title: Derivation of ventrical and atrial cardiomyocytes and maturation using biowires

city: Toronto

first: Brian

middle: Joseph

last: Cox

state: Ontario

address: 1 King's College Circle, Rm 3360

department: Physiology

institute: University of Toronto

summary: Tissue engineering using cardiomyocytes derived from human pluripotent stem cells holds a promise to revolutionise drug discovery, but only if limitations related to cardiac chamber specification and platform versatility can be overcome. We describe here a scalable tissue cultivation platform that is cell source agnostic and enables drug testing under electrical pacing. The plastic platform enabled on-line, non-invasive, recording of passive tension, active force, contractile dynamics and Ca2+ transients, as well as endpoint assessments of action potentials and conduction velocity. By combining directed cell differentiation with electrical field conditioning, we engineered electrophysiologically distinct atrial and ventricular tissues with chamber-specific drug responses and gene expression. We report, for the first time, engineering of heteropolar cardiac tissues containing distinct atrial and ventricular ends, and demonstrate their spatially confined responses to serotonin and ranolazine. Uniquely, electrical conditioning for up to 8 months enabled modeling of polygenic left ventricular hypertrophy starting from patient cells.

overall_design: human embryonic stem cells were cultured under conditions to generate either atrial or ventricle cardiomyocytes. The cardiomyocytes were placed into biowires that simulate normal cardiac sinus rhythm. Cell were harvested and assessed after a period of culture with or without electrical stimulation.

first: Milica

last: Radisic

last: Backx


title: mRNA-seq of wild-type or Otud1 deficient primary bone marrow derived macrophages (BMDM) after herpes simplex virus-1 or sendai virus infection

status: Public on Jan 23 2019

city: Beijing

first: Zeming

last: Zhang

address: 38 Xueyuan Rd , Haidian District,Beijing,China

country: China

institute: Institude of Systems Biomedicine

type: Expression profiling by high throughput sequencing

summary: Analysis of mRNA-seq of wild type bone marrow derived macrophages reveals how wild-type and Otud1 deficient bone marrow derived macrophages response to HSV-1 or SeV infection

overall_design: Primary bone marrow derived macrophages generated from bone marrow of WT or Otud1 knock out C57BL/6 mice were infected by HSV-1 or SeV for 0 or 6 hours, respectively.

first: Dandan

last: Wang

first: Fuping

last: You


title: REM sleep’s unique associations with corticosterone regulation, apoptotic pathways and behavior in chronic stress in mice

status: Public on Jan 24 2019

city: Guildford

first: Emma

last: Laing

address: Stag Hill

country: United Kingdom

institute: University of Surrey

summary: One of sleep’s putative functions is mediation of adaptation to waking experiences. Chronic stress is a common waking experience, however, which specific aspect of sleep is most responsive, and how sleep changes relate to behavioral disturbances and molecular correlates remain unknown. We quantified sleep, physical, endocrine, and behavioral variables, as well as the brain and blood transcriptome in mice exposed to 9 weeks of unpredictable chronic mild stress (UCMS). Comparing 46 phenotypical variables revealed that rapid-eye-movement sleep (REMS), corticosterone regulation, and coat state were most responsive to UCMS. REMS theta oscillations were enhanced, whereas delta oscillations in non-REMS were unaffected. Transcripts affected by UCMS in the prefrontal cortex, hippocampus, hypothalamus, and blood were associated with inflammatory and immune responses. A machine-learning approach controlling for unspecific UCMS effects identified transcriptomic predictor sets for REMS parameters that were enriched in 193 pathways, including some involved in stem cells, immune response, apoptosis, and survival. Only three pathways were enriched in predictor  sets for non-REMS. Transcriptomic predictor sets for variation in REMS continuity and theta activity shared many pathways with corticosterone regulation, in particular pathways implicated in apoptosis and survival, including mitochondrial apoptotic machinery. Predictor sets for REMS, and anhedonia shared pathways involved in oxidative stress, cell proliferation, and apoptosis. These data identify REMS as a core and early element of the response to chronic stress, and identify apoptosis and survival pathways as a putative mechanism by which REMS may mediate the response to stressful waking experiences.

overall_design: Study of transcriptomic changes in three stress- and sleep-related brain regions (prefrontal cortex, hippocampus, hypothalamus) and blood following 9 weeks of Unpredictable Chronic Mild Stress (UCMS) in mice.

first: Mathieu

last: Nollet

first: Harriet

last: Hicks

first: Andrew

middle: P

last: McCarthy

first: Huihai

last: Wu

first: Carla

middle: S

last: Moller-Levet

middle: E

first: Karim

last: Malki

first: Nathan

last: Lawless

first: Keith

middle: A

last: Wafford

first: Derk-Jan

last: Dijk

first: Raphaelle

last: Winsky-Sommerer


title: Targeting the NFAT:AP-1 transcriptional complex on DNA with a small-molecule inhibitor III

city: Los Angeles

first: Roberto

last: Spreafico

state: CA

address: UCLA

department: Institute for Quantitative and Computational Biosciences

country: USA

institute: University of Califonia Los Angeles

summary: The transcription factor NFAT has a key role in both T cell activation and tolerance and has emerged as an important target of immune modulation. NFAT directs the effector arm of the immune response in the presence of AP-1, and T cell anergy/exhaustion in the absence of AP-1. Envisioning a strategy for selective modulation of the immune response, we designed a FRET-based high-throughput screen to identify compounds that disrupt the NFAT:AP-1:DNA complex. We screened ~202,000 small organic compounds and identified 337 candidate inhibitors. We focus here on one compound, N-(3-acetamidophenyl)-2-[5-(1H-benzimidazol-2-yl)pyridin-2-yl]sulfanylacetamide (Compound 10), which disrupts the NFAT:AP-1 interaction at the composite ARRE-2 site without affecting the binding of NFAT or AP-1 alone to DNA. Compound 10 binds to DNA in a sequence-selective manner and inhibits the transcription of the Il2 gene and several other CsA-sensitive cytokine genes important for the effector immune response. This study provides proof-of-concept that small molecules can inhibit the assembly of specific DNA-protein complexes, and opens a potential new approach to treat human diseases where known transcription factors are deregulated.

overall_design: Comparison of total CD4+ T cells exposed to CsA vs vehicle

first: Giuliana

last: Mognol


title: Targeting the NFAT:AP-1 transcriptional complex on DNA with a small-molecule inhibitor

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

overall_design: Refer to individual Series


title: Targeting the NFAT:AP-1 transcriptional complex on DNA with a small-molecule inhibitor I

overall_design: Comparison of naive CD4+ T cells exposed to a chemical inhibitor of NFAT:AP-1 vs vehicle


title: Targeting the NFAT:AP-1 transcriptional complex on DNA with a small-molecule inhibitor II

overall_design: Comparison of total CD4+ T cells exposed to a chemical inhibitor of NFAT:AP-1 vs vehicle


title: Sequencing of  F4/40+ CD11b+ macrophages from adipose tissue of miR-146a WT or deficient mice on high fat or normal chow diet

city: Salt Lake City

first: Morgan

last: Nelson

state: Utah

address: 15 North Medical Drive

department: Pathology

institute: University of Utah

summary: We identify regulatory mechanisms that influence inflammation and metabolism during metabolic disease development. In addition to the other data represented in our paper, we performed RNA-seq to demonstrate a role for miR-146a, an anti-inflammatory miRNA, in regulating both inflammation and cellular metabolism during obesity.

overall_design: Each sample represents pooled cells from three mice of the same genotype and treatment group. Samples were pooled before FACS to ensure sufficient cell numbers for sorting and RNA collection. WT or miR-146a-/- mice were treated with either high fat diet or normal chow diet for 14 weeks starting from 6 weeks of age. Mice were sacrificed and live, singlet CD45+ CD11b+ F4/80+ cells were sorted from the stromal vascular fraction of adipose tissue using FACS Aria. RNA was collected from the sorted cells via Qiazol/RNeasy Kit (Qiagen) and library preparation used Illumina TruSeq Stranded RNA Kit with Ribo-Zero Gold. RNA-seq was performed using Illumina HiSeq 50 cycle single-read sequencing version 4. Sequence alignment was performed through the University of Utah Bioinformatics Core Facility.

first: Ryan

middle: M

last: O'Connell

middle: C

first: Marah

last: Runtsch


title: A comprehensive gene expression  analysis identifies novel  immune signatures in cesarean-born infants

city: Shanghai

first: Yongjie

last: Liu

address: 1665 kongjiang road

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

summary: The rate of cesarean delivery (CD) in China has risen sharply and the high rate was reported to be associated with increased risk of disease in the offspring. However, there is little research on the molecular mechanism of critical pathways and gene signatures involved in the neonatal immunity of cesarean-born infants. This study was undertaken to identify unique gene signatures which was involved in the neonatal immunity of cesarean-born infants through large-scale RNA-sequencing. Genes differentially expressed in cesarean-born infants were identified and further validated through quantitative real-time PCR (RT-qPCR). Moreover, we employed weighted gene co-expression network analysis (WGCNA) to identify highly connected genes that were correlated with neonatal inflammation. In total, 73 differentially expressed genes (DEGs) were identified between cesarean-born infants and normal vagina childbirth. The results obtained by secondary validation indicated that GATM, MIF, IFI27, IL1B, CA1, and EPHB1 were significantly upregulated in phenotype CD, while CYP2A6 and DLK1 were significantly down regulated. Further, functional and pathway enrichment analysis reveals perturbation of several DEGs involved in signaling pathways pertaining to immunoregulation, inflammation, apoptosis, and nervous development. Additionally, HLA-DOB popped out as a core gene in the process of inflammation, which might indicate the risk of cesarean-born infants for inflammatory disease. Notably, our study for the first time has documented gene signatures PIK3CA, PTPRC, SOS1, IL6ST, and MALT1, which were found to be involved in neonatal inflammation. Taken together, the full expression repertoire including the differentially expressed gene sets and core differentially co-expressed genes should provide an excellent resource for identifying potential biomarkers of cesarean-born infants with inflammation, and formulating new hypotheses for physiological functions and the discovery of novel therapeutic targets for inflammatory disease.

overall_design: The study samples were composed of 8 newborns by cesarean section delivery and 8 vagina childbirth.

first: Dan

last: Chen


title: Expression data from lung adenocarcinoma tissues and paired normal lung tissues

city: Zhoushan

first: yun

middle: li

last: Xu

address: No. 739, Dingshen Road, Lincheng Street, Dinghai District  Zhoushan City, Zhejiang Province, China

institute: Zhoushan hospital

summary:
Lung adenocarcinoma is the most common histologic subtype of non-small cell lung cancer. There exists a need to identify new molecular regulators for lung adenocarcinoma, providing insights into potential therapeutic targets.
We used microarrays to identify up-regulated genes in invasive lung adenocarcinoma.

overall_design: Invasive lung adenocarcinoma tissues and paired normal lung tissues were used for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain up-regulated genes in invasive lung adenocarcinoma

first: Liyun

first: Yanyan

last: Huang


title: Comparative analysis of mesenchymal stem cells derived from amniotic membrane, umbilical cord and chorionic plate under serum-free condition

first: Xiangxiang

last: Jiang

state: Beijing

address: 1 Beichen West Road, Chaoyang District

institute: Institute of Zoology, Chinese Academy of Sciences

summary: We performed RNA-Seq and identified the differnetially expressed gene information among human AM-MSC, UC-MSC, and CP-MSC(or named P-MSC).

