title: Expression data comparing BEL7402 HCC cells with or without PRMT6 stably repressed.

city: Hong Kong

first: Stephanie

last: Ma

address: Rm 47, 1/F, Lab Block, Faculty of Medicine Bldg, 21 Sassoon Rd, Pok Fu Lam

department: School of Biomedical Sciences

country: Hong Kong

institute: The University of Hong Kong

summary:
Systematic identification of altered genes downstream of PRMT6.
Platform used - Agilent SurePrint G3 Human Gene Expression v3 8x60K microarray kit.

overall_design: BEL7402 cells were transduced with lentivirus containing either non-target control (NTC) or shPRMT6 (clone 956) and stable pooled clones were selected by puromycin selection. Cells were harvested for RNA extraction by Qiagen kit.

middle: K


title: Transcriptional features of biological age maintained in cultured cardiac interstitial cells

status: Public on Dec 31 2020

city: San Diego

first: Oscar

middle: E

last: Echeagaray

state: CA

address: 5500 Campanile Drive

department: Biology

country: USA

institute: San Diego State University

type: Expression profiling by high throughput sequencing

summary: Single-cell RNA-seq (10X Genomics Chromium) to profile cultured cardiac interstitial cells derived from neonatal and adult cardiac tissue

overall_design: Transcriptional profiling of neonatal and LVAD derived cultured cardiac interstitial cells by scRNA-Seq approaches using 10X Genomics Chromium

first: Mark

middle: A

last: Sussman

first: Kim

last: Taeyong


title: Genomic and epigenomic adaptation in SP-R210 (Myo18A) isoform-deficient macrophages [ChIP-seq]

city: Hershey

first: Zissis

last: Chroneos

state: PA

address: 500 University Drive

department: Pediatrics

institute: Penn State College of Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Macrophages play fundamental roles in regulation of inflammatory responses to pathogens, resolution of inflammation and tissue repair, and maintenance of tissue homeostasis. The long (L) and short (S) isoforms of SP-R210/MYO18A, a macrophage receptor for surfactant protein A (SP-A) and C1q, regulate basal and inflammatory macrophage phenotype at multiple gene expression, translational, and subcellular levels in addition to their SP-A and C1q-mediated functions; disruption of L renders macrophages hyper-inflammatory, although the underlying mechanism had previously been unexplored. We questioned whether disruption of the L isoform would alter the global genomic responses. RNA sequencing analysis of SP-R210L(DN) macrophages revealed basal and influenza induced upregulation of genes associated with inflammatory pathways, including TLR, RIG-I, NOD, and cytoplasmic DNA signaling, whereas knockdown of both SP-R210 isoforms (L and S) only resulted in increased RIG-I and NOD signaling. Chromatin immunoprecipitation sequencing (ChIP-seq) analysis showed increased genome-wide deposition of the pioneer transcription factor PU.1 in SP-R210L(DN) compared to WT cells. ChIP-seq analysis of histone H3 methylation showed alterations in both repressive (H3K9me3 and H3K27me3) and transcriptionally active (H3K9me3) histone marks. Influenza A virus (IAV) infection, which stimulates an array of cytosolic and TLR-mediated antiviral mechanisms, resulted in differential redistribution between proximal promoter and distal sites and decoupling of PU.1 binding from Toll-like receptor regulated gene promoters in SP-R210L(DN) cells. Our findings suggest that SP-R210L-deficient macrophages are poised with an open PU.1-primed chromatin conformation to rapidly respond to inflammatory and metabolic stimuli.

overall_design: Total 17 samples were analyzed; 5 replicates each for uninfected WT and SP-R210L(DN) cells, 3 replicates for uninfected SP-R210(KO) cells, and 2 replicate each for IAV infected WT and SP-R210L(DN) cells

first: Eric

last: Yau

first: Yan

last: Chen

first: Chunhua

last: Song

first: Jason

last: Webb

first: Marykate

last: Carillo

first: Yuka

middle: I

last: Kawasawa

first: Zhenyuan

last: Tang

first: Yoshinori

last: Takahashi

first: Todd

middle: M

last: Umstead

first: Sinisa

last: Dovat

middle: C


title: RNA-seq Analysis of MoLID2 (MoKDM5)-dependent Genes in Magnaporthe oryzae 70-15

status: Public on Jan 01 2021

city: Hangzhou

first: Jianping

last: Lu

state: Zhejiang

address: 866 Yuhantang Road

department: College of Life Sciences

country: China

institute: Zhejiang University

summary:
Purpose: The goals of this study are to find out the genes regulated directly or indirectly by a trimethyl H3K4 histone demethylase Molid2 (MoKdm5) by RNA-seq in the rice blast fungus
Methods: Mycelial mRNAs of the wild type strain 70-15, ΔMolid2 incubated in H2O at 25˚C for 4 h, in triplicate independently for each strain, were extracted and isolated by RNeasy Plant mini kit (QIAGEN) and AMPure XP beads (Beckman). RNA-sequencing libraries were constructed using NEBNext RNA sample preparation kit (NEB). Samples were sequenced in a 1 x 100 nt way on Illumina Hiseq2500 instrument using TruSeq PE Cluster Kit v3 - cBot - HS (Illumina) and TruSeq SBS Kit v3-HS (Illumina).The M. oryzae genome database (MG8) (www.broadinstitute.org) was used as a reference gene database. Genome-wide transcript levels of genes were quantified in fragments per kilobase of exon model per million mapped reads (FPKM) (Trapnell 2010). Gene Ontology (GO) enrichment analyses for differentially expressed genes were performed using hypergeometric test with topGO, and p-values were adjusted with Bonferroni for multiple testing (Alexa 2006). And we selected FDR < 0.05 as enrichment terms.
Results and Conclusions: We identified 3400 genes regulated by Molid2 through RNA-seq.

overall_design: Mycelial mRNA profiles of wild type strain 70-15 (WT), ΔMolid2 incubated in H2O for 4 h were generated, in biologic triplicate, by Illumina Hiseq2500 in a 1 x 100 nt way

first: Jian

middle: P

first: Hui

middle: J

last: Cao

first: Li

middle: L

last: Zhang

first: Peng

middle: Y

last: Huang

first: Fu

last: Lin


title: Chromatin analysis of multiple myeloma cells following CBP/p300 inhibition and degradation (ChIP-Seq)

city: Boston

first: Christopher

last: Ott

state: MA

address: 149 13th Street

department: Cancer Center

institute: Masschusetts General Hospital

summary: We performed H3K27ac ChIP-seq on MM.1S cells treated with A-485, GNE-781, and the combination of both, or with dCBP-1, and CBP & p300 ChIP on MM.1S cells.

overall_design: Cells were treated for six hours with each inhibitor (or combination) at a concentration of 100 nM. Cells were then crosslinked (for ChIP-seq), lysed with appropriate lysis buffers, and ChIP-seq procedure was carried out.

first: Barbara

last: Karakyriakou


title: Chromatin analysis of multiple myeloma cells following CBP/p300 inhibition and degradation (ATAC-Seq)

summary: We performed ATAC-seq on MM.1S cells treated with A-485, GNE-781, and the combination of both, or with dCBP-1.

overall_design: Cells were treated for six hours with each inhibitor (or combination) at a concentration of 100 nM. Cells were then lysed with appropriate lysis buffers, and ATAC-seq procedure was carried out.


title: Temporal changes of a pivotal gene set defines plasticity of facultative CAM in Talinum triangulare

city: Düsseldorf

first: Andreas

middle: PM

last: Weber

address: Universitätsstr. 1

department: Institute for Plant Biochemistry

country: Germany

institute: Heinrich-Heine-University

overall_design:
RNA was extracted from leaves of Talinum triangulare plants (3 biological replicates) after plants were grown under 12 days of drought and 2 days of re-watering.

This series contains re-analyzed samples from GSE70601.

first: Dominik

last: Brilhaus


title: Transcriptional response of Corynebacterium glutamicum C1 to 3 mM indole-alanine dipeptide

city: Bielefeld

first: Christian

last: Ruckert-Reed

address: Sequenz 1

department: Medical School OWL

institute: Bielefeld University

summary: Differential gene expression analysis of C. glutamicum C1 in presence of 3 mM indole-alanine dipeptide compared to control conditions without indole-alanine dipeptide. C. glutamicum C1 cells were cultivated in CGXII minimal medium with 40 g per litre glucose in presence or absence of 3 mM indole-alanine dipeptide and harvested during exponential phase (o.d.600 6).

overall_design: Whole transcriptomes of Corynebacterium glutamicum C1 with and without the addition of 3 mM indole-alanine dipeptide as a treatment. Three independent cultivations were performed per condition. Total RNA isolated. Stable RNA was depleted and strand-specific cDNA libraries were constructed for each biological replicate and treatment.

first: Tatjana

last: Walter

first: Kareen

last: Veldmann

first: Tobias

last: Busche

first: Susanne

last: Goetker

first: Arman

middle: B

last: Kashkooli

first: Jannik

last: Paulus

first: Katarina

last: Cankar

first: Volker

middle: F

last: Wendisch


title: Single cell transcriptomic analysis (10x Genomics) of mouse colon LP CD4+ Tcells cells isolated from mouse under different infection conditions

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: To determine the states that Teff actually adopt in frontline tissues in vivo, we applied single-cell transcriptome and chromatin analysis on colonic Teff cells, in germ-free or conventional mice, or after challenge with a range of Teff subset-biasing microbes. Subsets were marked by expression of interferon-signature or myeloid-specific transcripts, but transcriptome or chromatin structure could not resolve discrete Th clusters. At baseline or at different times of infection, transcripts encoding cytokines or proteins commonly used as Teff markers distributed in a polarized continuum, which was also functionally validated. Clones derived from single progenitors gave rise to both IFN-γ and IL17-producing cells. Most transcriptional variance was tied to the infecting agent, independent of the cytokines produced, and chromatin variance primarily reflected activity of AP1 and IRF transcription factor families, not the canonical subset master regulators T-bet, GATA3, RORγ.

overall_design: Single cells were hashed and sorted by flow cytometry for single cell RNAseq library preparation (10x Genomics)

first: Evgeny

last: Kiner

first: Christophe

last: Benoist

first: Diane

last: Mathis


title: Transcriptomic analysis of mouse colon LP CD4+ Tcells cells isolated from mouse under different infection conditions

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

overall_design: Refer to individual Series


title: In vivo transcriptome profiling of control and GANAB-KD UMUC3 bladder carcinoma cells [bulk]

city: Shen Zhen

first: GuoYu

last: Peng

address: 47 Youyi Road, Luohu District

institute: Shenzhen Luohu Hospital Group

summary: Carcinoma cells achieve malignant progression and therapy resistance through de-differentiation. While differentiation therapy has proven to be highly efficient in acute promyelocytic leukemia, this therapeutic strategy has not been successfully applied in human solid tumors. Here, we identify α-Glucosidase II (GANAB) as a novel driver of bladder cancer de-differentiation using a systemic biology approach and demonstrate its potential to serve as a therapeutic target of solid tumor differentiation therapy. Partial knock-out of GANAB by CRISPR Cas9 differentiates one of the most aggressive bladder carcinoma line into a non-invasive papillary form in vivo and decreases chemotherapy resistance in vitro. As differentiation and de-differentiation program are mostly activated in vivo, we labelled control and GANAB-KD cells with a lentivirus to express a H2B-EGFP localized in the nuclei. After sorting by BD FACS Aria II, cells were lyzed for RNA-sequencing.

