, cause reduced attractive behavior in response to optogenetic activation of ORNs. Calcium imaging reveals that Orco mutant ORNs fully respond to optogenetic stimulation but exhibit altered temporal patterns of neural responses. These findings together suggest a critical role for prior activity in information processing upon ORN activation in Drosophila larvae, which in turn contributes to olfactory behavior control.

overall_design: Four control and five orco mutant samples with 20 dorsal organs each were isolated and subjected to mRNA-Seq analysis

first: Nao

last: Utashiro

first: Claire

middle: R

last: Williams

middle: Z

first: Kazuo

last: Emoto


title: Exosome-transmitted RVT1 from reactive astrocytes promotes recurrence glioblastoma proliferation

status: Public on Jun 08 2018

city: nanjing

first: chen

last: wanghao

state: jiangsu

address: Ding Jiaqiao 87th

department: School of Medicine

institute: southeast university

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

summary: Glioblastoma (GBM) remains among the most lethal brain tumors despite improvements in treatment. Surgical resection is a universal component of glioma therapy. However, the mechanism underlying postoperative recurrence remains a challenge due to limited information regarding the changes that occur in the postoperative microenvironment. Here, we show that a subtype of proinflammatory reactive astrocytes designated is induced by inflammatory cytokines or injury. We show that reactive astrocytes can secrete the long noncoding RNA (lncRNA) LOC646762 to promotes recurrence glioblastoma proliferation in an exosome-dependent manner.We firstly named this reactive astrocyte associated lnRNA as “lnc-RVT1”.

overall_design: The lncRNA expression profiles of glioblastoma, corresponding recurrence tumor tissues and astrocytes acquired from the peripheral area of edema in tumor tissues form three patients were studied by microarray.

first: Wanghao

last: Chen

first: Qiaoyu

first: Lukui


title: ChIP-seq data of QstR transcriptional regulator from Vibrio cholerae

city: Lausanne

first: Melanie

last: Blokesch

address: Station 19 / EPFL-SV-UPBLO

department: School of Life Sciences

country: Switzerland

institute: Swiss Federal Institute of Technology Lausanne (EPFL)

type: Genome binding/occupancy profiling by high throughput sequencing

summary: In this study, we studied the binding of the transcriptional regulator QstR to DNA through chromatin immunoprecipitation coupled with deep sequencing (ChIP-seq).

overall_design:
Comparison between ChIP samples derived from qstR-positive or qstR-negative V. cholerae strains.
Please note that the processed data *peaks.tsv was generated from both replicates and is linked as the corresponding 'replicate 1' sample supplementary file.


title: Cell culture-based model system for FOXO3 activity

status: Public on Jun 06 2018

city: Eindhoven

first: Henk

last: van Ooijen

address: High Tech Campus 11

department: Precision & Decentralized Diagnostics

country: Netherlands

institute: Philips Research

summary: MCF7 and MDA-MB-231 breast cancer cell lines were cultured in DMEM-F12 containing 10% FBS (Lonza) 100U/ml penicillin and 100 µg/ml streptomycin (Lonza). Transfecting third generation packaging vectors using Poly-ethylenimine into HEK293T cells generated lentiviral particles (17). MCF7 and MDA-MB-231 cells were stably transduced with lentivirus containing pINDUCER20-FOXO3.A3, allowing doxycycline induced expression of constitutively active FOXO3 (FOXO3.A3). Cells were treated with 20% FBS or 10 µM PI3K inhibitor LY294002 (Selleckchem) for 16 hours to activate and inactivate the endogenous PI3K pathway, respectively. FOXO3.A3 expression was induced by 16 hours treatment with 10 ng/ml doxycycline.

overall_design: 3 biological replicates per condition; each experiment contained at least a control and a stimulated condition

first: Boudewijn

middle: M

last: Burgering

first: Marten

last: Hornsveld

first: Anja

last: van de Stolpe


title: Amplification-based expression data show bias towards long gene misregulation in synaptic disorders

status: Public on Jun 05 2018

city: Houston,

first: Hari Krishna

last: Yalamanchili

state: TX

address: 1250 Moursund St #1125,

institute: Baylor College of Medicine

summary: Several recent studies have suggested that genes that are over 100 kb in length are particularly likely to be misregulated in neurological diseases associated with synaptic dysfunction, such as autism, Fragile X syndrome, and Rett syndrome. These length-dependent transcriptional changes seem to be modest, but, given the low sensitivity of high-throughput transcriptome profiling technology, the statistical significance of these results needs to be reevaluated. Here we show that transcriptional changes reflected in microarray and RNA-Sequencing benchmark datasets from the SEQC Consortium show a bias toward genes of greater length, even in the comparison of technical replicates. We hypothesized that PCR amplification, which is used in both microarray and RNA-Seq technologies, could be introducing this bias. We found that, when the fold-change values are small, PCR amplification in microarray and RNA-Seq technologies does produce a bias toward longer genes; we found no similar bias with nCounter technology, which is not based on PCR amplification. We provide an approach to more rigorously assess length-dependent changes that begins with comparing randomized control samples to estimate baseline gene length dependency and evaluate the statistical significance of gene length regulation.

overall_design: We purchased Universal Human Reference RNA from Agilent Technologies, Inc., and Human Brain Reference RNA from Life Technologies, Inc. For the nCounter experiments, we used the same RNA sample types as SEQC. We assessed RNA purity and integrity with Bioanalyzer (Agilent Technologies, Inc.) prior to use in the nCounter assays. Sample preparation and analysis were done using an nCounter Prep Station 5s and an nCounter Digital Analyzer 5s.

first: Huda

middle: Y

last: Zoghbi

first: Zhandong

last: Liu

first: Amy

last: Pohodich

first: Ayush

middle: T

last: Raman

first: Hari

middle: K

first: Ying

middle: W

last: Wan


title: Enhanced susceptibility of cancer cells to oncolytic rhabdo-virotherapy by expression of Nodamura virus protein B2 as a suppressor of RNA interference

status: Public on Jun 01 2018

city: Ottawa

first: Adrian

last: Pelin

state: Ontario

address: 501 Smyth Rd.

country: Canada

institute: Ottawa Hospital Research Institute

summary:
We have evaluated the response of M14 cells to VSV virus expressing eGFP or insect virus B2 protein.
We find interferon related genes to be at higher levels when cells are infected with VSV-B2

overall_design: Monolayers of M14 cells were treated at an MOI of 0.1 for 24h with either VSV-eGFP or VSV-B2.

first: Donal

last: Bastin

first: Carolina

middle: S

last: Ilkow


title: Early lineage segregation of multipotent embryonic mammary gland progenitors [expression]

status: Public on Jun 04 2018

city: Bruxelles

first: Alexandra

last: Van Keymeulen

address: 808, route de Lennik CP602

department: IRIBHM

country: Belgium

institute: Université Libre de Bruxelles

summary:
The mammary gland (MG) is composed of basal cells (BCs) and luminal cells (LCs). While it is generally believed that MG arises from embryonic multipotent progenitors (EMPs), it remains unclear when lineage restriction occurs and what are the mechanisms responsible for the switch from multipotency to unipotency during MG morphogenesis. Here, we performed multicolor lineage tracing and assessed the fate of single embryonic progenitors during mouse MG development. We demonstrated the existence of a developmental switch from multipotency to unipotency during embryonic MG development. Molecular profiling and single cell RNA-seq revealed the hybrid gene expression of EMPs, and the gene trajectory and lineage segregation occurring during MG development. In situ characterization showed that one of the earliest signs of lineage segregation consists in the restricted expression of p63 in the future BCs. Sustained p63 expression during MG development promotes unipotent BC fate in EMPs. Altogether, this study identifies the timing and the mechanisms mediating the switch from multipotency to unipotency during MG development.
To understand the molecular mechanisms regulating multipotency during embryonic development, we isolated EMPs by FACS at E14, performed their transcriptional profiling by microarray and compared their transcriptome to adult BCs and LCs

overall_design: Embryonic CD49f Hi Lgr5Hi mammary cells from E14 Lgr5-IRES-GFP female embryos were FACS isolated and RNA was extracted before being hybridized to Affymetrix microarrays. The three biological replicates samples were a pool of all female embryos from one litter.

first: Aline

last: Wuidart

first: Cédric

last: Blanpain

first: Audrey

last: Brisebarre


title: Effect of Mycoplasma hyorhinis infection on H292 lung adenocarcinoma cells

city: Novosibirsk

first: Mariya

middle: Alexandrovna

last: Smetanina

address: 8 Lavrentiev Avenue

country: Russia

institute: Institute of Chemical Biology and Fundamental Medicine SB RAS

summary: Analysis of H292 cells infected with Mycoplasma hyorhinis. Mycoplasma infection reduces the cytotoxic effect of Nutlin3 on H292 cells. The results provide insight into molecular mechanisms underlying the response of H292 cells to Nutlin3.

overall_design: Gene expression profiling of total RNAs extracted from human non-small cell lung cancer H292 cells infected (2 samples) and uninfected (2 samples) with Mycoplasma hyorhinis.

middle: A


title: Jun O-GlcNAcylatSchwann cell O-GlcNAcylation promotes peripheral nerve remyelination via attenuation of the AP-1 transcription factor JUNion promotes peripheral nerve remyelination after nerve injury

city: st. Louis

first: sungsu

last: kim

address: 600 S. euclid ave

institute: washington university

summary: To uncover abnormally regulated genes in OGT-KO SCs, we performed gene expression profiling experiments using sciatic nerves from 1-month-old OGT-SCKO and wildtype mice.

overall_design: Gene expression was measured in three independent pools of mouse Sciatic nerves from littermate controls and OGT-SCKO mice at 1 month of age

first: Kim

last: Sungsu

first: Milbrandt

last: Jeffrey


title: miRNA Expression Profiles of Premalignant and Malignant Arsenic-Induced Skin Lesions

city: Louisville

first: J.

middle: Christopher

last: States

state: KY

address: 505 S. Hancock St., Rm 304

department: Department of Pharmacology & Toxicology

institute: University of Louisville

summary: Total RNA was purified from keratinocytes isolated from FFPE arsenic-induced skin lesion samples collected from individuals exposed to high concentrations of arsenic exceeding 50 ppb in drinking water in Murshidibad district of West Bengal, India.

overall_design: The ΔCt values of miRNAs measured from malignant were compared to those of premalignant lesions or  ΔCt values malignant lesions (BCC &SCC) were also compared to

first: Laila

last: Al-Eryani

first: Samantha

last: Jenkins

first: J

middle: C

first: Vanessa


title: Effect of everolimus on clear cell renal cell carcinoma (ccRCC) cell lines - parental and stem cells

status: Public on May 31 2018

city: Warsaw

first: Anna

middle: Justyna

last: Kornakiewicz

address: Ksiecia Trojdena 2a

country: Poland

institute: School of Molecular Medicine

summary:
The aim of this study was to compare effect of everolimus on growth of different renal cell carcinoma (RCC) populations and develop design for experiments to measure the early response of everolimus in clear cell RCC (ccRCC) cell lines including renal cancer stem cells.
Gene expression profiling using microarray was performed to determine the early response to everolimus after 3 days of treatment with optimizied concentration of drug  in  two ccRCC cell lines 1) parental clear cell renal cell carcinoma ccRCC-PCSC (HKPCSC -human parental kidney cancer stem cells) and  2) ccRCC-CSC - clear cell renal cell carcinoma -cancer stem cells (HKCSC - human kidney cancer stem cells).

