title: Gene expression data from MCF7 cells stably expressing COX7RP

city: Hidaka

first: Kazuhiro

last: Ikeda

state: Saitama

address: 1397-1 Yamane

institute: Saitama Medical University

summary: To examine the role of COX7RP in breast cancer cells, MCF7 cells, which were stably transfected with COX7RP (COX7RP-MCF7) or control vector (vector-MCF7), were cultured in normoxic and hypoxic condition. Microarray analysis showed that COX7RP modulates metabolism-associated genes.

overall_design: Total RNA was extracted from COX7RP-MCF7 cells and vector-MCF7 cells, and then used for Affymetrix microarrays analysis.

first: Kuniko

last: Horie-Inoue

first: Satoshi

last: Inoue


title: Pro-BMP9 and sENG monomer:BMP9 complex signalling in human pulmonary arterial endothelial cells after 1.5 hours treatment

status: Public on Sep 23 2019

city: Cambridge

first: Wei

last: Li

address: Hills Road

department: Medicine

country: United Kingdom

institute: University of Cambridge

summary: This experiment was desinged to investigate the difference in global gene expression induced by the circulating form of BMP9, pro-BMP9, and BMP9 in complex with soluble endoglin (sENG:BMP9).

overall_design: Four independent PAECs (i.e. isolated from four different individuals) were purchased from Lonza. Each line was grown up and seeded separately for the treatment by pro-BMP9 and sENG:BMP9, both at 0.4 ng/ml of final growth factor domain concentration. Treatment was carried out for 1.5 hours at 37 C to allow the detection of the genes directly regulated by BMP9 ligand complexes.

first: Zhen

last: Tong

first: Nocholas

middle: W

last: Morrell


title: Developmental plasticity of stem cells in tooth and taste bud renewal

city: atlanta

first: Jeffery

last: Streelman

address: 950 atlantic drive

country: USA

institute: georgia institute of technology

type: Expression profiling by high throughput sequencing

summary: We use the continuously replacing dentition of Lake Malawi cichlid fishes to understand de-novo tooth replacement in adult vertebrates. In this system, each tooth is replaced in a one-for-one fashion every ~50 days. Here, we explore the source of epithelial stem cells for tooth replacement.

sample_organism:
Labeotropheus fuelleborni
Maylandia zebra

overall_design: Transcriptomes of replacement teeth and taste buds were obtained from Labeotropheus feulleborni and Metraclima zebra. Three replicates per species per tissue were collected.

first: Kawther

last: Abdilleh


title: RNA polymerases as moving barriers to condensin loop extrusion

city: Bloomington

first: Xindan

last: Wang

state: IN

address: 1001 E 3rd St

department: Biology

institute: Indiana University at Bloomington

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To separate replicated sister chromatids during mitosis, eukaryotes and prokaryotes have structural maintenance of chromosome (SMC) condensin complexes that were recently shown to organize chromosomes by a process known as DNA loop extrusion. In rapidly dividing bacterial cells, the process of separating sister chromatids occurs concomitantly with ongoing transcription. How transcription interferes with the condensin loop extrusion process is largely unexplored, but recent experiments show that sites of high transcription may directionally affect condensin loop extrusion. We quantitatively investigate different mechanisms of interaction between condensin and elongating RNA polymerases (RNAP) and find that RNAPs are likely steric barriers that can push and interact with condensins. Supported by new Hi-C and ChIP-seq data for cells after transcription inhibition and RNAP degradation, we argue that translocating condensins must bypass transcribing RNAPs within ~2 seconds of an encounter at rRNA genes and within ~10 seconds at protein coding genes. Thus, while individual RNAPs have little effect on the progress of loop extrusion, long, highly transcribed operons can significantly impede the extrusion process. Our data and quantitative models further suggest that bacterial condensin loop extrusion occurs by two independent, uncoupled motor activities; the motors translocate on DNA in opposing directions and function together to enlarge chromosomal loops, each independently bypassing steric barriers in their path. Our study provides a quantitative link between transcription and 3D genome organization and proposes a mechanism of interactions between SMC complexes and elongating transcription machinery relevant from bacteria to higher eukaryotes.

overall_design: Hi-C experiments were performed on wild type and mutant cells of Bacillus subtilis PY79 growing in rich media. ChIP-seq experiments were performed on cells growing in the same condition as in Hi-C experiments.

first: X

first: D

middle: Z

last: Rudner


title: CCL21 Expression in Beta Cells Induces Antigen-Expressing Stromal Cell Networks in the Pancreas and Prevents Autoimmune Diabetes in Mice

city: Miami

first: Anthony

last: Griswold

state: FL

address: 1501 NW 10th Ave, BRB 318

institute: University of Miami

summary: Tumors induce tolerance towards their antigens by producing the chemokine CCL21, leading to the formation of tertiary lymphoid organs (TLOs). Ins2-CCL21 transgenic, non-obese diabetic (NOD) mice express CCL21 in pancreatic β-cells and do not develop autoimmune diabetes. We investigated by which mechanisms CCL21 expression prevented diabetes.  Islet infiltrates of 4 week-old Ins2-CCL21 mice were enriched in naïve CD4+ T cells and compartmentalized within networks of CD45- gp38+ CD31- fibroblastic reticular cell (FRC)-like stromal cells. Importantly, 12 week-old Ins2-CCL21 NOD islets contained FRC-like cells with enhanced expression of β-cell autoantigens and gene expression profiles consistent with regulatory, anti-inflammatory properties and increased contractility. Consistently, transgenic mice harbored fewer autoreactive T cells and higher proportion of Tregs in the islets. Using adoptive transfer and islet transplantation models, we demonstrate that the formation of TLOs in Ins2-CCL21 transgenic islets is critical for regulation of autoimmunity and while the effect is systemic, the induction may be mediated locally by lymphocyte trafficking through TLOs.  Overall, our findings suggest that CCL21 promotes TLOs that differ from inflammatory TLOs associated with islets in T1D in that they resemble lymph nodes, contain FRC-like cells expressing β-cell autoantigens and are able to induce systemic and antigen-specific tolerance leading to diabetes prevention. These findings suggest that CCL21 may be exploited for novel immunoregulation approaches to treat autoimmune diabetes.

overall_design: Examination of lymph node derived Fibroblastic Reticular Cells (FRCs), FRC-like cells from pancreatic islets and islet infiltrating leukocytes in both Ins2-CCL21 transegnic NOD (TG+ samples) and non-transgenic NOD (TG- samples) mice

first: Freddy

last: Gonzalez Badillo

first: Flavia

last: Zisi Tegou

middle: J

first: Alice

last: Tomei


title: High-throughput sequencing Analysis of mouse BMDM cell Transcriptomes

city: HangZhou

first: Di

state: ZheJiang

address: No.866, Yuhangtang Road, Xihu District, Hangzhou

country: China

institute: ZheJiang university

summary:
Purpose: Mouse BMDM is the universal cell type of studying innate immunity.This study was to analyze LPS induced innate immune respone and the relationship between serine synthesis pathway and  LPS induced innate immune respone
Methods: BMDM cells were treated with or without LPS for 6 hours in the pressence of phgdh inhibitor or not. Then mRNA profiles of these samles were generated by High-throughput sequencing analysis, in triplicate, using illumina HiSeqTM 2000. And the differencial mRNA profiles were analyzed.
Results: mRNA profiles about 23002 genes were analyzed, and differencial expression profiles were compared .
Conclusions: Our study represents the first detailed analysis of transcriptomes of mouse BMDM treated with LPS and phgdh inhibitor, with biologic replicates, generated by RNA-seq technology. This data was useful to analyze the relationship between serine synthesis pathway and  LPS induced innate immune respone

overall_design: mRNA profiles of mouse BMDM treated with LPS and phgdh inhibitor were generated by High-throughput sequencing, in triplicate, using HiSeqTM 2000.

first: Weiwei

last: Yu


title: Selective and direct p53 inhibition by iASPP

city: Shanghai

first: Yun

last: Tan

state: Shanghai

address: Room 1109, Building 11, 197 Ruijin Er Rd

department: Shanghai Institute of Hematology

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

summary: We performed p53 ChIP-seq analysis of Nutlin-treated HCT116 cells to identify high-confident p53 regulated targets. And we performed ChIP-seq using an anti-p53 antibody in HCT116 cells treated with control or iASPP RNAi to identify iASPP regulated p53 targets.

overall_design: Identification of genes co-regulated directly by iASPP and p53

first: Shuo

last: Chen

first: Min

last: Lu


title: Analysis of the function of the Arabidopsis DRL1 gene in Botrytis cinerea-induced transcriptome changes

city: Durham

first: Jian-Liang

state: NC

address: 111 TW Alexander Dr

institute: NIEHS

summary: To define how DRL1 regulates Botrytis cinerea-induced transcriptional changes at the genome level, we performed a microarray experiment on B. cinerea-infected drl1 and wild-type plants to identify genes that were differentially expressed between drl1 and the wild type. A total of 200 defense response genes were differentially expressed between drl1 and the wild type at six hours post-inoculation. These genes include 20 ethylene (ET) responsive genes, 23 jasmonic acid (JA)/ET responsive genes, 50 JA responsive genes, and 107 other defense genes. All ET and JA/ET responsive genes and majorities of JA responsive and other defense genes were down-regulated in the drl1 mutant. Among the down-regulated genes are a group of well-characterized defense genes, including ORA59, ERF1, WRKY33, SIB1, PAD3, GLIP1, and CYP79B2, which have been demonstrated to function in resistance to necrotrophic fungal pathogens, indicating that DLR1 may contribute to B. cinerea resistance by modulating the expression of these defense genes.

overall_design: Botrytis cinerea-induced gene expression in drl1 and wild-type leaf tissues was measured at 0, 6, and 48 hours post-inoculation. Three independent experiments were performed at each time point (0, 6, or 48 hours) using different plants for each experiment.

first: Chenggang

first: Xudong

last: Zhang

first: Jian

middle: L

first: Yanping

first: Zhonglin

last: Mou


title: RNA-seq analysis of LSK from Oga(Vav-Cre) mice compared to wildtype

city: Bethesda

first: WeiPing

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

summary: In order to define HSC dysfunction in Oga mutant mice, we examined transcriptional deregulation in LSK cells from Oga(Vav-cre) mice in comparison to wildtype and found 41 downregulated and 12 upregulated genes

overall_design: RNA-Seq of LSK cells from 3 Oga(Vav-cre) female mice and 3 wildtype female mice

first: Lara

middle: K

last: Abramowitz

first: Chritelle

last: Harly

first: Avinash

last: Bhandoola

first: John

middle: A

last: Hanover


title: Rhesus Macaque Acute SIV Infection Study

first: Douglas Scott

last: Merrell

address: 4301 Jones Bridge Road

department: Dept. of Microbiology and Immunology

institute: Uniformed Services University

summary:
Question Addressed: How does Simian immunodeficiency virus (SIV) infection alter gene expression in memory CD4 T cell subsets very early during the 1st 10 days after infection? Memory CD4 T cells were sorted from rhesus macaque peripheral blood samples before infection and then at 4 and 10 days post SIV infection.   RNA was recovered from the sorted memory CD4 T cells samples. RNA from the time point prior to SIV infection from each individual animal was used as the reference for the post SIV infection time points for that same animal.  Thus, for each data set, the 4 and 10 day time points are being directly compared to the pre-infection data from the same animal. RNA samples as indicated above were used for reverse transcription reactions that directly incorporate Cy5 and Cy3 labeled nucleotides into the cDNA.
Time: Time after infection with SIV

overall_design: time series design

first: Joseph

last: Mattapallil


title: Expression data from NOD and B10 CD4 splenocytes

city: Sydney

first: Hugh

middle: John

last: French

state: New South Wales

address: UNSW

country: Australia

institute: UNSW

summary:
Because activation of the immune response is dependent on extensive changes in gene expression, it is likely that a major component of inter-individual variation in the immune response is ultimately mediated at the level of gene regulation. Here, we examine the influence of genetic variation on inducible gene expression in the murine immune response.
We report strain-specific genome-wide differences in mRNA expression between NOD and B10 inbred mice in CD4 splenocytes in basal, stimulated (4hr, PMA/I) states.