overall_design: mRNA profiles of  AM-MSC, UC-MSC, and CP-MSC from four individual donors were generated by deep sequencing.

first: Hongmei

last: Wang

first: Jiao

last: Ma


title: Polymyxin nephrotoxicity in kidney chip

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

summary: Drug-induced kidney injury, largely caused by proximal tubular intoxicants, limits development and clinical use of new and approved drugs. Assessing preclinical nephrotoxicity relies on animal models that are frequently insensitive, and thus, novel techniques, including human microphysiological systems, or “organs on chips,” are proposed to accelerate drug development and predict safety. Polymyxins are potent antibiotics against multidrug-resistant microorganisms; yet clinical use remains restricted because of high risk of nephrotoxicity and limited understanding of toxicological mechanisms. To mitigate risks, structural analogs of polymyxins (NAB739 and NAB741) are currently in clinical development. Using a microphysiological system to model human kidney proximal tubule, we exposed cells to polymyxin B (PMB) and observed significant increases of injury signals, including kidney injury molecule-1 KIM-1and a panel of injury-associated miRNAs (each P < 0.001). Surprisingly, transcriptional profiling identified cholesterol biosynthesis as the primary cellular pathway induced by PMB (P = 1.2 ×10–16), and effluent cholesterol concentrations were significantly increased after exposure (P < 0.01). Additionally, we observed no upregulation of the nuclear factor (erythroid derived-2)–like 2 pathway despite this being a common pathway upregulated in response to proximal tubule toxicants. In contrast with PMB exposure, minimal changes in gene expression, injury biomarkers, and cholesterol concentrations were observed in response to NAB739 and NAB741. Our findings demonstrate the preclinical safety of NAB739 and  NAB741 and reveal cholesterol biosynthesis as the novel (to our knowledge) pathway for PMB- induced injury. To our knowledge, this is the first demonstration of a human-on-chip platform used  for simultaneous safety testing of new chemical entities and defining unique toxicological pathway responses of an FDA-approved molecule.

overall_design: Cells from six donors were seeded into a total of 74 kidney chips, and effluents of kidney MPS were exposed for 48 hours of treatments

first: Elija

middle: J

last: Weber

first: Kevin

last: Lidberg

first: Lu

first: Theo

middle: K

last: Bammler

middle: W

first: Mavis

last: Li

first: Michelle

last: Redhair

first: William

last: Atkins

first: Cecilla

last: Tran

first: Kelly

last: Hines

first: Josi

last: Herron

first: Libin

first: Marla

last: Beatriz Monteiro

first: Susanne

last: Ramm

first: Vishal

last: Valdya

first: Martti

last: Varra

first: Timo

first: Jonathan

last: Himmelfarb

first: Edward

last: Kelly


title: Genes controlling the activation of natural killer lymphocytes are epigenetically remodeled in intestinal cells from germ-free mice

city: Copenhagen

first: Lars

middle: Roed

last: Ingerslev

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

type: Methylation profiling by high throughput sequencing

summary: Remodeling of the gut microbiota is implicated in various metabolic and inflammatory diseases of the gastrointestinal tract. We hypothesized that the gut microbiota affects the DNA methylation profile of intestinal epithelial cells (IECs) which could, in turn, alter intestinal function. Here, we used mass spectrometry and methylated DNA capture to respectively investigate global and genome-wide DNA methylation of intestinal epithelial cells from germ-free (GF) and conventionally raised mice (CONV-R). In colonic IECs from GF mice, DNA was markedly hypermethylated. This was associated with a dramatic loss of Ten-Eleven-Translocation activity, a lower DNA methyltransferase activity and lower circulating levels of the one carbon metabolites cobalamin and folate. At the gene level, we found an enrichment for differentially methylated regions at proximity of genes regulating cytotoxicity of Natural Killer cells (FDR < 8.9E-6), notably members of the natural killer group 2 member D ligand superfamily Raet. Our results suggest that altered activity of methylation-modifying enzymes in GF mice influences the IEC epigenome at genes involved in the crosstalk between intestinal and immune cells. Epigenetic reprogramming of IECs by the gut microbiota may modulate intestinal function in diseases associated with altered gut microbiota.

overall_design: MBD analysis of the 4 sections of the intestine of 7 germ free (GermFree) and 5 conventionalized (convR) mice

first: Audrey

last: Poupeau

first: Christian

last: Garde

first: Karolina

last: Sulek

first: Kiymet

last: Citirikkaya

first: Jonas

middle: T

last: Treebak

first: Manimozhiyan

last: Arumugam

first: David

last: Simar

first: Fredrik

last: Bäckhed

first: Romain

last: Barrès


title: Cellular acidosis triggers MondoA transcriptional activity by driving mitochondrial ATP production

first: Donald

last: Ayer

state: UT

address: 2000 Circle of Hope

department: Department of Oncological Sciences

summary: MondoA and its transcriptional target thioredoxin-interacting protein (TXNIP) constitute a regulatory loop that senses glycolytic flux and controls glucose availability. Cellular stress also triggers MondoA activity and TXNIP expression. To understand how MondoA integrates glucose and stress signals, we studied its activation by acidosis. We found that acidosis drives mitochondrial ATP (mtATP) synthesis. The subsequent export of mtATP from mitochondria via adenine-nucleotide transporter and voltage-dependent anion channel, and the enzymatic activity of mitochondria-bound hexokinase results in the production of glucose-6-phosphate (G6P), a known activator of MondoA transcriptional activity. MondoA localizes to the outer-mitochondrial membrane (OMM), and in response to G6P, shuttles to the nucleus and activates transcription. Our data suggests that MondoA is a required feature of a glucose- and mtATP-dependent, OMM-localized signaling center. We propose MondoA functions as a coincidence detector and its ability to sense glucose and cellular stress is coupled to the concerted production of G6P.

overall_design: mRNA sequencing of HeLa and HeLa:MondoA-KO cells treated with DMEM or DMEMAcidic for 4 hours

first: Blake

middle: R

last: Wilde

first: Zhizhou

last: Ye


title: Hif-1alpha deletion leads to adverse treatment efficacy in a mouse model of MLL-AF9 driven AML

city: Lund

first: Shamit

last: Soneji

address: Solvegatan 19

country: Sweden

institute: BMC

summary: This report explores the effect of Hif-1alpha deletion, using a conditional mouse model, together with standard chemotherapy regimen to evaluate leukemia stem cell (LSC) targeting in a murine model of MLL-AF9 driven acute myeloid leukemia (AML). This study reveals that Hif-1alpha-deleted leukemias displayed a faster disease progression after chemotherapy.

overall_design: Single cell RNA-seq data were generated on the 10X emulsion platform (10X Genomics, Pleasanton, CA) according to the manufactures instructions. The single-cell RNAseq from the Chromium platform was processed using CellRanger v1.3 using default settings, and subsequent normalization, QC, filtering, and differential gene expression analysis was performed in R using Seurat v1.4 (http://www.satijalab.org/seurat). Dimension reduction was performed using DDRTree over three components.

first: Talia

last: Velasco-Hernandez

first: Isabel

last: Hidalgo

first: Eva

last: Erlandsson

first: Jörg

last: Cammenga

last: Bryder


title: RNA Sequencing of Human iPS derived Cardiomyocytes

city: Farmington

first: Travis

last: Hinson

state: CT

address: 10 Discovery Drive

institute: The Jackson Laboratory

summary: To investigate transcriptional differences between HCM and WT cells

overall_design: Examination of HCM vs WT Cells, with 3 replicates of each sample

first: Rachel

last: Cohn


title: DNA methylation status predicts survival in metastasis free clear cell renal cell carcinoma

city: Umeå

first: Sofie

last: Degerman

state: Sweden

address: NUS, Blg 6M, 2nd floor

department: Medical Biosciensces

institute: Umeå University

summary:
Background: Clear cell renal cell carcinomas (ccRCCs) display divergent clinical phenotypes. Up to one third of patients with local disease at diagnosis will progress. Therefore, it is a need to identify patients at risk for recurrence. In the present study, we analyzed genome-wide promoter DNA methylation at diagnosis in relation to clinicopathological parameters, in order to identify DNA methylation profiles associated with risk for progress.
Method: DNA methylation status in 155,931 CpGs located in gene promoter regions was analyzed by Illumina HumanMethylation450K arrays in diagnostic tissue samples from 115 ccRCC patients. Methylation profiles were compared with genetic aberrations and clinicopathological parameters.
Results: The tumors separated into two clusters based on genome-wide promoter methylation status. The tumors in these clusters differed in tumor diameter (p < 0.001), TNM stage (p < 0.001), morphological grade (p < 0.001), and patients outcome (5 year cancer specific survival (pCSS5yr) 72 % in cluster A vs 26 % in cluster B, p < 0.001). When metastasis-status (M0/M1) and cluster A/B status at diagnosis were combined, we found poor survival in M1 patients regardless of cluster A/B status (pCSS5yr 9 % vs 6 %). In M0 patients, the cluster status clearly separated in survival (pCSS5yr 81 % vs 17 %; p < 0.001). We identified a methylation profile of 398 CpGs that was associated with progress of disease, which included differently methylated CpG sites in the SMAD6, SOCS3 and MX2 genes.
An integrated genomic and epigenomic analysis revealed significant correlations between the total number of genetic aberrations and hypermethylated CpGs (R = 0.435, p > 0.001), and predicted mitotic age (R = 0.407, p < 0.001).
Conclusion: DNA methylation analysis at diagnosis in ccRCC has the potential to improve outcome-prediction and therapy stratification.

overall_design: Bisulphite converted DNA from the clear cell renal cell carcinoma tumors and tumor free tisssue samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip

first: Emma

last: Evelönn

first: Mattias

last: Landfors

first: Zahra

last: Haider

first: Linda

last: Köhn

first: Börje

last: Ljungberg

first: Göran

last: Roos


title: Sex differences in gene regulation in the dorsal root ganglion after nerve injury

city: Baltimore

first: Sean

last: Taverna

state: MD

address: 855 N Wolfe St

department: Pharmacology & Molecular Sciences

institute: Johns Hopkins University

summary: Pain is a subjective experience derived from complex interactions among biological, environmental, and psychosocial pathways. Sex differences in pain sensitivity and chronic pain prevalence are well established. However, the molecular causes underlying these sex dimorphisms are poorly understood particularly with regard to the role of the peripheral nervous system. Here we sought to identify shared and distinct gene networks functioning in the peripheral nervous systems that may contribute to sex differences of pain after nerve injury. We performed RNA-seq on dorsal root ganglia following chronic constriction injury of the sciatic nerve in male and female rats. Analysis from paired naive and injured tissues showed that 1456 genes were differentially expressed between sexes. Appreciating sex-related gene expression differences and similarities in neuropathic pain models may help to improve the translational relevance to clinical populations and efficacy of clinical trials of this major health issue.

overall_design: examination of gene expression naïve and injured, male and female rats

first: Kimberly

last: Stephens

middle: D


title: Putative Biomarkers of malignant transformation of sinonasal inverted papilloma into squamous cell carcinoma

status: Public on Jan 22 2019

first: Zheng

last: Yang

address: No.1 Dongjiaominxiang

institute: Beijing Tongren Hospital

summary:
OBJECTIVE: Although the malignant transformation of sinonasal inverted papilloma (SNIP) into squamous cell carcinomas (SCC) has been reported in the literature, the molecular mechanisms driving this transformation have not been elucidated. This study compares genome-wide DNA methylation between SNIP and SCC arising in SNIP and further validates the expression of aberrantly methylated genes.
Methots:We used a comprehensive methylation profiling technique to investigate DNA methylation in CpG islands and promoters in six SNIP samples and seven SCC arising in SNIP samples.
A total of 11,201 nominally  differentially methylated sites were observed, between SNIP and SCC arising in SNIP.
This study is the first to compare the differences in global DNA methylation between SNIP and SCC arising in SNIP.

