title: Combinatorial knockout of RARα, RARβ, and RARγ completely abrogates transcriptional responses to retinoic acid in murine embryonic stem cells

first: Kristian

last: Laursen

address: 1300 York Ave.

department: Pharmacology

institute: Weill Cornell Medicine

summary: All-trans retinoic acid (ATRA) alters gene expression in CCE WT embryonic stem cells, but has no effect on gene expression in RAR-deficient TKO cells (devoid of Retinoic Acid Receptors α, β, and γ)

overall_design: Murine Embryonic Stem Cells (WT and RAR-deficient TKO cells) were treated with vehicle (ETOH) or all-trans retinoic acid (ATRA, 1uM) and expression profiling was performed by RNAseq

middle: B

first: Lorraine

last: Gudas


title: Deacetylation of miRNA-34a and miRNA-449 induces epithelial-mesenchymal transition and acquired resistance to ALK inhibitors

status: Public on May 28 2018

city: Seoul

first: Kyoung-Ho

last: Pyo

address: 50 Yonseiro

department: Avison Biomedical Research Center

country: South Korea

institute: Severance Hospital, Yonsei University College of Medicine

summary: Treatment with ALK tyrosine kinase inhibitors often elicits profound initial antitumor responses in ALK fusion-positive patients with lung adenocarcinoma. However, patients invariably develop acquired resistance to ALK inhibitors. In this study, we aimed to identify molecular events that limit the durable response to ALK inhibition using genetic and epigenetic approaches. To identify novel mechanisms of acquired resistance to ALK inhibitors, we established in vivo and in vitro models of acquired resistance to ceritinib and crizotinib using H3122 and H2228 cells. For in vivo model, mice with established H3122-derived tumors were treated with four doses of ceritinib (50mg/kg, 75mg/kg, 87.5mg/kg, 100mg/kg) to derive ceritinib-resistant tumors.

overall_design: To create ceritinib-resistant lines, H3122 was cultured with increasing concentrations of ceritinib starting with the one-third maximum inhibitory concentration (IC30). Doses were increased in a stepwise manner when normal cell proliferation patterns resumed. Fresh drug was added every 72-96h. Resistant cell (H3122-LR) that grew in 1µM ceritinib were derived after approximately 6 months of culturing in the continuous presence of drug

first: Mi-Ran

last: Yun

first: Sun-Min

last: Lim

first: Hun-Mi

last: Choi

first: Seong-Keun

last: Kim

first: Ji-Min

last: Lee

first: Youwon

first: Jae-Woo

first: Hye-Ryun

first: Min-Hee

last: Hong

first: Seon-Kyu

first: Keeok

last: Haam

first: Yong-Sung

first: Hyo-Sup

last: Shim

first: Ross

middle: A

last: Soo

first: James

middle: C

last: Yang

first: Mirang

first: Byoung-Chul

last: Cho


title: Distinct transcriptional profiles of anti-viral CD4+ T cells based on CD25 surface expression

status: Public on May 25 2018

city: Salt Lake City

first: Matthew

last: Williams

state: UT

address: 15 N. Medical Dr. E.

department: Pathology

country: USA

institute: University of Utah

type: Expression profiling by high throughput sequencing

summary: Trascriptional analysis of CD2 hi and CD25 lo CD4+ effector T cells during acute viral infection.  SMARTA cells were transferred into B6 mice, followed by infection with LCMV.  At day 5 post-infection, CD25 hi and CD25 lo SMARTA cells were isolated from the spleen by FACS. Consistent with our prior studies showing that CD25 lo early effector cells give rise to both Tfh effector cells and memory T cells, we observed gene expression in the CD25 lo population consistent with Tfh differentiation.  Conversely, CD25 hi effector cells expressed markers consistent with Th1 differentiation and short-term survival.

overall_design: mRNA profiles of monoclonal transgenic CD4+ T cells with divergent CD25 surface expression 5 days post LCMV infection in mice

first: Jeremy

middle: P

last: Snook


title: RNA-sequencing of isogenic primary, pre-malignant immortalized, and Ras-transformed human mammary epithelial cells

city: Durham

middle: Burk

last: Friedersdorf

state: NC

address: 207 Research Drive

department: Molecular Genetics & Microbiology

institute: Duke University

summary: Understanding changes in gene expression during tumor initiation and progression is critical to understanding how genetic alterations drive malignancy. We used a genetically defined cell culture model to study the progression of normal human mammary epithelial cells (HMECs) to malignancy. Primary HMECs were immortalized through the expression of hTERT, p53DD, cyclin D1, CDK4R24C and c-MYCT58A. This immortalization conferred limitless replicative potential as well as migratory capacity. These pre-malignant cells were subsequently HRASG12V transformed, which converted the immortalized cells to a fully tumorigenic state with significantly increased invasive capacity. We analyzed the cells using RNA-sequencing, and we report dramatic mRNA expression changes during the pre-malignant immortalization of primary cells, and very few mRNA expression changes occurring during oncogenic Ras transformation. RNA signatures in pre-malignant immortalized and Ras-transformed cells are consistent with previously reported epithelial-to-mesenchymal transition (EMT) signatures.

overall_design: RNA-sequencing in biological triplicate of three cell types (Primary HMECs, Immortalized HMECs, Transformed HMECs); Illumina HiSeq 2000 125bp PE (1 replicate) and Illumina HiSeq 4000 150bp PE (2 replicates)

first: Laura

middle: S

last: Bisogno

first: Jack

middle: D

last: Keene


title: aCGH analysis of human colon cancer C85 cell genome.

status: Public on May 24 2018

city: Warszawa

first: Magdalena

last: Dabrowska

address: 3 Pasteur

country: Poland

institute: Nencki Institute of Experimental Biology

summary: Chromosomal aberrations of C85 cell genome were identified by referral to normal colon epithelial CCD 841 CoN cell genome and Agilent Reference genomic DNA.

overall_design: Agilent SurePrint G3 Unrestricted CGH 1x1M array (GPL8737) was used per experimental variant.

first: Marek

last: Skoneczny


title: RNA-seq distinguished dominant inflammatory profile in placenta from a preterm labor mouse model and control

status: Public on May 26 2018

city: Guangzhou

first: Yi

last: Xiaochun

state: Guangdong

address: No. 107  West Road along the river, Yuexiu District

country: China

institute: Sun Yat-sen Memorial Hospital of the Sun Yat-sen University

summary:
Purpose: No gene expression profiles for the placenta in LPS-induced preterm labor mouse model have been published. The goal of this study was to obtain a comprehensive catalog of differentially expressed genes (DEGs) in the placenta using RNA-seq.
Methods: Preterm labor mouse model (P) and control pregnancy group (C) were gained using a protocol from R. Migale, et al., BMC MED 14 (2016):86. Briefly, on day 15.5 of gestation, an abdominal minilaparotomy was performed. The upper right uterine horn between the first and second sacs received injections of saline (C) or 20 mg E. coli LPS serotype O55:B5 (Sigma-Aldrich, Gillingham, UK) (P) to model preterm labor. Six hours after injections of LPS, the mice were sacrificed and placentas were excised and immediately snap-frozen in liquid nitrogen before being stored at −80°C for subsequent analysis. Placental mRNA profiles were generated by deep sequencing using Illumina seq 2500. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays.
Results: We mapped about 44 million sequence reads per sample to the mouse genome (build mm8) and 25307 transcripts with TopHat workflow. 155 differentially expressed genes (DEGs) in placenta were identified between the preterm group and control group, with a fold change ≥1.5 and p value <0.05. 61 inflammation-related genes occupied the dominant role. 7 of these were validated with qRT–PCR.
Conclusions: Our study represents the first detailed analysis of transcriptomes in placenta in LPS-induced preterm labor mouse model by RNA-seq technology. Dominant inflammatory profile in this model was gained, which gives us a better understanding of the exact molecular processes involved in the development of preterm labor after infection.

overall_design: Placentas from three control pregnancies and four preterm labors.


title: High-troughput expression profile of long non-coding and protein-coding RNAs in primary murine aortic endothelial cells (MAoECs)

city: Munich

first: Andreas

last: Schober

state: Bavaria

address: Pettenkoferstr. 9

department: Institute for Cardiovascular Prevention

country: Germany

institute: Ludwig-Maximilians-University

summary: strand specific sequencing of RNAs from MAoECs to determine the endothelial-specific expression profile of protein-coding and long non-coding RNAs

overall_design: Total RNA was isolated from cultured MAoECs (passage 4) and processed for a strand-specific RNA sequencing. The RNA purity and integrity were assessed using the Fragment Analyzer Automated CE System (Advanced Analytical). A RQN of 8.8 and a 28S/18S ratio of 2.2 were considered acceptable for next generation sequencing assay. Five µg of DNase-treated RNA were used to prepare Massive Analysis of cDNA ends (MACE) libraries needed to perform a DNA-Methylation-Sequencing (Meth-Seq) PCR bias free quantification with TrueQuant Technology, followed by a high-throughput sequencing on the Illumina Genome Analyzer II system (GenXPro GmbH, Frankfurt, Germany). The procedure consist in the extraction of poly-adenylated RNA from 5 µg RNA and reverse transcribed with biotinylated poly(T) primers. cDNA is fragmented to an average size of 250 bp. Biotinylated ends are captured by streptavidin beads and ligated to modified adapters (TrueQuant DNA adapter, GenXPro). The libraries are amplified by PCR, purified by SPRI beads and sequenced (2 x 100 bp Illumina HiSeq2000 TrueSeq, 2 x 20 Mio. Reads poly-A selected paired-end reads). Paired end sequencing of both DNA strands from each end is required for fragment strand specificity.

first: L

last: Natarelli

first: G

last: Csaba


title: RNA-seq profiling of  human thymic Tregs cultured in conditions containing Th1-cytokines, Retinoic acid or control conditions

city: Vancouver

first: Megan

middle: K

last: Levings

address: 950 West 28th Ave

country: Canada

institute: University of British Columbia

summary: To determine the effects of Th1-cytokines (IL-12 + IFN-gamma) or retinoic acid (RA) on expanding human Tregs isolated from pediatric thymus. Cells were stimulated after isolation and cultured for 13 days before RNAsequencing was performed.

overall_design: Human Tregs from pediatric thymus were isolated, stimulated via CD3/CD28 and expanded in vitro for 7 days (with IL-2 and rapamycin),  followed by CD3/CD28 restimulation and culture (with IL-2) until day 13. Cells were polarized to become Th1-Tregs by addition of IL-12 and IFN-gamma from day 0 to 7 of culture followed by neutral conditions from day 7 to 13 (Th1 -> 0) or from day 0 to 13 of culture (Th1 -> Th1). Retinoic acid was added from day 7 to 13 of culture (0 -> RA) to induce a gut-homing phenotype. Tregs without Th1-cytokines or RA served as controls (0 -> 0). Samples are from 3 subjects (PXX8, T016, T018) and each sample was used for all conditions (paired-design).

first: M

first: R

middle: E

last: Hoeppli


title: The ER membrane protein complex interacts cotranslationally to enable biogenesis of multipass membrane proteins

status: Public on May 29 2018

city: Cambridge

first: Jonathan

last: Weissman

state: MA

address: 455 Main St

department: HHMI, Biology

institute: Whitehead Institute for Biomedical Research, MIT

summary: The endoplasmic reticulum (ER) supports biosynthesis of proteins with diverse transmembrane domain (TMD) lengths and hydrophobicity. Features in transmembrane domains such as charged residues in ion channels are often functionally important, but could pose a challenge during cotranslational membrane insertion and folding. Our systematic proteomic approaches in both yeast and human cells revealed that the ER membrane protein complex (EMC) binds to and promotes the biogenesis of a range of multipass transmembrane proteins, with a particular enrichment for transporters. Proximity-specific ribosome profiling demonstrates that the EMC engages clients cotranslationally and immediately following clusters of TMDs enriched for charged residues. The EMC can remain associated after completion of translation, which both protects clients from premature proteasomal degradation and allows recruitment of substrate-specific and general chaperones. Thus, the EMC broadly enables the biogenesis of multipass transmembrane proteins containing destabilizing features, thereby mitigating the trade-off between function and stability.

