title: Differential gene expression in circulating CD14+ monocytes indicates the prognosis of critically ill patients with sepsis

status: Public on Feb 28 2020

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

type: Expression profiling by high throughput sequencing

summary: Critical illness and sepsis are characterized by drastic changes in the systemic innate immune response, particularly involving monocytes. Here we prospectively analyzed the gene expression profile of circulating CD14+ monocytes of selected samples by RNA Sequencing.

overall_design: Analysis of the RNA expression of circulating CD14+ monocytes of healthy volunteers and intensive care unit (ICU) patients with and without sepsis.

first: Anke

last: Liepelt

first: Philipp

last: Hohlstein

first: Hendrik

last: Gussen

first: Jia

last: Xue

first: Anna

middle: C

last: Aschenbrenner

first: Thomas

last: Ulas

first: Lukas

last: Buendgens

first: Klaudia

middle: T

last: Warzecha

first: Matthias

last: Bartneck

first: Tom

last: Luedde

first: Christian

last: Trautwein

middle: L

first: Alexander

last: Koch

first: Frank

last: Tacke


title: Transcriptom analysis of two types of cell death by RNA-seq

city: Sendai

first: AINAN

last: TIAN

address: Aramaki

country: Japan

institute: Tohoku University

summary: We established an Arabidopsis thaliana Columbia (Col-0) and Cucumber mosaic virus strain HYY [CMV(HYY)] patho-system and identified a necrotic cell death. The global gene expression analysis of the necrotic cell death and HR cell death developed in cucumber mosaic virus-inoculated leaves of A. thaliana was performed by RNA-seq, respectively. The samples for RNA-seq were collected from the cell death leaves showing HR cell death at 3dpi and showing necrotic cell death at 5dpi, respectively. The sequence data was first preprocessed by FASTQ in basespace of illumine.The sequence reads were processed with Trimmomatic (version 0.38) for adaptor trimming and quality trimming. The processed reads were mapped to the genome sequences of A.thaliana ecotype Col-0, CMV(Y) and CMV(Ho) with STAR (version 2.7) with its default settings. Read counts per each A.thaliana gene were retrieved by the quantification option of STAR. The obtained read counts were normalized and statistically tested using DESeq2 R package 3.7. Adjusted p-values were calculated with Benjamini-Hochberg procedure, and the threshold for adjusted p-value was set to 0.05 in the present study. The independent filtering in DESeq2 was performed to filter out the genes with low mean normalized counts, with an automatically optimized threshold; 5,906 genes which passed the independent filtering in both of the two comparisons (i.e, necrotic cell death vs mock and HR cell death vs control) were further analyzed for differential expression. Genes with adjusted p-value of <0.05 and a fold change of >4 or <0.25 were considered as DEGs. Of the 5,906 genes analyzed, 202 genes showed >4-fold up-regulation upon either HR cell death or necrotic cell death induction (adjusted p < 0.05). Thirty-five of them were common in HR cell death or necrotic cell death induction, while 149  and 18  were unique to HR cell death or necrotic cell death induction, respectively. Sixty-two genes showed <0.25-fold down-regulation upon either HR or necrosis induction (adjusted p < 0.05). Seven of them were common , while 43  and 12 were specific for HR cell death or necrotic cell death induction, respectively. Collectively, the necrotic cell death displayed a distinct gene expression pattern compare to HR cell death.

overall_design: Transcriptome analysis of "Necrosis" and HR cell death developed in cucumber mosaic virus-inoculated leaves of Arabidopsis thaliana was performed by RNA-seq, in triplicate, using TruSeq Stranded Total RNA Sample Preparation Kit.

first: Ainan

last: Tian

first: Shuhei

last: Miyashita

first: Sugihiro

last: Ando

first: Hideki

last: Takahashi


title: miRNA expression in high migratory cells

status: Public on Feb 27 2020

city: Tokushima

first: Kensei

last: Nishida

state: Tokushima

address: 3-18-15 Kuramoto-cho

institute: Tokushima University Graduate school

summary: microRNAs are small non-coding RNAs, which promote either mRNAs degradation or block their translation through binding to partially complementary sequences of their target mRNAs. We have previously isolated a subpopulation with accelerated baseline motility (MG cells) or an immotile one (non-MG cells) from a colon cancer cell line (HCT116). In this study, using these subpopulations, we identified miRNAs, which were involved in acquisition of a cell migratory phenotype.

overall_design: Total RNAs were isolated from the MG and non-MG cells, and then miRNAs gene expression was measured by human miRNA microarray (Agilent Technology).


title: Next Generation Sequencing Facilitates Quantitative Analysis of the effects of lack of autophagy on sorted mouse lung ILC2 Transcriptomes

city: Los Angeles

first: Lauriane

last: Galle

state: California

address: 1450 Biggy Street NRT 5509

country: USA

institute: University of Southern California

summary: Atg5, a key gene of the autophagy can affect ILC2 effector functions ex vivo. Increased ILC2 activation leads to the development of airway hyperreactivity and lung inflammation. Targeting Atg5 (autophagy) may therefore represent a novel therapeutic target to treat asthma.

overall_design: mRNA profiles of sorted  lung ILC2s from wild-type and Atg5-/-  were generated by deep sequencing, in triplicate, using a NextSeq 500 (Illumina) system.

last: Galle-Treger

first: Benjamin

middle: P

last: Hurrell


title: gdT cells and adipocyte IL-17RC control fat innervation and thermogenesis

city: Boston

first: Spiegelman

last: Lab

state: MA

address: 360 Longwood Avenue, Longwood Center

department: Cancer Biology

institute: Dana Farber Cancer Institute

summary: The sympathetic nervous system innervates peripheral organs to regulate their function and maintain homeostasis, whereas target cells also produce neurotrophic factors to promote sympathetic innervation. The molecular basis of this bi-directional communication remains to be fully elucidated. We use thermogenic adipose tissue as a model system to show that T cells, specifically gdT cells, play a critical role in promoting sympathetic innervation, at least in part through driving TGFβ1 expression in parenchymal cells via IL-17 Receptor C. Adipose-specific ablation of IL-17 Receptor C reduces TGFβ1 expression in adipocytes, impairs local sympathetic innervation and causes obesity and other metabolic phenotypes consistent with defective thermogenesis; innervation can be fully rescued by restoring TGFβ1 expression. Ablating gdT cells and the IL-17 Receptor C signaling pathway also impairs sympathetic innervation in salivary glands and the lung. These findings demonstrate T cell/parenchymal cell coordination to regulate sympathetic innervation.

overall_design: Gene expression profiles of brown adipose tissue from WT or AdIl17rc KO mice.

first: Bruce

last: Spiegelman

first: Bo

last: Hu


title: Chronic circadian misalignment accelerates immune senescence and abbreviates lifespan in mice

city: Kyoto

first: Kazuhiro

last: Yagita

address: Kawaramachi-Hirokoji, Kamigyo-ku

institute: Kyoto Prefectural University of Medicine

summary: Modern society characterized by a 24/7 lifestyle leads to misalignment between environmental cycles and endogenous circadian rhythms. Persisting circadian misalignment leads to deleterious effects on health and healthspan. However, the underlying mechanism remains not fully understood. Here, we subjected adult, wild-type mice to distinct chronic jet-lag paradigms, which showed that long-term circadian misalignment induced significant early mortality. Non-biased RNA sequencing analysis using liver and kidney showed marked activation of gene regulatory pathways associated with the immune system and immune disease in both organs. In accordance, we observed enhanced steatohepatitis with infiltration of inflammatory cells. The investigation of senescence-associated immune cell subsets from the spleens and mesenteric lymph nodes revealed an increase in PD-1+CD44high CD4 T cells as well as CD95+GL7+ germinal center B cells, indicating that the long-term circadian misalignment exacerbates immune senescence and consequent chronic inflammation. Our results underscore immune homeostasis as a pivotal interventional target against clock-related disorders.

overall_design: Examination of whole transcriptome in mouse liver and kidney exposing to ADV and LD conditions

first: Hitoshi

last: Inokawa

first: Yasuhiro

last: Umemura

first: Nobuya

last: Koike


title: Lactobacilli secretome-mediated negative regulator induction in HT-29 human IEC

status: Public on Feb 26 2020

city: Oshawa

first: Michael

last: Jeffrey

state: Ontario

address: 2000 Simcoe St N

department: Faculty of Science

country: Canada

institute: Ontario Tech University

summary: Recent evidence suggests that lactic acid bacteria (LAB) communicate with host cells via secretome components to influence immune responses, but less is known about gut pathogen secretomes, impact of LAB secretomes on host-pathogen interactions and the mechanisms underlying these interactions.   Genome-wide microarrays and cytokine profiling were used to interrogate the impact of the Lactobacillus rhamnosus R0011 secretome (LrS) on TNF-α and Salmonella enterica subsp. enterica serovar Typhimurium secretome (STS)-induced outcomes in human intestinal epithelial cells (IECs). The LrS attenuated both TNF-α- and STS-induced gene expression involved in NF-κB and MAPK activation, as well as expression of genes involved in other immune-related signaling pathways. Specifically, the LrS induced the expression of dual specificity phosphatase 1 (DUSP1), activating transcription factor 3 (ATF3) and tribbles pseudokinase 3 (TRIB3), negative regulators of innate immune signaling, in HT-29 IECs challenged with TNF-α or STS. TNF-α and STS-induced acetylation of H3 and H4 histones was attenuated by the LrS, as was the production of TNF-α and STS-induced pro-inflammatory cytokines and chemokines. Interestingly, the LrS induced production of macrophage migration inhibitory factor (MIF), a cytokine involved in host-microbe interactions at the gut interface. We propose that the LrS attenuates pro-inflammatory mediator expression through increased transcription of negative regulators of innate immune activity and changes in global H3 and H4 histone acetylation. These findings provide novel insights into the complex multifaceted mechanisms of action behind secretome-mediated interdomain communication at the gut-mucosal interface.

overall_design: HT-29 human intestinal epithelial cells were challenged with 8 different challenges. Briefly, HT-29 were challenged with Lactobacillus rhamnosus R0011 secretome, TNF-α (50ng/mL), Salmonella enterica subsp. enterica serovar Typhimurium secretome, L-lactic acid matched controls, or a combination of the treatments for 3 hours. There were 4 biological replicates for each challenge and the response to each challenge was compared to unchallenged controls.

first: Chad

middle: W

last: MacPherson

first: Olivier

last: Mathieu

first: Thomas

middle: A

last: Tompkins

first: Julia

middle: M

last: Green-Johnson


title: Sex-specific adipose tissue imprinting of regulatory T cells (RNA-seq)

city: Clayton

first: Wei

last: Shi

state: Victoria

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute

country: Australia

institute: Monash University

summary: Visceral adipose tissue (VAT) is a metabolically active endocrine organ that plays a critical role regulating organismal metabolism. Regulatory T (Treg) cells restrain VAT inflammation, and preserve insulin sensitivity and organismal metabolism. Here we report pronounced sexual dimorphism in VAT Treg cells, which were enriched specifically in males and differed strikingly from their female counterparts in phenotype, transcriptional landscape and chromatin accessibility. These differences were imprinted by the adipose tissue in a manner dependent on sex hormones. Male VAT was characterized by heightened inflammation, which resulted in CCR2-dependent recruitment of Treg cells. Sex hormones also regulated the differentiation of unique IL-33-producing stromal cell populations specific to the male VAT, which paralleled the local expansion of Treg cells and the induction of a transcriptional program controlled by transcription factor Blimp1. Overall our findings reveal a novel multi-layered feedback circuit depending on Treg cells and regulated by sex hormones to limit VAT inflammation.

