title: MeDIP-sequencing of shSRC-1 and shNT tamoxifen treated LY2 cells

city: Dublin

first: Leonie

last: Young

address: York Street

department: Surgery

country: Ireland

institute: Royal College of Surgeons, Ireland

summary: The steroid co-activator protein SRC-1 plays an important role in endocrine therapy resistant breast cancer. Its expression is associated with large high grade tumours, HER2 positivity, disease recurrence and resistance to endocrine therapy. While SRC-1 typically functions to activate gene expression, some evidence has pointed towards a potential role in repression. This study looks into the effects of a stable knockdown of SRC-1 in a tamoxifen resistant cell line, LY2, and the effects of this knock down on the methylation landscape.

overall_design: We report the MeDIP-sequencing of tamoxifen treated LY2 breast cancer cells treated with non-targeting shRNA or SRC-1 (NCOA1) targeting shRNA and examine the methylation differences.

middle: S

first: Ailis

last: Fagan

first: Elspeth

last: Ward


title: DNA methylation and expression profiles in wild-type and IDH1 R132H/WT human astroglial cells

status: Public on Jun 01 2018

city: Baltimore

first: Jie

last: Wang

state: Maryland

address: 400 N Broadway

country: USA

institute: Johns Hopkins University

type: Methylation profiling by genome tiling array

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Improved mapping and characterization of R-loop forming loci in fission yeast.

city: Davis

first: Frederic

last: Chedin

state: CA

address: 1 Shields Avenue

department: MCB

institute: UC Davis

type: Non-coding RNA profiling by high throughput sequencing

summary: R-loops both threaten genome integrity and act as physiological regulators of gene expression and chromatin patterning. To characterize R-loop forming loci in the fission yeast, we used the S9.6-based DRIPc-seq approach to obtain improved strand-specific maps of R-loop forming loci at near nucleotide resolution. We show that the weak affinity of the S9.6 antibody for double-stranded RNA (dsRNA) is sufficient to confound the mapping of genuine R-loops by this approach. dsRNA elimination allowed the identification of two distinct classes of R-loops that differ by their sensitivity to endogenous RNase H activity. Both classes associate with common chromatin features, which are similar to those associated with R-loop formation in human. We used RNA-seq to identify transcripts whose steady-state levels were affected by genome-wide manipulation of R-loop levels. gdh2 is such a transcript and we show that extra RNase H1 stimulates the cis-acting transcription interference between an upstream non-coding RNA and gdh2. Surprisingly, we found that most transcripts whose levels were altered by in vivo manipulation of R-loop levels did not form R-loops. Conversely, the abundance of only few R-loop forming transcripts was impacted by genome-wide variation of R-loop levels. We conclude that prolonged manipulation of R-loop levels imparts indirect effects on the transcriptome that could complicate the use of this strategy to understand R-loop functions.

overall_design: DNA-RNA immunoprecipitation strand-specific (DRIPc-seq) were performed on Schizosaccaromyces pombe cells from different genotypes (Wild-type, RNaseH1 overexpressed, RRP6 KO, RNaseH1+2 KO). Genomic DNA was treated with either RNaseA, RNaseA+H, RNaseA+III prior DRIPc-seq. Total RNA-seq was performed on Schizosaccaromyces pombe cells treated with several conditions (Wild-type, RNaseH1 overexpression, RNaseH1+2 KO). Small RNA-seq was performed on Schizosaccaromyces pombe Wild-type cells.

first: Stella

middle: R

last: Hartono

first: Amélie

last: Malapert

first: Pénélope

last: Legros

first: Pascal

last: Bernard

first: Vincent

last: Vanoosthuyse


title: Gene expression profile of WT and phoP mutant Mtb under heat-shock condition

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

summary: Heat-shock of 1 hr 30 min was given to WT and phoP mutant Mtb and gene expression profile was studied

overall_design: Organism : M.tuberculosis, Agilent's custom M.tb Gene Expression  8x15k Array (AMADID: 030010) designed by Genotypic technology Private Limited, Bangalore.

first: Ritesh

last: Sevalkar

first: Dibyendu

last: Sarkar


title: The transcription factor Grainyhead primes epithelial enhancers for spatiotemporal activation by displacing nucleosomes [evolutionary study]

status: Public on Jun 04 2018

city: Vienna

first: Jelle

last: Jacobs

address: Campus-Vienna-Biocenter 1

department: VBC

country: Austria

institute: Institute of molecular Pathology

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Transcriptional enhancers function as docking platforms for combinations of transcription factors to control gene expression. How enhancer sequences determine nucleosome occupancy, transcription factor recruitment, and transcriptional activation in vivo remains unclear. Using ATAC-seq across a panel of Drosophila inbred strains we found that SNPs affecting Grainyhead binding sites causally determine the accessibility of epithelial enhancers. We show that deletion or ectopic expression of Grh causes loss or gain of DNA accessibility, respectively. However, while Grh binding is necessary for enhancer accessibility, it is insufficient to activate enhancers. Finally, we show that human Grh homologs, GRHL1/2/3, function similarly. We conclude that Grh binding is necessary and sufficient for the opening of epithelial enhancers, but not for their activation. Our data support the model that complex spatiotemporal expression patterns are controlled by regulatory hierarchies in which pioneer factors, such as Grh, establish tissue-specific accessible chromatin landscapes upon which other factors can act.

sample_organism:
Drosophila ananassae
Drosophila erecta
Drosophila melanogaster
Drosophila mojavensis
Drosophila persimilis
Drosophila pseudoobscura
Drosophila sechellia
Drosophila simulans
Drosophila virilis
Drosophila yakuba
Drosophila willistoni

overall_design: ATAC-seq on 11 Drosophila Species to identify co-motifs in conserved Grainyhead enhancers.

first: J

first: S

last: Aerts


title: Hepatic lipid metabolism in chicken lines divergently selected for abdominal fat content

city: Harbin

first: Zhi-Qiang

last: Du

address: 59 Mucai Street, XiangFang District

country: China

institute: Northeast Agricultural University

summary: We performed gene expression profiling on chicken livers at five important embryonic developmental stages (E7, E12, E14, E17 and E21), which were selected from chicken lines with significant differences in abdominal fat content. Each developmental stage had its unique gene expression pattern and stage-specific differentially expressed genes (DEGs). Furthermore, the three rapid growth periods (E12, E14 and E17) had similar expression patterns. Between the two broiler lines, E17 had the largest number of significantly differentially expressed genes (979), specifically enriched in fatty acid metabolism and biosynthesis, PPAR signaling and glycolysis pathways. Therefore, genome-wide gene expression recapitulated the developmental pattern of chicken embryos, and found the important molecular pathways for hepatic lipid metabolism.

overall_design: digital gene expression on chicken embryo livers at different developmental stages

first: Hui

last: Li


title: The transcription factor Grainyhead primes epithelial enhancers for spatiotemporal activation by displacing nucleosomes [ATAC-seq]

overall_design:
ATAC-seq on inbred Drosophila Melanogaster strains from the DGRP project to identify Chromatin Accessibility QTLs.
ATAC-seq on the eye-antennal and wing imaginal discs of animals with stably integrated enhancer reporter constructs (PSA268-271).
ChIPmentation-seq on the transcription factor Grainyhead in eye-antennal and wing imaginal discs.


title: RNA-sequencing and MeDIP-sequencing of shSRC-1 and shNT tamoxifen treated LY2 cells

first: Leonie

last: Young

type: Methylation profiling by high throughput sequencing


title: Long noncoding RNA LNMAT1 promotes lymphatic metastasis in bladder cancer

city: Guangzhou

first: Changhao

last: Chen

state: Guangdong

address: Department of Urology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 107 Yan-Jiang Xi Road, Guangzhou, 510120, China

department: Department of Urology

institute: Sun yat-sen university

summary: Long non-coding RNAs (lncRNAs) are a large class of non-protein-coding transcripts that are over 200nt in length. LncRNAs have emerged as key regulator of biological process involved in the development and progression of bladder cancer. Bladder cancer is one of the most common genitourinary malignancies worldwide, with approximately 429,800 new cases and 165,100 deaths annually in the world. To identify critical lncRNAs that contributes to the progression of bladder cancer, Next generation sequencing (NSG) was performed in five paired high-grade muscle invasive bladder cancer (MIBC) and normal adjacent tissues (NAT), and in five lymph node (LN)-positive and LN-negative bladder cancer tissues. Our results indicate that the differential expressed lncRNAs in both MIBC tissues and LN-positive tissues associated in a variety of biological functions, such as metastasis.

overall_design: To identify critical lncRNAs that contributes to the progression of bladder cancer, NSG was performed in five paired high-grade muscle invasive bladder cancer and normal adjacent tissues and in five lymph node-positive and lymph node-negative bladder cancer tissues. The RNA of tissue was extracted and hybridized on illumina Hiseq 2500.

first: Tianxin

last: Lin


title: Assessing eRNAs associated with a cytokine-sensing mammary super-enhancer

city: Haining

first: Chaochen

last: Wang

address: 718 East Haizhou Rd

department: ZJU-UoE Institute

institute: Zhejiang University

summary: Enhancers are transcription factor platforms that also bind RNA polymerase II and  generate enhancer RNAs (eRNA). Although eRNAs have been suggested as predictors  of enhancer activities and possibly key components facilitating transcription, there is little  genetic evidence to support this. We address the biology of eRNAs in vivo and investigate  eRNA patterns, expression levels and possible functions within a mammary-specific  super-enhancer that is composed of three units with distinct transcriptional capacities. We  show that eRNA levels do not correspond with the activities of their respective enhancer  units. However, changes in eRNA expression upon deletion of individual enhancer units  reflect the change in overall super-enhancer activity. These data provide genetic evidence  that eRNA levels are not a reliable readout of individual enhancers, but they predict superenhancer  activity in the absence of constituent elements.

overall_design: ChIP-seq for H3K27ac, H3K4me3 and PolII in mammary tissues from mutant mice at lactation day 1 (L1).

first: Tyler

last: Kuhns

first: Christian

last: Reinbold

first: Michaela

last: Willi

first: Lothar

last: Hennighausen


title: Expression profiles in wild-type and IDH1 R132H/WT human astroglial cells [RNA-seq]

first: Jie

summary: Mutations in the isocitrate dehydrogenase 1 (IDH1) gene are critical to oncogenesis. The exact mechanism by which mutant IDH1 drives cell transformation is still not fully understood,  partially due to the difficulty of maintaining cells with endogenously mutated IDH1. We employed a “single base editing” technique and efficiently introduced the monoallelic point  mutation of IDH1 R132H (IDH1R132H/WT) into non-neoplastic human astroglial cells. Characterization of our cellular models revealed that IDH1R132H/WT inhibited cell proliferation  and promoted cell migration via mechanisms mediated by its oncometabolite 2-HG. Global gene expression and epigenetic analysis identified novel molecular targets of IDH1R132H/WT, namely  the Hippo pathway effector, Yes-associated protein (YAP), and its downstream signaling pathway Notch. In summary, the “single base editing” strategy introduces a new paradigm that  recapitulates the biological function of IDH1 R132H/WT and its oncometabolite 2-HG, which can be easily applied to other cell models. Our study provides a valuable model for novel discoveries of  molecular mechanisms during IDH1 R132H/WT-driven pre-cancerous events.

overall_design: We measured gene expression profiles of a wild-type and two IDH1R132H/WT clones from human astroglial cells

first: Shuang

last: Wei

first: Jiang

last: Qian

first: Shuli

last: Xia


title: Extracellular vesicle-mediated intercellular signaling between breast carcinoma cells and endothelial cells

city: BETHESDA

first: abdel

middle: G

last: Elkahloun

address: 50, SOUTH DRIVE

institute: NHGRI-NIH

summary: Huvec cells treated or not by exosomes from MDA-231 cell line.

first: Abdel

first: Sukhbir

last: Kaur


title: Functional study on the cooperation of ASXL1 and RUNX1 mutations for myeloid leukemia transformation

city: TauYau

first: Yun-Shien

last: Lee

state: Taiwan

address: TauYau

department: Dept. Biotechnology

country: Taiwan

institute: Ming Chuan Univ

summary:
BACKGROUND: Our previous studies showed that RUNX1 and ASXL1 mutations were frequently co-existed in chronic myelomonocytic leukemia (CMML) and clonal evolution of RUNX1 and/or ASXL1 occurred most frequently in chronic myeloid leukemia (CML) with myeloid blastic crisis. The molecular pathogenesis of cooperation of RUNX1 and ASXL1 mutations has not been reported yet.