overall_design: 6 samples were analyzed, including CTR-1, CTR-2, and CTR-3 for control UMUC3, and KD-1, KD-2, and KD-3 for GANAB-KD UMUC3.

first: Li

last: Yuqing

first: Peng

last: Guoyu

first: Zhu

last: Guanghui


title: In vivo transcriptome profiling of control and GANAB-KD UMUC3 bladder carcinoma cells [scRNA-Seq]

overall_design: 2 samples were analyzed, including CTR for control UMUC3, and KD for GANAB-KD UMUC3.


title: Transcriptional response of Corynebacterium glutamicum ATCC 13032 to 2.5 mM indole

first: Christian

last: Ruckert-Reed

summary: Differential gene expression analysis of C. glutamicum ATCC 13032 in presence of 2.5 mM indole compared to control conditions without indole. C. glutamicum ATCC 13032 cells were cultivated in CGXII minimal medium with 40 g per litre glucose in presence of 2.5 mM indole and harvested during exponential phase (o.d.600 4).

overall_design: Whole transcriptomes of Corynebacterium glutamicum ATCC 13032 with and without the addition of 2.5 mM indole as a treatment. Three independent cultivations were performed per condition. After total RNA isolation, samples were pooled based on treatment. Stable RNA was depleted and strand-specific cDNA libraries were constructed.


title: HTS based monitoring of the efficiency of somatic embryogenesis and meristem culture as a method used for virus elimination in grapevine

city: Godollo

first: Eva

last: Varallyay

address: 4 Szent-Györgyi Albert Street

department: Institute of Plant Protection

country: Hungary

institute: Hungarian University of Agriculture and Life Sciences

type: Non-coding RNA profiling by high throughput sequencing

summary: Meristem culture and somatic embryogenesis is an effective tool for virus elimination of vegetatively propagated crops including grapevine. While they both are proved to be useful to eliminate the main grapevine viruses their efficiency differs according to the virus and the variety. In our work we investigated their efficiency using small RNA high-throughput sequencing as virus diagnostic method. Field grown mother plants of four clones representing three cultivars, infected with different viruses and viroids were selected for sanitation via somatic embryogenesis and meristem culture. Our results show that the sanitation with SE was efficient against all of the presenting viruses, including grapevine Pinot gris virus, grapevine rupestris vein feathering virus and grapevine Syrah virus 1, having no data using somatic embryogenesis for their elimination. In case of other viruses and viroids such as GFkV, GRSPaV, GYSVd-1, HSVd this study confirms the findings of earlier researches, that SE is a possible way for elimination. While the efficiency of the elimination of different viruses was high, in case of viroids this ratio was lower. Our work demonstrated that efficiency of SE is comparable to the technically difficult meristem culture technique, and show promising way for the high demand of the production of virus-free grapevine in the future.

overall_design: 10 small RNA sequencing librarise were prepared (4 mother plants, 2 virus released line from meristem culture and 4 released lines using somatic embriogenezis

first: Mihaly

last: Turcsan

first: Emese

last: Demian

first: Tunde

last: Varga

first: Erno

last: Szegedi

first: Robert

last: Olah


title: Transfer RNA fragments replace microRNA regulators of the cholinergic post-stroke immune blockade III

city: Jerusalem

first: Katarzyna

last: Winek

state: Israel

address: The Edmond J. Safra Campus

department: ELSC

country: Israel

institute: Hebrew University of Jersusalem

summary: After ischemic stroke, the brain initiates intensive communication with the immune system, and acetylcholine contributes to this process. Stroke triggers peripheral immunosuppression leading to increased susceptibility to infections; and post-stroke pneumonia is linked with poor stroke outcome, but the responsible processes are yet unknown. We discovered a “change of guards” where microRNA levels decreased but small transfer RNA fragments (tRFs) accumulated in post-stroke blood cells. This molecular switch may re-balance acetylcholine signaling in CD14+ monocytes by regulating their gene expression and modulating post-stroke immunity. Our observations point to tRFs as new molecular regulators of post-stroke immune responses that may become potential therapeutic targets.

overall_design: Small RNA sequencing from whole blood of ischemic stroke patients two days post stroke and age matched controls

first: Sebastian

last: Lobentanzer

first: Hermona

last: Soreq


title: Genomic and epigenomic adaptation in SP-R210 (Myo18A) isoform-deficient macrophages [RNA-seq]

first: Zissis

last: Chroneos

first: Eric

last: Yau

first: Yan

last: Chen

first: Chunhua

last: Song

first: Jason

last: Webb

first: Marykate

last: Carillo

first: Yuka

last: Kawasawa

first: Zhenyuan

last: Tang

first: Yoshinori

last: Takahashi

first: Todd

last: Umstead

first: Sinisa

last: Dovat


title: Transfer RNA fragments replace microRNA regulators of the cholinergic post-stroke immune blockade I

overall_design: PolyA-selected long RNA sequencing from RAW 264.7 murine macrophages 24h after transfection with ssRNA tRF-22-WE8SPOX52 mimics and negative control


title: Identification of TOR-responsive slow-cycling neoblasts in planarians

city: Toronto

first: Alyssa

last: Molinaro

state: Ontario

address: 686 Bay Street

department: Molecular Genetics

country: Canada

institute: University of Toronto

summary: Epimorphic regeneration commonly relies on the activation of quiescent stem cells to drive new cell production. The planarian Schmidtea mediterranea is among the best regenerators in nature, thanks to its large population of adult stem cells, called neoblasts. While neoblasts have long been known to drive regeneration, whether a subset of neoblasts is reserved for this purpose is unknown. Here, we revisited the idea of reserved neoblasts by approaching neoblast heterogeneity from a regulatory perspective. By implementing a new fluorescence-activated cell sorting strategy in planarians, we identified a population of neoblasts defined by low transcriptional activity. These RNAlow neoblasts are relatively slow-cycling at homeostasis and undergo a morphological regeneration response characterized by cell growth at 48 hours post-amputation. At this time, RNAlow neoblasts proliferated in a TOR-dependent manner. Additionally, knockdown of the tumour suppressor Lrig-1, which is enriched in RNAlow neoblasts, resulted in RNAlow neoblast growth and hyperproliferation at homeostasis, and ultimately delayed regeneration. We propose that slow-cycling RNAlow neoblasts represent a regeneration-reserved neoblast population.

overall_design: Bulk or single cells from wild type animals were collected from FACS gates set based on DNA (Hoechst) and RNA (pyrnonin Y) content and libraries were prepared and sequenced.

first: Nicole

last: Lindsay-Mosher

first: Bret

last: Pearson


title: Disruption of the DNA damage pathway at different levels results in distinct phenotypes in a murine liver injury model

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

summary:
Background and aims: A coordinated stress and regenerative response is important following hepatocyte damage. Here, we investigate the phenotypes that result from genetic abrogation of individual components of the CHK2/ p53/ p21 pathway in a murine model of metabolic liver injury.
Methods: NTBC was reduced or withdrawn in Fah /  mice lacking Chk2, p53 or p21, and survival, tumor development, liver injury and regeneration were analyzed. Partial hepatectomies were performed and mice were challenged with the Fas-antibody Jo2.
Results: In a model of metabolic liver injury, loss of p53, but not of Chk2, impairs the oxidative stress re-sponse and aggravates liver damage, indicative of a direct p53-dependent protective effect on hepatocytes. Cell cycle control during chronic liver injury critically depends on the presence of both p53 and its downstream effector p21. In p53-deficient hepatocytes, unchecked proliferation occurs despite a strong induction of p21, revealing a complex interdependency between p21 and p53. The increased regenerative potential in the absence of p53 cannot fully compensate the surplus injury and is not sufficient to promote survival. Despite the different phenotypes as-sociated with the loss of individual components of the DNA damage response, gene expression patterns are dominated by the severity of liver injury, but reflect distinct effects of p53 on prolif-eration and the anti-oxidative stress response.
Conclusion: Characteristic phenotypes result from the genetic abrogation of individual components of the DNA damage response cascade in a liver injury model. The extent to which loss of gene function can be compensated, or affects injury and proliferation, depends on the level at which the cas-cade is interrupted.

overall_design: Microarray analysis on reverse transcribed RNA extracted from Fah-/-  and Fah/ p53-/-  mice with moderate (3 months on 2.5% NTBC) and their respective controls (100% NTBC) were peformed

first: Laura

last: Buitrago-Molina

first: Silke

last: Marhenke

first: Rober

first: Arndt

last: Vogel


title: Transfer RNA fragments replace microRNA regulators of the cholinergic post-stroke immune blockade

first: Katarzyna

last: Winek

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Transfer RNA fragments replace microRNA regulators of the cholinergic post-stroke immune blockade II

overall_design: PolyA-selected long RNA sequencing from whole blood of ischemic stroke patients two days post stroke and age matched controls

first: Sebastian

last: Lobentanzer

first: Hermona

last: Soreq


title: Chromatin analysis of multiple myeloma cells following CBP/p300 inhibition and degradation (RNA-Seq)

first: Christopher

last: Ott

summary: We performed RNA-seq on MM.1S cells treated with A-485, GNE-781, and the combination of both, or with dCBP-1.

overall_design: Cells were treated for six hours with each inhibitor (or combination) at a concentration of 100 nM. Cells were then lysed with appropriate lysis buffers, and RNA-seq procedure was carried out.

first: Barbara

last: Karakyriakou


title: Transcriptome analysis after BACE2 silencing in ocular melanoma cella

city: Shanghai

first: Fanglin

last: He

address: 639 Zhizaoju Rd

institute: Shanghai Ninth People's Hospital

summary: In order to study the mechanism of BACE2 and the development of melanoma, we established a model of low expression of BACE2 in melanoma. The results showed that the expression of tmem38b was decreased after BACE2 knockdown, and the intracellular calcium concentration was decreased. In order to reveal the interaction between BACE2 and tmem38b and the effect of intracellular Ca2 + concentration on the formation and development of melanoma, and to further explore BACE2 The relationship between the expression level and the survival time of OM patients provides new ideas for the treatment of malignant tumors

overall_design: Knockdown of BACE2 in melanoma cells affects its biological function

first: F

first: P

last: Chai

first: R

last: Jia


title: Crosstalk between vrille transcripts, proteins and regulatory elements controlling circadian rhythms and development in Drosophila

city: College Station

first: Paul

last: Hardin

state: Texas

address: 3258 TAMU Dept of Biology Buttler Hall room 100H

institute: Texas A&M University

summary: The vrille (vri) gene encodes a bZIP transcriptional repressor that is required for Drosophila patterning and cell proliferation during development as well as circadian behavior in adults. Three alternate first exons produce five different vri transcripts, where first exons 1a and 1b initiate two transcripts during development that produce the 610aa short VRI isoform and first exon 1c initiates three transcripts in adults that produce the 729aa long VRI isoform. To test whether long VRI is necessary for circadian clock function, we generated a mutant (vriΔ679) that eliminates transcripts encoding long VRI. The vriΔ679 mutant is viable, confirming that developmental functions of vri are driven by transcripts from exons 1a/1b, yet behavioral rhythms persist in vriΔ679 flies, demonstrating that vri transcripts encoding short VRI are sufficient for clock output. E-box regulatory elements upstream of exon 1c that drive rhythmic transcription in adults are also required for development, implying that these E-boxes also drive vri transcription from exons 1a/1b. Surprisingly, there is almost no long VRI present in adults even though the vast majority of transcripts encode long VRI, apparently because the ATG start codon for long VRI has a poor Kozak sequence context. Consequently, short VRI is the predominant isoform in adults and is sufficient for clock output. We conclude that vri-ADF transcripts driven by E-boxes upstream of exon 1c primarily control circadian rhythms by producing short VRI , whereas vri-E transcripts that are also regulated by E-boxes upstream of exon 1c mediate developmental patterning/cell proliferation through short VRI.