overall_design: Splenocytes from NOD and B10 inbred mouse strains were sorted for CD4 using autoMACS for RNA extraction and hybridization on Affymetrix microarrays. We examined the sorted cells at two time points; in the basal state (T0) and four hours after stimulation (T1) with a widely used, analogue of T cell receptor / CD28 co-stimulation signalling, namely phorbol 12-myristate 13-acetate (PMA) and ionomycin.


title: Influence of genetic variation on inducible gene expression in murine CD4+ splenocytes.

summary:
Because activation of the immune response is dependent on extensive changes in gene expression, it is likely that a major component of inter-individual variation in the immune response is ultimately mediated at the level of gene regulation. Here, we examine the influence of genetic variation on inducible gene expression in the murine immune response. We extracted primary CD4 splenocytes from inbred strains A/J, C57BL/6J, BALB/c, DBA/2J, and 129x1/SvJ (3 animals/strain) and measured mRNA transcript levels using microarrays in both basal state and four hours after stimulation with PMA/Ionomycin.
We report strain-specific genome-wide differences in mRNA expression between A/J, Balb/c, C57BL/6J, DBA/2J and 129X1/SvJ inbred mice in CD4 splenocytes in basal, stimulated (4hr, PMA/I) states.

overall_design: Splenocytes from A/J, Balb/c, C57BL/6J, DBA/2J and 129X1/SvJ inbred mouse strains were sorted for CD4 using autoMACS for RNA extraction and hybridization on Affymetrix microarrays. We examined the sorted cells at two time points; in the basal state (T0) and four hours after stimulation (T1) with a widely used, analogue of T cell receptor / CD28 co-stimulation signalling, namely phorbol 12-myristate 13-acetate (PMA) and ionomycin.


title: Expression  profile of lncRNAs in CSCs and non-CSCs of bladder cancer cell line

status: Public on Sep 22 2019

city: Guangzhou

first: Xu

state: Guangdong

address: 107. W. Yanjiang Road

department: Department of Urology

institute: Sun Yat-sen Memorial Hospital

summary: Bladder cancer stem cells (CSCs) contribute to tumorigenesis, recurrence and chemoresistance of bladder cancer. However, the molecular mechanisms underlying their self-renewal are poorly unknown. Long noncoding RNAs (lncRNAs) act as crucial regulators in a lot of human cancers, yet their potential roles and molecular mechanisms in bladder CSCs are poorly understood. The goal of this study is to identify the differentially expressed lncRNAs in bladder CSCs (UM-UC-3 4th spheres), its two differentiation sublines and bladder non-CSCs (UM-UC-3). Our study reveals that deregulation of lncRNAs is involved in the bladder CSCs.

overall_design: We first constructed a gemcitabine resistant bladder cancer cell line termed UM-UC-3 4th by consecutively passaging bladder cancer cells in NOD/SCID mice treated with chemotherapy. Next, we found that UM-UC-3 4th cells had stronger chemoresistant and self-renewal ability than parental UM-UC-3 cells in vitro and in vivo. Furthermore, UM-UC-3 4th formative spheres had contained more ALDH+ cells and increased CSCs marker expression, such as OCT4, SOX2 and NANOG. Therefore we used UM-UC-3 4th spheres as bladder CSCs for further study. Previous study showed that when the spheres were digested into single cells and cultured in 10% FBS medium, the CSCs was gradually differentiation. So we detected differentially expressed lncRNAs in bladder CSCs (UM-UC-3 4th spheres), bladder CSCs differentiation 10 hours, 1 day and bladder non-CSCs (UM-UC-3) by microarray.

first: Tianxin

last: Lin

last: Huang


title: Phosphodiesterase 3A deficient in breast cancer cell

status: Public on Sep 21 2019

city: Tianjin

last: Hao

address: 94, Weijin Road

institute: Nankai University

summary: Analysis of MDA-MB-231 breast tumor cell from knocking-down phosphodiesterase 3A (PDE3A), a cyclic nucleotide phosphodiesterase. Results provide insight into the role of PDE3A in breast tumor progression and metastasis.

overall_design: mRNA profiles of breast cancer MDA-MB-231-shNC and MDA-MB-231-shPDE3A were generated by deep sequencing, in triplicate, using BGISEQ-500.

first: Rong

last: Xiang

first: Yunping

last: Luo


title: RNAseq comparison of Ezh2 heterogygous knockout mesenchymal stromal cells verses wild type in young and aged mice

city: Melbourne

first: Melissa

last: Davis

state: Victoria

address: 1G Royal Parade

department: Bioinformatics Division

institute: Walter and Eliza Hall Institute of Medical Research

summary: Comparison of gene expression pattern profiles of bone derived Ezh2 heterozygous (Het) mesenchymal cells versuss wild type mesenchymal cells isolated from young (3 month old; 3M) and aged (12 month old; 12M) mice.

overall_design: RNAseq Comparisons (3 biological samples per group): Ezh2_WT_3M vs Ezh2_Het_3M; Ezh2_WT_3M vs Ezh2_WT_12M, Ezh2_Het_3M vs Ezh2_Het_12M, Ezh2_WT_12M vs Ezh2_Het_12M.

first: Soroor

last: Hediyeh-zadeh


title: Phenotypic characterisation of regulatory T cells in dogs reveals signature transcripts conserved in humans and mice

city: Philadelphia

first: Ying

last: Wu

state: Pennsylvania

address: 3900 Spruce Street

institute: University of Pennsylvania

summary: Regulatory T cells (Tregs) are a double-edged regulator of the immune system. Aberrations of Tregs correlate with pathogenesis of inflammatory, autoimmune and neoplastic disorders. Phenotypically and functionally distinct subsets of Tregs have been identified in humans and mice on the basis of their extensive portfolios of monoclonal antibodies (mAb) against Treg surface antigens. As an important veterinary species, dogs are increasingly recognised as an excellent model for many human diseases. However, insightful study of canine Tregs has been restrained by the limited availability of mAb. We therefore set out to characterise CD4+CD25high T cells isolated ex vivo from healthy dogs and showed that they possess a regulatory phenotype, function, and transcriptomic signature that resembles those of human and murine Tregs. By launching a cross-species comparison, we unveiled a conserved transcriptomic signature of Tregs and identified that transcript hip1 may have implications in Treg function.

overall_design: Transcriptomic profiles of CD4+CD25high and CD4+CD25- T cells isolated ex vivo from blood of five healthy dogs were generated by RNA-seq, using Illumina HiSeq 4000 System.

first: Oliver

last: Garden


title: Transcriptome-wide analysis of wild-type and SRSF3-knockout glioma stem-like cells

city: Chicago

first: Xiao

last: Song

state: IL

address: 303 E Superior St, Lurie 6-250

department: Neurology

institute: Northwestern University Feinberg School of Medicine

summary:
Purpose: The splicing factor SRSF3 is a member of serine- and arginine-rich proteins, which is frequently upregulated in various types of cancer. The aim of this study is to profile the alternative splicing (AS) events that were regulated by SRSF3 in glioma stem-like cells (GSCs).
Methods: Total RNAs isolated from GSC83 and GSC528 cells with SRSF3-konckout (KO) or control (WT) were subjected to paired-end RNA-seq using the Illumina NextSeq 500 system according to the manufacturer's instruction. Raw reads were subjected to quality control and then aligned with HISAT2 to the human genome hg19. Quantification was performed using HTSeq-count. Differential expression of genes was calculated by DESeq2. For the splicing analysis, the mapped reads were processed through the MISO pipeline to estimate expression of alternatively spliced isoforms. The PSI (Percent Spliced In) values were calculated for each annotated AS event.
Results:  We identified a total of 2752 and 2548 SRSF3-regulated AS events in GSC83 and 528 cells, respectively, with 1143 events shared by these two GSC cell lines.
Conclusions: Our study defines SRSF3 as a master regulator of glioma-associated AS program, implicating SRSF3 as an oncogenic factor for tumorigenesis and a potential therapeutic target for GBM treatment.

overall_design: Transcriptome profiles of GSC83-WT, GSC83-SRSF3-KO, GSC528-WT, and GSC528-SRSF3-KO were generated by next generation sequencing, using Illumina NextSeq 500 system.

first: Chang

last: Zeng

first: Wei

last: Zhang

first: Shi-yuan

last: Cheng


title: Gene expression profile analysis of ASGM1+ and ASGM1- CD8 T cells

city: Taipei

first: ChiChang

last: Sung

state: Taiwan

address: No.1 Ren Ai Rd.

department: Graduate Institute of Immunology

country: Taiwan

institute: College of Medicine, National Taiwan University

summary:
We found that ASGM1-positive CD8 T cells are the predominant intrahepatic ASGM1-positive immune cells in NFIL3 KO mice.
Our goal is using transcriptome analysis to reveal ASGM1-positive CD8 T cells had distinct gene profiles from ASGM1-negative ones.

overall_design: Total RNA extracted from ASGM1+ and ASGM1- CD8 T cells from the liver of naive NFIL3 KO mice were processed by Affymetrix Clariom D genechip.

first: Chi-Chang

first: Ping-Ning

last: Hsu


title: The zinc-responsive repressor Loz1 is the master regulator of zinc homeostasis in Schizosaccharomyces pombe

status: Public on Sep 20 2019

city: Columbus

first: Stevin

last: Wilson

state: Ohio

department: Molecular Genetics

institute: The Ohio State University

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

overall_design: Refer to individual Series


title: The zinc-responsive repressor Loz1 is the master regulator of zinc homeostasis in Schizosaccharomyces pombe [ChIP-seq]

summary: ChIP-seq to determine if the DNA binding activity of Loz1 is dependent upon zinc.

overall_design: Four independent replicates of the examination of Loz1-associated sites in the genome in response to growth in media with or without zinc suplementation.

first: Amanda

last: Bird


title: The zinc-responsive repressor Loz1 is the master regulator of zinc homeostasis in Schizosaccharomyces pombe [RNA-seq]

summary: RNA-seq to identify Loz1-dependent change in transcriptome in response to zinc supplementation.

overall_design: mRNA profiles of wild-type and loz1 deletion mutant S.pombe cells grown in EMM with zinc supplementation

first: Yi-Hsuan

last: Liu


title: Gene expression profiling of Foxr2-induced brain tumors

city: Minato-ku

first: Hideto

last: Koso

state: Tokyo

address: 4-6-1 Shirokanedai

country: Japan

institute: Institute of Medical Science, The University of Tokyo

summary: The goal of this study is profile gene expression patterns of Foxr2-induced brain tumor cells. Foxr2 overexpression in the brain induced tumor formation in the olfactory bulb (OB) and the brainstem (BS) under the p53 deficient background. Tumor cells were cultured in vitro, which resulted in sphere formation. Sphere-forming cells were used for gene expression analysis. Immortalized primary astroglia (AG) was analzyed for comparison.

overall_design: mRNA profiles of astroglia (AG), olfactory bulb (OB) tumor cells and brainstem (BS) tumor cells were generated by deep sequencing, in triplicate, using Illumina HiSeq3000.