METHODS: Lentiviral-mediated stable transduction of RUNX1-WT/MT (R135T) in K562 cells which harboring ASXL1-MT (Y591X). RNA was extracted from stable cell line and used for gene-expression microarray analysis.

RESULTS: For in vitro study, we overexpressed RUNX1-WT/MT (R135T) in K562 cells which harboring ASXL1-MT (Y591X). We found that RUNX1-MT augmented cell proliferation, colony formation, HOXA gene expression and inhibited megakaryocytic differentiation in ASXL1-MT K562 cells compared to RUNX1-WT or empty vector control. We performed gene expression profile of K562 cells overexpressed with EV, RUNX1-WT and RUNX1-R135T mutation. Gene expression microarray data revealed that 147 genes upregulated more than 2-fold in RUNX1-R135T expressing K562 cells compared to EV control cells. From gene expression data analysis, we found that inhibitor of DNA binding 1 (ID1), a key transcriptional regulator of hematopoietic stem cell (HSC) lineage commitment, is upregulated in RUNX1-R135T-transduced K562 cells compared to EV and RUNX1-WT-expressing cells.

overall_design: Lentiviral transduction mediated overexpressed RUNX1-WT/RUNX1-R135T in K562 cells. RNA extracted from stable cells and hybridization on Affymetrix microarrays.

first: Rabindranath

last: Bera

first: Lee

middle: Y

last: Shih

first: Ming

middle: C

last: Chiu

first: Ying

middle: J

last: Huang

first: Der

last: Liang

first: Yun


title: p63 regulates the switch from multipotency to unipotency during embryonic MG development

city: Brussels

first: Aline

last: Wuidart

address: Route de Lennik 808

country: Belgium

institute: ULB

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: Cédric

last: Blanpain


title: Effect of GFI1 KD vs GFI1 KO on expression profiling and AML occurence.

city: Montreal

first: Möröy

last: Tarik

state: Quebec

address: 110 Pine avenue West

country: Canada

institute: Insititut de Recherches Cliniques

summary: In order to indentify the transcriptional differences between GFI1 KD and GFI1 KO mice that may account for differences in occurence of AML between these mice, we performed exresiion profiling by RNA-Seq on healthy young and old mice mice from both genotypes. In the case of GFI1 KD, the older mice had developped AML whereas KO mice of comparable ages did not.

overall_design: For each genotype (Gfi1 KD and GFI1 KO), RNA was extracted from the bone marrow of 2 young healthy mice as a biological duplicate. Bone marrow RNA was also extracted from 2 older GFI1 KD mice with AML and 2 healthy GFI1 KO mice of comparable ages

first: Jennifer

last: Fraszczak

first: Tarik

last: Möröy

first: Charles

last: Vadnais


title: DNA methylation profiles in wild-type and IDH1 R132H/WT human astroglial cells [methylation]

first: Jie

last: Wang

summary: Mutations in the isocitrate dehydrogenase 1 (IDH1) gene are critical to oncogenesis. The exact mechanism by which mutant IDH1 drives cell transformation is still not fully understood, partially due to the difficulty of maintaining cells with endogenously mutated IDH1. We employed a “single base editing” technique and efficiently introduced the monoallelic point mutation of IDH1 R132H (IDH1R132H/WT) into non-neoplastic human astroglial cells. Characterization of our cellular models revealed that IDH1R132H/WT inhibited cell proliferation and promoted cell migration via mechanisms mediated by its oncometabolite 2-HG. Global gene expression and epigenetic analysis identified novel molecular targets of IDH1R132H/WT, namely the Hippo pathway effector, Yes-associated protein (YAP), and its downstream signaling pathway Notch. In summary, the “single base editing” strategy introduces a new paradigm that recapitulates the biological function of IDH1 R132H/WT and its oncometabolite 2-HG, which can be easily applied to other cell models. Our study provides a valuable model for novel discoveries of molecular mechanisms during IDH1 R132H/WT-driven pre-cancerous events.

overall_design: We profiled DNA methylation in one wild-type and two IDH1R132H/WT human astroglial cells

first: Shuang

last: Wei

first: Jiang

first: Shuli


title: Dual effect of the Nrf2 inhibitor for inhibition of HCV and cell proliferation

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

summary: We investigated whether brusatol, an Nrf2 inhibitor, has dual effects as anti-HCV and anti-hepatocellular carcinoma (HCC) and whether brusatol can enhance the similar dual effects of sorafenib. We showed that brusatol has dual effects as anti-HCV and anti-HCC and can enhance the similar in vitro effect by sorafenib and that there is potential of combination therapy of brusatol and sorafenib for HCV-related HCC.

overall_design: We performed microarray analysis for 2 samples;one from the control HPI cell, HCV-persistently infected Huh7.5 cell and the other from the HPI cell treated with brusatol, Nrf2 inhibitor, at a concentration of GI50.

first: Sugiyama

last: Kazuo

first: Murakami

last: Yuko

first: Ebinuma

last: Hirotoshi

first: Nakamoto

last: Nobuyuki

first: Saito

last: Hidetsugu


title: Spontaneous intake of essential oils after a negative postnatal experience has long-term effects on blood transcriptome in chickens

city: Bordeaux

last: FOURY

address: 146 rue Léo Saignat

country: France

institute: INRAE

summary: The perinatal period is critical for farm animals which are very sensitive to external challenges at this stage; this is partly due to the immaturity of their digestive and immune systems and high demand on behavioural and physiological adaptation. In addition, recent studies have shown that perinatal stressors can be responsible for increased disease risk in adulthood. We therefore hypothesized that correct welfare-health (WH) management of the young animal would improve its ability to cope with various challenges encountered not only during early post natal life but also throughout its whole production life. This programme aims to mimick field issues in experimental designs to assess their short- and long-term effects on WH. For the chicken, the negative experience will be exposure to experimental conditions that reproduce the conditions encountered between hatching and delivery to the farm.

overall_design: For 24h after leaving the hatchery, the chicks will be kept without food and water in containers and subjected to a lower room temperature (22°C = cold vs 27°C = control) and shaking movements mimicking transport. Control animals will not be subjected to stressors after leaving the hatchery and will be placed in standard rearing conditions.

first: Marie

middle: P

last: Moisan

last: Foury

first: Laurence

last: Guilloteau

first: Christine

last: Leterrier

first: Anne

last: Collin


title: Microfluidic low-input fluidized-bed enabled ChIP-seq device for automated and parallel analysis of histone modifications

city: Blacksburg

first: Chang

last: Lu

state: VA

address: 235 Goodwin Hall, 635 Prices Fork Road, Virginia Tech

department: Chemical Engineering

institute: Virginia Tech

summary: Genome-wide epigenetic changes such as histone modifications form a critical layer of gene regulations and have been implicated in a number of different disorders such as cancer and inflammation. Progress has made to decrease the input required for gold-standard genome-wide profiling tools like chromatin immunoprecipitation followed by next generation sequencing (i.e. ChIP-seq) to allow scarce primary tissues of specific type from patients and lab animals to be tested. However, there has been very little effort to rapidly increase the throughput of these low-input tools. In this report, we demonstrate LIFE-ChIP-seq (Low-Input Fluidized-bed Enabled Chromatin Immunoprecipitation combined with sequencing), an automated and high-throughput microfluidic platform capable of running multiple sets of ChIP assays in as little as 1 h with as few as 50 cells per assay. Our technology will enable testing of a large number of samples and replicates with low-abundance primary samples in the context of precision medicine.

overall_design: We examined genome-wide H3K4me3 profiles of GM12878 cell line starting with 1000 cells down to as few as 50 cells per assay. The ChIP experiment was performed using an automated microfluidic device (LIFE-ChIP), which performed 4 replicate experiments in every run under the same operating conditions. We also demonstrated that the device was capable of profiling two histone marks (H3K4me3 and H3K27ac) in one run with two replicates on each mark. The file name contains information on "cell number per assay"_"loading volume in microliters"_"washing time in minutes"_"no. of chamber"_"no. of device/histone mark (in the case of two marks being tested)". For example, "300_120L_20W_C1_H3K4me3" refers to the dataset taken by having 300 cells per assay, using 120 microliters of loading volume, 20 min of washing per buffer, and chamber 1 for characterizing H3K4me3 among the two histone marks profiled in the same run.

first: Travis

last: Murphy


title: Global gene expression analysis of HDF, HDF OBM, CiOB, MSC-OBs, pOBs

status: Public on Jun 06 2018

city: Kyoto

first: Kenta

last: Yamamoto

address: Kajicho 465

department: Immunology

institute: Kyoto Prefectural University of Medicine

summary:
Comparason of each cell mRNA expression pattern
We induced osteoblastic nature in human fibroblast using small compounds. To confirm CiOB gene expression pattern similarity to mesenchymals stem cells derived osteoblasts and primary osteoblasts, we analyzed and compared the gene expression profiles of the samples by cDNA microarry. The analysis revealed that CiOB are similar to osteoblasts.

overall_design: 5 samples

first: Osam

last: Mazda


title: Promoter DNA sequence guides factors that position the +1 nucleosome and facilitate TBP binding

city: Geneva

first: Slawomir

last: Kubik

address: quai Ernest-Ansermet 30

department: Molecular Biology Department

country: Switzerland

institute: University of Geneva

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

sample_organism:
Saccharomyces cerevisiae
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae W303

overall_design: Refer to individual Series


title: Global gene expression analysis of resistant and susceptible apple cultivars challenged with Penicillium expansum

city: Beaucouzé

first: Mathilde

last: ORSEL

address: 42, rue Georges Morel

institute: IRHS

summary:
Blue mold, caused by Penicillium expansum, is responsible for postharvest losses of apple fruit, and threatens human health through production of the potent mycotoxin patulin. No major gene(s) providing resistance have as yet been identified, but recent studies indicate a quantitative control of the disease. An AryANE chip covering 60K apple transcripts was used to identify possible candidate gene(s) that are differentially regulated between resistant and susceptible cultivars upon P. expansum infection. Induction of cell wall related gene (PGIP1), and three genes involved in the â€˜down-streamâ€™ flavonoid biosynthesis pathway (CHS, FLS and LDOX), shows the fundamental role of cell wall as an important barrier, and contents of polyphenolic compounds of fruits as a quantitative components in enhancing disease resistance to blue mold. Moreover, exogenous application of Jasmonic acid hormone enhanced the defense mechanism in fruits. This is the first report linking Jasmonic acid and activation of cell wall and flavonoid pathway genes in apple fruit resistance to blue mold. Results provide an initial categorization of genes that are potentially involved in the resistance mechanism, and should be useful for developing tools for gene marker-assisted breeding of apple cultivars with an improved resistance to blue mold.
SUBMITTER_CITATION: Ahmadi-Afzadi, M., Orsel Baldwin, M., Pelletier, S., Cournol, M., Proux-Wéra, E., Nybom, H., Renou, J.-P. (2018). Genome-wide expression analysis suggests a role for jasmonates in the resistance to blue mold in apple. Plant Growth Regulation, 85 (3), 375-387. , DOI : 10.1007/s10725-018-0388-2

overall_design: 4 cultivars (2 resistant and 2 susceptible), each in 3 technical replicates, were inoculated with fungal spores, and samples from control and inoculated fruits were taken in 3 time points.

