title: A Glis3-CD133-Wnt signaling axis regulating the self-renewal of adult murine pancreatic progenitor-like cells in colonies/organoids

status: Public on Jun 30 2019

city: Duarte

first: Xiwei

last: Wu

state: CA

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

country: USA

institute: City of Hope National Medical Center

type: Expression profiling by high throughput sequencing

summary: Adult pancreatic progenitor cells are a potential source of renewable insulin producing cells that can be used in regenerative medicine and cell replacement therapy for type-1 diabetes. We sought to understand the mechanisms by which adult pancreatic progenitor cells undergo self-renewal. The effects of knockdown of Glis3, CD133 (Prominin-1) and beta-catenin were investigated and we found that Glis3 and CD133 are capable of regulating self-renewal through Wnt gene expression.

overall_design: Total RNAs were extracted from 3-week-old colonies (grown in Matrigel- and RSPO1-containing culture) treated with lenti-shRNAs against Glis3, CD133 or control. RNAseq analysis was conducted subseuqently.

first: Hsun

middle: T

last: Ku

first: Jacob

middle: R

last: Tremblay


title: Hypoxia serum starved Flt-1 wild type and Flt-1 heterozygote BMDMs

city: Charlottesville

first: Vijay

middle: C

last: Ganta

state: VA

address: 454 Farrish Cir, Apt 3

institute: University of Virginia

summary: The goal is to identify differential gene expression between hypoxia serum starved (for 6 hours) Flt-1+/+ (wild type) and Flt-1+/- (VEGFR1 heterozygote) bone marrow derived macrophages

overall_design: Bone marrow derived macrophages (n=3) from wild type (Flt+/+) and Flt-1 heterozygote mice were challenged with hypoxia serum starvation and examined for differential gene expression by RNA-Seq analysis

first: Brian

middle: H

last: Annex


title: Circulating extracellular microRNAs predictive of human liver allograft status.

city: New York

first: Kemal

middle: Marc

last: Akat

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

type: Non-coding RNA profiling by high throughput sequencing

summary: Liver transplantation is the only lifesaving therapy for patients with irreversible liver failure, and 30% of the recipients experience acute rejection in the first 12 months following transplantation.  Acute rejection is diagnosed by core needle biopsy and noninvasive methods for predicting acute rejection could improve clinical care. MicroRNAs (miRNAs) are emerging as biomarkers of clinically significant events. We investigated whether circulating extracellular miRNA profiles in sera matched to liver allograft biopsies predict human liver allograft status. Small RNA sequencing and TaqMan low-density array analysis of RNA from biopsy matched sera identified that liver specific miR-122, and miRs -885, -210, -194, 193b, -192, -148a, -34a and -22 distinguish patients with acute rejection biopsies from those with biopsies without rejection features (false discovery rate of <0.15). We measured absolute levels of these informative 9 miRNAs using quantitative real-time PCR assays. Receiver-operating-characteristic (ROC) curve analysis of circulating levels of miRNA levels validated that all 9 miRNAs discriminate patients with acute rejection in their biopsies from those without rejection in their biopsies (P <0.01 to P<0.0001).  A parsimonious diagnostic signature of miR-122 and miR-194 was diagnostic of acute rejection with a sensitivity of 79% (95% confidence interval [CI], 49% to 95%) and a specificity of 88% (95% CI, 64% to 99%) (area under the curve, 0.91; 95% CI, 0.81 to 1.00; P<0.001 by ROC curve analysis). Our findings suggest that a molecular signature of miR-122 and miR-194 in serum offers a noninvasive means of diagnosing acute rejection including mild forms in human liver allografts.

overall_design: Total RNA was isolated from serum of patients after liver allograft transplantation (Clinical Trials of Transplantation-07 Study. A primary objective of the National Institutes of Health sponsored Clinical Trials in Organ Transplantation-07 observational study; CTOT-07 Study, ClinicalTrials.gov identifier: NCT01428700) and used for miRNA-sequencing and qPCR analysis.

middle: M

first: Thomas

last: Tuschl

first: Manikkam

last: Suthanthiran


title: Gene expression profiling of thymically-derived regulatory T cells from miR-142-deficient versus wild-type mice

status: Public on Jun 28 2019

city: London

first: Graham

last: Lord

address: 5th Floor Tower Wing, Guy's Hospital

department: Peter Gorer Department of Immunobiology

country: United Kingdom

institute: King's College London

summary: Regulatory T cells (Tregs) play a fundamental role in immune tolerance via control of self-reactive effector T cells (Teffs). The development and function of the Treg lineage is critically dependent on the transcription factor Forkhead box P3 (Foxp3). Mice with a Treg-specific deletion of miRNAs, also develop a spontaneous, lethal autoimmune disease virtually indistinguishable from that seen in Foxp3-decicient mice demonstrating that miRNAs are critical for establishment of Treg-mediated peripheral tolerance. However, the set of miRNAs responsible for this functional deficiency has yet to be fully defined. Using Foxp3 ChIP-seq data we identified Mir142 as the only miRNA gene associated with a super-enhancer bound by FOXP3 suggesting that miR-142 is important for Treg function. To identify genes directly regulated by miR-142 in Tregs we profiled the changes in gene expression upon conditional deletion of miR-142 in thymically-derived Treg cells.

overall_design: Tregs were obtained by magnetic positive selection of CD4+ cells from the lymph nodes and spleens of FoxP3YFP-Cre x Mir142fl/fl and FoxP3YFP-Cre x Mir142+/+ mice followed by flow-cytometric sorting of CD4+ CD25+ YFP+ cells to >95% purity. Complementary DNA (cDNA) from total RNA was prepared using the Nugen WT-Ovation Pico kit (Nugen Technologies) and hybridized to Affymetrix Mouse Gene ST 2.0 microarrays. All cell populations used for the microarray analysis were generated in duplicates and individually processed. Raw data were processed with the robust multi-array average (RMA) algorithm for probe-level normalization and differentially expression was estimated using the limma package in Bioconductor.

first: Nelomi

last: Anandagoda

first: Joanna

middle: D

last: Willis

first: Arnulf

last: Hertweck

first: Luke

middle: B

last: Roberts

first: Ian

last: Jackson

first: M

last: Refik Gökmen

first: Richard

middle: G

last: Jenner

first: Jane

middle: K

last: Howard


title: Gene expression profile in hearts of WT and endothelial S1pr1 knock-out mice 5 days after myocardial infarction

status: Public on Jun 27 2019

city: Shanghai

first: kuang

middle: ya

last: shu

state: Shanghai

address: 150 Jimo Rd, Pudong New District, Shanghai

department: Key Laboratory of Arrhythmias of the Ministry of Education of China, Research Center for Translational Medicine

country: China

institute: Shanghai East Hospital, Tongji University School of Medicine

summary: High-throughout RNA microarray results revealed different gene expression, including arg1, VEGF, TGF-beta, and IL-10, in ischemic myocardium of endothelial S1pr1 knock-out mice, compared to WT mice.

overall_design: We generated endothelial S1pr1 knock-out mice, and induced acute myocardial infarction by ligation of the left anterior descending coronary arteries in these mice and their corresponding WT mice. We applied high-throughout RNA microarray to study gene expression profile in the hearts 5 days after myocardial infarction in WT and endothelial S1pr1 conditional knock-out mice.

first: Zhang

last: Lin

first: Kuang

last: Yashu


title: Antitumour activity of Micromeria fruticosa on Cancer Cell Lines

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

country: India

institute: Genotypic Technology

summary: Investigate the mechanistic pathway for the antitumour activity of M. fruticosa on different cancer cell lines

overall_design: Organism : Homo sapiens, Agilent's Human Gene Expression  8x60k Array (AMADID: 072363)

first: Eman

last: Abu-Gharbieh

first: Bipin

last: Chand


title: Autophagy deficient melanocytes display a senescence associated secretory phenotype that includes oxidized lipid mediators

status: Public on Jun 29 2019

city: Vienna

first: Markus

last: Jeitler

address: Lazarettgasse 14

country: Austria

institute: Medical University Vienna

summary:
Autophagy is a recycling program for cells to adapt to metabolic needs and to stress. Defects in autophagy can affect metabolism, aging, proteostasis and inflammation.
We used microarrays to determine the changes in global gene expression in murine melanocyte upon genetic inactivation of the essential autophagy gene Atg7 and as secondary aim wheter the gene regulation by ultraviolet A light is affected by the Atg7 knockout

overall_design: This study was performed in biological duplicates for autophagy competent and deficient melanocytes.

first: Chunya

last: Ni

first: Marie-Sophie

last: Narzt

first: Ionela-Mariana

last: Nagelreiter

first: Cheng-Feng

last: Zhang

first: Lionel

last: Larue

first: Heidemarie

last: Rossiter

first: Johannes

last: Grillari

first: Erwin

last: Tschachler

first: Florian

last: Gruber


title: Immunosubtyping of breast cancer reveals distinct myeloid cell biology and immunotherapy resistance mechanisms

city: Houston

first: Ik Sun

last: Kim

state: TX

address: 1 Baylor Plaza

department: Lester and Sue Smith Breast Center

institute: Baylor College of Medicine

summary: Cancer-induced immune responses affect tumor progression and therapeutic response.  In multiple murine models and clinical datasets, we identified large variations of neutrophils and macrophages, which define “immune subtypes” of triple negative breast cancer (TNBC) including neutrophil-enriched (NES) and macrophage-enriched subtypes (MES). Different tumor-intrinsic pathways and mutual regulation between macrophages/monocytes and neutrophils contribute to the development of dichotomous myeloid compartment. MES contains predominantly macrophages that are CCR2-dependent and exhibit variable responses to immune checkpoint blockade (ICB). NES exhibits systemic and local accumulation of immunosuppressive neutrophils (or granulocytic myeloid-derived suppressor cells (gMDSCs), is resistant to ICB, and contains a minority of macrophages that appear to be unaffected by CCR2 knockout. A MES-to-NES conversion mediated acquired ICB resistance of initially sensitive MES models. Our results demonstrate diverse myeloid cell frequencies, functionality, and potential roles in immunotherapies, and highlight the need to better understand the inter-patient heterogeneity of the myeloid compartment.

overall_design: Transcritomic profiling of 1) eight different breast tumor cell lines cultured in vitro and 2) FACS-purified tumor-infiltrating neutrophils and macrophages from four breast tumors in vivo. Each sample was prepared in triplicate.

first: Xiang

first: Qianxing

last: Mo

first: Yuande

last: Tan


title: Haemophilus influenzae responds to the steroid beclomethasone used in asthma therapy by modulation of biofilm formation and antibiotic tolerance

city: Belfast

first: Shi-qi

last: An

address: Lisburn Road

institute: Queen's University Belfast

overall_design: mRNA profiles  of H. influenzae Rd KW20 strains (wild type, HI0628 mutant, wild type with beclomethoasome and  HI0628 mutant with beclomethoasome) were generated by deep sequencing, in triplicate, using Illumina MiSeq.

