title: Transcriptome data from ascorbic acid 2-glucose treated human or mouse embryonic stem cells

first: DONG-MYUNG

last: SHIN

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

overall_design: Refer to individual Series


title: Dual RNA-seq of zebrafish larvae infected with Shigella sonnei

status: Public on Nov 19 2019

city: London

first: Vincenzo

last: Torraca

state: London

address: Keppel street

country: United Kingdom

institute: LSHTM

type: Expression profiling by high throughput sequencing

summary: Shigella flexneri is historically regarded as the primary agent of bacillary dysentery, yet the closely-related Shigella sonnei is replacing S. flexneri, especially in developing countries. The underlying reasons for this dramatic shift are mostly unknown. Using a zebrafish (Danio rerio) model of Shigella infection, we discover that S. sonnei is more virulent than S. flexneri in vivo. Whole animal dual-RNAseq and testing of bacterial mutants suggest that S. sonnei virulence depends on its O-antigen oligosaccharide (which is unique among Shigella species). We show in vivo using zebrafish and ex vivo using human neutrophils that S. sonnei O-antigen can mediate neutrophil tolerance. Consistent with this, we demonstrate that O-antigen enables S. sonnei to resist phagolysosome acidification and promotes neutrophil cell death. Chemical inhibition or promotion of phagolysosome maturation respectively decreases and increases neutrophil control of S. sonnei and zebrafish survival. Strikingly, larvae primed with a sublethal dose of S. sonnei are protected against a secondary lethal dose of S. sonnei in an O-antigen-dependent manner, indicating that exposure to O-antigen can train the innate immune system against S. sonnei. Collectively, these findings reveal O-antigen as an important therapeutic target against bacillary dysentery, and may explain the rapidly increasing S. sonnei burden in developing countries.

sample_organism:
Shigella sonnei
Danio rerio

platform_organism:
Shigella sonnei
Danio rerio

overall_design:
Profiling of host and pathogen transcriptome for zebrafish larvae infected with Shigella sonnei at 24 hours post infection and comparison to transcriptome of control injected larvae and control bacteria grown in liquid culture

Grant: H2020-MSCA-IF-2015 700088; Grantee: Vincenzo Torraca; Type: European Union's Horizon 2020 research and innovation program
Grant: 772853 - ENTRAPMENT; Grantee: Serge Mostowy; Type: European Research Council Consolidator Grant
Grant: 206444/Z/17/Z; Grantee: Serge Mostowy; Type: Wellcome Trust Senior Research Fellowship
Grant: WT097411MA; Grantee: Serge Mostowy; Type: Wellcome Trust Research Career Development Fellowship
Grant: No code given; Grantee: Serge Mostowy; Type: Lister Institute of Preventive Medicine

first: Myrsini

last: Kaforou

first: Jayne

last: Watson

first: Gina

middle: M

last: Duggan

first: Hazel

last: Guerrero-Gutierrez

first: Sina

last: Krokowski

first: Michael

last: Hollinshead

first: Thomas

middle: B

last: Clarke

first: Rafal

middle: J

last: Mostowy

first: Gillian

middle: S

last: Tomlinson

first: Vanessa

last: Sancho-Shimizu

first: Abigail

last: Clements

first: Serge


title: Control of human hemoglobin switching by LIN28B-mediated regulation of BCL11A translation (Ribo-seq, RNA-seq)

status: Public on Nov 16 2019

city: New York

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

country: USA

institute: Memorial Sloan Kettering

summary: While BCL11A protein is not well synthesized at these earlier stages of development, its mRNA curiously continues to be associated with ribosomes. Through unbiased proteomic analyses in erythroid cells, we demonstrate that the RNA-binding protein LIN28B, which is developmentally expressed in a reciprocal pattern to BCL11A, directly interacts with ribosomes. We show that the observed suppression of BCL11A protein translation is mediated by LIN28B through a direct interaction with BCL11A mRNA and independent of its role in let-7 microRNA biogenesis. Finally, we show that BCL11A is the major functional target in LIN28B-mediated fetal hemoglobin induction. Our results reveal a previously unappreciated regulatory mechanism underlying human hemoglobin switching and illuminate opportunities for developing improved treatments for sickle cell disease and Beta-thalassemia

overall_design: Four replicates of ribosome profiling in adult and newborn erythroid cells with matching RNA-seq per sample.