first: Masoud

last: Ahmadi-Afzadi

last: Orsel

first: Sandra

last: Pelletier

first: Maryline

last: Bruneau

first: Estelle

last: Proux-Wéra

first: Hilde

last: Nybom

first: Jean-Pierre

last: Renou


title: Investigating the role of SMCHD1 in de novo X chromosome inactivation

status: Public on Jun 07 2018

city: Boston

first: Chen-Yu

last: Wang

state: MA

address: 185 Cambridge Street

department: Molecular Biology

institute: Massachusetts General Hospital

summary: To investigate the effect of Smchd1 ablation on de novo X chromosome inactivation (XCI), we derived clonal neural progenitor cells (NPCs) from Smchd1+/+ (wild-type, WT) and Smchd1-/- mouse embryonic stem cells (ES cells; ESC). We generated allele-specific RNA-seq datasets from WT and Smchd1-/- NPCs to examine the effect of Smchd1 ablation on gene silencing. In addition, we produced allele-specific ChIP-seq profiles of H3K4me3, H3K27me3, CTCF, and RAD21 and Xist CHART-seq profiles in WT and Smchd1-/- NPCs to investigate the role of SMCHD1 on the distribution of euchromatin, facultative heterochromatin, architectural proteins, and Xist RNA on the inactive X chromosome (Xi). To determine the localization of SMCHD1 on the Xi, we employed allele-specific DamID-seq to map SMCHD1-binding regions in female mouse embryonic fibroblasts. Furthermore, we performed in situ Hi-C on WT NPCs, Smchd1-/- NPCs, and female ES cells undergoing XCI, in order to explore the role of SMCHD1 in regulating the higher-order structure of the Xi.

overall_design: RNA-seq, ChIP-seq for H3K4me3, H3K27me3, CTCF, and RAD21, Xist CHART-seq, and in situ Hi-C in neural progenitor cell clones derived from WT and Smchd1-/- female mouse embryonic stem cells (ES cells). DamID-seq for SMCHD1 and CBX1 in female mouse embryonic fibroblasts. In situ Hi-C on WT female mouse ES cells at different stages of X chromosome inactivation.

first: Jeannie

middle: T

last: Lee


title: The transcription factor Grainyhead primes epithelial enhancers for spatiotemporal activation by displacing nucleosomes

first: Jelle

last: Jacobs

sample_organism:
Drosophila ananassae
Drosophila erecta
Drosophila melanogaster
Drosophila mojavensis
Drosophila persimilis
Drosophila pseudoobscura
Drosophila sechellia
Drosophila simulans
Drosophila virilis
Drosophila yakuba
Drosophila willistoni
Homo sapiens


title: Gene expressions of H9s in different culture systems

city: Lincoln

first: Chi

last: Zhang

state: NE

address: 1901 Vine Street

institute: University of Nebraska - Lincoln

summary: H9s were cultued in 2D, static 3D and dynamic 3D suspension and in the microspace cell culture system for 3 days. mRNAs were sequenced.

overall_design: RNA deep sequencing

first: Yuguo

last: Lei


title: Effect of Tmsb4x knockout on TGF-ß/MRTF signaling

city: Osaka

first: Tsuyoshi

last: Morita

address: Yamadaoka 2-2, Suita

department: Graduate School of Medicine

institute: Osaka University

summary: Myocardin-related transcription factors (MRTFs) are robust co-activator of Serum Reponse Factor, and regulate cell adhesion and motility by controlling the transcription level of cytoskeletal components. In tumor progression, MRTFs has been reported to contribute to metastatic potential. Previously, we reported thymosin-ß4 (Tß4, which is encoded by Tmsb4x gene) as an activator of MRTFs. Enhanced expression of Tß4 is frequently observed during tumor progression, and associated with poor prognosis. However, the relationships between MRTFs and Tß4 in tumor progression are largely unknown. Here we analyze the effect of Tß4 knockout on the transcription levels of MRTFs-target genes. In particular, we focused on their functions in TGF-ß signaling because both MRTFs and Tß4 are down-stream effectors of TGF-ß.

overall_design: Wild-type and Tmsb4x knockdown B16F1 cells were treated with 10 ng/ml of TGF-ß1 for 2 days. For the inhibition of  MRTF signaling, cells were also treated with 10 µM MRTF inhibitor CCG1423.

first: Ken'ichiro

last: Hayashi


title: miR-204 blocks MYCN expression and is a novel a tumor suppressor in neuroblastoma tumorigenesis

city: Randwick

first: Daniel

last: Carter

address: Lowy Cancer Research Centre

country: Australia

institute: Children's Cancer Institute

summary: Neuroblastoma is a pediatric cancer of the sympathetic nervous system. MYCN amplification is a key indicator of poor prognosis for the disease, however, mechanisms by which MYCN promotes neuroblastoma tumorigenesis are not fully understood. In this study, we analyzed global miRNA and mRNA expression profiles of tissues at different stages of tumorigenesis from TH-MYCN transgenic mice, a model of MYCN-driven neuroblastoma. Based on a Bayesian learning network model in which we compared pre-tumor ganglia from TH-MYCN+/+ mice to age-matched wild-type controls, we devised a predicted miRNA-mRNA interaction network. Among the miRNA-mRNA interactions operating during human neuroblastoma tumorigenesis, we identified that miR-204 is a tumor suppressor miRNA that inhibits a subnetwork of oncogenes strongly associated with MYCN-amplified neuroblastoma and poor patient outcome. Accordingly, we found that MYCN was bound to the miR-204 promoter and repressed miR-204 transcription, while in contrast, miR-204 directly bound MYCN mRNA and repressed MYCN expression. In support of a tumor suppressor role, miR-204 overexpression significantly inhibited neuroblastoma cell proliferation in vitro and tumorigenesis in vivo. Together these findings identify novel tumorigenic miRNA gene networks and miR-204 as a tumor suppressor that regulates MYCN expression in neuroblastoma tumorigenesis.

overall_design: BE(2)C neuroblastoma cells with stably incorporated miR.204 under the control of a doxcycline responsive promoter were treated with or without doxycline for 48 hours. RNA was isolated for hybridization on Agilent SurePrint G3 Human GE 8x60K microarrays. Each sample has two replicates


title: ChIP-on-chip Rad52 in cdc25-22 rif1∆ and cdc25-22 rif1∆rad3∆ in S. pombe

status: Public on May 31 2018

first: Pei-Yun Jenny

last: Wu

address: 1 Rue Camille Saint Saens

institute: Institute of Biochemistry and Cellular Genetics

type: Genome binding/occupancy profiling by genome tiling array

summary: ChIP-on-chip of Rad52 at time 90' after cdc25-22 release

overall_design: Each ChIP was compared to its reciprocially labeled input sample. Duplicates for every strain.

first: Blanca

last: Gómez-Escoda

first: Pei-Yun


title: Promoter DNA sequence guides factors that position the +1 nucleosome and facilitate TBP binding [array]

first: Slawomir

last: Kubik

summary: Here we present evidence that precise positioning of the +1 promoter nucleosome in yeast is critical for efficient TBP binding and pre-initiation complex assembly, and is determined, at least in part, by the action of two key factors, the essential chromatin remodeler RSC and one (or more) of a small set of ubiquitous pioneer transcription factors (PTFs). Despite their widespread co-localization, we show that RSC and PTFs often act independently to generate accessible chromatin. Furthermore, we present evidence that RSC binding, as well as the strength and directionality of its action on nucleosomes, depends upon the arrangement of two specific DNA motifs relative to nearby PTF binding sites. Our results provide insights into how promoter DNA sequence instructs trans-acting factors to precisely control nucleosome architecture and stimulate transcription initiation.

sample_organism:
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae W303

overall_design: Two-channel microarrays were used. RNA isolated from a large amount of wt yeast from a single culture was used as a common reference. This common reference was used in one of the channels for each hybridization and used in the statistical analysis to obtain an average expression-profile for each 30 minute depletion timepoint relative to time zero. Two independent cultures were hybridized on two separate microarrays. For the first hybridization, the Cy5 (red) labeled cRNA from the sample is hybridized together with the Cy3 (green) labeled cRNA from the common reference. For the replicate hybridization, the labels are swapped. Each gene is represented twice on the microarray, resulting in four measurements per strain/timepoint.

first: Eoghan

last: O'Duibhir

first: Wim

last: de Jonge

first: Stefano

last: Mattarocci

first: Benjamin

last: Albert

first: Jean

middle: L

last: Falcone

first: Maria

last: Bruzzone

first: Frank

last: Holstege

first: David

middle: M

last: Shore


title: Vesicle treatment of HCT8 cells

city: Oslo

first: Siv

last: Gilfillan

address: Gaustadaleen 21

department: Norwegian Center for Molecular Medicine

country: Norway

institute: University of Oslo

summary: ChIP-seq and FAIRE -Seq data of HCT8 cells after 5h treatment of vesicles from EC or VC

overall_design: Vesicles isolated from E.coli or Vibrio and HCT8 cells treated with these for 5 h

first: Svitlana

last: Vdovikova

first: Antoni

last: Hurtado

first: Sun

middle: N

last: Wai


title: Ribosomal Oxygenase 2 Constrains A Latent Anthelmintic Pathway In Intestinal Epithelial Cells

city: Memphis

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

summary: Expulsion of parasitic gastrointestinal nematodes requires diverse effector mechanisms coordinated by a Th2-type response. The evolutionarily conserved JmjC protein ribosomal oxygenase 2 (Riox2, formerly Mina) has been shown to repress IL4, a key Th2 cytokine, suggesting Riox2 may negatively regulate parasite expulsion. Here we report that expulsion of parasitic nematodes was indeed accelerated in Riox2 deficient mice. Unexpectedly, this was associated not with an elevated Th2 but rather an impaired Th1-type response. Further, in vitro T cell differentiation, reciprocal bone marrow chimera and conditional KO experiments demonstrated that retarded parasite expulsion and a normal Th1-type response both required Riox2 in intestinal epithelial cells (IECs). Gene profiling experiments in IECs revealed anti-microbial α-defensin peptides to be the major target of Riox2-dependent repression. In vitro exposure to recombinant α-defensin peptides caused cytotoxic damage to whipworms. These results identify a latent IEC-intrinsic anthelmintic pathway actively constrained by Riox2 and point to α-defensins as important effectors that together with Riox2 would be attractive therapeutic targets for the control of nematode infection.

overall_design: RNA-Seq analysis of enriched cecal epithelial cells of uninfected Villin-Cre+::Riox2(flox/flox) and Villin-Cre+::Riox2(+/+) littermates; and from ceca of Riox2(-/-) and Riox2(+/+) littermates 21 days following Trichuris muris (TM) infection.