overall_design: Experiments were performed to understand the gender difference in Visceral adipose tissue regulatory T cells. We are assessing the Treg extrinsic and intrinsic mechanisms that imprint these differences

first: Ajithkumar

last: Vasanthakumar

first: David

last: Chisanga

first: Jonas

last: Blume

first: Renee

last: Gloury

first: Nicholas

last: Collins

first: Tom

last: Sidwell

first: Li

last: Chaoran

first: Sebastian

last: Liene

first: Santiago

middle: V

last: Torres

first: Yifan

last: Zhan

first: Darren

last: Henstridge

first: Paul

last: Beavis

last: Gebhardt

first: Kara

last: Britt

first: Stephen

last: Nutt

first: Jeffrey

middle: D

last: Zajac

first: Rachel

last: Davey

first: Mark

last: Febbraio

first: Diane

last: Mathis

first: Axel

last: Kallies


title: Comparative and integrated functional genomics analysis of Klinefelter and Turner syndromes reveals network-wide effects of the sex chromosome dosage changes

city: Thousand Oaks

first: Xianglong

last: Zhang

state: CA

address: One Amgen Center Dr.

department: Department of Cardiometabolic Disorders

institute: Amgen Inc.

type: Methylation profiling by high throughput sequencing

summary:
Background: In both Turner syndrome (TS) and Klinefelter syndrome (KS) copy number aberrations of the X chromosome lead to various developmental symptoms. To date there has not been a comprehensive and directly comparative analysis of TS vs. KS regarding the changes on the molecular level
Methods: We analyzed gene expression patterns with RNA-Seq and DNA methylation patterns with the CpGiant assay in lymphocytes, and chromatin conformation with in situ Hi-C in lymphoblastoid cell lines, from TS and KS patients together with their same gender controls.
Results: In TS, differentially expressed escape genes were downregulated but differentially expressed inactive genes were upregulated. In KS, differentially expressed escape genes were upregulated while inactive genes appeared unchanged. Interestingly, 81 differentially expressed genes (DEGs) were associated with both TS and KS, and uniformly displayed expression changes into opposite directions. DEGs on the X chromosome and the autosomes were coexpressed in both TS and KS, indicating that there are molecular ripple effects of the changes in X chromosome dosage that extend to autosomes. Four potentially candidate genes (RPS4X, SEPT6, NKRF and CX0rf57) for KS were identified on Xq. Broad hypomethylation of the X chromosome is observed in TS whereas hypermethylation of chromosome X is present in KS. Only promoters of inactive genes were differentially methylated in both TS and KS while escape genes remained unchanged. The intrachromosomal contact map of the X chromosome in TS was partitioned into two superdomains and exhibited the structure of an active X chromosome.
Conclusions: Components of the molecular basis of TS and KS were identified on the levels of the transcriptome and the epigenome, with candidate central genes on Xp for TS and on Xq for KS. The discovery of shared DEGs indicates the existence of common molecular mechanisms for gene regulation in TS and KS that are transmitting the gene dosage changes to the transcriptome.

overall_design: A direct comparative analysis of TS versus KS and integrative analysis over three levels of genomic and functional genomic activity, in primary lymphocytes from patients and controls for levels of gene expression and levels of DNA methylation and in LCLs for chromosome folding patterns

first: David

last: Hong

first: Shining

last: Ma

first: Marcus

last: Ho

first: Thomas

last: Ward

first: Reenal

last: Pattni

first: Zhana

last: Duren

first: Atanas

last: Stankov

first: Sharon

last: Shrestha

first: Joachim

last: Hallmayer

first: Wing

last: Wong

first: Allan

last: Reiss

first: Alexander

last: Urban


title: cirRNA-seq of the fourth passage xenografts treated with 5-Fu and PBS

city: Guangzhou

first: li

middle: ping

last: gong

address: No.600 Tianhe Road

country: China

institute: The Third Affiliated Hospital, Sun Yat-sen University

summary:
In this study, we established a successive xenograft model to enrich Epstein-Barr virus-associated gastric carcinoma (EBVaGC) cancer stem cells (CSCs) through long-term treatment of EBVaGC cell line SNU719 with 5-Fluorouraci (5-Fu) in mice vivo passage. Simply, NOD/SCID mice injected in the subcutaneous with SNU719 were treated with 5-Fu weekly until xenografts reached 1.5 cm diameter and the mice were euthanizedand single-cell suspensions were obtainedby collagenasedigestion. Then the purified cells were passaged in 5-Fu-treated NOD/SCID mice as above. After four successive generations,we obtained theSNU-4th cells from the fourth passage xenografts treated with 5-Fu. Compared with parental SNU719 cells, SNU-4th cells possessed the stemness characters. Increasing evidence have proved that circular RNA (circRNA) play an important role in maintaining the tumor phenotype. So, we compared circRNAs expression between the fourth passage xenografts treated with 5-Fu and PBS by RNA-sequencing, hoping to find out which circRNAs were involved in the stemness regulation of EBVaGC.
we established a highly malignant EBVaGC cell line SNU-4th through long-term treatment of EBVaGC cell line SNU719 with 5-Fluorouraci in vivo passage, then we compared circRNAs expression between the fourth passage xenografts treated with 5-Fu and PBS by RNA-sequencing

overall_design: Profiling  the circular RNA  expression between the fourth passage xenografts treated with 5-Fu and PBS

first: Chun-kui

last: Shao

first: Li-ping

last: Gong


title: Progesterone, via yes-associated protein (YAP), promotes cardiomyocyte proliferation and cardiac repair

city: Chongqing

first: Cong

last: Lan

state: Chognqing

address: 10 Changjiangzhilu Road

department: Department of Cardiology

institute: Daping Hospital, The Third Military Medical University

summary: To explore effect of progesterone on gene expression of primary cultured cardiomyocytes isolated from 7-day-old SD rats

overall_design: We isolated and cultured  cardiomyocytes using 7-day-old SD rats and treated cells with control vehicle (control) or progesterone (10-7 M) (progesterone)  for 24 hours to prepare sample (three biological replicates for each group)  and RNA-sequencing (RNA-Seq) were performed using mRNA extracted from these samples.

first: Yuanzheng

last: Xue

first: Caiyu

last: Chen

first: Shuang

last: Qu

first: Chao

last: Fan

first: Hao

last: Luo

first: Cheng

last: Yu

first: Nian

last: Cao

first: Hongmei

last: Ren

first: Liangpeng

last: Li

first: Hongyong

last: Wang

first: Pedro

last: Jose

first: Zaicheng

last: Xu

first: Chunyu

last: Zeng


title: The developing lens transcriptome depends upon a counterbalance of Fgfr2- and Pten-regulated downstream signaling and transcription factor targets

city: Newark

first: Deepti

last: Anand

state: Delaware

address: 351 Wolf Hall, University of Delaware

department: Biological Sciences

institute: University of Delaware

summary: FGFR signaling plays important roles in development and disease pathogenesis. FGFR activation initiates phosphorylation-driven signaling cascades, most notably the RAS-RAF-MEK-ERK cascade and the PI3K-AKT cascade. PTEN antagonizes FGFR signaling by reducing both AKT and ERK activation. Lenses lacking FGFR2 exhibit lower levels of ERK and AKT phosphorylation accompanied by abnormally small lenses, widespread apoptosis, and defective fiber cell differentiation. In contrast, simultaneous deletion of both Fgfr2 and Pten restores ERK and AKT activation levels as well as lens size, cell survival and several aspects of fiber cell differentiation. A transcriptomic analysis of mouse lenses lacking Fgfr2, Pten or both Fgfr2 and Pten revealed molecular mechanisms that might explain how FGFR2 and PTEN signaling interact during development.  The FGFR2-deficient lens transcriptome suggested an overall loss of fiber cell identity with deregulated expression of 1,448 genes, nearly 60% of which returned to normal expression levels in lenses lacking both Fgfr2 and Pten. A specific set of parameters based on expression levels in each genotype identified 68 high priority candidate genes. The homeobox transcription factor, NKX6-1, encoded by one of these genes, had at least one binding motif in the putative promoters of 53 of these 68 genes. Furthermore, NKX6-1 activated the expression of the high priority candidate Rasgrp1, a RAS-activating guanine nucleotide exchange factor. Together, these data suggest a novel regulatory module in which NKX6-1 activates the expression of Rasgrp1 to restore the balance of ERK and AKT activation in the absence of both FGFR2 and PTEN.

overall_design: We collected RNA from the lenses of mice hemizygous for the Le-Cre transgene (control), or hemizygous for Le-Cre and homozygous for loxP flanked (floxed) alleles of Fgfr2, Pten ; or both Fgfr2/Pten. Lenses were dissected from the eye and carefully isolated from surrounding tissues including the cornea, retina, and tunica vasculosa lentis. Lenses were pooled into three biological replicates for each genotype, with each replicate containing six lenses from three mice.

first: Anand

last: Deepti

first: Michael

last: Robinson

first: Lachke

last: Salil


title: TBK1 Regulates Regeneration of Pancreatic b-cells

status: Public on Feb 29 2020

city: Rochester

first: Jin Sung

last: Jang

state: MN

address: 200 First St SW

institute: Mayo Clinic

summary: b-cell proliferation induction is one of the most tangible therapeutic strategies to restore b-cell mass. However, this approach has proven challenging due to a remarkable resistance of adult human b-cells to proliferation. Here we aim to unravel the role of a non-canonical IkB kinase TBK1 (TANK-binding kinase 1), which is predominantly expressed in b-cells in mammalian islets, in regulating cell cycle progression. Genetic silencing of TBK1 in INS-1 832/13 rat b-cell line promoted proliferation of b-cells. Proteomic and transcriptome analyses further revealed changes of proteins and genes critical for cell growth and proliferation, including upregulation of ribosomal proteins and cell cycle regulators, upon depletion of TBK1. TBK1 overexpression decreased sensitivity of b-cells to the elevation of cAMP levels and reduced proliferation of b-cells in a manner dependent on the activity of phosphodiesterase 3 (PDE3). Importantly, pharmacological inhibition of TBK1 using (E)3-(3-phenylbenzo[c]isoxazol-5-yl) acrylic acid (PIAA) augmented proliferation and function of rat and human embryonic stem cell (hESC)-derived insulin-producing b-cells under basal conditions. Diabetogenic insults further induced TBK1 expression and accordingly, PIAA protected b-cells against cytokine- and streptozotocin-induced diabetogenic challenges and promoted b-cell replication. Furthermore, PIAA increased proliferation of β-cells in normal and type 2 diabetic human islets with elevation in insulin secretion. Altogether, these data unveil novel and essential function of TBK1 as a key cell-autonomous negative regulator of b-cell replication and presenting PIAA as a valid therapeutic strategy for augmenting proliferation and function of b-cells.

overall_design: Transfected TBK1 siGENOME SMARTpool siRNA or negative control non-targeting siRNA into INS-1 832/13 beta-cells for 36 hours.

first: Chong

last: Shin

first: Jin


title: RNA-sequencing of NNK-exposed Gprc5a-/- lung tumors

city: Houston

first: Humam

last: Kadara

state: TX

address: 2130 W. Holcombe Blvd

institute: University of Texas MD Anderson Cancer Center

summary: We have previously found that tobacco carcinogen exposed Gprc5a-/- develop lung tumors including adenocarcinoma. We sought to understand the molecular pathology of these lung tumors by whole-transcriptome sequence (RNA-Seq) analysis.