overall_design: This study compared DNA methylation and gene expression between SNIP and SCC arising in SNIP.

first: Yang

last: Zhang


title: Whole genome characterization of in vitro generated mouse colonic monolayers

city: Chapel Hill

first: Nancy

last: Allbritton

state: NC

address: Room 012, Chapman Hall

department: Kenan Professor and Chair of the UNC/NC State Joint Department of Biomedical Engineering and Kenan Professor of Chemistry at UNC

institute: UNC

summary: We report whole genome data for in vitro mouse monolayers with different culture time/transepithelial electrical resistance and colonic crypts. Mouse colonic monolayers were generated on gradient cross-linked collagen scaffolds.

overall_design: A genomic comparison between in vitro generated monolayers and in vivo colonic tissue.

first: Dulan

middle: B

last: Gunasekara

first: Christopher

last: Sims

first: Scott

last: Magness

middle: L


title: Anti-apoptotic regulation contributes successful nuclear reprogramming using cryopreserved oocytes

city: Seoul

first: Chanhyeok

last: Park

address: 5, Hwarang-ro 14-gil

department: Brain Science Institute

country: South Korea

institute: KIST (Korea Institute of Science and Technology)

summary: The cryopreservation has a negative effect on the quality of oocytes and may be  closely associated with increased levels of reactive oxygen species (ROS) and  apoptotic events. The purpose of the present study was to evaluate the detrimental  effects on the developmental competence of somatic cell nuclear transferred (SCNT)-  mouse embryos using vitrified (cryopreserved) oocytes and to evaluate the recovery  effects of melatonin on cryo-damage in cloned embryos. Development of SCNT  embryos using cryopreserved oocyte cytoplasm (SCNT-CROC) was inferior to those  using fresh cytoplasm (SCNT-FOC). Using RNA-sequencing analysis, we found upregulation  of 8 pro-apoptotic-related genes (Cyct, Dapk2, Dffb, Gadd45g, Hint2, Mien1,  P2rx7, and Pmaip) in the SCNT-CROC group. Furthermore, the addition of melatonin,  an agent that reduces apoptosis and ROS production, enhanced blastocyst formation  rates in the SCNT-CROP group when compared with the melatonin-untreated group.  Additionally, melatonin-treatment increased the derivation efficiency of pluripotent stem  cells from cloned embryos using cryopreserved oocyte.

overall_design: Here we perform RNA-Seq experiment in melatonin-treated mouse 2-cell and blastocyst embryos, respectively.

first: D

last: Lee

first: A

first: C

middle: H

first: K

last: Hong


title: Global transcriptional changes in the JJN3 myeloma cell line that occur as a result of treatment with 2 pyrrolobenzodiazepine (PBD) monomers

city: CARDIFF

first: Peter

last: Giles

address: Heath Park

institute: Cardiff University

summary:
Background: This study characterises a group of Pyrrolo[2,1-c][1,4]benzodiazepine (PBD) monomeric hybrids to investigate the global transcriptional changes that occur as a result of treatment in these cells. It was also of interest to determine whether compounds show a selective inhibitory effect on the NF-kB consenus sequence and hence NF-kB signalling.
Methods: NF-kB is often overexpressed and over-active in multiple myeloma. Therefore, JJN3 myeloma cells were selected for this investigation. These cells were treated with 2 PBD monomers - DC-1-170 and DC-1-192 - at a concentration of 30nM, in triplicate alongside untreated controls. They were lysed in Trizol reagent (Thermo Fisher) and RNA was extracted using an RNeasy mini-prep kit (Qiagen). Isolated RNA was then taken forward for RNA-seq. Downstream analysis was performed using GenView2 software (in-house analysis tool developed by Peter Giles) and Ingenuity Pathway Analysis (Qiagen).
Results: RNA-seq analysis revealed an overall inhibitory effect on gene transcription as a result of treatment with both PBD monomers, with a small proportion of genes experiencing increased transcription. Approximately 80% of genes that were altered were common to both PBD compounds tested. Both PBD compounds also showed significant inhibition of NF-kB signalling.
Conclusions: RNA-sequencing confirmed gene set enrichment for NF-κB pathway genes although as expected, other canonical pathways were also affected. This could be linked with the toxicity that these cells experience as a result of treatment with PBD monomer hybrids.

overall_design: JJN3 cells were treated with 30nM of DC-1-170 and DC-1-192 for 4 hours alongside untreated controls in triplicate.

first: Thomas

last: Lewis

first: Chris

last: Pepper


title: Global distribution of DNA hydroxymethylation and DNA methylation in chronic lymphocytic leukemia

city: Gothenburg

first: Subazini

last: TK

address: Medicineragatan 9A

institute: Gothenburg university

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We studied global distribution of hydroxymethylation (5hmC) and DNA methylation (5mC) in during normal B-cell development and CLL maturation. To derive disease-specific epigenetic changes we have compared CLL subgroups to their corresponding cell of origin. Our data showed that naïve B-cells, compared to non-class switched and class switched memory B-cells, had higher levels of 5-hmC and 5-mC. By comparing with ChIP sequencing data of H3K27Ac and H3K4me1 modifications of CLL samples with 5hmC and 5mC levels, we observed an increase of 5-hmC at overall gene body regions, CpG island shores and regulatory elements. Comparing 5-hmC distribution with RNA sequencing we showed that genes with higher transcriptional activity had higher 5-hmC and vice versa. Thus, our study suggests that the global loss of 5-hmC levels, with significant increase at gene regulatory regions, constitute a novel hallmark of CLL pathogenesis.

overall_design: Investigating the global distribution óf 5hmC and 5mC levels, Transcriptome analysis followed by  H3K27Ac, H3K4me1 histone mpodifications using hMeDIP seq, MeDIP seq, RNA seq and ChIP sequencing for same CLL pateint samples and normal B cells.

first: Meena

last: Kanduri

first: Chandrasekhar


title: Promoter-proximal pausing mediated by the exon junction complex regulates splicing [RBP1 ChIP]

city: Lausanne

first: Jean-Yves

last: Roignant

address: genopode building

country: Switzerland

institute: University of Lausanne

summary: Promoter-proximal pausing of RNA polymerase II (Pol II) is a widespread transcriptional regulatory step across metazoans. Here we find that the nuclear exon junction complex (pre-EJC) is a critical and conserved regulator of this process. Depletion of pre-EJC subunits leads to a global decrease in Pol II pausing and to premature entry into elongation. This effect occurs, at least in part, via non-canonical recruitment of pre-EJC components at promoters. Failure to recruit the pre-EJC at promoters results in increased binding of the positive transcription elongation complex (P-TEFb) and in enhanced Pol II release. Notably, restoring pausing is sufficient to rescue exon skipping and the photoreceptor differentiation defect associated with depletion of pre-EJC components in vivo. We propose that the pre-EJC serves as an early transcriptional checkpoint to prevent premature entry into elongation, ensuring proper recruitment of RNA processing components that are necessary for exon definition.

overall_design: Pol II ChIP in  control and Mago depleted S2R+ cells from a previous lot and passage of S2R+ cells.

first: Akhtar

last: Junaid

first: Kreim

last: Nastasja


title: Impaired Liver X Receptor alpha phosphorylation affects hepatic chromatin H3K27 acetylation patterns

city: London

first: Ines

last: Pineda-Torra

address: 5 University Street

institute: University College London

summary: Liver X Receptors (LXRα and β) are ligand-activated transcription factors that play a key role in the control of lipid homeostasis, as well as modulation of immunity and inflammation. Besides ligand binding, LXR activity can be regulated by posttranslational modifications, such as phosphorylation. This study aims to assess how changes in the phosphorylation status of LXRα affect the H3K27Ac histone modification, a known marker for active regulatory elements in promoters and enhancers, in livers of mice mice that carry a whole-body phosphorylation deficient-version of LXRα (S196A) compared  to wild-type (WT), in response to a high fat-high cholesterol diet.

overall_design: High-throughput profiling of the H3K27Ac histone modification in liver of wild-type (WT) and LXRα-S196A female mice after being fed a High Fat-High Cholesterol diet for 6 weeks.

first: Natalia

last: Becares

first: Ning

last: Liang

first: Eckardt

last: Treuter


title: DAM ID sequencing of DAM fusion with Cdk9 in Control and Mago knockdown [Promoter-proximal pausing mediated by the exon junction complex regulates splicing]

overall_design: Cdk9-DamID in  control and Mago depleted S2R+ cells

first: Junaid

last: Akhtar

first: Nastasja

last: Kreim


title: Impact on erythroid progenitor type on erythroid differntiation

city: Cleveland Heights

first: Tolulope

last: Rosanwo

state: Ohio

address: 2741 Euclid Heights Blvd, Apartment 7

institute: Boston Children's Hospital

summary: We sought to compare mature iRBCs derived from WT or SCA hiPSCs to characterize observable disease phenotypes in culture. We performed bulk mRNA sequencing on PB cRBCs, WT iRBCs and SCA iRBCs.

overall_design: RNA-seq was performed to determine the genome-wide changes in expression in peripheral blood derived myelo-erythroid progenitors versus wild type and sickle cell iPS progentiors at different stages of erythropoiesis. Global transcriptomic analyses revealed that SCA iRBCs had elevated expression of hypoxia-responsive genes and decreased expression of metabolic pathways relating to lipid metabolism.

first: Melissa

last: Kinney

first: Trista

last: North

first: George

middle: Q

last: Daley


title: ChIP of Ser2P PolII from cells with Mago knockdown and control knockdown [Promoter-proximal pausing mediated by the exon junction complex regulates splicing]

overall_design: Ser2P ChIP in  control and Mago depleted S2R+ cells


title: Systems-level Analysis of Oxygen Exposure in Zymomonas mobilis: Implications for Isoprenoid Production

status: Public on Jan 21 2019

city: Madison

first: Daniel

last: Amador-Noguez

state: WI

address: 1550 Linden Dr

department: Bacteriology

institute: University of Wisconsin-Madison

summary: Zymomonas mobilis is an aerotolerant anaerobe and prolific ethanologen with attractive characteristics for industrial bioproduct generation. However, there is currently insufficient knowledge of the impact that environmental factors have on flux through industrially relevant biosynthetic pathways. Here, we examine the effect of oxygen exposure on metabolism and gene expression in Z. mobilis by combining targeted metabolomics, mRNA sequencing, and shotgun proteomics. We found that exposure to oxygen profoundly influenced metabolism, inducing both transient metabolic bottlenecks and long-term metabolic remodeling. In particular, oxygen induced a severe but temporary metabolic bottleneck in the methyl erythritol 4-phosphate pathway for isoprenoid biosynthesis caused by oxidative damage to the iron-sulfur co-factors of the final two enzymes of the pathway. This bottleneck was resolved with minimal changes in expression of isoprenoid biosynthetic enzymes. Instead, it was associated with pronounced upregulation of enzymes related to iron-sulfur cluster maintenance and biogenesis (i.e., flavodoxin reductase and the suf operon). We also detected major changes in glucose utilization in the presence of oxygen. Specifically, we observed increased gluconate production following exposure to oxygen, accounting for 18% of glucose uptake. Our results suggest that under aerobic conditions, electrons derived from the oxidation of glucose to gluconate are diverted to the electron transport chain where they can minimize oxidative damage by reducing reactive oxygen species such as H2O2. This model is supported by the simultaneous upregulation of three membrane-bound dehydrogenases, cytochrome c peroxidase, and a cytochrome bd oxidase following exposure to oxygen.