first: Meenu

last: Pillai

first: Belgacem

last: Mihi

first: Kenji

last: Ishiwata

first: Kiminori

last: Nakamura

first: Naoya

last: Sakuragi

middle: B

first: Toshinori

last: Nakayama

first: Tokiyoshi

last: Ayabe

first: Peter

last: Ratcliffe

first: Mathew

last: Coleman

first: Mark

last: Bix


title: ChIP-on-chip Rad52 in cdc25-22 and  cdc25-22 rad3∆ in Schizosaccharomyces pombe

first: Pei-Yun Jenny

last: Wu

summary: ChIP-on-chip of Rad52 at time 90' after cdc25-22 release.

overall_design: Each ChIP was compared to its reciprocially labeled input sample. Triplicates for every strain.

first: Blanca

last: Gómez-Escoda

first: Pei-Yun


title: Transcription Factors Dlx1 and Otp Segregate the Identity of Orexigenic/Anti-thermogenic- and Growth Promoting-Neurons in the Arcuate Nucleus

city: Gwangju

first: JANGHYUN

last: KIM

state: Gwangju

address: 33, YONGBONG-RO, BUK-GU, GWANGJU

department: Oral pathology

country: South Korea

institute: CNUDH

summary: The hypothalamic arcuate nucleus contains multiple types of neurons controlling critical physiological processes. However, the gene regulatory network directing their development remains rudimentary. Here we report that two transcription factors Otp and Dlx1 segregate the identity of orexigenic/anti-thermogenic NPY/AgRP- and growth-promoting GHRH-neurons in the developing arcuate nucleus. Otp-null and Dlx1-null mice lose NPY/AgRP and GHRH expression, respectively. Dlx1-null mice also show enhanced expression of Otp/NPY/AgRP, which is normalized in Dlx1;Otp-double mutant mice. Correspondingly, Dlx1-null mice exhibit decreased growth, lower body temperature and increased feeding. Furthermore, our genome-wide studies identify Otp as a negative target gene of Dlx1. Therefore, Otp is critical for NPY/AgRP-neuronal development, while Dlx1 promotes GHRH-neuronal development and antagonizes NPY/AgRP-neuronal development. These results identify a mechanism for segregating the identity of two functionally related neurons, and the Dlx1-Otp axis likely contributes to coordinating energy balance and growth by maintaining a proper ratio of NPY/AgRP- to GHRH-neurons.

overall_design: Chip-seq samples from wild-type hypothalamus were prepared for sequencing according to the Illumina protocol, and sequenced on the Illumina HiSeq 2500. We will then identified that Dlx1 could bind and regulate the gene transcription in hypothalamus development.

first: T

middle: K

last: An

first: J

middle: W

last: Lee


title: ChIP-on-chip of RPA (Ssb1) in cdc25-22 and cdc25-22 rad3∆ in S. pombe

summary: ChIP-on-chip of RPA at time 80' after cdc25-22 release


title: Replication origin mapping in cdc25-22 rif1∆ and  cdc25-22 rif1∆rad3∆ in S. pombe

summary: Identification of sites of replication initiation by copy number analysis, replicated DNA vs unreplicated DNA

overall_design: Comparison of samples before and after S phase entry; dye-swap experiments were performed and averaged. Triplicates for every condition


title: Radiation-induced molecular alterations after whole body irradiation in a mouse model

city: Northbrook

first: Michael

last: Falduto

state: IL

address: 1808 Janke, Unit M

institute: GenUs BioSystems, Inc.

summary: Long non-coding RNAs (lncRNAs) are emerging as key molecules in regulating many biological processes and have been implicated in development and disease pathogenesis. Biomarkers of cancer and normal tissue response to treatment are of great interest in precision medicine and for public health and medical management of disasters such as assessing radiation injury following accidental or intentional exposure. Circulating and functional RNAs, including microRNAs (miRNAs) and lncRNAs, in whole blood and other body fluids represent potential valuable candidates as biomarkers. Early prediction of possible acute, intermediate, and delayed effects of radiation exposure will enable timely therapeutic interventions. To address whether lncRNAs could serve as biomarkers for radiation bio-dosimetry, we performed whole genome transcriptome analysis in a mouse model after whole body irradiation. Differential lncRNA expression patterns were evaluated at 16-, 24-, and 48-hour time points post irradiation in total RNA isolated from whole blood of mice exposed to 1, 2, 4, 8, and 12 Gy of gamma-rays. Sham irradiated animals served as controls. Significant alterations in the expression patterns of lncRNAs were observed after different radiation doses at the various timepoints. We identified several lncRNAs known for DNA damage response as well as immune response as radiation induced biomarkers. Long non-coding RNA targets of tumor protein 53 (P53), Trp53cor1, Dino, Pvt1 and Tug1 and an upstream regulator of p53, Meg3 were altered in response to radiation. Gm14005 (Morrbid) and Tmevpg1 were regulated by radiation across all time points and doses. These two lncRNAs have important potential as blood based radiation biomarkers; Gm14005 (Morrbid) has recently been shown to play a key role in inflammatory response while Tmevpg1 has been implicated in the regulation of interferon-gamma. Precise molecular biomarkers will not only enable the development and effective use of medical countermeasures but also may be used to detect and circumvent or mitigate normal tissue injury in cancer radiotherapy treatments.

overall_design: 48 samples of mouse whole blood in batches of 3 biological replicates taken 6, 16, 24, or 48 hr after irradiation dose 0, 1, 2, 4, 8, or 12 Gy.

first: Molykutty

last: Aryankalayil

first: Sunita

last: Chopra

first: Joel

last: Levin

first: Iris

last: Eke

first: Adeola

last: Makinde

first: Shaoli

last: Das

first: Uma

last: Shankavaram

first: Claire

last: Vanpouille-Box

first: Sandra

last: Demaria

first: C


title: Replication origin mapping in nda3-km311 and  nda3-km311 rad3∆ in S. pombe

first: Pei-Yun Jenny

summary: Identification of sites of replication initiation by copy number analysis, replicated DNA (time 80) vs unreplicated DNA (time 0).

overall_design: Comparison of samples before and after S phase entry; dye-swap experiments were performed and averaged. Duplicates for every condition

first: Anthony

last: Perrot


title: VT257_DengueVaccination

city: Stanford

first: Stephen

last: Popper

department: Division of Infectious Diseases, Dept. of Medicine

institute: Stanford University

summary: Healthy flavivirus-naive volunteers (n=10) were vaccinated with the live attentuated dengue vaccine rDEN3∆30/31.  An additional 4 subjects received placebo (PBS).  Whole blood RNA (paxgene) for expression profiling was collected prior to vaccination (day 0), and on days 2,5,6,8,9,12,14,20,29,42, and 180. All samples from a given individual were extracted and prepared for hybridization at the same time; in some cases D0 samples were amplified and/or hybridized twice for quality control; results were averaged for subsequent analysis.  Comparisons between subjects were carried out after normalizing the data at each post-vaccination timepoint to the same subject's D0 (pre-vaccination) measurements


title: Protective effects of INSL6 on heart failure

first: Chia-Ling

last: Wu

address: 700Albany St

department: Whitaker Cardiovascular Institute

institute: Boston University

summary: Background: The insulin/IGF/relaxin family represents a group of structurally related but functionally diverse proteins. The family member Relaxin-2 has been evaluated in clinical trials for its efficacy in the treatment of acute heart failure. In this study, we assessed the role of Insulin-like peptide 6 (Insl6), another member of this protein family, in murine heart failure models using genetic loss-of-function and protein delivery methods. Methods and Results: Insl6-deficient (Insl6-KO) and wild-type (C57BL/6N) mice were administered angiotensin II or isoproterenol via continuous infusion with an osmotic pump or via intraperitoneal injection once a day, respectively for 2 weeks. In both models, Insl6-KO mice exhibited greater cardiac systolic dysfunction and left ventricular dilatation hypertrophy. Cardiac dysfunction in the Insl6-KO mice was associated with more extensive cardiac fibrosis and greater expression of fibrosis-associated genes. The continuous infusion of chemically synthesized INSL6 significantly attenuated left ventricular systolic dysfunction and cardiac fibrosis induced by isoproterenol infusion. Gene expression profiling suggests Lxr/ Rxr signaling is activated in the isoproterenol-challenged hearts treated with INSL6 protein. Conclusions: Endogenous Insl6 protein inhibits cardiac systolic dysfunction and cardiac fibrosis in angiotensin II- and isoproterenol-induced cardiac stress models. The administration of recombinant Insl6 protein could have utility for the treatment of heart failure and cardiac fibrosis.

overall_design: 3 groups with 2 comparisons. Normal heart vs. heart treated with Iso, and heart treated with Iso vs. heart treated with Iso and INSL6 protein.

first: Sonomi

last: Maruyama

first: Kenneth

last: Walsh


title: Gene expression in mouse ventromedial hypothalamus (VMH) after deletion of SIRT1 in SF1 neurons

first: Giorgio

last: Ramadori

address: Michel Servet 1

summary: VMH was dissected from 16-week-old mice with deletion of SIRT1 in SF1 neurons (Sf1-Cre; Sirt1loxP/loxP) and intact controls (Sirt1loxP/loxP) and fed on high calorie diet from 8 weeks of age.

overall_design: 3 control replicates, 3 SIRT1 deletion replicates.

first: Roberto

last: Coppari


title: CTCFL

status: Public on May 30 2018

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

country: Germany

institute: Justus-Liebig-University Giessen

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

overall_design: Refer to individual Series


title: Gene expression changes after Ctcfl overexpression in NIH3T3 cells.

summary: The two paralogous zinc finger factors CTCF and CTCFL differ in expression such that CTCF is ubiquitously expressed, whereas CTCFL is found during spermatogenesis and in some cancer types. Both factors share the highly conserved DNA binding domain and are bound to DNA sequences with an identical consensus. Here we analyzed the differential gene expression effect mediated by expression of Ctcfl in undifferentiated and differentiated NIH3T3 cell.

overall_design: NIH3T3 cells stably transfected with inducible Ctcfl expression vectors were used for RNA extraction and hybridization on Affymetrix microarrays. We analyzed gene expression in the presence/absence of Ctcfl.

first: Rainer

last: Renkawitz

first: Philipp

last: Bergmaier


title: Diverse AR-V7 cistromes in castration-resistant prostate cancer are governed by HoxB13

city: Durham

first: Zhong

last: Chen

state: NC

address: 905 S. LaSalle Street

department: Pathology

institute: Duke University

summary: The constitutively active androgen receptor (AR) splice variant 7 (AR-V7) plays an important role in the progression of castration-resistant prostate cancer (CRPC). Although biomarker studies established the role of AR-V7 in resistance to AR-targeting therapies, how AR-V7 mediates genomic functions in CRPC remains largely unknown. Using a ChIP-exo approach, we show AR-V7 binds to distinct genomic regions and recognizes a full-length androgen-responsive element in CRPC cells and patient tissues. Remarkably, we find dramatic differences in AR-V7 cistromes across diverse CRPC cells and patient tissues, regulating different target gene sets involved in CRPC progression. Surprisingly, we discover that HoxB13 is universally required for and colocalizes with AR-V7 binding to open chromatin across CRPC genomes. HoxB13 pioneers AR-V7 binding through direct physical interaction, and collaborates with AR-V7 to up-regulate target oncogenes. Transcriptional coregulation by HoxB13 and AR-V7 was further supported by their coexpression in tumors and circulating tumor cells from CRPC patients. Importantly, HoxB13 silencing significantly decreases CRPC growth through inhibition of AR-V7 oncogenic function. These results identify HoxB13 as a pivotal upstream regulator of AR-V7-driven transcriptomes that are often cell context-dependent in CRPC, suggesting that HoxB13 may serve as a therapeutic target for AR-V7-driven prostate tumors.