sample_organism:
Saccharomyces cerevisiae
Homo sapiens

platform_organism:
Saccharomyces cerevisiae
Homo sapiens

overall_design:
Ribosome profiling of whole cell or streptavidin-purified ribosomes biotinylated by ER-localized biotin ligase in yeast

This series includes re-analyzed samples from GSE61012 and GSE85686.

first: Elizabeth

last: Costa

first: Katerina

last: Popova

first: Nicole

middle: T

last: Schirle Oakdale

first: Calvin

middle: H

last: Jan


title: RNAseq of Breast cancer PDX samples

first: Alana

last: Welm

state: utah

address: 2000 Cir of Hope Dr

institute: Huntsman cancer institute

summary: RNAseq was done on Breast cancer PDX samples uisng Library protocol =llumina TruSeq Stranded Total RNA Kit with Ribo-Zero Gold , HiSeq 125 Cycle Paired-End Sequencing v4

overall_design: Paired end sequencing of PDX samples

first: David

last: Lum


title: Identification and single cell functional characterization of an endodermally-biased pluripotent sub-state in human embryonic stem cells

city: Los Angeles

first: Thomas

last: Allison

state: California

address: 615 Charles E Young Drive South

institute: UCLA

summary: Human embryonic stem cells (hESC) display substantial heterogeneity in gene expression, implying the existence of discrete substates within the stem cell compartment. To determine whether these substates impact fate decisions of hESC we used a GFP reporter line to investigate the properties of fractions of putative undifferentiated cells defined by their differential expression of the endoderm transcription factor, GATA6, together with the hESC surface marker, SSEA3. By single cell cloning, we confirmed that substates characterized by expression of GATA6 and SSEA3 include pluripotent stem cells capable of long term self-renewal. When clonal stem cell colonies were formed from GATA6-positive and GATA6-negative cells, more of those derived from GATA6-positive cells contained spontaneously differentiated endoderm cells than similar colonies derived from the GATA6-negative cells. We characterized these discrete cellular states using single cell transcriptomic analysis, identifying a potential role for SOX17 in the establishment of the endoderm biased stem cell state.

overall_design: Examination of 4 different cell substates within one human embryonic stem cell line as determine by the expression status of GATA6 and SSEA3

middle: F

first: Peter

last: Andrews


title: Functional dissection of lymphoid progenitor compartments resolves developmental trajectories in B-lymphocyte development

status: Public on May 23 2018

city: Lund

first: Shamit

last: Soneji

address: Solvegatan 19

country: Sweden

institute: BMC

summary: This report describes the identification and characterization of novel lymphoid progenitor populations in the mouse bone marrow. These data resolve the complexity of the classically defined pre-pro-B/FrA cell compartment and provide a model that can be used to develop a unifying view of the progression of early B-cell development.

overall_design: Single cell RNA-seq data were generated on the 10X emulsion platform (10X Genomics, Pleasanton, CA) according to the manufacturer's 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: Josefine

last: Åhsberg

first: Christina

last: Jensen

first: Tobias

last: Strid

first: Mikael

last: Sigvardsson


title: DNA methylation-mediated regulation of adipose tissue macrophages during high-fat diet-induced obesity

city: Columbia

first: Prakash

last: Nagarkatti

state: SC

address: 6439 Garners Ferry Road

institute: University of South Carolina School of Medicine

type: Methylation profiling by high throughput sequencing

summary: We used MeDIP-Seq to screen for genes that may be regulated by DNA methylation in macrophages isolated from adipose tissue of lean and obese mice.

overall_design: F4/80+ adipose tissue macrophages were isolated from epididymal fat of mice fed a 10% low fat diet, (LFD, lean mice) or 60% high-fat diet (HFD, obese mice) for 16 weeks.

first: Kathryn

last: Miranda

first: Xiaoming

last: Yang

first: Marpe

last: Bam

first: Mitzi


title: Role of NEDD4 E3s in CD4+ T cell activation

city: La Jolla

first: Aki

last: Daisuke

state: CA

address: 9420 Athena Cir

institute: La Jolla Institute

summary: Itch and WWP2 belongs to NEDD4 E3 family, and highly share the structural homology. However it remains elusive whether there are redundant or distinct roles in helper CD4+ T cell differentiation. Here we performed RNA seq analysis using WT, single and double knockout CD4+ T cells, and demonstrated the cooperative effect of the two E3s on Th2 differentiation.

overall_design: gene expression profile of phorbol 12-myristate 13-acetate plus ionomycin stimulated CD4+ T cells from 6 weeks old WT, single and double knockout mice.

first: Daisuke

last: Aki

first: Ashu

last: Sethi

first: Hui

last: Li

first: Wen

last: Zhang

first: Mingke

last: Zheng

first: Chris

last: Elly

first: Jee

last: Lee

first: Weiguo

last: Zou

first: Laurie

last: Glimcher

first: Yun-Cai

last: Liu


title: Regulation of mRNA half-life by an inhibitor of human decapping enzyme Dcp2 following transcription shutoff in HEK293T cells

city: West Haven

first: Sarah

last: Slavoff

state: CT

address: 300 Heffernan Dr

department: Chemistry

institute: Yale University

summary: We report the application of next generation sequencing for measurement of mRNA levels under the effect of a macrocyclic inhibtor of human decapping enzyme 2 (hDcp2).

overall_design: Examination of mRNA levels 0 h and 2 h after transcription block by actinomycin D in HEK293T cells treated by either 2 μM macrocyclic inhibitor CP25 or the same volume of vehicle for 18 h in triplicate.

first: Yang

last: Luo


title: Social Interaction-induced Activation of RNA Splicing in the Amygdala of Microbiome-Deficient Mice

city: Cork

first: Roman

middle: M

last: Stilling

address: Western Road

department: Anatomy and Neuroscience

country: Ireland

institute: University College Cork

summary: Social behaviour is regulated by activity of host-associated microbiota across multiple species. However, the molecular mechanisms mediating this relationship remain elusive. We therefore determined the dynamic, stimulus-dependent transcriptional regulation of germ-free (GF) and GF mice colonised post weaning (exGF) in the amygdala, a brain region critically involved in regulating social interaction. In GF mice the dynamic response seen in controls was attenuated and replaced by a marked increase in expression of splicing factors and alternative exon usage in GF mice upon stimulation, which was even more pronounced in exGF mice. In conclusion, we demonstrate a molecular basis for how the host microbiome is crucial for a normal behavioural response during social interaction. Our data further suggest that social behaviour is correlated with the gene-expression response in the amygdala, established during neurodevelopment as a result of host-microbe interactions. Our findings may help toward understanding neurodevelopmental events leading to social behaviour dysregulation.

overall_design: Equal amounts of RNA from two to three animals were pooled to yield 4 samples per group for naive animals (CON, GF, and exGF). Sample for social-interaction samples were sequenced infividually (n=8-12).  Comparisons for all relevant pairwise combinations were performed using DESeq2 and DEXSeq.

first: Gerry

last: Moloney

first: Feargal

middle: J

last: Ryan

first: Alan

last: Hoban

first: Thomaz

last: Bastiaanssen

first: Fergus

last: Shanahan

first: Gerard

last: Clarke

first: Marcus

last: Claesson

first: Timothy

middle: G

last: Dinan

first: John

last: Cryan


title: Cigarette smoking significantly alters sperm DNA methylation patterns

first: Kenneth

middle: Ivan

last: Aston

state: Select

address: 675 Arapeen Dr Suite 201

summary: Numerous health consequences of tobacco smoke exposure have been characterized, and the effects of smoking on traditional measures of male fertility are well described. However, a growing body of data indicates that pre‐conception paternal smoking also confers increased risk for a number of morbidities on offspring. The mechanism for this increased risk has not been elucidated, but it is likely mediated, at least in part, through epigenetic modifications transmitted through spermatozoa. In this study, we investigated the impact of cigarette smoke exposure on sperm DNA methylation patterns in 78 men who smoke and 78 never‐smokers using the Infinium Human Methylation 450 beadchip. We investigated two models of DNA methylation alterations: (i) consistently altered methylation at specific CpGs or within specific genomic regions and (ii) stochastic DNA methylation alterations manifest as increased variability in genome‐wide methylation patterns in men who smoke. We identified 141 significantly differentially methylated CpGs associated with smoking. In addition, we identified a trend toward increased variance in methylation patterns genome‐wide in sperm DNA from men who smoke compared with never‐smokers. These findings of widespread DNA methylation alterations are consistent with the broad range of offspring heath disparities associated with pre‐conception paternal smoke exposure and warrant further investigation to identify the specific mechanism by which sperm DNA methylation perturbation confers risk to offspring health and whether these changes can be transmitted to offspring and transgenerationally.

overall_design: We investigated the impact of cigarette smoke exposure on sperm DNA methylation patterns in 78 men who smoke and 78 never‐smokers using the Infinium Human Methylation 450 beadchip. We investigated two models of DNA methylation alterations: (i) consistently altered methylation at specific CpGs or within specific genomic regions and (ii) stochastic DNA methylation alterations manifest as increased variability in genome‐wide methylation patterns in men who smoke.

last: Jenkins

first: Emma

middle: R

last: James

first: David

last: Alonso

last: Hoidal

first: Patrick

last: Murphy

first: James

last: Hotaling

first: Bradley

last: Cairns

first: Douglas

last: Carrell

middle: I


title: Single cell transcriptomics reveal the dynamic of haematopoietic stem cell production in the aorta

city: Utrecht

first: Chloé

last: Baron

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: We present single-cell mRNA-Sequencing of various endothelial and hematopoietic populations isolated from the mouse embryonic aorta at E10 and E11. Our study reveals the transcriptional dynamics occuring during endothelial to hematopoietic transition, the process responsible for the production of hematopoietic stem cells.

first: Lennart

last: Kester

first: Anna

last: Klaus

first: Jean-Charles

last: Boisset

first: Roshana

last: Thambyrajah

first: Laurent

last: Yvernogeau

first: Valérie

last: Kouskoff

first: Georges

last: Lacaud

first: Alexander

last: van Oudenaarden

first: Catherine

last: Robin


title: A comparison of genome-wide DNA methylation profiles between Tibetan and Yorkshire pigs

city: Beijing

first: Bo

last: Zhang

address: No. 2 Yuanmingyuan West Road, College Animal Science & Technology, China Agriculture University, Beijing

institute: China Agricultural University

summary: We investigated the heart tissue whole-genome DNA methylation data of Tibetan and Yorkshire pigs raised at high and low altitudes using MeDIP-seq (methylated DNA immunoprecipitation sequencing) technologies, in order to comparatively analyze epigenetic regulation in the two breeds under normoxic and hypoxic conditions. In addition, we aimed to identify the key genes and molecular mechanisms that are involved in adaptation to high altitude in the Tibetan pig. The results of bisulphite sequencing and RT-qPCR indicated that the differentially methylated genes identified in MeDIP-seq were credible. Our results provide new insights into the molecular mechanisms and the epigenetic mechanism involved in hypoxic adaptation in pigs, and a greater understanding of human hypoxic diseases.