overall_design: Two condition experiment: 1) everolimus (E) treated and 2) untreated; 2 cell lines; parental clear cell renal cell carcinoma ccRCC-PCSC (P)  and ccRCC-CSC - clear cell renal cell carcinoma -cancer stem cells (M). Biological replicates: 3, technical replicates 4

last: Czarnecka

first: Cezary

last: Szczylik


title: MITE insertion-dependent expression of CitRKD1 with a RWP-RK domain regulates somatic embryogenesis in citrus nucellar tissues

city: Shizuoka

first: Hiroshi

last: Fujii

state: Shizuoka

address: 485-6 Okitsunakacho, Shimizu

department: Division of Citrus Research

country: Japan

institute: Institute of Fruit Tree Science, NARO

summary:
Somatic embryogenesis in nucellar tissues is widely recognized to induce polyembryony in major citrus varieties such as sweet oranges, satsuma mandarins and lemons. This capability for apomixis is attractive in agricultural production systems using hybrid seeds, and many studies have been performed to elucidate the molecular mechanisms of various types of apomixis. To identify the gene responsible for somatic embryogenesis in citrus, a custom oligo-DNA microarray including predicted genes in the citrus polyembryonic locus was used to compare the expression profiles in reproductive tissues between monoembryonic and polyembryonic varieties. The full length of CitRKD1, which was identified as a candidate gene responsible for citrus somatic embryogenesis, was isolated from satsuma mandarin and its molecular function was investigated using transgenic ‘Hamlin’ sweet orange by antisense-overexpression.
The candidate gene CitRKD1, predominantly transcribed in reproductive tissues of polyembryonic varieties, is a member of the plant RWP-RK domain proteins. CitRKD1 of satsuma mandarin comprised two alleles (CitRKD1-mg1 and CitRKD1-mg2) at the polyembryonic locus controlling embryony type (mono/polyembryony) that were structurally divided into two types with or without a miniature inverted-repeat transposable element (MITE)-like insertion in the upstream region. CitRKD1-mg2 with the MITE insertion was the predominant transcript in flowers and young fruits where somatic embryogenesis of nucellar cells occurred. Loss of CitRKD1 function by antisense-overexpression abolished somatic embryogenesis in transgenic sweet orange and the transgenic T1 plants were confirmed to derive from zygotic embryos produced by self-pollination by DNA diagnosis. Genotyping PCR analysis of 95 citrus traditional and breeding varieties revealed that the CitRKD1 allele with the MITE insertion (polyembryonic allele) was dominant and major citrus varieties with the polyembryonic allele produced polyembryonic seeds.

sample_organism: (Citrus unshiu x Citrus sinensis) x Citrus reticulata

overall_design: To identify the gene responsible for somatic embryogenesis in citrus, a custom oligo-DNA microarray including predicted genes in the citrus polyembryonic locus was used to compare the expression profiles in reproductive tissues between ‘Kiyomi’ and ‘Harumi’ as materials for monoembryonic and polyembryonic varieties, respectively. Eight independent experiment performed at 15, 30, 45 and 60 DAF (Day After Flowering) using whole young fruits in each variety.

first: Takehiko

last: Shimada


title: Rictor/mTORC2 signaling has opposing functions in adult glioma and childhood SHH medulloblastoma

city: Washington DC

first: Yuan

last: Zhu

state: DC

address: 111 Michigan Ave NW

institute: Children's National Medical Center

summary:
Primary glioblastoma, representing over 90% of adult glioblastoma, develop rapidly without preexisting lower-grade glioma. We have generated a mouse model of primary glioblastoma driven by a single p53 mutation. These p53-mutant gliomas lose the syntenic region of human chromosome 10q, which is mapped to mouse chr19 and chr7. Loss of mouse chr19, containing Pten, activates PI3K/Akt signaling.
Rictor/mTORC2 deletion inhibits Akt signaling, causing a significant delay in p53-mutant driven glioma formation. Unexpectedly, Rictor/mTORC2 loss promotes p53-mutant driven medulloblastomas with unique features of pediatric SHH medulloblastoma. Mechanistically, Rictor/mTORC2 loss inhibits the generation of glioma precursor cells from neural stem/progenitor cells in the adult brain, while causing a delay in differentiation of granule cell precursors in the developing brain, a cell-of-origin of SHH medulloblastoma.

overall_design: In this study we generate mouse models with (1) p53 loss (2) p53 loss combined with gemline Nf1 mutation (3) a conditional cis-p53/Nf1 mutation. We profiled the resultant tumors as well as normal forebrain and cerebellum as controls.


title: Effects of FGFRL1 deficiency on oesophageal squamous cell carcinoma cells

city: Kyoto

first: Yoshinori

last: Takei

address: 29-46 Shimoadachicho Yoshida

department: Graduate school of pharmaceutical science

institute: Kyoto University

summary: Several genes were indicated as genes strongly affected by FGFRL1-deficiency, through expression profiling of a total of 25,000 genes in 2 wild type KYSE520 human oesphageal squamous cell carcinoma cells and 2 FGFRL1-deficient kYSE520 cells

overall_design: Two FGFRL1-deficient KYSE 520 cell lines, clone No. 15 and No. 21, were established from KYSE520 human oesphageal squamous cell carcinoma cells with the CRISPR-Cas9 method.  As control, a  cell line of which FGFRL1 gene was intact, clone No. 1, was also established from KYSE520 cells treated with CRISPR-Cas9 method

first: Takafumi

last: Matsumura

first: Kazuaki

last: Watanabe

first: Tetsuo

last: Sudo

first: Kazuharu

last: Shimizu

first: Yutaka


title: Cerebellar gene expression from Mecp2-null and WT mice [Nanostring data set]

city: Cambridge

first: Ayush

last: Raman

state: MA

address: 75 Ames St

department: Epigenomics Program

institute: Broad Institute of MIT and Harvard

summary: Several recent studies have suggested that genes that are longer than 100 kb are more likely to be misregulated in neurological diseases associated with synaptic dysfunction, such as autism and Rett syndrome. These length-dependent transcriptional changes are modest in Mecp2 mutant samples, but, given the low sensitivity of high-throughput transcriptome profiling technology, the statistical significance of these results needs to be re-evaluated. Here, we show that the apparent length-dependent trends previously observed in MeCP2 microarray and RNA-Sequencing datasets, particularly in genes with low-fold changes, disappeared when compared to randomized control samples. As we found no similar bias with Nanostring technology, this bias seems to be particular to PCR amplification-based platforms. Transcriptional alterations with large fold-change values, however, can reveal an authentic long gene bias. Discriminating authentic from artefactual length-dependent trends requires establishing a baseline from randomized control samples.

overall_design: Nanostring cerebellum dataset

first: Huda

last: Zoghbi

first: Amy

middle: E

last: Pohodich

first: Laura

last: Lavery

first: Ying-Wooi

last: Wang

first: Zhandong

last: Liu


title: Expression data from GT1-7 cells after treatment with GnRH

city: Okinawa

first: Sayomi

last: Higa-Nakamine

address: 207 Uehara, Nishihara

department: Department of Biochemistry

institute: Graduate School of Medicine, University of the Ryukyus

summary:
Analysis of GT1-7 cells treated with GnRH.
In this dataset, we include the expression data obtained from GT1-7 cells after treatment with GnRH. We confirmed that GT1-7 cells expressed DUSP5 and DUSP6 after GnRH treatment. Results provide insight into the effect of GnRH on MAP kinase pathway.

overall_design: GT1-7 cells were treated with 50 nM GnRH for 30min.

first: Teruyuki

last: Higa

first: Hideyuki

last: Yamamoto


title: Epigenetic maintenance of topological domains in the rearranged gibbon genome [Hi-C]

status: Public on May 30 2018

city: Portland

first: Lucia

last: Carbone

state: Oregon

address: 3303 SW Bond Ave.

institute: Oregon Health & Science University

summary: The relationship between evolutionary genome remodeling and the three-dimensional structure of the genome remain largely unexplored. Here we use the heavily rearranged gibbon genome to examine how evolutionary chromosomal rearrangements impact genome-wide chromatin interactions, topologically associating domains (TADs), and their epigenetic landscape. We use high-resolution maps of gibbon-human breaks of synteny (BOS), apply Hi-C in gibbon, measure an array of epigenetic features, and perform cross-species comparisons. We find that gibbon rearrangements occur at TAD boundaries, independent of the parameters used to identify TADs. This overlap is supported by a remarkable genetic and epigenetic similarity between BOS and TAD boundaries, namely presence of CpG islands and SINE elements, and enrichment in CTCF and H3K4me3 binding. Cross-species comparisons reveal that regions orthologous to BOS also correspond with boundaries of large (400-600kb) TADs in human and other mammalian species. The co-localization of rearrangement breakpoints and TAD boundaries may be due to higher chromatin fragility at these locations and/or increased selective pressure against rearrangements that disrupt TAD integrity. We also examine the small portion of BOS that did not overlap with TAD boundaries and gave rise to novel TADs in the gibbon genome. We postulate that these new TADs generally lack deleterious consequences. Lastly, we show that limited epigenetic homogenization occurs across breakpoints, irrespective of their time of occurrence in the gibbon lineage. Overall, our findings demonstrate remarkable conservation of chromatin interactions and epigenetic landscape in gibbons, in spite of extensive genomic shuffling.

overall_design: Examination of Hi-C data and identification of TADs in one gibbon individual.

first: Nathan

last: Lazar


title: Epigenetic maintenance of topological domains in the rearranged gibbon genome [ChIP-seq]

overall_design: We performed ChIP-seq using H3K4me3 in two gibbon individuals (biological replicates).


title: Expression data from AMPKalpha1/2-double knockout murine embryonic fibroblasts stimulated or not with AICAR

city: Bordeaux

first: Michel

last: Moenner

address: 1, rue Camille Saint-Saens

department: IBGC CNRS UMR5095

country: France

institute: CNRS

summary:
AICAR is a metabolite with anti-tumoral properties. Its monophosphate derivative ZMP is an AMP mimetic activator of the protein kinases AMPK. However, AICAR  also mediates AMPK-independent effects.
A kinetic transcriptome analysis was therefore carried out in Ampkα1/α2 double knockout murine embryonic fibroblasts in response to AICAR in order to unveil these AMPK-independent functions,

overall_design: Ampkα1/α2 double knockout murine embryonic cells were incubated with 1 mM AICAR for 0, 1, 2, 4, 8, 12 and 24h. RNA extraction and hybridization on Affymetrix (Mouse MG-430 PM Array Strip Kit)  were then performed. Analyses were performed in triplicates (except t=8h in duplicate). The fold change in gene expression corresponds to the ratio between each incubation times with AICAR and control (t=0) without AICAR.