title: scRNA-seq of two triple knockout SCLC mouse models for subtyping

city: Nashville

first: Vito

last: Quaranta

state: TN

address: 2220 Pierce Ave

institute: Vanderbilt University

summary: Adopting a systems approach, we devise a general workflow to define actionable subtypes in human cancers. Applied to small cell lung cancer (SCLC), the workflow identifies four subtypes based on global gene expression patterns and ontologies. Three correspond to known subtypes, while the fourth is a previously undescribed neuroendocrine variant (NEv2). Tumor deconvolution with subtype gene signatures shows that all of the subtypes are detectable in varying proportions in human and mouse tumors. To understand how multiple stable subtypes can arise within a tumor, we infer a network of transcription factors and develop BooleaBayes, a minimally-constrained Boolean rule-fitting approach. In silico perturbations of the network identify master regulators and destabilizers of its attractors. Specific to NEv2, BooleaBayes predicts ELF3 and NR0B1 as master regulators of the subtype, and TCF3 as a master destabilizer. Since the four subtypes exhibit differential drug sensitivity, with NEv2 consistently least sensitive, these findings may lead to actionable therapeutic strategies that consider SCLC intratumoral heterogeneity. Our systems-level approach should generalize to other cancer types.

overall_design: 2 samples analyzed from 2 different triple knockout mouse models

first: Julien

last: Sage


title: Ex-vivo transcriptional analysis of splenic autophagy deficient dendritic cell subsets in an atherogenesis mouse model

city: Cambridge

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

institute: University of Cambridge

summary: Analysis of the transcriptional signature of FACS-purified splenic DC subsets from Ldlr deficient mice transplanted with control or Cd11c-cre Atg16l1flox/flox bone marrow and subjected to an atherogenic diet for 8 weeks

overall_design: Examination of 2 different cell subsets from 2 different strains of mice

first: Marc

last: Clement

first: Ziad

last: Mallat

first: Dimitrios

last: Tsiantoulas

first: Marcella

last: Ma


title: Preweaning nutrient supply alters mammary gland transcriptome expression relating to morphology, lipid accumulation, DNA synthesis and RNA expression in Holstein heifer calves.

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

summary: The objective of this study was to analyze the mammary gland transcriptome to determine how preweaning nutrient supply alters the molecular mechanisms that regulate preweaning mammary development. Holstein heifers were fed via milk replacer either an elevated level of nutrient intake (ELE; on average, 5.9 ± 0.2 Mcal ME in 8.4 L of milk replacer (MR)/d, n = 6) or a restricted amount of nutrients (RES; 2.8 ± 0.2 Mcal ME in 4L MR/day, n = 5) for 54 d postnatal, at which point they were slaughtered and samples of mammary parenchyma tissue were obtained. Parenchymal mRNA was analyzed and the fold changes (FC) of 18,111 genes (ELE relative to RES) were uploaded to Ingenuity Pathway Analysis (IPA) software for transcriptomic analysis. Using a threshold of P < 0.05, IPA identified that the FC of 1,931 of 18,811 differentially expressed genes (DEG) could be utilized for the analysis. A total 18 molecular and cellular functions were relevant (P < 0.05) to DE genes arising from the treatments, with Cell Death and Survival, Cellular Movement, Cellular Development, Cellular Growth and Proliferation, and Lipid Metabolism being the 5 most associated functions with DEG. Based on the directional FC of DEG, the mammary gland of ELE heifers was predicted to have increased Epithelial-Mesenchymal Transition (Z = 2.685) and Accumulation of Lipid (Z = 2.322), while the Synthesis of DNA (Z = -2.137), Transactivation of RNA (Z = -2.254), Expression of RNA (Z = -2.405), Transcription (Z = -2.482) and Transactivation (Z = -2.611) were all predicted to be decreased. Additionally, IPA predicted the activation status of 13 upstream regulators with direct influence on DEG as affected by ELE feeding that were either ligand-dependent nuclear receptors (n = 2), enzyme (n = 1), or transcription regulators (n = 10). Of these, 6 were activated (Z > 2) and 7 were inhibited (Z < -2). In summary, feeding ELE preweaning altered the mammary transcriptome of Holstein heifers affecting cell functions involved in the morphological and physiological development of the mammary gland.

overall_design: Holstein heifer calves were subjected to restricted or elevated nutrient supply through milk replacer during the preweaning phase. From day 18 onwards, calves were also offered a commercially available concentrate. At day 54 calves were killed, whereafter mammary gland tissue was subjected to gene expression profiling.

first: Koryn

middle: S

last: Hare

first: Leonel

middle: N

last: Leal

first: Josue

middle: M

last: Romao

first: Fernando

last: Soberon

first: Harma

last: Berends

first: Michael

middle: E

last: Van Amburgh

first: Javier

last: Martín-Tereso

last: Steele


title: Ultrasound-mediated ultra effective cellular reprogramming of human fibroblasts into neural progenitor-like cells [RNA-Seq]

city: Incheon Metropolitan City

first: Yong Seung

last: Lee

address: SimGokro 100gil 25

department: College of Medicine

country: South Korea

institute: Catholic Kwandong University

summary: We have developed an ultra effective method of triggering fast cellular reprogramming into neural progenitor cells (NPCs) with significant yields, called ultrasound-directed permeation of environmental transition-guided cellular reprogramming (Entr).

overall_design:
Three different culture time (1 day, 5 days (p1) and 30 days (p5)) of sample after ultrasound stimulus. Control and reference cells were used each HDF and hNSC

The HDF sample (GSM2308274) is identical to GSM2308280.

first: Yong

first: Hyejung

last: Heo

last: Park

first: Woon

middle: Y

last: Jung

first: Min

middle: G

first: Seung-Hun

last: Oh

first: Soonhag

last: Kim


title: Ultrasound-mediated ultra effective cellular reprogramming of human fibroblasts into neural progenitor-like cells [MBD-Seq]

type: Methylation profiling by high throughput sequencing

overall_design: DNA mehtylation profiles of 1-day-old HDF cells in NSC culture medium after ultrasound stimulus. Control and reference cells were used each HDF and hNSC

first: Yong-Seung

first: Yong-Keun

first: Woon-Yong

first: Min-Geun


title: Hepatic transcriptome profiling of liver-specific Elovl6 knockout mice fed a high-sucrose diet

city: Tsukuba

first: Takashi

last: Matsuzaka

state: Ibaraki

address: 1-1-1 Tennodai

department: Internal Medicine

institute: University of Tsukuba

summary: Elovl6 is a member of mammalian fatty acid elongase that is responsible for converting C16 saturated and monounsaturated fatty acids into C18 species. To understand the role of Elovl6 in liver, we generated liver-specific Elovl6 knockout mice (Albumin-Cre;Elovl6 fl/fl C57BL/6J). The goal of this experiment was to determine effects of hepatocyte Elovl6 deficiency on the murine liver transcriptome under lipogenic condition.

overall_design: Liver-specific Elovl6 knockout (LKO) and control mice (n=3 per group) were fed high-sucrose diet (D11725, Research Diets) for 14 days, fasted for 4 hr, then sacrificed. Livers were removed and flash frozen in liquid nitrogen. RNA was extracted and hybridized to Agilent SurePrint G3 Mouse Gene Expression 8x60K Microarrays.

first: Hitoshi

last: Shimano


title: Gene expression profiling in Acute Myeloid Leukemia (AML)

city: Cantanhede

first: Jacek

middle: Dariusz

last: Marzec

address: Biocant Park

country: Portugal

institute: CoLAB AccelBio

summary: The aim was to analyze the expression of genes in cytogenetically distinct cases of AML.

overall_design: We used total RNA obtained from 97 AML samples, consisting of 6 cytogenetically distinct subtypes,  to establish expression level of 27,868 individual human genes. Expression data from ABI Human Genome Survey Microarray were filtered, quantile-normalized and subjected to significance analysis of microarrays. We wanted to identify clusters of genes differentially expressed among AML subtypes.

first: Jun

last: Wang

first: Marwa

last: Saied

first: Bryan

middle: D

last: Young

first: Silvana

last: Debernardi


title: Enriched EWSR1 and EWS-FLI1 RNA-seq of HNRNPH1-silenced TC32 Ewing sarcoma and 293T human embryonic kidney cells.

first: Thomas

middle: Joshua

last: Meyer

state: Maryland

address: 41 Center Drive, Building 41, Room B620

department: National Cancer Institute

institute: National Institutes of Health

summary: Identification of EWSR1 and EWS-FLI1 transcript variants associated with the silencing of HNRNPH1 in TC32 Ewing sarcoma and 293T human embryonic kidney (HEK-293T) cells.

overall_design: TC32 Ewing sarcoma and HEK-293T cells were transfected with control siNeg or siHNRNPH1. RNA was harvested after 48 hours. Three samples in each group were analyzed.

first: Carla

last: Neckles

first: Robert

last: Walker

first: Suntae

first: Bong-Hyun

first: Natasha

last: Caplen


title: High-Throughput Single-Molecule R-loop Footprinting Reveals Principles of R-loop Formation

city: Davis

first: Frederic

last: Chedin

state: CA

address: 1 Shields Avenue

department: MCB

institute: UC Davis

summary: We have successfully characterized R-loop structures using non-denaturing bisulfite treatment coupled with single-molecule sequencing to reveal that R-loops form defined overlapping molecular clusters around promoter, gene body, and terminal regions of genes. Our results uncovers that R-loop formation is both driven by favorable DNA sequence as well as topological state.

sample_organism:
Escherichia coli
Homo sapiens

platform_organism:
Escherichia coli
Homo sapiens

overall_design: Characterization of R-loop formation of targeted human genes using single-molecule R-loop footprinting couple with Pacific Bioscience's long-read sequencing (SMRF-seq)

first: Maika

last: Malig

first: Stella

middle: R

last: Hartono

first: Jenna

last: Giafaglione

first: Lionel

last: Sanz

first: Frédéric

last: Chédin


title: Ultrasound-mediated ultra effective cellular reprogramming of human fibroblasts into neural progenitor-like cells

first: Yong Seung

last: Lee


title: Evolution of a Reverse Transcriptase to Map N1-Methyladenosine in Human mRNA

status: Public on Sep 24 2019

first: Huiqing

last: Zhou

state: Illinois

address: LOADING DOCK BEHIND 5741 S DREXEL AVE  929 E 57TH ST

institute: University of chicago

summary: Chemical modifications on mRNA are increasingly recognized as a critical regulatory layer of the flow of genetic information, but quantitative tools to monitor RNA modifications in a whole-transcriptome and site-specific manner are lacking. Here we describe a versatile directed evolution platform that rapidly selects for reverse transcriptases that install mutations during reverse transcription at sites of a given type of RNA modification, allowing for site-specific identification of the modification. To develop and validate the platform, we evolved the HIV-1 reverse transcriptase against N1-methyladenosine (m1A). Iterative rounds of selection yielded reverse transcriptases with both robust read-through and high mutation rates at m1A sites. We apply the evolved reverse transcriptase to identify thousands of statistically confident m1A sites in human mRNA, some of which can be detected in antibody-free RNA-seq libraries. Together, this work develops and validates the reverse transcriptase evolution platform and provides new tools, analysis methods, and datasets to study m1A biology.

overall_design: m1A-IP-seq and m1A-quant-seq experiments were performed on mRNA extracted from HEK-293T cells with three biological replicates.