overall_design: Gprc5a-/- mice were intraperitoneally administered 50 mg/kg body weight nicotine-derived nitrosamine ketone (NNK) three times per week for 8 weeks. Mice were followed up and different groups of mice were euthanised at four to seven months following NNK.  Six lung tumors that developed from lungs of five Gprc5a-/- mice at four to seven months post-NNK along with their respective five paired normal lung tissues (n=11 samples total) were sequenced.

first: Smruthy

last: Sivakumar


title: Global gene expression analysis of MGAS10870 serotype of Group A Streptococcus (Streptococcus pyogenes/GAS) in the absence or presence of 125µg/ml human calprotectin protein

city: HOUSTON

first: Muthiah

last: Kumaraswami

state: TEXAS

address: 6670 BERTNER AVE

department: Infectious Diseases

institute: Houston Methodist Research Institute

summary: The goal was to perform global transcriptome analysis on MGAS10870 serotype to investigate and compare the gene alterations of WT grown in the presence of 125µg/ml human calprotectin protein to WT grown in the absence of 125µg/ml human calprotectin protein

overall_design: There were 2 strains analyzed, each in duplicate replicates: 1) WT GAS grown to late exponential growth phase in the absence of 125µg/ml human calprotectin protein; 2) WT GAS grown to late exponential growth phase in the presence of 125µg/ml human calprotectin protein

first: Nishanth

last: Makthal


title: Celecoxib, Rofecoxib Chronically Treated Mice, with IL1beta, Aorta RNA-Seq

city: Philadelphia

first: Gregory

middle: Robert

last: Grant

state: PA

address: 3400 Civic Center Blvd.

department: Genetics

institute: University of Pennsylvania

summary: We screen for vascular off-target effects at therapeutic concentrations of celecoxib and rofecoxib using genomic approaches in a mouse model of vascular inflammatory responses. We assess whether therapeutic concentrations of celecoxib and rofecoxib might elicit distinct genomic effects in vivo in mice by comprehensive and unbiased analysis of the whole transcriptome sequencing. Drug specific differences in their expression profiles would be indicative of off-target effects.

overall_design: RNA-Seq 24 samples, mouse aorta. Treated with Celecoxib (100 mg/kg/day), Rofecoxib (50 mg/kg/day), or normal chow for three weeks then given IL-1beta stimulation. Mice were sacrificed four hours after IL-1beta stimulation. Eight biological replicates for each of the three conditions.

first: Emanuela

last: Ricciotti

first: Eun-Ji

last: Kim

middle: R

first: Tilo

last: Grosser

first: Garret

last: FitzGerald


title: The human gene FOXM1 promotes cortical folding and improves learning and memory ability in mice

city: Beijing

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

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

overall_design: Refer to individual Series


title: Expression data of FMN supplementation from Saccharomyces cerevisiae

city: Göteborg

first: Xin

last: Chen

address: Kemigården 4

department: Department of Biology and Biological Engineering

country: Sweden

institute: Chalmers University of Technology

summary: Alzheimer’s disease (AD) is hallmarked by progressive neurodegeneration. Aggregation of amyloid-β peptides (Aβ) is thought to play a pivotal role in driving AD pathogenesis, yet the underlying mechanisms remain unclear. Here, we use yeast genome-scale screening to study global synthetic genetic interactions and identify toxicity modifiers of Aβ42. We find that the gene encoding riboflavin kinase (FMN1) and its metabolic product flavin mononucleotide (FMN) are connected to AD. These relationship between Aβ42 and FMN was previously unknown. As a cofactor for flavoenzymes, FMN supplementation appears to attune many cellular processes to ameliorate Aβ42 toxicity.  RNA-seq analysis further confirms FMN’s cytoprotective mechanisms. Our findings provide increased understanding of FMN regulated cellular pathways which are associated with potential targets for AD treatment.

overall_design: The goal of the present study is to evaluate the impact of FMN supplementation on yeast strains. Saccharomyces cerevisiae expressing Aβ42 peptide or control (only promoter and terminator sequences) was pre-grown overnight, diluted to an initial OD600nm of 0.1 in medium. 5mM of FMN (Riboflavin 5’-monophosphate sodium salt) were supplemented to culture for continuous treatment. Samples were taken from biological triplicate cultures during exponential phase (EX).

first: Boyang

last: Ji

first: Xinxin

last: Hao

first: Xiaowei

last: Li

first: Thomas

last: Nyström

first: Dina

last: Petranovic


title: smallRNA-sequencing reveals microRNAs as endogenous Toll-like receptor ligands causing neuroinflammation

city: Freiburg

first: Ori

last: Staszewski

address: Breisacher Str. 64

department: Institute of Neuropathology

institute: University Medical Center Freiburg

type: Non-coding RNA profiling by high throughput sequencing

summary: To identify microRNAs as TLR-activating molecules we have induced apoptosis in primary cortical neurons to trigger specific microRNA release into media. smallRNA sequencing revealed potential microRNAs ligands derived from dying neurons and their corresponding media that harbor already described TLR7/8 activating sequences. In line with this finding, about 80% of our differentially present miRNAs were able to activate TLR7/8 reporter cell lines. Furthermore, microRNAs miR-340-3p and miR-132-5p induced a specific cytokine and chemokine release form microglia leading to neuronal death. Within our systematic approach, we have identified TLR paralog-specific activating microRNAs with the potential to serve as biomarkers for brain diseases.

overall_design: Apoptotic neurons release microRNAs as endogenous signaling molecules extracellular that are endosmal TLR7 and TLR8 ligands.

first: Seija

last: Lehnardt

last: Wallach


title: A single-cell transcriptome atlas during Cashmere goat hair follicle morphogenesis

status: Public on Oct 18 2020

city: Qingdao

first: Wei

last: Ge

state: Shandong Province

address: Changcheng Road

department: College of life sciences

institute: Qingdao Agricultural University

summary: Cashmere, also known as soft gold, is produced from secondary hair follicles in Cashmere goats and it’s therefore of significance to investigate the molecular profiles during Cashmere goat hair follicle development. However, our current understanding of the machinery underlying Cashmere goat hair follicle remains largely unexplored and researches regarding hair follicle development mainly used the mouse as a research model. To provides comprehensively understanding on the cellular heterogeneity and cell lineage cell fate decisions, we performed single-cell RNA sequencing on 19,705 single cells from induction (embryonic day 60), organogenesis (embryonic day 90) and cytodifferentiation (embryonic day 120) stage fetus Cashmere goat dorsal skin. Unsupervised clustering analysis identified 16 cell clusters and their corresponding cell types were also successfully characterized. Based on cell lineage inference, we revealed detailed transcriptional gene expression profiles during dermal and epidermal lineage cell fate decisions. These works together delineate unparalleled molecular profiles of different cell populations during Cashmere goat hair follicle morphogenesis and provide a valuable resource for identifying biomarkers during Cashmere goat hair follicle development.

overall_design: We performed single-cell RNA sequencing on 19,705 single cells from induction (embryonic day 60), organogenesis (embryonic day 90) and cytodifferentiation (embryonic day 120) stage fetus Cashmere goat dorsal skin.


title: The human gene FOXM1 promotes cortical folding and improves learning and memory ability in mice [P0]

summary:
Purpose: To gain further insight into how FOXM1 causes generation of cortical expansion and folding in mice, single cell RNA-seq was used to analyze the cell type changes resulting from the cerebral cortices of P0 FOXM1 conditional knock in mice and littermate wild-type.
Methods: Single cell isolation was prepared from P0 telencephalic tissue of wild-type (WT) and FOXM1f/+;Nestin-Cre mice. The fragmented cDNAs containing barcode and UMI sequences was built the library. Agilent 2100 Bioanalyzer was used to quality controlled and quantified. Single cell RNA-sequencing analysis was used by the Illumina HiSeq 2500 platform in Annoroad Genomics.
Results: Clustering and labeling of these cells visualized on a t-SNE plot between the wild-type (WT) and FOXM1f/+;Nestin-Cre mice brain cortex.
Conclusions: Single cell RNA-seq data would provide an overall understanding how FOXM1 gene contribute to generation of cortical expansion and folding in mice.

overall_design: Single cell isolation of P0 wild type (WT) and FOXM1f/+;Nestin-Cre mice were generated by deep sequencing, in triplicate, using Illumina HiSeq 2500.

first: Wenwen

last: Wang


title: Characterization of the menin-MLL interaction as therapeutic cancer target in solid tumor models

city: Berlin

first: Bernard

last: Haendler

address: Muellerstr. 178

institute: Bayer AG

summary:
Background: Inhibition of the interaction of the scaffold protein menin with the histone methyltransferase MLL1 (KMT2A) has recently emerged as a novel therapeutic strategy in different cancers.
Purpose: Here we validate the proposed pathogenic function of the menin-MLL interaction in cancer with a novel probe inhibitor BAY-155.
Methods: RNA-seq was used to investigate transcriptional effects of novel BAY-155 probe in thirteen cell lines from a range of solid tumor types.
Results: Menin-MLL inhibition by BAY-155 in colorectal (SW1463, LoVo, DLD-1), prostate (22RV1, LNCaP, VCaP), pancreas (PANC-1, MiaPaCa2), breast (BT-474, ZR-75-1, MCF7), bladder (JMSU-1) and kidney (G401) tissue derived cancer cell lines resulted in moderate gene expression changes. Surprisingly, for the reported role of MLL1 as a co-activator of gene expression, inhibition by BAY-155 led predominantly to up-regulation of genes. We could not observe any evidences of an overarching, menin driven expression program, which is in contrast to previous reports for e.g. the Hox gene cluster.
Conclusions: Our study adds important critical validation data to the menin-MLL interaction as therapeutic target in solid cancers. By using a more selective and potent inhibitor we propose that the potential therapeutic benefit of disrupting the menin-MLL interaction may be more restricted to specific cancers than previously predicted.

overall_design: RNA-sequencing of solid cancers-derived cell lines treated with BAY-155 inhibitor, combination of steroid hormone (ß-Estradiol or R1881 for breast and prostate cancer cell lines respectively) and BAY-155 or DMSO control.

first: Krzysztof

last: Brzezinka

first: Ekaterina

last: Nevedomskaya

first: Ralf

last: Lesche

first: Carlo

last: Stresemann


title: Profiling of histone modifications in GATA3 ZnFn2 mutant cells with progesterone treatment

city: Research Triangle Park

first: Paul

last: Wade

state: NC

address: 111 TW Alexander Drive

department: Laboratory of Molecular Carcinogenesis

institute: NIEHS

type: Genome binding/occupancy profiling by high throughput sequencing

summary: R330fs GATA3 mutant disrupts the progesterone network in T47D cells. We mapped active histone marks (H3K4me1 and H3K27ac) and repressive histone mark (H3K27me3) in the T47D GATA3  mutant cells after progesterone treatment. Control (vehicle) data has been posted under the accession number GSE130703.