overall_design: RNA-seq: mRNA profiles of heads from Drosophila wild type (WT) and vriΔ679 mutant at two different timepoints, ZT 02 and ZT 14

first: Kushan

last: Gunawardhana

first: Gustavo

last: Rivas

first: Courtney

last: Caster


title: Treatment of Neuroblastoma Cells with Inhibitors of Protein Disulfide Isomerase Upregulates NQO1 Activity

city: Copenhagen

first: Dennis

last: Özcelik

address: Universitetsparken 2

country: Denmark

institute: University of Copenhagen

summary:
Protein disulfide isomerase (PDI) is associated with many diseases including neurodegenerative disorders like Alzheimer’s disease and, hence, is considered a promising drug target. This study employs the two PDI inhibitors securinine and 16F16 in order to interrogate the role of PDI in the neurological disease and presents a novel link between PDI inhibition and NQO1 activity
Microarrays were used to analyze the global change in gene expression as a result of PDI inhibition in the human neuroblastoma cell line SH-SY5Y

overall_design: SH-SY5Y cells were treated with the PDI inhibitors securinine (30 uM) or 16F16 (4 uM) for 24 h followed by extraction of the global RNA. The RNA was subjected to an Affymetrix® Human Gene 2.0 ST Array


title: Receptor Notch-3 - role in kidney fibrosis using an UUO model

first: Robert

last: Geffers

summary: Gene array of kidney tissue of wild type and Notch-3 knockout mice was performed following unilateral ureteral obstruction (UUO).

overall_design: Kidney fibrosis and inflammation were analyzed following unilateral ureteral obstruction (UUO). UUO was performed with gender matched 12-16 weeks old mice. The right ureters of wild type and Notch3 knockout mice were ligated for 5 days. Both kidneys were collected for preparation of cortical RNA. Contralateral (left untretaed kidney) were harvested for comparative analyses. To gain insight into the mechanism(s) by which Notch3-deficiency alters the pattern of kidney damage, gene expression analysis of UUO kidneys is performed. The expression of fibrosis relevant genes, cytokines&chemokines as well as Notch receptor family members was compared in wild type UUO day 5 samples versus Notch3-/- UUO day 5 samples.

first: S

last: Brandt

middle: R

last: Mertens


title: MicroRNA-342-3p is a regulator of hepatocellular carcinoma regression

summary: Hepatocellular carcinoma (HCC) is a cancer with global impact and largely refractory to current treatments. Novel treatment options are therefore urgently needed. MicroRNAs play important regulatory roles in HCCs and are emerging as promising therapeutic options against HCC. We identified tumor suppressor miRNAs that may attenuate tumor development and contribute to HCC regression. We identified miR-342-3p as a promising tumor suppressor miRNA. To understand how miR-342-3p affects the global landscape of gene expression, we transfected Huh7 human hepatoma cells with either the scramble control, or a mimic for miR-342-3p and performed mRNA expression profiling.

overall_design: Huh7 human hepatoma cells were transfected with a scramble control or with a mimic for the tumor suppressor miRNA, miR-342-3p and following validation of miRNA expression, were subjected to gene expression profiling.

first: Asha

last: Balakrishnan


title: The effect of natural feline coronavirus infection on the host immune response: a whole-transcriptome analysis on the mesenteric lymph nodes of cats with and without feline infectious peritonitis

city: Zurich

first: giancarlo

last: russo

state: Schweiz

address: winterthurerstrasse 190

department: Functional Genomics Center Zurich

country: Switzerland

institute: ETH/University of Zurich

summary:
Purpose: Comparison of the effect on the host immune response of feline coronavirus infection with or without feline infectious peritonitis
Results: FIP was associated with higher pro-inflammatory pathway enrichment; whilst non-FIP FCoV-positive cats showed lower enrichment of humoral immunity pathways, below that of uninfected cats in the case of immunoglobulin production pathways
Conclusions: Reinforces host differences in disease susceptibility in addition to any viral factors, importance of cellular vs humoral response also highlighted.

overall_design: RNA was extracted from the MLN of cats with and without FIP, the latter divided also by the presence of FCoV infection in the MLN

first: Alexandra

last: Malbon

first: Giancarlo

last: Russo

first: Carole

last: Burgener

first: Emi

middle: N

last: Barker

first: Marina

last: Meli

first: Séverine

last: Tasker

first: Anja

last: Kipar


title: Chromatin analysis of multiple myeloma cells following CBP/p300 inhibition and degradation

first: Christopher

last: Ott

overall_design: Refer to individual Series


title: Regulation of Decay Accelerating Factor primes human germinal center B cells for phagocytosis

city: Umeå

first: Johan

last: Henriksson

address: 6K och 6L, Sjukhusområdet

country: Sweden

institute: Molecular Infection Medicine Sweden (MIMS)

summary: Germinal centers (GCs) are structures in secondary lymphoid organs, essential for an efficient humoral immune response. Complement interaction with B cells facilitates B cell activation, but little is known about the role of complement regulators during B cell activation and differentiation. By flow cytometric analysis, we could show that the majority of human GC B cells had decreased expression of the negative complement regulator Decay Accelerating Factor (DAF). Transcriptomic analysis revealed that DAFlo GC B cells upregulated genes associated with gene editing and proliferation, whereas DAFhi GC B cells had increased expression of genes involved in cell differentiation. We could confirm that DAFhi GC B cells expressed the transcription factor Blimp1 on protein level, which indicates that DAFhi GC B cells may be early plasmablasts/plasma cells. Then, we assessed the expression of the complement regulator CD59, which inhibits the membrane attack complex that lyses cells. We found that the expression was low in naïve and memory B cells, but increased in GC and plasmablasts/plasma cells. This suggests that DAFlo GC B cells may be primed for phagocytosis rather than lysis. By cell sorting, we could show that DAFlo GC B cells were phagocytosed to a greater extent than DAFhi GC B cells, both in presence and absence of complement. Stimulation of the B cell receptor on circulating B cells induced DAFlo cells.  Finally, we also identified specific downregulation of DAF during early B cell development in the human bone marrow. As a conclusion, we suggest that complement regulators serve specific functions at stages of B cell selection.

overall_design: DAFhi and DAFlo germinal center B cells (viable, CD3-, CD14-, CD19+, CD20+, CD38+, IgD-) were sorted in bulk (25.000 cells). RNA was extracted and hybridized to Affymetric Human Clariom D array.

first: Andy

last: Dernstedt

first: Jana

last: Leidig

first: Anna

last: Holm

first: Jenny

last: Mjösberg

first: Clas

last: Ahlm

first: Magnus

last: Hultdin

first: Mattias

last: Forsell


title: Enzalutamide resistance in C42-B prostate cancer cells

city: Cleveland

first: Sanjay

last: Gupta

state: Ohio

address: 10900 Euclid Avenue

department: Department of Urology

institute: Case Western Reserve University

summary: Castration resistant prostate cancer (CRPC) develops resistance to antiandrogens affecting Androgen Receptor (AR) signaling through a variety of mechanism. Because of this, the efficacy of androgen receptor targeted therapy remains limited for many patients with CRPC. We  developed C42B-enzalutamide (ENZU) and resistance cells to study changes in transcriptomic profile compared to parental cells.

overall_design: Genome wide expression of prostate cancer cells (C42B and C42B-enzalutamide resistant cells) were determined using RNA-seq. The RNA-seq experiment were performed with C42B cells were recurrently exposed to increasing concentrations of enzalutamide (1~ 20 μM) by passage in media containing enzalutamide for 6 months in 10% FBS and stored for further analysis. The resistant cells generated from 20 µM enzalutamide were always maintained in media containing 5µM enzalutamide were referred to as C42B Enzu (C42B enzalutamide resistance). Parental C42B cells treated with 1% DMSO were passaged alongside the enzalutamide treated cells as an appropriate control.C42B and C42B-Enzu cells were maintained in RPMI 1640 with 10% FBS. All cells were maintained at 37°C in a humidified incubator with 5% carbon dioxide.

first: Shiv

last: Shankar Verma


title: Enzalutamide resistance in prostate cancer cells

summary: Castration resistant prostate cancer (CRPC) develops resistance to antiandrogens affecting Androgen Receptor (AR) signaling through a variety of mechanism. Because of this, the efficacy of androgen receptor targeted therapy remains limited for many patients with CRPC. We  developed LNCaP-enzalutamide (ENZU) and resistance cells to study changes in transcriptomic profile compared to parental cells.

overall_design: Genome wide expression of prostate cancer cells (LNCaP and LNCaP-enzalutamide resistant cells) were determined using RNA-seq. The RNA-seq experiment were performed with LNCaP cells were recurrently exposed to increasing concentrations of enzalutamide (1~ 20 μM) by passage in media containing enzalutamide for 6 months in 10% FBS and stored for further analysis. The resistant cells generated from 20 µM enzalutamide were always maintained in media containing 5µM enzalutamide were referred to as LNCaP Enzu (LNCaP enzalutamide resistance). Parental LNCaP cells treated with 1% DMSO were passaged alongside the enzalutamide treated cells as an appropriate control. LNCaP and LNCaP-Enzu cells were maintained in RPMI 1640 with 10% FBS. All cells were maintained at 37°C in a humidified incubator with 5% carbon dioxide.

middle: S

last: Verma


title: Gene expression data of mRNA from mesenchymal stem cells derived from two different sorts of synovial membrane of German Landrace (DL) and Angeln Saddleback (AS) pigs

city: Dummerstorf

first: Siriluck

last: Ponsuksili

address: Wilhelm-stahl-allee 2

institute: FBN

summary: 47,845 probe-sets were screened, This study compared expression profiles of mesenchymal stem cells derived from the two breed DL and AS and then analyzed the expression profile genes between two different sorts of synovial membrane in each breed.

overall_design: RNAs of mesenchymal stem cells derived from two different sorts of synovial membrane of DL and AS were hybridized to Affymetrix Porcine Snowball Array


title: Gene expression of skin biopsie samples from juvenile myositis (JM) and childhood-onset lupus (cSLE).

city: Ann Arbor

first: Celine

last: Berthier

state: MI

address: 1150 W. Medical Center Dr, MSRB2

institute: University of Michigan

summary: Skin inflammaton heralds systemic disease in juvenile myositis (JM), yet we lack an understanding of pathogenic mechanisms driving skin inflammation in JM. The goal of this study is to define cutaneous gene expression signatures in JM and identify key genes and pathways that differentiate skin disease in JM from childhood-onset SLE (cSLE).

overall_design: Formalin formalin-fixed paraffin-embedded (FFPE) skin biopsy samples from JM, cSLE, and control (HC) patients were used to perform Affymetrix ST 2.1 microarray analysis and determine differentially expressed genes (DEGs; q-value ≤ 5%) between patient groups.