overall_design: Examination of heart tissue whole-genome DNA methylation  in Tibetan and Yorkshire pigs raised at high and low altitudes.

first: Hao


title: Increased FGF8 Signaling Promotes Chondrogenic Rather Than Osteogenic Development in the Embryonic Skull

city: Aurora

first: Trevor

last: Williams

state: CO

address: 12801 East 17th Ave

institute: University of Colorado Anschutz Medical Campus

summary: RNA-seq of RNA isolated from E14.5 mouse embryos- wildtype cranial base tissue, Msx2-Cre;CAGFgf8 mutant cranial vault, and wildtype cranial vault;  3 replicates of each group.

overall_design: E14.5 embryos, generated from an Msx2-Cre x CAGF8 cross, were dissected in ice-cold PBS.  From the mutant and control embryos, the skin was peeled away from the skull and the underlying cranial vault tissue was collected.  Subsequently, for the control embryos, the brain was removed and the cartilaginous sections of the cranial base were carefully collected as well.  All tissues from the mutant (cranial vault) and control embryos (cranial vault and cartilaginous cranial base) were stored in RNAlater (Ambion/Life Technologies) until RNA extraction.  RNA was extracted from 9 mutant and control cranial vaults as well as 9 cranial bases using RNeasy Lipid Tissue Mini Kit (Qiagen Cat. NO 74804) following the manufacturer’s protocol. Within each group, the 9 samples were pooled into three groups, with 3 samples making up each group, so that the RNA concentrations were similar.

first: Linnea

last: Schmidt


title: MLL-fusion-driven leukemia requires SETD2 to safeguard genomic integrity

city: Vienna

first: Thomas

last: Eder

address: Veterinaerplatz 1

department: Department for Biological Sciences and Pathobiology

country: Austria

institute: University of Veterinary Medicine, Vienna

type: Genome binding/occupancy profiling by high throughput sequencing

summary: MLL-fusions represent a large group of leukemia drivers, whose diversity originates from the vast molecular heterogeneity of C-terminal fusion partners of MLL. While studies of selected MLL-fusions have revealed critical molecular pathways, unifying mechanisms across all MLL-fusions remain poorly understood. We present the first comprehensive survey of protein-protein interactions of seven distantly related MLL-fusion proteins. Functional investigation of 128 conserved MLL-fusion-interactors identified a specific role for the lysine methyltransferase SETD2 in MLL-leukemia. SETD2 loss caused growth arrest and differentiation of AML cells, and led to increased DNA damage. In addition to its role in H3K36 tri-methylation, SETD2 was required to maintain high H3K79 di-methylation and MLL-AF9 binding to critical target genes, such as Hoxa9. SETD2 loss synergized with pharmacologic inhibition of the H3K79 methyltransferase DOT1L to induce DNA damage, growth arrest, differentiation and apoptosis. These results uncover a dependency for SETD2 during MLL-leukemogenesis, revealing a novel actionable vulnerability in this disease.

overall_design: ChIP-Seq with spike in Drosophila Melanogaster chromatin of 3 different histone modifications: H3K4me3, H3K36me3, H3K79me2 after inducible knockdown of Setd2 or Renilla (negative control); RNA-Seq performed after inducible knockdown of Setd2 or Renilla (negative control)

last: Skucha

first: Jessica

last: Ebner

first: Johannes

last: Schmöllerl

first: Mareike

last: Roth

first: Adrián

last: César-Razquin

first: Alexey

last: Stukalov

first: Sarah

last: Vittori

first: Matthias

last: Muhar

first: Bin

last: Lu

first: Martin

last: Aichinger

first: Julian

last: Jude

first: André

last: Müller

first: Balázs

last: Győrffy

first: Christopher

last: Vakoc

first: Peter

last: Valent

first: Keiryn

middle: L

last: Bennett

last: Zuber

first: Giulio

last: Superti-Furga

first: Florian

last: Grebien


title: Next generation sequencing of distal colon glial cells with DNBS-induced inflammation and neurokinin-2 receptor antagonism utilizing RiboTag mice

city: East Lansing

first: Brian

middle: David

last: Gulbransen

state: MI

address: 567 Wilson Rd

department: Physiology

institute: Michigan State University

summary:
Purpose:We have the first-reported set of glial-specific transcripts utilizing the Ribotag model. We use this model to explore glial changes in DNBS-induced inflammation and neurokinin-2 receptor (NK2R) antagonism.
Methods: Actively translated mRNA profiles of the distal colon myeneteric plexi of Rpl22(+/-)Sox10(+/-) male and female mice 8-10 weeks old were obtained utilizing the HA-tagged ribosomal immunoprecipitation and downstream RNA extraction. Samples meeting RNA quality standards by 18S and 28S rRNA peaks by 2100 Bioanalyzer and RNA 6000 Nano LabChip Kit (Agilent)  were deep sequenced with the Illumina HiSeq 4000.
Results: We mapped approximately 30-50 millions reads per sample to the mouse genome (v88) and identified approximately 100K ribosome-associated transcripts, with Tuxedo workflow, in distal colon glial cells with DNBS-induced inflammation and NK2R antagonism and their respective controls. Of these transcripts, changes in biological processes associated with inflammation and other important enteric nervous system communications between samples have been identified.
Conclusions: Our study demonstrates the first use of the Ribotag model to provide glial cell-specific actively-translated mRNA changes in DNBS-induced inflammation with and without functional NK2R signalling.

overall_design: Distal colon glial mRNA samples from Ribotag Rpl22(+/-)Sox10(+/-) mice administered either saline or DNBS and DMSO vehicle or NK2R antagonism.

first: Ninotchska

last: Delvalle

first: Christine

last: Dharshika


title: Gene expression profiles of primary samples of acute myeloid leukemia (AML)

city: Houston

first: Zhiqiang

last: Wang

state: Texas

address: 7455 Fannin St.

department: Lymphoma and Myeloma

institute: University of Texas MD Anderson Cancer Center

summary:
As part of a clinical trial of the MDM2 inhibitor DS-3032b, 41 primary tumor samples were obtained before treatment from 38 patients newly diagnosed with AML, or relapsed or refractory to standard induction chemotherapy
Gene expression features of pretreatment samples, along with TP53 mutation status, were found to correlate with clinical response to DS-3032b (manuscript under review).

overall_design:
Gene expression profiles were determined using Affymetrix U133_2.0 arrays. Random forest analysis with cross validation was used to identify features correlating with clinical response.
Clinical details for the samples will be provided in a Supplemental Table in the accompanying publication.

first: Jo

last: Ishizawa

first: Kenji

last: Nakamaru

first: Koichi

last: Tazaki

first: Wencai

last: Ma

first: Man

middle: C

first: R

last: Davis

first: Michael

last: Andreeff


title: Comparison of rectal patient data separated by their event of developing distant metastasis [RNA-Seq]

city: Goettingen

first: Alexander

last: Wolff

state: Lower Saxony

address: Humboldtallee 32

department: Medical Statistics

institute: UMG

summary:
The rectal cancer patient data set consists of 10 patients from a clinical study at the Surgery department of the University Medical Center Göttingen collected over a longer time. Patients were chosen based on the follow-up time and development of a distant metastasis. First a balanced sample size of five versus five patients with and without  a metastatic event was chosen. This needed to be changed to six versus four.
Two conditions of  rectal cancer patient data separates by the event of distant metastasis:  1. good prognosis, no event (4 samples),  2. bad prognosis, event (6 samples)
Single-end sequencing on a Illumina HiSeq 200 machine with the standard total_RNA protocol with 50 base pairs read length was used

overall_design:
Two conditions of  rectal cancer patient data separates by the event of distant metastasis:  1. good prognosis, no event (4 samples),  2. bad prognosis, event (6 samples)

** Raw data not provided due to patient privacy concerns **

first: Michaela

last: Bayerlová

first: Dieter

last: Kube

first: Jochen

last: Gaedcke

first: Tim

last: Beißbarth


title: Allele-specific control of replication timing and genome organization during development [RNA-Seq]

status: Public on May 22 2018

city: Tallahassee

first: David

last: Gilbert

state: FL

address: 319 Stadium Drive

department: Biology

institute: Florida State University

summary: DNA replication occurs in a defined temporal order known as the replication-timing (RT) program. RT is regulated during development in discrete chromosomal units, coordinated with transcriptional activity and 3D genome organization. Here, we derived distinct cell types from F1 hybrid musculus X castaneus mouse crosses and exploited the high single nucleotide polymorphism (SNP) density to characterize allelic differences in RT (Repli-seq), genome organization (Hi-C and promoter-capture Hi-C), gene expression (total nuclear RNA-seq) and chromatin accessibility (ATAC-seq). We also present HARP: a new computational tool for sorting SNPs in phased genomes to efficiently measure allele-specific genome-wide data. Analysis of six different hybrid mESC clones with different genomes (C57BL/6, 129/sv and CAST/Ei), parental configurations and gender revealed significant RT asynchrony between alleles across ~12% of the autosomal genome linked to sub-species genomes but not to parental origin, growth conditions or gender. RT asynchrony in mESCs strongly correlated with changes in Hi-C compartments between alleles but not SNP density, gene expression, imprinting or chromatin accessibility. We then tracked mESC RT asynchronous regions during development by analyzing differentiated cell types including extraembryonic endoderm stem (XEN) cells, 4 male and female primary mouse embryonic fibroblasts (MEFs) and neural precursor cells (NPCs) differentiated in vitro from mESCs with opposite parental configurations. We found that RT asynchrony and allelic discordance in Hi-C compartments seen in mESCs was largely lost in all differentiated cell types, coordinated with a more uniform Hi-C compartment arrangement, suggesting that genome organization of homologues converges to similar folding patterns during cell fate commitment.

overall_design: We characterized the allelic differences in RT (Repli-seq), genome organization (Hi-C and promoter-capture Hi-C), gene expression (total nuclear RNA-seq) and chromatin accessibility (ATAC-seq) in distinct cell types from F1 hybrid musculus X castaneus mouse crosses.

first: Juan

last: Rivera-Mulia


title: Allele-specific control of replication timing and genome organization during development [ATAC-Seq]


title: Allele-specific control of replication timing and genome organization during development [Repli-Seq]

summary: DNA replication occurs in a defined temporal order known as the replication-timing (RT) program. RT is regulated during development in discrete chromosomal units, coordinated with transcriptional activity and 3D genome organization. Here, we derived distinct cell types from F1 hybrid musculus X castaneus mouse crosses and exploited the high single nucleotide polymorphism (SNP) density to characterize allelic differences in RT (Repli-seq), genome organization (Hi-C and promoter-capture Hi-C), gene expression (nuclear RNA-seq) and chromatin accessibility (ATAC-seq). We also present HARP: a new computational tool for sorting SNPs in phased genomes to efficiently measure allele-specific genome-wide data. Analysis of 6 different hybrid mESC clones with different genomes (C57BL/6, 129/sv and CAST/Ei), parental configurations and gender revealed significant RT asynchrony between alleles across ~12 % of the autosomal genome linked to sub-species genomes but not to parental origin, growth conditions or gender. RT asynchrony in mESCs strongly correlated with changes in Hi-C compartments between alleles but not SNP density, gene expression, imprinting or chromatin accessibility. We then tracked mESC RT asynchronous regions during development by analyzing differentiated cell types including extraembryonic endoderm stem (XEN) cells, 4 male and female primary mouse embryonic fibroblasts (MEFs) and neural precursors (NPCs) differentiated in vitro from mESCs with opposite parental configurations. Surprisingly, we found that RT asynchrony and allelic discordance in Hi-C compartments seen in mESCs was largely lost in all differentiated cell types, coordinated with a more uniform Hi-C compartment arrangement, suggesting that genome organization of homologues converges to similar folding patterns during cell fate commitment.