overall_design: Genome-wide mapping of chromatin architectures in P4-treated GATA3 mutant T47D cells

first: Motoki

last: Takaku

first: Sara

last: Grimm


title: Light effect via Opn3 on the activity of brown adipocytes

city: Boston

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

summary: Opsin3 (Opn3) is a transmembrane heptahelical G-protein-coupled receptor (GPCR) with the potential to produce a non-visual photoreceptive effect. Interestingly, anatomical profiling of GPCRs reveals that Opn3 mRNA is highly expressed in adipose tissue. The photosensitive functions of Opn3 in mammals are poorly understood, and whether Opn3 has a function in fat is entirely unknown. In this study, we found that Opn3-knockout (Opn3-KO) mice were prone to diet-induced obesity and insulin-resistance. At the cellular level, Opn3-KO brown adipocytes cultured in darkness had decreased glucose uptake and lower nutrient-induced mitochondrial respiration than wild-type (WT) cells. Light exposure promoted mitochondrial activity and glucose uptake in WT adipocytes but not in Opn3-KO cells. Using RNA sequencing, we identified several novel light-sensitive and Opn3-dependent molecular signatures in brown adipocytes. Importantly, direct exposure of BAT to light in living mice significantly enhanced thermogenic capacity of BAT, and this effect was diminished in Opn3-KO animals. These results uncover a previously unrecognized cell-autonomous, light-sensing mechanism in brown adipocytes via Opn3-GPCR signaling that can regulate fuel metabolism and mitochondrial respiration in vitro and thermogenesis in vivo. Our work also provides a molecular basis for developing light-based treatments for obesity and its related metabolic disorders.

overall_design: Brown adipocytes and their precursors were isolated from newborn wild-type and Opn3-KO mice by collagenase digestion, and were immortalized. Cells were differentiated into adipocytes for 8 days. Total RNA was extracted from cells using the spin column kit (Zymo Research). The integrity and purity of total RNA were assessed using an Aligent 2100 Bioanalyzer (Agilent Technologies). The Illumina TruSeq Stranded mRNA protocol was used for the preparation of RNA sequencing (RNA-Seq) libraries and sequenced on a HiSeq2500 machine (Illumina), as paired-end, 100 base pairs (bp) reads.

first: Mari

last: Sato

first: Yu-Hua

last: Tseng


title: PROP1-Dependent Retinoic Acid Signaling Regulates Developmental Pituitary Morphogenesis and Hormone Expression

city: Stony Brook

first: Leonard

middle: YM

last: Cheung

state: New York

address: 101 Nicolls Road

institute: Stony Brook University

summary: Dietary vitamin A is metabolized into bioactive retinoic acid in vivo and regulates the development of many embryonic tissues.  Retinoic acid signaling is active in the oral ectoderm-derived tissues of the neuroendocrine system, but its role there has not yet been fully explored.  We show here that retinoic acid signaling is active during pituitary organogenesis and dependent on the pituitary transcription factor Prop1.  Prop1-mutant mice show reduced  expression of the aldehyde dehydrogenase gene Aldh1a2, which metabolizes the vitamin A-intermediate retinaldehyde into retinoic acid.  In order to elucidate the specific function of RA signaling during neuroendocrine development, we studied a conditional deletion of Aldh1a2 and a dominant-negative mouse model of inhibited retinoic acid signaling during pituitary organogenesis.  These models partially phenocopy Prop1-mutant mice by exhibiting embryonic pituitary dysmorphology and reduced hormone expression, especially of thyroid-stimulating hormone.  These findings establish the critical role of retinoic acid in embryonic pituitary stem cell progression to differentiated hormone cells and raise the question of gene-by-environment interactions as contributors to pituitary development and disease.

overall_design: 10x Chromium single-cell RNA sequencing data of pituitary cells from one P4 female Hesx1Cre/+ and one P4 female Hesx1Cre/+; R26dnRAR/dnRAR mouse

first: L

middle: Y

first: S

last: Camper


title: New Pathogenesis Mechanisms and Translational Leads Identified by Multidimensional Analysis of Necrotizing Myositis in Primates

first: Priyanka

last: Kachroo

address: 6670 Bertner Avenue

summary:
Purpose: We used dual RNA-seq to analyze the transcriptomes of serotype M1 S. pyogenes and host skeletal muscle recovered contemporaneously from infected nonhuman primates (NHPs). We identified genes important for necrotizing myositis, made isogenic deletion mutants and performed RNA-seq comparing one of those deletion mutant strains (dahA) grown in vitro and compared to its parental wild-type strain.
Methods: We grew the emm1 reference strain MGAS2221 in rich media (growth in vitro), and collected samples in triplicate at both mid-exponential (ME), and early stationary (ES) phase, to perform RNA-seq analysis. In addition, three NHPs were injected in the quadriceps skeletal muscle with the same GAS strain, necropsied after 24 h, samples were excised in concentric sections (from 1, at the inoculation site, to 5 on the periphery), and analyzed by dual RNA-seq (growth in vivo). Mock-infected skeletal muscle tissue was collected as negative control. Isogenic mutant for dahA and its parental wild-type strain were grown under the same conditions. Quality of the total RNA, rRNA-depleted RNA, and cDNA libraries was evaluated with RNA Nano, RNA Pico, and DNA high-sensitivity kits (Agilent Technologies, respectively, using an Agilent 2100 Bioanalyzer. For each sample, the cDNA library concentration was measured fluorometrically with Qubit™ dsDNA HS assay kits (Invitrogen). The cDNA libraries were diluted, pooled, and sequenced with an Illumina NextSeq 550 instrument. .cDNA libraries for the dahA isogenic mutant and its parental wild-type strain, grown in vitro, were generated using Epicentre Scriptseq for bacteria and sequenced on Illumina NextSeq 500 instrument.

sample_organism:
Streptococcus pyogenes
Macaca fascicularis

overall_design:
RNA-seq was performed on MGAS2221 grown in THY (triplicates) and dual RNA-seq was performed on the in-vivo samples (infected and mock infected NHP tissues). RNA-seq was also performed on the dahA isogenic mutant strain and its  parental wild-type.

Please note that the Samples 25-39 are mock-infected samples (separate sections from site of infection) have no processed data since they were combined to generate the samples 40-42.
The raw files for all mock-infected samples (Samples 25-42) are included for users who may try to analyze the data with all the mock-samples as controls.

first: James

last: Musser

first: Jesus

last: Eraso


title: Integrative analysis of lncRNAs, miRNAs, and mRNA-associated ceRNA network in lung tissue of aging mice and changes after intervention of Codonopsis pilosula

city: Lanzhou

first: Dongmei

last: Chen

address: No. 35 Dingxi east road, chengguan district, Lanzhou, Gansu province

institute: Gansu University of Chinese Medicine

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


title: Integrative analysis of lncRNAs, miRNAs, and mRNA-associated ceRNA network in lung tissue of aging mice and changes after intervention of Codonopsis pilosula (lncRNA, mRNA datasets)

summary: Codonopsis pilosula, a kind of traditional Chinese medicine, possesses anti-aging effect. However, the anti-aging effect of Codonopsis pilosula on lung remains largely unknow and the exact molecular mechanism of Codonopsis pilosula anti-aging also needs to be further studied. Thus, we investigated the protective effect of Codonopsis pilosula on aging lung and the exact molecular mechanism of Codonopsis pilosula anti-aging. To test this hypothesis, we established the aging mice model, and then used Codonopsis pilosula to intervene. Microarray analysis and bioinformatics methods were used to comprehensively analyze lncRNA-miRNA-mRNA (ceRNA) network. Our results showed that the aging mice model was established. From the microarray analysis, 138 lncRNAs, 128 mRNAs and seven miRNAs significantly changed after aging, whereas, 282 lncRNAs, 283 mRNAs and 19 miRNAs were dysregulated after intervention of Codonopsis pilosula. KEGG pathway analysis was performed to explore the signaling pathways involved. Compared with the ceRNA network in aging mice and after intervention of Codonopsis pilosula, we found three mRNAs (Hif3a, Zbtb16, Plxna2) and one lncRNA (NONMMUT063872) associated with Codonopsis pilosula anti-aging and they were validated by qRT-PCR. Altogether, our results showed that Codonopsis pilosula has the protective effect on aging lung and the ceRNA network plays an important role in Codonopsis pilosula anti-aging.

overall_design: Total RNA was extracted from lung tissues in the control group, the model group and high dose Codonopsis pilosula intervention group (n=3 mice).

first: Jiajia

last: Liu

first: Jie

last: Meng

first: Dandan

last: Li

first: Pan

last: Zhao

first: Yongqiang

last: Duan

first: Li

first: Jing

last: Wang


title: RNA-seq in Prdm16 KO doudenal and villi

first: Patrick

last: Seale

address: Smilow Center for Translational Research, 12th Floor 3400 Civic Center Blvd. Bldg 421

department: Institute for Diabetes, Obesity & Metabolism

summary: RNA was extracted from duodenal villi from crontrol and Prdm16 KO mice 3 days after deletion

overall_design: RNA was isolated from duodenal villi of WT (Prdm16loxP/loxP) or KO (Rosa26CreERT2; Prdm16loxP/loxP ) mice 3 days after tamoxifen injection.  Total RNA was extracted from isolated crypts or villi using TRIzol (Invitrogen) combined with Purelink RNA Mini columns (Fisher).  RNA-seq libraries were generated using  a Truseq RNA Sample Preparation kit (Version 2, Illumina, RS-122-2001). RNA-seq was performed by the University of Pennsylvania Next Gen Sequencing Core using a HiSeq 2000 high output sequencer.  Differential expression was determined using the EdgeR software package using log2 fold change of KO divided by WT. 0-1 False Discovery Rates were calculated from the p-value using a Benjamini-Hochberg correction.

first: Rachel

last: Stine


title: An ontogenetic switch in the positive and negative selection of B cells [bone marrow and fetal liver]

city: Oxford

first: Adam

last: Cribbs

address: Windmill Road

department: NDORMS

country: United Kingdom

institute: University of Oxford

summary: Developing B cells can differentiate into a variety of different subsets, but the mechanisms that determine these outcomes are incompletely understood, with theories based on separate lineages or the positive and negative selection by self-antigens.  In particular, the development of the B-1 B cell subset arises mainly from precursors in early ontogeny and is subject to positive selection by self-antigens, whereas the follicular B-2 B cell subset arises later and is subject to negative control. In this study we show how a cell intrinsic switch from Lin28b to Let7 gene expression changes a B cell’s susceptibility from positive to negative selection during ontogeny. Ectopic expression of a Lin28b transgene in B cells restores the positive selection of autoreactive B-1 B cells by self-antigen in adult bone marrow.  Analysis of antigen-specific immature B cells in early and late ontogeny identifies Lin28b-dependent genes associated with B-1 B cell development, including Arid3a and Bhleh41, and Lin28b-independent effects associated with the presence or absence of self-antigen. These findings identify cell intrinsic and extrinsic determinants of B cell fate during ontogeny and reconcile lineage and selection theories of B cell development. They explain how changes in the balance of positive and negative selection may be able to adapt to meet the immunological needs of an individual during its lifetime.

overall_design: Examination of the transcriptome from B cells isolated from bone marrow or neonatal liver

first: Xijin

last: Xu


title: Single-cell RNA-seq analysis identifies meniscus progenitors and reveals the progression of meniscus degeneration

city: Guangzhou

first: Hao

last: Sun

state: Guangdong

address: Zhongshan 2nd Road

department: Joint surgery

institute: First Affiliated Hospital of Sun Yat-sen University,

summary: We identified seven clusters in healthy human meniscus, including five empirically-defined populations and two novel populations. Pseudotime analysis showed EC and FCP existed at the pseudospace trajectory start. MCAM (CD146) was highly expressed in two clusters. CD146+ meniscus cells differentiated into osteoblasts and adipocytes and formed colonies. We identified changes in the proportions of degenerated meniscus cell clusters and found a cluster specific to degenerative meniscus with progenitor cell characteristics. The reconstruction of four progenitor cell clusters indicated that FCP differentiation into DegP was an aberrant process. Interleukin-1β stimulation in healthy human meniscus cells decreased CD146+ cells and increased CD318+ cells, while TGFβ1 attenuated the increase in CD318+ cells in degenerated meniscus cells.