first: Jessica

last: Turnier

first: Lauren

last: Pachman

first: Lori

last: Lowe

first: Lam

last: Tsoi

first: Sultan

last: Elhaj

first: Rajasree

last: Menon

first: Gabrielle

last: Morgan

first: Johann

last: Gudjonsson

first: J

last: Kahlenberg


title: Differential gene expression in WT versus Hem1 KO macrophages

first: Robert

last: Geffers

summary: Gene profiling, using microarray technology, was used to identify differentially expressed genes in bone marrow-differentiated macrophages of Hem1 KO versus Hem1 WT mice

overall_design: Bone marrow of two distinct mice of each genotype was differentiated in vitro into macrophages and cells were collected for analysis

first: S

last: Stahnke

first: T

last: Stradal

first: R


title: A dataset of lncRNAs and mRNAs during embryonic development of common carp, Cyprinus carpio

city: Wuxi

first: Lanmei

last: Wang

address: East Shanshui Road 9

institute: Freshwater Fisheries Research Centre of Chinese Academy of Fishery Sciences

summary: The Cyprinus carpio is one of the most important food fish with over hundred varieties in the world. It shows many morphological and genetic variations after selection breeding. It is also considered an alternative vertebrate fish model to zebrafish.  MicroRNAs (miRNAs) and long non-coding RNAs (lncRNAs) have been suggested to have a crucial role in embryonic development. However, systemic research on the lncRNAs and miRNAs during embryonic development of C. carpio has not been reported yet. In this study, we investigated the miRNA, lncRNA and mRNA expression profiles during six main embryonic development stages (cleavage (2 hours post-fertilization hpf)), blastocyst (6 hpf), gastrulation (12 hpf), organ formation (20 hpf), hatching (64 hpf) and 1 day post-hatching). A total of 323.43 Gb high-quality reads  were obtained from lncRNA  library. After filtering, 51,979 lncRNAs were identified. The results would open the way for future genetic, genomic, and evolutionary studies and enable better understanding of gene regulation during embryonic development of C. carpio.

overall_design: mRNAs and lncRNAs in embryonic development stages of common carp were detected by strand-specific RNAseq using Illumina HiSeq X-TEN.

first: Feibiao

last: Song

first: Wenbin

last: Zhu

first: Jianjun

last: Fu

first: Zaijie

last: Dong

first: Pao

last: Xu


title: Expression analysis in Arabidopsis comparing combined salt-stress and subsequent Botytis infection with single stresses

city: Tuebingen

first: Andrea

middle: A.

last: Gust

state: BW

address: Auf der Morgenstelle 32

department: Center for Plant Molecular Biology (ZMBP)

institute: University of Tuebingen

summary:
Investigation of whole genome gene expression level changes in wild-type Arabidopsis leaves upon application of either salt-stress or Botrytis-infection or both stresses in combination
Plants have evolved effective defense mechanisms to cope with various microbial attacks. However, triggering of immune responses needs to be tuned to the local environment to balance between defense and growth. Here, we investigated the impact of salt which is a prominent environmental factor in arid regions on the Arabidopsis innate immune response. An in-depth analysis of combined salt-stress with Botrytis infection revealed an up-regulation of a unique set of genes, which is not induced upon single stress application.

overall_design: A 15 chip study using total RNA recovered from each three biological replicates of 1. control treatment (t=0 days), 2. normal watering (t=4 days), 3. salt-watering (t=4 days), 4. normal watering (for 4 days) plus Botrytis infection on day 4 for additional 3 days, 5. salt-watering (for 4 days) plus Botrytis infection on day 4 for additional 3 days.  Each chip measures the expression level of the whole genome from Arabidopsis thaliana accession Columbia 0 (Col-0).

first: Thorsten

last: Nürnberger


title: Transcriptomic analysis of C. elegans infected with Myzocytiopsis humicola or treated with its extract

city: London

first: Michalis

last: Barkoulas

address: SAF Building, South Kensington

country: United Kingdom

institute: Imperial College London

summary: We used RNA-seq to identify gene expression changes in C. elegans after 1 hr, 4 hr, 12 hr and 24 hr of exposure to Myzocytiopsis humicola extract; and after 12 hr, 24 hr and 48 hr of infection with Myzocytiopsis humicola

overall_design: Total RNA was extracted from L4 stage C. elegans after exposure to Myzocytiopsis humicola or its extract at appropriate time points

first: Manish

last: Grover


title: Comprehensive circular RNA expression profiling and competitive endogenous RNAs regulatory networks in distal cholangiocarcinoma

city: Beijing

first: Xinxue

last: Zhang

state: Beijing

address: 8 Gongti South Street

institute: Beijing Chaoyang Hospital

summary: To explore the differentially expressed (DE) circular (circ)RNAs, competing endogenous RNAs networks, and potential biomarkers in distal cholangiocarcinoma (dCCA), using microarray analysis, a comprehensive circRNA expression profiling was constructed with six paired dCCA tumor and adjacent normal samples. A total of 171 DE circRNAs were identified. Three upregulated (hsa_circ_0060144, hsa_circ_0008274, and hsa_circ_0000673) and two downregulated circRNAs (hsa_circ_0139402 and hsa_circ_0001714) were validated with RT-qPCR in 40 dCCA patients. Among them, hsa_circ_0000673 had an idea prognostic efficiency (AUC=0.85, p<0.01) and high level of hsa_circ_0000673 was associated with late tumor stage (p<0.01), poor histodifferentiation (p=0.041), and residual tumor (p=0.044). Gene ontology analysis of the host genes of 171 DE circRNAs showed that “response to nutrient”, “adherens junction”, and “cell adhesion molecule binding” were mainly enriched in terms of biological process, cellular component, and molecular functions respectively. Nine target micro(mi)RNAs of the five DE circRNAs were screened out and enriched in cancer associated pathways. Thereafter, 188 DE mRNAs were predicted as target genes of the nine miRNAs. Finally, protein-protein interaction networks were constructed and 20 hubgenes were identified. This research provided a landscape of DE circRNAs in dCCA, constructed circRNA-miRNA-mRNA regulating networks, and identified hsa_circ_0000673 as a potential biomarker and target for treating dCCA.

overall_design: Using microarray analysis, a comprehensive circRNA expression profiling was constructed with six paired dCCA tumor and adjacent normal samples. A total of 171 DE circRNAs were identified. Three upregulated (hsa_circ_0060144, hsa_circ_0008274, and hsa_circ_0000673) and two downregulated circRNAs (hsa_circ_0139402 and hsa_circ_0001714) were validated with RT-qPCR in 40 dCCA patients. Among them, hsa_circ_0000673 had an idea prognostic efficiency (AUC=0.85, p<0.01) and high level of hsa_circ_0000673 was associated with late tumor stage (p<0.01), poor histodifferentiation (p=0.041), and residual tumor (p=0.044). Gene ontology analysis of the host genes of 171 DE circRNAs showed that “response to nutrient”, “adherens junction”, and “cell adhesion molecule binding” were mainly enriched in terms of biological process, cellular component, and molecular functions respectively. Nine target micro(mi)RNAs of the five DE circRNAs were screened out and enriched in cancer associated pathways. Thereafter, 188 DE mRNAs were predicted as target genes of the nine miRNAs. Finally, protein-protein interaction networks were constructed and 20 hubgenes were identified. This research provided a landscape of DE circRNAs in dCCA, constructed circRNA-miRNA-mRNA regulating networks, and identified hsa_circ_0000673 as a potential biomarker and target for treating dCCA.

first: Xin

last: Zhao

first: Zhigang

first: Zhe

last: Liu

first: Jiqiao

first: Shaocheng

last: Lyu

first: Lixin

last: Li

first: Ren

last: Lang

first: Qiang

last: He


title: Adeno-associated virus-mediated delivery of anti-miR-199a tough decoys attenuates cardiac hypertrophy

city: Chengdu

first: Hualin

last: Yan

state: Sichuan

address: No.37, Guoxuexiang,

institute: West China Hospital, Sichuan University

summary: MicroRNAs (miRNAs) are important regulators in the process of cardiac hypertrophy and heart failure. Previous studies showed that miR-199a is upregulated in pressure-overload cardiac hypertrophy and overexpression of miR-199a induces cardiac hypertrophy in vivo. However, the therapeutic role of anti-miR-199a treatment in cardiac hypertrophy is of little known. Here, we showed a novel and effective way to treat mice cardiac hypertrophy and restored cardiac function through injection of adeno-associated virus (AAV) which expressed anti-miR-199a tough decoys (TuDs). We performed the RNA-seq profiling in both AAV9-EGFP control and AAV9-anti-miR-199a TuDs injected cardiac hypertrophic mice. The transcriptome analysis indicates that genes related to cytoplasmic translation, mitochondrial respiratory chain complex assembly were upregulated by anti-miR-199a treated recovered hearts.

overall_design: Examine expression of mRNAs in AAV9-EGFP and AAV9-anti-miR-199a tough decoys(TuDs) injected hypertrophic hearts

first: Yifei

first: Yimin

last: Hua

first: Yan

last: Luo


title: Transducin β-like protein 1 controls multiple oncogenic networks in diffuse large B cell lymphoma

city: Columbus

first: Hatice Gulcin

last: Ozer

state: OH

address: 1800 Cannon Dr

department: Biomedical Informatics

institute: The Ohio State University

summary: ChIP-Seq analysis showed that TBL1 occupancy was not significantly globally affected after treatment with tegavivint supporting the notion that TBL1 functions as an adaptor protein that facilitates the exchange between co-repressor and coactivators

overall_design: Chip-seq was performed in two DLBCL cell lines (Riva and Pfeiffer) to assess the genome-wide localization of TBL1 in the presence or absence of tegavivint for 12 hours

first: Youssef

last: Youssef

first: Vrajesh

last: Karkhanis

first: Wing

middle: K

last: Chan

first: Frankie

last: Jeney

first: Alessandro

last: Canella

first: Xiaoli

first: Shelby

last: Sloan

first: Alexander

last: Prouty

first: Liudmyla

last: Tsyba

first: Walter

last: Hanel

first: Xuguang

last: Zheng

first: Pu

first: Ji-Hyun

last: Chung

first: David

last: Lucas

first: Zachary

last: Kauffman

first: Karylin

last: Larkin

first: Anne

last: Strohecker

first: Hatice

middle: G

first: Rosa

last: Lapalombella

first: Hui

last: Zhou

first: Zijun

last: Xu-Monette

first: Ken

last: Young

first: Ruolan

last: Han

first: lmar

last: Nurmemmedov

first: Gerard

last: Nuovo

first: Kami

last: Maddocks

first: John

last: Byrd

first: Robert

last: Baiocchi

first: Lapo

last: Alinari


title: Intermittent treatment on exemestane acquired resistance

city: Duarte

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

summary: MCF7aro cells were cultured in hormone-stripped medium and treated with EXE continuously or intermittently (2 weeks on and 1 week off) in the presence of 1nM testosterone. At week 14, EXE-treated cells as well as MCF7aro cells were hormone-stripped for 48h were harvested and RNA was extracted.Gene expression profiles in each cell line were analyzed by the Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays.