first: Liang

last: Yang


title: Defects of mitochondrial RNA turnover lead to the accumulation of double-stranded RNA in vivo

city: Solna

middle: Andreas

last: Schober

address: Solnavägen 9

department: Department of Medical Biochemistry and Biophysics (MBB)

country: Sweden

institute: Karolinska Institutet

summary: The RNA helicase SUV3 and the polynucleotide phosphorylase PNPase are involved in the degradation of mitochondrial mRNAs but their roles in vivo are not fully understood. Additionally, upstream processes, such as transcript maturation, have been linked to some of these factors, suggesting either dual roles or tightly interconnected mechanisms of mitochondrial RNA metabolism. To get a better understanding of the turn-over of mitochondrial RNAs in vivo, we manipulated the mitochondrial mRNA degrading complex in Drosophila melanogaster models and studied the molecular consequences. Additionally, we investigated if and how these factors interact with the mitochondrial poly(A) polymerase, MTPAP, as well as with the mitochondrial mRNA stabilising factor, LRPPRC. Our results demonstrate a tight interdependency of mitochondrial mRNA stability, polyadenylation and the removal of antisense RNA. Furthermore, disruption of degradation, as well as polyadenylation, leads to the accumulation of double-stranded RNAs, and their escape out into the cytoplasm is associated with an altered immune-response in flies. Together our results suggest a highly organised and inter-dependable regulation of mitochondrial RNA metabolism with far reaching consequences on cellular physiology.

overall_design: Mitochondrial and cytosolic RNA of Drosophila mutants with defects in mitochondrial RNA turnover was enriched with anti-dsRNA J2 antibody and deep sequenced.

first: Aleksandra

last: Pajak

first: Isabelle

last: Laine

first: Paula

last: Clemente

first: Najla

last: El-Fissi

middle: A

first: Camilla

last: Maffezzini

first: Javier

last: Calvo-Garrido

first: Rolf

last: Wibom

first: Roberta

last: Filograna

first: Ashish

last: Dhir

first: Anna

last: Wedell

first: Christoph

last: Freyer

last: Wredenberg


title: Effects of transcription on genome - nuclear lamina interactions: DamID-seq data

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

summary: In mammalian nuclei, transcriptionally active genomic regions tend to localize to the interior of the nucleus while inactive regions are often located at at the nuclear lamina.  In this study we activated specific genes in lamina-associated domains by TALE-VP64 or CRISPRa-mediated activation. We also reduced transcription of individual genes by knockout of promoter/enhancer regions, or by insertion of a transcription termination sequence. In each case we  generated  genome-wide DamID maps to determine changes in nuclear lamina interactions, and in selected cases we also generated Repli-seq maps and/or RNAseq data.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Transcription was locally manipulated in mouse and human cell lines by using several techniques: random integration of a hPGK-EGFP expression cassette, TALE-VP64, CRISPRa, deletion of endogenous gene promoters or truncation of an endogenous transcript. Changes in 3D genome architecture were assesses by mapping lamina interaction with DamID.

first: Laura

last: Brueckner

first: Tom

last: van Schaik

first: Daan

last: Peric-Hupkes

first: Christ

last: Leemans

first: Jiao

last: Sima

first: Peiyao

last: Zhao

first: David

last: Gilbert


title: Effects of transcription on genome - nuclear lamina interactions: Repli-seq data

overall_design: Transcription of individual genes was manipulated in  human RPE-1 cells by CRISPRa. Changes in replication timing were determined by Repli-seq.


title: RNA-Sequencing analysis of reproduction/meiosis in Selaginella moellendorffii

city: shanghai

first: luoyan

last: zhang

address: songhu Road 2005

institute: fudan university

summary: To investigate global gene expression during meiosis in S. moellendorfii, digital gene-expression profiling of a series of sporangia at different developmental stages was performed by Illumina HiSeq™ 2000 sequencing platforms, with young leaves being used as a control. The samples were collected from South Mountain, Chongqing (29°33'44.18"N; 106°37'35.62"E) and stored in RNAlater solution. Total RNAs were extracted using the TRIzol solution. The clean reads were aligned to the genome sequence of S. moellendorfii at JGI database by SOAP2. Gene expression levels were calculated from the number of uniquely aligned clean reads and then normalized into units of Reads Per Kilobase per Million reads mapped (RPKM). Genes were considered to be differentially expressed if they had an FDR < 0.05, P-value < 0.05, and the absolute value of log2Ratio ≥ 1 between reproductive and vegetative samples. As a result, 5416 genes were found to be up-regulated in reproductive/meiotic samples.

overall_design: Gene expression patterns of a series of sporangia at different developmental stages was detected by Illumina HiSeq™ 2000 sequencing platforms, with young leaves being used as a control.

first: Ji

last: Yang

first: Luoyan

last: Zhang


title: Identifying signals from the skeletal muscle niche that regulate satellite cell function

city: Stevenage

first: Paul

last: Wilson

state: Hertfordshire

address: GlaxoSmithKline Medicine Research Centre

department: Target Sciences

institute: GSK

summary: Skeletal muscle is the most common tissue in the body. Its continued maintenance and regeneration throughout life is essential to the function of the organism. Satellite cells are critical to regeneration of the skeletal muscle and strategies to improve function of satellite cells are of great importance. Muscle-resident Fibro-Adipogenic Precursors (FAPs) cells are a critical component of the satellite cell niche and help orchestrate efficient muscle regeneration and potentiate satellite cell differentiation via soluble or secreted factors. Populations with similar phenotype and function to muscle FAPs have been isolated from the skin and white adipose tissue. Interactions between tissue-specific FAP cells and resident stem cells in those tissues might be conserved. Therefore, defining specific factors that mediate the relationship between muscle FAPs and satellite cells would have implications for other organs.

overall_design: Use parabiosis as a model to determine if muscle FAPs can enter cross-circulation.  Perform RNA sequencing of muscle and lung FAPs to identify transcripts that stimulate satellite cell differentiation

first: Amy

last: Wagers

first: Rohan

last: Manohar


title: Effects of transcription on genome - nuclear lamina interactions

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

overall_design: Refer to individual Series


title: Effects of transcription on genome - nuclear lamina interactions: RNA-seq data

overall_design: Transcription of individual genes was manipulated in human RPE-1 cells by  CRISPRa. Changes in gene expression were assayed by RNA-seq.


title: SIN3 LIKE genes mediate long-day induction of flowering but inhibit the floral transition in short days through histone deacetylation in Arabidopsis

first: fei

last: huang

address: No. 3888 Chenhua Road, Shanghai 201602, P. R. China

institute: Chinese Academy of Sciences (CAS)

summary: We show that in Arabidopsis SIN3 LIKE (SNL)family genes encoding a scoffold protein for assembly of histone deacetylase complex, directly regulate the expression of an FT activator and three FT repressors to regulate the transition to flowering in short days and long days, respectively. Under inductive long days, SNLs including SIN3 LIKE 1(SNL1) to SNL5, function in partial redundancy to repress the expression of three AP2 family transcription factors that repress FT expression, and thus mediate long-day induction of FT expression and promote the transitiion to flowering. In contrast, under non-inductive short days SNLs act to inhibit the floral transition, partly through direct repression of a MADS box transcriptional factor that promotes FT expression. Thus, our results reveal that SNLs, through histone deacetylation, play a novel dual role for the control of flowering in the long-day plant Arabidopsis: inhibiting flowering when the day length is shorter and promoting the floral transition when days become longer than a threshold length.

overall_design: Total RNAs were extracted from the aerial parts of 11-day-old seedlings of LDs grown wild type(WT) and snl1/2/3/4/5 quintuple mutant (snl1-5) (harvested at ZT5) by Rneasy Plus mini kit (Qiagen). Total RNAs (1.0μg) form each sample were used for library preparation with NEBNext Ultra Directional RNA Library Prep kit for Illumina (New England BioLabs, E7420L) flowering the manufacturer's instructions. Prepared libraries were assessed for quality using NGS High-Seneitivity kit on a fragment analyzer (AATI) and quantified using a Qubit 2.0 fluorometer(Thermo Fisher Scientific). All libraries were sequenced on an Illumina HiSeq sequencer. Three biological replicated of each genotype were sequenced.

first: He

last: Yuehui

first: Huang

last: Fei


title: Paf1C regulates RNA polymerase II progression by modulating elongation rate

first: Liming

last: H ou

institute: NYU Langone Health

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Elongation factor Paf1C regulates several stages of the RNA polymerase II (Pol II) transcription cycle, although it is unclear how it modulates Pol II distribution and progression in mammalian cells. We found that conditional ablation of Paf1 resulted in the accumulation of unphosphorylated and Ser5 phosphorylated Pol II around promoter proximal regions and within the first 20-30 kb of gene bodies, respectively. Paf1 ablation did not impact the recruitment of other key elongation factors, namely, Spt5, Spt6, and the FACT complex, suggesting that Paf1 function may be mechanistically distinguishable from each of these factors. Moreover, loss of Paf1 triggered an increase in TSS-proximal nucleosome occupancy, which could impose a considerable barrier to Pol II elongation past TSS-proximal regions. Remarkably, accumulation of Ser5P in the first 20-30 kb coincided with reductions in histone H2B ubiquitylation within this region. Furthermore, we show that nascent RNA species accumulate within this window, suggesting a mechanism whereby Paf1 loss leads to aberrant, prematurely terminated transcripts and diminution of full-length transcripts. Importantly, we found that loss of Paf1 results in Pol II elongation rate defects with significant rate compression. Our findings suggest that Paf1C is critical for modulating Pol II elongation rates by functioning beyond the pause-release step as an "accelerator" over specific early gene body regions.

overall_design: ChIP-seq, Pro-seq, ssRNA-seq, MNase-seq and ATAC-seq after conditional knockout Paf1 or siRNA-mediated knockdown of Paf1 in mouse C2C12 myoblast cells

last: Hou

first: Yating

last: Wang

first: Yu

last: Liu

first: Ilya

last: Shamovsky

first: Evgeny

last: Nudler

first: Bin

last: Tian

first: Brian

last: Dynlacht


title: Transcriptome characterization of radiation-induced sarcomas

city: Toulouse

first: Frédéric

last: Chibon

address: 2 avenue Hubert Curien

department: Team 19 - INSERM UMR1037

country: France

institute: Cancer Research Center of Toulouse

summary: We performed RNA sequencing on secondary sarcomas, arising from previous radiation therapies. We investigated whether such radiation-induced tumours harbour specific genomic and/or transcriptomic alterations compared to sporadic (primary) sarcomas.

overall_design: We compared 77 radiation-induced (secondary) sarcomas to 93 sporadic (primary) sarcomas. Transcriptome is studied by RNA-seq (Illumina) and genome is studied by array-CGH (Affymetrix SNP6 and CytoScan HD) plus gene fusions identified using RNA-seq.

first: Tom

last: Lesluyes


title: Expression profiling in exosomal miRNAs of human bone marrow stromal cells derived from myelodysplastic syndrome patients

status: Public on Jun 26 2019

city: Shinjyuku

first: Tomohiro

last: Umezu

state: Tokyo

address: 6-1-1 Shinjyuku

department: Department of Molecular Pathology

country: Japan

institute: Tokyo Medical University

summary:
Myelodysplastic syndromes (MDS) constitute a heterogeneous group of clonal hematological disorders characterized by the presence of peripheral cytopenias and an increased risk of transformation into acute myeloblastic leukemia (AML). These hematological disorders are complex and their origin in a clonal hematopoietic stem cell disorder is accepted. In the last few years, the importance of the bone marrow (BM) microenvironment has been highlighted. Bone marrow stromal cells (BMSCs) are a non-hematopoietic BM cell population considered to be the osteoblastic progenitors and a key component of the hematopoietic microenvironment. As usual, it was considered that intercellular communication could be achieved by direct cell-to-cell contact or the exchange of soluble factors and intercellular adhesion molecule. Recently, a new mechanism of intercellular communication based on the secretion of extracellular esicles (EVs) has been described. Such a mechanism modifies the functional properties of recipient cells by the transfer of bioactive molecules such as mRNA, proteins and micro-RNAs, among others.
BMSCs play an important role in bone marrow environment. Recent evidences suggest that EVs act as a mediator of cell-cell interaction in hematologic neoplasms. To clarify the possible association between the cargo of BMSC-EVs and disease severity, we performed miRNA profiling in BMSC-EVs derived from MDS patients.