overall_design: scRNA-seq was used to identify cell subsets and their gene signatures in healthy human and degenerated meniscus cells

first: Zhiqi

last: Zhang


title: An ontogenetic switch in the positive and negative selection of B cells [IgHEL]

overall_design: Examination of the transcriptome from B cells isolated from bone marrow following 10 weeks and 3 weeks from IgHEL transgenic mice


title: Effect of restricted dissolved oxygen on expression of Clostridium difficile toxin A subunit from E. coli.

city: Bethesda

first: Ashish

middle: K

last: Sharma

state: MD

address: 14 Service Rd West Building 14A Room 176 MS-5522

department: National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)

institute: National Institute of Health

summary: We used microarray to identify the global gene expression profile of recombinant E.coli culture expressing repeating unit of the C. difficile toxin A (rARU) C-terminal region. Controlled condition batch runs were performed with E.coli expressing rARU at both restricted and unrestricted DO conditions for collecting samples of log and late-log phases at unrestricted and restricted DO.

overall_design: Time point mRNA profiling of E.coli expressing rARU at both restricted and unrestricted DO conditions for gene expression profiling.

first: A

first: J

last: Shiloach


title: RNA Seq In Isolated Crypts from Duodenum, Jejunum, and Ileum

summary: RNA was extracted from crypts from the three portions of the small intestine

overall_design: mRNA profiles of crypts from murine Duodenum, Jejunum, and Ileum, were generated by deep sequencing in triplicate. Followed by DESeq2 analysis with outputs of pairwise comparisons of differential expression in the three cell types.

first: Sakers

last: Alexander


title: An ontogenetic switch in the positive and negative selection of B cells [B cell subsets]

overall_design: Examination of the transcriptome from B cells isolated from peripheray (B cell subsets A:anergic,B:Follicular,C:MZ B cell, D: B1 B cell)


title: Physiological responses of Saccharomyces cerevisiae to industrially relevant conditions: slow growth, low pH and high CO2 levels

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

country: Netherlands

institute: Delft University of Technology

summary: Engineered strains of Saccharomyces cerevisiae are used for industrial production of succinic acid. Optimal process conditions for dicarboxylic-acid yield and recovery include slow growth, low pH and high CO2. To quantify and understand how these process parameters affect yeast physiology, this study investigates individual and combined impacts of low pH (3.0) and high CO2 (50 %) on slow-growing chemostat and retentostat cultures of the reference strain S. cerevisiae CEN.PK113-7D. Combined exposure to low pH and high CO2 led to increased maintenance-energy requirements and death rates in aerobic, glucose-limited cultures. Further experiments showed that these effects were predominantly caused by low pH. Growth under ammonium-limited, energy-excess conditions did not aggravate or ameliorate these adverse impacts. Despite the absence of a synergistic effect of low pH and high CO2 on physiology, high CO2 strongly affected genome-wide transcriptional responses to low pH. Interference of high CO2 with low-pH signaling is consistent with low-pH and high-CO2 signals being relayed via common (MAPK-)signaling pathways, notably the cell wall integrity (CWI), high osmolarity glycerol (HOG) and calcineurin pathways. This study highlights the need to further increase robustness of cell factories to low pH for carboxylic-acid production, even in organisms that are already applied at industrial scale.

overall_design: Compare expression of glucose growth S. cerevisiae CEN.PK113-7D in chemostat cultures at d = 0.025 h-1 for low pH (pH3), high CO2 (50%) conditions as well as in retentostats when going from 0.025 h-1 to near-zero growth rates. Both datasets are compared to 'standard laboratory' conditions.

first: Pascale

last: Daran-Lapujade

first: Marcel

last: van den Broek

first: Xavier

last: Hakkaart


title: MBOAT7 loss of function in clear cell Renal Carcinoma (ccRCC)

city: Chicago

first: Matthew

middle: J.

last: Schipma

state: IL

address: 750 N. Lake Shore Drive

department: Biochemistry and Molecular Genetics

institute: Northwestern University

summary: We demonstrated an increase in MBOAT7 and downstream phosphatidylinositol products in ccRCC. This RNAseq was of two loss of function clones and wild-type in the Caki-1 cell model (ccRCC cell line).

overall_design: We used CRISPR/Cas9 to generate knockout cell lines validated using Sanger and Western Blotting. The knockout clones were then RNA sequenced against a wild-type counterpart.

first: Chase

last: Neumann

last: Brown


title: An ontogenetic switch in the positive and negative selection of B cells

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

overall_design: Refer to individual Series


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and MPG-/- Transcriptomes

city: Trondheim

first: Nicola

middle: Pietro

last: Montaldo

address: Erling Skjalgssons gt 1

department: Department of Clinical and Molecular Medicine (IKOM)

country: Norway

institute: NTNU

summary: mRNA profiles of HAP1 wild type (WT) and MPG-/- cells were generated by deep sequencing using Complete Genomics

overall_design: mRNA profiles of HAP1 wild type (WT) and AAG-/- cells were generated by deep sequencing using Complete Genomics


title: mRNA map of HUVECs treated with HeLa exosome and Human Cervical Epithelial cell (Hcer)exosome [RNA-seq]

city: Hangzhou

first: lin

last: yinuo

address: Jiefang Road NO.88

institute: Second Affiliated Hospital of Zhejiang University

summary: we aimed to compare the mRNA profile between HUVECs treat with HeLa exosome and Hcer cell exosome. Cells were treated with HeLa exosomes or Hcer exosomes for 48 hours (3 repeat samples for each group) and then RNA of each group was collected.RNAs were sequenced on Proton Sequencers according to Ion PI Sequencing 200 Kit v2.0 (Life Technologies).According to the results,we found a total of 2493 different genes reach to 2 fold difference between two groups.

overall_design: HUVEC cell treated with HeLa exo or HCer exo, analysed using deep sequencing, in triplicate.

first: Hong

last: Yu

first: Yinuo

last: Lin


title: PRDM16 ChIP-Seq in Prdm16 WT and KO duodenal crypts

city: Philadelphia

first: Patrick

last: Seale

institute: University of Pennsylvania

summary: PRDM16 ChIP was perfomed in control and Prdm16 KO crypts isolated from the duodenum of 6 week old mice 3 days  after inducible gene deletion

overall_design: 6 samples

first: Rachel

last: Stine


title: Genome-wide binding of Arabidopsis growth regulating factors uncovers their broad regulatory functions in plant growth, development and stress response

city: Knoxville

first: Sarbottam

last: Piya

state: Tennessee

address: 2431 Joe Johnson Dr.

department: Plant Science

institute: University of Tennessee


title: exosomal microRNA maps of HeLa cell exosome vs human cervical epithelial cell exosome [miRNA-seq]

summary: We aimed to compare the exosomal microRNA profile form HeLa cell line with that from human cervical epithelial cell(Hcer)line.exosomes were isolated from conditioned medium of HeLa cell and HCer cell,3 samples for each group.Exosomal microRNAs were sequenced on Proton Sequencers according to Ion PI Hi-Q Sequencing 200 Kit (Life Technologies).According to the results of miRNA sequencing, we found a total 371 different miRNAs the amount of which reach to 10 fold differece between two groups.

overall_design: exosomal microRNA profiles of HeLa cell exosome vs human cervical epithelial cell (HCER) analysed using deep sequencing, in triplicate, using Illumina GAIIx.

first: Chi

last: Zhang


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type (WT), AAG-/-, and ELP1-/-  Transcriptomes

summary: mRNA profiles of HEK293T wild type (WT), AAG-/-, and ELP1-/- cells were generated by deep sequencing, in triplicate, using Illumina HiSeq 2500.

first: Barbara

last: vanLoon


title: Regulation of the heat shock response is built into the spatial organization of the proteostasis network

first: David

last: Pincus

institute: University of Chicago

summary: How heat shock induces the heat shock response (HSR) - a gene expression program encoding chaperones and other protein homeostasis (proteostasis) factors - remains an unresolved question in eukaryotic cell biology. Here we show that subcellular localization of the conserved J-protein Sis1 is a key regulator of the HSR in yeast. Under nonstress conditions, nucleoplasmic Sis1 promotes interaction between the chaperone Hsp70 and the transcription factor Hsf1 to repress the HSR. Heat shock triggers Sis1 to localize to the periphery of the nucleolus and to condense on the ER surface. Sis1 recruits the proteasome to this spatial network along with disaggregases and the ribosome quality control complex. Through localization dynamics, Sis1 relays the condition of the proteome to Hsf1. We conclude that the activation state of the HSR is determined by the spatial organization of the proteostasis network.

overall_design: We performed 12 RNA seq of polyA+ mRNA from yeast cells over two time courses: following heat shock at 39C and following nuclear depletion of the J-protein Sis1 using the "anchor away" approach. For both time series, the time points were 0, 15, 30, 60, 90 and 120 minutes.


title: Emory University African American Microbiome in Pregnancy Cohort.

city: Atlanta

first: Anna

last: Knight

state: Georgia

address: 101 Woodruff Circle NE

institute: Emory University

summary: All subjects were enrolled from Grady Memorial and Emory Midtown Hospitals. Subjects provided blood samples at two timepoints during pregnancy.

overall_design: Subjects provided blood samples at two timepoints during pregnancy, which were processed into peripheral blood mononuclear cells (PBMC). DNA was extracted usingthe AllPrep RNA/DNA Mini Kit (Qiagen). DNA methylation was assessed on the HumanMethylation450 BeadChip.


title: Attenuation of progesterone driven mammary stem cells population by telapristone acetate

first: Seema

middle: Ahsan

last: Khan

address: 303 E. Superior Street, 4-111

summary: ovariectomized mice treated with E2+Progesterone, E2+Progesterone+TPA,  E2+Progesterone+RU486 and sham for 14 days, followed by isolation of luminal mature, luminal progenitor and mammary stem cells through FACS and RNASeq performed for each cell lineage population. TPA and RU486 treated mice show significant decline in mammary stem cell pool pulation comapared to EP treated mice

overall_design:
RNA-seq of luminal mature, luminal progenitor and mammary stem cells from ovariectomized mice treated with  E2+Progesterone, E2+Progesterone+TPA,  E2+Progesterone+RU486 or sham for 14 days.

contributor: Artificial Intelligene (AI, www.artificialintelligene.com)

first: Manish

last: Ranjan


title: Activin A impacts on the allocation of the epiblast stem cells to the ectoderm lineage

city: WESTMEAD

first: PIERRE

last: OSTEIL

state: NSW

address: 214 Hawkesbury Road

department: Embryology

institute: CMRI

summary: The modulation of TGFb activity is critical for the specification of mesendoderm tissue progenitors in the multipotent early epiblast and the repression of TGFb activity enhances the ectoderm lineage potency of the epiblast cells.

overall_design: 2 different lines with 3 replicates each.