first: Anindita

last: Basak

first: Mathias

last: Munschauer


title: Chromatin dynamics reveal circadian control of human in vitro islet maturation [WGBS]

city: Cambridge

first: Juan

middle: R

last: Alvarez-Dominguez

state: MA

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

institute: Harvard University

type: Methylation profiling by high throughput sequencing

summary: Stem cell-derived tissues could transform disease research and therapy, yet most methods generate functionally immature products. We investigate how human stem cells differentiate into pancreatic islets in vitro by profiling DNA methylation, chromatin accessibility, and histone modification changes. We find that enhancer potential is reset upon lineage commitment, and show how pervasive epigenetic priming steers endocrine cell fates. Modeling islet differentiation and maturation regulatory circuits reveals genes critical for generating endocrine cells and identifies circadian control as limiting for in vitro islet function. Entrainment to circadian feeding/fasting cycles triggers islet metabolic maturation by inducing cyclic synthesis of energy metabolism and insulin secretion effectors, including antiphasic insulin and glucagon pulses. Following entrainment, stem cell-derived islets gain persistent chromatin changes and rhythmic insulin responses with a raised glucose threshold, a hallmark of functional maturity, and function within days of transplantation. Thus, stem cell-derived tissues are amenable to functional improvement by circadian modulation.

overall_design: Whole-genome bisulfite sequencing of purified live cells at defined developmental stages from stem cells to mature pancreatic islet α/β cells


title: Chromatin dynamics reveal circadian control of human in vitro islet maturation [ChIP-seq]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: ChIP-sequencing of purified fixed cells at defined developmental stages from stem cells to mature pancreatic islet α/β cells


title: Control of human hemoglobin switching by LIN28B-mediated regulation of BCL11A translation [RNA-Seq]

overall_design: Gene expression analysis using RNA-sequencing on CD34+ HSPCs (Hematopoietic Stem and Progenitor Cells) from adult and newborn, differentiated until maturation to proerythroblasts and basophilic erythroblasts.


title: Contribution of synergism between PHF8 and HER2 signalling to breast cancer development and drug resistance

status: Public on Nov 15 2019

city: Iowa City

first: Hank

last: Qi

state: IA

address: 1-632 Bowen Science Building

institute: University of Iowa

summary: HER2 plays a critical role in tumorigenesis and is associated with poor prognosis of patients with HER2-positive breast cancers. Although anti-HER2 drugs are beneficial benefits for treating breast cancer, de novo, or acquired resistance often develops. Epigenetic factors are increasingly targeted for therapy; however, such mechanisms that interact with HER2 signaling are poorly understood. RNA sequencing was performed to identify PHF8 targets downstream of HER2 signaling. CHIP-qPCR were used to investigate how PHF8 regulates HER2 transcription. ELISA determined cytokine secretion. Cell-based assay revealed a feed forward loop in HER2 signaling and then evaluated in vivo. We report the synergistic interplay between histone demethylase PHF8 and HER2 signaling. Specifically, PHF8 levels were elevated in HER2-positive breast cancers and upregulated by HER2. PHF8 functioned as a coactivator that regulated the expression of HER2, markers of the HER2-driven epithelial-to-mesenchymal transition and cytokines. The HER2-PHF8-IL-6 regulatory axis was active in cell lines and in newly established MMTV-Her2/MMTV-Cre/Phf8-floxed  mouse models, which revealed the oncogenic function of Phf8 in breast cancer for the first time. Further, the PHF8-IL-6 axis contributed to the resistance to trastuzumab in vitro and may play a critical role in the infiltration of T cells in HER2-driven breast cancers. These findings provided informative mechanistic insight into the potential application of PHF8 inhibitors to overcome resistance to anti-HER2 therapies.

overall_design: mRNA profiles of MCF10A cells stably expressing a scramble shRNA, PHF8 shRNA, and HER2 overexpression were generated by RNA-seq, in duplicate, using HiSeq2500 instrument.

first: Qi

last: Liu

first: Nicholas

last: Borcherding

first: Peng

last: Shao

middle: H


title: Control of human hemoglobin switching by LIN28B-mediated regulation of BCL11A translation [RIP-Seq]

overall_design: Two replicates of LIN28B CLIP-seq in newborn erythroid cells with matching input for each sample. One replicate is rRNA depleted.


title: Dynamic changes in gene expression profile during differentiation of iPS into MSCs

city: Singapore

first: Tongming

address: 60 Biopolis street

department: Cancer stem group

country: Singapore

institute: Genome Institute of Singapore

summary: Analysis of gene expression profile at different developmental stages of MSCs.  iPS cells from human fibroblasts are differentiated into MSCs undergoing primitive streak and mesoderm. Results provide important information of dynamic changes in gene expression profile during MSC development.

overall_design: Total RNA is obtained from human fibroblasts,  iPS, primitive streak, mesoderm cells, MSCs and bone marrow MSCs. Different stages of cells are compared with iPS cells.

first: Tong

first: Bing

last: Lim


title: Direct role of MUTE in cell state switch and symmetric cell division to create stomata

city: Austin

first: Keiko

middle: U.