overall_design: Microarray analysis of gene expression in exemestane intermittently or continuously-treated ER+ breast cancer MCF7aro cells

first: Masri

last: Selma

first: Chen

last: Shiuan


title: Differential BET protein recruitment to IL-6 and IL-8 promoters and suppression of innate immunity and cell cycle genes by BET inhibitors in TNFalpha/IL-17 stimulated human keratinocytes

city: Newcastle

first: Simon

last: Cockell

address: Framlington Place

institute: Newcastle University

summary:
Background:  Epigenetic mechanisms are implicated in chronic inflammatory pathogenesis.  Bromodomain Extra-Terminal (BET) proteins are druggable epi-reader proteins which bind acetylated histones and transcription factors regulating gene expression, including inflammatory genes.
Objectives:  To evaluate the role of specific histone acetylation events and BET protein interactions in promoting keratinocyte inflammatory and transcriptional responses, to determine the effects of pharmacological inhibition of BET proteins and thereby test the hypothesis that BET proteins represent an effective therapeutic target to treat cutaneous inflammation.
Methods:  Primary human keratinocytes were stimulated with tumour necrosis factor alpha and interleukin 17 (TNFalpha + IL-17), +/- BET inhibitor (I-BET151). Cytokine induced interleukin 6 and 8 (IL-6 /-8) responses were determined by qPCR and ELISA. Chromatin immunoprecipitation (ChIP) assays were undertaken to characterise epigenetic changes at the IL-6 and IL-8 gene promoters, while the effect of I-BET151 treatment on keratinocyte transcriptional response was determined by Illumina array.
Results:  TNFalpha + IL-17 induced gene-specific epigenetic changes, including: histone hyperacetylation, recruitment of BET proteins (BRD2/3/4) to the promoter regions of IL-6/-8 and activation of RNA polymerase II (PolII(S2P)), correlating with increased IL-6/-8 expression.  I-BET151 reduced recruitment of BRD4 and activation of PolII(S2P), at the IL-6 promoter, and BRD3/4 and PolII(S2P), at the IL-8 promoter; which is consistent with I-BET151 inhibitory effects on TNFalpha + IL-17-induced IL-6/-8 expression.  A ~10-fold enrichment of BRD4/p65 was observed at the IL-6 promoter compared to the IL-8 promoter.  Transcriptomics analysis showed that I-BET151 modulated expression of genes involved in cell cycle, cell proliferation and the innate immune response in keratinocytes stimulated with TNFalpha + IL-17.
Conclusions:  In human keratinocytes, disease-relevant stimuli induced dynamic epigenetic changes at inflammatory gene loci.  BET proteins played a critical role in keratinocyte innate immune responses and displayed differential effects; for example BRD4/p65 was particularly enriched at the IL-6 promoter, indicating that BRD4 may be a critical factor in integrating inflammatory stimuli via NF-B in chronic skin inflammation.  Inhibition of these responses by I-BET151 highlights BET proteins as potential therapeutic targets in inflammatory skin disease.

overall_design: Gene expression profiling by Illumina BeadArray of human primary keratinocyte cells with stimulation (TNF⍺/IL-17) and treatment with BET inhibitor (I-BET151).  Samples from consenting human donors (12 donors, 4 conditions, 2 timepoints = 96 total samples).

first: Keith

first: Nick

last: Reynolds


title: DNA Methyltransferase 3A Mediates the Sustained Effects of Stress on Synaptic Functions and Behaviors

city: Tallahassee

first: Nicholas

middle: James

last: Waddell

state: FL

address: 319 Stadium Dr

department: Biological Sciences

institute: Florida State University

type: Methylation profiling by high throughput sequencing

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


title: Transcriptional response to a dietary Comfrey supplement in broiler chickens

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

department: Genome Biology

institute: FBN Dummerstorf

summary: in vivo microarray study of transcriptional changes in chicken whole blood cells due to dietary intake of Comfrey (Symphytum spp.)

overall_design: whole blood of 16 broiler chickens per dietary group were sampled for expression profiling

first: Michael

last: Oster

first: Henry

last: Reyer

first: Siriluck

last: Ponsuksili


title: Gene expression in stage III colorectal cancer

city: Changsha

first: Xiangping

last: Song

state: Hunan

address: 87 Xiangya Road

institute: Xiangya Hospital

summary: Profile of differentially expressed genes in stage III colorectal cancer  compared to paired normal tissue by whole genome microarray expression test

overall_design: Both cancer tissue and paired adjacent non-cancerous tissue were collected and stored in liquid nitrogen. 12 samples from six patients diagnosed with stage III CRC post-surgery were used for microarray analysis.

first: Qian

last: Pei

first: Haiping


title: Differences in transcription in Angelman syndrome and control person iPSC-derived neurons

city: Essen

first: Laura

last: Steenpass

address: Hufelandstrasse 55

department: Institute of Human Genetics

institute: University Hospital Essen, University Duisburg-Essen

summary: Angelman syndrome is caused by loss of funtional ubiquitin E3 ligase UBE3A and results in severe deley in cognitive and motor development. In neurons, UBE3A locates to the synapse and to the nucleus. Loss of nuclear UBE3A results in development of Angelman syndrome like symptoms in mice. UBE3A can function as transcriptional coactivator of steroid hormone receptors, but the entire function of UBE3A in the nucleus is still not clear. So we wanted to study differences in the transcriptome in neurons differentiated from iPSCs that were derived from patients with Angleman syndrome and normal controls.

overall_design: Differentiation of iPSCs into cortical neurons, 3 samples Angelman syndrome, 3 samples controls


title: Trancriptome sequencing of BGC823 with or without ZBTB7A knockdown

city: Jinan

first: Yujing

last: Sun

state: Shandong

address: 44 Wen Hua Xi Road

department: Department of pathology

institute: School of Basic Medical Sciences, Shandong University

summary: Tumor budding (TB), clusters of less than 5 cells dissociated from the tumor mass, is reported to predict nodal involvement and recurrence in multiple human cancers including gastric carcinoma (GC). However, it is not clear how TB forms. In this study, we determined the expression pattern of GAGE12I, CTNND1, Kif26B, CREB1 and ZBTB7A in human GC samples by IHC attempting to find any TB-related markers. The results showed that TB could predict lymph node metastasis and is negatively associated with the overall survival of GC patients. The expression of ZBTB7A in the tumor margin (invasive front), rather than the other four markers, was much higher than that inside the tumor and was positively correlated with TB score. Moreover, patients with higher marginal ZBTB7A expression had poorer prognosis. ZBTB7A could enhance the migration and invasion capabilities of GC cells in vitro. Mechanically, ZBTB7A might activate EGFR-MAPK-ERK and PI3K-AKT-mTOR pathway, which resulted in epithelial-mesenchymal transition (EMT) to induce the formation of TB. Thus, we concluded that higher ZBTB7A expression in the tumor margin may contribute to the dissociation of tumor cells from the tumor mass to form TB by initiating EMT via EGFR-MEK-ERK and PI3K-AKT-mTOR pathway.

overall_design: BCG823 cells of control and that with siZBTB7A treated were analyzed. No replication.

first: Peng

last: Gao


title: Post-implantation developmental defects induced by mtDNA mutation derive from altered DNA methylome in oocytes

first: Wenjie

last: Shu

address: Taiping Road 27

institute: Beijing Institute of Radiation Medicine

summary: Accumulating evidences suggest a link between mitochondrial dysfunction and female reproduction decline. To directly and systematically figure out the influence of mitochondrial DNA (mtDNA) mutation on oocyte quality and embryo development, we used an mtDNA mutator mouse model (D257A) that harbors a proofreading-deficient version of PolgA. Here we showed that D257A mice developed a profound reduction of fertility at 19-week of age, and accumulated twofold more increase in the levels of point mutations in oocyte mtDNA. Following ovarian hyper-stimulation, we found oocyte numbers retrieved from WT and D257A mice were comparable until 19 weeks of age, while with a half reduced number of oocyte ovulated in D257A mice thereafter. We further found the oocyte quality based on mitochondrial distribution, meiotic spindle assembly, chromosomal segregation and ATP content at 19 weeks of age was identical in both group. Meanwhile, the ovulated oocytes can initiate and sustain early embryo development after in vitro fertilization, and reach the blastocyst stage with no obvious defects compared to WTs. Of note, post-implantation developmental defects were observed in D257A embryos, as revealed by fetal growth retardation and decreased ratios of pups delivered. Furthermore, genome-wide methylation analysis revealed global hypomethylation across the genome of D257A oocytes, with a dramatic reduce in genome repetitive-elements, like DNA transposon, LINEs and SINEs regions. In conclusion, our study presents the direct experimental investigation of the effect of mtDNA mutation on oocyte and embryo competence, and demonstrates altered DNA methylation in oocyte may represent a critical mechanism that mediates the phenotypic defects of mtDNA mutation in post-implantation development.

overall_design: Two groups with three replicates were used.

first: Longsen

last: Han


title: Gene expression in Semimembranosus skeletal muscles in pig using the GenmascqChip (custom 15K Agilent microarray)

city: SAINT GILLES

first: Frederic

last: Herault

address: 16 le Clos

department: Animal Genetic

country: France

institute: INRAE

summary: eQTL analysis of Semimembranosus muscle in pig

overall_design: The 112 pigs (females and barrows) used in gene expression analyses are part of a larger F2 population of 1,000 animals, setup within the framework of a QTL detection program. These animals were produced as a second generation intercross between two commercial sire lines (F016, Pietrain type line, and FH019, synthetic line from Hampshire, Duroc and Large-White founders, FRANCE-HYBRIDES, St Jean de Braye, France).

first: Marie

last: Damon

first: Annie

last: Vincent

first: Frédéric

last: Hérault


title: Changes in mouse femoral head transcriptome after FGFR3 constitutive activation

city: PARIS

first: laurent

last: SCHIBLER

address: 24 Boulevard du Montparnasse

department: Imagine Institute, UMR 1163

institute: INSERM

summary:
Achondroplasia (ACH), the most common form of human dwarfism is caused by a mutation in the Fibroblast Growth Factor Receptor 3 (FGFR3) gene, resulting in constitutive activation of the receptor. In order to gain insight into molecular mechanisms involved in the physiopathology, a conditional mouse model carrying the Y367C mutation corresponding to the human Y373C TDI mutation was produced (fgfr3neoY367C/+). Crossing these mice with CMV-CRE mice produces dwarf fgfr3Y367C/+ and fgfr3+/+ controls littermates.
Dwarf fgfr3Y367C/+ mice exhibited skeletal dysplasia at birth, the phenotype becoming progressively more pronounced as the mice got older, with reduced length of long bone, narrow trunk, short ribs and macrocephaly. Histological examination of epiphyseal growth plates showed a disorganized growth plate, with reduced size of the hypertrophic and proliferative zone and an accelerated secondary ossification center formation (full phenotype description in Pannier S et al, Activating Fgfr3 Y367C mutation causes hearing loss and inner ear defect in a mouse model of chondrodysplasia. Biochimica et biophysica acta 2009; Pannier S et al, Delayed bone age due to a dual effect of FGFR3 mutation in Achondroplasia. Bone 2010; Jonquoy A et al, A novel tyrosine kinase inhibitor restores chondrocyte differentiation and promotes bone growth in a gain-of-function Fgfr3 mouse model. Human molecular genetics 2012; Martin L et al, Constitutively-active FGFR3 disrupts primary cilium length and IFT20 trafficking in various chondrocyte models of achondroplasia. Human molecular genetics 2018).

overall_design: Three pairs of Fgfr3Y367C/+ female and Fgfr3+/+ controls littermates were produced at 4 time points (d7, d14, d21 and d28).

first: Laurent

last: Schibler

first: Laurence

last: Legeai-Mallet


title: Transcriptional reprogramming of cancer cells upon loss of the PPM1G/PP2Cγ phosphatase

city: Dallas

first: Ivan

last: D'Orso

state: TX

address: 5323 Harry Hines

department: Microbiology

institute: UT Southwestern Medical Center

summary: Dysfunction of cell signaling–transcriptional regulatory circuits promotes malignant transformation, tumor development, and resistance to cancer therapy. However, the molecular mechanisms by which these abnormal programs translate into tumorigenesis are not entirely understood. The PPM1G/PP2Cγ phosphatase is frequently mutated and deleted in cancer but the functional consequences remain unknown. Here we measure steady-state and nascent RNA changes in parental and PPM1G knockout colorectal cancer cells, and define the transcriptional signatures deregulated upon PPM1G loss leading to aberrant, increased cell proliferation indicating PPM1G is a novel tumor suppressor.