first: Pierre

last: Osteil

last: Tam


title: RNA-seq in Prdm16 KO duodenal crypts

summary: The adult intestinal epithelium is maintained by a continuous replacement of differentiated cells from stem cells. Previous studies suggest that cellular metabolic pathways regulate intestinal stem cell activity and differentiation. However, little is known about the cell-intrinsic factors that control these metabolic programs. Here, we identify the transcription factor PRDM16 as a critical regulator of intestinal metabolic programing and stem cell differentiation. Acute deletion of Prdm16 in adult mice causes severe intestinal wasting, apoptosis, and an accumulation of poorly differentiated cells in the crypt.  Prdm16-deficient crypts display decreased expression levels of fatty acid oxidation (FAO) genes and reduced rates of FAO. PRDM16 binds, along with its protein partners PPARγ and PPARα, to the promoter and enhancer regions of many FAO genes. The loss of Prdm16 or inhibition of FAO impaired the transition of intestinal stem cells into transit amplifying cells.  Notably, PRDM16 expression is highest in the duodenum and declines distally along the intestine. This gradient of PRDM16 expression controls the region-specific expression of the FAO program and underlies the differential reliance of region-specific stem cells on FAO.  Altogether, this study establishes PRDM16 as a regional-specific regulator of metabolism and stem cell differentiation in the intestine.

overall_design:
RNA was extracted from duodenal crypts isolated from crontrol and Prdm16 KO crypts 3 days after deletion
RNA was isolated from duodenal crypts of WT (Prdm16loxP/loxP) or KO (Rosa26CreERT2; Prdm16loxP/loxP ) mice 3 days after tamoxifen injection.  Total RNA was extracted from isolated crypts or enteroids (following one ice cold PBS wash to dissolve Matrigel) using TRIzol (Invitrogen) combined with Purelink RNA Mini columns (Fisher) and then reverse transcribed into cDNA using the ABI High-Capacity cDNA Synthesis kit.  RNA-seq libraries were generated using  a Truseq RNA Sample Preparation kit (Version 2, Illumina, RS-122-2001).  RNA-seq was performed by the University of Pennsylvania Next Gen Sequencing Core using a HiSeq 2000 high output sequencer.  Differential expression was determined using the EdgeR software package using log2 fold change of KO divided by WT. 0-1 False Discovery Rates were calculated from the p-value using a Benjamini-Hochberg correction.


title: H3K27Ac ChIP-Seq in Prdm16 KO duodenal crypts

summary: The adult intestinal epithelium is maintained by a continuous replacement of differentiated cells from stem cells. Previous studies suggest that cellular metabolic pathways regulate intestinal stem cell activity and differentiation. However, little is known about the cell-intrinsic factors that control these metabolic programs. Here, we identify the transcription factor PRDM16 as a critical regulator of intestinal metabolic programing and stem cell differentiation. Acute deletion of Prdm16 in adult mice causes severe intestinal wasting, apoptosis, and an accumulation of poorly differentiated cells in the crypt.  Prdm16-deficient crypts display decreased expression levels of fatty acid oxidation (FAO) genes and reduced rates of FAO. PRDM16 binds, along with its protein partners PPAR? and PPAR?, to the promoter and enhancer regions of many FAO genes. The loss of Prdm16 or inhibition of FAO impaired the transition of intestinal stem cells into transit amplifying cells.  Notably, PRDM16 expression is highest in the duodenum and declines distally along the intestine. This gradient of PRDM16 expression controls the region-specific expression of the FAO program and underlies the differential reliance of region-specific stem cells on FAO.  Altogether, this study establishes PRDM16 as a regional-specific regulator of metabolism and stem cell differentiation in the intestine.

overall_design: H3K27Ac was performed on control and Prdm16 KO crypts isolated from the duodenum of 6 week old mice injected with tamoxifen 3 days before crypt extraction


title: Genome-Wide DNA Methylation Meta-analysis in the Brains of Suicide Completers I

city: Exeter

first: Stefania

last: Policicchio

state: Devon

address: RILD building, BARRACK ROAD, Albion Place

institute: University of Exeter, Medical School

summary:
Suicide is the second leading cause of death globally among young people representing a significant global health burden. Although the molecular pathology of suicide remains poorly understood, it has been hypothesised that epigenomic processes may play a role. The objective of this study was to identify suicide-associated DNA methylation changes in the human brain by utilising previously published and unpublished methylomic datasets. We analyzed prefrontal cortex (PFC, n = 211) and cerebellum (CER, n = 114) DNA methylation profiles from suicide completers and non-psychiatric, sudden-death controls, meta-analyzing data from independent cohorts for each brain region separately. We report evidence for altered DNA methylation at several genetic loci in suicide cases compared to controls in both brain regions with suicide-associated differentially methylated positions enriched among functional pathways relevant to neuropsychiatric phenotypes and suicidality, including nervous system development (PFC) and regulation of long-term synaptic depression (CER). In addition, we examined the functional consequences of variable DNA methylation within a PFC suicide-associated differentially methylated region (PSORS1C3 DMR) using a dual luciferase assay and examined expression of nearby genes.  DNA methylation within this region was associated with decreased expression of firefly luciferase but was not associated with expression of nearby genes, PSORS1C3 and POU5F1. Our data suggest that suicide is associated with DNA methylation, offering novel insights into the molecular pathology associated with suicidality.
DNA from bulk post-mortem brain (human cerebellum) from 58 individuals

overall_design: Bisulphite converted DNA from the 58 samples were hybridised to the Illumina Infinium 850K Human Methylation Beadchip

first: Sam

last: Washer

first: Joana

last: Viana

first: Artemis

last: Iatrou

first: Joe

last: Burrage

first: Eilis

last: Hannon

first: Gustavo

last: Turecki

first: Zachary

last: Kaminsky

first: Jonathan

last: Mill

first: Emma

last: Dempster

first: Therese

last: Murphy


title: Ventral midbrain-type neural stem/precursor cells (VM-NSCs) derived from human midbrain organoids as a stable source for treating symptoms of Parkinson’s disease

city: Seoul

first: Seungwon

middle: Thomas

last: Kim

address: Wangsimniro 222

department: Department of Biochemistry and Molecular Biology

country: South Korea

institute: Hanyang University

summary: In this study, midbrain-like organoids were yielded from hPSCs to prepare cells used for PD therapy. Neural stem/precursor cells (NSCs) isolated from midbrain organoids (Og-NSCs) expanded stably and differentiated into mDA neurons, and an unprecedentedly high proportion express midbrain-specific factors.

overall_design: mRNA profile of 2D culture system derived NSCs, Midbrain Organoid derived NSCs, Midbrain-like organoids. GSM4039143 and GSM4039144 are included in this article as PD ips 2D-NSC samples.

first: Sang-Hun

last: Lee

first: Mi-Yoon

last: Chang

first: Seung

first: Hye

middle: J

last: Woo


title: Control of region-specific intestinal metabolism and maintenance by PRDM16

first: Patrick

last: Seale


title: Expression data from gastric cancer cell line HGC27 after knockdown of SNAIL

status: Public on Feb 25 2020

city: kyoto

first: Ru

last: chen

address: kawahara-cho 53, shogoin, sakyo-ku

institute: kyoto university

summary: SNAIL, which is a key factor in EMT, has high expression levels in the gastric spheres. To investigate SNAIL-regulated genes, we knocked down this gene in the gastric cancer cell line HGC-27 and compared the gene expression of these cells with those of the parental cells by microarray.

overall_design: The lentivirus package system: pMDLg/pRRE (Addgene, plasmid #12251), pRSV-Rev (Addgene, plasmid #12253) and pMD2.G (Addgene, plasmid #12259) together with the shRNA plasmid targeting the human SNAIL gene as well as the control vector: pLKO.1puro (Addgene, plasmid #8453) were co-transfected into 293T cells by Lipofectamine 3000 (Invitrogen). SNAIL-targeting short-hairpin RNA (MISSION shRNA) duplex (A: 5-TGCTCCACAAGCACCAAGAGTC-3; B: 5-CCACTCAGATGTCAAGAAGTAC-3) was purchased from Sigma-Aldrich Co. LCC. (St. Louis, MO, USA). About 48 to 72 hours later, virus supernatant was collected for concentration. For shRNA knockdown, HGC27 cells were seeded onto 6-well plates and infected with optimal virus concentrations supplemented with 6 µg/mL Polybrene (Sigma, St. Louis, MO, USA), then incubated for 12 hours before replacing with fresh medium. Cells were then selected by puromycin (INVIVOGEN, Japan) at the concentration of 1.8 µg/ml for 2 weeks.

last: Chen

first: Shigeo

last: Takaishi


title: Longitudinal measures of RNA expression and disease activity in FSHD muscle biopsies

city: Seattle

first: Stephen

last: Tapscott

state: WASHINGTON

address: 1100 Fairview N. Ave

department: Human Biology

institute: Fred Hutch Cancer Research Center

summary: Advances in understanding the pathophysiology of facioscapulohumeral dystrophy (FSHD) have led to the discovery of candidate therapeutics and it is important to identify markers of disease activity and progression to inform clinical trial design. For drugs that inhibit the expression of DUX4, measuring DUX4 or DUX4 target gene expression might be an interim outcome measure of drug activity, however, only a subset of muscle biopsies in FSHD show evidence of DUX4 expression. Our prior study showed that MRI T2-STIR positive muscles had a higher probability of showing DUX4 expression than muscles with normal MRI characteristics. In the current study, we performed a one-year follow-up assessment of the same muscle with repeat MRI and muscle biopsy. There was very little change in the muscle MRI characteristics over the one-year period and, similar to the initial evaluation MRI T2-STIR-postive muscles had a higher expression of DUX4 regulated genes, as well as genes associated with inflammation, extracellular matrix, and cell cycle. Compared to the initial evaluation, overall the level of expression in these gene categories remained stable over the one-year period, however, there was some variability for each individual muscle biopsied. We pooled the data from both the initial and one-year follow-up evaluations and identified several subgroups based on gene expression, as well as a set of genes that distinguished all of the FSHD samples from the controls that include DUX4-regulated genes, inflammatory immune genes, and cell cycle control genes. These candidate markers of disease activity need to be validated on independent datasets, but will hopefully be useful in studies of disease progression and response to therapy.

overall_design:
A total of 36 patients were recruited through the Seattle Paul D. Wellstone Muscular Dystrophy Cooperative Research Center.  35 patients (mean age 54, range 19-75; 22 male/13 female; clinical severity score 0-8) underwent muscle biopsy at the first visit.  All patients had genetically confirmed FSHD1 or 2.  31 patients had muscle biopsies at the second visit.  The inital visit RNA-seq biopsy samples were deposited to GSE115650. This raw dataset includes the RNA-seq performed on 27 out of the 31 follow-up biopsies plus the eight control muscle biopsies from the initial investigation.