first: Chloé

last: Philippe

first: Benoît

last: Pinson

first: Jim

last: Dompierre

first: Véronique

last: Pantesco

last: Viollet

first: Bertrand

last: Daignan-Fornier


title: Epigenetic maintenance of topological domains in the rearranged gibbon genome [WBGS]

type: Methylation profiling by high throughput sequencing

sample_organism:
Macaca mulatta
Nomascus leucogenys

platform_organism:
Macaca mulatta
Nomascus leucogenys

overall_design: Whole genome bisulfite sequencing (WGBS) was performed on blood samples from one gibbon and one rhesus macaque.


title: The surveillance of pre-mRNA splicing is an early step in C. elegans RNA interference of endogenous genes.

status: Public on May 28 2018

city: Boston

first: Martin

last: Newman

address: 185 Cambridge St, CPZN-7250

department: Molecular Biology

institute: Massachusetts General Hospital

type: Non-coding RNA profiling by high throughput sequencing

summary: Here we examine the role of mRNA splicing in Caenorhabditis elegans RNAi.  We find that viable null mutations in U1 and U2-snRNP-specific splicing factor genes cause defects in RNAi.  The U1A orthologue rnp-2 is required for normal ERGO-1 Argonaute-class 26G siRNA biogenesis, trans-splicing of the eri-6/7 transcript and targeting of poorly conserved gene transcripts by WAGO Argonaute-class 22G siRNAs.  We find that poorly spliced gene transcripts engaged by the siRNA generating machinery are poorly conserved, possess few introns, and often have introns that are divergent from introns found in highly conserved genes.

overall_design: Analysis of small RNA populations in wildtype and splicing mutant embryos using next-generation sequencing

first: Fei

last: Ji


title: The whole genome effects of the PPARα agonist fenofibrate on livers of hepatocyte humanized mice

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

summary: The role of PPARα in gene regulation in mouse liver is well characterized. However, less is known about the effect of PPARα activation in human liver. The aim of the present study was to better characterize the impact of PPARα activation on gene regulation in human liver by combining transcriptomics with the use of hepatocyte humanized livers. To that end, chimeric mice containing hepatocyte humanized livers were given an oral dose of 300 mg/kg fenofibrate daily for 4 days. Livers were collected and analysed by hematoxilin and eosin staining, qPCR, and transcriptomics. Transcriptomics data were compared with existing datasets on fenofibrate treatment in normal mice. The human hepatocytes exhibited excessive lipid accumulation. Fenofibrate increased the size of the mouse but not human hepatocytes, and tended to reduce steatosis in the human hepatocytes. Quantitative PCR indicated that induction of PPARα targets by fenofibrate was less pronounced in the human hepatocytes than in the residual mouse hepatocytes. Transcriptomics analysis indicated that, after filtering, a total of 282 genes was significantly different between fenofibrate- and control-treated mice (P<0.01). 123 genes were significantly lower and 159 genes significantly higher in the fenofibrate-treated mice, including many established PPARα targets such as FABP1, HADHB, HADHA, VNN1, PLIN2, ACADVL and HMGCS2. According to gene set enrichment analysis, fenofibrate upregulated interferon/cytokine signaling-related pathways in hepatocyte humanized liver, but downregulated these pathways in normal mouse liver. Also, fenofibrate downregulated pathways related to DNA synthesis in hepatocyte humanized liver but not in normal mouse liver. The results support the major role of PPARα in regulating hepatic lipid metabolism, and underscore the more modest effect of PPARα activation on gene regulation in human liver compared to mouse liver. The data suggest that PPARα may have a suppressive effect on DNA synthesis in human liver, and a stimulatory effect on interferon/cytokine signalling.

overall_design: Chimeric mice with humanized livers were given an oral dose of 300 mg/kg fenofibrate daily for 4 days after which the hepatic transcriptome was analyzed.

first: Montserrat

last: de la Rosa Rodriguez

first: Go

last: Sugahara

first: Yuji

last: Ishida

first: Chise

last: Tateno

first: Sander

last: Kersten


title: Different gene expression between CENPK knockdown and control hepatocellular carcinoma cell line BEL-7404

city: Xi’an

first: Jianlin

last: Wang

state: shaanxi

address: 127 West Changle Street

institute: Fourth Military Medical University

summary:
We sought to find out the molecular mechanism of CENPK displayed in hepatocellular carcinoma.
Microarray experiments were carried out to identify different gene expression between CENPK-knockdown BEL-7404 cell line and Scramble BEL-7404 cell lines.

overall_design: Lentiviral expression vector of CENPK short hairpin RNA and the control group of scramble sequence was both used to infect the BEL-7404 cell line. Total RNA was extracted and analyzed by the Agilent 4x44K whole human genome oligo microarray.

first: Kaishan

last: Tao


title: Genome-wide analysis of gene expression upon BMI1 inhibition in human cortical neurons.

city: Montreal

first: Gilbert

last: Bernier

state: Quebec

address: 5415 Boul. l’Assomption

institute: Hopital Maisonneuve-Rosemont

summary: Study of gene expression regulated by BMI1 in human cortical neurons.

overall_design: Total RNA from undifferentiated hESC line HUES9, hESC-derived neurons and shBMI1 hESC-derived neurons was extracted and subjected to illumina BeadArray transcriptomic platform.

first: Anthony

last: Flamier


title: RNA Profiling in Patients' tumor infiltrating lymphocytes

status: Public on May 26 2018

first: Andrew

last: Weinberg

address: 4805 NE Glisan St 2N35

institute: Agonox

summary:
Identifying tumor antigen-specific T cells from cancer patients has been a goal of tumor immunologists for several decades. Co-expression of CD103 and CD39 on CD8 TIL highly enriches for tumor-reactive T cells. CD39+CD103+ CD8 TIL have a distinct TCR repertoire compared to other CD8 TIL subsets and are clonally expanded within the tumor.
They are highly enriched for tumor antigen recognition and efficiently killed autologous tumor cells. Patients with head and neck cancer whose CD8 TIL contained a higher frequency of CD39+CD103+ cells experienced a greater overall survival. This work describes a simple and effective method for detecting tumor-reactive CD8 TIL.

overall_design: Labeled target cDNA was prepared from 15 human total RNA samples. Samples were amplified and labeled using NuGEN Ovation Pico WTA System with Encore Biotin Module protocol (3'IVT assay). Each sample target was hybridized to a Human PrimeView GeneChip array. Image processing and expression analysis were performed using Affymetrix GeneChip Command Console (AGCC) v. 3.1.1 and Affymetrix Expression Console v. 1.1 software, respectively.

first: Duhen

last: Thomas

first: Montler

last: Ryan

first: Weinberg

last: Andrew


title: Deacetylation of miRNA-34a and miRNA-449 induce epithelial-mesenchymal transition and acquired resistance to ALK inhibitors

city: Seoul

first: Kyoung-Ho

last: Pyo

address: 50 Yonseiro

department: Avison Biomedical Research Center

country: South Korea

institute: Severance Hospital, Yonsei University College of Medicine

summary: Treatment with ALK tyrosine kinase inhibitors often elicits profound initial antitumor responses in ALK fusion-positive patients with lung adenocarcinoma. However, patients invariably develop acquired resistance to ALK inhibitors. In this study, we aimed to identify molecular events that limit the durable response to ALK inhibition using genetic and epigenetic approaches. To identify novel mechanisms of acquired resistance to ALK inhibitors, we established in vivo and in vitro models of acquired resistance to ceritinib and crizotinib using H3122 and H2228 cells. For in vivo model, mice with established H3122-derived tumors were treated with four doses of ceritinib (control, 75mg/kg, 87.5mg/kg, 100mg/kg) to derive ceritinib-resistant tumors.

overall_design: For in vivo model, mice with established H3122-derived tumors were treated with four doses of ceritinib (control, 75mg/kg, 87.5mg/kg, 100mg/kg) to derive ceritinib-resistant tumors. Xenograft tumors showed initial dose-dependent decrease in tumor volume and subsequently developed acquired resistance within 24-108 days.

first: Mi

last: Yun

first: Sun

last: Lim

first: Kyoung

middle: H

first: Yong

last: Kim

first: Seon

first: Mirang

first: Byoung

last: Cho


title: Defining the role of the General Stress Response regulators, SigT and GsrN, in control of the hyperosmotic stress response in Caulobacter crescentus

city: East Lansing

first: Sean

last: Crosson

state: Michigan

address: 567 Wilson Rd

department: Dept. Microbiology and Molecular Genetics

institute: Michigan State University

summary: We report gene expression responses of Caulobacter crescentus to osmotic upshock (150 mM sucrose). The goal of this study is compare the transcriptional responses of wild type, sigT deletion, and gsrN overexpression (gsrN++) strains. The data provide a high resolution view of how two major regulators of the general stress response (sigT and gsrN) shape transcription upon shift to a hyperosmotic environment.

overall_design: Caulobacter crescentus wild type, ΔsigT and gsrN++ strains were grown to mid log phase. Cultures were split, and either treated with 150 mM sucrose (to induce hyperosmotic shock) or untreated. After treatment, cells were rapidly pelleted and resuspended in Trizol for RNA purification.

first: Matthew

last: Tien

first: Benjamin

middle: J

last: Stein


title: Bilophila wadsworthia worsens high-fat diet-induced metabolic impairments in inflammation dependent and independent manners

city: Saint-Malo

first: Phuong

middle: Hang

last: PHAM

address: 7 allée Métis

department: Data science

institute: Parean Biotechnologies

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

sample_organism:
Mus musculus
uncultured bacterium

platform_organism:
Mus musculus
uncultured bacterium

overall_design: Refer to individual Series


title: Transcriptome profile in ore15-1D and ore15-2 at DAE 4

city: Jeju-si

first: Jeongsik

state: Jeju

address: 102 Jejudaehakroe

department: Faculty of Science Education

institute: Jeju National University

summary: To understand the role of ORE15 in the early leaf development, we have employed transcriptional profiling of wild type Col-0, ore15-1D, and ore15-2KO at 4 days after leaf emergence. Agilent's Whole Arabidopsis Gene Expression Microarray (G2519F-021169, V4, 4x44K) was used.

overall_design: Transcriptional profiling comparision between Col, ore15-1D and ore15-2 at early development (DAE 4). 2 independent biological samples.

first: Jin-Hee

first: Hye-Ryun

last: Woo


title: Bilophila wadsworthia worsens high-fat diet-induced metabolic impairments in inflammation dependent and independent manners [bacterial gene expression]

summary: Dietary lipids favor the growth of the pathobiont Bilophila wadsworthia, but the relevance of this expansion in metabolic syndrome pathogenesis remains unknown. Here, we showed that B. wadsworthia synergize with HFD to promote higher inflammation, intestinal barrier dysfunction and bile acid dysmetabolism, leading to higher glucose dysmetabolism and hepatic steatosis. Host-microbiota transcriptomics analysis unraveled pathways, particularly butanoate metabolism, which may underlie the metabolic effects mediated by B. wadsworthia. Pharmacological suppression of B. wadsworthia-associated inflammation unmasked the bacterium’s intrinsic capacity to induce a negative impact on glycemic control and hepatic function. Finally, the probiotic Lactobacillus rhamnosus CNCM I-3690 was able to limit B. wadsworthia-induced immune and metabolic impairment by limiting its expansion, reducing inflammation and reinforcing intestinal barrier. Our results support a new avenue for interventions against western diet-driven inflammatory and metabolic diseases.

overall_design:
RNA-seq analysis of bacterial RNA to look at abundances of bacterial transcripts in mouse feces of mice subjected to different diets and/or inoculations.