sample_organism: Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821

overall_design: Oxygen exposure timecourse. Z. mobilis cultures grown under anaerobic conditions were transferred to aerobic conditions during mid-log phase. A time zero sample was taken just before transfer. mRNA extractions were performed at 5, 15, 30, 45, 60, and 120 minutes after transfer to oxygen. 4 replicates for samples transferred to aerobic conditions (O2). Control samples were also collected from cultures that remained under anaerobic conditions at 60 and 120 minutes after the time zero sample. 3 replicates for anaerobic controls (An).

first: Julia

middle: I

last: Martien


title: Identification of cis elements for temporal and spatial control of DNA replication [Repli-Seq KLF4]

city: Tallahassee

first: David

last: Gilbert

state: FL

address: 319 Stadium Drive

department: Biology

institute: Florida State University

summary: DNA replication occurs in units of chromatin higher order organization (Topologically Associating Domains, or TADs; replication domains, or RDs), which self-organize in 3D into sub-nuclear compartments of early or late replicating chromatin. However, identification of cis-elements regulating replication timing (RT) and sub-nuclear compartments has been a major challenge in the field. Through an extensive series of CRISPR mediated deletion and inversions at a pluripotency associated domain (DppA2/4) in mouse embryonic stem cells (mESCs), we have identified cis-regulatory “early replication control elements” (ERCEs) that mediate early replication and A/B compartmentalization. We show that CTCF/cohesin loops, including the TAD boundaries, were dispensable, and multiple internal DNA segments were necessary for the domain’s early replication in a partially redundant fashion. These segments were also sufficient to maintain early replication in the context of large inversions, irrespective of TAD boundaries. High-resolution capture Hi-C of this region revealed three sites of major contact that also displayed prominent chromatin features. Targeted deletion of all three contact points, which do not include the major mapped replication origins, caused a complete shift to late replication and association with compartment B, equivalent to the switch during lineage commitment. Individual and pair-wise deletions confirmed their partial redundancy and interdependency in giving rise to domain-wise RT patterns, and suggest the importance of long-range interactions. ERCEs are enriched in properties of strong or super-enhancers, and regulate gene expression, although transcription itself is not sufficient in driving early replication. In sum, our results have revealed the first cis-elements regulating the temporal and spatial control of DNA replication that is independent of transcription.

overall_design: Genome-wide replication timing profiles.

first: Jiao

last: Sima


title: Identification of cis elements for temporal and spatial control of DNA replication [Repli-Seq YY1]


title: Py2T long term cells and mesenchymal breast cancer cells (MTΔECad) treated with different inhibitors

city: Basel

first: Ravi Kiran Reddy

last: KALATHUR

state: Basel

address: Mattenstrasse 28

department: Departement Biomedizin

institute: University of Basel

summary: Cancer cell plasticity facilitates the development of therapy resistance and malignant progression. De-differentiation processes, such as an epithelial-mesenchymal transition (EMT), are known to enhance cellular plasticity. Here, we demonstrate that cancer cell plasticity can be exploited therapeutically by forcing the trans-differentiation of EMT-derived breast cancer cells into post-mitotic and functional adipocytes. Delineation of the molecular pathways underlying such trans-differentiation has motivated a combination therapy with a MEK inhibitor and the anti-diabetic drug Rosiglitazone in various mouse models of murine and human breast cancer in vivo. This combination therapy provokes the conversion of invasive and disseminating cancer cells into post-mitotic adipocytes leading to the repression of primary tumor invasion and metastasis formation

overall_design: Py2T long term cells and mesenchymal breast cancer cells (MTΔECad) were harvested at day7 and treated with different inhibitors (two biological replicates per time-point)

first: Dana

last: Ishay-Ronen

first: Maren

last: Diepenbruck

first: Ravi

last: kalathur

first: Robert

last: Ivanek

first: Gerhard

last: Christofori


title: Identification of cis elements for temporal and spatial control of DNA replication [Repli-Seq CTCF Auxin]


title: RNA Polymerase II CTD Tyrosine 1 is Required for Efficient Termination by the Nrd1-Nab3-Sen1 Pathway

city: Montreal

first: Francois

last: Robert

state: QC

address: 110 av des Pins Ouest

country: Canada

institute: IRCM

type: Genome binding/occupancy profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Identification of cis elements for temporal and spatial control of DNA replication [4C-seq]

overall_design: 4C-seq profiles in mESCs with a bait in DppA2/4 domain.


title: Identification of cis elements for temporal and spatial control of DNA replication [Bru-seq]

overall_design: Bru-seq capturing nascent RNA transcripts.


title: RNA Polymerase II CTD Tyrosine 1 is Required for Efficient Termination by the Nrd1-Nab3-Sen1 Pathway (NET-Seq)

summary: Transcription termination is key to gene regulation as it prevents transcription interference with neighboring genes. In Saccharomyces cerevisiae, termination at protein-coding genes is coupled to the cleavage of the nascent transcript, while most non-coding RNA transcription relies on a cleavage-independent termination pathway involving Nrd1, Nab3 and the helicase Sen1 (NNS pathway). In both pathways, the recruitment of termination factors involves phosphorylated forms of the RNA polymerase II C-terminal domain (CTD) but the contribution of individual CTD residues was never systematically investigated. Here, we investigated the impact of mutating phosphorylation sites in the CTD on termination. We observed widespread termination defects at protein-coding genes in mutants for Ser2 or Thr4 but rare defects in Tyr1 mutants for this class of genes. Instead, mutating Tyr1, or its phosphatase Glc7, led to widespread termination defects at non-coding genes known to terminate via the NNS pathway. These defects can be suppressed by slowing down transcription, suggesting that Tyr1 mediates termination via the regulation of elongation or pausing. Our work redefines the role of Tyr1 in termination at protein-coding genes in budding yeast and highlights its key role in termination by the NNS pathway.

overall_design: NET-seq experiments of WT RNAPII and an RNAPII mutant where the CTD is mutated such that all 26 repeats contain an Y1F substitution. Cells express either Flag-tagged WT RPB1 or Flag-tagged Y1F mutant RPB1 on a centromeric plasmid under the control of the RPB1 promoter. The endogenous RPB1 gene is Myc-tagged. NET-seq experiments were performed using an anti-Flag antibody in duplicate, for a total of four samples.

first: Pierre

last: Collin

first: Célia

last: Jeronimo

first: Christian

last: Poitras

first: François


title: Identification of cis elements for temporal and spatial control of DNA replication [Repli-seq epha4]


title: Histone acetyltransferase Kat2a stabilises pluripotency with control of transcriptional heterogeneity

status: Public on Jan 20 2019

city: Cambridge

first: Cristina

last: Pina

address: Long Road

department: Haematology

institute: University of Cambridge

summary: Cell fate transitions in mammalian stem cell systems have often been associated with transcriptional heterogeneity, however existing data have failed to establish a functional or mechanistic link between the two phenomena. Experiments in unicellular organisms support the notion that transcriptional heterogeneity can be used to facilitate adaptability to environmental changes and have identified conserved chromatin-associated factors that modulate levels of transcriptional noise. By inhibiting the paradigmatic histone acetyl-transferase, and candidate noise modulator, Kat2a (yeast orthologue Gcn5) in mouse embryonic stem cells, we show destabilisation of pluripotency-associated gene regulatory networks through increased global and locus-specific transcriptional heterogeneity. Functionally, network destabilisation associates with reduced pluripotency and accelerated mesendodermal differentiation, with increased probability of transitions into lineage commitment. Thus, we functionally link transcriptional heterogeneity to cell fate transitions through manipulation of the histone acetylation landscape of mouse embryonic stem cells and establish a general paradigm that could be exploited in other normal and malignant stem cell fate transitions.

overall_design:
Differential chromatin H3K9 acetylation of mouse embryonic stem (ES) cells treated with Kat2/Gcn5 inhibitor MB-3 or vehicle (DMSO) for 48 hours in the presence of serum and leukaemia inhibitory factor (LIF).

This series includes gene expression profiling of mouse embryonic stem (ES) cells treated with Kat2/Gcn5 inhibitor MB-3 or vehicle (DMSO).

first: D

last: Seyres

first: C

first: N

last: Moris


title: DNA methylation analysis of normal and HBx transgenic mouse liver

first: Young-Joon

last: Kim

address: Yonsei-ro 50

institute: Yonsei university

summary: A genome-wide integrated DNA methylation analysis of the early stage of hepatocellular carcinoma development that induced by HBx. The HBV x (HBx) protein, which plays a critical role in the development of HCC, was shown to interact with several epigenetic factors, such as DNMT3A and HDAC1. Most HBx transgenic (TG) mice spontaneously develop HCC at about 1 year of age, providing genetic validation of the oncogenic potential of HBx even in the absence of viral integration and chronic inflammation. Therefore, it would be intriguing to study the regulatory role of HBx in the epigenome and its impact on HCC development. We performed a genome-wide analysis to examine the differences in DNA methylation enrichment pattern between cancer and normal liver cells.

overall_design: Methylated-CpG island recovery assay (MIRA) of at 3 mouth old age mouse liver

first: Sun-Min

last: Lee


title: Epigenome analysis of cohorts infants and toddlers: children raised in orphanages and children raised in biological families

city: Houston

first: Oxana

middle: Yu.

last: Naumova

state: TX

address: 4849 Calhoun Rd, TIMES, Rm 373

department: Psychology

institute: University of Houston

summary: Genome wide DNA methylation profiling of whole blood cells. The the Illumina Infinium MethylationEPIC microarray was used. Two children's cohorts were studied: 29 children residing in the orphanages (institutional care group, IC) and 29 children being raised in biological families (biological family care group, BFC)

overall_design: Bisulphite converted DNA from the 58 samples were hybridised to the Illumina Infinium MethylationEPIC Beadchip.

middle: Y

first: Elena

last: Grigorenko


title: Identification of cis elements for temporal and spatial control of DNA replication

first: David

middle: M

last: Gilbert

overall_design:
Refer to individual Series

The GSE114139_ERCEs_predicted_mm10.txt file was created using all of the data from the series of experiments that are part of Superseries GSE114139. For genome-wide prediction of ERCEs, CTCF-independent Hi-C interactions (20kb resolution, FDR 5%) were retrieved using the auxin-induced CTCF depletion HiC (Nora et al., 2017) with Fit-Hi-C program (Ay et al., 2014). The significant interactions were then filtered based on their overlap with P300-binding sites, non-lamin-associated domains and Oct4, Sox2 and Nanog (OSN) triple peaks on both sides of the interaction. The final set of interactions were then flattened into 1D regions, which were further processed to merge multiple sites as the predicted ERCEs.