middle: C

last: Dickinson

first: Chuan

last: He


title: RNA sequencing and small RNA sequencing in WT and mir-138 DKO CAD cell lines

status: Public on Sep 19 2019

first: Jennifer

last: Cherone

state: Ma

address: 400 Main Street, 68-259

institute: Massachusetts Institute of Technology

type: Non-coding RNA profiling by high throughput sequencing

summary: MicroRNAs (miRNAs) play roles in diverse developmental and disease processes. Distinct miRNAs have hundreds to thousands of conserved mRNA binding sites, but typically direct only modest repression via single sites. Cotargeting of individual mRNAs by different miRNAs could potentially achieve stronger and more complex patterns of repression. Comparing target sets of different miRNAs, we identified hundreds of pairs of miRNAs that share more mRNA targets than expected (often by two-fold or more) relative to stringent controls, with particularly high levels of cotargeting among brain-enriched miRNAs. We profiled miRNA expression changes over a cell culture model of neuronal differentiation, and selected the non-homologous cotargeting miRNA pair miR-138 and miR-137 to study functionally. We generated a CRISPR-mediated mir-138 double knockout (DKO) cell line in the murine CAD cell culture model of neuronal differentiation. mir-138 DKO cells lacking both mir-138 loci were unable to differentiate and project neurites following serum withdrawal. Further characterization of the DKO cells by RNA-seq showed that loss of miR-138 resulted in a de-differentiated state compared to WT cells. Specificity of the mir-138 DKO was confirmed by the rescue of neurite growth upon addition of a miR-138 mimic. Interestingly, addition of a miR-137 mimic, but not mimics of other neuronal miRNAs, could also rescue the neurite growth phenotype and allow mir-138 DKO cells to differentiate, and transcriptome profiling revealed similar gene expression changes. Clustering of all cotargeting pairs revealed a group of 9 predominantly brain-enriched miRNAs that share many targets. In reporter assays, subsets of these miRNAs together repressed gene expression by 5- to 10-fold, often exhibiting cooperative repression. Together, our results uncover an unexpected pattern in which combinations of miRNAs collaborate to robustly repress cotargets, and suggest important developmental roles for cotargeting.

overall_design: Small RNA-seq from CAD cells in serum and 4 days post serum withdrawal in triplicate sequenced on an Illumina HighSeq Sequencer in triplicate. RNA-seq of WT and mir-138 DKO CAD cells across serum withdawal-induced neuronal differentiation (0 and 1 day sequenced in duplicate) and (0 and 4 days from WT sequenced in triplicate) , and additional RNA-seq from mir-138 DKO CAD cells transfected with miR-138 or miR-137 mimics or a pUC19 DNA control in triplicate (2 days after transfection and 4 days after transfection) sequenced on an Illumina NextSeq sequencer.

first: Christopher

middle: B

last: Burge


title: Identification of Klf9-regulated genes in HT22 tissue culture cells

city: Palo Alto

first: Joseph

middle: Riley

last: Knoedler

address: 1201 Welch Road

department: Psychiatry and Behavioral Sciences

institute: Stanford Univesity


title: miRNA expression of exosomes from Treponema pallidum-stimulated macrophages

city: nanjing

first: Wenlong

last: Hu

address: Jiangwangmiao Street

department: Institute of Dermatology

institute: Chinese Academy of Medical Science & Peking Union Medical College

summary: We performed a comprehensive miRNA profiling analysis of exosomes by Treponema pallidum-stimulated microarrays. A total of 2×106 macrophages were obtained by THP-1 differentiation and grown in RPMI-1640 containing 10% exosome-free FBS. Exosomes were acquired from macrophage culture supernatants with (n = 7) or without (n = 3) T. pallidum. Briefly, macrophages were washed in PBS twice and further grown in fresh medium for 12 h (n = 2), 24 h (n = 2) and 48 h (n = 3) to collect exosomes. Exosomal miRNA microarray assays were carried out with Agilent Human miRNA (8*60K) array.

overall_design: A total of 2×106 macrophages were obtained by THP-1 differentiation and grown in RPMI-1640 containing 10% exosome-free FBS. Exosomes were acquired from macrophage culture supernatants with (n = 7) or without (n = 3) T. pallidum. Briefly, macrophages were washed in PBS twice and further grown in fresh medium for 12 h (n = 2), 24 h (n = 2) and 48 h (n = 3) to collect exosomes, and exosomal miRNA microarray assays were carried out.

first: Wen-long

first: Bu-Fang

last: Xu

first: Qian-Qiu

last: Wang


title: Differential messenger RNA expression in Granulosa Cells from polycystic ovary syndrome with Normoandrogen and Hyperandrogen: Identification of gene sets through bioinformatic Filtering analysis

city: Shenyang

first: Wensu

last: Liu

state: Liaoning

address: 77 Puhe Road, Shenyang North New Area

institute: China Medical University

summary: PCOS is a widespread disease that primarily caused in-pregnancy in pregnant-age women. Normoandrogen (NA) and Hyperandrogen (HA) PCOS are distinguished under distinct level of testosterone, while markers and expression patterns for both subtypes were not adequately studied. Text-mining analysis stated the correlation for PCOS with granusola cells and thus we performed microarray analysis on granusola cells from HA PCOS, NA PCOS and normal tissue from individuals, and afterwards downloaded RNA-seq and microarray data from NCBI GEO database on granusola cells from PCOS and normal ovary. Applying our newly developed method using Monte Carlo algorithm and text mining method on combined data, we identified several potential markers for HA and NA PCOS. RT-PCR and Western blotting results validated the expression pattern of these markers for HA and NA PCOS as bioinformatical prediction. Further gene ontology (GO) and text-mining analysis discovered that (1) NA PCOS was highly correlated with estrogen-driven tumors including ovarian, breast and endometrial cancer as compared with normal granusola cells. NA PCOS specific genes IL6R and CD274 were bioinformatically predicted and experimentally validated and thus might be the key factor behind the mechanism responsible for the tumor-like pattern for NA PCOS; (2) HA PCOS showed high correlation with keratinization, epidermis development, GTPase activity, glomerular basement membrane development and apoptosis corresponding to the fact HA PCOS patients express characteristic of hirsutism, diabetes and obesity. Meanwhile HA PCOS was sustantially lowerly related with estrogen-driven tumors as compared with normal granusola cells.

overall_design: A total of 18 subjects were enrolled and 12 of the subjects were divided into three groups (control, NA PCOS and HA PCOS) with 4 subjects in each group. Recruitment took place from December 2015 to January 2016.

first: Zeyu

last: Yang

first: Tianyu

last: Tang

first: Chunyu

first: Lin

last: Lin

first: Tao

last: Wen

first: Shengli

first: Ge

last: Sun

first: Kai

last: Zeng

first: Renlong

last: Zou

first: Xiuxia

first: Yue

last: Zhao


title: Expression profiling of murine rhabdoid tumor model

city: PARIS

first: Joshua

last: Waterfall

state: Please select:

address: 26 rue d'Ulm

department: Department of Translational Research and Inserm U830

country: France

institute: Institut Curie

summary: To characterize tumors developing in our SMARCB1 deficient mouse model, we performed mRNA sequencing of tumors and control normal tissues

overall_design: Bulk mRNAseq was done on 14 separate tumors and 3 biological replicates of healthy mouse brain

middle: J

first: Franck

last: Bourdeaut

first: Amaury

last: Leruste


title: Androgen Receptor is a Backdoor Inhibitor of Wildtype and Mutant Estrogen Receptors in Refractory Hormone Receptor-Positive Breast Cancers

city: Boston

first: Xintao

last: Qiu

state: MA

address: 440 brookline ave

institute: Dana Faber Cancer Institute

summary: Ligand-activated AR inhibits wildtype and mutant-refractory ER activity in PDXs by reprogramming the ER and FOXA1 cistrome and rendering tumor-growth inhibition. These findings suggest that ligand-activated AR may function as a backdoor inhibitor of ER and that AR agonists may offer a safe and effective treatment for ER-positive breast cancer.

overall_design: Tumor xenograft PDX models: AR, ER, and FOXA1 ChIP-Seq

first: Ramesh

last: Narayanan

first: Henry

middle: W

last: Long


title: Identification of Klf9 genomic binding sites in HT22 tissue culture cells [ChIP-Seq]

first: Joseph

last: Knoedler

summary: Krueppel-like factor 9 (Klf9) is a DNA-binding transcription factor that has been implicated in neuronal development and regeneration, but none of its genomic targets are known in neurons. We used the mouse hippocampus-derived cell line HT22 to identify Klf9’s genomic binding sites in neurons. We stably transfected HT22 cells with the biotin ligase BirA with or without co-transfection of a Klf9 fusion protein with an n-terminal FLAG tag and a biotin ligase recognition peptide. This allowed us to precipitate Klf9 in chromatin using streptavidin. This permits the use of more stringent wash conditions, improving signal-to-noise ratio. We conducted high-throughput sequencing on DNA precipitated from these lines and identified 3,378 regions where Klf9 associated in chromatin. We found that Klf9 associated near transcription start sites and that its genomic targets were enriched for genes related to cytoskeletal regulation and apoptosis.

overall_design: We used chromatin-streptavidin precipitation to identify Klf9 genomic targets in mouse hippocampal neurons.

first: Robert

last: Denver


title: Identification of Klf9-regulated genes in HT22 tissue culture cells [RNA-Seq]

summary: Krueppel-like factor 9 (Klf9) is a DNA-binding transcription factor that has been implicated in neuronal development and regeneration. We used mouse hippocampus-derived HT22 cell line to identify genes differentially regulated by forced Klf9 expression. We stably transfected HT22 cells with pCDNA6:TR (encoding the Tet repressor) and pCDNA6:TO-Klf9 (encoding Klf9 downstream of the Tet operator), allowing doxycycline(dox)-inducible expression of Klf9. We chose a stably transfected clone with baseline Klf9 mRNA level similar to that of untransfected HT22 cells (parent line) and approximately 10-fold induction after dox treatment. We conducted RNA-seq on stably transfected HT22 cells treated with or without dox for 8 hours; we also conducted RNA-seq on parent cells subjected to the same dox treatment to separate nonspecific effects of dox from the effects of forced Klf9 expression. Analysis of RNA-seq data found 217 gene repressed and 21 upregulated by forced Klf9 expression (FDR-adjusted p<.005; because fold changes were small we used a stringent p value cutoff to ensure that we were studying genes likely to be bona fide targets), showing that Klf9 functions primarily as a transcriptional repressor. Gene ontology analysis showed that Klf9-repressed genes were enriched in cytoskeletal and Wnt signaling-related genes.

overall_design: We used doxycycline-inducible cells to identify Klf9-regulated genes in mouse neuronal tissue culture cells.