overall_design: Human BMSCs of elderly (68 and 72 years old) healthy donors (Normal-BMSCs) were purchased from Lonza. BMSCs from 29 patients (22 patients with MDS, and 7 with post-MDS AML), age 22~87,  were obtained by classical adhesion methods after obtaining a written informed consent (IRB approval no.2684). We tentatively separated MDS patients into two groups according to the IPSS-R: low-risk group (n=13; very low to intermediate risk) and high-risk group (n=9; high and very high risk group). The extracellular vesicules (EVs) from culture medium of BMSCs were isolated by Total exosome isolation regent (Invitrogen). Total RNA from each EV fractions (2 Normal-BMSCs, 13 low-risk MDS-BMSCs,  9 high-risk MDS-BMSCs,and 7 AML-BMSCs) was extracted by the miRneasy mini kit (Qiagen). The EV-miRNA profiling was done using a TaqMan low-density array (ABI), and Student’s t-test was used to determine statistical significance for comparisons between low-risk and high-risk  groups using R software.


title: Bangladeshi women living in UK: Buccal cell DNA methylation analysis

city: Nottingham

first: Reinhard

last: Stoger

address: Sutton Bonington Campus

department: School of Biosciences

institute: Universityf Nottingham

type: Methylation profiling by genome tiling array

summary: Prior studies of Bangladeshi migrants in the UK revealed that reproductive function is adaptive, responding to different environments during childhood by adjusting the timing of puberty, reproductive lifespan and overall reproductive function. Here we aimed to understand the basis of this plasticity. Our goals were to establish whether epigenetic mechanisms play a role in the plasticity of this adaptive reproductive phenotype. We hypothesized that women growing up in Bangladesh would have distinct DNA methylation signatures compared to those who moved to the UK at a young age or were born to Bangladeshi parents in the UK. Some of these environmentally induced epigenetic differences would be detected in buccal cell DNA and reflect the divergent gene expression responsible for the altered reproductive function. The women of the study who grew up in Bangladesh were relatively affluent, well-nourished and rarely performed manual work, but a significant confounding factor in their early life was the level of disease load presenting a chronic immune challenge

overall_design: buccal cell DNA samples from 31 adult  Bangladeshi women (age 28.1 ± 5.0) living in London, UK were interogated for their methylation levels using Illumina-MethylationEpic arrays. Sample #12 loaded twice on the array. Quality controls following analysis of the raw data led to the removal of data derived from samples #6, #7 and #10.  Usable data: Bangladeshi women experienced their childhoods in Bangladesh  (n=15), or in the UK (n=13).

first: Ben

last: Bar-Sade

first: Or

last: Eden

first: Lilach

last: Pnueli

first: Kurshida

last: Begum

first: Gregory

last: Leeman

first: Richard

last: Emes

last: Stöger

first: Gillian

last: Bentley

first: Philippa

last: Melamed


title: RNAseq based trascript profilling of MCF7-xenograft mice treated with one of three CDK4/6 inhibitiors

city: Boston

first: Kartik

last: Subramanian

address: 200 Longwood Avenue

institute: Harvard Medical School

summary: We compare differences in gene expression induced after treating MCF7-xenograft mice with either ribociclib, palbociclib, or abemacicilb daily for 4 days.

overall_design: Mice were engrafted with MCF7 cells in each flank and allowed to grow to ~300 mm3. The animals were then randomly assigned to treatment groups, and treated daily for four days with ribociclib (150 mg/kg), palbociclib (150 mg/kg), abemaciclib (25, 75, 100, 125, or 150 mg/kg), or vehicle control (0.5% (w/v)

first: Marc

last: Hafner

first: Caitlin

last: Mills

first: Sarah

last: Boswell


title: Multiomics Profiling Establishes the Polypharmacology of FDA-Approved CDK4/6 Inhibitors and the Potential for Differential Clinical Activity.

first: Peter

last: Sorger

state: MA

department: Department of Systems Biology

summary: We compared three CDK4/6 inhibitors that have recently emerged as highly promising agents for advanced breast cancers by performing transcriptional profiling (mRNA-Seq) on a panel of seven breast cancer cell lines following 6 or 24 hours of drug exposure at concentrations ranging from 0.3 to 3.0 uM.

overall_design: mRNA levels for 7 breast cancer cell lines treated with one of three CDK4/6 inhibitors (abemaciclib, palbociclib, or ribociclib) at either 0.3 uM, 1.0 uM (only for MCF7), or 3.0 uM for either 6 or 24 hours.

first: Chris

last: Chen


title: Integrative transcriptomic analysis reveals mechanisms controlling the reciprocity of epithelial and mesenchymal genes during epithelial-to-mesenchymal transition

city: Yokohama

first: Kazuhide

last: Watanabe

state: Kanagawa

address: 1-7-22 Suehiro-cho Tsurumi-ku

department: Center for Integrative Medical Sciences

institute: Riken

summary: Epithelial-to-mesenchymal transition (EMT) is an important developmental process that is also activated during disease progressions. Many genes involved in EMT have been identified to date, but the key molecules governing the coupling between the dynamics of epithelial genes and that of the mesenchymal genes are unclear. In addition, it has been shown that there is a remarkable diversity of EMT phenotypes in different pathological conditions or microenvironments, but its mechanistic basis remains elusive. In this study, we used transcriptomic analysis to identify the roles of an EMT-inducing transcription factor ZEB1 in controlling epithelial and mesenchymal genes. We found that the mesenchymal genes exhibit a significant diversity in terms of their responsiveness to ZEB1. We applied machine learning approaches to the transcriptome data and identified three groups of M-genes that are controlled by EMT promoting factors via different types of regulatory circuits. We inferred the functional differences among the M-gene clusters in motility regulation of cultured cells and in survival of breast cancer patients. We characterized the roles of ZEB1 in controlling the reciprocity and reversibility of EMT using mathematical modeling. Our integrative analysis reveals the key roles of ZEB1 in coordinating the dynamics of a large number of genes during EMT, and it provides new insights into the mechanisms for the diversity of EMT phenotypes.

overall_design: MCF10A cells were treated by combinations of perturbations as follows: recombinant TGF-beta (200 nM) for 4 weeks, CRISPR/Cas9-mediated ZEB1 knockout, doxycycline-inducible expression of exogenous ZEB1, and TGF-beta type1 receptor inhibiotr (SB-431542, 10microM) treatment


title: Epithelial signatures of chemical-induced lung adenocarcinoma

city: Munich

first: Georgios

last: Stathopoulos

state: Bayern

address: Max-Lebsche-Platz

department: Comprehensive Pneumology Center

country: Germany

institute: Helmholz Zentrum Munich


title: Digital gene expression (DGE) based transcript profiling of CDK inhibitors

summary: We compare differences in gene expression induced after 6 hours of exposure to one of three CDK4/6 inhibitors or a pan-CDK inhibitor

overall_design: mRNA levels for 7 breast cancer cell lines or PDX models treated with one of three CDK4/6 inhibitors (abemaciclib, palbociclib, or ribociclib)  at 4 concentrations (0.1, 0.3, 1, 3 um) or the pan-CDK inhibitor alvocidib at 2 concentrations (0.1, 1 um) in triplicate.


title: Neuroligin-4 Regulates Excitatory Synaptic Transmission in Human Neurons

city: Stanford

first: Samuele

last: Marro

state: California

address: 256 Campus Drive

institute: Stanford University

summary: The autism-associated synaptic-adhesion gene Neuroligin-4 (NLGN4) is poorly conserved evolutionarily, limiting conclusions from Nlgn4 mouse models for human cells. Here, we show that the cellular and subcellular expression of human and murine Neuroligin-4 differ, with human Neuroligin-4 primarily expressed in cerebral cortex and localized to excitatory synapses. Overexpression of NLGN4 in human neurons resulted in an increase in excitatory synapse numbers but a remarkable decrease in synaptic strength. Human neurons carrying the syndromic autism mutation NLGN4-R704C also formed more excitatory synapses but with increased functional synaptic transmission due to a postsynaptic mechanism, while genetic loss of NLGN4 did not significantly affect synapses in the human neurons analyzed. Thus, the NLGN4-R704C mutation represents a change of function mutation. Our work reveals contrasting roles of NLGN4 in human and mouse neurons, suggesting human evolution has impacted even fundamental cell biological processes generally assumed to be highly conserved.

overall_design: We compared the global gene expression profiles of induced neuronal (iN) cells. iN cells were derived from human embryonic stem cells (H1) by expression of transcription factors. Ngn2 was used to generate Ngn2-iN, Alsc1 and Dlx2 to generate AD-iN cells and Alsc1 and Myt1l to generate AM iN cells. AM and Ngn2 iN cells are glutamatergic neurons whereas AD iN cells are GABAergic. Mature iN cells cultured with mouse glia (6 weeks after transgene induction) were dissociated with Trypsin and FACS-sorted in Trizol LS. To distinguish from glial cells, iN cells were transduced with a lentiviral vector expressing EGFP under the control of CAG promoter together with the reprogramming transcription factors.

first: Marius

last: Wernig


title: Aging-Associated Decrease in the Histone Acetyltransferase KAT6B Causes Myeloid-Biased Hematopoietic Stem Cell Differentiation

city: Bar Harbor

first: Jennifer

last: Trowbridge

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

summary: Purpose: Gene expression profiling of long term hematopoietic stem cells (LT-HSCs) transduced with Kat6b shRNA and Non-Targeting Control (NTC)

overall_design: LT-HSCs were transduced with viral supernatant containing shRNA against Kat6b and Non-Targeting Control (NTC) in triplicates. Transduced cells were sorted in RLT buffer after 2 days in culture and send for sequencing

first: Eraj

middle: S

last: Khokhar

first: Sneha

last: Borikar

first: Elizabeth

last: Eudy

first: Tim

last: Stearns

first: Kira

last: Young

middle: J


title: Gene expression of hiPSC-derived DA Neurons harboring SNCA A53T mutation or genome Corrected and hESC-derived WT DA Neurons and  SNCA A53T mutation introduced Corrected

status: Public on Jun 25 2019

city: Guelph

first: Scott

last: Ryan

state: ON

address: 50 Stone Rd E

country: Canada

institute: University of Guelph

summary: A53T mutant human DA neurons or their isogenic control counterparts were differentiated to DA-Neurons for 35 days. Gene expression profile was analysed to assess the effect of  the genetype on gene expression.

overall_design: In the current study, Isogenenic hiPSCs and hESC differing exclusively at a single amino acid (A53T)  were differentiated into dopamine producing neurons.  Gene expression profile was analysed to assess the effect of both genetype on gene expression.


title: RNA-seq transcriptome profiling of young gametophytes and capsules at different developmental stages of Pogonatum aloides

first: luoyan

last: zhang

summary: To investigate global gene expression during development in Pogonatum aloides, digital gene-expression profiling of capsules at different developmental stages was performed by Illumina HiSeq™ 2000 sequencing platforms, with the young gametophyte being used as a control. The samples of P. aloides were collected from Jiming Mountain, Ningde (26°56'39.34"N; 118°57'21.45"E, and stored in RNAlater solution. Total RNAs were extracted using the TRIzol reagent. The RNA-Seq reads were assembled into transcripts using SOAPdenovo v1.04. Gene expression levels were calculated from the number of uniquely aligned clean reads and then normalized into units of Reads Per Kilobase per Million reads mapped (RPKM). Genes were considered to be differentially expressed if they had an FDR < 0.05, P-value < 0.05, and the absolute value of log2Ratio ≥ 1 between reproductive and vegetative samples. As a result, 4007 genes were found to be up-regulated in reproductive/meiotic samples.