overall_design: Genome-wide replication timing profiles were constructed from hybrid F1 cell lines derived from crosses of mouse subspecies and strains


title: Genes regulated by soluble guanylyl cyclase in VCaP prostate cancer cells

city: Boston

first: Dong

last: Han

address: 100 Morrissey Blvd

department: Biology-CPCT

institute: Umass Boston

summary: The aberrant activation of the ERG oncogenic pathway due to TMPRSS2-ERG gene fusions is the major driver of prostate cancer initiation and progression. We identified the alpha1 and beta1 subunits of soluble guanylyl cyclase (GUCY1A1, GUCY1B1) as major ERG-regulated genes in prostate cancer cells. Soluble guanylyl cyclase (sGC) is the major mediator of nitric oxide signaling in cells that, upon nitric oxide binding, catalyzes the synthesis of cGMP and subsequently activates PKG. We showed in ERG-positive PCa cells (VCaP) that cGMP synthesis was significantly elevated by ERG, leading to increased PKG activity and cell proliferation. To further understand the functions of sGC-cGMP pathway in prostate cancer cells, we performed RNA-seq analyses in VCaP cells to identify genes that are regulated by sGC.

overall_design: Firstly, we performed RNA-seq analyses to examine genes differentially regulated by alpha1 or beta1 subunit of sGC in VCaP cells transfected with siRNA against non-target-control (siNTC), GUCY1A1 (siGUCY1A1), or GUCY1B1 (siGUCY1B1). Secondly, we also performed RNA-seq to examine the gene expression profile in VCaP cells treated with vehicle or ODQ, an sGC inhibitor that blocks cGMP synthesis.

first: Feng

last: Zhou

first: Shuai

last: Gao

first: Changmeng

last: Cai


title: RNA-sequencing analysis of CD4 T cells following ipilimumab therapy

city: Nanjing

first: Shiping

last: JIAO

state: Jiangsu

address: Zhongshan Road #321

department: Department of Hepatobiliary Surgery

institute: Nanjing Drum Tower Hospital

summary: We sorted CD4 T cells from patients with metastatic melanoma at baseline and after three doses of ipilimumab.

overall_design: We examined the differential expression of epigenetic enzymes

first: Padmanee

last: Sharma

first: Sangeeta

last: Goswami


title: CRISPR/Cas9-mediated knock-in of an optimized TetO repeat for live cell imaging does not cause heterochromatinization of endogenous loci

city: Urbana

first: Ipek

last: Tasan

state: IL

address: 600 S. Mathews Avenue

institute: University of Illinois at Urbana-Champaign

summary: We recently developed an easy, efficient and scalable method for tagging and live cell imaging of non-repetitive, endogenous chromosome regions via CRISPR/Cas9 mediated knock-in of a TetO repeat. For this purpose, we created optimized and irregular 48-mer and 96-mer TetO repeats. Since it is known that repetitive regions in the human genome can induce H3K9me3-mediated heterochromatin formation, we tested whether 48-mer and/or 96-mer TetO repeats induce H3K9me3 flanking their insertion sites. Using a newly developed method called as CUT&RUN, we showed that there was no significant difference in the H3K9me3 pattern flanking the insertion sites of TetO repeats when compared to wild-type cells.

overall_design: We performed CUT&RUN using an antibody specific for H3K9me3 to identify H3K9me3 enriched regions in the genome. We controlled H3K9me3 enrichment flanking one of the target sites we named as ‘region 3’ (gRNA target site is chr6:31,813,898-31,813,920 (hg19)), where we integrated TetO repeats by CRISPR/Cas9-mediated knock-in. We compared clones with 96-mer or 48-mer TetO integration at ‘region 3’ (clones 96-8 and 48-15, respectively) versus wild-type cells. We used non-transduced wild-type cells (wt) and TetR-EGFP transduced wild-type (wtGFP) as controls. The experimental samples analyzed were 96-8 and 48-15 clones transduced with TetR-EGFP. Experiments were performed in duplicates (8 samples total).

first: Tasan

last: Ipek

first: Zhao

last: Huimin


title: BRG1 governs Glucocorticoid Receptor interactions with chromatin and pioneer factors across the genome

city: Research Triangle Park

first: Jackson

middle: Andrew

last: Hoffman

state: North Carolina

address: 111 TW Alexander Dr, Building 101 Room C432

department: DIR

institute: NIEHS

summary: The Glucocorticoid Receptor (GR) alters transcriptional activity in response to hormones by interacting with chromatin at GR binding sites (GBSs) throughout the genome. Our work in human breast cancer cells identifies three classes of GBSs with distinct epigenetic characteristics and reveals that BRG1 interacts with GBSs prior to hormone exposure. The GBSs pre-occupied by BRG1 are more accessible and transcriptionally active than other GBSs. BRG1 is required for a proper and robust transcriptional hormone response and knockdown of BRG1 blocks recruitment of the pioneer factors FOXA1 and GATA3 to GBSs. Finally, GR interaction with FOXA1 and GATA3 binding sites was restricted to sites pre-bound by BRG1. These findings demonstrate that BRG1 establishes specialized chromatin environments that define multiple classes of GBS. This in turn predicts that GR and other transcriptional activators function via multiple distinct chromatin-based mechanisms to modulate the transcriptional response.

overall_design: ChIP-seq and RNA-seq in A1-2 and A1A3 cells (both derived from T47D human breast cancer cells)

middle: A

first: Kevin

middle: W

last: Trotter

first: James

last: Ward

first: Trevor

last: Archer


title: Melanopsin retinal ganglion cells regulate cone photoreceptor positioning in the mouse retina

city: Montreal

first: Michel

last: Cayouette

state: Québec

address: 110 Ave des Pins O

department: Cellulary Neurobiology

institute: Institut de Recherches Cliniques de Montreal

summary: We performed RNA sequencing on melanopsin deleted retinas (Opn4-DTA/DTA) to determine potential cues involved in instructing cone photoreceptor positioning

overall_design: RNAseq of whole P8 retinal extracts from wild-type littermate vs. Opn4DTA/DTA mice

first: Adele

last: Tufford

first: Tiffany

last: Schmidt


title: Activity-dependent aberrations in gene expression and alternative splicing in a mouse model of Rett syndrome

city: Stony Brook

first: Nurit

last: Ballas

state: NY

address: 100 Nicolls Road

department: Department of Biochemistry and Cell Biology

institute: Stony Brook University

summary: Rett syndrome (RTT) is a severe neurodevelopmental disorder that is caused by mutations in the gene methyl-CpG-binding-protein-2 (MECP2). However, the molecular mechanism by which these mutations mediate the RTT neuropathology remains enigmatic. In this study, we stimulated MeCP2-null cortical neurons (in vitro) and brains (in vivo) of a RTT mouse model to explore the effect of the loss of MeCP2 function on the activity-dependent transcriptomes of the cortex and hippocampus, respectively, using RNA-seq. These analyses revealed that the loss of MeCP2 results in aberrant global pattern of gene expression, characterized predominantly by higher levels of expression of activity-dependent genes, and anomalous alternative splicing events, specifically in response to neuronal activity.

overall_design: For in vitro experiments, RNA-seq was performed on MeCP2-null (MT) and wild-type (WT) neuron-enriched cortical cultures that were either treated (T) with KCl for 3hr or not treated (N), after 10 days in culture. For in vivo experiments, RNA-seq was performed on hippocampi of MeCP2-null (MT) and wild-type (WT) mice that were either treated with kainic acid for 40 or 68 minutes, or not treated.

first: Sivan

last: Osenberg

first: Ariel

last: Karten

first: Jialin

last: Sun

first: Jin

last: Li

first: Shaun

last: Charkowick

first: Christy

last: Felice

first: Mary

last: Kritzer

first: Minh

middle: V

last: Nguyen

first: Peng

last: Yu


title: Early-onset pediatric atopic dermatitis is characterized by Th2/Th17/Th22- centered inflammation and lipid alterations

status: Public on May 21 2018

city: New York

last: Israel

address: 1425 Madison Avenue

department: Department of Dermatology

institute: Icahn School of Medicine at Mount Sinai

summary:
Background: While atopic dermatitis (AD) often starts in early childhood, detailed tissue profiling of early-onset AD in children is lacking, hindering therapeutic development for this patient population with a particularly high unmet need of better treatments.
Objective: We sought to globally profile the skin of infants with AD compared to adults with AD and healthy controls.
Methods: We performed microarray, RT-PCR and fluorescence microscopy studies in infants and young children (<5yo) with early-onset AD (<6mo) compared to age-matched controls and adults with longstanding AD.
Results: Transcriptomic analyses revealed profound differences between early-onset pediatric vs. longstanding adult AD, not only in lesional but also non-lesional tissues. While both patient populations harbored Th2-centered inflammation, pediatric AD also showed significant Th17-skewing, but lacked the Th1 upregulation that characterizes adult AD. Defects in lipid barrier (e.g. ELOVL3, DGAT2) and tight junction regulation (e.g. Claudins 8 and 23) were evident in both groups but, unlike adult AD which showed the classic downregulation of epidermal differentiation and cornification products, pediatric AD exhibited relatively normal expression of these genes. Some lipid-associated mediators (such as FAR2 and FA2H) even showed preferential downregulation in pediatric AD, and lipid barrier genes (FA2H, DGAT2) showed inverse correlations with transepidermal water loss/TEWL, a functional measure of the epidermal barrier.
Conclusions: Children and adult AD skin samples share lipid metabolism and tight junction alterations, but epidermal differentiation complex defects are only present in adult AD, potentially resulting from chronic immune aberration that is not yet present in early-onset disease.

overall_design: We performed microarray studies in skin from lesional and non-lesional tissue in infants and young children (<5yo) with early-onset AD (<6mo), and adults with longstanding AD compared to age-matched controls.

first: Patrick

last: Brunner

first: Emma

last: Guttman-Yassky


title: Gastrointestinal Stromal Tumor Enhancers Support a Transcription Factor Network Predictive of Clinical Outcome

city: Worcester

first: Matthew

last: Hemming

state: MA

address: 364 Plantation Street

institute: UMass Medical School

summary: Activating mutations in the KIT or PDGFRA receptor tyrosine kinases are hallmarks of gastrointestinal stromal tumor (GIST). The biological underpinnings of recurrence following resection or disease progression beyond kinase mutation are poorly understood. Utilizing chromatin immunoprecipitation with sequencing (ChIP-seq) of tumor samples and cell lines, we describe the enhancer landscape of GIST, highlighting genes that reinforce and extend our understanding of these neoplasms. A group of core transcription factors can be distinguished from others unique to localized and metastatic disease. The transcription factor HAND1 emerges in metastatic disease, binds to established GIST-associated enhancers and is required for GIST cell proliferation and KIT gene expression. The pattern of transcription factor expression in primary tumors is predictive of metastasis-free survival in GIST patients. These results provide insight into the enhancer landscape and transcription factor network underlying GIST, and define a new strategy for predicting clinical behavior of this disease.

overall_design: RNA-seq from GIST cell lines, tumors and a patient-derived xenograft

first: James

middle: E

last: Bradner


overall_design: ChIP-seq of cell lines and human GIST tumors with input control.


overall_design: ATAC-seq of GIST cell lines.