title: HDAC3 restrains cytokine signaling during thymocyte development for the generation of CD4 T cells (RNA-Seq)

city: Rochester

first: Virginia

middle: Smith

last: Shapiro

state: MN

address: 200 First St SW

department: Immunology

institute: Mayo Clinic

summary: CD4 and CD8 T cells are vital components of the immune system.  According to the kinetic signaling model, commitment to the CD4 or CD8 lineage is determined by whether persistent TCR signaling or cytokine signaling predominates, respectively.  We found histone deacetylase 3 (HDAC3) is critical for the development of CD4 T cells, as its deletion leads to the generation of only CD8SP thymocytes.  In the absence of HDAC3, MHC Class II-restricted OT-II thymocytes are redirected to the CD8 cytotoxic lineage.  Analysis of histone acetylation and RNA-seq reveals HDAC3-deficient DP thymocytes are biased towards the CD8 lineage prior to positive selection.  In addition, HDAC3-deficient DP thymocytes have increased IL-21R expression and STAT5 activation.  As a result, HDAC3 is required to restrain cytokine signaling in DP thymocytes and is required for the generation of CD4 T cells.

overall_design: We used mRNA-seq to identify changes in gene expression and ChIP-seq to map epigenetic marks in DP thymocytes and TCR-int/CD69-positive thymocytes.

middle: S


title: HDAC3 restrains CD8-lineage genes to maintain a bi-potential state in CD4+CD8+ thymocytes for CD4-lineage commitment


title: ESRP1 knockdown in breast cancer cells

status: Public on Jan 19 2019

city: Indianapolis

first: Sunil

last: Badve

state: IN

address: 635 Barnhill Drive, MS A-128

institute: Indiana University

summary: ESRP1 was knocked down in endocrine resistant LCC2 and LCC9 cells

overall_design: Analysis of importance of ESRP1 in breast cancer

first: Yesim

last: Gokmen-Polar


title: HDAC3 restrains cytokine signaling during thymocyte development for the generation of CD4 T cells (ChIP-Seq)


title: Identification of cis elements for temporal and spatial control of DNA replication [repli-Seq]

overall_design: Genome-wide replication timing profiles

first: Jiao

last: Sima


title: Interferon-beta-inducible genes in human monocyte-derived macrophages (MDMs)

city: Los Angeles

first: Priscila

middle: Ribeiro

last: Andrade

state: CALIFORNIA

address: 615 Charles E Young Drive South, room 246

department: Medicine

institute: UCLA

summary: Transcriptome analysis of human macrophages stimulated with Interferon Beta at different time points. Control Media data for all different time points can be found at Series GSE82227.

overall_design: RNA sequencing of human monocyte differentiated macrophages stimulated with Interferon Beta at 2, 6 and 24h (285u/ml). Control media data for each time point is available at Series GSE82227.

first: Dennis

last: Montoya

first: Susan

last: Realegeno

first: Robert

last: Modlin


title: Maintenance of nucleolar homeostasis by CBX4 alleviates senescence and osteoarthritis

city: Beijing

first: Zunpeng

last: Liu

address: Beichen West Road

department: Institute of Zoology, Chinese Academy of Sciences

institute: State Key Laboratory of Stem Cell and Reproductive Biology

summary: CBX4, a component of polycomb repressive complex 1 (PRC1), plays important roles in the maintenance of cell identity and organ development through epigenetic silencing. However, whether CBX4 regulates the homeostasis of human stem cells remains unclear. Here, we demonstrate that CBX4 counteracts human mesenchymal stem cell (hMSC) aging via the maintenance of nucleolar homeostasis. CBX4 protein is decreased in aged hMSCs, and targeted CBX4 knockout in young hMSCs results in destabilized nucleolar heterochromatin, increased ribosome biogenesis and protein translation, and accelerated cellular senescence. CBX4 maintains nucleolar homeostasis by recruiting nucleolar protein fibrillarin and heterochromatin organization associated protein KAP1 at nucleolar rDNA, limiting the excessive expression of rRNAs. Importantly, overexpression of CBX4 alleviates physiological hMSC aging and attenuates the development of posttraumatic osteoarthritis in mice. Taken together, our findings reveal a novel role of CBX4 in counteracting senescence by maintaining nucleolar homeostasis, providing a potential therapeutic target for aging-associated disorders.

overall_design: Transcriptome analysis of knee joints tissues upon the treatment of lentiviruses expressing Luc, CBX4 in anterior cruciate ligament transection (ACLT) induced osteoarthritis (OA) mouse model.

first: Guanghui


title: Transcriptomic analysis of RCH-ACV cells whose SETDB2 was knocked down by shRNA

city: Stanford

first: Stephen HK

last: WONG

state: California

address: G2035 SIM1 Bldg

institute: Stanford University

summary: RCH-ACV cells was depleted for SETDB2 by shRNA lentivirus construct co-expressing mCherry fluorescent. After sorting of mCherry positive cells, the cells were cultured and expanded and total RNA was extracted for Microarray experiment.

overall_design: 6 samples, 2 conditions

first: Chiou-Hong

last: Lin

first: Stephen

last: Wong

first: Michael

last: Cleary


title: Noninvasive ultrasound stimulation of the spleen to treat inflammatory arthritis - single cell RNA sequencing of splenic leukocytes

city: Minneapolis

first: Rachel

middle: Stegeman

last: Graham

address: 2101 6th St SE

department: Pediatrics

institute: University of Minnesota

summary: Purpose: The goal of this study was to characterize splenic leukocytes in arthritic and non-arthritic mice with and without ultrasound treatment

overall_design: Method: Splenocytes were sorted for live, singlet CD45+ cells which were made into libraries using the 10X Genomics Chromium Single Cell 3’ Library & Gel Bead Kit (v2) and sequenced on an Illumina NovaSeq Sequencer.

first: Daniel

middle: P

last: Zachs

first: Sarah

middle: J

last: Offutt

first: Yohan

last: Kim

first: Jerel

last: Mueller

first: Jennifer

last: Auger

first: Nathaniel

last: Schuldt

first: Claire

last: Kaiser

first: Abigail

last: Heiller

first: Raini

last: Dutta

first: Hongsun

last: Guo

first: Jamu

middle: K

last: Alford

first: Bryce

middle: A

last: Binstadt

first: Hubert

last: Lim


title: Genome-wide maps of chromatin remodeler binding in acute myeloid leukemia cell line.

city: Kolkata

first: Amitava

last: Sengupta

state: West Bengal

address: CN 6, Sector V, Salt Lake

department: Cancer Biology & Inflammatory Disorder Division

country: India

institute: CSIR - Indian Institute of Chemical Biology (Translational Research Unit of Excellence)

summary: We have used chromatin immunoprecipitation followed by high throughput sequencing to map regions of chromatin remodeler binding in Control and KDM6A knock down AML cells. We have used this data to determine KDM6A contribution to chromatin remodeler binding and thus understand its role in leukemogenesis.

overall_design: Binding profile of the core ATP-ase subunit of the NuRD chromatin remodeler in Control and KDM6A knock down AML cell line.


title: Fine Mapping and Functional Characterization of Genetic Variants in the FAM13A Chronic Obstructive Pulmonary Disease GWAS locus using Massively Parallel Reporter Assays

city: BOSTON

first: Dandi

last: Qiao

state: MA

address: 181 Longwood Avenue

institute: Brigham and Women's Hospital and Harvard Medical School

summary:
Background: The identification of causal variants responsible for disease associations from genome-wide association studies (GWAS) facilitates functional understanding of the disease mechanisms implicated by GWAS. One of the earliest GWAS associations to COPD spans an intragenic region within FAM13A, but the causal variants at this loci have not yet been identified. Massively parallel reporter assays (MPRA) can be used to prioritize functional regulatory variants in a high-throughput manner.
Methods: We used an integrated approach using fine-mapping in over 10,000 subjects from COPD GWAS studies, two MPRA experiments, traditional reporter assays, chromatin conformation capture, and CRISPR-based gene editing to characterize COPD-associated regulatory variants in FAM13A in human bronchial epithelial cell lines.
Results: Conditional genetic association and fine mapping analyses identified two independent COPD association signals in FAM13A. MPRA identified 45 common functional regulatory variants, and six COPD-associated putative functional variants were prioritized for further functional investigation. Three variants demonstrated significant activity in traditional reporter assays, and one variant, rs2013701, was selected for further testing in the endogenous genomic context based on a direction of effect consistent with postulated mechanisms of FAM13A-mediated COPD susceptibility. CRISPR-based genome editing for this variant confirmed allele-specific effects on FAM13A expression and altered rates of cellular proliferation, providing multiple levels of functional characterization for this COPD-associated variant.
Conclusions: Comprehensive screening for regulatory variants near FAM13A identified the presence of extensive functional regulatory variation within a 250kb window of FAM13A in HBECs. Focused functional evaluation of the COPD-associated functional variants in LD with the two independent association signals in this region prioritized the common variant rs2013701, for which multiple parallel lines of functional evidence confirm allelic effects on FAM13A regulation.

first: Xiaobo

last: Zhou

first: Peter

last: Castaldi

first: Feng


title: Cdk8 and Ssn801 regulate oxidative stress resistance and virulence in Cryptococcus neoformans

status: Public on Jan 18 2019

city: St. Louis

first: Yiming

last: Kang

state: MO

address: 1 Brookings Dr

department: Computer Science and Engineering

institute: Washington University in St. Louis

summary: Cryptococcus neoformans is an important pathogen that annually kills 200,000 people worldwide. It survives in the environment as a yeast or spore and can also proliferate within host macrophages after being inhaled into the lungs. In conditions of immunocompromise, cryptococcal cells can escape from the lungs to the brain, where they cause a deadly meningoencephalitis that is both difficult and expensive to treat. Cryptococcal adaptation to the harsh lung environment is a critical first step in its pathogenesis, and consequently a compelling topic of study. This adaptation is mediated by a complex transcriptional program that integrates cellular responses to environmental stimuli. Although several key regulators in this process have been examined, one important protein complex that modulates transcription yet remains understudied in C. neoformans is the Mediator complex. In other organisms, this complex promotes transcription of specific genes by increasing the assembly of the RNA Polymerase II pre-initiation complex. We have focused on the Kinase Module of the Mediator complex, which consists of cyclin C (Ssn801), cyclin-dependent kinase 8 (Cdk8), and two other proteins (Med12 and Med13). This module provides important inhibitory control of Mediator complex assembly and activity. Using a transcriptomics approach, we discovered that Cdk8 and Ssn801 together regulate cryptococcal functions relevant to pathogenesis, including the response to oxidative stress. Deletion of CDK8 resulted in altered mitochondrial morphology and the dysregulation of genes involved in oxidation-reduction processes, such that this strain exhibited increased susceptibility to oxidative stress. This resulted in an inability of mutant cells to proliferate within phagocytes, decreased lung burdens, and attenuated virulence in in vivo studies. These findings increase our understanding of cryptococcal adaptation to the host environment and its regulation of oxidative stress resistance and virulence.

overall_design: 7 independent strains are prepared in triplicate and analyzed. CNAG_00000 is the KN99alpha WT strain. CNAG_06086_WT is the WT control reference strain for the strain expressing a kinase dead Cdk8 (CNAG_06086_KD)

first: Andrew

last: Chang

first: Kang

last: Yiming

first: Tamara

last: Doering


title: Compare of gene expression between p16INK4A positive and negative Colon cancer [2018HC346]

city: swon

first: Tea jun

last: Park

address: 206, World cup-ro, Yeongtong-gu

department: Biochemistry and Molecular Biology

institute: Ajou University School of Medicine

summary: To evaluate gene expression in an in colon cancer, we analyzed the gene expression profile of p16INK4A positive or negative expressed colon cancer region by RNA sequencing.