Definitions:
sizeFactor: normalization factor calculated by DESeq2
T1_rating: MRI signal: T1 fat rating
fat_fraction: MRI signal: T1 fat fraction
STIR_rating: MRI signal: STIR rating
Inflammation: Histopathologic inflammations core
Variability.in.Fiber.Size: Pathology score: Variabilituy in fiber size
Extent.of.Central.Nucleation: Pathology score: Extent of centrl nucleation
Necrosis.Regeneration.Inflammation: Pathology score: Variabilituy in fiber size
Fibrosis: Pathology score: Fibrosis
Pathology.Score: Accumulated pathology score
dux4.rlogsum: DUX4 score = summation of four DUX4 biomarkers
dux4.group: Group by DUX4 score

first: Chao-Jen

last: Wong

first: Leo

middle: H

last: Wang

first: Seth

last: Frieman

first: Dennis

last: Shaw

first: Chris

middle: B

last: Budech

first: Amy

middle: E

last: Campbell

first: Richard

last: Lemmers

first: Silevere

middle: m

last: van der Maarel

first: Rabi

middle: N

last: Tawil


title: RNA_Sequencing Facilitates Quantitative Analysis of macrophages transcriptomes from Wild Type and miR_7 deficiency mice Transcriptomes

city: Zunyi

first: HUIZI

last: CHEN

state: GuiZhou

address: Honghuagang District

department: Zunyi Medical University

institute: Zunyi Medical University

summary: Purpose: The goals of this study are to analyze  the differential gene expression of miR_7 deficiency mice macrophages before and after activation, and  screen out miR_7 candidate target genes.

overall_design: Total RNA of  macrophages (from WT or miR_7 deficiency mice) stimulated with 100 ng/mL LPS for 12 hrs or left unstimulated was purified using TRIzol reagent. Total RNA of each sample was submitted to the TSRI Next Generation Sequencing Core for deep sequencing. Total RNA was enriched for polyA_containing RNAs and deep sequencing of those samples was performed on a HiSeq 2000 (Illumina). Data analysis was performed with Pipeline Software (Casava v1.8.2) and Cutadapt. Alignment to the mouse genome was performed with mRNA_Seq TopHat v2.0.13 with Bowtie2, and the exon annotation retrieved with Partek. Total read counts for each gene was calculated and used to identify protein coding genes downregulated by miR_7.

first: Huizi

first: Lin

last: Xu


title: EPI-00649-2019 New insights into the early mechanisms of epileptogenesis in a zebrafish model of Dravet syndrome

city: Esch-sur-Alzette

first: Kamil

last: Grzyb

email: kamilgen@gmail.com, kamil.grzyb@uni.lu

address: 2, avenue de l'Université

country: Luxembourg

institute: University of Luxembourg - LCSB

summary: We report early mechanisms of epileptogenesis in a zebrafish model of Dravet syndrome caused by missense mutation in scn1lab gene.

overall_design: Single-cell RNA-Sequencing experiments were performed on a total of 4 samples. These correspond to zebrafish brain 5 and 8 days post fertilization (comparing wild-type to a scn1Lab homozygote mutation).

first: Ettore

last: Tiraboschi

first: Silvia

last: Martina

first: Wietske

last: van der Ent

first: Kinga

last: Gawel

first: Maria

last: Cordero-Maldonado

first: Suresh

last: Kumar Poovathingal

first: Sarah

last: Heintz

first: Somisetty

last: Venkata Satheesh

first: Jarle

last: Brattespe

first: Ju

first: Maximiliano

last: Suster

first: Alexander

last: Skupin

first: Camila

middle: V

last: Esguerra


title: Gene expression profiling identifies a gene signature that predicts progression to active tuberculosis several years before disease onset

city: Newark

first: Padmini

last: Salgame

state: NJ

address: 185 South Orange Ave

department: Medicine

institute: Rutgers New Jersey Medical School

summary: We evaluated the predictive ability of various gene signatures in baseline peripheral blood mononuclear cell samples to distinguish Mtb-infected individuals who eventually progress to TB disease (progressors) or who remain asymptomatic (non-progressors) during clinical follow-up; we also compare long-term Mtb-infected non-progressors from patients with TB disease

overall_design: Transcriptome profiles via RNAseq of progressors, non-progressors, and TB patients in a Brazilian household contact cohort were used to identify a gene signature predictive of progression to TB

first: W

last: Johnson

first: Samantha

last: Leong

first: Yue

last: Zhao


title: α-Synuclein Translocates To The Nucleus To Activate Retinoic Acid- Dependent Gene Transcription

status: Public on Feb 24 2020

city: Fort Lauderdale

first: Lubov

last: Nathanson

state: Florida

address: 3321 College Ave.

department: INIM

institute: Nova Southeastern University

summary: α-Synuclein (α-Syn) is a protein implicated in the pathogenesis of Parkinson’s disease (PD). It is primarily cytosolic and reversibly interacts with cell membranes. α-Syn also occurs in the nucleus, however, the mechanisms involved in its nuclear localization are poorly understood. We analyzed alterations in gene expression following induced α-Syn expression in SH-SY5Y cells. Analysis for upstream regulators pointed at alterations in transcription activity of retinoic acid receptors (RAR)s and additional nuclear receptors. We show that α-Syn binds RA and translocates to the nucleus to selectively enhance gene transcription. Nuclear translocation of α-Syn is regulated by calreticulin, in a leptomycin-B independent mechanism. Importantly, nuclear translocation of α-Syn following RA treatment enhances its toxicity in cultured neurons and the expression levels of PD-associated genes, among which are two familial PDassociated genes, ATPase cation transporting 13A2 (ATP13A2) and PTEN-induced kinase 1 (PINK1). The results link a physiological role for α-Syn in the regulation of RAmediated gene transcription and its toxicity in the synucleinopathies.

overall_design: SH-SY5Y cells induced to express α-Syn (with 1 μg/ml doxycycline) and treated for 16 hours in DMEM supplemented with 0.1% serum and  RA (5 μM). Cells were collected and analyzed following 72 hours from induction of α-Syn expression. Control samples included an identical set up but without induced α-Syn expression.

first: Dana

last: Davidi

first: Meir

last: Schechter

first: Suaad

last: Abd ElHadi

first: Adar

last: Matatov

first: Ronit

last: Sharon


title: A pan-cancer transcriptome analysis to identify the molecular mechanism of prexasertib resistance [microarray]

city: Indianapolis

first: Ricardo

last: Martinez

state: IN

address: 307 E Merrill St

institute: Eli Lilly and Company

summary:
The combined influence of oncogenic drivers, genomic instability, and/or DNA damage repair deficiencies increases replication stress in cancer. Cells with high replication stress rely on the upregulation of checkpoints like those governed by CHK1 for survival. Previous studies of the CHK1 inhibitor prexasertib demonstrated activity across multiple cancer types. Therefore, we sought to (1) identify markers of prexasertib sensitivity and (2) define the molecular mechanism(s) of intrinsic and acquired resistance using preclinical models representing multiple tumor types. Our findings indicate that while cyclin E dysregulation is a driving mechanism of prexasertib response, biomarkers associated with this aberration lack sufficient predictive power to render them clinically actionable for patient selection. Transcriptome analysis of a pan-cancer cell line panel and in vivo models revealed an association between expression of E2F target genes and prexasertib sensitivity and identified innate immunity genes associated with prexasertib resistance. Functional RNAi studies supported a causal role of replication fork components as modulators of prexasertib response. Mechanisms which protect cells from oncogene-induced replication stress may safeguard tumors from such stress induced by a CHK1 inhibitor, resulting in acquired drug resistance. Furthermore, resistance to prexasertib may be shaped by innate immunity.
We included microarray data here as part of the study. RNAseq data was uploaded separately.

overall_design: Prexasertib resistant cell lines from different cancer types were generated using a long-term drug concentration escalation protocol. With at least 3 biological replicates in both resistant and parental lines, Affymetrix microarrays were used to identify differentially expressed genes, which helped to understand molecular mechanism of acquired resistance.

first: Xi

last: Rao


title: Comparative transcriptome analysis of a series of high stepper mutant mice to better understand mutational effect and Rorb function

city: Bar Harbor

first: Abigail

last: Tadenev

state: ME

address: 600 Main St

institute: The Jackson Laboratory

summary: To better understand the effects of high stepper (hstp) mutations on expression from the Rorb locus, we performed RNAseq on samples of whole brain from WT, Rorbh1/h1, Rorbh2/h2, and Rorbh4/h4 mice.  Abnormal transcripts in Rorbh1/h1 brain, mapping upstream of exon 1, likely result from the >326kb duplication in this region, which is thought to cause the hstp phenotype.  A similar yet distinct pattern of aberrant transcripts ~150kb farther upstream in Rorbh2/h2 brain may indicate the presence of a different as-yet-undetermined structural mutation in this line.  Comparison of all datasets reveals that the dramatic high stepper gait phenotype can occur despite very few changes to the transcriptome of the brain as a whole.

overall_design: Brains were harvested from n=3 mice per genotype of WT, Rorbh1/h1, Rorbh2/h2, and Rorbh4/h4 mice, RNA prepared, and RNAseq performed.

middle: L

first: Robert

middle: W

last: Burgess


title: Senataxin, the helicase mutated in AOA2 and ALS4, plays a role in autophagy regulation [HTS]

city: Bridgewater

first: Wencheng

last: Li

state: NJ - New Jersey

institute: PTC Therapeutics

summary: Senataxin (SETX) is an RNA/DNA helicase that has been implicated in transcriptional regulation and the DNA damage response, through resolution of R-loop structures. Mutations in SETX result in either of two distinct neurodegenerative disorders. SETX dominant mutations result in a juvenile form of ALS (amyotrophic lateral sclerosis) named ALS4, while recessive mutations are responsible for an ataxia called AOA2 (ataxia with oculomotor apraxia type 2). How mutations in the same protein can lead to different phenotypes is still unclear. To elucidate AOA2 disease mechanisms, we first examined gene expression changes following SETX depletion. We observed effects on both transcription and RNA processing, but surprisingly observed decreased R-loop accumulation in SETX depleted cells. Importantly, we discovered a strong connection between SETX and the autophagy pathway, reflecting a direct effect on the transcription of autophagy genes. We show that SETX depletion inhibits the progression of autophagy, leading to an accumulation of ubiquitinated proteins, decreased ability to clear protein aggregates, as well as mitochondrial defects. Analysis of AOA2 patient fibroblasts also revealed a perturbation of the autophagy pathway. Our work has thus identified a novel function for SETX in the regulation of autophagy, whose modulation may have a therapeutic impact for AOA2.

overall_design: 3'READS profiling of U87 cells treated with SETX siRNA or control siRNA

first: Mainul

last: Hoque

first: Patricia

last: Richard

first: Shuang

last: Feng

first: Yueh-Lin

last: Tsai

first: Ubayed

last: Muhith

first: Juan

last: Irizarry-Cole

first: Katharine

last: Stolz

first: James

last: Manley

first: Bin

last: Tian


title: Ellagic acid activated PPAR signaling pathway to protect ileums against castor oil-induced diarrhea in mice: Application of transcriptome analysis in drug screening

city: Harbin

first: Jianqing

last: Chen

address: Changjiang Road

institute: Northeast Agricultral University

summary: Background: Acute diarrhea is still a common and serious disease. The causes of acute diarrhea are very complicated. Therefore, we need to find a medicine to control diarrhea symptoms, save time for diagnosis of pathogens, and prevent drug abuse. Ellagic acid (EA), a natural polyphenol drug, has anti-diarrhea effects. However, the action mechanisms of EA for non-specific diarrhea have not been characterized. Materials and methods: To study the mechanisms of EA, mice were divided into four groups (group C were intraperitoneally injected with 0.1 ml physiological saline and orally given 0.2 ml physiological saline, and then after experiment began 0.5 h, orally administered 0.3 ml physiological saline. Group D were intraperitoneally injected with 0.1 ml physiological saline and orally given 0.2 ml castor oil, and then after experiment began 0.5 h, orally administered 0.3 ml physiological saline. Group E were intraperitoneally injected with 0.1 ml physiological saline and orally given 0.2 ml castor oil, and then after experiment began 0.5 h, orally administered 0.3 ml EA (10 mg/ml). Group V were intraperitoneally injected with 0.1ml GW9662 (1m g/ml) and orally given 0.2 ml castor oil, and then after experiment began 0.5 h, orally administered 0.3 ml EA (10 mg/ml).) Transcriptome were performed on ileum tissues of mice in group D and E. Histological examination and qRT-PCR were performed on ileum tissues of mice in group C, D, E and V. Results: We found that a total of 273 differentially expressed genes (DEGs) were obtained, including 160 up-regulated DEGs and 113 down-regulated DEGs. The DEGs were enriched in 458 Gene Ontology (GO) terms and 15 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, respectively. The peroxisome proliferator activated receptor (PPAR) signaling pathway was the most significantly enriched in KEGG pathways. We used the PPAR-specific antagonist GW9662 to validate the anti-diarrhea and anti-inflammatory effect of EA in group V compared with group E. Conclusively, EA protected ileums against castor oil-induced inflammation and diarrhea by activating the PPAR signaling pathway and a method was used to study the mechanism of EA.