last: Torii

state: TX

address: MNS 5.104A 2506 Speedway

institute: The University of Texas at Austin

summary: Precise cell division control is critical for developmental patterning. For the differentiation of a functional stoma, a cellular valve for efficient gas exchange, the single symmetric division of an immediate precursor is absolutely essential. Yet, the mechanism governing the single division event remains unclear. Here we report the complete inventories of gene expression by the Arabidopsis bHLH protein MUTE, a potent inducer of stomatal differentiation. We found that MUTE switches the gene expression program initiated by its sister bHLH, SPEECHLESS and directly induces a suite of cell-cycle genes and their transcriptional repressors. The architecture of the regulatory network initiated by MUTE represents an Incoherent Type 1 Feed-Forward Loop. Our study delineates the role for MUTE in orchestrating a transcriptional cascade leading to stomatal differentiation, and unravels a core regulatory circuit.

overall_design: RNA-seq profile of estradiol-inducible MUTE

first: S

middle: K

last: Han

first: T

middle: A

last: Endo

first: K

middle: U


title: Synthetic lethality between VPS4A and VPS4B triggers   an inflammatory response in colorectal cancer

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

country: Poland

institute: Uniwersytet Warszawski

summary: Somatic copy number alterations play a critical role in oncogenesis. Loss of chromosomal regions containing tumor suppressors can lead to collateral deletion of passenger genes. This can be exploited therapeutically if synthetic lethal partners of such passenger genes are known and represent druggable targets. Here, we report that VPS4B gene, encoding an ATPase involved in ESCRT-dependent membrane remodeling, is such a passenger gene frequently deleted in many cancer types, notably in colorectal cancer (CRC). We confirmed downregulation of VPS4B mRNA and protein levels from CRC patient samples. We identified VPS4A paralog as a synthetic lethal interactor for VPS4B in vitro and in mouse xenografts. Depleting both proteins profoundly altered the cellular transcriptome and induced cell death accompanied by the release of immunomodulatory molecules that mediate inflammatory and anti-tumor responses. Our results identify a pair of novel druggable targets for personalized oncology and provide a rationale to develop VPS4 inhibitors for precision therapy of VPS4B-deficient cancers.

overall_design: The aim of the study was to analyze transcriptional changes upon single depletion of VPS4A or VPS4B  and double depletion of VPS4A and VPS4B (VPS4A+B) in human colorectal HCT116 cell line. For RNA-seq analysis 4 biological replicates were prepared, each encompassing following samples: 1/ non-transfected HCT116 (NT),  2/ HCT116 transfected with non -targeting siRNA (siCTRL#1), 3/ HCT116 transfected with non -targeting siRNA (siCTRL#2), 4/ HCT116 transfected with siRNA targeting VPS4A, sequence #1 (siVPS4A#1), 5/ HCT116 transfected with siRNA targeting VPS4A, sequence #2 (siVPS4A#2), 6/ HCT116 transfected with siRNA targeting VPS4B, sequence #1 (siVPS4B#1), 7/ HCT116 transfected with siRNA targeting VPS4B, sequence #2 (siVPS4B#2), 8/ HCT116 transfected with combination of siRNAs targeting VPS4A and VPS4B  (siVPS4A#2 and VPS4B#1, referred thereafter as siVPS4A+B#1), 9/ HCT116 transfected with combination of siRNAs targeting VPS4A and VPS4B  (siVPS4A#1 and VPS4B#2, referred thereafter as siVPS4A+B#2). Non-transfected and siCTRL#1-transfected cells served as reference samples.

first: Ewelina

last: Szymańska

first: Paulina

last: Nowak

last: Kolmus

first: Magdalena

last: Cybulska

first: Edyta

last: Derezińska-Wołek

first: Anna

last: Szumera-Ciećkiewicz

first: Marta

last: Brewińska-Olchowik

first: Aleksandra

last: Grochowska

first: Katarzyna

last: Piwocka

first: Monika

last: Prochorec-Sobieszek

first: Michał

last: Mikula

last: Miączyńska


title: Small non-coding RNA discovery and profiling with sRNAtools based on high-throughput sequencing

city: Beijing

first: Qi

last: Liu

state: Beijing

address: Dong xiaofu No 1, Xiangshan Road, Haidian District

department: State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry

country: China

institute: Chinese Academy of Forestry

type: Non-coding RNA profiling by high throughput sequencing

summary: Small non-coding RNAs (sncRNAs) are generated from different genomic loci and have important roles in biological processes, such as cell proliferation and regulation of gene expression. Next-generation sequencing (NGS) has provided an unprecedented opportunity to discover and quantify diverse kinds of sncRNAs, such as tRFs (tRNA-derived small RNA fragments), phasiRNAs (phased, secondary, small interfering RNAs), piRNAs and plant specific 24-nt short interfering RNAs (siRNAs). However, currently available web-based tools do not provide approaches to comprehensively analyze all these diverse sncRNAs. A novel web server, sRNAtools (https://bioinformatics.sc.cn/sRNAtools), is presented that can be used in conjunction with high-throughput sequencing to discover, profile and functionally annotate sncRNAs, including miRNAs, isomiRs, piRNAs, tRFs, tRNAs, snRNAs, snoRNAs, rRNAs, phasiRNAs, and plant specific 24-nt siRNAs for 21 species. In this study, sRNAtools has been used in sncRNA profiling in poplar wood tissues, which identified many wood related sncRNAs expression patterns.We believe that sRNAtools will greatly benefit the scientific community as an integrated tool to study sncRNAs.