overall_design: Examination of p16INK4A positive expressed colon cancer (A) region each compared with  p16INK4A negative expressed colon cancer (B).

first: Tae

first: Young

last: Kim


title: Identify novel TGF-β-regulated genes by RNA-sequencing from MCF10A cells

city: Iowa City

first: Hank

last: Qi

state: IA

address: 1-632 Bowen Science Building

institute: University of Iowa

summary: TGF-β signaling and its induced EMT (Epithelial to mesenchymal transition) play fundamental roles in development and disease including cancers. Although, TGF-β-regulated genes have been extensively studied, with RNA-sequencing (RNA-seq) analysis, new TGF-β-regulated genes are still been identified. Moreover, many significantly regulated genes by TGF-β are not emphasized. This study employs RNA-seq on MCF10A cells treated by TGF-β for 1.5 (this GEO), 24, 48, and 72 (GSE74377) hours and aims to identify novel TGF-β-regulated genes. With 1.5 fold gene expression change (log2 0.58) and p<0.05 at any length of the treatment, 1166 and 861 genes were found to be upregulated and downregulated by TGF-β, respectively. These genes were analyzed for their enrichments in KEGG pathways and prognostic markers of cancers. Several genes of interest were further analyzed for their regulation by TGF-β across cell lines and their functions in context of TGF-β were further studied. This study systematically analyzed TGF-β-regulated genes and revealed novel factors mediating the pro-migratory role of TGF-β signaling, hence, sheds a light on the understanding of the mechanisms underlying the role of TGF-β signaling in cancer development.

overall_design: mRNA profiles of MCF10A cells stably expressing a scramble shRNA with TGF-β1 treatment for 0, 1.5 hours were generated by RNA-seq, in duplicate, using HiSeq2500 instrument.

first: Qi

last: Liu

first: Nicholas

last: Borcherding

first: Peng

last: Shao

first: Huojun

last: Cao

first: Weizhou

last: Zhang


title: Compare of gene expression between p16INK4A positive and negative regions of colon cancer from five patients

overall_design: Refer to individual Series


title: Compare of gene expression between p16INK4A positive and negative Colon cancer [2018HC067]

overall_design: Examination of p16INK4A positive expressed colon cancer (I) region each compared with  p16INK4A negative expressed colon cancer (C).


title: Compare of gene expression between p16INK4A positive and negative Colon cancer [2018HC100]


title: RNA-seq and ChIP-seq to study how transcription factor Foxp1 regulates Foxp3 binding to chromatin and coordinates regulatory T cell function

city: Princeton

first: Yuri

last: Pritykin

state: NJ

address: 245 Carl Icahn Lab, Lewis-Sigler Institute for Integrative Genomics

institute: Princeton University

summary: Regulatory T (Treg) cells, whose differentiation and function are controlled by transcription factor Foxp3, express high amounts of a closely related family member Foxp1, which is also expressed in quiescent naive T cells. Here we explored Foxp1 function in Treg cells. We found that a large number of Foxp3-bound genomic sites in Treg cells were occupied by Foxp1 in both Treg and conventional T cells. In Treg cells, Foxp1 markedly increased Foxp3 binding to these sites, which were enriched for canonic forkhead and Ets binding motifs. Foxp1 deficiency in Treg cells resulted in their impaired function and competitive fitness associated with markedly reduced CD25 expression and interleukin-2 (IL-2) responsiveness, diminished CTLA-4 and increased SATB1 expression. The characteristic patterns of CD25, Foxp3, and CTLA-4 expression in Treg cells were rescued, at least in part, upon strong IL-2 signaling. Our studies suggest that in addition to the Foxp1-mediated regulation of quiescence that is common to Treg and conventional T cells, Foxp1 has an essential non-redundant function in Treg cells by enforcing Foxp3-mediated regulation of gene expression and enabling efficient IL-2 signaling in these cells.

overall_design: Foxp1 ChIP-seq in Treg (triplicates) and conventional T cells (duplicates), with genetic controls; Foxp3 ChIP-seq in wildtype (duplicates) and Foxp1-deficient (triplicates) Treg cells, with genetic controls; RNA-seq in naïve and activated wildtype and Foxp1-deficient Treg cell (triplicates)

first: Catherine

last: Konopacki

first: Yury

last: Rubtsov

first: Christina

last: Leslie

first: Alexander

last: Rudensky


title: Compare of gene expression between p16INK4A positive and negative Colon cancer [2017HC070]


title: Compare of gene expression between p16INK4A positive and negative Colon cancer [2018HC173]


title: An evolutionarily-conserved Wnt3/β-catenin/Sp5 feedback loop restricts head organizer activity in Hydra [RNA-Seq]

city: Geneva

first: Leonardo

last: Beccari

address: 30 Quai Ernest Ansermet

department: Genetics and Evolution

institute: University of Geneva

summary: Head regeneration in Hydra requires the transformation of gastric tissue into a head organizer that produces a head activator and a head inhibitor. Here we report the decipherment of a long-standing question in developmental biology, the identification of the transcription factor Sp5 as a key head inhibitory component. We show that Sp5 has an apical to basal graded expression pattern in intact Hydra, its expression is induced upon Wnt/β-catenin signaling activation and when knocked-down triggers the formation of multiple heads and axes in homeostatic and regenerative conditions. Our data indicate that Sp5 acts in a feed-forward loop to robustly regulate its own expression and that Sp5 prevents head formation by repressing the Wnt3 promoter. This Sp5 mediated Wnt antagonism is conserved and was invented early in metazoan evolution to set up axial patterning. To gain insights on the evolution of the transcriptional properties of the Sp5 gene, we analyzed the capacity of the hydra Sp5 and zebrafish Sp5a paralogs to bind to cis-regulatory elements of the contitutively active human genome and to regulate the expression of the corresponding target genes. To this end, we transfected HEK293 cells with plasmids encoding for either hySp5 or zfSp5a proteins and we performed ChIPseq and RNAseq experiments to analyze their genomic occupancies and the changes in the transcriptional profiles induced upon transfection.

overall_design: Cells were transfected either with a control plasmid or with plasmids encoding for HySp5 and ZfSp5a proteins. Plasmids encoding for mutant versions of these genes, lacking the DNA binding domain (HySp5-dDBD  and ZfSp5-dDBD respectively), were also transfected. In order to evaluate the ability of HySP5 and ZfSp5a proteins to regulate gene expression via cooperation with beta-catenin, HEK293 cells were cotransfected with a combination of plasmids encoding for these factors. HEK293 cells were also transfected either with the b-CATENIN coding plasmid alone or with a combination of plasmids encoding for HySp5-dDBD or ZfSp5-dDBD together with b-catenin.

first: M

last: Vogg

first: L


title: Molecular interactions between Hel2 and RNA supporting ribosome-associated quality control

city: Edinburgh

first: Marie-Luise

last: Winz

address: Max Born Crescent

department: Wellcome Centre for Cell Biology

institute: University of Edinburgh

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


title: A Novel Glioma-specific Enhancer Maintains Glioma Temozolomide Sensitivity By Regulation of RasGRP3 Expression via Long-range Chromosome Interactions

city: Tianjin

first: Bohan

last: Chen

address: NO.94 Weijin Road

institute: Nankai University

summary: In this study, we report the identification of a glioma-specific enhancer that confers sensitivity to TMZ by upregulation of the mitogen-associated protein kinase activator RasGRP3. Deletion of either the active domain of RasGPR3 or the enhancer using CRISPR/Cas9, was sufficient to restore sensitivity to TMZ in a resistant population of cells that was reversed with overexpression of RasGRP3. The project include RNA-seq, Hi-C, Capture Hi-C between DMSO-treated U251 and TMZ-treated U251.

first: Wange

last: Lu


city: London

first: Rasha

middle: Noureldin

last: Saleh

address: 30 Guilford street

institute: University College London

summary: HIRA is a histone chaperone that modulates gene expression through the deposition of H3.3. Conditional knockout of Hira in embryonic mouse hearts leads to cardiac septal defects. However, the effects of HIRA on the gene expression profile at earlier stages of cardiogenic mesoderm differentiation has not yet been studied. Differentiation of mouse embryonic stem cells (mESCs) towards cardiomyocytes mimics some of these events and is an accepted model of these early stages. We performed RNA-Seq and H3.3-HA ChIP-seq on both WT and Hira-null mESCs and early cardiomyocyte progenitors of both genotypes. Analysis of our RNA-seq data showed differential down regulation of cardiovascular development-related genes in Hira-null cardiomyocytes compared to WT cardiomyocytes. Correlating these data with H3.3 enrichment showed that HIRA is required for the expression of the transcription factors (TFs) Gata6, Meis1 and Tbx2. These TFs displayed diminished HIRA-dependent H3.3 enrichment in their gene bodies or at their transcription start site in the absence of HIRA. Our results reveal new transcription factors through which HIRA influences cardiogenesis in vitro and potentially in vivo.

overall_design: Genome wide enrichment of H3.3 in WT and Hira-null embryonic stem cells and day 15 differentiated cardiac progenitor.

first: Tony

last: Brooks

first: Peter

last: Scambler

first: Ariane

last: Chapgier


title: Molecular interactions between Hel2 and RNA supporting ribosome-associated quality control [I]

summary: Ribosome-associated quality control (RQC) pathways monitor and respond to stalling of translating ribosomes. Using a newly developed technique based on in vivo UV crosslinking and mass spectrometry, we identify a C-terminal region in Hel2/Rqt1 as an RNA binding domain, with amino acids L501/K502 directly interacting with RNA. In vivo crosslinking of Hel2 revealed binding to 18S rRNA and translating mRNAs. Consistent with the 18S binding site located between mRNA entrance and exit channels, Hel2 preferentially bound mRNA both upstream and downstream of the termination codon. A C-terminal truncation that deleted L501/K502, abolished crosslinking to 18S rRNA, altered mRNA binding patterns, and reduced Hel2 function comparable to hel2∆. Asc1, also participates in RQC and ASC1 deletion impaired Hel2 18S and mRNA binding. We conclude that Hel2 is recruited or stabilized on translating 40S ribosomal subunits by interactions with 18S rRNA and Asc1. Ribosome-bound Hel2 interacts with mRNA, predominately during translation termination.

overall_design: CRAC was performed with yeast BY4741 strains containing HTP-tagged Hel2 (only version, under native promotor).

first: Lauri

last: Peil

first: Tomasz

middle: W

last: Turowski

first: Juri

last: Rappsilber

first: David

last: Tollervey


title: Molecular Profiling defines evolutionarily conserved transcription factor signatures of major vestibulospinal neuron groups

status: Public on Jan 17 2019

city: Boston

first: Benjamin

last: Okaty

address: 77 Avenue Louis Pasteur

institute: Harvard Medical School

summary: Vestibulospinal neurons are organized into discrete groups projecting from brainstem to spinal cord, enabling vertebrates to maintain proper balance and posture. The two largest groups are the lateral vestibulospinal tract (LVST) group and the contralateral medial vestibulospinal tract (cMVST) group, with different projection lateralities and functional roles. In search of a molecular basis for these differences, we performed RNA sequencing on LVST and cMVST neurons from mouse and chicken embryos followed by immunohistofluorescence validation. Focusing on transcription factor (TF)-encoding genes, we identified TF signatures that uniquely distinguish the LVST from the cMVST group and further parse different rhombomere-derived portions comprising the cMVST. Immunohistofluorescence assessment of the CNS from spinal cord to cortex demonstrated that these TF signatures are restricted to the respective vestibulospinal groups and some neurons in their immediate vicinity. Collectively, these results link the combinatorial expression of TFs to developmental and functional subdivisions within the vestibulospinal system.