overall_design: To identify AR-V7 and HoxB13 binding sites in CRPC, ChIP-exo and ATAC-seq were performed in CRPC cells and tissues. RNA-seq was performed to examine AR-V7 and HoxB13 regulated profiles. Each experiment includes two biological replicates.

first: Qianben

last: Wang


title: Distinct roles of cohesin-SA1 and cohesin-SA2 in 3D chromosome organization

city: Madrid

first: Ana

last: Losada

state: Madrid

address: C/ Melchor Fernández Almagro, 3.

department: Molecular Oncology Programme

country: Spain

institute: Centro Nacional de Investigaciones Oncológicas (CNIO)

summary: In addition to mediating sister chromatid cohesion, cohesin plays a central role in DNA looping and segmentation of the genome into contact domains (TADs). Two variant cohesin complexes that contain either STAG/SA1 or SA2 are present in all cell types. Here we addressed their specific contribution to genome architecture in non-transformed human cells. We found that cohesin-SA1 drives stacking of cohesin rings at CTCF-bound sites and thereby contributes to the stabilization and preservation of TAD boundaries. In contrast, a more dynamic cohesin-SA2 promotes cell type-specific contacts between enhancers and promoters within TADs independently of CTCF. SA2 loss, a condition frequently observed in cancer cells, results in increased intra-TAD interactions, likely altering the expression of key cell identity genes.

overall_design: ChIP-seq for cohesin subunits SMC1, SA1 and SA2 was performed in 3 different cell lines (MCF10A, HMEC, HCAEC) and peak calling was done against the input sample from the corresponding cell line. RNA-seq was performed in triplicates in MCF10A cells control depleated from SA1, SA2 or CTCF by means of Dharmacon SMART pool siRNAs. HiC-seq was performed in two replicates in MCF10A cells control and depleated from SA1 and SA2 by means of Dharmacon SMART pool siRNAs. 4C-seq was performed in MCF10A cells control and depleated from SA2 or CTCF.

first: Aleksandar

last: Kojic

last: Cuadrado

first: Daniel

last: Gimenez

first: Magali

last: De Koninck

first: Miriam

last: Rodríguez-Corsino

first: Gonzalo

last: Gómez-López

first: François

last: Le Dily

first: Marc

middle: A

last: Marti-Renom


title: Blood and Nasal Epigenetics Correlate to Allergic Rhinitis Symptom Development in the Environmental Exposure Unit

city: Vancouver

first: Michael

middle: S.

last: Kobor

state: BC

address: 950 West 28th Avenue

department: Medical Genetics

institute: Centre for Molecular Medicine and Therapeutics / University of British Columbia

summary: Epigenetic alterations may represent new therapeutic targets and/or biomarkers of allergic rhinitis (AR). Our aim was to examine genome-wide epigenetic changes induced by controlled pollen exposure in the Environmental Exposure Unit (EEU). 38 AR-sufferers and 8 non-allergic controls were exposed to grass pollen for 3h on two consecutive days. We interrogated DNA methylation at baseline and 3h in peripheral blood mononuclear cells (PBMCs) using the Infinium Methylation 450K array. We corrected for demographics, cell composition, and multiple testing (Benjamini-Hochberg), and verified hits using bisulfite PCR-pyrosequencing and qPCR. To extend these findings to a clinically relevant tissue, we investigated DNA methylation and gene expression of mucin 4 (MUC4), in nasal brushings from a separate validation cohort exposed to birch pollen. In PBMCs of allergic rhinitis participants, 42 sites showed significant DNA methylation changes of 2% or greater. DNA methylation changes in tryptase gamma 1 (TPSG1), schlafen 12 (SLFN12) and MUC4 in response to exposure were validated by pyrosequencing.  SLFN12 DNA methylation significantly correlated with symptoms (p<0.05), and baseline DNA methylation pattern was found to be predictive of symptom severity upon grass allergen exposure (p<0.05). Changes in MUC4 DNA methylation in nasal brushings in the validation cohort correlated with drop in peak nasal inspiratory flow (Spearman r = 0.314, p = 0.034), and MUC4 gene expression was significantly increased (p<0.0001). This study revealed novel and rapid epigenetic changes upon exposure in a controlled allergen challenge facility, identified baseline epigenetic status as a predictor of symptom severity.

overall_design: This cohort consist of genomic DNA extracted from lymphocyte-enriched blood samples from 15 Atopic and 8 non atopic participants. DNA was bisulphite converted and hybridized to the Illumina Infinium HumanMethylation450 Beadchip for genome wide DNA methylation profiling.

first: Michelle

last: North

first: Meaghan

last: Jones

first: Julia

last: MacIsaac

first: Alexander

last: Morin

first: Lisa

last: Steacy

last: Gregor

first: Anne

last: Ellis


title: SETDB2 links E2A-PBX1 to cell cycle dysregulation in acute leukemia through CDKN2C repression [sequencing]

first: Stephen HK

last: WONG

state: California

address: G2035 SIM1 Bldg

summary: Acute lymphoblastic leukemia (ALL) is associated with significant morbidity and mortality necessitating further improvements in diagnosis and therapy.  Targeted therapies directed against epigenetic regulators, which are frequently mutated or misregulated in acute leukemia, are emerging as candidate approaches in preclinical studies and early trials.  However, the epigenetic factors involved in most ALLs are not well defined or functionally characterized.  In this study, we demonstrate an oncogenic role for the protein lysine methyltransferase SETDB2 in leukemia pathogenesis.  It is over-expressed in a wide spectrum of leukemias, required for their maintenance in vitro and in vivo, and its elevated expression correlates with a poor prognosis in clinical cohorts.  In a subset of ALL with the preBCR+ phenotype, SETDB2 expression is maintained as a direct target gene of the chimeric transcription factor E2A-PBX1.  In this subset, SETDB2 epigenetically suppresses expression of the cell cycle inhibitor CDKN2C through histone H3K9 tri-methylation thus establishing a novel oncogenic pathway subordinate to E2A-PBX1 that silences a major tumor suppressor in ALL.  In contrast, SETDB2 was relatively dispensable for normal hematopoietic stem and progenitor cell proliferation.  In addition to targeting SETDB2 alone, its knockdown significantly enhanced sensitivity to kinase and epigenetic inhibitors suggesting a potential approach to future combination treatments.  Our studies define an epigenetic role for SETDB2 in leukemia pathogenesis, and provide a mechanistic rationale for targeting SETDB2 therapeutically in a subset of leukemia.

overall_design: For RNAseq experiment, E2A-PBX1 was specifically knocked down by two shRNAs in two human E2A-PBX1+ cell lines (RCH-ACV, 697). Finally, two cell lines with two shRNAs plus corresponding control in triplicates are submitted to RNAseq sequencing. For ChIP-seq, RCH-ACV cells depleted of SETDB2 by shRNA were immuoprecipitated with anti-H3K9me3 antibody, and together with input control were constructed for ChIP-seq libraries and submitted to single-end ChIP-sequencing (detailed protocol referred to, Wong et al., 2015, Cancer Cell).

first: Stephen

middle: H

last: Wong

first: Chiou-Hong

last: Lin

last: Cleary

first: Jason

last: Kurzer

first: Corina

last: Schneidawind

last: Wei

first: Jesus

last: Duque-Afonso

first: Johan

last: Jeong


title: Gene expression profiling coupled with the Connectivity Map database-mining reveals potential therapeutic drugs for Hirschsprung disease

city: Guangzhou

first: Liang

last: Zhang

address: Xingnan Road 521

department: Translational Medicine Research Center

institute: Guangdong Women and Children Hospital

summary: Hirschsprung disease (HD) is a congenital intestinal anomaly, which derives from a failure to form enteric ganglia in the lower bowel. Surgery is a major therapeutic strategy and neural stem cells transplantation is believed as a promising approach. However, we still face many challenges. To better characterize the pathology of HD, we used Agilent microarrays to analyze the gene expression profiles of surgically resected bowel tissue from 8 HD patients and 8 controls. A total of 253 genes were differentially expressed between the two groups using SAM software with threshold set at fold-change >2.0 and q-value <0.05. Gene Ontology analysis demonstrated that genes related to regulation of neuron development were significantly enriched. Differentially expressed genes (DEGs) involved in neuron development were further validated by quantitative real-time PCR (qRT-PCR) and immunohistochemistry. Moreover, in an attempt to seek potential drugs for HD, we correlated the observed gene expression patterns in HD to those of small molecule compounds via the Connectivity Map (cMap) database. Several compounds were screened that could rescue the dysregulated molecular signature in HD, proposing a testable hypothesis about possible therapeutic agents as a novel remedy for HD. In conclusion, our work may enhance our understanding the molecular changes in HD. More importantly, this study opens new fields of investigation into pharmacological intervention for HD.

overall_design: A total of 8 children diagnosed with congenital megacolon, 7 boys and 1 girl, age range from 1 to 6 months, were recruited in our series. The dual-color approach was employed in this experiment. Individual diseased samples and their paired adjacent normal tissues were all labeled with Cy3 and hybridized with a common reference consisted of 8 normal controls labeled with Cy5.

first: Shangjie

last: Xiao

first: Xiaochun

last: Zhu

first: Hua

last: Deng

first: Weiping

last: Zhou

first: Wenyi

last: Yang

first: Like

last: Yuan

first: Jiangyu

first: Huimin

last: Xia


title: Reprogramming of rabbit induced pluripotent stem cells toward Inner Cell Mass cells and chimeric competency with Krüppel-like factors

city: Jouy-en-Josas

first: Jouneau

last: Luc

address: Domaine de Vilvert

institute: INRA

summary: Rabbit induced pluripotent stem cells (rbiPSCs) essentially display the characteristic features of primed pluripotency as defined in rodents and primates. In this study, we reprogrammed rbiPSCs using human Krüppel-like factors (KLFs) 2 and 4 and cultured them in a medium supplemented with fetal calf serum and leukemia inhibitory factor. These cells (designated rbEKA) were propagated by enzymatic dissociation for at least 30 passages, during which they maintained a normal karyotype. This new culturing protocol resulted in transcriptional and epigenetic reconfiguration, as evidenced by the expression of transcription factors and histone marks associated with naïve pluripotency. Furthermore, microarray analysis of rbiPSCs, rbEKA cells, rabbit ICM cells, and rabbit epiblast revealed that the global gene expression profile of the reprogrammed rbiPSCs was more similar to that of rabbit ICM and epiblast cells. Injection of rbEK cells into 8-cell and 16-cell stage rabbit embryos resulted in extensive colonization of ICM in 10% mid-blastocysts (E4) and embryonic disk in 1.4% pre-gastrulae (E6). Thus, these results indicate that KLF2 and KLF4 triggered the conversion of rbiPSCs into epiblast-like, embryo colonization-competent PSCs. Our results highlight some of the requirements to achieve bona fide chimeric competency.

overall_design:
In the present work, we analyzed the transcriptome of rabbit iPS cells before and after reporgramming to a naïve-like state of pluripotency. The cell lines include: (1) two independent iPS cells (referred to as B19 and B29) produced by somatic cell reprogramming with human OCT4, SOX2, c-MYC and KLF4 (described in Osteil et al. 2013 Biol Open. 2:613-628); (2) a derivative of B19, referred to as B19-EOS cells, resulting from infectioon of B19 cells with L-SIN-EOS-C(3)-EiP (EOS) lentiviral vector (Hotta et al., 2009 Nat Methods. 6:370-376); (3) two derivatives of B129-EOS, referred to as rbEKA-30 and rbEKA-9 cells, obtained by transfection of a PiggyBac vector expressing human KLF2 and KLF4. We included rabbit inner cell mass and epiblast samples as reference for naïve and primed pluripotency, respectively.