ASF = altered Schaedler flora

first: Jane

last: Natividad

first: Bruno

last: Lamas

first: Hang

middle: P

last: Pham

first: Marie-Laure

last: Michel

first: Dominique

last: Rainteau

first: Chantal

last: Bridonneau

first: Gregory

last: da Costa

first: Johan

last: van Hylckama Vlieg

last: Sovran

first: Celia

last: Chamignon

first: Julien

last: Planchais

first: Mathias

last: Lavie-Richard

first: Philippe

last: Langella

first: Patrick

last: Veiga

first: Harry

last: Sokol


title: Epigenetic maintenance of topological domains in the rearranged gibbon genome

first: Lucia

last: Carbone


title: Expression data from Astro-D2KO mice experiencing a Status Epilepticus (SE)

status: Public on May 25 2018

city: Chicago

first: Gustavo

middle: Werpel

last: Fernandes

state: IL

address: 5841 South Maryland Av.

department: Endocrinology

institute: University of Chicago

summary:
Status Epilepticus (SE) is an abnormally prolonged seizure that results from either a failure of mechanisms that terminate seizures or from initiating mechanisms that inherently lead to prolonged seizures.
Here we report an unbiased analysis of the hippocampal transcriptome of mice with targeted disruption of Dio2 in the astrocytes (Astro-D2KO mouse) undergoing 3 h SE.

overall_design: Astro-D2KO mice were selected  for RNA extraction and hybridization on Affymetrix microarrays. Here, we sought to identify whether SE modifies thyroid hormone metabolism/action in the brain and how it affects the hippocampal acute transcriptional response.

first: Bruna

last: Nascimento

first: Antonio

last: Bianco

first: Miriam

middle: O

last: Ribeiro


title: Bilophila wadsworthia worsens high-fat diet-induced metabolic impairments in inflammation dependent and independent manners [mouse gene expression]

first: Phuong

last: PHAM

overall_design: Microarray analysis was performed by using total tissue from caecum tip of mice on week 5 post-treatment.

first: Jane

middle: M

last: Natividad

first: Bruno

last: Lamas

first: Hang

last: Pham

last: Michel


title: Podoplanin is a marker but no driver for malignant progression in glioblastoma

city: Heidelberg

first: Peter

last: Angel

address: Im Neuenheimer Feld 280

department: Signal Transduction and Growth Control

institute: German Cancer Research Center

summary:
Genome-wide expression analysis of PDPNhigh and PDPNlow subpopulations of human glioblastoma cells
The aim of this expression study was to identify genes that are differentially expressed between the two populations and to determine a PDPN-associated gene signature

overall_design: Six human glioblastoma cultures were sorted for high and low PDPN expression, RNA extracted and genome-wide expression analysis performed


title: MicroRNA regulation of adipose tissue macrophages during high-fat diet-induced obesity.

status: Public on May 22 2018

city: Columbia

first: Prakash

last: Nagarkatti

state: SC

address: 6439 Garners Ferry Road

institute: University of South Carolina School of Medicine

summary: We used microRNA microarrays to identify dysregulated microRNAs in macrophages isolated from adipose tissue of lean and obese mice.

overall_design: F4/80+ adipose tissue macrophages (ATMs) were isolated from epididymal fat of mice fed normal chow diet (NCD, lean mice) or 60% high-fat diet (HFD, obese mice) for 16 weeks.

first: Kathryn

last: Miranda

first: Mitzi


title: Transcriptional control of adipose tissue macrophages during high-fat diet-induced obesity.

summary: We used transcriptome microarrays to identify gene expression changes in macrophages isolated from adipose tissue of lean and obese mice.

overall_design: F4/80+ adipose tissue macrophages were isolated from epididymal fat of mice fed normal chow diet (NCD, lean mice) or 60% high-fat diet (HFD, obese mice) for 16 weeks.


title: Expression data from allergic patients to profilin

city: Madrid

first: Leticia

last: Mera

state: Madrid

address: Carretera Boadilla km 5300

country: Spain

institute: CEU San Pablo University

summary:
Prevalence and severity of allergic diseases have increased worldwide. To date, respiratory allergy phenotypes are not fully characterized and, along with inflammation progression, treatment is increasingly complex and expensive. Profilin sensitization constitutes a good model to study the progression of allergic inflammation.
We have used microarrays to understand the underlying mechanisms of severe profilin-mediated reactions using a model that includes patients with different levels of sensitization to profilin (non-allergic, mild, moderate and severe)

overall_design: Our aim was to identify the underlying mechanisms and the associated biomarkers of allergic progression, focusing on severe phenotypes, using microarrays.

first: Paloma

last: Fernández

first: Isabel

last: Martín-Antoniano


title: G1P3 (IFI6), a Mitochondrial Localized Antiapoptotic Protein, Promotes Metastatic Potential of Breast Cancer Cells through mtROS

status: Public on May 24 2018

city: Commerce

first: Venugopalan

last: Cheriyath

address: 2600 S Neal Street

department: Biological and Environmental Sciences

institute: Texas A&M University-Commerce

summary:
G1P3 (IFI6) was associated with poor distance metastasis free survival (DMFS) in breast cancer cases. Therefore, we tested the hypothesis that G1P3-induced mitochondrial redox deregulation confers metastatic potentials in breast cancer cells. Our results demonstrate that coordinated action of multiple pathways elicited by G1P3-induced mtROS augment actin-containing migratory structures to promote breast cancer cell migration and invasion
Comparative network analysis identified upregulation of antioxidant, acin remodeling, and EMT networks in G1P3 overexpressing MCF-7 cells.

overall_design: Total RNA obtained from MCF-7 cells stably expressing vector or G1P3 were subjected to expression array to investigate the effect of G1P3 on gene expression in ER+ breast cancer cell line


title: Gene expression in cord blood links genetic risk for neurodevelopmental disorders with maternal psychological distress and adverse childhood outcomes

city: New York

first: Michael

last: Breen

state: NY

address: 1468 Madison Ave

department: Depts. of Psychiatry, Genetics and Genomic Sciences

institute: Ichan School of Medicine at Mount Sinai

summary: Prenatal  exposure  to  maternal  stress  and  depression  has  been  identified  as  a risk  factor for  adverse behavioral  and neurodevelopmental  outcomes  in  early  childhood.  However, the  molecular  mechanisms through  which  maternal  psychopathology  shapes offspring development  remain  poorly  understood. We  analyzed  transcriptome-wide  gene  expression  profiles  of  149 UCB  samples  from  neonates  born to  mothers  with  prenatal  PTSD  (n=20),  depression (n=31)  and  PTSD  with  comorbid  depression  (PTSD/Dep;  n=13),  compared  to  neonates born  to  carefully  matched  trauma  exposed  controls  without  meeting  PTSD  criteria  (TE; n=23)  and  healthy  mothers  (n=62).  We  also evaluated  physiological  and  developmental measures in these infants at birth, six months and twenty-four months. A multistep analytic approach  was  used  that  specifically  sought  to:  1)  identify  dysregulated  genes,  molecular pathways  and  discrete  groups  of  co-regulated  gene  modules  in  UCB  associated  with prenatal  maternal  psychopathologies;  and  2)  to  determine  the  impact  of  perinatal  PTSD and depression on early childhood development outcomes.

overall_design: Transcriptome-wide gene expression assays were applied to umbilical cord blood samples from neonates born to mothers with posttraumatic stress disorder (PTSD; n=20), depression (n=31) and PTSD with comorbid depression (n=13) compared to carefully matched trauma exposed controls (n=23) and healthy mothers (n=62).


title: Effect of LIMD1 knockdown on gene expression in Human Bronchial Epithelial Cells (HBECs)

city: London

first: Tyson

middle: V.

last: Sharp

address: John Vane Science Centre, Charterhouse Square

department: Barts Cancer Institute

country: United Kingdom

institute: Queen Mary University of London

summary: HBECs were untreated, treated with scrambled siRNA (80nM) or LIMD1 targeting siRNA (80nM) for 72 hours. Total RNA was extracted and gene expression was measured using Illumina HumanHT-12 v4 Expression BeadChip array.

overall_design: 12 total samples, 4 replicates per treatment condition

first: Daniel

last: Foxler

first: Katherine

last: Bridge

first: John

middle: G

last: Foster

first: Paul

last: Grevitt

first: Sean

last: Curry

first: Kunal

last: Shah

last: Davidson

first: Ai

last: Nagano

first: Emanuela

last: Gadaleta

first: Hefin

middle: I

last: Rhys

middle: T

last: Kennedy

first: Miguel

last: Hermida

first: Ting-Yu

last: Chang

last: Shaw

first: Louise

last: Reynolds

first: Tristan

middle: R

last: McKay

first: Hsei-Wei

last: Wang

first: Paulo

last: Plevin

first: Dimitris

last: Lagos

first: Nicholas

last: Lemoine

first: Prabhakar

last: Rajan

first: Trevor

last: Graham

first: Claude

last: Chelala

first: Kairbaan

last: Hodivala-Dilke

first: Ian

last: Spendlove

middle: V


title: Transcriptomic profiling of trigeminal nucleus caudalis (TNC) and spinal cord dorsal horn (SC)

city: Glostrup

first: Lisette

last: Kogelman

address: Nordre Ringvej 67

department: Danish Headache Centre

country: Denmark

institute: Rigshospital Glostrup

summary: RNA-Sequencing of the trigeminal nucleus caudalis and spinal cord, dorsal horn in male naive rats (Wistar Han) of 10 weeks old

overall_design: 6 naive rats were killed after 2 weeks of arrival, both trigeminal nucleus caudalis and spinal cord dorsal horn were dissected using laser capture microdissection of each rat.

first: Rikke

last: Elgaard-Christensen

first: Sara

last: Pedersen

first: Thomas

middle: F

last: Hansen

first: Inger

last: Jansen-Olesen

first: Jes

last: Olesen


title: Transcriptomic analysis of gene profile in KSHV+ PEL cells changed by bacterial quorum sensing molecules [BCP-1_OdDHL]

city: New Orleans

first: Zhiqiang

last: Qin

state: LA

address: 1700 Tulane Ave

institute: LSUHSC-NO

summary: KSHV-related primary effusion lymphoma is mostly seen in immunocompromised individuals such as HIV+ patients, who frequently suffering polymicrobial infections including different opportunistic pathogens. It is interesting to explore the host gene profile in PEL altered by bacterial quorum sensing molecules, the key systems regulating virulence factors in many bacteria.

overall_design: BCP-1 were incubated with 25μM of OdDHL from P. aeruginosa for 48 h, then the HumanHT-12 v4 Expression BeadChip (Illumina) was used to detect gene profile altered within PQS treated PEL when compared to vehicle-treated cells.