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and FGR Transcriptomes

city: Shanghai

first: Li

last: Ma

email: mary_wyyx@126.com, mary_wyyx@163.com

address: Siping road

institute: Tongji University

summary: Our study represents the detailed analysis of midbrain transcriptomes generated by RNA-seq technology. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of midbrain mRNA profiles of 3-day-old wild-type (WT) and FGR mice.

overall_design: brain mRNA profiles of 3-day old wild type (WT) and FGR mice were generated by deep sequencing.

first: Mengxue

last: Tian


title: MiR-145-5p is Down-Regulated in Human Extrahepatic Cholangiocarcinoma and Regulates SRGAP2 and Rac1

status: Public on Sep 18 2019

city: Seoul

first: HONG JOO

last: KIM

address: 29, Saemunan-Ro, Jongno-Gu

institute: Kangbuk Samsung Hospital

summary: The overall objective of this study was to explore aberrantly expressed microRNAs (miRNAs) and investigate their clinical significances in patients with extrahepatic cholangiocarcinoma (ECCA).

overall_design: Eighty-two patients who underwent curative resection for histologically confirmed ECCA at our institution from October 2004 to November 2015 were enrolled. miRNA expression microarrays for SNU-1196 and SNU-245 ECCA cell lines and normal human biliary epithelial cells (NHBEC) were performed. Real time quantitative polymerase chain reactions (RT-qPCR) for each cell lines and surgically resected ECCA tissue microarrays were also conducted.

first: Nam

middle: H

last: Kim

first: Hong

first: Dong

first: Seoung

last: Chae

first: Jin

last: Sohn


title: Argopecten irradians, gills, exposed to Thiazolidinedione derivatives 49

first: Cheng

last: Chi

address: weigang road

institute: Nanjing Agricultural University

summary: Differential expression analysis of gill tissues of bay scallop (Argopecten irradians) exposed to Thiazolidinedione derivatives 49 at a concentration of 0.64 μM for 48 h.

overall_design: Each sample consists in total RNA was extracted from pooled tissues of 18 individuals.

first: Chi

last: Cheng


title: Next-gen sequencing for transcriptomic differences in livers of mice with acetaminophen toxicity

city: Bronx

first: Sanjeev

last: Gupta

state: NY

address: 1300 Morris Park Ave.

department: Medicine

institute: Albert Einstein College of Medicine

summary:
The goal of the study is to compare transcriptome profile of mouse liver with acetaminophen toxicity to potentially therapeutic healthy blood serum exosome or cytokine treatments along with acetaminophen
Studies also included sequencing of miRNA from exosomes isolated  from pooled serum of several healthy anonimous human donors and livers of mice that received the exosome treatment along with acetominophen.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Exosomal and tissue small RNAs and tissue total RNA from healthy and injuried states were used to perfom high throughput sequensing by Ion Torrent Proton instrument

first: Yogeshwar

last: Sharma

first: Tatyana

last: Tchaikovskaya

first: Fadi

middle: L

last: Jaber

first: Preeti

last: Viswanathan

first: Charles

last: Rogler

first: Alexander

last: Maslov

first: Wilber

last: Quispe-Tintaya


title: Indoxyl sulfate stimulates angiogenesis by regulating reactive oxygen species production via CYP1B1

city: Utrecht

first: Caroline

state: Nederland

address: Heidelberglaan 100

department: Nephrology and Hypertension

institute: Universitair Medisch Centrum Utrecht

summary:
Introduction: Indoxyl sulfate (IS) is an accumulated protein-bound uremic toxin found in patients with kidney disease. Although it is known that IS impairs the vascular endothelium, the precise underlying mechanism remains unclear.
Methods: We performed RNA sequencing in human umbilical vein endothelial cells (HUVECs) that were treated with either IS or control medium. Gene enrichment analyses were performed based on differentially expressed genes. We further examined the main enriched biological processes at the functional level.
Results: We identified 1,293 genes that were affected in IS-treated HUVECs when compared to control and gene enrichment analysis indicated altered vascular formation and cell metabolism. We observed decreased viability and increased cell senescence due to IS treatment at the functional level. Furthermore, we demonstrated that IS exposure of HUVECs promoted angiogenesis as shown by the increase in total tubule length in a 3D HUVECs/pericytes co-culture assay. We also observed an increase in ROS production in IS-treated endothelial cells. Notably, the pro-angiogenic response of IS and the increased ROS production were abolished when CYP1B1, one of the main target genes that was upregulated by IS, was silenced.
Conclusion: IS promotes angiogenesis and CYP1B1 is an important factor in IS-activated angiogenic response.

overall_design: The transcriptiome profile of HUVECs cultured in IS or control medium, in triplet, were obtained using RNA sequencing on the Nextseq500 system (Illumina).


title: Genome-wide expression analysis of murine sciatic nerve of young and old mice

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

country: Germany

institute: Leibniz Institute on Aging - FLI

summary: The regenerative capacity of peripheral nerves declines during aging, contributing to the development of neuropathies, limiting organism function. Changes in Schwann cells prompt failures in instructing maintenance and regeneration of aging nerves; altered inflammatory environment leading to a defective Schwann cell response, as an underlying mechanism of impaired nerve regeneration during aging. Chronic inflammation was detected in intact uninjured old nerves, characterized by increased macrophage infiltration and raised levels of monocyte chemoattractant protein 1 (MCP1) and CC chemokine ligand 11 (CCL11). Schwann cells in the old nerves appeared partially dedifferentiated, accompanied by an activated repair program independent of injury. Upon sciatic nerve injury, an initial delayed immune response was followed by a persistent hyperinflammatory state accompanied by a diminished repair process. As a contributing factor to nerve aging, we showed that CCL11 interfered with Schwann cell differentiation in vitro and in vivo. Our results indicate that increased infiltration of macrophages and inflammatory signals diminish regenerative capacity of aging nerves by altering Schwann cell behavior. The study identifies CCL11 as a promising target for anti‐inflammatory therapies aiming to improve nerve regeneration in old age.

overall_design: In total, 12 samples of sciatic nerve tissue were analyzed of which 6 are from young mice and 6 are from old mice

first: Robert

last: Buettner

first: Thomas

last: Mindos

first: Philipp

last: Koch


title: Biochemical analysis of chromatin targeting by Tn5 transposase

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

institute: Medical Institute of Bioregulation

summary: Tn5 transposase is used as a tool for detecting nucleosome-free regions of genomic DNA in eukaryotes, but its DNA target site in chromatin has not been understood. In the present study, the well-positioned dinucleosomes were reconstituted, and the Tn5 transposase target sites were mapped in the dinucleosomes in vitro. We found that Tn5 transposase preferentially targets near the entry-exit DNA region within the nucleosome, if the linker DNA exists between two nucleosomes. This specific DNA targeting by Tn5 did not depend on the linker DNA length and DNA sequence. Tn5 transposase becomes to target the middle of the linker DNA, in addition to the entry-exit site of the nucleosome, if the linker DNA length extends to 30 base pairs. These in vitro data provide direct evidence for the Tn5 target sites in the nucleosome, resulting important information for interpretation of the Tn5-transposase-based genomics methods, which have been interpreted as linker or nucleosome-free DNA regions in genomes.

overall_design: To understand the Tn5 transposase target site in nucleosomal DNA, four dinucleosomes with different linker DNA lengths and DNA sequences were reconstituted as substrates, and the Tn5 transposase reactions were performed in vitro.

first: Shoko

last: Sato

first: Yasuhiro

last: Arimura

first: Tomoya

last: Kujirai

first: Akihito

last: Harada

first: Kazumitsu

last: Maehara

first: Jumpei

last: Nogami

first: Hitoshi

last: Kurumizaka


title: Effect of Lithum on adult white matter

city: Padova

first: Andrea

middle: Domenico

last: Rivera

address: Via Gabelli 67

department: Neuroscience

country: Italy

institute: University of Padova

summary:
Analysis of adult murine optic nerves cultured for 3 days in vitro (DIV) ex-vivo in organotypic media containing saline or Lithium Chloride.
Results provide insight on the mechanism of action of Lithium on glial cells.

overall_design: Optic nerves from 6 C57BL/6 between P35-45 per group were cultured in organotypic media containing saline or Lithium Chloride (20mM) for 3DIV.  Total RNA was extracted and subsequent subjected to microarray analysis using Affymetrix Mouse GeneChip 430 2.0 according to manufacturer conditions

first: A

last: Butt


title: miR-1,miR-122,miR-124 overexpression in 293T cells

city: Nanjing

first: Yan

last: Zeng

address: No.1, Weigang

summary: To identify miR-1, miR-122 and miR-124 target genes in 293T cells using RNA-seq.

overall_design: Total RNA was isolated from control, miR-1, miR-122 or miR-124 overexpressing 293T cells after 48h of transfection and RNA-seq analysis was performed.


title: A high protein model alters the endometrial transcriptome of mares

city: Lexington

first: Barry

middle: A.

last: Ball

state: Kentucky

address: 108 Gluck Equine Research Center,

department: Veterinary Scinece

institute: University of Kentucky

summary: We developed an experimental model to elevate BUN during diestrus. There were both urea and control treatments (7 mares/treatment), done in a crossover design. Urea treatment consisted of a loading dose of urea (0.03 g/kg of urea) and urea injections over 6 hours (0.03 g/kg/hr). Control mares received the same volume of saline solution. Blood samples were collected to measure BUN. Uterine and vaginal pH were evaluated after the last intravenous infusion, then endometrial biopsies were collected for RNA-sequencing

overall_design: A uterine biopsy was collected from the base of the uterine horn six hours after the start of the treatment (n= 7 per treatment). Total cellular RNA was extracted from endometrial samples using TRIzol Reagent (Thermo Fisher Scientific) following the manufacturer’s recommendations. A total of 1 μg of RNA was treated with DNase I (Ambion Inc., Austin, TX) for 30 minutes at 37℃ to remove genomic DNA according to manufacturer’s instructions. Paired-end reads with 150 nucleotides in length were produced. The RNAseq libraries were prepared with Illumina's TruSeq Stranded mRNAseq Sample Prep kit (Illumina, San Diego, CA). Read 1 aligns to the antisense strand and Read 2 aligns to the sense strand. The libraries were quantitated by qPCR and sequenced on one lane for 101 cycles from each end of the fragments on a HiSeq 4000 using a HiSeq 4000 sequencing kit version 1.  The lane produced a total of 700 million reads. Fastq files were generated and demultiplexed with the bcl2fastq v2.17.1.14 Conversion Software (Illumina). The Fastq files were evaluated for read quality using FastQC 0.11.4. Subsequently, Trim Galore 0.4.1 was used for adapter and read quality trimming (Phred score threshold of 30). Reads were mapped to the Equus caballus reference genome (EquCab 3.0) using the software STAR 2.5.3a, then annotated with the equine reference annotation from NCBI using Cufflinks 2.2.1. Fragments per kilobase per million (FPKM) were used to determine the expression level of genes. Lastly, we used Cuffdiff 2.2.1 to calculate differentially expressed genes (DEG) between samples from the control and urea groups. Significance level was set at FDR-adjusted p-value of the test statistic < 0.1 using a Benjamini-Hochberg correction.

first: Yatta

last: Boakari

first: Hossam

last: El-Sheikh Ali

first: Pouya

last: Dini

first: Shavahn

last: Loux

first: Claudia

last: Faernandes

first: Kirsten

last: Scoggin

first: Alejandro

last: Esteller-Vico

first: Laurie

last: Lawrence


title: Impact of urine from cranberry-treated volunteers on global gene expression of uropathogenic Escherichia coli

status: Public on Sep 17 2019

city: Muenster

first: Ulrich

last: Dobrindt

state: NRW

address: Mendelstrasse 7

department: Institute of Hygiene

institute: University of Münster

summary: Growth in urine of cranberry extract-treated volunteers did not markedly affect the transcirptome of UPEC strain UTI89. Expression of bacterial adhesin determinants (P fimbriae, S fimbrae, curli) was not markedly changed upon growth in the urine samples, while a slight, but non-significant upregulation of type 1 fimbriae was observed.

overall_design: Examination of the transcriptome of uropathogenic E. coli after 2 h incubation in urine of cranberry extract-treated human volunteers (one replicate) in comparison to 2 h incubation in urine of the same volunteers before cranberry treatment (one replicate).

first: Birte

last: Scharf

first: Christoph

last: Stork

first: Andreas

last: Hensel


title: RNA sequencing of wildtype-KRAS HKE3 (wtHKE3) and mutant-KRAS HKE3 (mtHKE3) colorectal cancer cell lines before and after stimulation with TGF-alpha

city: Adelaide

first: Sriganesh

last: Srihari

state: SA

address: North Terrace

department: Infection and Immunity

institute: South Australian Health and Medical Research Institute

summary: RNA sequencing was performed on wtHKE3 and mtHKE3 colorectal cancer cell lines (obtained from Shirasawa [1]) before stimulation (timepoint 0) and at 15, 30, 60, 90 and 120 mins post-stimulation with transforming growth factor alpha (TGF-α) (0.01 µg/mL, Abcam). Three replicates were sequenced at each timepoint. [1] Tsunoda, Ishikura, Doi et al., Anticancer Res 2015, 35(8):4453-4459.

overall_design: RNAseq profiles from wtHKE3 and mtHKE3 cells before and after stimulation with TGF-alpha. In total, 36 cDNA libraries (2 cell lines X 6 time-points X 3 replicates per timepoint) were generated for sequencing.

first: Theodosia

last: Charitou

first: David

last: Lynn


title: Non-CYP2D6 variants selected by GWAS improved the prediction of impaired tamoxifen metabolism in breast cancer patients

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

country: Poland

institute: Uniwersytet Warszawski

summary:
Background: Current reports suggest that a certain minimum plasma concentration of (Z)-endoxifen is required for breast cancer patient to benefit from tamoxifen therapy. A reliable prediction of which patients are at risk for insufficient exposure to (Z)-endoxifen would be relevant for optimizing treatment, e.g. by adjusting the dose, from the very beginning. The objective of this study was to search for new DNA variants that could be helpful in the preemptive prediction of impaired tamoxifen to endoxifen metabolism.