sample_organism:
Gallus gallus
Mus musculus

platform_organism:
Gallus gallus
Mus musculus

overall_design: Transcriptome profiles of small pools of retrogradely labeled, acutely dissociated, manually sorted vestibulospinal neurons from mouse and chicken embryos with 3-6 biological replicates per sample condition (projection target). RNAseq libraries prepared from medially adjacent tissue served as a control for both mouse and chicken samples (4 biological replicates), and for the mouse an additional control group was comprised of unlabeled, acutely dissociated and manually sorted cells from caudally adjacent tissue (4 biological replicates).

first: Anders

last: Lunde


title: Using Next-Generation Sequencing Transcriptomics to Determine Markers of Post-traumatic Symptoms  - preliminary findings from a post-deployment cohort

city: Toronto

first: Stephen

last: Scherer

state: Ontario

address: 686 Bay Street

department: Genetics and Genomic Biology

institute: The Hospital for Sick Children

summary: Post-traumatic stress disorder is a concerning psycho behavioral disorder thought to emerge from the complex interaction between genetic and environmental factors. For soldiers exposed to combat, the risk of developing this disorder is two-fold and diagnosis is often late, when much sequela has set in. To be able to identify and diagnose in advance those at “risk” of developing PTSD, would greatly taper the gap between late sequelae and treatment. Therefore, this study sought to test the hypothesis that the transcriptome can be used to track the development of PTSD in this unique and susceptible cohort of individuals. Gene expression levels in peripheral blood samples from 85 Canadian infantry soldiers (n = 58 subjects negative for PTSD symptoms and n = 27 subjects with PTSD symptoms) were determined by RNA sequencing technology following their return from deployment to Afghanistan. Count-based gene expression quantification, normalization and differential analysis (with thorough correction for confounders) revealed significant differences in two genes, LRP8 and GOLM1 . These preliminary results provide a proof-of-principle for the diagnostic utility of blood-based gene expression profiles for tracking symptoms of post-traumatic stress disorder in soldiers returning from tour. It is also the first to report transcriptome-wide expression profiles alongside a post-traumatic symptom checklist.

overall_design: Peripheral blood samples from 85 Canadian infantry soldiers (n = 58 subjects negative for PTSD symptoms and n = 27 subjects with PTSD symptoms)

first: Cathy

last: Boscarino

first: Thomas

last: Nalpathamkalam

first: Giovanna

last: Pellecchia

first: Weili

last: Li

first: Bhooma

last: Thiruvahindrapuram

first: Daniele

last: Merico


title: High-dimensional transcriptional analyses of UC Colon comparing RNALater to DMSO collection method

city: Cambridge

first: Scott

last: Jelinsky

address: 610 Main Street

department: Inflammation and Immunology

institute: Pfizer

summary: Simultaneous analyses of peripheral and mucosal immune compartments can yield insight into the pathogenesis of mucosal-associated diseases. Although methods to preserve peripheral immune cells are well established, studies involving mucosal immune cells have been hampered by lack of simple storage techniques. We provide a cryopreservation protocol allowing for storage of gastrointestinal (GI) tissue with preservation of viability and functionality of both immune and epithelial cells.

overall_design: Multiple biopsies were taken from UC subjects to and placed into different collection media to compare the ability to extract total RNA and use total RNAseq to study the difference between inflamed and non-inflamed tissue


title: Comparison of liver mRNA expression between Control AA and Low AA diet fed mice

city: Madison

first: Dudley

last: Lamming

address: 2500 Overlook Terr

institute: University of Wisconsin-Madison

summary: The goal of the experiment was to examine hepatic gene expression differences induced by a low protein high carbohydrate diet. We used chemically defined diets based on naturally defined diets first published and completely described in Fontana et al., 2016, Cell Reports.

overall_design: 9 week old C57BL/6J mice were fed either Control (TD.140711) or Low AA (TD.140712) diets for 4 months and then sacrificed after an overnight ~16 hour fast. 8 total samples were examined - 4 from Control AA and 4 from Low AA diet fed mice.


title: PLZF targets developmental enhancers for activation during osteogenic differentiation of human mesenchymal stem cells (ChIP-seq)

city: Copenhagen N

first: Mads

last: Lerdrup

address: Blegdamsvej 3C

department: Department of Cellular and Molecular Medicine

institute: University of Copenhagen

summary: The PLZF transcription factor is essential for osteogenic differentiation of hMSCs, however, its regulation and molecular function during this process is not fully understood. Here we revealed that the ZBTB16 locus encoding PLZF, is repressed by Polycomb (PcG) and H3K27me3 in naïve hMSCs. At the pre-osteoblast stage of differentiation, the locus lost PcG binding and H3K27me3, gained JMJD3 recruitment, and H3K27ac resulting in high expression of PLZF. Subsequently, PLZF was recruited to osteogenic enhancers, influencing H3K27 acetylation and expression of nearby genes important for osteogenic function. Furthermore, we identified a latent enhancer within the ZBTB16/PLZF locus itself that became active, gained PLZF, p300 and Mediator binding and looped to the promoter of the nicotinamide N-methyltransferase (NNMT) gene. The increased expression of NNMT correlated with a decline in SAM levels, which is dependent on PLZF and is required for osteogenic differentiation.

overall_design: ChIP-Sequening for histone modification: H3K27me3, H3K27ac, H3K4me1, H3K4me3, and PLZF binding in hMSC

first: Shuchi

last: Agrawal Singh

first: Ana-Luisa

middle: R

last: Gomes

first: Harmen

last: Van de Werken

first: Jens

last: Vilstrup Johansen

first: Robin

last: Andersson

first: Albin

last: Sandelin

first: Kristian

last: Helin

first: Klaus

last: Hansen


title: PLZF targets developmental enhancers for activation during osteogenic differentiation of human mesenchymal stem cells (RNA-seq)

overall_design: Effect of PLZF knockdown on osteogenic differentiation of hMSC (RNAseq)


title: Estrogen Signaling in Arcuate Kiss1 Neurons Suppresses a Sex-Dependent Circuit That Promotes Dense Strong Bones in Female Mice

city: San Francisco

first: Holly

last: Ingraham

state: CA

address: 1550 4th Street, 284F

department: Cellular and Molecular Pharmacology

institute: University of California, San Francisco

summary: Purpose: To characterize the estrogen receptor α (ESR1)-dependent transcriptome of neurons in the arcuate nucleus that regulate female bone density

overall_design: Method: Using RNA-Seq we compared gene expression profiles of microdissected arcuate nuclei from 3 control (Esr1fl/fl) and 3 conditional knockout (Esr1fl/fl;Nkx2-1-Cre) female mice.

first: William

middle: C

last: Krause


title: Targeting JNK Pathway Expands Human Hematopoietic Stem Cells

city: Beijing

first: xiong

last: xiao

address: 5 Yiheyuan Rd

institute: peking university

summary: The limited number of human hematopoietic stem cells (HSCs) has restrained their widespread clinical application. Despite great efforts in recent years, the in vitro expansion of HSCs remains a challenge due to incomplete understanding of the signaling networks underlying HSC self-renewal. Here we show that culturing human cord blood (CB) CD34+ cells with JNK-IN-8, an inhibitor of the JNK signaling pathway, can enhance the self-renewal of HSCs with a 6-fold increase in number. These expanded CD34+ cells repopulated recipient mice for 20 weeks and can form secondary engraftment that lasted for more than 21 weeks. Knockdown of c-Jun, a major downstream target in the JNK pathway, significantly promoted the expansion of hematopoietic stem and progenitor cells (HSPCs). Our findings demonstrate a critical role of JNK pathway in regulating HSC expansion, provide new insights into HSC self-renewal mechanism, and may lead to improved clinical application of HSCs.

overall_design: The progeny mRNA profiles of cord blood CD34+ cells with a 7-days culture were generated by RNA sequencing, in duplicate, using Illumina hiseq XTen.

first: Xiong

last: Xiao

first: Hongkui

last: Deng


title: Probing the Global Cellular Responses to Lipotoxicity Caused by Saturated Fatty Acids

first: Laura

last: Bond

address: 655 Huntington Avenue

department: Genetics and Complex Diseases

institute: Harvard School of Public Health

summary: RNA sequencing technology was applied to determine the transcriptional changes due to palmitate treatment, RNF213 knockdown, and GPAT4 knockdown.

overall_design: Total RNA was isolated from K562 cells using an RNeasy Kit. The library construction and sequencing were performed by the TUFTS sequencing core (tucf-genomics.tufts.edu/). Briefly, the RNA was run on a Bioanlayzer (Agilent) to assess RNA quality and quantification. The biological triplicates were pooled at this point. The library preparation was performed using the TruSeq Stranded mRNA Library Prep Kit (Illumina). The samples were sequenced by HiSeq 2500, Rapid Paired-End 100 (RL-PE100) or HiSeq 2500, High Output v4 Paired-End 100 (HI-PE100, Illumina). All reads were mapped to the UCSC hg19 human reference genome using Tophat2 with multi-read correction, followed by normalization, quantification and differential expression analysis using Cuffdiff.

first: Manuele

last: Piccolis

first: Robert

last: Farese Jr

first: Tobias

last: Walther


title: Gene expression analysis of prostate cancer cells treated with fatty acid synthase (FASN) inhibitor IPI-9119

city: boston

first: giorgia

last: zadra

address: 450 Brookline ave

department: Oncologic pathology

institute: DFCI

summary: Alterations in gene expression following fatty acid synthase inhibtion were evaluated in androgen sensitive LNCaP cells and castration resistant 22Rv1 and LNCaP-95 cells.  Cell were exposed to 2 concentrations (0.1 and 0.5 uM) of  FASN inhibitor IPI-9119 or DMSO for 6 days.

overall_design: Differential gene expression anlaysis in 3  prostate cancer cell lines treated with FASN inhibitor IPI-9119

first: Giorgia

last: Zadra

first: Massimo

last: Loda


title: Transcriptional profiling at the DLK1/MEG3 domain explains clinical overlap between imprinting disorders

city: Paris

first: Walid

last: Abi Habib

address: 28 avenue du dr arnold netter

country: France

summary: we performed transcriptomic profiling on fibroblasts cultures from controls, TS14 and SRS patients in order to study the effect of hypomethylation at imprinted loci on genes expression

overall_design: RNA seq was perfromed from fibroblasts mRNA of: 4 controls. 4 TS14 patients, 5 SRS patients and one SRS/TS14 patient

first: Irene

last: Netchine


title: RNA-seq of human iPS derived  macrophages with or without KLF1- transcription factor Activation

status: Public on Jan 16 2019

first: Martha

last: Lopez Yrigoyen

address: 5 Little France Dr

institute: Centre for Regenerative Medicine

summary: Red blood cells (RBCs) mature within a specialized niche (the erythroblastic island (EI)), which consists of a central  macrophage surrounded by differentiating erythroblasts. Human Induced Pluripotent Stem Cell derived macrophages (iPSC-DMs) enhance proliferation and terminal maturation of Umbilical Cord Blood (UCB) CD34+ derived erythroid cells and iPSC derived erythroid cells. These effects are further increased when an inducible KLF1-ERT2 fusion protein is activated in iPSC-DMs.  To assess the mechanism of action, we sought to compare the transcriptome of iPSC-DMs with and without KLF1 activation. For this, we used an inducible IPSC line (iKLF1.2) in which upon tamoxifen addition, the KLF1 transcription factor is translocated to nucleus and consequently KLF1 downstream targets are expressed. The identification and characterisation of could identify factors involved in erythroid maturation and thus helpful to improve current protocols to manufacture RBCs  in vitro.