first: Lu

last: Dai

first: Jovanny

last: Zabaleta


title: Transcriptomic analysis of gene profile in KSHV+ PEL cells changed by bacterial quorum sensing molecules [BCBL_OdDHL]

overall_design: BCBL-1 were incubated with 25μM of OdDHL from P. aeruginosa for 48 h, then the HumanHT-12 v4 Expression BeadChip (Illumina) was used to detect gene profile altered within OdDHL treated PEL when compared to vehicle-treated cells.


title: Transcriptomic analysis of gene profile in KSHV+ PEL cells changed by bacterial quorum sensing molecules [BCP-1]

overall_design: BCP-1 were incubated with 25μM of PQS from P. aeruginosa for 48 h, then the HumanHT-12 v4 Expression BeadChip (Illumina) was used to detect gene profile altered within PQS treated PEL when compared to vehicle-treated cells.


title: Transcriptomic analysis of gene profile in KSHV+ PEL cells changed by bacterial quorum sensing molecules [BCBL-1]

overall_design: BCBL-1 were incubated with 25μM of PQS from P. aeruginosa for 48 h, then the HumanHT-12 v4 Expression BeadChip (Illumina) was used to detect gene profile altered within PQS treated PEL when compared to vehicle-treated cells.


title: Transcriptomic analysis of gene profile in KSHV+ PEL cells changed by bacterial quorum sensing molecules

overall_design: Refer to individual Series


title: Transcriptional profiling of human monocyte-derived macrophages

city: Vienna

first: Anna

last: Ohradanova-Repic

address: Lazarettgasse 19

country: Austria

institute: Medical University of Vienna

summary: In this study we compared the response of human monocyte-derived macrophages differentiated with either granulocyte-macrophage colony-stimulating factor (GM-CSF) or macrophage colony-stimulating factor (M-CSF) to the most common activation stimuli: LPS plus interferon-γ to induce macrophage polarization towards the M1 type or IL-4 to induce macrophage polarization towards the M2a type. Additionally, IL-10 was used to drive M-CSF-primed macrophages into the M2c state. We used the the whole-human genome microarray to determine genes that were up- or downregulated by the activation stimuli in both macrophage lineages, with focus on genes implicated in immune response.

overall_design: We generated 7 different macrophage subtypes in three biological replicates: Isolated monocytes of three healthy donors (biological replicates) were differentiated with either 25ng/ml GM-CSF or 50ng/ml M-CSF for 7d. GM-CSF-differentiated macrophages were then either mock-activated with culture medium only (control; condition 1) or activated with 100 ng/ml LPS + 25ng/ml IFNγ (condition 2), or 20 ng/ml IL-4 (condition 3) for 2d (48 h). This activation regime was also used to activate M-CSF-differentiated macrophages, which were in additionally activated with 20 ng/ml IL-10 (condition 4) for 2d (48 h).

first: Christian

last: Machacek

first: Hannes

last: Stockinger


title: Super-enhancer Driven Core Regulatory Circuitry in MYCN-amplified Neuroblastoma [array]

city: Cambridge

first: Richard

middle: A

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: Transcriptional dysregulation plays a major role in the development and progression of human tumors such as pediatric neuroblastoma. Therefore, we sought to elucidate the relationship between genes required for neuroblastoma cell growth and survival and the transcriptional core regulatory circuitry (CRC) that controls the gene expression program. A genome-scale CRISPR-Cas9 screen for oncogenic dependencies revealed that 143 genes are essential for cell survival and growth in neuroblastoma relative to other cancers, including many super-enhancer (SE) regulated transcription factors. Genome-wide occupancy analysis of transcription factor binding demonstrated that at least six of these transcription factors were both dependency genes and components of the CRC in MYCN-amplified neuroblastoma including: HAND2, ISL1, PHOX2B, GATA3, TBX2, and MEIS2.  Binding sites for these transcription factors were clustered within a few hundred base pairs in their own enhancers and the enhancers of downstream target genes, which surprisingly included  40% of the independently determined neuroblastoma dependency genes. This profound level of transcriptional control of oncogenesis through self-reinforcing transcriptional circuits led us to test combinatorial pharmacological inhibition of transcriptional initiation and elongation, which synergistically induced tumor cell death, supporting drugging transcription  as a means to advance the treatment of high risk neuroblastoma.

overall_design: Array-based expression profiling of neuroblastoma cells treated with JQ1 and 125nM THZ1 for up to 12hrs.

first: Adam

middle: D

last: Durbin

first: Mark

middle: W

last: Zimmerman

first: Neekesh

last: Dharia

first: Brian

last: Abraham

first: Amanda

last: Balboni

first: Nina

last: Weichert-Leahey

first: Shuning

last: He

first: John

last: Krill-Burger

first: Francisca

last: Vazquez

first: David

last: Root

first: Aviad

last: Tsherniak

first: William

middle: C

last: Hahn

first: Todd

last: Golub

first: Kimberly

last: Stegmaier

first: A

last: Look


title: Near-term fetal sheep pulmonary artery endothelial cells in a model of intrauterine growth restriction (IUGR)

city: Aurora

first: Reuben

middle: Blair

last: Dodson

state: CO

address: 13123 East 16th Ave

department: Surgery

institute: University of Colorado Denver

summary: Isolated PAECs gene expression was tested in cultured cells from control or hyperthermia-treated pregnant sheep (IUGR model) to measure gene expression changes.

overall_design: Control PAECs (n=4) compared to IUGR PAECs (n=4)

first: R

middle: B

first: Steven

last: Abman

first: Cristina

last: Alvira

last: Astling


title: ZNFX-1 Functions Within Perinuclear Nuage to Balance Epigenetic Signals

status: Public on May 18 2018

city: Worcester

first: Craig

last: Mello

address: 368 Plantation Street

department: RNA Therapeutics Institute

institute: UMASS Med School/HHMI

summary: Animal cells have a remarkable capacity to adopt durable and heritable gene expression programs or epigenetic states that define the physical properties and diversity of somatic cell types. The maintenance of epigenetic programs depends on poorly understood pathways that prevent gain or loss of inherited signals. In the germline, epigenetic factors are enriched in liquid-like perinuclear condensates called nuage. Here we identify the deeply conserved helicase-domain protein, ZNFX-1, as an epigenetic regulator and component of nuage that interacts with Argonaute systems to balance epigenetic inheritance. Our findings suggest that ZNFX-1 promotes the 3’ recruitment of machinery that propagates the small RNA epigenetic signal and thus counteracts a tendency for Argonaute-targeting to shift 5’ along the mRNA.  These functional insights support the idea that recently identified subdomains of nuage, including ZNFX-1 granules or “Z-granules,” may define spatial and temporal zones of molecular activity during epigenetic regulation.

overall_design:
Small RNA bound to WAGO-9 or CSR-1, as well as total small RNA, from wildtype or znfx-1 mutant animals were cloned in triplicates and sequenced.
Please note that both IPs were done using anti-flag mouse monoclonal antibody M2 from Sigma (Cat#F1804) since both CSR-1 and WAGO-9 were tagged with FLAG peptide.

first: Takao

last: Ishidate

first: Ahmet

last: Ozturk


title: Differential expression of host cell genes and their implications in PCV2 infection

status: Public on May 16 2018

city: St. Paul

first: Cheryl

last: Dvorak

state: MN

address: 1971 Commonwealth Avenue

department: Veterinary and Biomedical Sciences

institute: University of Minnesota

summary: We examined the differential gene expression in VR1BL cells in vitro with and without PCV2 infection

overall_design: VR1BL cells were infected with PCV2b strain (GenBank ID JF290418) at an MOI of 1 for 4 days and control cells were mock infected for 4 days. Total RNA was isolated from 3 control and 3 infected replicates and RNA-seq was performed using an illumina GAIIx.

first: Sumathy

last: Puvanendiran

first: Michael

middle: P

last: Murtaugh


title: The coupling of transcriptome and proteome adaptation during development and heat stress response of tomato pollen

status: Public on May 15 2018

city: Greifswald

first: Stefan

last: Simm

address: Walter-Rathenau-Straße 48

department: Bioinformatics

institute: University Medicine Greifswald

summary:
Pollen development is central for plant reproduction and is assisted by changes of the transcriptome and the proteome. At the same time, pollen is largely heat sensitive, particularly at early developmental stages. To define the changes during development and the response of different stages to elevated temperatures we investigated the transcriptome and proteome of pollen at tetrad, post-meiotic and mature stage before and after application of elevated temperatures. We used Solanum lycopersicum as an economically important crop. We demonstrate that the number of transcripts declines from tetrad to mature stage, while the protein content shows the opposite trend. Comparison of the transcriptome and proteome led to the discovery of two translational modes assigned as direct translation – transcripts increased in a specific pollen stage lead to increased translation in the same stage – and delayed translation – transcripts are produced for translation in later stages. The response to elevated temperatures is with ~5% of all genes being upregulated comparable to general plant behavior. The alteration at proteome level marked the mature pollen as least responsive and the post-meiotic stages as most responsive with altered levels of 40% of the identified proteins. For a subset of the genes with direct translation we observed a downregulation of protein levels after heat stress, whereas some of the genes with delayed translation showed a shift from delayed to direct translation when heat stress is applied. Further, Hsps, proteasome subunits, ribosomal proteins as well as eukaryotic initiation factors are the most drastically affected groups. On the example of Hsps we document that the response at transcriptome and proteome levels in e.g. the post-meiotic and mature stage does not correlate. Moreover, while all stages respond to heat stress with regulation of transcript abundance of Hsps in a comparable manner, changes at proteome level are distinct. Thus, we demonstrate that the difference in heat stress response in different stages of pollen development is rather manifested by significant changes of protein than transcript abundance.
-------------------------------------------------------
Solanaceae Pollen Thermotolerance Initial Training Network (SPOT-ITN) Consortium

overall_design: 12 samples (3 developmental stages under 2 conditions (control and heat stress) with 2 biological replicates)

first: Mario

last: Keller

first: Spot-ITN

last: Consortium


title: Characterization of imprinted genes in rice reveals regulation and imprinting conservation at some loci in plant species

city: Yangzhou

first: Chen

last: Chen

state: Jiangsu

address: 12 E. Wenhui Rd.

department: Agricultural College

institute: Yangzhou University

summary: Genomic imprinting is an epigenetic phenomenon by which certain genes display differential expression in a parent-of-origin-dependent manner. Hundreds of imprinted genes have been identified from several plant species. Here we identified, with a high level of confidence, 208 imprinted candidates from rice. Imprinted genes of rice showed limited association to the transposable elements, which contrasts with findings from Arabidopsis. Generally, imprinting in rice is conserved within species, but intraspecific variation was detected as well.