title: Lipoxins Regulate the  Egr-1 Network and Reverse Diabetic Kidney Disease

city: Melbourne

first: Mark

middle: D

last: Ziemann

state: VIC

address: 85 Commercial Rd

department: Bioinformatics Working Group

country: Australia

institute: Burnet Institute

summary: The failure of spontaneous resolution underlies chronic inflammatory conditions including microvascular complications of diabetes such as diabetic kidney disease. The identification of endogenously generated molecules which promote the physiologic resolution of inflammation suggests that these bioactions may have therapeutic potential in the context of chronic inflammation. Lipoxins (LXs) are lipid mediators which promote the resolution of inflammation. Here we investigated the potential of LXA4 and a synthetic LX analogue [Benzo-LXA4] as therapeutics in a murine model of diabetic kidney disease. Diabetes was induced with streptozotocin in ApoE-/- mice and kidney disease was observed. The development of  diabetes-induced albuminuria, mesangial expansion and collagen deposition was attenuated by LXs. It is noteworthy that LXs also attenuated established kidney disease in diabetic mice administered LXs 10 weeks after disease onset, with evidence of preserved kidney function. Kidney transcriptome profiling defined a diabetic signature [725 genes; FDR P≤0.05]. Comparison of this murine gene signature with human DKD identified shared renal pro-inflammatory/pro-fibrotic signals (TNF-α, IL-1β, NF-κB). In diabetic mice we identified 20 and 51 transcripts regulated by LXA4 and Benzo-LXA4, respectively, and pathway analysis identified established (TGF-β1, PDGF, TNF-α, NF-κB) and novel (Early growth response-1 - EGR-1) networks activated in diabetes and regulated by LXs. Using human renal epithelial cells, we demonstrate that LXs attenuate TNF-α driven Egr-1 activation, with Egr-1 important for cellular responses to TGF-β1 and TNF-α. These data demonstrate for the first time that LXs can reverse established  diabetic complications and support a therapeutic paradigm to promote the resolution of inflammation.

overall_design: RNA-seq was performed to understand gene expression changes caused by injection of lipoxin and benzo-lipoxin a compared to the ethanol vehicle in diabetic and non-diabetic mice. N=6 replicates were profiled.

first: Eoin

middle: P

last: Brennan

first: Muthukumar

last: Mohan

first: Aaron

last: McClelland

first: Christos

last: Tikellis

first: Antony

last: Kaspi

first: Stephen

last: Gray

first: Raelene

last: Pickering

first: Shimin

last: Tan

first: Syed

middle: T

last: Ali-Shah

last: Guiry

first: Assam

last: El-Osta

first: Karin

last: Jandeleit-Dahm

last: Cooper

first: Catherine

last: Godson

first: Phillip

last: Kantharidis


title: Comprehensive profiling of translation initiation in influenza-virus infected cells

status: Public on May 20 2018

city: Seattle

first: Rasi

last: Subramaniam

address: 1100 Fairview Ave N

institute: Fred Hutch

summary: Cellular stress is often accompanied by non-canonical initiation of translation at alternate start codons in mammalian cells. Here we systematically investigate the extent and impact of alternate translation initiation in the context of influenza virus infection. We use ribosome profiling with the initiation inhibitor lactidomycin to experimentally delineate translation initiation sites in a human lung epithelial cell line infected with influenza virus.

overall_design: We use genome-wide methods (Ribo-Seq and RNA-Seq) to examine how translation initiation is altered in influenza virus infected lung-epithelial cells

first: Heather

last: Machkovech

first: Arvind


title: Mouse embryonic stem cells (mESCs) differentiation towards ventral hindbrain neuronal cell types [d0-d3.5]

city: Stockholm

first: Johan

last: Ericson

address: Solnavägen 9

department: Cell and Molecular Biology

institute: Karolinska Instituet

summary: mESCs treated with retinoic acid (RA) and a Shh agonist (SAG) recapitulated ventral hindbrain development and produced a population of neural progenitors with a minor presence of other cell types.

overall_design: The differentiation in mESCs was induced by RA and SAG in monolayer condition. The cells were collected every day and processed for RNA isolation and RNA-seq.

first: Zhanna

last: Alekseenko


title: RNA-seq of medullary thymic epithelial cell (mTEC) subsets in inducible Aire-lineage tracing mice

status: Public on May 19 2018

city: San Francisco

first: Joshua

last: Pollack

address: 2 Tower Pl.  Ste 800

institute: Pionyr Immunotherapeutics

summary: The goal of the study was to sequence mRNA expression from sorted medullary thymic epithelial cell (mTEC) subsets in inducible Aire-CreERT2.R26-Stopfl-tdTomato lineage tracing mice after a pulse chase. Four cell subsets were sorted 7 days after a single 2mg pulse of tamoxifen administered by oral gavage. 4 biological replicates (1,2,3,4) were collected derived from 12 pooled thymi per replicate. From the DAPI-;CD45-;EpCAM+ TEC pool, cells were sorted as: pre-Aire (MHCIIlo;RFP-), early-Aire (MHCIIhi;RFP-), late-Aire (MHCIIhi;RFP+), and post-Aire (MHCIIlo;RFP+). The data were used to identify differentially expressed genes across the four mTEC subsets to examine mTEC heterogeneity and identify novel mTEC subpopulations.

overall_design: Four biological replicates (12 pooled thymi per replicate) of each of four mTEC subsets were sorted from Aire-lineage tracing mice 7 days after pulse-chase with tamoxifen.

first: Corey

middle: N

last: Miller

first: Imran

middle: S

last: Khan

first: Todd

last: Metzger

first: David

last: Erle

first: Mark

last: Anderson


title: Expression data of C.pn treated foam cell

status: Public on May 18 2018

city: Los Angeles

first: Shuang

last: Chen

address: 8700 Beverly blvd

department: Pediatrics

institute: Cedars Sinai Medical Center

summary:
C.pn potentiated hyperlipidemia-induced inflammasome activity in cultured macrophages and in foam cells in atherosclerotic lesions of Ldlr–/– mice.  We discovered that C.pn-induced extracellular IL-1β triggers a negative feedback loop to inhibit GPR109a and ABCA1 expression and cholesterol efflux leading to accumulation of intracellular cholesterol and foam cell formation.  Gpr109a and Abca1 were both upregulated in plaque lesions in Nlrp3–/– mice in both hyperlipidemic and C.pn infection models.
We sued microarrays to detail the  gene expression underlying C.pn and ox-LDL treatment on mice periteneal macrophages to study the regulating of ABCA1 related genes with NLRP3 manutation

overall_design: WT and NLRP3 KO periteneal macrophage were treated for RNA extraction and hybridization on Affymetrix microarrays.  Four-condition experiment using peritoneal macrophages: WT PBS; WT  [Cpn + oxLDL ] 8h; NLRP3 KO PBS;NLRP3 KO [Cpn + oxLDL] 8h to analyze  the expression profiles.

first: G

last: Tumurkhuu

first: S


title: Allele-specific control of replication timing and genome organization during development [Promoter Capture Hi-C]

middle: M

last: Gilbert

overall_design: We characterized the allelic differences in RT (Repli-seq), genome organization (Hi-C and promoter-capture Hi-C), gene expression (total nuclear RNA-seq) and chromatin accessibility (ATAC-seq) in distinct cell types from F1 hybrid musculus X castaneus mouse crosses.

first: Juan

last: Rivera-Mulia


title: Global chromatin accessibility of gene locus in CD4+ T cells activated with or without OX40 costimulation

city: HOUSTON

first: Xiaolong

last: Zhang

address: 6670 Bertner Avenue, R7-211

department: Immunobiology & Transplant Research Center

institute: Houston Methodist Research Institute

summary: OX40 is a T cell costimulatory molecule in the tumor necrosis factor receptor (TNFR) superfamily. Unlike other costimulatory molecules, OX40 is not expressed by naive T cells, but its expression is rapidly induced following T cell activation, and OX40 costimulation plays a critical role in cell survival, proliferation, and generation of memory cells. We used ATAC-seq to detail the chromatin accessibility of gene locus of activated CD4 T cells with or without OX40 costimulation in the presence of  TGF-β1 and IL-2 and identified distinct classes of genes after OX40 costimulation.

overall_design: Naive CD4+ T cells (CD62LhighCD44lowFoxp3−) were sorted from C57/Bl6 Foxp3-eGFP reporter mice, and activated in vitro with soluble anti-CD3 mAb and mitomycin C-treated Wt APCs or OX40L-Tg APCs in the presence of  TGF-β1 and IL-2 in 96-well round bottom tissue-culture plates. Forty-eight hours later, living CD4+ T cells were sorted from cultures by flow cytometry. ATAC-seq was performed at Active Motif (Carlsbad, CA).

first: Xian

last: Li

first: Bo

last: Xia

first: Xiang

last: Xiao

first: Kaifu


title: TCR signal strength controls thymic differentiation of iNKT cell subsets

city: Aurora

first: Laurent

last: Gapin

department: Immunology and Microbiology

institute: University of Colorado Anschutz Medical campus

summary: Three major phenotypically and functionally distinct invariant Natural Killer T (iNKT) cell subsets (iNKT1, iNKT17 and iNKT2), each with propensity to traffic to different tissues and to secrete different cytokines upon activation, have been defined. These fate assignments can be conferred upon iNKT cells during development in the thymus, but the cues that direct these decisions remain unclear. Here, we show that T cell antigen receptor (TCR) signal strength governs the development of iNKT cell subsets in the thymus, with high signaling strength necessary for iNKT2 and iNKT17 development. Alteration of TCR diversity and/or signaling dramatically diminished iNKT2 and iNKT17 cell subset development in a cell intrinsic manner. Decreased TCR signaling affected the persistence of Egr2 expression and the upregulation of PLZF both in vivo and in vitro. Genome-wide chromatin accessibility analysis revealed subset-specific activity of regulatory elements associated with unique signatures of transcription factor binding sites. NFAT and Egr binding motifs were found preferentially enriched in chromatin regulatory regions specifically accessible in iNKT2 cells that were lost in iNKT2 cells that had developed with reduced TCR signaling. Altogether, these data suggest a model of iNKT cell subset development where variable TCR signaling induces changes in chromatin accessibility at NFAT and Egr binding sites which exerts a determinative influence on the dynamic of gene enhancer accessibility that affects the developmental fate of iNKT cells.

overall_design: ATAC-seq of invariant Natural Killer T cell populations from 2 genotypes of mice


title: GoldCLIP: Gel-omitted Ligation-dependent CLIP

city: Beijing

first: Ming

last: Wang

state: Beijing

address: #15 Datun Road, Chaoyang, Beijing 100101, China

department: Key Laboratory of RNA Biology

institute: Institute of Biophysics, Chinese Academy of Sciences

type:
Other
Third-party reanalysis

summary: Protein-RNA interaction networks are essential to understand gene regulation control. Identifying the binding sites of RNA-binding proteins (RBPs) by CLIP (UV-crosslinking and immunoprecipitation) represents one of the most powerful methods to map in vivo protein-RNA interactions. However, the traditional CLIP protocol is technically challenging, which requires radioactive labeling and suffers from material loss during PAGE-membrane transfer procedures. Here we introduce a super-efficient CLIP method (GoldCLIP) that omits all gel purification steps. This nonisotopic method allowed us to perform highly reproducible CLIP experiments with classical RBP such as PTB in human cell lines. In principle, our method guarantees sequencing library constructions, providing the protein of interest can be successfully crosslinked to RNAs in living cells. GoldCLIP is readily applicable to diverse factors to uncover their endogenous targets.

overall_design:
Gel-omitted Ligation-dependent CLIP applied to characterize the in vivo protein-RNA interactions

This series includes re-analyzed data from ERP016865; Array Express accession ID: E-MTAB-5027. The re-analyzed data file is: PTB_iCLIP2.bed.gz, available below. This file contains data from all samples in ERP016865. The methods used to produce these CLIP peaks are identical to those listed for the samples in this series.