overall_design: Gene expression patterns of capsules at different developmental stages of P. aloides were detected by Illumina HiSeq™ 2000 sequencing platforms, with the young gametophyte being used as a control.

first: Ji

last: Yang

first: Luoyan

last: Zhang


title: Epithelial-mesenchymal transition markers screenedina cell-based model and validated in lung adenocarcinoma

city: wuhan

first: dong

last: chen

state: Hubei

address: GaoXin 2nd Road

institute: ablife

summary: The epithelial-to-mesenchymal transition (EMT) process in cancer enables the migratory and invasive capabilities associated with metastatic competence. The cancer microenvironment plays an important role in inducing the occurrence of EMT. A number of extracellular stimuli and associated signaling pathways have been identified to promote EMT, however, molecular features during the early stages of EMT are poorly understood. Here we have established a novel in vitro EMT-inducing system that mimi cs tumor microenvironment and allows for close monitoring of the EMT progress. Using RNA-seq and miRNA-seq, we analyzed the transcriptomic transitions accompanying the progression of EMT, and pinpointed several molecular features during early EMT of the lung carcinoma cells.

overall_design: CAF conditioned medium treated and control A549 cells were collected at six different time points (3h, 6h, 12h, 24h, 48h, 72h) for RNA-seq and miRNA-seq, two biological replicates for each sample.

first: Jing

last: Song

first: Wenqing

last: Wang

first: Yi

first: Qi


title: Assessment of the effect of RNase A-treated Enterococcus feacalis strain EC-12(EC-12) or untreated EC-12 on transcriptome profiles in human peripheral blood mononuclear cells

city: Kyoto

first: Ryo

last: Inoue

address: 1-5, Hangi-cho, shimogamo

institute: Kyoto Prefectural University

summary: Whole blood was collected from healthy adult and peripheral blood mononuclear cells (PBMC) were isolated.  PBMCs were cultured in medium or stimulated with RNase treated EC-12 or untreated EC-12 for 6hours. Then transcriptome profiles in PBMC were obtained.

overall_design: Comparison: control PBMC (medium) vs PBMC situmulated with untreated EC-12, and control PBMC vs PBMC situmulated with RNase-treated EC-12, PBMC stimulated with untreated EC-12 vs PBMC stimualted with RNase treated EC-12. Biological replicates; 3 donors; 2 control(medium), 3 untreated EC-12, 3 RNase-treated EC-12.

first: R

last: Tamaki


title: Differential Gene expression of C. elegans larvae following tunicamycin treatment in the absence of manf-1

city: Bethesda

first: WeiPing

last: Chen

state: MD

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

department: GCL

institute: NIDDK/NIH

summary: Microarray analysis was performed to evaluate the changes in gene expression that are associated with manf-1 deficiency with and without exposure to tunicamycin. RNA was isolated from four groups, (wildtype (N2) and manf-1 mutant (tm3603) L1 stage larve with and without 5 hours exposure to tunicmycin (5microgram/milliliter)) for transcriptomic profiles analysis

overall_design: Identification of genes expressed after tunicamycin treatment in two groups (wildtype and manf-1 mutant) with three replications per group.

first: Christopher

last: Richie

first: Brandon

last: Harvey

first: Jessica

last: Hartman

first: Joel

last: Meyer


title: Stromal Mir-20a modulates paracrine CXCL8 secretion in colitis and colon cancer

city: Cleveland

first: Emina

last: Huang

state: OH

address: 9500 Euclid Ave

department: Stem Cell

institute: Lerner Research Institute/Cleveland Clinic

summary: We report the results of RNA-Seq on fibroblasts cultivated from cancerous, colitic and normal primary patient colon tissues

overall_design: Transcriptome analysis of fibroblasts isolated from cancerous/colitic and normal primary tissues.

first: E


title: Gene expression study of human endometrial receptivity in IVF implantation failure patients undergoing ovarian stimulation II

city: Mumbai

first: Indira

last: Hinduja

address: 15, Dr. G. Deshmukh Marg

institute: Jaslok Hospital and Research centre

summary: Endometrial receptivity on genomic level is one of the major cause of implantation failure in IVF patients with unexplained infertility and is a main obstacle in success of IVF. Gene expression profiles of implantation failure cases of unexplained infertility were compared with proven healthy oocyte donors as controls, both undergoing ovarian stimulation. The results provide additional information about gene expression profile related to endometrial receptivity in implantation failure cases especially under the influence of ovarian stimulation during IVF cycle.

overall_design: Total RNA isolated from endometrial tissue collected during implantation window from implantation failure cases with unexplained infertility (having normal hormones and endometrium with 8mm and above, triple layered) were compared with oocyte donors as healthy proven fertile controls under the influence of long protocol of ovarian stimulation during IVF.

first: Amruta

last: Pathare

first: Kusum

last: Zaveri


title: Inhibiting neutrophils activation by long-term administration of 5-amino salicylic acid reduces colitis-associated colorectal tumor burden in ApcMin/+ mice

city: Sunto-gun

first: Yoko

last: Ono

state: Shizuoka

address: 1188, Shimotogari, Nagaizumi-cho

institute: Kyowa Hakko Kirin Co., Ltd

summary: Objective  The risk of ulcerative colitis (UC)-associated colorectal cancer (CRC) increases with the duration of UC. Oral 5-aminosalicylic acid (5-ASA) formulations are the first-line treatment for mild-to-moderate UC; nevertheless, preventive effect of oral 5-aminosalicylic acid (5-ASA) formulations on UC-associated CRC remains unsolved. We investigated the impact of 5-ASA to colitis-associated neoplasia in C57BL/6J-ApcMin heterozygous (ApcMin/+) mice.  Design  ApcMin/+ mice exposed to 1.5 w/v% dextran sulfate sodium (DSS) ad libitum for 3 days followed by 25 days of tap water to develop colitis-associated neoplasia. Mice were intracolorectally administrated with 5-ASA to evaluate the effects on the number of tumors. The mechanism of action was presumed by microarray analysis using in vivo samples and was confirmed by in vitro culture of HT-29, a human colorectal adenocarcinoma cell line with supernatant of human primary neutrophils.  Results  A remission between acute and recurrent episodes of diarrhea, which were ameliorated by 5-ASA treatment were observed in this model. The number of tumors was reduced by continuous 5-ASA administration in this model. This reduction was abolished by withdrawal of 5-ASA in remission period compared to continuous 5-ASA administration. Microarray analysis revealed that neutrophils were involved in the protective mechanism of 5-ASA against proliferation of tumors. Additionally, calprotectin production from human primary neutrophil as activation marker was strongly correlated with proliferation of HT-29.

overall_design: ApcMin/+ mice were given drinking water supplemented with 1.5 w/v% dextran sulphate sodium (DSS) for 3 days to induce colitis, and were intracolorectally administrated with 5-aminosalicylic acid (5-ASA) or Saline (Control) for 28 days.  ApcMin/+  mice (Sham) were given drinking water alone for 28 day.  Mice of each groups (Sham, 5-ASA and Control) were sacrified and were collected macroscopically distinguished non-tumor regions in colon on day 28.

first: Yasumasa

last: Kanai

first: Akiko

last: Katsumata

first: Toshio

last: Ota


title: Mayo GBM Patient Derived Xenograft National Resource

city: ROCHESTER

first: Shulan

last: Tian

state: Minnesota

address: 200 1st street SW

department: Health Science Research

institute: Mayo Clinic

summary: Genome wide DNA methylation profiling of GBM xenografts. The Illumina EPIC 850k Human DNA methylation array used to obtain DNA methylation profiles across approximately 800,000 CpGs in GBM xenograft samples. Samples included xx GBM xenografts.

overall_design: Bisulphite converted DNA from the 78 samples were hybridised to the Illumina Infinium Human MethylationEPIC Beadchip

first: Jann

last: Sarkaria


title: HDL protects against myocardial ischemia reperfusion injury via miR-34b and miR-337 expression which requires STAT3

city: Geneva

first: Celine

last: Delucinge

address: 1 rue Michel Servet

department: iGE3 Genomics Platform

country: Switzerland

institute: University of Geneva

summary: We  investigated whether the cardioprotective effect of HDL modulates miRNAs as a downstream target of STAT3 activation.

overall_design: miRNAs profile was analysed by microarray. The analysis was divided in 6 groups: 3 experimental protocols (sham=no ischemia, IR=ischemia reperfusion protocol and IR+HDL= ischemia reperfusion protocol, treated with HDL at the onset of reperfusion) and 2 mouse genotype (WT=willd type, STAT3_KO=STAT3 cardiac-restricted KO). This microarray  analysis includes 3 mice per group.

first: Sarah

last: Pedretti

first: Marie-Claude

last: Brulhart-Meynet

first: Fabrizio

last: Montecucco

first: Sandrine

last: Lecour

first: Richard

middle: W

last: James

first: Miguel

last: Frias


title: Gene expression profile of TE1 cell line with siFOXM1 treatment

city: Rio de Janeiro

first: Pedro

last: Nicolau Neto

state: RJ

address: 37 Andre Cavalcanti Street

department: PCM

country: Brazil

institute: INCA

summary: To identify the differently expressed genes after silencing of FOXM1 in TE1 cell line using siRNA

overall_design: To compare the gene expression profile in TE1 cell line treated with siFOXM1 or with scramble

middle: P

last: Nicolau-Neto

first: Paulo

last: Santos

first: Luis

middle: L

last: Pinto


title: Using Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes as a Model to Study Trypanosoma cruzi Infection

status: Public on Jun 24 2019

first: Joseph

last: Wu

state: Carlifornia

address: Stanford University School of Medicine

institute: Stanford University School of Medicine

summary: Human cardiomyocyte responses to Chagas disease

overall_design: hiPSC-CMs replicates in both control and disease conditions.

first: Adriana

last: Bozzi


title: Comparison of gene expression profiles between a bone marrow-derived primary mesenchymal stromal cell clone (MSC2) without osteoblastic induction and with 14 days or 28 days of ostoblastic induction

city: Birmingham

first: Qiling

last: He

state: AL

address: 1825 University Blvd, Shelby Building

department: Microbiology

institute: University of Alabama at Birmingham

summary: Multiple hypothesis testing using a false discovery rate of p<0.01 and fold-change of 1.5 detected 4257 genes that were differentially expressed at least between two groups among MSC2 without osteoblastic induction, MSC2 with osteoblastic induction for 14 or 28 days

overall_design: 9 samples were analyzed. Among the 9 samples, 3 independent replicates for MSC2 without osteoblastic induction, 3 independent replicates for MSC2 with 14 days of osteoblastic induction, and 3 independent replicates for MSC2 with 28 days of osteoblastic induction

first: C

last: Swindle

first: Chao

last: Wan

first: Robert

last: Flynn

first: Dongquan

last: Chen

first: Christopher

last: Klug


title: RNA sequencing data

city: Madrid

first: Osvaldo

last: Graña

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Structural Biology

country: Spain

institute: CNIO

summary: RNA sequencing data of AdGFP cell from mouse PDAC

overall_design: 6 mouse PDAC cell lines were infected with Adeno GFP

first: Carolina

last: Navas

first: Carmen

last: Guerra


title: H3K36 methylation and the chromodomain protein Eaf3 are required for proper co-transcriptional spliceosome assembly

city: Los Angeles

first: Stephen

last: Douglass

state: CA

address: 5128 TLSB Terasaki Life Sciences Building, 610 Charles Young Drive East

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

summary: In the eukaryotic cell, spliceosomes assemble onto pre-mRNA cotranscriptionally. The fact that spliceosome assembly takes place in the context of a dynamic chromatin environment suggests that the state of the chromatin may affect splicing. The molecular details and mechanisms through which chromatin regulates RNA splicing, however, are still unclear. Here, we show a widespread role for the histone methyltransferase Set2 and its histone modification, H3K36 methylation, in pre-mRNA splicing through high-throughput sequencing. Moreover, we find that the effect of H3K36 methylation on pre-mRNA splicing is not dependent on changes in RNA polymerase II elongation, but are driven by the chromodomain protein Eaf3. We find that Eaf3 is recruited to intron-containing genes and that Eaf3 physically interacts with the splicing factor Prp45. Eaf3 acts with Prp45 and Prp19 after formation of the pre-catalytic B complex around the time of splicing activation revealing the step in splicing that is regulated by H3K36 methylation. These studies support a model whereby H3K36 facilitates recruitment of an “adapter protein” to support efficient, constitutive splicing.