overall_design: Woody plants provide large amounts of biomass, which can serve as raw material for the production of renewable energy and other commercial products. Poplar is a model system to study woody plants. miRNAs has been revealed playing important roles in the formation of poplar wood. To fully understand the characteristics of poplar sncRNAs, especially in wood formation, we used sRNAtools based on sRNA-seq to study sncRNAs in all poplar wood tissues (xylem, phloem, and cambium) and leaves.

first: Xiaoqiang

last: Lang

first: Changjun

last: Ding

first: Xiaohua

last: Su


title: The mevalonate pathway is required for pyrimidine synthesis and survival of p53-deficient colon cancer cells in metabolically compromised environments

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

country: Germany

institute: University of Wuerzburg

summary: In this study, we have investigated the effect of p53 deletion on the metabolic activity of colon cancer cells exposed to metabolic stress. In order to recreate the simultaneous reduction in oxygen and nutrient availability found in tumors, we cultured cancer cells as multicellular tumor spheroids. Under these conditions, p53 deficient cancer cells activate the expression of enzymes of the mevalonate pathway via the sterol regulatory element binding protein 2 (SREBP2). Moreover, inhibition of mevalonate pathway activity with statins selectively induced apoptosis in p53 deficient cancer cells exposed to metabolic stress. This effect was mediated by the requirement of p53 deficient cancer cells to synthesise ubiquinone (coenzyme Q10) to maintain TCA cycle activity, respiration and the production of pyrimidine nucleotides. Our study has revealed a novel link between isoprenoid synthesis by the mevalonate pathway and the electron transport function of ubiquinone, which is required for nucleotide biosynthesis. As a consequence, maintaining mevalonate pathway activity is essential for p53 deficient cancer cells to proliferate and survive under the metabolic constraints of the tumor microenvironment.

overall_design: RNAseq experiments in HCT116 p53WT or -deficent cells analyzing gene expression changes in monolayer or 3D culture conditions and after treatment with simvastatin.

first: Irem

last: Kaymak

first: Werner

last: Schmitz

first: Beatrice

last: Dankworth

first: Carina

last: Maier

first: Carsten

last: Ade

first: Susanne

last: Walz

first: Mathias

last: Rosenfeldt

first: Andrew

last: Campbell

first: David

last: Gay

first: Grace

last: McGregor

first: Owen

last: Sansom

first: Almut

last: Schulze


title: Control of human hemoglobin switching by LIN28B-mediated regulation of BCL11A translation

first: Caleb

last: Lareau


title: Cell-type specific dysregulation of RNA alternative splicing in short tandem repeat mouse knockin models of myotonic dystrophy

city: Gainesville

first: Maurice

last: Swanson

state: FL

address: 2033 Mowry Road,, Cancer & Genetics Research Complex, Swanson Lab, Room 220G

institute: University of Florida

summary: Short tandem repeats (STRs) are prone to expansion mutations that cause multiple hereditary neurological and neuromuscular diseases. To study pathomechanisms using mouse models that recapitulate the tissue specificity and developmental timing of an STR expansion gene, we used rolling circle amplification and CRISPR/Cas9-mediated genome editing to generate Dmpk CTG expansion (CTGexp) knockin models of myotonic dystrophy type 1 (DM1). We demonstrate that skeletal muscle myoblasts and brain choroid plexus epithelial cells are particularly susceptible to Dmpk CTGexp mutations and RNA mis-splicing. Our results implicate dysregulation of muscle regeneration and cerebrospinal fluid homeostasis as early pathogenic events in DM1.

overall_design: RNAseq profiles were generated for tibialis anterior, differentiated myotubes and choroid plexus from either WT mice, or mice containing CTG repeat expansions as indicated, e.g.Dmpk 480 allele includes 480 CTG repeats.

first: Curtis

middle: N

last: Nutter

first: Jodi

middle: L

last: Bubenik

first: Ruan

last: Oliveira

first: Franjo

last: Ivankovic

first: Lukasz

last: Sznajder

first: Benjamin

last: Kidd

first: Belinda

last: Pinto

first: Brittney

last: Otero

first: Helmut

last: Carter

first: Eric

last: Vitriol

middle: T

last: Wang


title: Chromatin dynamics reveal circadian control of human in vitro islet maturation [ATAC-seq]

first: Juan

last: Alvarez-Dominguez

overall_design:
ATAC-sequencing of purified live cells at defined developmental stages from stem cells to mature pancreatic islet α/β cells
ATAC-sequencing of purified live cells differentiated from human pluripotent stem cells from Stage 6 week 0 to Stage 6 week 4.