first: Jiaqi

last: Gu

first: Yang

last: Yang

first: Ding

last: Qiu

first: Yiquan

first: Jinbiao

last: Ma

first: Yu

last: Zhou

first: Gregory

middle: J

last: Hannon

last: Yu


title: Altered thymic differentiation and modulation of arthritis by invariant NKT cells expressing mutant ZAP70 [RNA-Seq]

status: Public on May 17 2018

city: San Diego

first: Meng

last: Zhao

address: 9420 Athena Cir

institute: La Jolla Institute of Allergy and Immunology

summary: Various subsets of invariant natural killer T (iNKT) cells with different cytokine productions develop in the mouse thymus, but the factors driving their differentiation remain unclear.  Here we show that hypomorphic alleles of Zap70 or chemical inhibition of Zap70 catalysis lead to an increase of IFN-g-producing iNKT cells (NKT1 cells), suggesting  NKT1 cells may require a lower TCR signal threshold. Zap70 mutant mice develop IL-17-dependent arthritis. iNKT cells and therapeutic induction of IFN-g secretion by activating iNKT cells are protective in this model, but the representation of IFNg versus IL-17 secreting iNKT cells in the joint change in favor of IL-17 producers as disease worsened. NKT1 cells are also present in the synovial fluid of arthritis patients, where they could be beneficial. Our data therefore suggest that TCR signal strength during thymic differentiation may influence not only IFNg production, but also the protective function of iNKT cells in arthritis.

overall_design: Three subsets of iNKT cells from the thymi of WT control and SKG mice were analyzed. Three independent experiments were carried out. Triplicates of each sample were analyzed

first: Mattias

last: Svensson

first: Koen

last: Venken

first: Ashu

last: Chawla

first: Shu

last: Liang

first: Isaac

last: Engel

first: Piotr

last: Mydel

first: Jeremy

last: Day

first: Dirk

last: Elewaut

first: Nunzio

last: Bottini

first: Mitchell

last: Kronenberg


title: Altered thymic differentiation and modulation of arthritis by invariant NKT cells expressing mutant ZAP70

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

overall_design: Refer to individual Series


title: Transcriptome profiling of microRNA-mediated neuronal reprogramming with REST repression at day 7

city: Saint Louis

first: Bo

last: Zhang

state: MO

address: 660 S. Euclid Avenue

department: Developmental Biology

institute: Washington University School of Medicine

summary: Ectopic expression of neuronal microRNAs (miRNAs), miR-9/9* and miR-124 (miR-9/9*-124) in adult human fibroblasts has been found to evoke extensive reconfigurations of the chromatin and direct the fate conversion to neurons. We found that miR-9/9* and miR-124 led to the repression of REST, a transcriptional repressor of neuronal genes, during microRNA-mediated neuronal conversion and knockdown of REST enhanced the activation of BAF53b, a mature neuronal marker. Furthermore, time series analysis of the transcriptome of cells undergoing the miR-9/9*-124-induced conversion indicated upregulated genetic pathways that were predicted to be targeted by REST although the transcript level of REST remained unchanged (Abernathy et al., 2017). Therefore, we reasoned that knocking down REST in addition to miR-9/9*-124 at an early time point (day 7), in which REST repression is minimally evident during neuronal conversion, would speed up the adoption of neuronal identity. We performed the RNA-seq analysis to compared differentially expressed genes (DEGs) between human adult fibroblasts expressing control shRNA (shCTL) and reprogramming cells expressing shCTL or shREST at day 7. Finally, we found that the repression of REST constitutes an important component of microRNA-mediated neuronal reprogramming of human fibroblasts.

overall_design: RNA-seq analysis in 6 samples (2 replicates each) of human adult fibroblasts expressing control shRNA (shCTL) and reprogramming cells expressing shCTL or shREST at day 7.

first: Seong

last: Lee

first: Andrew

last: Yoo


title: RNA-sequencing analysis of regulatory T cells differentiated in presence or absence of CPI-1205

city: Nanjing

first: Shiping

last: JIAO

institute: Nanjing Drum Tower Hospital

summary: We differentiated naïve CD4 T cells isolated from FoxP3-eGFP mice into inducible regulatory T cells in presence or absence of CPI-1205. Differentiated regulatory T cells were then sorted by flow cytometry based on GFP expression.

overall_design: DEG analysis of inducible regulatory cells differentiated in presence or absence of CPI-1205 was performed.

first: Padmanee

last: Sharma

first: Sangeeta

last: Goswami


title: Induction of human SST and PV neurons by expressing a single transcription factor LHX6

first: Fang

last: Yuan

address: 101Longmian Avenue

institute: Nanjing Medical University

summary: To systematically explore the effect of LHX6 on neural development and differentiation, we performed RNA-sequencing (RNA-seq) of hPSC-derived GINs at day 50 in vitro.RNAseq results could also confirm alteration of GINs identity with the overexpression of LHX6.

overall_design: RNAs-seq assay of two groups of GABAergic neurons (control and LHX6 overexpression)

first: Yuan

last: Fang

first: Kai-Heng

first: Xin

last: Chen

first: Yuanyuan

last: Wang

first: Mingyan

last: Lin

first: Shi-Bo

last: Xu

first: Hai-Qin

last: Huo

first: Min

first: Lixiang

last: Ma

first: Yuejun

first: Shuijin

last: He

first: Yan

last: Liu


title: Profiling of lung tumor-infiltrating CD8 T cells according to their expression status of CD39

city: Singapore

first: Kaibo

last: Duan

address: 8A Biomedical Grove, Immunos Building, Level 4

country: Singapore

institute: Singapore Immunology Network

summary: Human tumors are infiltrated by various immune cells, including CD8 T cells. CD8 T cells express unique receptors that can recognize peptides at the host’s cells, including tumor cells. After probing the antigen specificity of ex-vivo tumor-infiltrating CD8 T cells from human tumors, we hypothesized that expression of CD39 was correlated with tumor-specificity. The present experiment aims at better characterizing ex-vivo CD39+ vs CD39- CD8 T cells.

overall_design: CD39- and CD39+ CD8 T cells were FACS sorted from 8 fresh tumor samples and their RNA extracted for transcriptomic profiling.

first: Yannick

last: Simoni

first: Josephine

last: Lum

first: Evan

last: Newell


title: Profiling of colorectal tumor-infiltrating CD8 T cells according to their expression status of CD39

overall_design: CD39- and CD39+ CD8 T cells were FACS sorted from 8 fresh tumor samples and their RNA extracted for transcriptomic profiling. Additionally, Effector memory and Naive CD8+ T cells were FACS sorted from 5 healthy donors’ peripheral blood.


title: Cohesin interacts with a panoply of splicing factors required for cell cycle progression and genomic organization

first: Jie

state: WA

address: 3720 15th Ave NE

department: Genome Sciences

institute: UW

summary: The cohesin complex regulates sister chromatid cohesion, chromosome organization, gene expression, and DNA repair. Here we report that endogenous human cohesin interacts with a panoply of splicing factors and RNA binding proteins, including diverse components of the U4/U6.U5 tri-snRNP complex and several splicing factors that are commonly mutated in cancer. The interactions are enhanced during mitosis, and the interacting splicing factors and RNA binding proteins follow the cohesin cycle and prophase pathway of regulated interactions with chromatin. Depletion of cohesin-interacting splicing factors results in stereotyped cell cycle arrests and alterations in genomic organization. These data support the hypothesis that splicing factors and RNA binding proteins control cell cycle progression and genomic organization via regulated interactions with cohesin and chromatin.

overall_design: Performed in situ DNase Hi-C on SF3B1-depleted HeLa cells

first: Jung-Sik

last: Kim

first: Xiaoyuan

first: Zhijun

first: Taeyeon

first: Julia

last: Gerard

first: Brian

first: William

last: Lane

last: Noble

first: Bogdan

last: Budnik

first: Todd

last: Waldman


title: Profiling of tumor-infiltrating CD8 T cells according to their expression status of CD39


title: CTCF boundary remodels chromatin domain and drives aberrant HOX gene transcription in acute myeloid leukemia

city: Hangzhou

first: Huacheng

last: Luo

state: Zhejiang

address: No. 150, Fucheng Road, Qiantang District

institute: Hangzhou Institute of Medicine (HIM), The Chinese Academy of Sciences

summary: We analyzed RNA-seq, ATAC-seq, ChIP-seq and 4C-seq data to find that  CTCF binding site located between HOXA7 and HOXA9 genes (CBS7/9) is critical for establishing and maintaining aberrant HOXA9-HOXA13 gene expression in AML. Disruption of the CBS7/9 boundary resulted in spreading of repressive H3K27me3 into the posterior active HOXA chromatin domain that subsequently impaired enhancer/promoter chromatin accessibility and disrupted ectopic long-range interactions among the posterior HOXA genes. Consistent with the role of the CBS7/9 boundary in HOXA locus chromatin organization, attenuation of the CBS7/9 boundary function reduced posterior HOTTIP lincRNA and HOXA gene expression and altered myeloid specific transcriptome profiles important for pathogenesis of myeloid malignancies.

overall_design: We have submitted our RAW sequence datasets into SRA database (SRP115103 and Bioproject: PRJNA396046),  including RNA-SEQ, ATAC-seq, ChIP-seq and 4C-seq for WT and CBS7/9KO MOLM13 leukemia cells

first: Suming

last: Huang


title: Leukaemic alteration of IKZF1 primes stemness and malignancy programs in human lymphocytes

first: ruoyan

last: Li

address: Yiheyuan street

institute: Peking University

summary: We uncovered upregulated stem cell program in leukaemic lymphoblasts of patients with IKZF1 alterations by analyzing the archived gene-expression profiling datasets. We then used a frequent IKZF1 deletion, IK6, as a model via transduction into human primitive haematopoietic cells, followed by xenotransplantation in mice. Immunophenotypically defined stem, pro-B, and immature/mature (IM/M)-B cells were collected from primary recipients for functional assay and transcriptome profiling. Successful reconstitution in secondary recipient mice revealed the stemness of IK6+ pro-B and IM/M-B cells. Upregulated stemness and malignancy programs in IK6+ cells confirmed IK6 effects. Interestingly, these programs corresponded to distinct canonical pathways. Remarkably, the pathway profile mapped in the modelled cells well mirrored that in patients’ leukaemic cells; therefore, our study provides a seminal insight into the cancerous reprogramming of somatic cells.

overall_design: Examination of gene expression in 7 cell types, triple replicates were used.

first: Fan

last: Bai

first: Deng-Li

last: Hong


title: Intestinal and thymic tuft cell RNA-seq

first: Joshua

last: Pollack

state: CA

summary: The goal of the study was to sequence mRNA from tuft cells (identified as CD45-;EpCAM+;IL-25+ using Flare25 reporter mice) in the epithelia of thymus and small intestine. As a control, non-tuft epithelial cells (CD45-;EpCAM+;IL-25-) were also isolated. The data were used to compare tuft cell markers between the small intestine and thymus.