overall_design: RNA sequence data of 4 samples with two biological replicates each were analyzed, including wildtype, set2 deletion, eaf3 deletion, and H3K36A point mutation.  ChIP sequence of RNA polymerase II S2P of three samples, wildtype with 2 technical replicates, H3K36A point mutation without replication, and eaf3 deletion without replication were also analyzed along with ChIP-seq of wildtype H3K36 trimethylation without replication.  For ChIP sequencing, we analyzed as compared to three input libraries, including one replicate each for wildtype, H3K36A, and eaf3 deletion.

first: Calvin

last: Leung

first: Marco

last: Morselli

first: Matthew

last: Obusan

first: Marat

last: Pavlyukov

first: Matteo

last: Pellegrini

first: Tracy

last: Johnson


title: Expression data form P90 mouse hippocampus - various mutant condition

city: Daejeon

first: Jina

last: Park

address: 291 Daehak-ro, Yuseong-gu

department: Biological Science

country: South Korea

institute: KAIST

summary:
The level of Synaptotagmin-2 (Syt2) was altered by deletion of IPMK protein in the male mouse brain. We investigated gene expression changes in the hippocampal region of IPMK conditional knockout (cKO) mice by performing genome-wide transcriptome analyses.
In this dataset, we include the expression data obtained from dissected mouse hippocampus using loss-of-function IPMK mutants. These data are used to obtain 5 genes that are differentially expressed in response to IPMK signaling

overall_design: 4 Total samples were analyzed. We prepared two sample mRNA of each group, IPMK WT & IPMK cKO. Genes with an FDR≤10% and a fold-change ≥1.5 were selected.

first: Seyun

last: Kim


title: Applying genome-wide CRISPR screens for therapeutic discovery in FSHD

city: New Haven

first: Monkol

last: Lek

state: CT

address: 300 Cedar st

institute: Yale University School of Medicine

summary: The emergence of CRISPR gene-editing technologies and genome-wide CRISPR libraries enables a new mechanism to efficiently perform unbiased genetic screens that can accelerate the process of therapeutic discovery for genetic disorders. This represents a significant leap forward from the extensive studies of genetic and biochemical interactions typically required to understand disease pathogenesis and development of targeted therapy. In this study, we demonstrate the utility of a genome-wide CRISPR loss-of-function library to identify therapeutic targets for facioscapulohumeral muscular dystrophy (FSHD), a genetically complex subtype of muscular dystrophy for which there is currently no treatment available. In FSHD, both genetic and epigenetic changes can lead to misexpression of DUX4, the FSHD causal gene that encodes the highly cytotoxic DUX4 protein. We performed a genome-wide CRISPR screen to identify genes whose loss-of-function conferred survival when DUX4 was expressed, thus reducing the pathogenic impact of the genetic defect. Emerging genes from our screen illuminated ‘druggable’ pathways that can be targeted with small molecule inhibitors. Treatment with PI3K/Akt/mTOR signaling inhibitors resulted in reduced DUX4 protein expression and a reduction of FSHD disease biomarkers in patient myogenic lines, as well as improved structural and functional properties of a zebrafish model of FSHD. Our genome-wide perturbation of pathways affecting DUX4 expression has empowered us to rapidly identify existing compounds with potential therapeutic benefit for FSHD. Thus, the experimental pipeline described in this paper presents an accelerated paradigm towards therapeutic discovery and is translatable to other genetic diseases with well-established phenotypic selection assays.

overall_design: Identifying genes and pathways that rescue DUX4 induced toxicity in myoblast

first: Angela

first: Louis

last: Kunkel


title: BCL6 modulates tissue neutrophil survival and exacerbates pulmonary inflammation following influenza infection

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: Epidemics of influenza virus are of great challenges to the public concern. The lung inflammation and injury caused by excessive inflammatory cell infiltration into the lungs and overproduction of inflammatory mediators are major consequences during influenza virus infection. Neutrophils are vital for anti-microbial defense. However, the roles of neutrophils during viral infections are less clear. Furthermore, the molecular regulation of neutrophil fate and function at the viral infected sites is largely elusive. We found that BCL6 deficiency in neutrophils, but not in monocytes nor lung macrophages, attenuated host inflammation and morbidity following influenza infection. Mechanistically, BCL6 bound to the neutrophil gene loci involved in cellular apoptosis specifically at the site of infection. As such, BCL6 disruption resulted in increased expression of apoptotic genes in neutrophils in the respiratory tract, but not in the circulation nor bone marrow. Consequently, BCL6 deficiency promoted tissue neutrophil apoptosis. Our results have revealed a previously unappreciated role of BCL6 in modulating neutrophil apoptosis at the site of infection for the regulation of host disease development following viral infection.

overall_design: Neutrophils were flow sorted based on their surface expression of CD11b and Ly6G from total lung cells of MRP8-Cre Bcl6 or Bcl6 fl/fl mice at day 6 post influenza virus infection. Total RNA was isolated and RNA-seq was performed.

first: Bibo

last: Zhu

first: Jie

last: Sun


title: KMT9a writes the H4K12me1 histone mark and controls metabolism and proliferation of castration-resistant prostate cancer cells

city: Freiburg

first: Eric

last: Metzger

address: Breisacherstr. 66

institute: Uniklinik-Freiburg

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

Posttranslational modifications of histones such as methylation regulate chromatin structure and gene expression. Methylation of histone lysine residues is generally performed by SET domain methyltransferases. Here, we identify the heterodimeric C21orf127/TRMT112 complex as a histone methyltransferase. Assembly of the seven-b-strand protein C21orf127 (also named Hemk2, N6amt1 or PrmC) with TRMT112 is essential to form an active enzyme, hereafter named KMT9 that writes the histone mark H4K12me1 in vitro and in vivo. We characterized the recognition mode of H4K12 by KMT9 that is formed by the assembly of KMT9a with KMT9b by solving the co-crystal structure. Genome-wide analyses revealed KMT9 and H4K12me1 enrichment at promoters of KMT9 target genes. By controlling expression of genes involved in cell cycle regulation, KMT9 regulates proliferation of androgen receptor-dependent and -independent prostate tumour cells. Importantly, KMT9 depletion severely affects proliferation of castration- and enzalutamide-resistant prostate cancer cells and xenograft tumours. Together, our data link the writing of the H4K12me1 histone mark by KMT9 with KMT9-dependent gene expression, which in consequence regulates cell cycle and proliferation. KMT9 executes these functions independently of androgen receptor and androgen signalling thus, providing a promising paradigm for the treatment of castration resistant prostate cancer.

overall_design: Refer to individual Series


city: Seattle

first: Amit

last: Sharma

state: WA

address: 1100 Fairview Ave N

department: Human Biology

institute: Fred Hutchinson Cancer Research Center

summary: In order to identify IFNα-induced host factor(s) that might inhibit replication of unadapted chimeric SIV/HIV-1 viruses (SHIVs), we measured IFNα-induced gene expression in immortalized pig-tailed macaque (Ptm) CD4+ lymphocytes. Triplicate cultures of Ptm lymphocytes were left untreated or treated with 1000 U/ml of IFNα. Twenty-four hours later, RNA was isolated, and RNA-seq libraries were prepared for sequencing. A total of 198 genes were found to be significantly differentially expressed (|logFC| ≥ 0.585 & FDR 5%) upon IFNα treatment. 147/198 genes were found to be significantly upregulated and 51/198 genes were found to be significantly downregulated regulated upon IFNα treatment.

overall_design: IFNα-induced gene expression in immortalized pig-tailed macaque CD4+ lymphocytes left untreated or treated with 1000 U/ml of IFNα.

first: Julie

last: Overbaugh


title: Defining genetic variation in widely used congenic and backcrossed mouse models reveals varied regulation of genes important for immune responses

first: Amy

last: Weinmann

address: 1825 UNIVERSITY BLVD

department: Department of Microbiology

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


title: Exploring differential transcriptome between jejunum and cecum tissue of broiler

city: bologna

first: PAOLO

middle: o

last: BOSI

state: BOLOGNA

address: Viale Fanin, 46

department: DISTAL

country: Italy

institute: UNIVERSITY OF BOLOGNA

summary:
A more in-depth exploration of gut functional aspects may be interesting in order to provide hints for action (e.g. dietary strategies) to favor gut balance maintenance (Sinha et al., 2017),  given the important role of the intestine in development of possible metabolic diseases. A careful survey on the differential gene expression may help to scouting new interesting functions and identify potential markers for testing various experimental factors.
The transcriptomes of the jejunum and cecum mucosae of  19 broiler chickens were compared.
At slaughter age (day 42), on 38 birds, selected with a homogeneous body weight, jejunum and cecum mucosae were collected by gently scraping after tissues rinsing in PSB to remove residues of digesta, and immediately frozen in liquid nitrogen and then stored at -80°C. From both tissues, total RNA was extracted using GeneJET RNA Purification Kit (Thermo Scientific)

overall_design: The analysis of whole mRNA transcript expression was done by Affymetrix© GeneChip Chicken 1.0 ST Array and hybridized arrays were scanned on Affimetrix© GeneChip Scanner 3000 7G System (Affymetrix, Santa Clara, California, USA). Data analysis was carried out on the CEL ﬁles using Transcriptomic Analysis Console (TAC) Affymetrix© software (4.0.1.36)  and Transcripts ID’s were associated to human gene names, based on Chicken Ensemble

first: Micol

last: Bertocchi

first: Federico

last: Sirri

first: Orazio

last: Palumbo

first: Giuseppe

last: Maiorano

first: Paolo

last: Bosi

last: Trevisi


title: Defining genetic variation in widely used congenic and backcrossed mouse models reveals varied regulation of genes important for immune responses [RNA-seq]

summary: In our study, we developed an alternative next-generation sequencing dataset processing strategy to identify genetic variation in backcross mouse models.  We used this approach to define SJL genetic content in B6.SJL-CD45.1 mice from different vendor sources.

overall_design: We performed RNA-seq experiments on CD4+ Th1 cells isolated from C57BL/6 or B6.SJL-Ptprca Pepcb/Boy mice from three different vendor sources.  We also performed RNA-seq experiments on CD4+ Th1 cells isolated from Tbx21-/- mice.