title: Expression data from medial vestibular nucleus neuronal subtypes of mouse

city: Baltimore

first: Sascha

last: du Lac

state: MD

address: 720 Rutland Avenue

department: Otolaryngology HNS

institute: Johns Hopkins University School of Medicine

summary: Medial vestibular nucleus (MVN) neurons were functionally classified by single-cell gene expression profiling. The transcriptional diversity across MVN neuronal subtypes was further examined by microarray analysis.

overall_design: Single-cell cDNA prepared from individual MVN neurons were first classified into 8 cell types (E1, E2, E3, I1a, I1b, I2, I3a, I3b) by expression profiles of transmitter-related genes, ion channels, and cell-type markers (Kodama et al., 2012 J Neurosci). Single-cell cDNAs belonging to each cell type were pooled and subjected to microarray analysis.

first: Takashi

last: Kodama


title: Real-time quantitative PCR analysis of phenotype of osteochondral tissue chip

status: Public on Nov 14 2019

city: Pittsburgh

first: Zixuan

last: Lin

state: PA

address: 450 Technology Dr

department: Department of Orthopaedic Surgery

institute: University of Pittsburgh

summary: In this study, we aimed to develop microphysiological osteochondral (OC) tissue chips derived from human induced pluripotent stem cells (iPSCs) to model the pathologies of OA. We first induced iPSCs into mesenchymal progenitor cells (iMPCs) and optimized the chondro- and osteo-inductive conditions for iMPCs. Then iMPCs were encapsulated into photocrosslinked gelatin scaffolds and cultured within a dual-flow bioreactor, in which the top stream was chondrogenic medium and the bottom stream was osteogenic medium. After 28 days of differentiation, biphasic OC tissue and monophasic chondral (CH) tissue chips were successfully generated and phenotypes were confirmed by real time RT-PCR. The OC tissues were cut into Top and Bottom (Bot), and both parts were compared with each other. CH tissue were compared with their phenotype on Day 0. Total RNA was extracted from the samples and processed for qPCR according to the manufacturer's instructions.

overall_design: qPCR gene expression profiling: OC and CH tissue chip were generated and compared as indicated in summary. Total RNA from each sample was used for gene expression analysis and normalized to RPL13A.

first: Lin

last: Hang

last: Zixuan


title: Tuber transcriptome profiling of eight potato cultivars with different cold-induced sweetening responses to cold storage

city: Fredericton

first: Martin

last: Lague

state: New Brunswick

address: 850 Lincoln Rd.

country: Canada

institute: Agriculture and Agri-Food Canada

summary: Tubers are vegetative reproduction organs formed from underground extensions of the plant stem.  Potato tubers are harvested and stored for months.  Storage under cold temperatures of 2 - 4 °C is advantageous for supressing sprouting and diseases. However, development of reducing sugars can occur with cold storage through a process called cold-induced sweetening (CIS).  CIS is undesirable as it leads to darkened color with fry processing.  The purpose of the current study was to find differences in biological responses in eight cultivars with variation in CIS resistance.  Transcriptome sequencing was done on tubers before and after cold storage and three approaches were taken for gene expression analysis: 1. Gene expression correlated with end-point glucose after cold storage, 2. Gene expression correlated with increased glucose after cold storage (after-before), and 3. Differential gene expression before and after cold storage.  Cultivars with high CIS resistance (low glucose after cold) were found to increase expression of an invertase inhibitor gene and genes involved in DNA replication and repair after cold storage.  The cultivars with low CIS resistance (high glucose after cold) showed increased expression of genes involved in abiotic stress response, gene expression, protein turnover and the mitochondria. There was a small number of genes with similar expression patterns for all cultivars including genes involved in cell wall strengthening and phospholipases.  It is proposed that the pattern of gene expression is related to chilling-induced DNA damage repair and cold acclimation and that genetic variation in these processes are related to CIS.

overall_design: Tubers from eight Solanum tuberosum potato cultivars (15329-03, 15323-04, 15328-26, 575.04.01, Crop 20, Summer Delight, Doremi, and Lady Claire) sampled at two time points: 1. with two weeks of harvest  (before cold storage) and 2. after three months of cold storage at 4 °C (after cold storage).  Three replicate samples were done for each cultivar at each time point.  At each time point, 3 tubers were sampled at three locations (rose end, bud end and mid section) using a 6 mm Harris Unicore biopsy punch.  The total number of tuber core punches was 9 per sample.