overall_design: Four replicates of tuft cells were sorted from both tissues. As a reference, four replicates of non-tuft cells were also sorted from the small intestine. One tuft replicate from the small intestine was discarded because it failed QC. One non-tuft replicate was also discarded because of failed QC

first: Corey

last: Miller

first: Jakob

last: von Moltke

first: Richard

last: Locksley

first: David

last: Erle

first: Mark

last: Anderson


title: Single-cell analysis of progenitor cell dynamics and lineage specification of the human fetal kidney

city: Ann Arbor

first: Rajasree

last: Menon

state: Michigan

address: 4544E, MSRB2, Catherine Street, University of Michigan

department: Department of Computational  Medicine and Bioinformatics

institute: University of Michigan

summary: In order to shed light on human kidney development, we have used single-cell transcriptomics to characterize gene expression in different cell population, and to study individual cell dynamics and lineage trajectories during development

overall_design: We have used DropSeq to perform single cell sequencing on 3,865 cells from 3 developing human kidneys

first: Cristina

last: Cebrián

first: Edgar

last: Otto

first: Jason

middle: R

last: Spence

first: Matthias

last: Kretzler


title: Enhancing human kidney organoid differentiation from pluripotent stem cells with high-throughput automation

summary: Organoids derived from human pluripotent stem cells are a potentially powerful tool for high-throughput screening (HTS), but the complexity of organoid cultures poses a significant challenge for miniaturization and automation. In this study, single-cell RNA sequencing identify within organoids previously-undetected parietal and interstitial compartments. We discovered that addition of vascular endothelial growth factor (VEGF) during the differentiation process resulted in an approximately ten-fold increase in endothelial cells, without compromising the formation of the organoids. Although VEGF clearly increased the number of endothelial cells by immunofluorescence, relatively few endothelial cells were captured by scRNA-seq and only a modest increase in endothelial cells was observed. This suggested that either a substantial number of endothelial cells were lost or destroyed before sequencing, or that a spectrum of maturation states was present in the cultures.

overall_design: We have used DropSeq to perform single cell sequencing on  human kidney organoids.Organoids included in this analysis were generated by treatment  with and without VEGF. We did a bulk RNA analysis on the organoids treated with and without VEGF

first: Jennifer

last: Harder

first: Benjamin

last: Freedman


title: Expression data from NPY Y1R-deficient osteoblastic cells

status: Public on May 16 2018

city: Sydney

first: Nicola

last: Lee

state: NSW

address: 384 Victoria Street

department: Neuroscience

institute: Garvan Institute of Medical Research

summary:
NPY signalling via osteoblastic Y1 receptors has been shown to control bone mass but also contributes significantly to the control of whole-body insulin secretion and glucose homeostasis in mice through the release of novel factor(s) which are different from the previously implicated osteocalcin.
We used microarrays to identify novel endocrine factors regulated by Y1 receptors and involved in the regulation of bone mass and whole-body homeostasis.

overall_design: Microarrays were performed on GFP-positive osteoblastic cells isolated from either WT (n=4) or Y1-deficient mice (n=2) expressing GFP under control of a 3.6kb fragment of the rat alpha1(I)-collagen promotorand the data were analysed for

first: Herbert

last: Herzog


title: Transcription factor IRF8 orchestrates the adaptive natural killer cell response

city: Ithaca

first: Colleen

last: Lau

state: New York

address: 930 Campus Road

department: Microbiology & Immunology

institute: Cornell University

summary: Natural killer (NK) cells are innate lymphocytes that have been recently appreciated to display features of adaptive immunity in response to viral infection. Biallelic mutations in the IRF8 gene have been reported to cause familial NK cell deficiency and susceptibility to severe viral infection in humans; however, the precise role of this transcription factor in regulating NK cell function remained unknown. Here, we show that IRF8 is required in a cell-intrinsic manner for NK cell-mediated protection against mouse cytomegalovirus (MCMV) infection. During exposure to MCMV, IRF8 is robustly upregulated in NK cells by IL-12 and STAT4, which promotes epigenetic remodeling of the Irf8 locus. Moreover, IRF8 facilitates the proliferative burst of virus-specific NK cells by promoting expression of a suite of DNA replication and cell cycle genes, and directly regulating Zbtb32, a master regulator of NK cell proliferation during viral challenge. These results identify a novel function and cell-type specific regulation for IRF8 in host antiviral immunity, and provide a mechanistic understanding of virus susceptibility in patients with IRF8 mutations.

overall_design: RNA-seq was performed on NK cells harvested during in-vivo infection

first: Joseph

last: Sun


title: WGBS assessment of global methylation alterations in Dnmt3a1KO , Dnmt3a2KO, Dnmt3aKO, Tet1KO and DKO mouse embryonic stem cells

city: seattle

first: xueqiu

last: lin

state: wa

institute: FRED HUTCHINSON CANCER CENTER

summary: Using WGBS we assessed global DNA methylation changes in Dnmt3a1KO/Dnmt3a2KO/Dnmt3aKO/Tet1KO/DKO  mouse embryonic stem cells. Compared with WT cells, Dnmt3aKO cells but not Dnmt3bKO cells showed genome-wide hypomethylation.

overall_design: Genomic DNA from WT, Dnmt3a1KO, Dnmt3a2KO, Dnmt3aKO, Tet1KO and DKO J1 ES cells wes isolated, treated with bisulfite and sequenced with Illumina HiSeq sequencing systems.

first: Sean

last: Cullen

first: Xueqiu

last: Lin

first: Wei

last: Li

first: Margaret

last: Goodell


title: Genome-wide maps of histone modifications (SpikeIn) and Suz12 in WT, Dnmt3a-/-, Tet1-/- J1 and DKO ES cells.

summary: Using ChIP-seq to assess changes of histone modifications in response to Dnmt3a or Tet1 deficiency.

overall_design: Examination of H3K4me3, H3K27me3 and Suz12 in WT, Dnmt3a-/-, Tet1-/-  and DKO ES cells.

first: Tianpeng

last: Gu


title: Human blastocysts of normal and abnormal karyotypes display distinct transcriptome profiles: an analysis of every mono and trisomy

city: Manhattan

first: Tenzin

last: Lhakhang

address: 550 First Avenue

institute: NYU School of Medicine

summary: Characterization of the transcriptome of normal and abnormal embryos.

overall_design: Gene expression profiling of every mono and trisomy.


title: TCR signal strength controls thymic differentiation of iNKT cell subsets

first: Kent

middle: Augustus

last: Riemondy

state: Colorado

department: Biochemistry and Molecular Genetics

institute: University of Colorado School of Medicine

summary: Three major phenotypically and functionally distinct invariant Natural Killer T (iNKT) cell subsets (iNKT1, iNKT17 and iNKT2), each with propensity to traffic to different tissues and to secrete different cytokines upon activation, have been defined. These fate assignments can be conferred upon iNKT cells during development in the thymus, but the cues that direct these decisions remain unclear. Here, we show that T cell antigen receptor (TCR) signal strength governs the development of iNKT cell subsets in the thymus, with high signaling strength necessary for iNKT2 and iNKT17 development. Alteration of TCR diversity and/or signaling dramatically diminished iNKT2 and iNKT17 cell subset development in a cell intrinsic manner. Decreased TCR signaling affected the persistence of Egr2 expression and the upregulation of PLZF both in vivo and in vitro. Genome-wide chromatin accessibility analysis revealed subset-specific activity of regulatory elements associated with unique signatures of transcription factor binding sites. NFAT and Egr binding motifs were found preferentially enriched in chromatin regulatory regions specifically accessible in iNKT2 cells that were lost in iNKT2 cells that had developed with reduced TCR signaling. Altogether, these data suggest a model of iNKT cell subset development where variable TCR signaling induces changes in chromatin accessibility at NFAT and Egr binding sites which exerts a determinative influence on the dynamic of gene enhancer accessibility that affects the developmental fate of iNKT cells.

overall_design: mRNA-Seq of invariant Natural Killer T cell populations from 2 genotypes of mice

first: S

middle: H

last: Krovi

first: Jay

last: Hesselberth

first: Laurent

last: Gapin


title: Gene expression profiling of hematopoietc stem cells from heterozygous Asxl1 KI mice

city: Tokyo

first: Masahiro

last: Uni

address: 7-3-1, Hongo, Bunkyo-ku

department: Department of Hematology and Oncology

country: Japan

institute: Graduate School of Medicine, The University of Tokyo

summary: We performed RNA-seq with

overall_design: mRNA expression profiles of hematopoietc stem cells obtained from eight weeks old  Asxl1+/+ mice and eight Asxl1G643fs/+ mice were generated by deep sequencing, in duplicate, using Illumina Hiseq 2000.

first: Mineo

last: Kurokawa


title: Determining ELL2 direct targets via ChIPseq

status: Public on May 15 2018

city: Pittsburgh

first: Christine

last: Milcarek

state: PA

address: 200 Lothrop Street

department: Immunology

institute: University of Pittsburgh

summary: A plasma cell line was used to determine which genes have ELL2 protein bound to them.

overall_design: Three biological replicates of cells were grown in CMs lab, fixed with 1% formaldehyde and sent frozen to Active Motif along with our 4502 anti-ELL2 antibody where ChIP seq was performed on a fee for service basis.  ELL2 antibody had been previously evaluated by Active Motif and found suitable for the analyses.

first: Ashley

last: Nelson


title: RNA-Seq analysis of JIB-04 effects on global cellular transcription and HIV in 2D10 T cells

city: La Jolla

first: Max

last: Chang

address: 9500 Gilman Drive

institute: University of California, San Diego

summary: Measuring the effects of the compound JIB-04 on global transcription, NFkB pathway-related genes, and integrated HIV proviral DNA.

overall_design: RNA-seq analysis of mRNAs from DMSO or JIB-04 treated 2D10 T cells at 0 h or 6 h TNFalpha induction to identify genes that are altered by JIB-04 and TNFalpha.  .

first: Muyu

last: Xu


title: Tissue-resident macrophages in the intestine are long-lived and defined by Tim-4 and CD4 expression

city: Manchester

first: Tovah

last: Shaw

address: 46 Grafton Street

department: Division of Infection, Immunity and Respiratory Medicine

country: United Kingdom

institute: University of Manchester

summary: A defining feature of resident gut macrophages is their high replenishment rate from blood monocytes, attributed to tonic commensal-stimulation of this site. In contrast, almost all other tissues contain locally maintained macrophage populations, which co-exist with monocyte-replenished cells at homeostasis. Here, we identified three transcriptionally distinct murine gut macrophage subsets that segregate based on expression of Tim-4 and CD4. Challenging current understanding, Tim-4+CD4+ gut macrophages were found to be locally maintained, while Tim-4–CD4+ macrophages had a slow turnover from blood monocytes; indeed, Tim-4–CD4– macrophages were the only subset with the high monocyte-replenishment rate currently attributed to gut macrophages. Moreover, all macrophage subpopulations required a live microbiota to sustain their numbers, not only those derived from blood monocytes. These findings oppose the prevailing paradigm that all macrophages in the adult murine gut rapidly turnover from monocytes in a microbiome-dependant manner; instead, supplanting it with a model of ontogenetic diversity, where locally maintained subsets co-exist with rapidly replaced, monocyte-derived populations.

overall_design: Tim-4–CD4–, Tim-4–CD4+ and Tim-4+CD4+ macrophages were isolated by fluorescence-activated cell sorting (FACS) from the small intestines of 3 pooled wild type adult male C57/BL6 mice, on four separate occasions. Similarly, Ly6Chi peripheral blood monocytes from 3-4 pooled wild type adult male C57/BL6 mice were isolated, on three separate occasions. Cells were sorted directly into RLT buffer (Qiagen) and stored on dry ice before storage at -80oC for subsequent RNA extraction. RNA was extracted from 120,000 – 200,000 cells using an RNeasy micro kit (Qiagen) following manufacturer’s instructions. RNA was quantified using a Qubit 2.0 Fluorometer (Thermo Fisher Scientifc) and quality was assessed using an RNA ScreenTape Assay and 2200 TapeStation (Agilent Technologies). Strand-specific RNA-seq libraries were prepared using the Illumina workflow with the TruSeq® Stranded mRNA Sample Preparation Kit. Paired-end reads (65bpx65bp) were generated from each sample. From 48 to 192 million reads were obtained from each sample. The fastq files generated by an Illumina  HiSeq4000 platform were analysed with FastQC (Andrew S.; FastQC: A Quality Control tool for High Throughput Sequence Data, available online. Any low quality reads and contaminated barcodes were trimmed with Trimmomactic (Bolger et al., 2014). All libraries were aligned to GRCm38.p4 assembly of mouse genome using STAR-2.4.2 (Dobin et al., 2013) and only uniquely mapped reads were used in differential gene expression analysis. The mapped reads were counted by genes with HTSeq (Anders et al., 2015) agaist gencode.vM11.annotation.gtf. The differentially expressed (DE) genes were identified using DESeq2 (Love et al., 2014) by pairwise comparisons between the experimental groups. The DE genes with 0.05 were selected for further validation and analysis.