first: Danielle

last: Chisolm

first: Wayne

last: Cheng

first: Shelby

last: Colburn

first: Aaron

last: Silva-Sanchez

first: Selene

last: Meza-Perez

first: Troy

last: Randall


title: Complex regulatory mechanisms underlying mineral nutrient acquisition in soybean roots responsive to low pH stress

city: 广州

first: Chen

middle: Qian

last: Qian

state: 广东省

address: 天河区五山街道

institute: 华南农业大学

summary: Proton toxicity is one of the major environmental stresses limiting crop production, and becomes increasingly serious because of anthropogenic activities. To understand acid tolerance mechanisms, the plant growth, mineral nutrient accumulation and global transcriptome changes in soybean (Glycine max) in response to long-term acid stress were investigated. Results showed that acid stress significantly inhibited soybean root growth, but exhibited slight effects on the shoot growth. Moreover, concentrations of essential mineral nutrients were significantly affected by acid stress, mainly dependent on soybean organs and mineral nutrient types. The concentrations of phosphorus (P) and molybdenum (Mo) in both leaves and roots, nitrogen (N) and potassium (K) in roots and magnesium (Mg) in leaves were significantly decreased, respectively. Whereas, the concentrations of calcium (Ca), sulfate (S) and iron (Fe) were increased in both leaves and roots. Transcriptome analyses in soybean roots resulted in identifying 419 up-regulated and 555 down-regulated genes under acid conditions. A total of 38 differentially expressed genes (DEGs) were involved in mineral nutrient transportation. Among them, all the detected five GmPTs and GmZIPs, two GmAMTs and GmKUP genes, together with GmIRT1, GmNramp5, GmVIT2.1, GmSKOR, GmTPK5 and GmHKT1, were significantly suppressed. Moreover, the genes encoding transcription factors (e.g., GmSTOP2s and a GmPHL1), and genes involved in pH stat metabolic pathways were significantly up-regulated by low pH stress in soybean roots. Taken together, it strongly suggested that maintaining pH stat and mineral nutrient homeostasis are adaptive strategies of soybean responses to acid stress, which might be regulated by a complex signaling network.

overall_design: Transcriptome analyses were carried out using pH4.2 as acid treatment and pH5.8 as control, every treatment had three replicates.

first: Qianqian

last: Chen

first: Weiwei

last: Wu

first: Tong

last: Zhao

first: Wenqi

last: Tan

first: Jiang

last: Tian

first: Cuiyue

last: Liang


title: Transcriptomic landscapes provide a framework of native gene expression from which to imagine new connections in cell biology

city: Clayton

first: Traude

last: Beilharz

state: VIC

address: Wellington Rd

country: Australia

institute: Monash University

summary: The Poly(A)-Test RNA-seq, ( PAT-seq ) approach was utilized to determine  gene expression and poly(A)-site change in S. cerevisiae during colony maturation.

overall_design: Investigating the link (or lack thereof) between gene expression and APA

middle: H

first: Paul

middle: F

last: Harrrison

first: Michael

last: See


title: RNA-sequencing analysis for gene expression profiles affected by CASC9 knockdown

city: Wenzhou

first: jingwen

last: geng

address: 270  Xueyuan Road

institute: Wenzhou Medical University

summary: Genome-wide association studies of tumor samples have identified a large number of lncRNAs associated with various types of cancer including colorectal cancer. To elucidate the mechanism by which CASC9 regulates colorectal cancer cell growth, RNA-sequencing was performed to analyze the gene expression profile affected by CASC9 knockdown. A total of 249 significantly upregulated genes and 491 significantly downregulated genes (absolute fold change ≥ 2, P < 0.05) were found in CASC9 knockdown HCT-116 cells.

overall_design: Comparing gene expression profiles of HCT-116 cells transfected with CASC9 GapmeR (GapC9) and the control GapmeR (GapNC)

first: Jianmin

first: Kaili

last: Luo

first: Jingwen

last: Geng


title: Alterations in hepatic gene expression and DNA methylation as underlying mechanisms of disturbed metabolism in adult mouse offspring after exposure to a prenatal high fat diet

city: Maastricht

first: Sven

last: Rouschop

address: Universiteitssingel 50

department: Pharmacology and Toxicology

institute: Maastricht University

summary:
Exposure to a prenatal high fat (HF) diet leads to an impaired metabolic phenotype in mouse offspring. The underlying mechanisms, however, are not yet fully understood. Therefore, this study investigated whether the impaired metabolic phenotype could have been mediated through altered hepatic DNA methylation and gene expression.
In this study, both parent mice received a HF or low fat (LF) diet before and during pregnancy, and throughout lactation, after which offspring was weaned onto a HF diet. Previous work showed that at 12 weeks of age, the offspring displayed postprandial hypertriglyceridemia, which related to an impaired clearance of lipids from the blood into the liver after a HF meal. To study the mechanisms underlying the impaired metabolic phenotype after prenatal exposure to a HF diet, hepatic genome-wide gene expression was studied using whole transcript microarrays. In addition, hepatic DNA methylation of selected genes was assessed by bisulphite pyrosequencing.

overall_design: Male offspring mice were sacrificed at 12 and 28 weeks of age. Livers were obtained and total RNA was isolated for microarray hybridization. In total, 32 samples were included: for week 12, n=7 per group (prenatal HF or LF) and for week 28, n=9 per group.

first: Vera

last: Schrauwen-Hinderling

first: Antoon

last: Opperhuizen

first: Roger

last: Godschalk

first: Frederik

last: van Schooten


title: SYMPK is essential for meiosis in mouse germ cells

status: Public on Jun 22 2019

city: Wuhan

first: Mengcheng

address: 185 Donghu Road

institute: Wuhan University

summary: Because SYMPK has been reported to regulate the alternative splicing (AS) in somatic cells(293 cells), we asked whether SYMPK also regulates AS in germ cells. Whole transcriptome RNA-seq analysis was performed using total RNA extracted from wt and Sympk cKOStra8-Cre testes.

overall_design: Examination of different transcriptional levels in wt and Sympk cKO mouse testes.

first: Rui


title: Social status-dependent regulation of the hepatic miRNAome in  rainbow trout, Oncorhynchus mykiss

city: Houston

first: Kyle

middle: Ryan

last: Navel

state: Texas

address: 2575 W. Bellfort Ave. Ste 270

department: Sales

country: USA

institute: LC Sciences

summary:
Purpose: Next-generation sequencing (NGS) of small RNAs allows transcriptome level analysis of the miRNAome. The goals of this study are to identify differentially regulated hepatic miRNAs in response to a dominant or subordinate social status using small RNA next generation sequencing. Specific quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods were used to validate optimal high-throughput data analysis, and in silico prediction to identify bona fide target pathways regulated by differentially regulated miRNAs following these social interactions.
Method: Small RNA sequencing was performed using four randomly selected samples from each treatment group were used for sequencing. The quality of total RNA was confirmed by RNA Integrity Numbers greater than 9.0 using an Agilent Technologies 2100 Bioanalyzer. Nucleotide fractions (15-50) of small RNA were isolated from the total RNA using polyacrylamide gel electrophoresis and were ligated to a 30 adapter followed by a 50 adapter (Illumina, San Diego, CA, USA). The small RNA ligated to the adaptors was reverse transcribed to cDNA, PCR amplified and gel purified. The gel-extracted cDNA was used for library preparation, which was further used for cluster generation on Illumina's Cluster Station before sequencing using Illumina GAIIx. Raw sequence data was obtained from image data using Illumina's Sequencing Control Studio software version 2.8 (SCS v2.8) following real-time sequencing image analysis and base-calling by Illumina's Real-Time Analysis version 1.8.70 (RTA v1.8.70). The ACGT101-miR v4.2 pipeline (LC Sciences) was used to analyze sequenced data. Sequences with low Q scores, reads mapped to mRNA, RFam, Repbase and piRNA database were deleted and unique families were generated from identical sequences. These filtered unique sequences were then mapped to fish pre-miRNA and miRNA using miRBase or to the rainbow trout genome (Berthelot et al., 2014) to identify conserved miRNA following ACGT-101 User's Manual. Unique or novel miRNAs were identified after the BLAST performed against fish miRNAs from miRbase database (release 21) and published miRNAs from rainbow trout (Mennigen et al., 2016). The miRNAs that do not match any sequences in the specified databases and have the propensity of forming hairpin structure with the extended sequences at the mapped positions were classified as unique miRNAs. These unique miRNAs were further classified into different groups depending on the mappable reads to selected miRNAs in miRbase. Differentially expressed miRNAs were identified using the statistical software R (Version 3.2.2) package DESeq2 for one-way ANOVA comparison of all three treatment groups. Real-time RT–PCR validation was performed using SYBR Green assays
Results: 24 miRNAs are differentially regulated by social status. 9 miRNAs are higher expressed in dominant trout. 15 miRNAs are higher expressed in subordinate trout.
Conclusions: Our study represents the first detailed analysis of the rainbow trout miRNAome in response to nutritional stimuli. Specifically, we here identify common hepatic miRNAs differentially regulated by refeeding following a short-term fast (2d), as well as miRNAs differentially regulated in the postprandial state depending on the dieatary stimulus (no carbohydrates compared to >20% dietary carbohydrates)

overall_design: Hepatic miRNA profiles of 4-day paired trout with dominant or subordinate social status were generated by deep sequencing, in three replicates per experimental group, using Illumina GAIIx.

first: D

last: Kostniuk

first: B

middle: M

last: Culbrt

first: K

last: Gilmur

last: Zhang

first: C

last: Martniuk

first: J

last: Menngen


title: Hypoxia-induced metabolic dysfunction in WAT

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

institute: Wageningen University

summary: Background: Excessive white adipose tissue (WAT) expansion as in obesity is generally associated with chronic inflammation of WAT, which contributes to obesity associated complications. Low oxygen availability in WAT is hypothesized to be the initiator of this inflammatory response.  Hypothesis: We examined the hypothesis that local tissue hypoxia is responsible for the initiation of inflammation in WAT.  Research design and methods: Diet-induced obese male C57BL/6JOlaHsd mice, housed at thermoneutrality, were exposed to mild environmental oxygen restriction (OxR, to 13% oxygen) for five days and compared with mice kept at normoxia, after which WAT and serum were collected. Body composition, systemic metabolic parameters, WAT macrophage infiltration (as marker for tissue inflammation) and whole genome microarray analysis, and circulating adipokines were measured.  Results: Five days OxR decreased body weight and fat mass, and increased blood levels of haemoglobin and haematocrit, as well as lactate to glucose ratio, which indicated systemic hypoxia. No difference in adipose tissue inflammation was found, which was supported by down regulation of inflammation-associated transcript levels of S100a8, Saa1, and Saa3. Serum metabolomics revealed an increase of branched chain amino acid Valine and propionylcarnitine. Adipokines CCDC3, CCK, and Adiponectin are reduced by OxR on transcript (Cck) or serum protein level (Adiponectin), or both (CCDC3).  Conclusions: Mild oxygen restriction does not increase white adipose tissue inflammation in obese mice. However, a systemic adaptation together with a metabolic response in WAT was observed.

overall_design: C57BL/6JOlaHsd wildtype male mice, aged 9 weeks, were fed a purified low fat diet (BIOCLAIMS, Hoevenaars et al., Genes and Nutrition 2012) for 3 weeks to acclimatize, followed by 12 weeks a BIOCLAIMS high-fat diet (HFD), all at thermoneutrality (29 degrees Celsius). Subsequently, mice were divided into 2 different treatment groups: i) control group which remained under normoxia for 5 days, ii) 5 days oxygen restriction to 13% ambient oxygen in an indirect calorimetry system. Mice were killed immediately after taking them out of the indirect calorimetry system by decapitation. After sacrification, epididymal WAT was immediately dissected and snap frozen in liquid nitrogen. Total RNA was isolated, quantified and qualified, and subsequently used for global gene expression profiling using Agilent 8x60K microarrays.