Methods: The molecular ratio (MR) was defined as (Z)-endoxifen plasma concentration divided by the sum of concentrations of tamoxifen and other measured metabolites. The MR of 0.0146, previously delineated as corresponding to (Z)-endoxifen 6 ng/ml efficacy threshold level, was adopted as a cut-off value in a genome-wide association study (GWAS) comprising 287 breast cancer patients receiving tamoxifen 20 mg daily. Multivariate binary logistic regression was used for the pre-selection of variables that showed independent impact on MR and to develop models predictive for MR value below the threshold.

Results: In total, 13 GWAS-selected single nucleotide polymorphisms (SNPs) located outside the CYP2D6 gene and two known CYP2D6 variants were significantly associated with the MR value below 0.0146. The strongest association was observed for rs8138080 in WBP2NL (p = 1.78 x 10-15). The minor allele of six SNPs was associated with a decreased risk of impaired tamoxifen metabolism. CYP2D6 genotype was found by Nagelkerke pseudo-R2 to explain 42.7% of a total variation observed in MR, while rs8138080 alone explained 33.7% of this variability. Two alternative models for MR prediction have been developed. The prediction accuracy of Model 1, including rs7245, rs6950784 and rs1320308 in addition to CYP2D6 genotype, was considerably higher than predictive performance of CYP2D6 genotype alone (AUC increase from 0.758 to 0.879). The AUC of 0.830 achieved for the Model 2, developed with the same three SNPs as in Model 1 and rs8138080 instead of CYP2D6 genotype, makes it an interesting, simplified alternative to the costly and time-consuming testing of full CYP2D6 genotype.

Conclusions: The four novel SNPs, tested alone or in addition to CYP2D6 genotype, improved the prediction of impaired tamoxifen to endoxifen metabolism, allowing for adjustments in dosing regimen before the treatment begins.

overall_design:
192 DNA samples were selected from previously described, based on the ratio of the sum of two tamoxifen active metabolites ((Z)-endoxifen and (Z)-4-OH-Tam) plasma concentration to the sum of the concentration of tamoxifen and the remaining measured compounds; 96 samples represented the highest ratio and the next 96 samples the lowest one.

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first: Ewa

last: Hennig

first: Magdalena

last: Piątkowska

first: Ewelina

last: Pośpiech

first: Agnieszka

last: Paziewska

first: Jakub

last: Karczmarski

first: Anna

last: Kluska

first: Elżbieta

last: Brewczyńska

first: Jerzy

last: Ostrowski


title: Transcriptome of CRPV-induced wart tissues

city: Bethesda

first: Thomas

last: Meyer

address: 41 Center Drive, Building 41, Room B620

institute: National Institutes of Health

summary: Cottontail rabbit papillomavirus (CRPV) infection in susceptible animals represents an important model for studying papillomavirus pathogenesis and tumorigenesis. The goal of this project is to determine a comprehensive transcriptome of CRPV-induced wart tissues generated by different routes of infection.

overall_design: The New Zealand rabbits with prewounded back skin were infected with CRPV Hershey strain via two routes of infection: a) cutaneuosly by scratching the pre-wounded back skin; b) intravenous injection into ear vein. The medium-size tumors occurred at the pre-wounded back skin area were harvested. The total RNA was isolated using TRIpure Reagent (Roche) and DNase-treated on column using RNeasy kit (Qiagen). Total stranded RNA-seq was performed on Ribo-minus RNA using True-seq kit with 125 bp modality and 100 million reads depth.

first: Zhi-Ming

last: Zheng

first: Vladimir

last: Majerciak

first: Pengfei

last: Jiang


title: miRNA expression profiles of aneurysmal tissues

city: Luxembourg

first: Yvan

last: Devaux

address: 120 route d'Arlon

country: Luxembourg

institute: LIH

summary: To identify miRNAs which could be involved in TAA (Thoracic Aortic Aneurysm) pathogenesis, we first performed miRNAs microarrays using the aortic media of healthy controls and TAA patients. 473 miRNAs were detected in at least half samples. Among them, 232 miRNAs were differentially expressed with adjusted p value < 0.05 and log2 transformed fold change > 0.5 or < -0.5.

overall_design: Total RNA was extracted from aortic media of 19 patients and 19 healthy controls and was hybridized with Agilent microarray G3 Human miRNA Microarray Kit, which contained 5893 probes corresponding to 2549 miRNAs from miRBase release 21.

first: A

last: Boileau

first: L

last: Zhang

first: Y


title: Lymph node metastasis evolution drives cancer immune evasion and drug resistance

city: London

first: Matthew

last: Davies

address: Fulham Road

institute: Institute of Cancer Research

summary:
Gastro-esophageal adenocarcinomas (GEAs) are aggressive cancers and multiple trials of targeted therapies recently failed to improve survival in these tumors. Intratumor heterogeneity (ITH) is suspected to contribute to poor outcomes. Here we investigate the degree of ITH in multiple primary and metastatic regions of gastric adenocarcinoma tumours.
ITH increased significantly with lymph node metastasis formation and subclonal aberrations activating the Mitogen Activated Protein Kinase (MAPK)-pathway were significantly enriched in nodal metastases. This shows that selection pressures in the lymph node ecosystem differ from those in the primary tumor, leading to evolutionary convergence of distinct tumors when they spread to lymph nodes.

overall_design: We used Oncoscan arrays to analyse multiple regions from nine GEA primary tumors and associated lymph node metastases. Somatic mutation and DNA copy number analysis identified ITH in all tumors. Eight chromosomally instable GEAs predominantly evolved through DNA copy number aberrations whereas a microsatellite instable tumor exclusively evolved through point mutations and showed evidence for parallel evolution.    We used Oncoscan arrays to analyse multiple regions from nine GEA primary tumors and associated lymph node metastases. Somatic mutation and DNA copy number analysis identified ITH in all tumors. Eight chromosomally instable GEAs predominantly evolved through DNA copy number aberrations whereas a microsatellite instable tumor exclusively evolved through point mutations and showed evidence for parallel evolution.    We used Oncoscan arrays to analyse multiple regions from nine GEA primary tumors and associated lymph node metastases. Somatic mutation and DNA copy number analysis identified ITH in all tumors. Eight chromosomally instable GEAs predominantly evolved through DNA copy number aberrations whereas a microsatellite instable tumor exclusively evolved through point mutations and showed evidence for parallel evolution.

middle: N

first: Marco

last: Gerlinger


title: Drivers of topoisomerase II poisoning mimic and complement cytotoxicity in AML cells

city: Mainz

first: Piyush

last: More

address: Langenbeckstrasse 1

department: Department of Pharmacology

institute: University Medical Center, Johannes Gutenberg University of Mainz

summary: Recently approved cancer drugs remain out-of-reach to most patients due to prohibitive costs and only few produce clinically meaningful benefits. An untapped alternative is to enhance the efficacy and safety of existing cancer treatments. We hypothesized that the response to topoisomerase II poisons, the most successful group of cancer drugs, can be improved by considering treatment-associated transcript levels, taken as surrogates for protein expression. To this end, we analyzed transcriptomes from Acute Myeloid Leukemia (AML) cell lines treated with the topoisomerase II poison etoposide. Using complementary criteria of co-regulation within networks and of essentiality for cell survival, we identified and functionally confirmed 11 druggable drivers of etoposide cytotoxicity. Drivers with pre-treatment expression predicting etoposide response (e.g. PARP9) generally synergized with the drug. Drivers repressed by etoposide (e.g. PLK1) displayed standalone cytotoxicity. Drivers, whose modulation evoked etoposide-like gene expression changes (e.g. mTOR), were cytotoxic both alone and in combination with etoposide. In summary, both pre-treatment gene expression and treatment-driven changes contribute to the cell killing effect of etoposide. Inhibitors of protein products of the involved genes can be used to enhance the efficacy of etoposide. This strategy can be used to identify combination partners or even replacements for other classical anticancer drugs, especially those interfering with DNA integrity and transcription.

overall_design: AML cell lines were treated with either vehicle control (media) or cell-specific IC50 concentrations of etoposide for 24 hours. Total RNA was extracted and single-end RNA sequencing was performed to idendify etoposide-evoked changes in the gene expression. The experiment was perfomed using 3 biological replicates, each for vehicle control- and etoposide-treated cells.

first: Leszek

last: Wojnowski


title: Expression data from PC3 cells treated with astragalus polysaccharides

city: Tianjin

first: Xingkang

address: Hexi

department: Urology

institute: Tianjin Institute of Urology

summary:
Astragalus polysaccharides (APS), as one of the main effective components of astragalus, have been reported to regulate the processes of inflammation, metabolism, and carcinogenes.
We used microarrays to detect the different expression of mRNA in PC3 cells upon APS treatment.

overall_design: PC3 cells were treated with APS at 10mg/mL and negative control for 48h. Then, total RNAs were extracted by using Trizol reagent (Invitrogen). The mRNA array data were analyzed by using the GeneSpring softwore V13.0 (Agilent). To select the differentially expression genes, we used thresholdvalues of ≥2 and ≤2-fold change and a T-test p value of 0.05.