first: Stephanie

last: Houston

first: Kelly

last: Wemyss

first: Hayley

last: Bridgeman

first: Thomas

last: Barbera

first: Tamsin

last: Zangerle-Murray

first: Patrick

last: Strangward

first: Amanda

last: Ridley

first: Ping

last: Wang

first: Samira

last: Tamoutounour

first: Judith

last: Allen

first: Joanne

last: Konkel

first: John

last: Grainger


title: Molecular analysis of high-grade serous ovarian carcinoma with and without associated serous tubal intra-epithelial carcinoma [RNA-Seq; normal samples]

city: Baltimore

first: leslie

last: cope

state: MD

address: 550 N. Broadway

institute: leslie cope

summary: Many high-grade serous carcinomas (HGSCs) of the pelvis are thought to originate in the distal portion of the fallopian tube.  Serous tubal intraepithelial carcinoma (STIC) lesions are the putative precursor to HGSC and identifiable in ~50% of advanced stage cases. To better understand the molecular etiology of HGSCs, we report a multi-center integrated genomic analysis of advanced stage tumors with and without STIC lesions and normal tissues. The most significant focal DNA SCNAs were shared between cases with and without STIC lesions. RNA sequence and miRNA data did not identify any clear separation between cases with and without STIC lesions.  HGSCs had molecular profiles more similar to normal fallopian tube epithelium than ovarian surface epithelium or peritoneum. The data suggest that the molecular features of HGSCs with and without associated STIC lesions are mostly shared, indicating a common biologic origin, likely to be the distal fallopian tube among all cases.

overall_design: In this study, 96 previously untreated high-grade serous carcinoma samples were selected to have half with STIC lesions and half without.    Molecular assays were performed that included RNAseq, microRNA expression, and copy number variation.  A total of 10 pools of normal epithelium brushings obtained from ovary (4 pools), peritoneum (3 pools), and fallopian tube (3 pools) for RNA sequencing and molecular barcode analyses.

first: Douglas

last: Levine

first: Leslie

last: Cope


title: Total RNA-seq of cancer cells with inhibition of DNA and/or histone methylation

city: Chikusa-ku

first: Hitoshi

last: Ohtani

state: Nagoya

address: Furo-cho

department: Graduate School of Bioagricultural Sciences

institute: Nagoya University

summary: Endogenous Retroviruses (ERVs) silencing mechanism depend on DNA methylation, heterochromatin conformation and the PRC2 complex. However, extensive maps of ERVs distribution and the associated epigenetic marks have not yet been provided in human cancer cells. Our purpose in this study is to investigate ERVs expression changes after inhibition of DNA and/or histone methylations. Total RNA-seq in human colon cancer HCT116 cells following DNA methylation inhibitor treatment or knockdown of individual H3K9me2/3 histone methyltransferases revealed that about 1,000 of evolutionary young ERVs were predominantly silenced by DNA methylation, whereas about 800 of intermediate age ERVs were silenced by histone methylations. ERVs therefore have undergone an epigenetic switch in silencing mechanism during host genome evolution.

overall_design: Total RNA-seq were performed in four human cancer cell lines (HCT116, HL60, MCF7 and HepG2) following DNA methylation inhibitor (5-aza-CdR) treatment or knockdown of individual H3K9me2/3 histone methyltransferases (G9a, SETDB1, SETDB2, SUV39H1 and SUV39H2), H3K27me3 (EZH2) or a scaffold protein TRIM28. Dual inhibition of DNA methylation and histone modifications were conducted after 5-aza-CdR treatment and knockdown of individual histone methyltransferases (G9a, SETDB1, SETDB2, SUV39H1, SUV39H2 and EZH2) and TRIM28.

first: Peter

last: Jones


title: Pseudomonas aerugiosa tctED deletion strain compared to wildtype

city: Ottawa

middle: Kyle

last: Taylor

state: Ontario

address: 4125 Roger Guindon Hall 451 Smyth Rd

department: Biochemistry, Microbiology, and Immunology

institute: University of Ottawa

summary:
Purpose of study was to investigate whole genome expression changes of a strain with deletion of the two-component system TctD-TctE and determine genes dysregulate relative to the parental wildtype to gain insight into possible regulatory targets of TctD-TctE.
TctD-TctE is a two-component system in Pseudomonas aeruginosa that responds to and regulates uptake of tricarboxylic acids such as citric acid. It accomplishes this through derepression of the porin encoding the gene opdH, thereby regulating influx of citrate metabolites from the surrounding environment. Deletion of the tctED operon (ΔtctED) resulted in a reduced growth phenotype when citric acid is present in media. In the ΔtctED strain the presence of citric acid was found to have an inhibitory effect on growth. When the alternative carbon source arginine was present, wildtype levels of growth could not be restored. Static cultures of ΔtctED had low cell density in the presence of citric acid but maintained the same levels of biofilm formation compared to conditions when no citric acid was present. This suggests a dysregulation of biofilm formation in the presence of citric acid. In the ΔtctED strain there was also greater accumulation of tobramycin within the biofilm compared to the PA14 wildtype strain. Additionally, analysis of whole-genome expression found that multiple metabolic genes were dysregulated in ΔtctED. Here it is concluded that TctD-TctE is involved in biofilm tolerance to tobramycin in the presence of citrate metabolites.

overall_design: A total of 8 samples were analyzed. Conditions of planktonic and biofilm growth were performed for both the tctED strain and wildtype (4 samples for each strain). Wildtype expression in this study was used as a basis to determine tctED expression relative to wildtype.

middle: K

first: Thien-Fah

last: Mah


title: Novel human full-thickness, three-dimensional non-keratinized mucous membrane model for pharmacological studies in wound healing

city: Aachen

first: Sebastian

last: Huth

address: Pauwelsstr. 30

institute: Uniklinik RWTH Aachen

summary: Efforts are increasingly aiming to develop in vitro models that can provide effective alternatives to in vivo experiments. The main aim of this study was the establishment of an in vitro model of the non-keratinized mucous membrane that can be used as a standardized tool to evaluate biological and therapeutic effects of pharmaceuticals for mucosal wound healing. Performing histological and immunofluorescence analyses with known differentiation markers we proved that our model mimics the two distinctive layers of the mucous membrane – the stratified squamous epithelium and the lamina propria. In our study we used our model to investigate molecular effects of a dexpanthenol-containing ointment that is widely used in the wound treatment of the oral mucosa. For that purpose our model exhibits a unique feature in that dexpanthenol and proliferation enhancing additives that may interfere with our studies are not required for the maintenance of the model culture. After setting standardized lesions with a CO2 laser, topical treatment with the dexpanthenol-containing ointment enhanced wound closure in our non-keratinized mucous membrane model compared to placebo and untreated controls. Furthermore, microarray analysis revealed that the treatment of our laser wounded model with the dexpanthenol-containing ointment evoked an upregulated expression of various genes related to accelerated wound healing. Overall, we verified that our mucous membrane model can be utilized in future to monitor ex vivo effects of various topical therapies on mucosa morphology, physiology, and gene expression. Our findings confirm the potential of the non-keratinized mucous membrane model as an in vitro tool for the replacement of pharmacological in vivo studies regarding mucosal wound healing.

overall_design: Two samples were analyzed: Comparison between 3D mucous membrane model after laser injury and treatment with the dexpanthenol-containing vs. the placebo treated control.

first: Laurenz

last: Schmitt

first: Yvonne

last: Marquardt

first: Ruth

last: Heise

first: Verena

last: von Felbert

first: Philipp

last: Amann

first: Timm

last: Steiner

first: Frank

last: Hölzle

first: Jens

last: Baron


title: Single cell RNA-seq and ATAC-seq of EMT induced by TGFbeta stimulation and Zeb1 overexpression

city: New Haven

first: David

last: van Dijk

state: CT

address: 333 Cedar street

department: Genetics, Computer Science

institute: Yale University

summary: We report the application of single cell RNA-sequencing using indrop on an HMLE breast cancer cell line that we induced to undergo EMT. We measured 7523 single cells after 8 and 10 days of stimulation with TGFbeta. In addition, we measured 3496 single cells in an engineered HMLE cell line with Dox inducible Zeb1, after 2 days of stimulation with Doxycycline. Finally, we performed ATAC-seq on CD44 sorted HMLE cells after 8 days of stimulation with TGFbeta.

overall_design: Single cell RNA-seq on two different cell lines and ATAC-seq on one cell line


title: Differential expression analysis from MV4-11 cells treated with or without APTO-253 for 6 hours.

city: San Diego

first: Hongying

last: Zhang

address: 3550 General Atomics Court, MS G02/420

institute: Aptose Biosciences

summary: RNA-seq and differential gene expression analysis were used to detect specific genes and pathways either up or down regulated in the AML cell line MV4-11 after treatment with novel small molecule APTO-253. The aim of the analysis was to elucidate genes or pathways that are key to the celular phenotype of APTO-253 mechanism of action in killing AML cells. W detected an effect on MYCexpression, DNA damage and cell stress response pathwyas and cell cycle arrest.

overall_design: Expression profiles were generated from MV4-11 (AML cell line) cells treated with either DMSO (as a control) or APTO-253 for 6 hrs. Duplicate samples for each condition were analyzed using Illumina Tru-seq and Hi-seq2000

first: Hannah

first: Andrea

last: Local


title: Cryptococcus neoformans sexual reproduction is controlled by a quorum sensing peptide

city: beijing

first: lei

last: chen

address: NO.1 Beichen West  Road, Chaoyang District, Beijing 100101, China

institute: the institute of microbiology chinese academy of sciences

summary: Mating pheromone is the best-known fungal paracrine signal whose essentiality in determining sexual reproduction has been recognized since six decades ago. We demonstrate that the pheromone cannot induce mating response during unisexual mating due to the lack of a compatible receptor from the same unisexual population. We identify a quorum sensing (QS) peptide Qsp1 in place of pheromone as a specific intercellular signal directing Cryptococcus unisexual reproduction.  A typical zinc finger regulator Cqs2 as the master regulator of QS signaling induces unisexual reproduction in response to Qsp1. Collectively, these data demonstrate that QS activation rather than pheromone induction as the pivotal social control mechanism underlies unisexual reproduction in C .neoformans.

overall_design: 64 samples contain wild type, cqs1delta ,opt1delta and cqs2delta, expression profiles of wild-type (WT) and the cqs1delta mutant in the presence of glucose or galactose of  two replicates.

first: Xiuyun

last: Tian

first: Guangjun

last: He

first: Pengjie

last: Hu

first: Lei

last: Chen

first: Changyu

last: Tao

first: Ying-Lu

last: Cui

first: Lan

last: Shen

first: Weixin

last: Ke

first: Haijiao

last: Xu

first: Youbao

last: Zhao

first: Qijiang

first: Fengyan

last: Bai

first: Bian

last: Wu

first: Ence

last: Yang

first: Xiaorong

last: Lin

first: Linqi

last: Wang