first: F

last: Hoevenaars

first: E

first: I

last: van der Stelt

last: Keijer


title: LncRNA/mRNA sequencing analysis on cerebral cortex of P301S mutant Tau transgenic mice (PS19).

status: Public on Jun 23 2019

city: Singapore

first: Joonki

last: Kim

address: 2 Medical drive, Blk MD9

department: Physiology, School Of Medicine

country: Singapore

institute: National University of Singapore

summary: Aggregation of the microtubule-associated protein, tau, can lead to neurofibrillary tangle formation in neurons and glia, the hallmark of tauopathy. The cellular damages induced by the tau overexpression and aggregation may lead to multiple pathologic features of tauopathy. However, the effect of aging on tauopathy has not been elucidated yet. Here, we conducted lncRNA/mRNA sequencing analysis on P301S mutant Tau transgenic mouse model (PS19) with different ages to track the genetic changes occurred by the aging and progression of tau overexpression.

overall_design: P301S TG mice and their wild type mice were raised in animal facility at National University of Singapore. At 3 and 10 months-old age, both type of mice were sacrificed and cerebral cortex was dissected and kept frozen. Total RNA was extracted from the collected cerebral cortex tissues and lncRNA/mRNA sequencing was conducted using Illumina HiSeq 4000 system by Novogene.

first: Thiruma

middle: V

last: Arumugam


title: Convergence of BMI1 and CHD7 on ERK signalling in medulloblastoma

city: Toronto

first: Michael

middle: D

last: Taylor

state: Ontario

address: 686 Bay St

department: Developmental and Stem Cell Biology

institute: Hospital for Sick Children

summary: We describe a novel molecular convergence between BMI1 and CHD7 in the initiation of medulloblastoma. We show that CHD7 controls differentiation of G4 MB cells and its silencing renders them susceptible to Bmi1-mediated ERK1/2-induced proliferation control. We show that BMI1-mediated repression of the ERK1/2 inhibitor DUSP4 leads to increased proliferation and tumour burden in primary human MB cells.

overall_design: Two biological replicates of the following knockdown conditions were used: shBMI1, shCHD7, double shBMI1/shCHD7, and scrambled controls.

first: Silvia

last: Marino


title: Single-cell transcriptomic analysis reveals lineage hierarcies and communications for second heart lineage deployment

city: Beijing

first: Haiqing

last: Xiong

state: Beijing

address: 5 Yiheyuan Road,  Haidian District

country: China

institute: Peking University


title: Chemotherapeutic drugs inhibiting Topoisomerase 1 activity inhibit TNF-induced inflammatory gene expression

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

institute: Justus-Liebig-University Giessen

summary: Inhibitors of DNA topoisomerase I (TOP1), an enzyme relieving torsional stress of DNA by generating transient single-strand breaks, are clinically used to treat ovarian cancer, small cell lung cancer and cervical cancer. As torsional stress is generated by replication and transcription we tested the effects of clinically used TOP1 inhibitors Topotecan and SN-38 on TNF-induced gene expression. RNA-seq experiments showed that inhibition of TOP1 activity interfered with the vast majority of TNF-triggered genes, while interference with TOP2 activity had only a minor impact. TOP1 inhibition affected the expression of early and late induced genes and the relative strength of gene induction played no role in the sensitivity to TOP1 interfering drugs. These data raise the possibility that the inhibition of inflammatory gene expression contributes to the increased risk of infection seen in some patients treated with TOP1 inhibtors.

overall_design: The effect of the various toposomerase I inhibitors on inflammatory NF-kB target genes were examined using qPCR and RNA-Seq

first: Lienhard

last: Schmitz

first: Tabea

last: Riedlinger

first: Tobias

last: Zimmermann


title: Single-cell transcriptomics reveals chemotaxis mediated intra-organ crosstalk during cardiogenesis [ChIP-seq]

summary: We used single-cell RNA-seq to reconstruct differentiation paths of cardiac progenitors in two sequential waves during early heart development. Further analysis identified six major cell types and multiple differentiation trajectories of cardiac progenitors derived from distinct heart fields. We also constructed TF regulatory networks controlling SHF CPC differentiation. Interlineage crosstalk through signaling pathways and chemotactic guidance played a potent role in SHF CPC deployment. The mechanisms regulating SHF CPC migration and differentiation was further confirmed by Nkx2-5 enhancer knock out. Our work provides a cardiac lineage hierarchy and new insights into SHF CPC development. Mechanistically, NKX2-5 directly bound the Cxcr2 genomic locus and activated its transcription.

overall_design: We performed NKX2-5 ChIP-seq using an Nkx2-5 allele in which the endogenous gene has been modified to incorporate FLAG and bio (flbio) epitope tags, where bio is specifically biotinylated by the enzyme BirA (He et al. 2014; Zhou et al. 2017). SHF (largely SpM and pharyngeal mesoderm) and HT regions were separately micro-dissected for a modified bioChIP-seq in Nkx2-5flbio/+::Rosa26BirA/+ mouse embryos at E8.25-8.75.

first: Yingjie

last: Luo

first: Aibin

last: He


title: IL-11 neutralising therapies for the treatment of nonalcoholic steatohepatitis

first: Giuseppe

middle: Alessandro

last: D'Agostino

state: Singapore

address: 11 Mandalay Road

institute: Lee Kong Chian School of Medicine - NTU

summary:
Background and aims: Here we investigate the role of IL-11 signalling in the pathogenesis of nonalcoholic steatohepatitis (NASH).
Methods: HSCs or hepatocytes were stimulated with IL-11 and effects assessed using cellular and high content imaging, immunoblotting, ELISA and invasion assays. Genetic and pharmacological IL-11 gain- or loss-of-function experiments were performed in vitro and in vivo. IL-11 signaling was studied using ERK inhibitors. The effects of anti-IL-11 or anti-IL11RA therapy were assessed in three preclinical NASH models using methionine/choline deficient diets or a Western diet with liquid fructose. Phenotyping was performed using hydroxyproline assay, qPCR, RNA-seq, Western blotting, histology, CyTOF, lipid and metabolic biomarkers.
Results: When stimulated with NASH factors HSCs secrete IL-11, which drives an autocrine, ERK-dependent signaling loop required for the HSC-to-myofibroblast transformation. IL-11 is upregulated in human and murine NASH, Il-11 injection causes liver damage, inflammation and fibrosis in mice and Il11ra1 deleted mice are protected from NASH in two preclinical models. Therapeutic antibodies against IL11RA or IL-11 consistently inhibit and reverse fibrosis and steatosis in three murine NASH models. Unexpectedly, IL-11 causes hepatocyte damage and promotes stromal-mediated inflammation and anti-IL-11 therapies reverse NASH-associated hepatotoxicity and hepatitis. Genetic or pharmacologic inhibition of IL-11 signaling in NASH is associated with lower serum triglyceride, cholesterol and glucose.
Conclusion: We show an unappreciated and central role for IL-11 in liver pathobiology. Targeting IL-11 signalling with neutralizing antibodies reverses fibrosis, steatosis, hepatocyte death and inflammation across the spectrum of NASH. This novel therapeutic approach is associated with a favorable cardiometabolic profile.

overall_design: Mouse liver samples (each category in triplicate): 3 weeks of normal chow diet (NCD),  6 weeks of NCD, 3 weeks of High Fat Methionine- and Choline-deficient Deficient (HFMCD) diet with IgG treatment, 6 weeks HFMCD with IgG treatment, 3 weeks of HFMCD with X203 treatment, 6 weeks of HFMCD with X203 treatment, 3 weeks of HFMCD with X209 treatment, 6 weeks of HFMCD with X209 treatment. Human hepatic stellate cells (HSCs), each category in triplicate: HSCs with no stimulation and HSCs with 24h stimulation with TGFB1 + IgG

first: Anissa

last: Widjaja

first: Brijesh

middle: K

last: Singh

first: Eleonora

last: Adami

first: Sivakumar

last: Viswanathan

first: Jinrui

last: Dong

first: Benjamin

last: Ng

first: Wei

last: Lim

first: Jessie

last: Tan

first: Bhairav

last: Paleja

first: Madhulika

last: Tripathi

first: Sze

middle: Y

first: Shamini

last: Guna Shekeran

first: Sonia

last: Chothani

first: Anne

last: Rabes

first: Martina

last: Sombetzki

first: Eveline

last: Bruinstroop

first: Lio

last: Min

first: Rohit

last: Sinha

first: Salvatore

last: Albani

first: Paul

last: Yen

first: Sebastian

last: Schafer

first: Stuart

last: Cook


title: Single-cell transcriptomic analysis reveals lineage hierarcies and communications for second heart lineage deployment [RNA-seq]

first: Haiqing

last: Xiong

summary: We used single-cell RNA-seq to reconstruct differentiation paths of cardiac progenitors in two sequential waves during early heart development. Further analysis identified six major cell types and multiple differentiation trajectories of cardiac progenitors derived from distinct heart fields. We also constructed TF regulatory networks controlling SHF CPC differentiation. Interlineage crosstalk through signaling pathways and chemotactic guidance played a potent role in SHF CPC deployment. The mechanisms regulating SHF CPC migration and differentiation was further confirmed by Nkx2-5 CPC enhancer knock out. Our work provides a cardiac lineage hierarchy and new insights of SHF CPC development.

overall_design: Single cells were derived for scRNA-seq from mice carrying Isl1Cre::Rosa26tdTomato or  Nkx2-5Cre::Rosa26tdTomato at E7.75, E8.25, E8.75, E9.25

first: Yingjie

last: Luo

first: Aibin

last: He


title: Chronic, Chemogenetic Stimulation of The Nucleus Accumbens Produces Lasting Effects on Binge Drinking and Ameliorates Alcohol-Related Transcriptional and Morphological Changes

status: Public on Jun 21 2019

city: Portland

first: Angela

middle: Renee

last: Ozburn

state: OR

address: 3710 SW US Veterans Hospital Rd

department: Behavioral Neuroscience

institute: OHSU

summary: We report RNA-Seq data obtained from nucleus accumbens tissue of HDID-1 mice subjected to chronic stimulation via CNO/DREADDs within a Drinking in The Dark (DID) Paradigm. Here, we found that chronically increasing NAc activity (via CNO/hM3Dq) decreased binge-like drinking, an effect lasting for at least 7 days . CNO did not alter intake in hM4Di- or GFP-expressing mice. We observed interesting and significant changes in expression of several plasticity-related genes (e.g. Hdac4 was increased with binge drinking, and ameliorated with CNO).

overall_design: Examination of Nac tissue in 2 fluid types (EtOH and H2O) with 2 treatments (CNO and VEH).

middle: R

first: Dar'ya

last: Pozhidayeva


title: Transcriptomic analysis of 5637 bladder cancer cell line transfected with MAT1A plamid, 48 hours post transfection

city: Livermore

first: Kelly

last: Martin

address: 7000 East Ave

institute: LLNL

overall_design: 5637 bladder cancer cell line (human) were transfected to overexpress MAT1A using a MAT1A plasmid obtained from Origene (2 ug/ul) at 50% confluency in a 24-well plate using Lipofectamine 3000 (following manufacturer guidelines). RNA was collected directed into Qiagen RLT RNA storage buffer supplemented with beta-mercaptoethanol for RNA sequencing preparation, 48h post transfection.

middle: A

first: Aimy

last: Sebastian

first: Gabriela

middle: G

last: Loots


title: Ribosome profiling of A549 cells depleted of RPLP1 and RPLP2 and infected with DENV.