overall_design: iKLF1.2 iPSCs were differentiated to macrophages and then split into 2 groups, one was treated with tamoxifen for the last 4 days of culture to activate KLF1. The other group was not treated with tamoxifen. Four biologically independent differentiation experiments were carried out and so 8 samples were generated: 4 samples of untreated iKLF1.2 iPSCs-derived macrophages and 4 samples of tamoxifen treated iKLF1.2 iPSC-derived macrophages. Total RNA was extracted from each sample and RNA integrity was of a high enough quality for library preparation, as all RIN values were above 9 for every sample.

last: Lopez-Yrigoyen

first: Jonathan

last: Manning

first: Lesley

last: Forrester


title: Branched-chain Amino Acid Aminotransferase-1 Regulates Self-Renewal and Pluripotency of Mouse Embryonic Stem Cells through Ras Signaling

first: Shaohui

last: Chen

address: NO.38 Tongyan Road

summary: Embryonic stem cells (ESCs) can self-renew indefinitely and have the potential to differentiate into all cell types in the adult organism. Although the developmental plasticity of ESCs is mainly controlled by transcription factors, the intrinsic regulation of this process remains elusive. Here, using whole transcriptome RNA-sequencing analysis, we identified branched-chain amino acid aminotransferase-1 (Bcat1) as highly expressed in mouse ESCs. Further, deletion of the Bcat1 gene was found to impair the pluripotency and self-renewal of mouse ESCs and made cells more inclined to differentiate toward epiblast stem cells. Conversely, overexpression of Bcat1 in mouse ESCs resulted in robust self-renewal and the repression of differentiation. Mechanistically, Bcat1 regulates the expression of RAS protein activator like 1 (Rasal1), leading to activation of Ras-Erk/MAPK signaling axis, which controls the expression of a set of core transcription factors that maintain pluripotency and self-renewal. In summary, we identified for the first time that Bcat1 is essential for mouse ESCs self-renewal and pluripotency and that this effect is mediated by the Ras pathway.

overall_design: In order to figure out the possible regulator which maintains the mouse Embryonic stem cells pluripotency and self-renewal, we performed RNA-seq in WT (cultured in normal medium with 2i and lif) and differential (cultured in the medium lacking of 2i and lif for 7 days) E14 cells (in three replicates, using Illumina HiSeq-2000). By analyzing the RNA-seq data, we found Bcat1 was highly expressed in WT E14 cells and decreased in differential E14 cells, and further studies showed that Bcat1 is essential for maintaining mESCs self-renewal and pluripotency. Next, we want to figure out how Bcat1 functions in mESCs. Mouse Embryonic stem cells -E14 mRNA of wild type (WT) and Bcat1-/- were generated by deep sequencing, in two replicates, using Illumina HiSeq-2000.

first: Bohan

first: Wange

last: Lu


title: Escherichia coli O157:H7 responds to phosphate starvation by modifying LPS involved in biofilm formation

city: Saint-Hyacinthe

first: Philippe

last: Vogeleer

address: 3200 rue Sicotte

institute: Université de Montréal

summary:
Pathogens like E. coli O157:H7 are responsible for many outbreaks and can be found and survive in poor inorganic phosphate (Pi) environments. In E. coli the phosphate homeostasis is regulated by the Pst system and the two-component system PhoB/R. In a Δpst mutant, PhoB is constitutively activated and biofilm formation is increased.
To understand how PhoB activation lead to biofilm increase, we compared the transcriptomes of EDL933 the WT strain and  Δpst mutant both grown in MOPS Pi rich medium, using the Affymetrix GeneChip® E. coli Genome 2.0 Array.

overall_design: EDL933WT strain and its isogenic mutant Δpst were grown in Pi+ conditions until the OD600 reached respectively 0.55 to 0.6. Samples equal to 5.10e8 CFU were taken from this mid log phase and processed for transcriptomes analysis. Ten µg of RNAs were extracted and retro-transcripted. One µg of the fragmented and biotinylated cDNAs, were hybridized onto Affymetrix GeneChip® E. coli. The data were processed using the FlexArray® software; RMA normalization and the levels of transcription obtained from 3 biological replicates of each experimental condition were compared using the EB (Wright & Simon) algorithm. We then conducted comparisons between Δpst mutant and EDL933WT both grown in Pi+. The differentially expression conditions corresponded to 2-fold change (FC) cut-off and p-value < 0.05.

first: Samuel

last: Chekabab

first: Antony

middle: T

last: Vincent

first: Steve

last: Charrette

first: Alexey

last: Novikov

first: Martine

last: Caroff

first: Francis

last: Beaudry

first: Mario

last: Jacques

first: Josée

last: Harel


title: Transcriptomics analysis of Colon tumor xenograft model in streptozotocin-induced diabetic mice

city: Madrid

first: Pablo

last: Minguez

state: Madrid

address: Av. Reyes Catolicos 2

department: Genetics and Genomics

country: Spain

institute: Health Research Institute Fundación Jiménez Díaz (IIS-FJD), UAM

summary: This is a transcriptomics analysis contributing to a bigger project that tries to shed light on the role of type 2 diabetes mellitus (T2DM) as a risk factor for colon cancer (CC). Here we present a gene expression screening of 7 colon tumor xenograft samples, 2 with diabetic mice and 5 with normal blood glucose levels. For xenograft model details see: Prieto I, et al. (2017) Colon cancer modulation by a diabetic environment: A single institutional experience. PLoS One 12(3):e0172300

overall_design: In this dataset we include the expression data from 7 samples of colon cancer tumor xenograft samples, 2 with diabetic mice and 5 with normal blood glucose levels.

first: Laura

last: Del Puerto-Nevado


title: Lysine specific demethylase 1 inactivation enhances differentiation and promotes cytotoxic response when combined  with all-trans retinoic acid in acute myeloid leukemia across   subtypes

city: Amsterdam

first: Tesa

last: Severson

address: 121 Plesmanlaan

department: Molecular Carcinogensis

country: Netherlands

institute: Netherlands Cancer Institute

summary: Combined treatment with all-trans retinoic acid and GSK2879552 results in synergistic effects on gene expression, cell proliferation, markers   of differentiation, and, most importantly, cytotoxicity.

overall_design: Gene expression analysis of DMSO, single and combination treatment (ATRA and GSK2879552) on 6 AML cell lines at two time-points with two replicates (paired end RNA-seq on 96 samples in total)

first: Helai

last: Mohammad

first: Kimberly

middle: N

last: Smitheman

first: Satyajit

last: Rajapurkar

first: Michael

last: McCabe

first: Natalie

last: Karpinich

first: James

last: Foley

first: Melissa

middle: B

last: Pappalardi

first: Ashley

last: Hughes

first: Wendy

last: Halsey

first: Elizabeth

last: Thomas

first: Christopher

last: Traini

first: Kelly

middle: E

last: Federowicz

first: Jenny

last: Laraio

first: Fredrick

last: Mobegi

first: Geraldine

last: Ferron-Brady

first: Rabinder

last: Prinjha

middle: L

last: Carpenter

first: Ryan

middle: G

last: Kruger

first: Lodewyk

last: Wessels


title: Transcriptomics analysis of paired tumor and normal mucosa samples in a cohort of patients with colon cancer, with and without T2DM.

first: Pablo

last: Minguez

summary: This is a transcriptomics analysis contributing to a bigger project that tries to shed light on the role of type 2 diabetes mellitus (T2DM) as a risk factor for colon cancer (CC). Here we present a gene expression screening of paired tumor and normal colon mucosa samples in a cohort of 42 CC patients, 23 of them with T2DM. Using gene set enrichment, we identified an unexpected overlap of pathways over-represented in diabetics compared to non-diabetics, both in tumor and normal mucosa, including diabetes-related metabolic and signaling processes. An integration with other -omic studies suggests that in diabetics, the local micro-environment in normal colon mucosa may be a factor driving field cancerization which may promote carcinogenesis. Several of these pathways converged on the tumor initiation axis TEAD/YAP-TAZ. Cell culture studies confirmed that high glucose concentrations upregulate this pathway in non-tumor colon cells. In conclusion, diabetes is associated to deregulation of cancer-related processes in normal colon mucosa adjacent to tissue which has undergone a malignant transformation. These data support the existence of the field of cancerization paradigm in diabetes and set a new framework to study link between diabetes and cancer.

overall_design: In total we collected FFPE 2 types of samples from 42 patients with colon cancer: i) tumor samples and ii) normal colonic mucosa. The cohort is composed by 23 non-diabetic patients and 19 diabetics.

first: Laura

last: Del Puerto-Nevado


title: PLZF targets developmental enhancers for activation during osteogenic differentiation of human mesenchymal stem cells

first: Mads

last: Lerdrup

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

overall_design: Refer to individual Series


title: Etv6-dependent positive and negative gene regulatory network controls vegfa expression in vivo [RNA-seq]

city: Oxford

first: Lei

last: Li

address: University of Oxford

department: Radcliffe Department of Medicine

institute: WIMM

summary: VEGFA signaling is crucial for physiological and pathological angiogenesis and hematopoiesis. Although many context-dependent signaling pathways downstream of  VegfA have been uncovered, vegfa transcriptional regulation in vivo is unclear. Here, we show that ETS transcription factor Etv6 positively regulates vegfa expression during blood stem cell development through multiple transcriptional inputs. In agreement with its established repressive functions, Etv6 directly inhibits expression of vegfa repressor foxo3. Surprisingly, it also directly activates expression of vegfa activator klf4. Finally, it indirectly binds to vegfa promoter by the recruiment of Klf4. Thus, our work uncovers a dual function for Etv6, as both a transcriptional repressor and activator, in controlling a major signaling pathway.

overall_design: RNA-seq was performed on three independent biological samples obtained from the somites of wild-type (WT) or etv6 morpholino injected stage 22 embryos. Indexed libraries were then generated, pooled and sequenced using a NextSeq 500 sequencer.

first: Rossella

last: Rispoli

first: Roger

last: Patient

first: Aldo

last: Ciau-Uitz

first: Catherine

last: Porcher


title: Expression data from murine colorectal tumors of mice fed a normal chow diet and a high fat diet

city: Cologne

first: thomas

last: wunderlich

state: NRW

address: Gleueler Str. 50

country: Germany

institute: MPI for Metabolism Research

summary: Obesity increases colorectal cancer despite other disturbances. We have used the AOM/DSS protocol to induce colitis-associated cancer in normal chow diet and high fat diet fed animals. Tumors were microdissected and global gene expression was analysed using microarray.

overall_design: Upon weaning animals were either fed a normal chow (NCD) or a high fat diet (HFD) for 14 weeks. Azoxymethane (AOM) (10mg/kg) was injected at week 8 and 4 days later 1.5% dextrane sodium sulphate (DSS) was supplied in the drinking water for 5 days. Mice were sacrificed 62 days after AOM injection and colorectal tumors were microdissected and processed for RNA isolation.

first: F

last: Wunderlich

first: Claudia

middle: M