overall_design:
To explore imprinted genes in rice, we used three-line hybrid rice strains to construct reciprocal crosses. A cytoplasmic male sterile (CMS) line carries a sterility gene encoded in the cytoplasmic genome, such that the pollen produced is sterile. A “maintainer” line shares the same nuclear genome as its corresponding CMS line but has a distinct cytoplasmic genome. Due to the absence of the cytoplasmic sterility gene, the maintainer line is fertile. Using rice CMS and maintainer lines for crossing greatly increases the efficiency of hybridization and enables us to rigorously control the timing of fertilization and to avoid false hybridization events. Here, we used the japonica CMS lines (Liuqianxin-A and Yu6-A) and their maintainer lines (Liuqianxin-B and Yu6-B), and the indica CMS lines (Rongfeng-A and Wufeng-A) with their corresponding maintainer lines (Rongfeng-B and Wufeng-B) to make two distinct reciprocal-cross sets, which we refer to as Liuqianxin-A/Rongfeng-B (LR), Rongfeng-A/Liuqianxin-B (RL), Yu6-A/Wufeng-B (YW), and Wufeng-A/Yu6-B (WY). The LR and RL reciprocal crosses, and YW and WY reciprocal crosses are indicated as LR-RL and YW-WY hereafter for convenience. Meanwhile, we made crosses of Wufeng-A/Wufeng-B (WW), Rongfeng-A/Rongfeng-B (RR), Liuqianxin-A/Liuqianxin-B (LL), and Yu6-A/Yu6-B (YY), which resembled selfing inbred lines as controls to validate imprinting.
The following crosses are represented in this Series:  liuqianxinA-liuqianxinB, liuqianxinA-rongfengB, rongfengA-liuqianxinB, rongfengA-rongfengB, wufengAyu6B, yu6A-wufengB


title: 1-day styrene inhalation dose response in three strains of C57Bl/6 mice: wild-type (WT), CYP2F2 knockout (KO), and CYP2F1 humanized (TG) mice, and CD-1 mice

city: Research Triangle Park

middle: B.

last: Black

state: North Carolina

address: 100 Capitola Dr., Suite 106

institute: Scitovation, LLC.

summary: These data examine transcriptomic changes in Lung tissue after a single day's exposure to Styrene inhalation in male C57Bl/6 and CD-1 mice.  Styrene causes increased lung tumors in mice, but not in rats.  Mouse lung tumors were found mostly at the conclusion of a life-time (104 weeks for males) exposure study and most were benign.  Styrene is largely negative in genotoxicity assays.  Styrene metabolism by CYP2F2 produced a different metabolite pattern in mouse lung than in liver or in rats or humans.  The purpose of this study was to use genomic analyses to further investigate potential modes of action (MoA) of styrene in mice after a short term exposure to styrene.  Mice strains exposed were C57Bl/6 wild-type (WT), CYP2F2 knockout (-/-; KO) and CYP2F21 humanized transgenic (2F2-KO + 2F1,2A13,2B6-transgenic, TG), and CD-1 male mice using 10, 40 & 120 ppm styrene at 6 hr/day for a single day.  Lungs were analyzed by Affymetrix whole genome microarrays for each strain relative to strain specific vehicle controls for each strain.  Both RMA normalization and statistical analsis (ANOVA) was performed on each strain separately.  Affymetrix control probes (AFFX-prefix, 104 probes) have been excluded from the data matrix.

overall_design: Lung gene expression was evaluated in male CD-1 and C57Bl/6 WT, KO & TG mice following a single 6-hr inhalation exposure of styrene at 0, 10, 40, and 120 ppm

first: Melvin

middle: E

last: Andersen


title: The QstR regulon of Vibrio cholerae

city: Lausanne

first: Melanie

last: Blokesch

address: Station 19 / EPFL-SV-UPBLO

department: School of Life Sciences

institute: Swiss Federal Institute of Technology Lausanne (EPFL)

summary: In this study, we compared the QstR regulon to the TfoX regulon (and TfoY regulon) of V. cholerae in WT strain A1552 and its ΔhapRΔvpsA derivative using RNA-seq to better understand QstR's function.

overall_design: mRNA profiles of a V. cholerae strains A1552-Tn, A1552-TntfoX-strep, A1552-TntfoY-strep, A1552-TnQstR and A1552ΔvpsA::FRTΔhapR::FRT-Tn, A1552ΔvpsA::FRTΔhapR::FRT-TntfoX-strep, A1552ΔvpsA::FRTΔhapR::FRT-TntfoY-strep, A1552ΔvpsA::FRTΔhapR::FRT-TnQstR. 3 independent biological replicates are provided for each bacterial strain. The bacteria were grown to high cell density and in the presence of arabinose as inducer.


title: 5-day styrene inhalation dose response in CD-1 mice (lung)

summary: Styrene causes increased lung tumors in mice, but not in rats.  Mouse lung tumors were found mostly at the conclusion of a life-time (104 weeks for males) exposure study and most were benign.  Styrene is largely negative in genotoxicity assays.  Styrene metabolism by CYP2F2 produced a different metabolite pattern in mouse lung than in liver or in rats or humans.  The purpose of this study was to use genomic analyses to further investigate potential modes of action (MoA) of styrene in mice.  Lungs were analyzed by whole genome microarrays for each strain at each dose.  Male CD-1 mice were exposed to 6 inhalation concentrations of styrene: 0, 1, 5, 10, 20, 40, and 120 ppm for a single 6 hour exposure. This was intended to gain dose-response data at low-observed-adverse-effect-levels (LOAELs) of styrene (≥ 20 ppm) and at no-observed-adverse-effect-levels (NOAELs) of styrene (< 20 ppm) for comparison with gene expression from similar Styrene inhalation exposures in a second strain of mice (C57Bl/6).  Affymetrix control probes (AFFX-prefix, 104 probes) have been excluded from the data matrix.

overall_design: Lung gene expression was evaluated in male CD-1 mice following a single 6-hr inhalation exposure of styrene at 0, 1, 5, 10, 20, 40, and 120ppm


title: SOX-2 mediated upregulation of CD24 promotes adaptive resistance towards targeted therapy in melanoma

city: Heidelberg

first: Jochen

last: Utikal

address: Im Neuenheimer Feld 280

department: Clinical Cooperation Unit Dermato-Oncology

institute: German Cancer Research Center

summary: Melanoma is one of the most aggressive types of skin cancer and is often characterized by a constitutively activate RAS-RAF-MEK-ERK pathway. For targeted therapy, BRAF inhibitors are available that are powerful in the beginning but resistance occurs rather fast. A better understanding of the underlying mechanisms of resistance is urgently needed to increase the success of the treatment. Here, we observed that in targeted therapy resistant, melanoma-derived induced pluripotent cancer cells (iPCCs) SOX2 and CD24 are upregulated. It is known that both SOX2 and CD24 expression promote an undifferentiated and cancer stem cell like phenotype, which is associated with higher therapy resistance. We therefore elucidated the role of SOX2 and CD24 in targeted therapy resistance in more detail. We found that SOX2 and CD24 are upregulated upon BRAF inhibitor treatment and that SOX2 is able to upregulate the expression of CD24 by binding to the CD24 promoter. Furthermore, we show that SOX2 or CD24 overexpression significantly increase the resistance towards BRAF inhibitors, while SOX2 knock-down rendered cell sensitive towards treatment. Moreover, CD24 and SOX2 are able to upregulate Src and STAT3 activity which could contribute to the increased resistance. Importantly, CD24 knockdown or Src inhibition in resistant SOX2 overexpressing cells, the sensitivity towards BRAF inhibitors was re-established. Hence, we suggest a novel mechanism of adaptive resistance whereby BRAF inhibition is circumvented via the upregulation of CD24 by SOX2 resulting in increased activity of Scr and STAT3. Thus, to prevent adaptive resistance it might be beneficial to use Src or STAT3 inhibitors together with MAPK pathway inhibitors.

overall_design: Total RNA from A375 DMSO treated cells was compared to A375 cells treated with 3 µM vemurafenib for 24h

first: Laura

last: Hüser


title: Expression of small RNAs during epigenetic disturbances of Tetrahymena DNA elimination

city: Montpellier

first: Kazufumi

last: Mochizuki

address: 141 rue de la Cardonille

institute: Institute of Human Genetics, CNRS

summary: Epigenetic inheritance of acquired traits is widespread among eukaryotes but how and to what extent such information is trans-generationally inherited is still unclear. The patterns of programmed DNA elimination in ciliates are epigenetically and trans-generationally inherited, and it has been proposed that small RNAs, which shuttle between the germline and the soma, regulate this epigenetic inheritance. In this study, we test the existence of such small RNA-mediated communication by epigenetically disturbing the pattern of DNA elimination in Tetrahymena. We show that the pattern of DNA elimination is indeed determined by the selective turnover of small RNAs, which is induced by the interaction between germline-derived small RNAs and the somatic genome. In addition, we show that DNA elimination of an element is regulated by small RNA-mediated communication with other eliminated elements. By contrast, no evidence obtained thus far supports the notion that transfer of epigenetic information from the soma to the germline, if any, regulates DNA elimination. Our results indicate that small RNA-mediated trans-nuclear and trans-element communication, in addition to unknown information in the germline genome, contributes to determining the pattern of DNA elimination.

overall_design: In this study, we aim to test the following three predictions regarding small RNA-directed DNA elimination in Tetrahymena by epigenetically disturbing DNA elimination: 1) selective turnover of Early-scnRNAs in scnRNA selection shapes the pattern of DNA elimination through communication between the MIC, the parental MAC and the developing new zygotic MAC; 2) trans-recognition between IESs via scnRNAs and the cis-spreading of Late-scnRNA production in the new MAC buffer against fluctuations in Early-scnRNA accumulation to ensure robust DNA elimination; and 3) IES-biased Early-scnRNA production in the MIC is determined at the end of the preceding conjugation by scnRNAs that translocate from the MAC to the new MIC.

first: Tomoko

last: Noto


title: Tumor analysis: Freeze-thawing cycle of triple negative breast cancer cells changes tumor CD24/CD44 profile and percentage of tumor-infiltrating immune cells

status: Public on May 12 2018

city: Rennes

first: Patrick

last: Legembre

address: CRLCC Eugène Marquis, Rue Bataille Flandres Dunkerque, Bat. D

department: Chemistry Oncogenesis Stress Signalling

institute: Inserm U1242

summary: We studied the impact of cryopreservation on the transcriptome of tumorosphere derived from freshly dissociated triple negative breast cancer (TNBC) tumors. RNA expression of tumorospheres derived from freshly dissociated or frozen then thawed dissociated tumor cells from 3 patients was analysed.

overall_design: Dissociated tumor cells from three TNBC patients were collected and either immediately cultured or cryopreserved for 15 days then thawed. Fresh or cryopreserved dissociated cells were cultured in mammocult medium (stemcell technologies) in low attachment plates.  After two weeks mammospheres were collected and total RNA was extracted. Cell immunophenotyping was performed at dissociation, after thawing and at RNA collection with flow cytometry.