first: Shan-qi

last: Guo


title: The transcription factor Bhlhe40 programs mitochondrial regulation of resident CD8+ T cell fitness and functionality

city: San Antonio

first: Zhenqing

last: Ye

state: TX

address: 8403 Floyd Curl Dr

department: 6Department of Population Health Sciences

institute: UT Health San Antonio

summary: Tissue-resident memory CD8+ T cells (Trm) share characteristics and core residency gene programs with tumor-infiltrating lymphocytes (TILs). However, the transcriptional, metabolic and epigenetic regulation of Trm cell and TIL differentiation, maintenance and function are largely undefined. Furthermore, it is unknown whether metabolic and epigenetic manipulations can be employed to promote Trm/TIL functional programs for cancer immunotherapy. Here we report a critical mechanism programming the mitochondrial and epigenetic regulation of Trm/TIL functionality in situ. We found that mouse and human Trm/TIL expressed the transcription factor BHLHE40 and the BHLHE40-associated gene signature. Bhlhe40 was specifically required for Trm and TIL development and polyfunctionality. Local PD-1 signaling inhibited TIL Bhlhe40 expression, and Bhlhe40 was critical for TILs reinvigoration following anti-PD therapy. Mechanistically, Bhlhe40 sustained Trm/TIL mitochondrial fitness for the promotion of a functional epigenetic state. Building on these findings, we also identified an epigenetic and metabolic regimen that promoted Trm/TIL gene signatures associated with tissue residency and poly-functionality through in vitro T cell screening. Strikingly, this regimen empowered the anti-tumor activity of CD8+ T cells and possessed therapeutic potential even at an advanced tumor stage in mouse models. Our results provide mechanistic insights on the local regulation of Trm and TIL function, and offer a viable strategy for developing novel immunotherapeutic means for cancer.

overall_design: Examination of RNA expression in: in vitro activated CD8+ T cell from WT or Bhlhe40 deficient mice; TIL cells and Splenic CD8+ T cells from B16-OVA bearing WT mice; Trm cells from IAV infected WT or Bhlhe40 deficient mice and Splenic CD8+ T cells from IAV infected WT mice.

first: Chaofan

last: Li

first: Jie

last: Sun


title: A novel P300 inhibitor reverses DUX4-mediated global histone H3 hyperacetylation, target gene expression and cell death

city: Minneapolis

first: Michael

last: Kyba

state: MN

address: 2231 6th St SE

institute: University of Minnesota

summary: DUX4-induced gene expression was compared in the presence vs. absence of the p300 inhibitor, iP300w

overall_design: LHCN-M2 immortalilzed human myoblasts carrying rtTA and a dox-inducible DUX4 gene were cultured in the presence of dox and presence or absence of inhibitor.  Negative control was the parent line carrying rtTA only but not DUX4.  This eliminated any potential dox-specific effect.

first: Darko

last: Bosnakovski

first: Ce

last: Yuan


title: C9orf72 Intermediate Repeats are Associated with Corticobasal Degeneration, Increased C9orf72 Expression and Disruption of  Autophagy

city: Philadelphia

first: Edward

last: Lee

state: PA

address: 613A Stellar Chance Laboratories; 422 Curie Blvd

institute: University of Pennsylvania

summary: Microsatellite repeat expansion disease loci can exhibit pleiotropic clinical and biological effects depending on repeat length. Large expansions in C9orf72 (100s-1000s of units) are the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal degeneration (FTD). However, whether intermediate expansions also contribute to neurodegenerative disease is not well understood. Several studies have identified intermediate repeats in Parkinson’s disease patients, but the association was not found in autopsy confirmed cases. We hypothesized that intermediate C9orf72 repeats are a genetic risk factor for corticobasal degeneration (CBD), a neurodegenerative disease that can be clinically similar to Parkinson’s but has distinct tau protein pathology.  Indeed, intermediate C9orf72 repeats were significantly enriched in autopsy-proven CBD (n=354 cases, odds ratio=3.59, p-value=0.00024).  While large C9orf72 repeat expansions are known to decrease C9orf72 expression, intermediate C9orf72 repeats result in increased C9orf72 expression in human brain tissue and CRISPR/cas9 knockin iPSC derived neural progenitor cells. In contrast to cases of FTD/ALS with large C9orf72 expansions, CBD with intermediate C9orf72 repeats was not associated with pathologic RNA foci or dipeptide repeat protein aggregates.  Knock-in cells with intermediate repeats exhibit numerous changes in gene expression pathways relating to vesicle trafficking and autophagy. Additionally, overexpression of C9orf72 without the repeat expansion leads to defects in autophagy under nutrient starvation conditions. These results raise the possibility that therapeutic strategies to reduce C9orf72 expression may be beneficial for the treatment of CBD.

overall_design: Samples are isogenic CRISPR edited Neural progenitor cells differentiated from iPSCs using dual SMAD inhibition. C9orf72 repeat size was edited in the parental PBWT iPSC line, and clonal lines were generated. 3 cell lines with low repeat numbers and 3 cell lines with intermediate repeats and 2 technical replicates per line were sequenced.

first: Christopher

middle: P

last: Cali


title: Gene expression in quiescent NSCs (qNSCs) after bafilomycin A (BafA) treatment

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

summary: To evaluate the role of enhanced lysosomes in qNSCs, lysosomal function was inhibited with BafA, a specific inhibitor of the vacuolar-type H(+)-ATPase (V-ATPase).

overall_design: Gene expression in BafA-treated (BafA) and non-treated (control) qNSCs was analyzed at 4 and 24 hours after changing medium from 2 samples per condition.

first: Taeko

last: Kobayashi

first: Ryoichiro

last: Kageyama


title: The effect of an NAD+ precursor vitamin B3, niacin, on muscle transcriptomic profiles of mitochondrial myopathy patients and healthy controls

city: Helsinki

first: Virginia

last: Brilhante

state: Uusimaa

address: Haartmaninkatu 8

department: Stem Cells and Metabolism Research Program

country: Finland

institute: University of Helsinki

summary:
Purpose: We examined the impact of niacin on muscle gene expression in mitochondrial myopathy patients and healthy controls.
Methods: Muscle transcriptomics profiles were generated using global transcriptomics analysis by RNA sequencing which was performed by the Beijing Genomic Institute (BGI) using their standard protocols
Results: The pathway enrichment analysis of RNA-sequencing data indicated that phagosome formation, serine/glycine/one-carbon pathways (de novo serine biosynthesis, purine degradation, glutathione metabolism),  LXR/RXR activation, eicosanoid, glycoprotein 6, atherosclerosis, iron homeostasis and cAMP-mediated signalling pathways were among the most significantly changed in patients. Only five and two of the disease associated pathways remained significantly changed after 4- and 10-month supplementation, respectively, in patients as compared to controls. The most prominent niacin-related transcriptomic change in patients’ muscle (patient 10-months on niacin vs patient baseline) was wide-spread downregulation of mTOR-dependent cytoplasmic translation, involving a large number of cytoplasmic ribosome subunits as well as translation initiation factor eIF1. In patients, niacin activated also the peroxisome proliferator-activated receptor signaling pathway, known to induce mitochondrial biogenesis. Niacin also led to decreased atherosclerosis signaling including lowered apolipoprotein expression in patients. The healthy control muscles showed only few changes after 4-months of niacin. To examine in detail the effects of NAD-booster niacin in the mitochondrial integrated stress response (ISRmt),  we studied the effects NAD+ boosting for the expression of 24 ISRmt target genes in the patients’ muscle. The analysis confirmed wide-spread induction of these genes, but their expression was unaffected by niacin (ATF5 and its targets ASNS, TRIB3, FGF21, GDF15, MTHFD2, and MTHFD1L; de novo synthesis of serine, PSAT1, PHGDH and SHMT2;  glutathione metabolism GPX3 and GSR; and unfolded protein response ER CHOP).
Conclusions: These results showed that niacin modulated the expression of disease associated pathways and suppressed mTOR signalling in patients but niacin did not affect disease-related ISRmt signalling.

overall_design: In this small open-label study, we recruited five PEO patients either with sporadic single mtDNA deletions or a mutation in a mtDNA maintenance gene Twinkle. For every patient, two gender- and age-matched healthy controls were recruited. Two controls discontinued after 2 months. Patients manifested with only myopathic symptoms. Study subjects were supplemented with a 1 g/day dose of niacin, which is an NAD+ precursor vitamin B3 form with a proven safety record in humans. Clinical examinations and collection of blood samples and muscle biopsies were performed in patients at the time points 0, 4 and 10 months and in controls at 0 and 4 months.

first: Eija

last: Pirinen

first: Anu

last: Suomalainen Wartiovaara


title: The cross-talk between TGF-b and periostin can be targeted for pulmonary fibrosis [AR2857]

city: SAGA

first: Yasuhiro

last: Nanri

address: 5-1-1 Nabeshima

institute: Saga university

summary: Idiopathic pulmonary fibrosis (IPF) is a devastating disease characterized as progressive and irreversible fibrosis in the interstitium of lung tissues. There is still an unmet need to develop a novel therapeutic drug for IPF. We have previously demonstrated that periostin, a matricellular protein, plays an important role in the pathogenesis of pulmonary fibrosis. However, the underlying mechanism of how periostin causes pulmonary fibrosis remains unclear. In this study, we sought to see whether the cross-talk between transforming growth factor-b (TGF-b), a central mediator in the pathogenesis of pulmonary fibrosis, and periostin in lung fibroblasts leads to generation of pulmonary fibrosis and whether taking advantage of the cross-talk between TGF-b and periostin, inhibitors for integrin aVb3, a periostin receptor, can block pulmonary fibrosis in the model mice. We found that there exists a cross-talk between TGF-b and periostin signals via aVb3/b5 converging into Smad3. This cross-talk is important for expression of several downstream molecules of TGF-b including serpin family E member 1, CCN family member 2/connective tissue growth factor, insulin-like growth factor binding protein-3, and IL-11, all of which have been already shown to be important for pulmonary fibrosis. We, moreover, found several potent integrin inhibitors to block the cross-talking with TGF-b signals and CP4715, one of the compounds, improved bleomycin-induced pulmonary fibrosis in mice. These results suggest that the cross-talk between TGF-b and periostin can be targeted for pulmonary fibrosis and that CP4715 can be a potential therapeutic agent to block the cross-talk between TGF-b and periostin.

overall_design: To explore the possibility that there exists the cross-talk between TGF-beta and periostin in lung fibroblasts leading to pulmonary fibrosis, we first compared the gene expression profiles of normal human lung fibroblasts (NHLFs) with or without stimulation of 1 ng/ml TGF-beta and with or without of periostin knockdown by DNA microarray analysis

first: Kenji

last: Izuhara


title: The cross-talk between TGF-b and periostin can be targeted for pulmonary fibrosis

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

overall_design: Refer to individual Series


title: Maternal immune activation impairs cognitive flexibility and alters transcription in frontal cortex

city: La Jolla

first: Chi-Yu

last: Lai

state: California

address: 10010 North Torrey Pines Road

institute: Salk Institute

summary: We examined mRNA expression differences in frontal cortex of adult offspring of Poly(I:C)- and Saline-exposed mice

overall_design: RNA-seq in offspring of Poly(I:C)- and Saline-exposed mice

first: Dionisio

middle: A

last: Amodeo

first: Omron

last: Hassan

first: Eran

last: Mukamel

first: M

middle: M

last: Behrens

first: Susan

last: Powell


title: The cross-talk between TGF-b and periostin can be targeted for pulmonary fibrosis [AR2819]


title: Deconvolution of Transcriptional Networks Identifies TCF4 as a Master Regulator in Schizophrenia

first: Kai

last: Wang

state: Pennsylvania

address: 3501 Civic Center Boulevard, 5th Floor CTRB

institute: The Children's Hospital of Philadelphia Research Institute

summary: We report the data generated upon knockdown of TCF4 in hiPSC-derived neural progenitor cells and glutamatergic neurons.

overall_design: Examination of TCF4 knockdown to probe its contribution to schizophrenia.

first: Abolfazl

last: Doostparast Torshizi


title: Transcriptome analyses of ovarian stroma: tunica albuginea, interstitium and theca interna

first: Katja

last: Hummitzsch

address: Level 5, North Tce/George Street

department: Obstetrics& Gynaecology

institute: The University of Adelaide

summary: The ovary has specialized stromal compartments, including the tunica albuginea, interstitial stroma and theca interna, which develops concurrently with the follicular antrum. To characterize the molecular determinants of these compartments, stroma adjacent to preantral follicles (pre-theca), interstitium and tunica albuginea were laser microdissected (n = 4 per group) and theca interna was dissected from bovine antral follicles (n = 6).