overall_design: Nascent and steady-state RNA expression levels in Ctrl vs PPM1G KO cells.

first: Zheng

last: Ma

first: Holly

last: Ruess

first: Iván


title: Gene expression in Longissimus lumborum skeletal muscles in pig using the GenmascqChip (custom 15K Agilent microarray)

summary: eQTL analysis of Longissimus lumborum muscle in pig

overall_design: The 325 pigs (females and barrows) used in gene expression analyses are part of a larger F2 population of 1,000 animals, setup within the framework of a QTL detection program. These animals were produced as a second generation intercross between two commercial sire lines (F016, Pietrain type line, and FH019, synthetic line from Hampshire, Duroc and Large-White founders, FRANCE-HYBRIDES, St Jean de Braye, France).


title: Insight into the regulation of prodigiosin production by temperature in Serratia marcescens through transcriptome analysis

city: WUXI

first: YANG

last: SUN

address: LIHU ROAD

institute: JIANGNAN UNIVERSITY

summary: We report the application of transcriptome sequencing technology for high-throughput profiling of Serratia marcescens for producing prodigiosin. By obtaining over 163 million bases of sequence from Serratia marcescens genome DNA, we generated transcriptome -state maps of Serratia marcescens 12h cells, 24h cells, and 36h cells at 30C and 37C,respectively. We explored the mechanism of S. marcescens response temperature regulation at the transcription level through transcriptome sequencing technology. We found that the pig gene cluster at low temperature would favor at the transcriptional level, however, higher temperature resulting in instability and loss of enzyme activity. Numerous amino acid metabolic pathways involved in prodigiosin biosynthesis in S. marcescens responded to temperature changes, and metabolic fluxes were directed towards prodigiosin biosynthesis. At the same time, quorum sensing, two-component regulatory system and sRNA were stimulated by temperature to regulate PG biosynthesis and involve strain virulence and exclusive genes. Moreover, inhibition factors was the one reason for S. marcescens incapable synthesis of prodigiosin at 37C. This study laid a good foundation for understanding the biological functions of prodigiosin, improving the temperature tolerance of industrial strains, and excavating temperature-sensitive regulatory elements.

overall_design: Examination of the influence on prodigiosin production in Serratia marcescens between 30℃ and 37℃ .

first: Zhiming

last: Rao

first: Yang


title: Discrepancy in SATB1 expression reflects the heterogeneity in cutaneous T cell lymphoma

first: Yumei

address: No.8 Xishiku Street, Xi Cheng District

department: Department of Dermatology and Venereology

institute: Peking University First Hospital

summary: SATB1 is an important T-cell specific chromatin organizer in cutaneous T cell lymphoma, while its expression and function in Mycosis fungoides (MF) remain ambiguous. RNA-sequencing was conducted to investigate the genes regulated by SATB1 in MF-derived MJ cells by RNA-sequencing after SATB1-knockdown. With the criteria of P<0.05 and |fold change|>1.3, there were 988 genes upregulated and 1373 genes downregulated in SATB1-silencing MJ cells and further subjected to KEGG analysis. SATB1 silencing in MJ cells showed that SATB1 upregulated genes involved in eosinophil recruitment, including STAT3 and IL13, and downregulated genes in cell cycle progression.

overall_design: Gene expression was compared between MJ cells transfected with SATB1-shRNAs and scrambled shRNA to investigate genes regulated by SATB1 in MJ cells.

first: Fengjie

last: Liu

first: Jingru

first: Yujie

last: Wen

first: Ping

last: Tu

last: Wang


title: Chip-chip of Snt1, of PolII, and of H3K4me2 from budding yeast cells

city: Taipei

first: Gan-Guang

last: Liou

state: Taiwan

address: Institute of Molecular Biology, Academia Sinica., 128 Sec. 2, Academia Rd, Nankang,

country: Taiwan

type: Genome binding/occupancy profiling by genome tiling array

summary: Chromatin immunoprecipitation of Snt1, of PolII, and of H3K4me2, respectively, applied with tilling array chip (ChIP on chip of Snt1, of PolII, and of H3K4me2, respectively) analysis demonstrated that a compared genomic occupancy of Snt1, of PolII, and of H3K4me2 in Saccharomyces cerevisiae wild type cells compared anong those in Hst1 deleted, Hos2 deleted and Hst2 & Hos2 double deleted cells

overall_design: Comparison the distributions of Snt1, of PolII, and of H3K4me2 on whole chromatin region among the wild  type, Hst1 deleted, Hos2 deleted and Hst2 & Hos2 double deleted cells

first: Gunn-Guang

first: Shu-Yun

last: Tung


title: Transgenerational epigenetic and transcriptomic effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin exposure in rat [Bisulfite-Seq]

city: Toronto

first: Stephenie

last: Prokopec

address: 661 University Avenue, Suite 510

institute: Ontario Institute for Cancer Research

summary: In rats, direct exposure to TCDD causes myriad toxicities. Exposed rats experience hepatotoxicity, wasting syndrome and immune suppression, amongst others. “Inherited exposure”, as occurs in the F3 generation of directly exposed F0 animals, has also been shown to cause toxicity: both male and female F3 rats demonstrate an increased incidence of adult onset disease while males show increased incidence of kidney disease and an altered sperm epigenome. Here, we employ bisulfite-sequencing to explore the methylation profile of male F3 Sprague-Dawley rats bred through the paternal germ line from F0 dams exposed to a single dose of TCDD (0 or 1000 ng/kg body weight) by oral gavage. We identified multiple significant differentially methylated regions (DMRs) affecting receptor genes, including multiple olfactory receptors, as well as Egfr and Mc5r, typically with increased methylation among the TCDD-exposed lineage relative to control lineage.

overall_design: On gestational day 11, groups of pregnant female Sprague-Dawley rats (n=6-8) were treated with a single dose of TCDD (0 or 1000 ng/kg bodyweight) dissolved in corn oil by oral gavage. Adult male F1 progeny were mated with untreated female rats to achieve F2 generations. The above procedure was repeated to further achieve F3 generations. At the end of the examination period, rats were euthanized by carbon dioxide exposure and subjected to tissue sampling. Testicular tissue was shipped on dry ice to the analytical laboratory for processing.

middle: D

first: Mattie

last: Viluksela

first: Hanna

last: Miettinen

first: Paul

last: Boutros

first: Raimo

last: Pohjanvirta


title: Circular ANRIL isoforms switch from repressors to activators of p15/CDKN2B expression during RAF1 oncogene-induced senescence

city: Toulouse

first: Estelle

last: Nicolas

address: 118 route de Narbonne

summary: Long non-coding RNAs (ncRNAs) are major regulators of gene expression and cell fate. The INK4 locus encodes the tumour suppressor proteins p15INK4b, p16INK4a and p14ARF required for cell cycle arrest and whose expression increases during senescence. ANRIL is a ncRNA antisense to the p15 gene. In proliferative cells, ANRIL prevents senescence by repressing INK4 genes through the recruitment of Polycomb-group proteins. In models of replicative and RASval12 oncogene-induced senescence (OIS), the expression of ANRIL and Polycomb proteins decreases, thus allowing INK4 derepression. Here, we found in a model of RAF1 OIS that ANRIL expression rather increases, due in particular to an increased stability. This led us to search for circular ANRIL isoforms, as circular RNAs are rather stable species. We found that the expression of two circular ANRIL increases in several OIS models (RAF1, MEK1 and BRAF). In proliferative cells, they repress p15 expression, while in RAF1 OIS, they promote full induction of p15, p16 and p14ARF expression. Further analysis of one of these circular ANRIL shows that it interacts with Polycomb proteins and decreases EZH2 Polycomb protein localization and H3K27me3 at the p15 and p16 promoters, respectively. We propose that changes in the ratio between Polycomb proteins and circular ANRIL isoforms allow these isoforms to switch from repressors of p15 gene to activators of all INK4 genes in RAF1 OIS. Our data reveal that regulation of ANRIL expression depends on the senescence inducer and underline the importance of circular ANRIL in the regulation of INK4 gene expression and senescence.

overall_design: Strand-specific RNA-seq datasets in senescent WI38 hTERT RAF1-ER cells-treated with siRNAs against circANRIL e16-e5 (2 different control siRNAs and 2 different circANRIL e16-e5 siRNAs, 2 replicates).

first: Lisa

last: Muniz

first: Marion

last: Aguirrebengoa

first: Didier

last: Trouche


title: Chip-chip of Set3, of PolII, and of H3K4me2 from budding yeast cells

institute: Institute of Molecular Biology, Academia Sinica.

summary: Chromatin immunoprecipitation of Set3, of PolII, and of H3K4me2, respectively, applied with tilling array chip (ChIP on chip of Set3, of PolII, and of H3K4me2, respectively) analysis demonstrated that a compared genomic occupancy of Set3, of PolII, and of H3K4me2 in Saccharomyces cerevisiae wild type cells compared anong those in Hst1 deleted, Hos2 deleted and Hst2 & Hos2 double deleted cells

overall_design: Comparison the distributions of Set3, of PolII, and of H3K4me2 on whole chromatin region among the wild  type, Hst1 deleted, Hos2 deleted and Hst2 & Hos2 double deleted cells


title: The zinc cluster transcription factor Rha1 is a positive filamentation regulator in Candida albicans

city: London

first: Vanessa

last: Dumeaux

address: Elgin Dr

department: Anatomy and Cell Biology

institute: Western University

summary: The regulatory mechanism for filamentation includes a complex network of transcription factors that play roles in regulating hyphae associated genes.  We identify here a new regulator of filamentation from the zinc cluster transcription factor family. We present evidence suggesting that this transcription factor assists the Nrg1/Brg1 switch regulating hyphal development.

overall_design: Two biological replicates of both SC1604GAD1A and the Wild-type SC5314 strains were diluted to OD600=0.1 in YPD and inoculated to reach OD600 =0.8-1.

first: Raha

last: Parvizi Omran

first: Malcolm

last: Whiteway


title: RNA-seq analysis of Withania somnifera after exposure to high salt concentrations

city: Stellenbosch

first: Anna-Maria

last: Oberholster

state: Western Cape

address: JC Smuts Building, Van der Bijl Street

department: Genetics

country: South Africa

institute: University of Stellenbosch

summary: RNA was extracted from leaf samples obtained from 3 Withania somnifera control plants (WC) that were watered with Hoagland’s solution and 3 experimental plants (WS) that were watered with Hoagland’s solution supplemented with 100mM NaCl (for one week).

overall_design: 3 control Withania somnifera plants were watered with Hoagland’s solution and 3 experimental Withania somnifera plants were watered with Hoagland’s solution supplemented with 100mM NaCl for 1 week. Three leaves per plant were collected and ground into powder with liquid nitrogen. RNA was extracted, library prep commenced with Ribo-zero protocols and sequenced on Illumina NovaSeq 6000 system.

last: Botha-Obertholster

first: N

last: Burger


title: Transgenerational epigenetic and transcriptomic effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin exposure in rat [array]

summary: In rats, direct exposure to TCDD causes myriad toxicities. Exposed rats experience hepatotoxicity, wasting syndrome and immune suppression, amongst others. “Inherited exposure”, as occurs in the F3 generation of directly exposed F0 animals, has also been shown to cause toxicity: both male and female F3 rats demonstrate an increased incidence of adult onset disease, females also display reproductive abnormalities and increased incidence of ovarian diseases while males show increased incidence of kidney disease and an altered sperm epigenome. Here, we explore the hepatic transcriptomic profile of male and female F3 Sprague-Dawley rats bred through the paternal germ line from F0 dams exposed to a single dose of TCDD (0, 30, 100, 300 or 1000 ng/kg body weight) by oral gavage. We hypothesize that RNA transcripts with altered abundance in livers of unexposed F3 progeny of treated F0 Sprague-Dawley rats may result from epigenetic modifications to the genome. Female F3 rats demonstrated more TCDD-mediated hepatic transcriptomic changes than males, with differences primarily in the lowest dose group.