first: Helen

last: Tai


title: Oligodendrocyte Progenitor Cell Transcriptome in White Matter Stroke

city: Los Angeles

first: Giovanni

last: Coppola

state: CA

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

summary: Tissue progenitors maintain the integrity of organ systems through aging and stress. The brain’s white matter regions experience ischemic lesions and age-dependent degeneration. Brain white matter contains progenitors, oligodendrocyte precursor cells (OPCs), which can repair some insults. The response of OPCs to white matter ischemia and aging is not known. We characterized the response of OPCs to white matter stroke using OPC reporter mice, cell migration tracking, OPC specific RNA sequencing, and mechanistic studies in candidate biochemical pathways in the aged brain. White matter stroke induces initial proliferation of local OPCs but blocks differentiation, shunting a portion into astrocytes. Candidate signaling pathways for this differentiation block including novel interactions of inhibin and matrilin-2 and new roles of NgR1 ligands following white matter stroke. Stroke induces inhibin expression in astrocytes and downregulates OPC matrilin-2 that contributes into OPC differentiation block. Antagonism of NgR1 ligands promotes OPC differentiation by attenuating the OPC astrocytic transformation and enhances functional recovery from stroke in aged animals.

overall_design: RNA-sequencing of laser-capture oligodendrocyte precursor cell with a without white matter stroke

first: Elif

middle: G

last: Sozmen

first: R

last: Rosenzweig

first: M

last: Machnicki

first: Roman

last: Giger

first: Jason

middle: D

last: Hinman

first: Harry

last: Vinters

first: S

last: Carmichael


title: Epigenetic Code of Host Chromosome Docking Sites for Epstein-Barr Virus (EBV) Latent Episomes

city: Eugene

first: Hideki

last: Tanizawa

state: OR

address: 1370 Franklin Blvd

department: Institute of Molecular Biology

institute: University of Oregon

summary: Epstein-Barr virus (EBV) genomes persist in latently infected cells as extrachromosomal plasmids that attach to host chromosomes through the tethering functions of EBNA1, a viral encoded sequence-specific DNA binding protein. Here we employed circular chromosome conformation capture (4C) analysis to identify genomewide associations between EBV episomes and host chromosomes. We found that EBV episomes in Burkitt lymphoma (BL) cells preferentially associate with EBNA1 sequence-specific DNA binding sites in the cellular genome that are also enriched for B-cell factors EBF1 and RBP-jK, the repressive histone mark H3K9me3, and surrounded by AT-rich sequence. These attachment sites corresponded to transcriptionally silenced genes with enrichment in neuronal function. Depletion of EBNA1 from EBV latently infected BL cells led to a transcriptional de-repression of these silenced genes. EBV attachment sites in lymphoblastoid cells (LCLs) showed different correlations, suggesting that latency types are functionally linked to the epigenetic environment of host chromosome attachment sites.

overall_design: 4C-seq, ChIP-seq, and RNA-seq data

first: Kyoung-Dong

last: Kim

first: Andrew

last: Kossenkov

first: Fang

last: Lu

first: Louise

middle: C

last: Showe

first: Kenichi

last: Noma

first: Paul

last: Lieberman


title: Expression analysis of colonic neurons stimulated with AhR agonist (3-methylcholanthrene)

status: Public on Nov 13 2019

first: Vassilis

last: Pachnis

address: 1 Midland Road

department: Development and Homeostasis of the Nervous System Laboratory

institute: The Francis Crick Institute

summary:
Neural control of visceral organ function is essential for homeostasis and health. Intestinal peristalsis is critical for digestive physiology and host defence and is often dysregulated in gastrointestinal (GI) disorders. Luminal factors, such as diet and microbiota regulate neurogenic programs of gut motility, but the underlying molecular mechanisms remain unclear. Here we show that the transcription factor Aryl hydrocarbon Receptor (AhR) functions as a biosensor in intestinal neural circuits linking their functional output to the microbial environment of the gut lumen. Using nuclear RNA sequencing of mouse enteric neurons representing distinct intestinal segments and microbiota states, we demonstrate that the intrinsic neural networks of the colon exhibit unique transcriptional profiles controlled by the combined effects of host genetic programmes and microbial colonisation. Microbiota-induced expression of AhR in neurons of the distal gastrointestinal tract enables them to respond to the luminal environment and induce expression of neuron-specific effector mechanisms. Neuron-specific deletion of Ahr or constitutive overexpression of its negative feedback regulator CYP1A1, results in reduced peristaltic activity of the colon, similar to that observed in microbiota-depleted mice. Finally, expression of Ahr in enteric neurons of antibiotic-treated mice partially restores intestinal motility. Taken together, our experiments identify AhR signalling in enteric neurons as a regulatory node that integrates the luminal environment with the physiological output of intestinal neural circuits towards gut homeostasis and health.
The enteric nervous system (ENS) encompasses the intrinsic neural networks of the gastrointestinal (GI) tract, which regulate most aspects of intestinal physiology, including peristalsis. In addition to host-specific genetic programmes, microbiota and diet have emerged as critical regulators of gut tissue physiology and changes in the microbial composition of the lumen often accompany GI disorders. We found that gut environmental sensor Aryl hydrocarbon receptor (AhR) is induced in colonic neurons in response to microbiota colonisation and regulates intestinal peristalsis in an AhR ligand-dependent manner. In this experiment, we used RNA sequencing to identify genes regulated in mouse colonic neurons by AhR activation.