first: Jian-Qing

first: Hong-Liang

last: Yang

first: ZunLai

last: Sheng


title: Differentially expressed transcriptomes of P7 mouse tendon cells with targeted deletion of TGF-beta signaling

city: Portland

first: Zheng

last: Xia

state: Oregon

address: 3181 SW Sam Jackson Park Rd

department: Department of Biomedical Engineering

institute: Oregon Health & Science University

summary:
Background: Our group has previously shown that disruption of TGFβ signaling in mouse limb mesenchyme resulted in arrested tendon formation (Pryce et at, 2007). To examine the role of TGFβ signaling in later stages of tendon development, the TGF-beta type II receptor gene (Tgfbr2) was targeted in the Scleraxis (Scx)-expressing cell lineage using the Cre-lox recombination system. We find that tendon development was not disrupted in mutant (Tgfbr2;ScxCre) embryos. However, shortly after birth tenocytes underwent dedifferentiation in which the cell lost differentiation markers and reverted to a more stem/progenitor state.
Purpose: To determine gene expression changes in Tgfbr2;ScxCre mutant tendon cells.
Methods: We performed scRNA-seq for transcriptome changes in P7 mutant tendon cells, a stage at which the majority of the mutant cells is dedifferentiated. Briefly, tendons from P7 mutant and wild-type (as a control) pups were harvested and enzymatically digested. The released cells were then subjected to scRNA-seq  analysis using 10x Genomics platform.
Results: Using unsupervised hierarchical clustering, we identified two major clusters corresponding to mutant (dedifferentiated) cells and wild-type tenocytes in the respective samples. Findings from the pairwise comparison of the gene set between the P7 wild-type tenocyte and mutant cell clusters do not only lend support to our notion that the mutant cells lost their differentiation state, but also suggest the possibility of induction of some developmental programs in these cells, a general feature in cellular dedifferentiation.
Conclusions: TGF-beta signaling is critical for maintenance of the tendon cell fate.

overall_design: Tendon mRNA profiles of 7-day old Tgfbr2;ScxCre mutant and wild type (as a control) mice were generated by deep sequencing using Illumina NextSeq (MidOutput 150). Two samples were submitted, in which each sample consist of enzymatically-released tendon cells that were harvested and pooled from 2 pups.

first: Guak-Kim

last: Tan

first: ChaoJie

last: Wang

first: Ronen

last: Schweitzer


title: Ethyl acetate fraction of Lentinula edodes (LEA) inhibits osteoclastogenesis by suppressing NFATc1 expression

city: Cheongju

first: Kyunghwan

last: Kim

address: Rm #202a, Bldg. S1-5, 1 chungdae-ro

institute: Chungbuk National University

summary: To screen for altered gene expression during osteoclastogenesis,  BMM cells treated with RANKL or RANKL+LEA were subjected to gene expression profiling.

overall_design: Transcriptome profiles of RANKL- or RANKL+LEA-treated BMMswere generated by deep sequencing, in duplicate, using HiSeq 2500.


title: Circular RNAs in nasopharyngeal carcinoma cell lines with different metastasis potential

city: Guangzhou

first: Yingqin

last: Li

address: Room 927, Building 2, No. 651 Road Dong Feng East

institute: Sun Yat-sen University Cancer Center

summary: Increasing evidence has demonstrated a significant role for circular RNAs (circRNAs) in tumorigenesis. However, their functions in nasopharyngeal carcinoma (NPC) metastasis remain largely unknown. In this study, a model compared high and low metastatic NPC cell lines (S18 vs. S26) was constructed to determine the expression profile of circRNAs using the RNA sequencing analysis.

overall_design: Using Illumina HiSeqTM2000, we performed RNA-sequencing analysis of ribosomal RNA-depleted and RNase-R-treated RNA to acquire different expression profiles of circRNAs in a pair of NPC cell lines with different metastatic potential (the high-metastasis S18 cell and the low-metastasis S26 cell).

first: Jun

last: Ma

first: Xiaohong

last: Hong

last: Liu


title: Genome wide anaylsis of transcriptome modifications in male mice exposed to tributyltin during development

city: Houston

first: Cheryl

last: Walker

state: TX

address: 1 Baylor Plaza

department: Center for Precision Environmental Health

institute: Baylor College of Medicine

summary:
Purpose: To identify alterations induced by developmental exposure to tributyltin at different stages of life
Methods: Dams were treated with tributyltin during gestation and lactation in drinking water and pups were euthanized at different ages
Results: We identified a number of changes in transcriptomic activity in 5 month, and ten month old pups after tributyltin exposure. Male animals exposed to tributyltin also developed fatty liver 5 months of age and adenomas of the liver at ten months of age.

overall_design: Liver was isolated from animals exposed to tributyltin during development at 5 months and 10 months. At 10 months of age adenomas were also collected.

first: Cristian

last: Coarfa


title: Human nasopharyngeal carcinoma cells : S18 with high metastasis potential vs. S26 with low metastasis potential

summary: Metastasis is the major reason of treatment failure in nasopharyngeal carcinoma. miRNAs have been identified to regulate tumor metastasis. We aimed to identify metastasis-associated miRNAs  in nasopharyngeal carcinoma.

overall_design: Using Agilent Human miRNA (8*60K) V19.0 Chips, we profiled the miRNA expressions between high-metastatic nasopharyngeal carcinoma cell line S18 and low-metastatic  nasopharyngeal carcinoma cell line S26 to identify metastasis-related miRNAs.


title: The Golgi Glycoprotein MGAT4D is an Intrinsic Protector of Testicular Germ Cells From Mild Heat Stress

city: Bronx

first: Ayodele

last: Akintayo

address: 1300 Morris Park Ave

department: Cell Biology

institute: Albert Einstein College of Medicine

summary:
Male germ cells are sensitive to heat stress and testes must be maintained outside the body for optimal fertility. However, no germ cell intrinsic mechanism that protects from heat has been reported.
Here, we identify the germ cell specific Golgi glycoprotein MGAT4D as a protector of male germ cells from heat stress. Mgat4d is highly expressed in spermatocytes and spermatids.
Unexpectedly, when the Mgat4d gene was inactivated globally or conditionally in spermatogonia, or mis-expressed in spermatogonia, spermatocytes or spermatids, neither spermatogenesis nor fertility were affected. On the other hand, when males were subjected to mild heat stress of the testis (43 °C for 25 min), germ cells with inactivated Mgat4d were markedly more sensitive to the effects of heat stress, and transgenic mice expressing Mgat4d were partially protected from heat stress.
Bioinformatics analyses of microarray data from heat stressed versus control germ cells showed that germ cells lacking Mgat4d generally mounted a similar heat shock response to control germ cells, but could not maintain that response. Several pathways activated by heat stress in wild type were induced to a lesser extent in Mgat4d[−/−] heat-stressed germ cells (NFκB response, TNF and TGFβ signaling, Hif1α and Myc genes). Thus, the Golgi glycoprotein MGAT4D is a novel, intrinsic protector of male germ cells from heat stress.

overall_design: We aimed to obtain insights into gene expression changes in germ cells of Mgat4d[-/-] versus control males after their testes were subjected to mild heat stress. Male mice of two months, on C57BL6/J background, were treated for 25 min at 43ºC or 33°C (no heat stress control) and allowed to recover.  Total germ cells were isolated 8 hr after treatment and cDNA prepared for gene expression analysis using microarrays.

first: Meng

last: Liang

first: Boris

last: Bartholdy

first: Frank

last: Batista

first: Jennifer

last: Aguilan

first: Jillian

last: Prendergast

first: Afsana

last: Sabrin

first: Subha

last: Sundaram

first: Pamela

last: Stanley


title: LncRNA LUCRC regulates colorectal cancer cell proliferation and tumorigenesis by targeting endoplasmic reticulum stress response

city: Xiamen

first: Jiancheng

last: Ding

state: Fujian

address: School of Pharmaceutical Sciences, Xiamen University Xiang`an South Road

institute: Xiamen University

summary: Colorectal cancer (CRC) is the second most common cause of cancer-related death worldwide, and is well known for its strong invasiveness, rapid recurrence and poor prognosis. Long non-coding RNAs (lncRNAs) have been shown to be involved in the development of variety types of cancers, including colorectal cancer. Here, through transcriptomic analysis and functional screening, we reported that lncRNA LUCRC (LncRNA Upregulated in Colorectal Cancer) is highly expressed in colorectal tumor samples and is required for colorectal cancer cell proliferation, migration and invasion in cultured cells and tumorigenesis in xenografts. LUCRC was found to regulate target gene expression of unfolded protein response (UPR) in endoplasmic reticulum (ER), such as BIP. The clinical significance of LUCRC is underscored by the specific presence of LUCRC in blood plasma of patients with colorectal cancers. These findings revealed a critical regulator of colorectal cancer development, which might serve as a therapeutic target in colorectal cancer.

overall_design: RNA-seq was performed to identify target genes of a lncRNA termed LUCRC in colorectal cancer cell HCT116.

first: Wen

first: Jian-Cheng

first: Xue

last: Chen


title: RNA sequencing facilitates quantitative analysis of siRNA circHIPK2 transfected neural stem cells and siRNA circCon transfected neural stem cells transcriptomes

city: Nanjing

first: guangtian

last: wang

address: Dingjiaqiao 87

department: Department of Pharmacology

institute: School of Medicine, Southeast University

summary: We report the application of Illumina paired-end RNA-seq approach for transcriptome of siRNA circHIPK2 transfected neural stem cells and siRNA circCon transfected neural stem cells . By removing sequence-dependent bias and amplification noise using UMI-tools. The mapped reads of each sample were assembled using StringTie. After the final transcriptome was generated, StringTie and edgeR was used to estimate the expression levels of all transcripts. By obtaining a total of million paired-end reads of sequence from neural stem cells , we generated transcriptome profiles of siRNA circHIPK2 transfected neural stem cells and siRNA circCon transfected neural stem cells , respectively. We found 201 differentially expressed genes (DEGs) between siRNA circHIPK2 transfected neural stem cells and siRNA circCon transfected neural stem cells. This study provides a detailed analysis of the underlying mechanisms of stroke，such as neuronal injury and long-term effect, generated by RNA-seq technology.

overall_design: Transcriptome profiles of siRNA circHIPK2 transfected neural stem cells and siRNA circCon transfected neural stem cells, respectively, were generated by paired-end sequencing, in triplicate, using Illumina Novaseq 6000.

first: Honghong

last: Yao

first: Guangtian

last: Wang