city: Galveston

first: Rafael

last: Kroon Campos

address: 11th street and mechanic

institute: UTMB

summary: We used ribosome profiling to evaluate viral and cellular translation in RPLP1/2-depleted cells. This revealed that ribosomes pause in the sequence coding for the N-terminus of the envelope protein, immediately downstream of sequences encoding two adjacent transmembrane domains (TMDs). RPLP1/2 function to enhance ribosome elongation at this position and increase viral protein stability, possibly by improving co-translational folding of DENV proteins. We also analyzed the effects of RPLP1/2 depletion on cellular translation. We find that RPLP1/2 moderately affects ribosome density for a small subset of cellular mRNAs. However, meta-analysis of ribosome positions on all cellular mRNAs revealed slightly increased accumulation of ribosomes downstream of start codons in RPLP1/2-depleted cells, suggesting that RPLP1/2 enhance elongation efficiency. Importantly, we found that ribosome density on mRNAs encoding multiple TMDs was disproportionately affected by RPLP1/2 knockdown, suggesting a role for RPLP1/2 in transmembrane protein biogenesis. Together, our findings reveal insights into the function of RPLP1/2 in DENV and cellular translation.

overall_design: A549 cells were plated at 1.5 x 106 cells per 10 cm dish. Three 10cm dishes were transfected with NSC siRNA whereas three other dishes were transfected with either siP1_1, siP2_1 or siP2_4 siRNAs as described in the transfections section. 48 h later cells were infected as described previously with DENV-2 (NGC strain) at MOI of 10 in a total volume of 10 ml, rocked every 15 minutes for 1 h and the infection was allowed to proceed for more 1.5 h (2.5 h total time). Cells were then flash frozen in liquid nitrogen without cycloheximide pretreatment and cold lysis buffer containing CHX was used to lyse the cells on ice. The RIBOseq strategy was adapted from Ingolia and colleagues with a few modifications described next. After nuclease digestion, samples were run in a polysome gradient and the ribosome fractions were collected. As described by Reid and colleagues, fractions were extracted using Trizol LS (Thermo Fisher Scientific), and rRNAs were removed using the Ribo-Zero gold rRNA removal kit (Illumina, San Diego CA) according to the manufacturer's protocol. For adapter ligation and library building we used NEBNext Small RNA Library Prep Set (Illumina).

last: Campos

first: Sagara

last: Wijeratne

first: Premal

last: Shah

first: Mariano

last: Garcia-Blanco

first: Shelton

middle: S

last: Bradrick


title: A transcriptomic analysis of primary mature adipocytes from lean, obese, and type 2 diabetic subjects: role of the extracellular matrix

city: Linköping

first: Peter

last: Str lfors

address: Lasarettsgatan

department: Department of Biomedical and Clinical Sciences (BKV)

institute: Linköping University

summary: Type 2 diabetes is associated with obesity, and is characterized by insulin resistance in target tissues of the hormone combined with insufficient systemic insulin. Insulin resistance apparently begins in subcutaneous adipocytes that fail to further accumulate triacylglycerol. To understand the pathogenesis of transition from lean to obesity and to diabetes, we performed transcriptome profiling by RNA-sequencing of isolated primary human adipocytes. Half of identified transcripts were protein-coding and shared between individuals, while non-protein-coding transcripts were subject specific. Differential gene expression between lean and diabetes reflected corresponding changes in 7 of 12 characterized insulin-signaling proteins. In the tissue, adipocytes are surrounded by extracellular matrix (ECM) providing a dynamic scaffold. However, excess ECM is implicated in obesity and diabetes. Bioinformatic analyses of transcriptomes revealed major upregulation of genes related to ECM in obese compared with lean, which was reversed in diabetes. However, biochemical analysis of adipose tissue demonstrated reduced ECM in obesity or diabetes compared with lean. We conclude that marked changes in the adipocyte transcriptome related to ECM do not reflect global adipose tissue fibrosis, but likely control the pericellular milieu surrounding the adipocyte; and excess ECM is not a feature of subcutaneous adipose tissue in obesity or diabetes.

overall_design:
Adipocyte mRNA profiles from lean, obese and type 2 diabetic subjects, 6 samples each

>>>Submitter states that the raw data cannot be made available due to patient privacy concerns<<<

first: Meenu

last: Rajan

first: Simon

last: Söderholm

first: Rasmus

last: Magnusson

first: Mika

last: Gustafsson

last: Strålfors


title: Progression of liver tumor was promoted by tris(1,3-dichloro-2-propyl)phosphate through the induction of inflammatory responses in krasV12 transgenic zebrafish

city: Tianjing

first: Chen

last: Sheng

address: Wuqing

institute: Novogene

summary: In this study, krasV12 genetically modified zebrafish, Tg(fabp10:rtTA2s-M2; TRE2:EGFP-krasG12V), an inducible liver tumor model, was used to evaluate the promotion potential of TDCIPP for liver tumor. Briefly, krasV12 transgenic females were exposed to 0.3 mg/L TDCIPP, 20 mg/L doxycycline (DOX) and a binary mixture of 0.3 mg/L TDCIPP with 20 mg/L DOX, and liver size, histopathology, and transcriptional profiles of liver were tested. Treatment with TDCIPP increased the liver size and caused more aggressive hepatocellular carcinoma (HCC). Furthermore, compared with the exposure to DOX, TDCIPP in the presence of DOX up-regulated the expression of genes relevant with salmonella infection and the toll-like receptor signaling pathway, implying an occurrence of inflammatory reaction, which was sustained by the increase in the amount of infiltrated neutrophils in the liver of Tg(lyz:DsRed2) transgenic zebrafish larvae. Collectively, our results suggested that TDCIPP could promote the liver tumor progression by induction of hepatic inflammatory responses.

overall_design: Liver mRNA prolifie of 3 months old kras zebrafish which were treated with DMSO, TDCIPP, DOX, DOX with TDCIPP were generated by deep sequencing, in triplicate.

first: Sheng

last: Chen

first: Chunsheng

last: Liu


title: Liver macrophages inhibit the endogenous antioxidant response in obesity-associated insulin resistance [RNA-Seq]

city: Huddinge

first: Ping

address: Alfred Nobels allé 8

department: Department of Laboratory Medicine

institute: Karolinska Institutet

summary: Liver Macrophages exacerbate oxidative stress induced by hepatic steatosis in obesity by blocking the endogenous anti-oxidant response.

overall_design: Kupffer cell mRNA profiles of wild type and obese mice at 9 and 14 weeks were generated by deep RNA sequencing, in replicates, using Illumina HiSeq 3000.

first: Valerio

last: Azzimato

first: Jennifer

last: Jager

first: Myriam

last: Aouadi


title: Transcriptional regulation by IRF1 and IRF2 in the mouse DC3.2 cell line in the presence or absence of interferon

city: Worcester

first: Pranitha

last: Vangala

state: MA

address: 55 Lake Avenue North

institute: University of Massachussets Medical School

summary: We analyzed the classes of genes influenced by IRF1 and IRF2 under basal conditions and upon stimulation with interferon.

overall_design: Examination of differentially expressed genes in WT, IRF1-KO, IRF2-KO, or IRF1/IRF2-DKO DC3.2 lines after 2 hours of stimulating with 5,000U/mL IFNα, 2ng/mL IFNγ, or media alone.

first: Barry

last: Kriegsman

first: Manuel

last: Garber

first: Kenneth

middle: L

last: Rock


title: Transcriptome profiles reveals potential core genes in the black skin of Xichuan Black-bone chickens（Gallus gallus）

city: Zhengzhou

first: Donghua

last: Li

state: China

address: Wenhua Road 95, Zhengzhou City

institute: Henan Agricultural University

summary: High throughput sequencing technology was used to sequence the transcriptome of breast muscle tissue of control group and test group IV, the results of bioinformatics analysis showed that 417 mRNAs were differentially expressed between control group and test group IV (fold change ≥ 2.0, P < 0.05). Among them, 160 mRNAs presented upregulated and 257 were downregulated. The differentially expressed mRNAs were mainly involved in Melanogenesis, Calcium signaling pathway, Wnt signaling pathway, mTOR signaling pathway, and Vascular smooth muscle contraction.

overall_design: control group(A) and test group IV(E-1)

first: Guoxi


title: Liver macrophages inhibit the endogenous antioxidant response in obesity-associated insulin resistance [miRNA-Seq]

overall_design: Kupffer cell miRNA profiles of wild type and obese mice at 9 and 14 weeks were generated by small-RNA sequencing, in replicates, using Illumina HiSeq 3000.


title: Expression data from ME180 cells transfected with siControl and siSGK1

city: Dalian

first: Hailing

last: Cheng

address: 467 Zhongshan Road

institute: The Second Hospital of Dalian Medical University

summary: SGK1 knockdown-induced transcriptional changes in ME180 cells.

overall_design: ME180 cervical cancer cells were transfected with siControl or siSGK1 for 48 hours, followed by RNA extraction and RNA sequencing analysis. Each has three biological repeats.

first: Min

last: Wang

first: Zhiwei

last: Tao

first: Pixu


title: Transcriptome profiling reveals significant changes in the gastric muscularis externa with obesity that partially overlap those that occur with gastroparesis

city: Indianapolis

first: Brian

middle: Paul

last: Herring

state: IN

address: 635 Barnhill Drive, MS309

department: Cellular and Integrated Physiology

institute: Indiana University School of Medicine

summary: The goal of the current study was to identify changes in gene expression in the stomach muscularis that may be contributing to altered gastric motility in gastroparesis and obesity.

overall_design: Stomach muscularis biopsies were obtained from human subjects with low BMI and normal gastric motility (low BMI control, n=6), subjects with high BMI but normal gastric motility (high BMI control, n=6), subjects with low BMI and gastroparesis (low BMI gastroparesis, n=6) and from subjects with high BMI and gastroparesis (High BMI gastroparesis, n=4). RNA was isolated and subjected to whole transcriptome sequencing.

first: Paul

first: Guanglong

last: Jiang


title: Liver macrophages inhibit the endogenous antioxidant response in obesity-associated insulin resistance

first: Ping

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

overall_design: Refer to individual Series


title: Gene expression levels od Troponin T Amino Acid Mutation (ΔK 210) Knock-in Mice as a Neonatal Dilated Cardiomyopathy Model at 0day and 1week after birth

city: Tokyo

first: Jun

last: Tanihata

address: 3-25-8 Nishishinbashi, Minato-ku

institute: The Jikei Univ Sch of Med

summary: Cardiac phenotypes of homozygous ΔK210 knock-in (TNNT2ΔK210/ΔK210) mice including comprehensive gene expression profiles were investigated to establish an animal model of neonatal DCM and to identify early progression factors of pediatric DCM.

overall_design: Microarray analysis with pooled left ventricular tissues from wild-type and TNNT2ΔK210/ΔK210 mice at 0-day old (n=2, respectively) and 1-week old (n=2, respectively) were performed.

first: Susumu

last: Minamisawa


title: Segmental chick eye transcriptome analysis at embryonic days 5, 6, 7

city: Edinburgh

first: Joe

last: Rainger

state: Midlothian

address: Easter Bush

department: Roslin Institute

country: United Kingdom

institute: University of Edinburgh

summary: Ocular tissue RNAseq from WT embryos

overall_design: Three biological replicates each of four tissues at 3 timepoints

first: James

last: Prendergast


title: Identification of transcription factors involved in the regulation of flowering in Adonis amurensis through combined RNA-seq transcriptomics and iTRAQ proteomics

city: Habin

first: Ai min

last: Zhou

address: 59 wood street, xiangfang district

institute: Northeast Agricultural University

summary: Molecular mechanisms of flowering in Adonis amurensis

overall_design: investigated global gene expression profiles at different developmental stages of flowering in A. amurensis by RNA-seq transcriptome

first: Aimin