first: Matthieu

last: Le Gallo

first: Thibault

last: de la Motte Rouge

first: Amanda

last: Poissonnier

first: Vincent

last: Lavoué

last: Tas

first: Jean

last: Leveque

first: Florence

last: Godey


title: A PDGFRα-driven mouse model of Glioblastoma reveals a Stathmin1-mediated mechanism of sensitivity to Vinblastine

city: Beijing

first: Hua-Jun

last: Wu

state: Beijing

address: 8 science park road, zhongguancun life science park

department: School of Basic Medical Sciences

institute: Peking University Health Science Center

summary: Glioblastoma multiforme (GBM) is an aggressive primary brain cancer that includes focal amplification of PDGFRα and for which there are no effective therapies. Herein, we report the development of a genetically engineered mouse model of GBM based on autocrine, chronic stimulation of PDGFRα and the analysis of GBM signaling pathways using proteomics. We discovered the tubulin-binding protein Stathmin1 (STMN1) as a PDGFRα phospho-regulated target and that this mis-regulation conferred selective sensitivity to vinblastine (VB) cytotoxicity. Treatment of PDGFRα GBMs with VB in mice drastically prolonged survival and was dependent on STMN1. Our work provides a rationale for evaluating genotype-specific anti-microtubule drugs as cancer treatment in select GBM patient populations.

overall_design: Total RNA was isolated from flash frozen tumors freshly excised from mice using Qiagen RNeasy RNA Isolation Kit. Gene expression analysis was conducted using the GeneChip® Mouse 2.0 ST Array (Affymetrix) at the Yale Center for Genome Analysis. Three biological replicates were profiles for each condition

first: Hyun-Jung

last: Jun

first: Al

last: Charest


title: TIGIT+ iTregs elicited by human regulatory macrophages control T cell immunity

status: Public on May 14 2018

city: Regensburg

first: James

middle: Alexander

last: Hutchinson

state: Bavaria

department: General Surgery

institute: University Hospital Regensburg

summary: Human regulatory macrophages (Mreg) have shown early clinical promise as a cell-based, adjunct immunosuppressive therapy in solid organ transplantation. It is hypothesised that recipient CD4+ T cell responses are actively regulated through direct allorecognition of donor-derived Mregs. Here we show that human Mregs convert allogeneic CD4+ T cells to IL-10-producing, TIGIT+ FoxP3+ induced regulatory T cells that non-specifically suppress bystander T cells and inhibit dendritic cell maturation. Differentiation of Mreg-induced Tregs (miTregs) relies on multiple, non-redundant mechanisms that are not exclusive to interaction of Mregs and T cells, including signals mediated by indoleamine 2,3-dioxygenase, TGF-β, retinoic acid, Notch and progestagen-associated endometrial protein. Preoperative administration of donor-derived Mregs to living-donor kidney transplant recipients results in an acute increase in circulating TIGIT+ Tregs. These results suggest a feed-forward mechanism by which Mreg treatment promotes allograft acceptance through rapid induction of direct pathway Tregs.

overall_design: To better characterise the phenotype of human miTregs, whole genome gene expression profiling studies by microarray were performed. Mregs and IFN-γ Mφ were generated from CD14+ monocytes of 5 healthy donors. Seven days later, CD3+ T cells were isolated from 5 unrelated healthy donors and split into two lots: From the first lot, a pure population of fresh CD4+ T cells was obtained by flow-sorting and total RNA was extracted; the second lot of T cells was added into direct co-culture with allogeneic Mregs or IFN-γ Mφ at a 1:1 ratio for 5 days, or were cultured alone without stimulation for 5 days. After coculture, CD4+ and CD8+ T cells were flow-sorted and total RNA was extracted. Microarray analysis was performed on the Agilent Whole Human Genome Oligo Microarray 8x60K platform. Hence, a dataset was generated comprising eight sample groups (S1-S8) representing four CD4+ T cell populations and four CD8+ T cell populations from 5 independent donors produced by single-colour hybridisations.

first: Paloma

last: Riquelme

first: Stefan

last: Tomiuk


title: Transcriptomic profiling of liver of Ctnnb1-KO and WT mice after 12 weeks exposure to Phenobarbital (miRNA)

status: Public on May 11 2018

city: Basel

first: Jonathan

last: Moggs

address: Fabrikstrasse 2

institute: Novartis

summary: Signaling through the Wnt/b-catenin pathway is a crucial determinant of hepatic zonal gene expression, liver development, regeneration, and tumorigenesis. The gene encoding b-catenin is called Ctnnb1. We have previously shown that liver tumour promotion mediated by the model tumour promoter phenobarbital (PB) is completely lost in mice, where Ctnnb1 has been conditionally knocked out in hepatocytes (CTNNB1KO mice; Rignall et al., Carcinogenesis 32, 52-57, 2010). In the present study, the effect of a 12 weeks PB exposure on the liver miRNA expression pattern was  investigated, in order to potentially get information on the nature of the loss of promotional activity in the CTNNB1KO mice.

overall_design: For animal used and experimental details see Braeuning et al., Histochem. Cell Biol 134, 469-481, 2010.

first: Albert

last: Braeuning

first: Michael

last: Römer

last: Schwarz


title: Analysis of gene expression profile in LPS-stimulated Maf-deficient BMDM

city: Hachioji

first: Kenta

last: Kikuchi

state: Tokyo

address: 1432-1, Horinouchi

institute: Immune regulation lab

summary: To characterize Maf-regulated gene clusters, we globally compared mRNA expression in LPS-stimulated Maf+/- and Maf-/- bone marrow derived macrophages.

overall_design: Gene expression in BMDM was measured 5 hours after stimulation with 100 ng/ml LPS.

first: Kenichi

last: Asano


title: Tissue damage signaling is essential for protective neutrophil recruitment to microbial infection in zebrafish (Danio rerio)

city: New York

first: Philipp

last: Niethammer

address: 430 East 67th street

institute: MSKCC

summary: RNAseq was performed on zebrafish larvae infected with bacteria under different osmotic pressures. The trascriptome profile generated here reveals the differential immune gene expression pattern.

overall_design: Pseudomonas aeruginosa resuspended in either standard or isotonic E3 were injected into the otic vesicle of zebrafish larvae. Uninjected zebrafish larvae served as control. Total RNA was extracted after 1 hour of infection and processed to following sequencing.

first: C

last: Huang

first: P


title: Recapitulation of pharmacogenomic data reveals that invalidation of SULF2 enhance sorafenib susceptibility in liver cancer

city: Suwon

first: Hyun Goo

last: Woo

address: 164 Worldcup-ro Yeongtong-gu

institute: Ajou University School of Medicine

summary: Gene mutations play critical roles during cancer development and progression, and therefore represent targets for precision medicine. Here we recapitulated the pharmacogenomic data to delineate novel candidates for actionable mutations and therapeutic target drugs. As a proof-of-concept, we demonstrated that the loss-of-function of SULF2 by mutation (N491K) or inhibition enhanced sorafenib sensitivity in liver cancer cells and in vivo mouse models. This effect was mediated by deregulation of EGFR signaling and downstream expression of LCN2. We also report that the liver cancer patients non-responding to sorafenib treatment exhibit higher expression of SULF2 and LCN2. In conclusion, we suggest that SULF2 plays a key role in sorafenib susceptibility and resistance in liver cancer via deregulation of LCN2. Diagnostic or therapeutic targeting of SULF2 (e.g., OKN-007) and/or LCN2 can be a novel precision strategy for sorafenib treatment in cancer patients.

overall_design: The analysis of gene expression profiling according to SULF2 condition.

first: H


title: Genome-wide analysis of gene expression in Panc-1 and BxPC-3 cells subjected to iExosomes treatment and control treatments

status: Public on May 09 2018

city: Houston

first: Valerie

last: LeBleu

state: TX

address: 1881 East Road

institute: MDACC

summary: In this study Panc-1 cells and BxPC-3 cells were cultured. The cells were harvested (untreated control 'cont') for RNA extraction, or treated for 3 hours with various exosomes preparations. The exosomes were collected from BJ human foreskin fibroblast culture supernatant without further processing (control exosomes or 'CE'), or engineered to contain scrambled siRNA ('scr') or KRASG12D siRNA ('iExo). Two or three distinct wells of cells were evaluated per treatment condition and assigned a well number (well -1, -2 or 3).

overall_design: RNA from cultured Panc-1 and BxPC-3 human pancreas cancer cells was harvested. Controls included untreated cells, and cells treated with control exosomes and scramble siRNA containing exosomes. The exosomes were obtained from  BJ human foreskin fibroblast culture supernatant. The recipient cells were incubated for 3 hours with the indicated treatments. The cells were also treated with iExosomes, which consist in  exosomes obtained BJ human foreskin fibroblast culture supernatant and electroporated with siRNA that target KRASG12D.


title: Gene expression profiling of mouse small intestinal myofibroblast after stimulation with homogenate of intestinal eosinophil

city: Minato-ku

first: Naoki

last: Takemura

address: 4-6-1 Shirokanedai

department: International Research and Development Center for Mucosal Vaccines

institute: Institute of Medical Science, The University of Tokyo

summary: GeneChip® Mouse Gene 2.0 ST Array was used to comprehensively investigate the changes of gene expression of small intestinal myofibroblasts of mice after stimulation with homogenates of intestinal eosinophils in vitro.

overall_design: Intestinal subepithelial myofibroblasts were obtained from small intestine of wild-type BALB/c mice. Myofibroblasts were incubated in the absence or presence of homogenate of intestinal eosinophils (5 mg/ml) for 1 day. Cells were cultured in triplicate. Total RNA was extracted, pooled, and subjected to analysis by GeneChip® Mouse Gene 2.0 ST Array.

first: Satoshi

last: Uematsu


title: Integrative analysis of gut microbiota composition, host colonic gene expression and intraluminal metabolites in aging C57BL/6J mice

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

summary: Diminished colonic health is associated with various age-related pathologies. In this study, we applied an integrative approach to reveal potential interactions between determinants of colonic health in aging C57BL/6J mice. Analysis of gut microbiota composition revealed an enrichment of various potential pathobionts, including Desulfovibrio spp., and a decline of the health-promoting Akkermansia spp. and Lactobacillus spp. during aging. Intraluminal concentrations of various metabolites varied between ages and we found evidence for an increased gut permeability at higher age. Colonic gene expression analysis suggested that during the early phase of aging (between 6 and 12 months), expression of genes involved in epithelial-to-mesenchymal transition and (re)organization of the extracellular matrix were increased. Differential expression of these genes was strongly correlated with Bifidobacterium spp. During the later phase of aging (between 12 and 28 months), gene expression profiles pointed towards a diminished antimicrobial defense and were correlated with an uncultured Gastranaerophilales spp. This study demonstrates that aging is associated with pronounced changes in gut microbiota composition and colonic gene expression. Furthermore, the strong correlations between specific bacterial genera and host gene expression may imply that orchestrated interactions take place in the vicinity of the colonic wall and potentially mediate colonic health during aging.

overall_design: Male C57BL/6J mice were randomly distributed into four groups that were sacrificed at 6, 12, 24 and 28 months. Mice were housed individually and fed an ad libitum semi-synthetic (AIN-93W) control diet.  Upon sacrifice at 6, 12, 24 or 28 months of age, colonic scrapings were collected and RNA was isolated for microarray analyses.

first: Benthe

last: van der Lugt

first: Fenni

last: Rusli

first: Carolien

last: Lute

first: Andreas

last: Lamprakis

first: Ethel

last: Salazar

first: Mark

last: Boekschoten

middle: J

last: Müller

first: Jacques

last: Vervoort

first: Sander

last: Kersten

first: Clara

last: Belzer

first: Dieuwertje

last: Kok

first: Wilma

last: Steegenga


title: Expression analysis of platinum sensitive and resistant epithelial ovarian cancer patient samples.