Please note that the EPI and ICM samples are re-used samples from previous study [GSE79195]. However the sample titles referred in the manuscript associated with the current study are different from the previous study and correpsond to the previous titles as shown below;

GSM accn.   GSE79195 [PMID: 27594588]  -- current study
GSM2087654  Epiblast sample 1  --  Epiblast sample 1
GSM2087655  Epiblast sample 2  --  Epiblast sample 4
GSM2087656  Epiblast sample 3  --  Epiblast sample 3
GSM2087657  Epiblast sample 4  --  Epiblast sample 2
GSM2087658  Inner Cell Mass sample 1  --  Inner Cell Mass sample 3
GSM2087659  Inner Cell Mass sample 2  --  Inner Cell Mass sample 4
GSM2087660  Inner Cell Mass sample 3  --  Inner Cell Mass sample 1
GSM2087661  Inner Cell Mass sample 4  --  Inner Cell Mass sample 2

first: Yann

last: Tapponnier

first: Marielle

last: Afanassieff

first: Luc

last: Jouneau

first: Catherine

last: Archilla

first: Barbara

last: Schmaltz-Panneau

first: Pierre

last: Osteil

first: Jérome

last: Lecardonnel

first: Véronique

last: Duranthon

last: Savatier


title: Epigenetic modifications of hematopoietic differentiation are recapitulated in humanized mice

status: Public on May 25 2018

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

institute: RWTH Aachen University

summary: Transplantation of human hematopoietic stem cells into immunodeficient mice is a valuable technique to gain insight into stemness and hematopoietic development in an in vivo environment. In this study we analyzed if transplanted hematopoietic cells in humanized mice recapitulate epigenetic changes of normal hematopoietic development. Hematopoietic stem and progenitor cells (CD34+) were isolated from human umbilical cord blood (CB) and 50,000 cells were intravenously injected into five 7 to 9 week old KIT-deficient NOD/SCID Il2rg-/-KitW41/W41 (NSGW41). 19 weeks after transplantation bone marrow was harvested, sorted for hCD45+ cells, and DNA methylation profiles were analyzed with Infinium HumanMethylation450 BeadChips (Illumina). DNA methylation patterns of normal hematopoietic development are overall recapitulated in the xenogeneic microenvironment – particularly those of normal early B cell progenitor cells.

overall_design: DNA from sorted human CD45+ cells from bone marrow of five humanized mice was bisulfite converted and hybridized to the Illumina Infinium 450k Human Methylation BeadChip.

first: Joana

last: Frobel

first: Susann

last: Rahmig

first: Julia

last: Franzen

first: Claudia

last: Waskow


title: NFkB signaling and ISGylation associated with BRCA1-mutated fallopian tube epithelium

city: Toronto

first: carl

last: virtanen

state: Ontario

address: 101 College St

department: Princess Margaret Genomics Centre

institute: University Health Network

summary: Germline BRCA1 or BRCA2 mutations (mtBRCA1 and mtBRCA2) dramatically increase risk for high-grade serous ovarian cancer (HGSOC), the most commonly diagnosed histotype.  Other risk factors for this cancer, which originates primarily in the distal fallopian tube epithelium (FTE), implicate ovulation.  To test whether mtBRCA1 or mtBRCA2 FTE cells respond differently to peri-ovulatory follicular fluid (FF) exposure than control patient FTE, gene expression profiles from primary FTE cultures were compared at baseline, 24h after FF exposure, and 24h after FF replacement with culture medium.  Hierarchical clustering revealed both FF exposure and BRCA mutation status affect gene expression, with BRCA1 mutation having the greatest impact. Analysis revealed increased NFκB and EGFR signaling at baseline, with increased interferon signaling after recovery from FF exposure in mtBRCA1 samples.  Inhibition of EGFR signaling and ISGylation by increased BRCA1 expression was verified in an immortalized FTE cell line, OE-E6/E7, stably transfected with BRCA1.  Suppression of ISG15 and ISGylated protein levels by BRCA1 expression was found to be mediated by decreased NFκB signaling and was transiently suppressed by FF exposure.  This study demonstrates increased NFκB signaling associated with decreased BRCA1 expression resulting in increased ISG15 and ISGylation following FF exposure, which could represent potential targets for chemoprevention.

overall_design: Fallopian tube epithelium from BRCA1 and BRCA2 mutation carriers and non-mutated women were seeded in collagen-IV coated transwells (n=8 for mtBRCA1, mtBRCA2 and control). The lower chamber contained cuture medium for the duration of the experiment. Upper chamber first contained culture medium, this was replaced with follicular fluid for 24h, and this was then replaced with fresh culture medium for 24h. RNA was extracted from cells after 24h FF exposure (F24), and after recovery from FF exposure (FC). Cells maintained only in culture medium were used as a control (C24).

last: Hollingsworth

first: Angela

last: Lau

first: Alicia

last: Tone

first: Alexandra

last: Kollara

first: Lisa

last: Allen

first: Terry

last: Colgan

first: Valerie

last: Dube

first: Barry

last: Rosen

first: K

last: Murphy

first: Ellen

last: Greenblatt

first: Tomer

last: Feigenberg

first: Carl

last: Virtanen

first: Theodore

last: Brown


title: Promoter DNA sequence guides factors that position the +1 nucleosome and facilitate TBP binding [sequencing]

city: Geneva

first: Slawomir

last: Kubik

address: quai Ernest-Ansermet 30

institute: University of Geneva

summary: Here we present evidence that precise positioning of the +1 promoter nucleosome in yeast is critical for efficient TBP binding and pre-initiation complex assembly, and is determined, at least in part, by the action of two key factors, the essential chromatin remodeler RSC and one (or more) of a small set of ubiquitous pioneer transcription factors (PTFs). Despite their widespread co-localization, we show that RSC and PTFs often act independently to generate accessible chromatin. Furthermore, we present evidence that RSC binding, as well as the strength and directionality of its action on nucleosomes, depends upon the arrangement of two specific DNA motifs relative to nearby PTF binding sites. Our results provide insights into how promoter DNA sequence instructs trans-acting factors to precisely control nucleosome architecture and stimulate transcription initiation.

overall_design:
Nucleosome occupancy as well as TBP binding was measured upon depletion of Abf1, Reb1, Rap1 and/or the catalytic subunit of chromatin remodeler RSC.

For the yeast strain background used in this study, Rapamycin causes depletion from the nucleus of the proteins tagged with the FRB peptide following the "anchor away" protocol published in PMID: 18922474.

first: Eoghan

last: O'Duibhir

first: Wim

last: de Jonge

first: Stefano

last: Mattarocci

first: Benjamin

last: Albert

first: Jean

last: Falcone

first: Maria

last: Bruzzone

first: Frank

last: Holstege

first: David

last: Shore


title: Resetting the Epigenetic Balance of Polycomb/COMPASS Function at Enhancers for Cancer Therapy

status: Public on May 27 2018

city: Chicago

first: Ali

last: Shilatifard

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

summary: MLL3/KMT2C is a COMPASS family member and tumor suppressor that functions as a histone H3K4 mono-methyltransferase at enhancers. Human cancer genome sequencing studies have identified frequent MLL3 point mutations, however, the question of how these mutations alter MLL3 function and contribute to oncogenesis remains unanswered. Here, we have characterized a cancer mutational hot spot in the MLL3 Plant Homeo Domain (PHD) repeats that correlates with poor patient survival. Cancer-associated mutations in the MLL3-PHD disrupt interaction with the BAP1 deubiquitinase complex. BAP1 loss-of-function in cancer cells significantly reduces MLL3 recruitment to enhancers regions, resulting in reduced H3K4me1 and increased H3K27me3 levels at these loci. Notably, we find that increased H3K27me3 levels in BAP1 null cells are due to decreased MLL3/UTX/COMPASS occupancy. Reducing H3K27me3 through PRC2 catalytic inhibition resets the pattern of gene expression in cells with defective MLL3- BAP1-UTX activity and impairs tumor proliferation in cancer cells with MLL3 mutations. This study provides a molecular mechanism to explain the role of MLL3 PHD mutations in cancer pathogenesis. Therefore, based on these observations, we propose a potential therapeutic strategy for cancers harboring MLL3/COMPASS mutations by resetting the Polycomb/COMPASS epigenetic balanced state of gene expression.

overall_design: To examine changes in histone modification and gene expression after depletion of MLL3/BAP1/UTX or EZH2 inhibition in human cell lines.

first: Lu

last: Wang

first: Clayton

last: Collings


title: Genome-wide profiles of replication initiation, single-stranded DNA accumulation, and Rad52 binding in cells exposed to replication stress

city: Bordeaux

first: Pei-Yun Jenny

last: Wu

address: 1 Rue Camille Saint Saens

institute: Institute of Biochemistry and Cellular Genetics


title: RNA-Seq analysis of localization along animal-vegetal axis of Xenopus laevis

city: Vestec by Prague

first: Radek

last: Šindelka

address: Průmyslová 595

country: Czech Republic

institute: Institute of Biotechnology, Czech Academy of Science, v.v.i.

summary: We combined cryosectining of oocytes along the animal-vegetal axis (first developmental axis) and RNA-Seq to determine localization profiles of coding and noncoding RNAs. It provides complete view on RNA localization. We found that nearly all RNAs are localized, but only small percentage is actively transported during oogenesis.

overall_design: RNA profiles (mRNA, lncRNA, other RNA) were generated by deep sequencing, in biological triplicates (each oocyte divided into five segments), using Illumina HiSeq.

last: Sindelka

first: Pavel

last: Abaffy


title: Epigenetic characterization of NKG2C high cells of primigravid decidual NK, multigravid decidual NK, nulligravid endometrial NK and multigravid endometrial NK

city: Jerusalem

first: Ofer

last: Mandelbaum

state: Select a State or Province

address: Hebrew University Medical School

department: The Lautenberg Center for General and Tumor Immunology

country: Israel

institute: The Hebrew University Faculty of Medicine, Jerusalem, Israel

summary: Natural killer cells (NKs) are abundant in the human decidua. Several diseases of poor placental development are associated with first pregnancies, and we thus looked to characterize differences in decidual NKs in first versus repeated pregnancies. We discovered a population unique to repeated pregnancies, which possesses a novel transcriptome and epigenetic signature, characterized with high expression levels of the receptors NKG2C and LILRB1. Activation of these receptors leads to increased production and secretion of IFNγ and VEGFa, the latter found to support vascular sprouting and trophoblast-tumor growth. We propose that this population represents NK “memory” of pregnancy, and have named these cells Pregnancy Trained decidual NK cells (PTdNKs). We further suggest that the precursors of PTdNKs are found in the endometrium. PTdNKs may prove useful in understanding and treating disorders of poor placentation.