overall_design: On gestational day 11, groups of pregnant female Sprague-Dawley rats (n=6-8) were treated with a single dose of TCDD (0, 30, 100, 300 and 1000 ng/kg bodyweight) dissolved in corn oil by oral gavage. Adult male F1 progeny were mated with untreated female rats to achieve F2 generations. The above procedure was repeated to further achieve F3 generations. At the end of the examination period, rats were euthanized by carbon dioxide exposure and subjected to tissue sampling. Hepatic tissue was shipped on dry ice to the analytical laboratory for processing.

middle: M


title: DNA Methyltransferase 3A Mediates the Sustained Effects of Stress on Synaptic Functions and Behaviors [RRBS]

first: Nicholas

last: Waddell

summary: Emerging evidence suggests that epigenetic mechanisms regulate aberrant gene transcription in stress-associated mental disorders. However, it remains to be elucidated about the role of DNA methylation and its catalyzing enzymes, DNA methyltransferases (DNMTs), in this process. Here we found that rats exposed to chronic (2-week) unpredictable stress exhibited a substantial reduction of Dnmt3a after stress cessation in the prefrontal cortex (PFC), a key target region of stress. Treatment of unstressed control rats with DNMT inhibitors recapitulated the effect of chronic unpredictable stress on decreased AMPAR expression and function in PFC. In contrast, overexpression of Dnmt3a in PFC of stressed animals prevented the loss of glutamatergic responses. Moreover, the stress-induced behavioral abnormalities, including the impaired recognition memory and aggressive behaviors, were ameliorated by Dnmt3a expression in PFC of stressed animals. Lastly, we found genome-wide DNA methylation changes in PFC of stressed rats are selectively enriched at several pathways, such as axon guidance, Wnt signaling and neurotransmission. These findings have therefore recognized the role of DNA epigenetic modification in stress-induced disturbance of synaptic functions and cognitive & emotional processes.

overall_design: 4 samples (PFC tissue from one rat/sample) in each group are analyzed

first: Jing

last: Wei

first: Jia

last: Cheng

first: Zi-Jun

last: Wang

first: Xiaodong

last: Pang

first: Aiyi

last: Liu

first: Javed

last: Chitaman

first: Lara

last: Duffney

first: Jinfeng

last: Zhang

first: David

last: Dietz

first: Jian

last: Feng

first: Zhen

last: Yan


title: Transgenerational epigenetic and transcriptomic effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin exposure in rat

first: Stephenie

last: Prokopec

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

overall_design: Refer to individual Series


title: Single-cell RNA-Seq analysis reprogramming of T to ITNK

city: Guangzhou

first: zhiwu

last: jiang

address: 190 Kai Yuan Avenue, Science Park

institute: GIBH

summary: To further decipher the cell fate continuum during reprogramming of T cells to ITNKs, we investigated the gene expression dynamics of T and ITNK cells from a CB sample at single-cell level using micro-well based scRNA-seq technology at different time points post BCL11B ablation

overall_design: T cells that were electroplated with PX458-BCL11B at day 0 (2263 cells), day 5 (1565 cells), day 10 (498 cells), day 15 (204 cells), and day 20 (418 cells), based on sc-RNA seq analysis.

first: Zhiwu

last: Jiang

first: Peng

last: Li


title: DNA Methyltransferase 3A Mediates the Sustained Effects of Stress on Synaptic Functions and Behaviors [RNA-seq]

address: 319 Stadium Dr


title: Identification of mode of action for cell-based immunotherapy with ex-vivo expanded and activated autologous killer cells (AKCs) to recurrent glioblastoma (GBM) patients

city: seongnam

first: Kyunggi

last: Cho

address: yatap 59

department: neurosurgery

country: South Korea

institute: CHA bundang medical center

summary:
The 12 recurrent GBM patients were participated. NanoString nCounter pancancer IO 360 panel (750 genes) assay was conducted with GBM patients tissue which was extracted at postoperative after recurrent event.
The goal of this study was to extract significant genes which were associated with overall survival (OS) and durable response within AKC-treated recurrent GBM patients.

overall_design: Tumor tissues were obtained from AKC-treated recurrent GBM patients with 5 durable and 7 poor responders. NanoString assay was performed.

first: Jaejoon

last: Lim

first: YoungJoon

last: Park


title: EZH2 protects tumor-infiltrating lymphocytes from metabolic-stress induced cell death and exhaustion [RNA-seq]

city: Little Rock

first: Allen

last: Gies

state: AR

address: 4301 W. Markham

department: Biochemistry and Molecular Biology

institute: University of Arkansas for Medical Sciences

summary: Direct competition between tumor-infiltrating lymphocytes (TIL) and cancer cells for metabolic resources often renders T cells dysfunctional. Here, we report an epigenetic mechanism contributing to the development of metabolic exhaustion in TILs. T cells undergo a loss of the histone methyltransferase EZH2 (Enhancer of Zeste Homolog 2) during tumor infiltration. Using a multi-omics approach, we have defined a mechanism by which EZH2 inhibition leads to mitochondrial dysfunction and the resultant metabolic exhaustion. Reprogramming T cells to express a gain-of-function EZH2 mutant resulted in an enhanced ability of T cells to inhibit tumor growth. Our studies suggest that manipulation of EZH2 in T cells might represent a potential strategy to protect tumor-specific T cells during metabolic stress.

overall_design: Comparison of gene expression analysis between control and EZH2 inhibited CD8+ T cells using next generation sequencing (RNA-seq).

first: Brian

last: Koss

first: Bradley

last: Shields

first: Erin

last: Taylor

first: Aaron

last: Storey

first: Stephanie

last: Byrum

first: Charity

last: Washam

first: Samrat

last: Choudhury

first: JeongHyun

last: Ahn

first: Hidetaka

last: Uryut

first: Jason

last: Williams

first: Kimberly

last: Krager

first: Tung-Chin

last: Chiang

first: Samuel

last: Mackintosh

first: Rick

last: Edmondson

first: Thomas

last: Gajewski

first: Nukhet

last: Aykin-Burns

first: Gang

first: Alan

last: Tackett


title: Expression data from Vehicle, MP and MP+CSE_Bu treated SD rats

city: Lucknow

first: Naibedya

last: Chattopadhyay

state: Uttar Pradesh

address: Sector 10, Jankipuram extension, Sitapur road

department: Endocrinology

country: India

institute: CSIR-CDRI

summary:
Understanding the mechanism of action of CSE-Bu on gene level in osteogenic effect.
We used microarray to detail the effect of MP and MP+CSE_Bu on gene expression in SD rats and identified various classes of genes that are either upregulated or down-regulated.

overall_design: Rats were divided into 3 groups and treated with Vehicle, MP (methylprednisolone) and MP+CSE_Bu (methylprednisolone and Cassia occidentalis extract's butanolic fraction), respectively. All treatments were given for 4 weeks. After treatment total RNA was isolated from femur bone of each group by Trizol method as instructed by the manufacturer.

first: Chirag

last: Kulkarni

first: Subhashis

last: Pal

first: Neetu

last: Singh

first: Dinesh

last: Kumar Sahu

first: Pratap

last: Shankar


title: Interleukin-17A suppresses granular layer formation in a three-dimensional human epidermis model via regulation of terminal differentiation genes

city: Fukuoka

first: Emi

last: Sato

state: Fukuoka

address: 7-45-1Jyonan-ku, Nanakuma

department: Faculty of Medicine

country: Japan

institute: Fukuoka University

summary: Immunotherapies targeting IL-17 greatly improve plaque psoriasis. Most previous studies on IL-17 focused on the Th17 immune response, but investigation of the effects of IL-17A on psoriatic epidermal structure are limited. Using an in vitro three-dimensional (3D) human epidermis model, we investigated the effects of IL-17A and IL-17C on morphological changes and gene expression. IL-17A directly suppressed the formation of the granular layer, whereas IL-17C did not. IL-17A significantly downregulated the gene expression of profilaggrin (FLG), which is a major component of keratohyalin granules in the granular layer. Global gene expression analysis of this 3D epidermis model showed that both IL-17A and IL-17C upregulated S100A7A and type 1 interferon-related genes including MX1, IFI44L, XAF1 and IFIT1. However, only IL-17A directly downregulated keratinocyte differentiation-related and cornified envelope-related genes including FLG, LOR, C1ORF68, LCE1E, LCE1B, KRT10, CST6 and RPTN. In conclusion, IL-17A, a systemic inflammatory cytokine, affected keratinization in our 3D epidermis model. In contrast, IL-17C, a locally produced cytokine, did not have strong effects on keratinization. Targeting IL-17A does not only reduce inflammation but it may also directly affect epidermal differentiation in psoriasis.

overall_design: Normal human epidermal keratinocytes were used to establish 3D skin constructs by seeding them on devitalized human dermis with recombinant human IL-17A, IL-17C or distilled water (dH2O)

first: Narumi

last: Yano

first: Yuka

last: Fujita

first: Shinichi

last: Imafuku


title: EZH2 protects tumor-infiltrating lymphocytes from metabolic-stress induced cell death and exhaustion

first: Allen

last: Gies

overall_design: Comparison of H3K27me3 and H3K36me3 ChIP-Seq on control and EZH2 inhibited T cells.


title: Evolutionary Origin of Vertebrate Oct4/POUV Functions in Supporting Pluripotency

city: Copenhagen

first: Josh

last: Brickman

address: 3B Blegdamsvej

department: reNEW

institute: Copenhagen University

summary: Pluripotency is the capacity of early embryonic cells to make all the future lineages of the organism, and the existence of a pluripotent population of cells is important to both germ cell function and the pool of progenitor cells that enable vertebrate development to proceed over time through the process of gastrulation. Oct4, a class V POU transcription factor, is required for maintenance of pluripotency in embryonic stem cells (ESCs) and induction of pluripotency via transcription factor reprogramming. Homologues of Oct4 have been identified in other gnathostomes and classified into two different paralogues: POU5F1 and POU5F3. Here we provide evidence that these proteins are probably derived from a single POUV gene through ancient whole genome duplication events. To approach this issue, we compared the functional conservation and divergence of different POUV proteins in their capacity to support naïve pluripotency in mouse ESCs. We found a strong correlation between POU5F1 activity in naïve pluripotency and the regulation of germ cell specification programs. In contrast, POU5F3 exhibited reduced capacity to support naïve ESCs and its activity in ESCs correlated with the expression of genes associated with pre-gastrulation stages, or primed pluripotency. We detected evidence of this functional segregation as early as Sarcopterygian ancestors, based on the activities of coelacanth POUV proteins. Furthermore, we were able to identify earlier POUV homologues in lamprey and shark, indicating that the earliest point at which mammalian-level pluripotency of both POUV paralogues emerged is between the osteichthyan-chondrichthyan split and the gnathostome-cyclostome split.Taken together, our work highlights the evolutionary history of POUV activities across jawed vertebrates, suggesting that evolutionary pressure has facilitated maintenance of both paralogues over long periods of evolutionary history. In species with both paralogues, subfunctionalization of these proteins appears conserved.  However, in many branches of vertebrate evolution, one of these paralogues is lost, suggesting a high level of plasticity in function and precarious balance between retaining both proteins and the overall levels of POUV activity in different developmental systems.  While the conserved subfunctionalization of POUV activities evolved at some point just before the appearance of tetrapods, the additional divergent activities of this protein family appear to have evolved independently in each vertebrate lineage after gnathostome radiation.