city: Tampere

first: Mauro

last: Scaravilli

address: Arvo Ylpön katu 34 D253

department: BioMediTech

country: Finland

institute: University of Tampere

summary: The objective of this work was to identify potential cancer biomarkers by analyzing microarray and protein expression data from platinum-sensitive and -resistant ovarian cancer patient samples. The gene expression profiles of the samples were ompared based on platinum sensitivity status and PARP levels.

overall_design: 6 clinical samples of platinum sensitive and 6 samples of resistant.

first: Kristina

last: Veskimäe

first: Serafiina

last: Jaatinen


title: Atrial Molecular Asymmetry Precedes the Emergence of Cardiac Septation II

city: Bad Nauheim

first: Almary

middle: Victoria

last: Guerra Rodríguez

state: Hessen

address: Ludwigstrasse 43

department: Dept. III Developmental Genetics

country: Germany

institute: Max Planck Institute for Heart and Lung Research

summary: For the study of possible downstream targets of Meis2b, we compared the following expression profiles: 48hpf whole larvae of meis2bs988/s988 to meis2b+/+ siblings, whole heart of 3 wpf meis2bs988/s988 to meis2b+/s988 siblings, atria of 3 mpf meis2bs988/s988 to meis2bs988/+ siblings, and ventricle to atrium of 3 mpf WT zebrafish.

overall_design: Meis2b mutants

last: Guerra

first: Raoul

last: Germano

first: Oliver

last: Stone

first: Rima

last: Arnaut

first: Benoit

last: Vanhollebeke

first: Didier

last: Stainier

first: Sven

last: Reischauer


title: Atrial Molecular Asymmetry Precedes the Emergence of Cardiac Septation I

summary: Comparison of total RNA of atrial and ventricular chambers from adult zebrafish heart. The goal was to identify chamber specific transcripts and atrial enriched transcripts that can be linked to atrial or ventricular septal defects in mammals.

overall_design: The hearts of 12 adult zebrafish (6mpf) were extracted and the atria were dissected from the ventricles. The total RNA of the atria was compared to the total RNA from the ventricles.


title: Identification of SoxC-regulated genes during neurogenesis in the developing spinal cord [chicken]

status: Public on May 10 2018

city: Erlangen

first: Michael

last: Wegner

address: Fahrstr. 17

department: Institut of Biochemistry

summary:
The HMG-domain containing SoxC transcription factors Sox4 and Sox11 are expressed in the vertebrate central nervous system in neuronal precursors and neuroblasts. They are required during early stages of neurogenesis.
Here we perform micorarray analysis to identify genes that are downstream of these SoxC proteins during spinal cord neurogenesis in chicken. The identified genes represent potential direct target genes of Sox4 and Sox11.

overall_design: The neural tube of chicken embryos were electroporated at HH9 stage with shRNA expression plasmids . Electroporated cells were obtained by FACS from neural tubes at HH11 and used to prepare total RNA. Overall gene expression patterns were compared between control transfected cells and cells transfected with Sox11- and Sox4-shRNAs using Affymetrix microarrays.

first: Franziska

last: Fröb

first: Johannes

last: Thalhammer

first: Elisabeth

last: Sock


title: Differential gene expression profile of human neutrophils cultured with Plasmodium falciparum-parasitized erythrocytes

status: Public on May 07 2018

city: Obihiro

first: Ryo

last: Takano

state: Hokkaido

address: Inada-cho

department: National Research Center for Protozoan Diseases

institute: Obihiro University of Agriculture and Veterinary Medicine

summary: Neutrophils (PMNs) are the most abundant cellular component of our innate immune system, where they play central roles in the pathogenesis of and resistance to a broad range of diseases. However, their roles in malarial infection remain poorly understood. Therefore, we examined the transcriptional gene profile of human PMNs in response to Plasmodium falciparum-parasitized erythrocytes (iRBCs) by using oligonucleotide microarrays. Results revealed that PMNs induced a broad and vigorous set of changes in gene expression in response to malarial parasites, represented by 118 upregulated and 216 downregulated genes. The transcriptional response was characterized by the upregulation of numerous genes encoding multiple surface receptors, proteins involved in signal transduction pathways, and defense response proteins. This response included number of genes which are known to be involved in the pathogenesis of malaria and other inflammatory diseases. Gene enrichment analysis suggested that the biological pathways involved in the PMNs responses to the iRBCs included insulin receptor, Jak-STAT signaling pathway, mitogen activated protein kinase (MAPK), and interleukin and interferon-gamma signaling pathways. The current study provides fundamental knowledge on the molecular responses of neutrophils to malarial parasites, which may aid in the discovery of novel therapeutic interventions.

overall_design: Polymorphonuclear leukocytes (PMNs; neutrophils) were co-cultured with un-infected red blood cells (RBCs) or P. falciparum parasite-infected RBCs (iRBCs). At 1 hour post co-cultivation, the cells were harvested and subjected to microarray analysis (four technical replicates per each group)

first: Alaa

last: Terkawi Mohamad


title: Drosophila CNS mitochondrial dysfunction with Ras/MAPK inhibition microarray

status: Public on May 05 2018

city: London

first: Joseph

middle: M.

last: Bateman

state: (Click to Select US State)

address: Guy's campus

institute: King's College London

summary:
Mitochondrial dysfunction causes biophysical, metabolic and signalling changes that alter homeostasis and reprogram cells. We used a Drosophila model in which TFAM is overexpressed in the nervous system with or without Ras/MAPK pathway inhibition, by knock-down of the ETS transcription factor pointed, to investigate the how mitochondrial dysfunction and Ras/MAPK signalling affect the transcriptome.
We used microarray analysis to investigate gene expression in cases of mitochondrial dysfunction in the CNS with or without Ras/MAPK pathway inhibition by knock-down of pointed (Pnt) and anterior open (Aop).

overall_design: RNA was purified from the late third instar larval CNS from control larvae, or larvae over-expressing mitochondrial transcription factor A (TFAM) in post-mitotic neurons using the neuron specific driver nSyb-Gal4, or larvae over-expressing TFAM in combination with knock-down of Pnt or Aop.  nSyb-Gal4 driving Pnt or Aop knock-down alone conditions were also included. Three replicates are included for all conditions.

middle: M

first: Olivia

last: Duncan


title: FACS-sorted Six2-positive nephron progenitor cells at embryonic day 15.5: wildtype (WT) vs. conditional HDAC1&2-null (MUT)

status: Public on May 08 2018

city: New Orleans

first: Samir

middle: S

last: El-Dahr

address: 1430 Tulane Ave

department: Pediatrics

institute: Tulane University School of Medicine

summary: Transcriptional profiling of FACS-sorted Six2-positive nephron progenitor cells from Six2CreEGFP mice without (WT) or with (MUT) homozygously floxed HDAC1 and HDAC2 alleles at the age of embryonic day 15.5. This experiment aimed to uncover the genome-wide alternation in gene expression resulting from the removal of HDAC1&2 in the nephron progenitor population and successive changes to the series of events in kidney development.

overall_design: Two-condition experiment, WT vs. MUT cells. Biological replicates: 4 WTs and 4 MUTs.

first: Liu

last: Hongbing

first: Chen

last: Shaowei

first: Yao

last: Xiao

first: Li

last: Yuwen

last: Jiao

first: Saifudeen

last: Zubaida

first: El-Dahr

last: Samir


title: miR-585-5p overexpression effect on tongue cancer cells

first: Heyu

last: Zhang

address: 22 South Zhongguancun Avenue, Haidian District

country: China

institute: Peking university school of stomatology

summary:
Analysis of SCC-9 tongue cancer cells overexpressing miR-585-5p. miR-585-5p is frequently downregulated in primary tongue cancer. Results provide insight into the role of miR-585-5p in the pathogenesis of tongue cancer.
We used micorarrays to detailed the genes regulated by miR-585-5p in SCC-9 cells.

overall_design: We trasfected SCC-9 cells with miR-NC (control) or miR-585-5p mimics (30nM). 36 hours later,  RNA was extracted by Qiangen RNA Isolation Kit.

first: Yongmei

last: Song

first: Qimin

last: Zhan

first: Tiejun

last: Li


title: iac gene expression in the indole-3-acetic acid-degrading soil bacterium Enterobacter soli LF7

city: Davis

first: Johan

last: Leveau

state: CA

address: One Shields Ave

department: Plant Pathology

country: USA

institute: University of California, Davis

summary:
We show for soil bacterium Enterobacter soli LF7 (synonym Enterobacter asburiae LF7a) that possession of a iac (indole 3-acetic acid catabolic) gene cluster is causatively linked to the ability to utilize the plant hormone indole 3-acetic acid (IAA) as a carbon and energy source. Genome-wide transcriptional profiling by mRNA sequencing revealed that these iac genes chromosomally arranged as iacHABICDEFG and coding for the transformation of IAA to catechol, were the most highly induced (>29-fold) among the relatively few (<1%) differentially expressed genes in response to IAA. Also highly induced and immediately downstream of the iac cluster were genes for a Major Facilitator Superfamily protein (mfs) and enzymes of the β-ketoadipate pathway (pcaIJD-catBCA), which channels catechol into central metabolism. This entire iacHABICDEFG-mfs-pcaIJD-catBCA gene set was constitutively expressed in a iacR deletion mutant, confirming the role of iacR, annotated as coding for a MarR-type regulator and located upstream of iacH, as a repressor of iac gene expression.

The research described here was funded from grants #2010-03544 and #2013-02075 awarded to JHJL by the United States Department of Agriculture (USDA) National Institute of Food and Agriculture (NIFA) Agriculture and Food Research Initiative (AFRI)

overall_design: Orthogonal comparison of gene expression profiles generated by illumina sequencing of RNA from two bacterial strains, i.e. wildtype (wt or WT) Enterobacter soli LF7 and its  iacR targeted deletion mutant ΔiacR::cat (mut or DeltaR),  growing on succinate, and spiked with 200uM indole-3-acetic acid (+IAA or IAA200) or not (-IAA or H2O).

middle: H

first: Isaac

middle: V

last: Greenhut


title: Evaluating Mice lacking Serum Carboxylesterase as a Behavioral Model for Nerve Agent Intoxication

status: Public on May 04 2018

city: Aberdeen Proving Ground

first: Heidi

last: Hoard-Fruchey

state: MD

address: 2900 Ricketts Point Rd

institute: USAMRICD

summary:
Mice and other rodents typically used for nerve agent research have high concentrations of carboxylesterase in the blood that can act as natural scavengers for nerve agents.
To develop an improved rodent system for the study of chemical warfare nerve agents, a serum carboxylesterase knock out mouse model was made (Es-1 knock out).
This study utilized mRNA analysis to evaluate the effects of knocking out the serum carboxylesterase in a mouse model.

overall_design:
Brain, heart, kidney, liver, and lung tissues were collected from naïve knock out mice. Both male and female animals were included in the study.
Total RNA was isolated and processed for hybridization to Affymetrix GeneChip HT MG-430 PM oligonucleotide microarrays.

first: Emily

last: Dunn

first: C

middle: L

last: Cadieux