overall_design: Four compartments of bovine ovarian stroma were selected for analysis. Tunica albuginea, interstitial stroma and stroma close to follicles were collected by lasercapture microdissection (n=4 for each group). Theca layer samples were collected by follicle dissection of healthy small antral follicles (< 5mm). Thecal samples were from individual follicles and animals, whereas tunica albuginea, interstitial stroma and stroma near the follicle were pooled from different animals.

first: Nicholas

last: Hatzirodos

first: Anne

last: McPherson

first: Jeff

last: Schwartz

first: Raymond

last: Rodgers

first: Helen

middle: F

last: Irving-Rodgers


title: Effect of circPTPRM on the biological behaviors of hepatocellular carcinoma cells in vitro and its clinical significance.

city: Shenyang

first: Zhun

last: Luo

address: 155 Nanjing North Street

department: Infectious Diseases

institute: the First Affiliated Hospital, China Medical University

summary: In this paper, a new circRNA was discovered by RNA sequencing, and its relationship with hepatocarcinoma proliferation, apoptosis, invasion and migration and clinical correlation of hepatocellular carcinoma were verified from different angles, providing a basis for further discussion on the mechanism of promoting the occurrence and development of hepatocellular carcinoma.

overall_design: RNA sequencing was performed on 3 pairs of hepatocellular carcinoma and their adjacent paired tissues, and 3 differentially expressed circRNAs were selected and verified by Real time PCR in 30 pairs of tissue samples, hepatoma cells and normal liver cells, and clinical data were analyzed. From which candidate circRNAs are selected. Then, the anti-candidate circRNA si RNA-1 and si RNA-2 were transfected into the hepatoma cell line, and the biological behavior of the hepatoma cells after silencing of the candidate circRNA was detected by cell proliferation, plate cloning, flow cytometry and transwell.

first: Wei

last: Cui


title: Identification of the genes regulated by the 5-HT2B serotonin receptor agonist BW723C86 in human M-CSF-primed monocyte-derived macrophages

city: Madrid

first: Angel

last: Corbí

state: Madrid

address: Ramiro de Maeztu 9

department: Molecular Microbiology and Infection Biology

country: Spain

institute: Consejo Superior de Investigaciones Científicas

summary: Peripheral serotonin (5-HT) exacerbates or limits inflammatory pathologies (pulmonary arterial hypertension, cardiac valve degeneration, systemic sclerosis, gut disorders, neuroendocrine neoplasms, arthritis) through interaction with seven types of 5-HT receptors (5-HT1-7). As central regulators of inflammation, macrophages are critical targets of 5-HT, which promotes their anti-inflammatory and pro-fibrotic polarization primarily via the 5-HT7-Protein Kinase A (PKA) axis. However, anti-inflammatory human macrophages are also characterized by the expression of 5-HT2B, an off-target of anesthetics, anti-parkinsonian drugs and Selective Serotonin Reuptake Inhibitors (SSRI) that contributes to 5-HT-mediated pathologies. Since 5-HT2B prevents mononuclear phagocyte degeneration in amyotrophic lateral sclerosis and modulates motility of murine microglial processes, we sought to determine the functional and transcriptional consequences of 5-HT2B activation in human macrophages.  Ligation of 5-HT2B by the 5-HT2B-specific agonist BW723C86, which exhibits antidepressant- and anxiolytic-like effects in animal models, significantly modified the cytokine profile and the transcriptional signature in macrophages. Importantly, 5-HT2B agonist-induced transcriptional changes were partly mediated through activation of the Aryl hydrocarbon Receptor (AhR), a ligand-dependent transcription factor that regulates immune responses and the biological responses to xenobiotics. Besides, BW723C86 triggered transcriptional effects that could not be abrogated by 5-HT2B antagonists and impaired monocyte-to-osteoclast differentiation. Therefore, our results demonstrate the existence of a functional 5-HT2B-AhR link in human macrophages and indicate that the commonly used 5-HT2B agonist BW723C86 exhibits 5-HT2B-independent effects.

overall_design: Human peripheral blood monocytes from three independent healthy donors (1, 2 and 3) were isolated by anti-CD14-labeled magnetic microbeads. CD14+ monocytes were cultured for 5 days in RPMI 10% FCS containing M-CSF (M1). After 5 days, cells were maintained in serum-free medium for 48 hours. Then, the resulting macrophages were treated with DMSO (Control), BW723C86 (10mM), SB204741 (1mM) [5-HT2B antagonist] or BW723C86 plus SB204741 during 6 hours.Total RNA from each condition was extracted and purified using the RNA isolation kit (Macheray-Nagel). Labelled RNA was used as hybridization probes on human Agilent SurePrint G3 Human Gene Expression 8x60K (G4851A). All experimental procedures were performed following manufacturer instructions. Microarrays were scanned on an Agilent G2539A scanner. Scanned images and raw data were pre-processed with GeneSpring GX (Agilent).

last: Corbí López

first: Concha

last: Nieto

first: Miguel

last: Vega Palacios


title: Identification of potential miR-215 target genes in patient-derived tumor-initiating cell (TIC) cultures

city: Belvaux

first: Elisabeth

last: Letellier

address: 6, Avenue du Swing

department: Life Sciences Research Unit

institute: University of Luxembourg

summary:
Stable overexpression of miR-215 in patient-derived TIC culture T51
The main focus of the study was the identification and validation of potential target genes of hypoxia-responsive miR-215 in colon TICs

overall_design: 3 vs 3 technical replicates for T51 TICs that were stably transduced with a miR-215 or a corresponding control vector


title: Identification of differentially expressed miRNAs in hypoxic tumor-initiating cell (TIC) cultures

summary:
Patient-derived TIC cultures T6 and T18 were used to study the effect of normoxic vs. hypoxic culture conditions
The main focus of the study was the identification and validation of new hypoxia-responsive miRNAs and target genes in such colon TICs

overall_design: 4 vs 4 technical replicates for T6 and 3 vs 3 technical replicates for T18 were used to compare normoxia vs hypoxia


title: H3K27me3-mediated silencing of structural genes is required for zebrafish heart regeneration

city: Charlestown, MA

first: Raz

last: Ben-Yair

address: 13th st.

department: CVRC

institute: MGH

summary: Deciphering the genetic and epigenetic regulation of cardiomyocyte proliferation in organisms capable of robust cardiac renewal represents an attractive inroad towards regenerating the human heart. In the highly regenerative zebrafish heart, cardiomyocytes near the wound edge undergo dramatic changes in gene expression concomitant with sarcomere disassembly, loss of cell-cell adhesion, and detachment from the extracellular matrix (ECM), which leaves them poised to divide and give rise to new muscle cells that colonize the wound. Using integrated highthroughput transcriptional and chromatin analyses, we identified correlations between gene expression changes and activating H3K4me3 and/or repressive H3K27me3 dynamics8 in cardiomyocytes following injury. Within the category of downregulated genes that gain H3K27me3, transcripts encoding sarcomere and cytoskeletal components were significantly overrepresented. To investigate a functional requirement for H3K27me3-mediated gene silencing during zebrafish heart regeneration, we generated an inducible transgenic strain expressing a mutant version of histone 3, H3.3K27M, which allowed us to inhibit H3K27me3 catalysis in cardiomyocytes during the regenerative window. Hearts composed of H3.3K27M-expressing cardiomyocytes fail to regenerate with wound edge myocardium showing heightened expression of structural genes and prominent sarcomere structures. Although cell cycle re-entry was unperturbed, cytokinesis and wound invasion were significantly compromised. Collectively, our study identifies a requirement for H3K27me3-mediated silencing of structural genes during zebrafish heart regeneration and suggests that repression of similar structural components in the border zone of the infarcted human heart might improve its regenerative capacity.


title: H3K27me3 deposition over sarcomeric and cytoskeletal promoters is required for cardiomyocyte cytokinesis and wound invasion during zebrafish heart regeneration [ChIP-seq]

summary: Deciphering the genetic and epigenetic regulation of injury-induced heart regeneration in organisms capable of robust cardiac renewal represents an attractive inroad towards regenerating the human heart. In the highly regenerative zebrafish heart, cardiomyocytes near the wound edge undergo dramatic gene expression changes concomitant with sarcomere disassembly, loss of cell-cell adhesion, and detachment from the extracellular matrix (ECM), which leaves them poised to divide and give rise to new muscle cells that colonize the wound. Using integrated high-throughput transcriptional and chromatin analyses, we identified correlations between gene expression changes and activating H3K4me3 and/or repressive H3K27me3 dynamics in cardiomyocytes following injury. Within the category of downregulated genes that gain H3K27me3, transcripts encoding sarcomere and cytoskeletal components were significantly overrepresented. To investigate a functional requirement for H3K27me3-mediated gene silencing during zebrafish heart regeneration, we generated an inducible transgenic strain expressing a mutant version of histone 3, H3.3K27M, which allowed us to inhibit H3K27me3 catalysis in cardiomyocytes during the regenerative window. Hearts composed of H3.3K27M-expressing cardiomyocytes fail to regenerate with wound edge myocardium showing heightened expression of structural genes and prominent sarcomere structures. Although cell cycle re-entry was unperturbed, cytokinesis and wound invasion were significantly compromised. Collectively, our study identifies a requirement for H3K27me3-mediated silencing of structural genes during zebrafish heart regeneration and suggests that repression of similar structural components in the border zone of the infarcted human heart might improve its regenerative capacity.

overall_design: Examination of 2 different histone modifications in enriched cardiomyocyte samples from uninjured and regenerating zebrafish hearts with three biological replicates.

first: Vincent

last: Butty

first: Laurie

last: Boyer

first: Alon

last: Goren

first: Michele

last: Busby

first: C

middle: G

last: Burns

first: Caroline

middle: E


title: Differential gene expression profiling in response to paraquat using a Drosophila Parkinson's disease model

status: Public on Sep 16 2019

city: Tuscaloosa

first: Urmila

last: Maitra

state: Alabama

address: 1325 Science and Engineering Complex, Box 870344

department: DEPARTMENT OF BIOLOGICAL SCIENCES

institute: University of Alabama

summary: Transcriptomic profiling using Drosophila heads reveals early gene expression responses to transient paraquat exposure. We performed RNAseq profiling of heads from the wild type (WT) Drosophila strain, Canton S (males only), that were fed either 2.5% sucrose (control) or 5 mM PQ in 2.5% sucrose for 12 h.

overall_design: Transcriptomic profiling was performed using independent biological replicates per feeding. Age-matched adult Canton S male flies were fed either 2.5% sucrose (control) or 5 mM PQ in 2.5% sucrose for 12 h and the heads were collected for RNA extraction. For paired-end library preparation, NEBNext mRNA Library Prep Reagent Set for Illumina was used and the library concentration was analyzed by utilizing a DNA 1000 Chip on an Agilent 2100 Bioanalyzer. Paired-end sequencing (25 million, 50-bp, paired-end reads) was performed using a 200 Cycle TruSeq SBS HS v4 Kit on an Illumina HiSeq2500 sequencer (Illumina, Inc., San Diego, CA, USA) at the HudsonAlpha Institute for Biotechnology, Huntsville, AL. TopHat v2.0 were used to map raw reads to the reference Drosophila melanogaster genome dm3

first: Janis

last: O'Donnell