overall_design: NKG2Chigh (and negative) decidual and endometrial NK cells, from nulligravid, primigravid and multigravid women

last: Mandelboim

first: Moriya

last: Gamliel


title: Transcriptome signature identifies distinct cervical pathways induced in lipopolysaccharide-mediated preterm birth

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

country: USA

institute: UT Southwestern Medical Center

summary: Cervical inflammasome activation and subsequent protease upregulation are potential mechanisms of downstream extracellular matrix disruption in LPS-mediated preterm birth.

overall_design: Using RNA-seq to compare cervices from day 15 gestation intrauterine-LPS treated mice to nontreated day 15, intrauterine water (sham), and day 18 samples.

first: Alexandra

last: Willcockson

first: Tulip

last: Nandu

first: Shanmugasundaram

last: Nallasamy

first: Cheuk-Lun

last: Liu

first: Lee

first: Mala

last: Mahendroo


title: BCR-ABL1 inhibitors decrease cholesterol and atherosclerosis, and activate coagulation in a translational mouse model

status: Public on May 24 2018

city: Zeist

first: Lars

last: Verschuren

address: Utrechtseweg 48

department: Microbiology and Systems Biology

country: Netherlands

institute: TNO

summary:
Objectives: Treatment with the second and third generation BCR-ABL1 tyrosine kinase inhibitors (TKIs) increases cardiovascular risk in chronic myeloid leukemia (CML) patients. We investigated the multifactorial process of TKI-induced vascular adverse effects in a translational model for atherosclerosis, the APOE3*Leiden.CETP mouse.
Approach and results: Mice were treated for sixteen weeks with imatinib (150 mg/kg BID), nilotinib (10 and 30 mg/kg QD) or ponatinib (3 and 10 mg/kg QD), giving similar drug exposures as in CML-patients. Cardiovascular risk factors were analyzed throughout the study, and histopathological analysis of atherosclerosis and transcriptome analysis of the liver was performed. Imatinib and ponatinib decreased plasma cholesterol (imatinib, -69%, :<0.001; ponatinib 3mg/kg, -37%, P<0.001; ponatinib 10 mg/kg -44%, P<0.001) and atherosclerotic lesion area (imatinib, -78%, P<0.001; ponatinib 3 mg/kg, -52%, P=0.014; ponatinib 10 mg/kg, -48%, P=0.001), which were not affected by nilotinib.  In addition, imatinib increased plaque stability. Gene expression and pathway analysis predicted that ponatinib may lead to a pro-coagulant state by adversely affecting coagulation factors of both the contact activation (intrinsic) and tissue factor (extrinsic) pathways. The coagulation factor VII in plasma was increased by ponatinib, whereas nilotinib increased FVIIa.
Conclusion: Imatinib showed a beneficial cardiovascular risk profile, whereas nilotinib and ponatinib increase the cardiovascular risk through induction of a pro-thrombotic state.

overall_design: In total, one control group, one reference group (L-NAME) and 3 treatment groups (imatinib, nilotinib, ponatinib) were inlcuded in the analysis. Of each group, 8 samples were analysed.

last: verschuren

first: Martien

last: Caspers

first: Elsbeth

last: Pieterman

first: Hans

last: Princen

first: C

last: Kluft

first: R

last: Garcia

first: J

last: Aman

last: Jukema

first: M

last: Pouwer


title: miR-200b is associated with cisplatin sensitivity in bladder cancer cells

city: Sapporo

first: Hiromu

last: Suzuki

state: Hokkaido

address: S1, W17, Chuo-ku

department: Department of Molecular Biology

institute: Sapporo Medical University

summary: We aimed to clarify the role of miR-200b in cisplatin (CDDP) sensitivity in bladder cancer (BCa). CDDP resistant T24 cells (T24RC) were transfected with a miR mimic negative control (NC) or a miR-200b mimic, after which cells were treated with or without CDDP. We found that ectopic miR-200b expression re-sensitized the T24RC cells to CDDP. Gene expression microarray analysis revealed that the combination of miR-200b and CDDP affected genes involved in CDDP sensitivity and cytotoxicity.

overall_design: CDDP resistant T24 cells (T24RC) were transfected with a miR mimic negative control (NC) or a miR-200b mimic using Lipofectamine RNAiMAX and incubated for 72 h. Transfectants were then  treated with or without 1.6 μg/ml of CDDP for additional 72 h. Total RNA was extracted using a TRI Reagent.

first: Tetsuya

last: Shindo


title: Targeted mutagenesis recapitulates brain tumor initiation in cerebral organoids

city: Vienna

first: Thomas

middle: Rainer

last: Burkard

address: Dr. Bohrgasse 7

country: Austria

institute: IMBA

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

overall_design: Refer to individual Series


title: Gene expression signatures for CD8αβ+ intraepithelial lymphocytes and CD8αβ+ splenocytes.

city: Hefei

first: Banru

last: Chen

address: 443 Huangshan Road

country: China

institute: School of Life Sciences, University of Science & Technology of China

summary:
CD8αβ+ intraepithelial lymphocytes (IELs) are a subset of “effector-memory-like” T cells scattered along the intestinal epithelium. To investigate if CD8αβ+ IEL can function in ways other than the conventional cytotoxic effect of CD8αβ+ T cells,CD8αβ+ IELs  were compared with CD8αβ+ splenocytes (SPL) by RNA-seq.
We used microarrays to identify new functions of CD8αβ+ IELs .

overall_design: CD8αβ+ IELs and CD8αβ+ SPLs were sorted from intraepithelium of small intestines and spleens of WT mice (8–12w).

first: Haiming

last: Wei


title: High resolution annotation of Zebrafish transcriptome using long-read sequencing

city: New York

first: Stuart

last: Sealfon

state: NY

address: One Gustave L. Levy Place

department: Department of Neurology

institute: Icahn School of Medicine at Mount Sinai

summary: With the emergence of zebrafish as an important model organism, a concerted effort has been made to study its transcriptome. This effort is limited by gaps in zebrafish annotation, which is especially pronounced concerning transcripts dynamically expressed during zygotic genome activation (ZGA). To date, short read sequencing has been the principal technology for zebrafish transcriptome annotation. In part because these sequence reads are too short for assembly methods to resolve the full complexity of the transcriptome, the current annotation is rudimentary. By providing direct observation of full-length transcripts, recently refined long-read sequencing platforms can dramatically improve annotation coverage and accuracy. Here, we leveraged the SMRT platform to study the early ZGA-stage zebrafish transcriptome. Our analysis revealed additional novelty and complexity in the zebrafish transcriptome, identifying 2748 high confidence novel transcripts that originated from previously unannotated loci and 1835 new isoforms in previously annotated genes.

overall_design: Pooled RNA of α-amanitin / untreated embryos were collected and profiled with long-read sequencing. Temporally corresponding pre/post ZGA pooled embryonic RNA samples were profiled with short-read RNA-seq. Long-read raw data were assembled into transcripts using IsoSeq  (PMID: 27407110), mapped to the reference GRCz10 genome using GMAP [PMID:15728110] and annotated against the reference transcriptome using Cuffcompare [PMC3334321]. Novel transcripts were compared to short-read data and computationally validated in constructing a final long-read augmented transcriptome.

first: German

last: Nudelman

first: Antonio

last: Frasca

first: Kirsten

last: Edepli-Sadler

first: Martin

last: Walsh

first: Elena

last: Zaslavsky


title: Dual inhibition of HDMX and HDM2 as a Therapeutic Strategy in Leukemia

city: Bronx

first: Luis

last: Carvajal

address: 1300 Morris Park Ave

department: Department of Cell Biology

institute: Albert Einstein College of Medicine

summary: The p53 protein is the most frequently inactivated tumor suppressor in human cancer. While p53 mutations are found in 50% of all cancers, the p53 pathway can also be suppressed by its interaction with endogenous inhibitors HDMX and HDM2, which are frequently overexpressed in patients with acute myeloid leukemia and other cancers. Thus, pharmacological disruption of both these interactions is an attractive strategy to restore p53-dependent tumor suppressor activity in AML with wild type P53. Strategies targeting HDM2 have recently generated promising results; however, cancer cells are still left vulnerable to p53 inhibition by HDMX, particularly in cancers such as leukemia that overexpress HDMX. In this study, we demonstrate that dual HDMX/HDM2 inhibition using a stapled alpha-helical peptide (ALRN-6924), which has recently entered clinical testing, leads to striking anti-leukemic effects.  ALRN-6924 robustly activates p53-dependent transcription at the single cell and single molecule level, and exhibits biochemical and molecular biological on-target activity in leukemia cells in vitro and in a patient who received ALRN-6924 treatment. Dual HDMX/HDM2 inhibition by ALRN-6924 inhibits cellular proliferation by inducing cell cycle arrest and apoptosis in cell lines and primary AML patients’ cells, including in leukemic stem cell-enriched populations, and disrupts functional clonogenic and serial replating capacity. Furthermore, ALRN-6924 leads to significantly improved survival in an AML xenograft model in vivo. At the molecular level, dual HDMX/HDM2 inhibition leads to global transcriptional activation of p53-dependent pathways in leukemia cells. Our study provides insight into the effects of dual HDMX/HDM2 inhibition and proof-of-concept for ALRN-6924 as a novel therapeutic approach in AML and other cancers with high HDMX levels.

overall_design: Total mRNA expression profiles of vehicle (1:10 DMSO) or 1 uM ALRN-6924 treated AML cells (6 hours) were generated by deep sequencing, in triplicates, using the Illumnia HiSeq 2500 instrument.

first: Daniela

last: Ben-Neriah

first: Adrien

last: Senecal

first: Lumie

last: Benard

first: Swathi-Rao

last: Narayanagari

first: Charles

last: Kenworthy

first: Victor

last: Thiruthuvanathan

first: Vincent

last: Guerlavais

first: D

last: Annis

first: Boris

last: Bartholdy

first: Britta

last: Will

first: Jesus

middle: D

last: Anampa

first: Ioannis

last: Mantzaris

first: Manuel

last: Aivado

first: Robert

last: Singer

last: Coleman

first: Amit

last: Verma

first: Ulrich

last: Steidl


title: Replication origin mapping in cdc25-22 and cdc25-22 rad3∆ in S. pombe

first: Pei-Yun Jenny

last: Wu

summary: Identification of sites of replication initiation by copy number analysis, comparing samples before and after entry into S phase.

overall_design: Comparison of samples before and after S phase entry; dye-swap experiments were performed and averaged. Triplicates for every condition

first: Blanca

last: Gómez-Escoda

first: Pei-Yun


title: RNA-seq of Kras-Usp22WT and Kras-Usp22KO myeloid progenitors

city: Memphis

first: John

last: Crispino

state: Tennessee

address: 262 DANNY THOMAS PL

institute: St. Jude Children's Research

summary: Ras mutations are commonly observed in Juvenile Myelomonocytic Leukemia (JMML) and Chronic Myelomonocytic Leukemia (CMML). JMML and CMML transform into Acute Myeloid Leukemia (AML) in about 10% and 50% of patients respectively. However, how additional events cooperate with Ras to promote this transformation are largely unknown. We show that absence of the Ubiquitin-Specific-peptidase 22 (USP22), a component of the SAGA chromatin-remodeling complex linked to cancer progression, unexpectedly promotes AML transformation in mice expressing oncogenic KrasG12D/+. USP22 deficiency in KrasG12D/+ mice resulted in shorter survival compared to control mice. This was due to a block in myeloid cell differentiation leading to the generation of AML. This effect was cell autonomous since mice transplanted with USP22-deficient KrasG12D/+ cells developed an aggressive disease and died rapidly. The transcriptome profile of USP22-deficient KrasG12D/+ progenitors resembled leukemic stem cells and was highly correlated with genes associated with poor prognosis in AML. We show that USP22 functions as a PU.1 deubiquitylase by positively regulating its protein stability and promoting the expression of PU.1 target genes. Reconstitution of PU.1 overexpression in USP22-deficient KrasG12D/+ progenitors rescued their differentiation. Our findings uncovered an unexpected role for USP22 in Ras-induced leukemogenesis and provide further insights into the function of USP22 in carcinogenesis.