overall_design: 6 samples

first: Joshua

first: Woranop

last: Sukparangsi


title: Nonclinical  cardiovascular safety evaluation of romosozumab, an inhibitor of sclerostin for the treatment of osteoporosis in postmenopausal women at high risk of fracture

city: San Diego

first: Jun

last: Yin

state: CA

address: 10901 N Torrey Pines Rd

department: Bioinformatics Core

institute: Sanford Burnham Prebys Medical Discovery Institute

summary: Romosozumab is a humanized monoclonal antibody that inhibits sclerostin, an extracellular inhibitor of the canonical Wnt signaling pathway, expressed in osteocytes. Romosozumab results in increased bone formation and decreased bone resorption and has been approved in several countries for the treatment of osteoporosis in postmenopausal women at high risk of fracture. Sclerostin is also expressed in aortic vascular smooth muscle cells, the function of which is unclear but has been proposed to be an inhibitor of vascular calcification, atheroprogression, and associated inflammation. A slight  increase in serious cardiovascular adverse events (CV AEs) was observed in romosozumab-treated subjects in a clinical trial comparing alendronate with romosozumab (ARCH; NCT01631214) but was not observed in a placebo-controlled trial (FRAME; NCT01575834). To investigate biological plausibility of the role of romosozumab in cardiovascular disease, a comprehensive nonclinical package with additional cardiovascular studies was conducted including studies in two murine models of atherosclerosis. Results of these studies demonstrated that the effects of romosozumab or a surrogate sclerostin antibody were either a direct or indirect consequence of its pharmacodynamic effects on bone. There were with no functional or morphologic effects on the cardiovascular system in animal models in the presence or absence of atherosclerosis. The totality of these nonclinical data has not identified a biologically plausible mechanism to explain the increase in serious CV AEs in the ARCH trial.

overall_design: The objective of this substudy was to evaluate transcriptional changes in the aorta in response to sclerostin antibody (Scl-Ab) treatment in high fat diet-fed ovariectomized (OVX) wild-type (WT) and Apolipoprotein E (ApoE) knockout mice. RNA-seq analyses were applied to satellite animals in the vehicle, Scl-Ab–treated WT, and HFD-fed ApoE-OVX groups. All groups of satellite animals were analyzed in the AngII-infused ApoE KO study.

first: James

last: Turk

first: Aimee

last: Deaton

first: Marina

last: Stolina

first: Melanie

last: Felx

first: Gabrielle

last: Boyd

first: Jean

last: Bienvenu

first: Gill

last: Holdsworth

first: Charles

last: Glaus

first: Yudong

last: He

first: Rogely

middle: W

last: Boyce


title: SPANX control of Lamin A/C modulates nuclear architecture and promotes melanoma growth

city: Rockville

first: Tongwu

last: Zhang

state: MD

address: 9609 Medical Center Drive

department: Division of Cancer Epidemiology & Genetics

institute: National Cancer Institute

summary:
Purpose: To investigate mechanisms underlying SPANX knockdown phenotypes, we monitored changes in gene expression profiles in A375 melanoma cells subjected to SPANX KD (RNA-Seq).
Methods: RNASeq Libraries were prepared from isolated total RNA using the QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina from Lexogen, (Vienna, Austria). Barcoded libraries were pooled and single end sequenced (1X75) on the Illumina NextSeq 500 using the High output V2.5 kit (Illumina Inc., San Diego CA). Raw data FASTQ files were generated by standstard illumina base calling pipeline and stored in illumina cloud service BaseSpace. Reads were aligned with the STASR aligner. Analyses of differentially expressed genes (DEGs) were subsequently performed using a negative binomial test method (edgeR)10 implemented using SARTools R Package
Results: Of 609 genes deregulated by both shRNA, 454 were upregulated and 123 were downregulated. Networks associated with cell division were downregulated following SPANX KD, while those associated with 3-phosphoinositide biosynthesis were upregulated. Notably, IPA analysis identified the cell cycle as the primary pathway deregulated, and further analysis using the reactome database revealed that most of those genes were associated with the G1/S transition.

overall_design: RNA was prepared 7 days following SPANX knockdown, and triplicates were used for RNAseq analysis.

first: Ikrame

last: Lazar

first: Bertrand

last: Fabre

first: Yongmei

last: Feng

first: Ze’ev

middle: A

last: Ron


title: MiRNA-mRNA expression profiles and functional network after injection of botulinum toxin type A into submandibular gland [microarray]

city: Beijing

first: Mao

last: Qianying

address: No. 22 Zhong Guan Cun South Street, Haidian District,

department: Oral and Maxillofacial Surgery

institute: Peking University School and Hospital of Stomatology

summary:
Backgroud: Botulinum toxin type A (BTXA) is widely used for the treatment of sialorrhea and other glandular hypersecretion diseases. Micro ribonucleic acid (miRNA) plays an important role in the occurrence and development of salivary diseases, but it is still unclear which role miRNA plays during the inhibition of salivary secretion triggered by BTXA. This work was aimed to explore the miRNA-mRNA expression profiles and functional network after injection of BTXA into submandibular gland.
Methods: The differentially expressed (DE) miRNAs and mRNAs between the control group and BTXA group were identified through high-throughput sequencing and bioinformatic analyses and were confirmed by qRT-PCR. Bioinformatic analyses were performed to identify the critical biological functions and signalling pathways and established the functional network.
Results: A total of 19 DE miRNAs and 1072 DE mRNAs were identified between the control group and BTXA group. We confirmed 6 DE miRNAs through the qRT-PCR validation. Bioinformatic analysis identified that several pathways may be associated with the inhibition of salivary secretion, such as MAPK signaling pathway, Tight junction and Cytokine-cytokine receptor interaction. We predicted the target genes of these 6 DE miRNAs and established the miRNA-mRNA interaction network. The intersection of DE mRNAs and target genes was performed and finally obtained 7 mRNAs: EGR2, PAQR9, ZKSCAN1, USP6N, lCYB561A3, ZFHX4 and CLIC5.
Conclusions: Our study describes the miRNA and mRNA expression profiles and functional network after injection of BTXA into submandibular gland. These findings explore the mechanism of BTXA in inhibiting salivary secretion, and probably provide a new idea for the clinical application.
Key words: miRNA-mRNA, BTXA, submandibular gland

overall_design: Detection of expression profiles of miRNA and mRNA in submandibular glands of control group and BTXA group, and analysis of GO and KEGG pathways.

first: Ruolan

last: Xiang

first: Qianying

last: Mao


title: RNA data from melanoma-derived exosomes and melanoma cell lines

city: Nantes

first: Delphine

last: Fradin

address: 8 quai Moncousu

institute: CRCI2NA, Inserm UMR1307, CNRS UMR6075

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

summary: characterize lncRNA and mRNA present in melanoma-derived exosomes

overall_design: We used microarray to identified RNA abundant in exosomes or differentially expressed between exosomes from different melanoma cell lines


title: Expression Profiles in Low- and High-Altitude Individuals

first: Cuiying

last: Li

address: 30 Fucheng

institute: Air Focre Medical Center, PLA

summary: The Qing-Tibet Plateau is characterized by low oxygen pressure, which is an important biomedical and ecological stressor. However, the variation in gene expression during periods of stay on the plateau has not been well studied. We recruited eight volunteers to stay on the plateau for 3, 7 and 30 days. Human Clariom D arrays were used to measure changes in the mRNA expression profiles in these volunteers. ANOVA indicated that 699 genes were significantly differentially expressed in response to entering the plateau during hypoxic exposure. The genes with changes in transcript abundance were involved in the terms phosphoprotein, acetylation, protein binding, and protein transport. Furthermore, numerous genes involved in hematopoietic functions, including erythropoiesis and immunoregulation, were differentially expressed in response to acute hypoxia. This phenomenon may also explain why the majority of people entering the plateau do not have excessive erythrocyte proliferation and are susceptible to infection.

overall_design: The peripheral white cells were obtained from volunteers with the indicated hypoxic exposure times (exposure to hypoxia for 3, 7, and 30 days). We globally analyzed peripheral white cells mRNA expression profiles from the eight peripheral white cells samples using mRNA expression arrays.

first: Jun

last: Xiao


title: Barrier-to-autointegration factor 1 protects against a basal cGAS-STING response

city: Columbus

first: Patrick

middle: Leonard

last: Collins

address: 770 BRT,  460 W 12th Ave

department: Microbial Infection and Immunity

institute: Ohio State University

summary: Although the pathogen recognition receptor pathways that activate cell-intrinsic antiviral responses are well delineated, less is known about how the host regulates this response to prevent sustained signaling and possible immune-mediated damage. Using a genome-wide CRISPR-Cas9 screening approach to identify host factors that modulate interferon (IFN) stimulated gene (ISG) expression, we identified the DNA binding protein Barrier-to-autointegration factor 1 (Banf1), a previously described inhibitor of retrovirus integration, as a modulator of basal cell-intrinsic immunity. Ablation of Banf1 by gene editing resulted in enhanced chromatin accessibility of host defense genes and increased expression of ISGs including Oas2, Rsad2 (viperin), Ifit1, ISG15 and Cxcl10. The phenotype in Banf1-deficient cells occurred through a cGAS, STING, and IRF3-dependent signaling axis, was associated with reduced infection of RNA and DNA viruses, and was reversed in Banf1 complemented cells. Confocal microscopy and biochemical studies revealed that a loss of expression of Banf1 resulted in higher level of cytosolic double-stranded DNA at baseline. Our study identifies an undescribed role for Banf1 in regulating levels of cytoplasmic DNA and cGAS-dependent ISG homeostasis and suggests possible therapeutic directions for promoting or inhibiting cell-intrinsic innate immune responses.

overall_design: Examination of different chromatin activity by H3K27ac native ChIP-seq, and paired RNA-seq, in three different BV2 genotypes

first: Collins

last: Patrick

first: Diamond

last: Michael

first: Hongming

last: Ma

first: Eugene

last: Oltz


title: The infection cushion: a fungal weapon for plant-biomass destruction

city: VILLEURBANNE

first: MATHIAS

last: CHOQUER

address: 10, rue Raphaël Dubois

institute: UNIVERSITE LYON1

summary: Full transcriptomes of the Botrytis cinerea wild-type strain B0510, cultured in liquid medium or on cellophane sheets placed on PDB 1/4-agar plates, were compared to identify genes differentially expressed  when infection cushions are formed from vegetative mycelium.

overall_design: Botrytis cinerea conidia were spread onto cellophane sheets placed on PDB 1/4-agar plates and harvested after 44h of culture when infection cushions (IC) represented about 40% of the surface of the plates. Control samples corresponding to mycelium grown in liquid PDB 1/4 were harvested after 44h of culture. 4 and 3 replicates were performed for IC and mycelium, respectively. The 7 total-RNA samples were used for hybridization on Nimblegen 4plex gene expression arrays (20,885 gene models from Botrytis cinerea with three 60-mer probes per gene)

first: Mathias

last: Choquer

first: Christine

last: Rascle

first: Isabelle

last: Gonçalves

first: Christophe

last: Bruel

first: Nathalie

last: Poussereau

first: Amélie

last: deVallée