overall_design: We developed an adeno-associated virus (AAV)-based strategy for isolation and RNA sequencing of enteric neuron nuclei (nRNAseq) representing different intestinal segments and microbiota states. For isolation of neuronal nuclei from the myenteric plexus, mice were injected intravenously with AAV9-CaMKII-EGFPKASH. 5 weeks after intravenous injection of AAV, the longitudinal smooth muscle layer and associated myenteric plexus were peeled off the wall of the smal intestine (SI) and colon and subjected to Dounce homogenization. After filtering the homogenate to remove large debris, samples were centrifuged at 1000 x G for 10 min at 4°C to obtain a pellet containing muscularis externa nuclei. For flow cytometric analysis, doublet discrimination gating was applied to exclude aggregated nuclei, and intact nuclei were determined by subsequent gating on the area and height of DAPI intensity. Both EGFP+ (neuronal) and EGFP- (non-neuronal) nuclear populations were collected directly into 1.5mL tube containing Trizol LS reagent.

first: Yuuki

last: Obata

first: Stefan

last: Boeing


title: AhR signalling in enteric neurons

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

overall_design: Refer to individual Series


title: Expression analysis of enteric neurons from the mice housed in different animal facilities (the Francis Crick institute and the University of Bern)

summary:
Neural control of visceral organ function is essential for homeostasis and health. Intestinal peristalsis is critical for digestive physiology and host defence and is often dysregulated in gastrointestinal (GI) disorders. Luminal factors, such as diet and microbiota regulate neurogenic programs of gut motility, but the underlying molecular mechanisms remain unclear. Here we show that the transcription factor Aryl hydrocarbon Receptor (AhR) functions as a biosensor in intestinal neural circuits linking their functional output to the microbial environment of the gut lumen. Using nuclear RNA sequencing of mouse enteric neurons representing distinct intestinal segments and microbiota states, we demonstrate that the intrinsic neural networks of the colon exhibit unique transcriptional profiles controlled by the combined effects of host genetic programmes and microbial colonisation. Microbiota-induced expression of AhR in neurons of the distal gastrointestinal tract enables them to respond to the luminal environment and induce expression of neuron-specific effector mechanisms. Neuron-specific deletion of Ahr or constitutive overexpression of its negative feedback regulator CYP1A1, results in reduced peristaltic activity of the colon, similar to that observed in microbiota-depleted mice. Finally, expression of Ahr in enteric neurons of antibiotic-treated mice partially restores intestinal motility. Taken together, our experiments identify AhR signalling in enteric neurons as a regulatory node that integrates the luminal environment with the physiological output of intestinal neural circuits towards gut homeostasis and health.
The enteric nervous system (ENS) encompasses the intrinsic neural networks of the gastrointestinal (GI) tract, which regulate most aspects of intestinal physiology, including peristalsis. In addition to host-specific genetic programmes, microbiota and diet have emerged as critical regulators of gut tissue physiology and changes in the microbial composition of the lumen often accompany GI disorders. However the molecular mechanisms by which gut enviromental factors regulate ENS homeostasis remain unknown. In order to address this issue, we used RNA sequencing to identify genes specifically upregulated in mouse colonic neurons in response to microbial colonisation.


title: Expression analysis of colonic and small intestinal neurons in the germ-free (GF) and specifric pathogen-free (SFP) mice


title: Genome-wide differences in RNA expression in Drosophila melanogaster leg imaginal discs based on time and presence/absence of broad-based gene regulation

city: Lawrence

first: Clinton

middle: Allen

last: Rice

state: Kansas

address: 1200 Sunnyside Ave

department: Molecular Biosciences

institute: University of Kansas

summary: We report on changes in gene expression resulting from the ecdysone-directed broad-based transcriptional regulatory hierarchy in Drosophila melanogaster leg imaginal discs by comparing expression in white1118  third-instar larvae (-18 hrs relative to pupariation) and white prepupae (0 hrs) to examine the transcriptional effects of the late larval ecdysone pulse, as well comparing expression in white1118 and broad5 white prepupal leg imaginal discs to examine the transcriptional effects of the early ecdysone responder, broad. Using this approach, we were able to identify critical leg disc elongation genes that are differentially regulated in broad mutants

overall_design: RNA sequencing of leg imaginal discs in white1118 larvae/prepupae at -18 hrs and 0 hrs and in broad5 prepupae at 0 hrs. Each genotype/timepoint combination was sequenced in triplicate.