overall_design: mRNA expression profile of myeloid progenitors (cKit_Linlow/-) from 7-9 weeks old Kras-Usp22WT and Kras-Usp22KO mice

first: Johanna

last: Melo-Cardenas

first: Yuanming

last: Xu

first: Juncheng

last: Wei

first: Can

last: Tan

first: Sinyi

last: Kong

first: Beixue

last: Gao

first: Elena

last: Montauti

first: Gina

last: Kirsammer

first: Jonathan

last: Licht

first: Jindan

last: Yu

first: Peng

last: Ji

first: Deyu

last: Fang


title: Mapping of CTCF and CTCFL binding sites in 3T3 and p19 cells

city: Giessen

first: Marek

last: Bartkuhn

address: Aulweg 132

institute: Justus-Liebig-University Giessen

summary: Study of the differential binding behavior of the paralogous factors CTCF and CTCFL by ChIP-seq in mouse NIH3T3 and p19 cells.

overall_design: ChIP-seq of CTCF and CTCFL in 3T3 and p19 cells

first: Rainer

last: Renkawitz

first: Philipp

last: Bergmaier


title: Genome-Wide Identification and Comprehensive Analysis of Conserved MicroRNAs and Phased small Interfering RNAs in Watermelon [degradome]

status: Public on May 23 2018

city: Kunming

first: Yun

last: Zheng

state: Yunnan

address: 452 Fengyuan Road

institute: Yunnan Agricultural University

summary: MicroRNAs (miRNAs) are a class of endogenous small non-coding RNAs involved in the post-transcriptional gene regulation and play a critical role in plant growth, development and stress responses. Watermelon (Citrullus lanatus L.) is one of the important agricultural crops worldwide. Here we carried out computational and experimental analysis of miRNAs and phased small interfering RNAs (phasiRNAs) in watermelon by analyzing 14 small RNA profiles from roots, leaves, androecium, flowers, and fruits, and one published small RNA profile of mixed tissues. To identify the targets of miRNAs and phasiRNAs, we generated a degradome profile for watermelon leaf which is analyzed with the SeqTar algorithm. We identified 97 conserved pre-miRNAs, of which 58 have not been reported previously and 348 conserved mature miRNAs without precursors. We also found 9 novel pre-miRNAs encoding 18 mature miRNAs. One hundred and one 21 nucleotide (nt) PHAS loci, and two hundred and forty one 24 nt PHAS loci were also identified. We identified 120 conserved targets of the conserved miRNAs and TAS3-derived tasiRNAs by analyzing a degradome profile of watermelon leaf. The presented results provide a comprehensive view of small regulatory RNAs and their targets in watermelon.

overall_design: Identification and comprehensive analysis of conserved microRNAs and phased small interfering RNAs in watermelon or whole plant using Illumina HiSeq 2000 sequencer.


title: RNA-seq of Scyliorhinus retifer electroreceptors

status: Public on May 29 2018

city: San Francisco

first: Duncan

last: Leitch

department: Physiology

institute: University of California - San Francisco

summary: Transcriptional profiling from adult Scyliorhinus retifer from electrosensory cells of the ampullae of Lorenzini, forebrain, skin, and skeletal muscle shows differential gene expression of voltage-activated ion channels related to sensory transduction.

overall_design: Examination of gene expression in ampullary cells, brain, non-electroreceptive skin, and muscle in one adult Scyliorhinus retifer chain catshark prepared from poly A+ RNA using Illumina TruSeq Stranded mRNA Library Prep Kit

first: Nicholas

last: Bellono

first: David

last: Julius


title: LONG NON-CODING RNAs ASSOCIATED WITH METABOLIC TRAITS IN HUMAN WHITE ADIPOSE TISSUE

city: Stockholm

first: Ingrid

last: Dahlman

address: Karolinska Huddinge

country: Sweden

institute: Karolinska

summary:
The aim of this study was to identify novel long noncoding RNAs (lncRNAs) that are differentially expressed in the subcutaneous region either in obesity or insulin resistance.
A number of novel lncRNAs were differentially expressed in the subcutaneous region either in obesity or insulin resistance. Two lncRNAs (termed here as adipocyte specific insulin resistance related lncRNAs (ADLNRIs), ADLNRI 1 and ADLNRI 2) were influenced by both conditions and enriched in adipocytes. Knockdown of either by antisense oligonucleotides in fat cellsadipocytes altered lipolysis and adiponectin secretion, respectively.

overall_design: The 80 women included in this study were selected from the extremes of insulin sensitivity as measured by homeostasis model assessment of IR (HOMAIR) among 220 obese women who participated in a clinical trial on the effect of bariatric surgery (NCT01785134 at www.clinicaltrials.gov). All sampling and measurements were performed before or during bariatric surgery (laparoscopic gastric bypass). Participants were investigated at 8 AM after an overnight fast. Insulin sensitivity was assessed by HOMAIR and was calculated from fasting measures of glucose and insulin. High HOMAIR values indicate IR. The 40 women with the highest HOMAIR values and the 40 women with the lowest values were selected for inclusion in the present study.  Differential gene expression analysis was conducted at the gene level using Limma, selecting for genes with a false discovery rate of <0.05


title: Expression data from murine splenic erythroblasts in stress erythropoiesis.

status: Public on May 28 2018

city: State College

first: K. Sandeep

last: Prabhu

state: Pennsylvania

address: 115 Henning Building, University Park

department: Veterinary and Biomedical Sciences

institute: Pennsylvania State University

summary:
In absence of selenium, proerythroblasts exhibited delay in differentation into basophilic erythroblasts during phenylhydrazine induced stress erythropoiesis.
This microarray project was aiming to explore gene expression patterns in erythroblasts in the function of selenium status.

overall_design: Proerythroblasts and basophilic erythroblasts were FACS sorted from spleen of selenium deficient or adequate mice on day 3 post phenylhydrazine treated mice. RNA was extracted and processed for microarray.

first: Chang

last: Liao

first: K

middle: S

first: Robert

middle: F

last: Paulson


title: Global expression of sebacous gland carcinoma

city: Whitechapel

first: John

last: Bladen

address: 4 Newark Street

department: Blizard Institute

country: United Kingdom

institute: QMUL

type:
Expression profiling by array
Other


title: RNA-seq insights into primary root apical meristem exhaustion and determinate root growth in Pachycereus pringlei (Cactaceae)

city: Cuernavaca

first: Gustavo

last: Rodriguez-Alonso

state: Morelos

address: Av.Universidad 2001, Col. Chamilpa

department: Biología Molecular de Plantas

country: Mexico

institute: Instituto de Biotecnología

summary: Many Cactaceae species exhibit determinate growth of the primary root as a consequence of root apical meristem (RAM) exhaustion. The genetic regulation of this root growth pattern is unknown.    We de novo assembled and annotated the root apex transcriptome of the Pachycereus pringlei primary root at three developmental stages with active or exhausted RAM. The assembled transcriptome was characterized and used to evaluate differential transcript expression, identify RT-qPCR reference genes, and infer a transcriptional regulatory network.   We generated a robust and comprehensive transcriptome of the primary root apex of P. pringlei and identified putative orthologs of Arabidopsis regulators of RAM maintenance, as well as putative lineage-specific transcripts. Furthermore, the transcriptome contained putative orthologs of most proteins involved in housekeeping processes, hormone signaling, and metabolic pathways.  Specific transcriptional programs operate in the root apex at specific developmental time points. The transcriptional state of the P. pringlei root apex as the RAM becomes exhausted is comparable to that of cells from the meristematic, elongation, and differentiation zones of Arabidopsis roots. We suggest that the genetic program underlying the drought stress response is induced during development of the Cactaceae root, and that lineage-specific transcripts could contribute to root apical meristem exhaustion in Cactaceae.

overall_design: 1 mm of the apex of the Pachycereus pringlei primary root was collected. 350, 450, and 600 root tips were pooled per samples (developmental stage) at the initial, intermediate, or terminal growth stage, respectively. Two biological replicates were included per developmental stage. Total RNA was extracted and mRNA-seq was performed on the Illumina HiSeq Platform at BGI-Tech, Hong Kong.

last: Rodríguez-Alonso

first: Marta

last: Matvienko

first: Svetlana

last: Shishkova


title: Global gene expression in response to X rays in mice deficient in Parp1

first: Sally

last: Amundson

department: Center for Radiological Research

institute: Columbia University

summary: There is a current interest in the development of biodosimetric methods for rapidly assessing radiation exposure in the wake of a large-scale radiological event.  The initial focus of this work has largely centered on determining the exposure dose to an individual using biological indicators.  Gene expression signatures are showing promise for biodosimetric application, but little is known about how these signatures might translate for the assessment of radiological injury in radiosensitive individuals, who comprise a significant fraction of the general population, and who would likely require treatment following lower doses.  Using Parp1-/- mice as a model radiation sensitive genotype, we have investigated the effect of this DNA repair deficiency on the gene expression response to radiation.  Although Parp1 is known to play general roles in regulating transcription, the pattern of gene expression changes observed 24 h after exposure to a potentially lethal LD50 dose of radiation was remarkably similar in the two genotypes, and indicated similar levels of activation of both the p53 and NFκB radiation response pathways.  In contrast, exposure of wild-type mice to a sub-lethal dose that was equal to the LD50 dose given to the Parp1-/- mice, resulted in a reduced gene expression response.  Gene expression classifiers trained on the wild-type data correctly identified all wild-type samples as unexposed, exposed to a sub-lethal dose, or exposed to a potentially lethal dose.  All unexposed samples from the Parp1-/- mice were also correctly classified, and 80% of the irradiated samples were identified as exposed to a potentially lethal dose.  The results of this study suggest that, at least for some genotypes, gene expression has the potential to accurately detect the extent of radiological injury, rather than being useful only as a surrogate of physical radiation dose.

overall_design: Parp1-/- or wild-type mice were either exposed to a LD50/30 dose of x rays, or were sham-irradiated as controls, and then sacrificed 24h later. Wild-type mice were also exposed to the dose corresponding to LD50/30 in Parp1-/-.  5 replicates, representing individual mice, were used for each condition, with the exception of wild types exposed to the LD50/30 (8.8 Gy), for which four replicates were used.

first: Suresh

last: Kumar

first: Evagelia

middle: C

last: Laiakis

first: Albert

last: Fornace Jr.


title: Murine intestinal organoids resemble intestinal epithelium in their microRNA profiles

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

summary: To compare miRNA expression profiles between freshly isolated intestinal epithelial cells and cultured organoids in mice. Intestinal organoids largely resembled intestinal epithelial cells in their miRNA profiles. Although the expression levels of some miRNAs were different between crypt and villus epithelial cells, such expression patterns were not reproduced during the maturation of intestinal organoids.

overall_design: miRNA expression levels in the crypt and villus epithelial cells isolated from murine small intestine and in the organoids cultured from murine small intestinal crypts were analyzed by microarray.

first: Kei

last: Sonoyama