first: Stuart

last: Macdonald

first: Robert

middle: E

last: Ward IV


title: Loss of epigenetic modifications on the inactive X chromosome and sex-biased gene expression profiles in B cells from NZB/W F1 mice with lupus-like disease

city: Philadelphia

first: Montserrat

last: Anguera

address: 3800 Spruce Street, Rosenthal Room 390EB

department: Biomedical Sciences

institute: University of Pennsylvania School of Veterinary Medicine

summary: We report loss of epigentic silencing marks on the inactive X on female mice with lupus like disease, and find novel sex differences in gene expression between female and male mice with late stage disease.

overall_design: Comparison of gene expression changes between female and male mice with lupus-like disease

first: Isabel

last: Sierra


title: Mutagenesis sensitizes murine models of triple negative breast cancer to immunotherapy

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

summary: This study identifies mechanisms of response to immune checkpoint inhibition in mouse models of triple negative breast cancer.

overall_design: Single-Cell RNA-seq profiling of response to immune checkpoint inhibitors in mouse models of triple negative breast cancer.

middle: M

first: Daniel

middle: P

last: Hollern


title: Impact of Early Antiretroviral Therapy Initiation on HIV-Specific CD4 and CD8 T Cell Function in Perinatally Infected Children

city: Cleveland

first: Mark

last: Cameron

state: OH

address: 10900 Euclid Ave

department: Population and Quantitative Health Sciences

institute: Case Western Reserve University

summary: 14 children vertically HIV infected ART treated within 6 months of life (ET) and 6 children vertically HIV infected ART treated after 12 months of life were studied to understand the effect of early ART initiation on HIV specific CD4+ T cells and CD8+ T cells functionalities. Additionally, RNAseq on unstimulated PBMC was performed to also evaluate the impact of early ART on the immune transcriptome.

overall_design: RNA extracted from PBMC from early (<6months), late (>12months) ART treated HIV perinatally infected individuals and 6 healthy individuals  was sequenced and compared to identify differences in their background transcriptome

first: S

last: Rinaldi

last: Pallikkuth

first: M

first: L

last: de Armas

first: N

last: Cotugno

first: R

last: Pahwa

first: B

last: Richardson

last: Lain

last: Williams

first: P

last: Palma


title: ERα over-expression does not accelerate development of p53-deficient mammary tumors in mice [RNA-Seq]

city: Amsterdam

first: Lisette

last: Cornelissen

address: Plesmanlaan 121

country: Netherlands

institute: The Netherlands Cancer Institute

summary: About 75% of all breast cancers express the nuclear hormone receptor oestrogen receptor α (ERα). However, the majority of mammary tumors from genetically engineered mouse models are ERα-negative. To model ERα-positive breast cancer in mice, we exogenously introduced expression of mouse and human ERα in an existing p53-deficiency driven breast cancer mouse model. After initial ERα expression during development of the mammary gland, expression was reduced or lost in adult glands and p53-deficient mammary tumors. ChIP-sequencing analysis of primary mouse mammary epithelial cells (MMECs) derived from these models, in which expression of the ERα constructs was induced in vitro, confirmed interaction of ERα with the DNA. In human breast and endometrial cancer, the pioneer factor FOXA1 is known to be essential to facilitate ERα/DNA binding. Surprisingly, the ERα binding sites identified in primary MMECs, but also in mouse mammary gland and uterus, showed a high enrichment of ERE motifs, but were devoid of Forkhead motifs. Furthermore, exogenous introduction of FOXA1 and GATA3 in ERα-expressing MMECs was not sufficient to promote ERα-responsiveness of these cells. Together, this suggests that species-specific differences in ERα-cistromes between mouse and human are dictated by the DNA sequence, resulting in ERα-dependencies in mice that are not FOXA1 driven and potentially not tumorigenic. These species-specific differences in ERα-biology can limit the use of mouse models in ERα-positive breast cancer research.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNAseq data of MCF7 cells and primary MMECs derived from WcrH;P53F/F mice or WcrH;P53F/F mice expressing HA-tagged human ERa or HA-tagged mouse ERa

first: Linda

last: Henneman

first: Anne

last: Paulien Drenth

first: Eva

last: Schut

first: Roebi

last: de Bruijn

first: Wilbert

last: Zwart

first: Jos

last: Jonkers


title: Gene expression profiles of 4 non-pathogenic mutants in the phytopathogenic fungus Botrytis cinerea

city: Palaiseau

first: Adeline

last: SIMON

address: 22 place de l'agronomie

country: France

institute: INRAE

summary: Full transcriptomes of the Botrytis cinerea wild-type strain B0510 and 4 non-pathogenic mutants, grown in a cucumber liquid medium, were compared to identify differentially expressed genes.

overall_design: Botrytis cinerea WT and 4 non-pathogenic mutant strains were grown in a cucumber liquid medium. 3 or 4 replicates were performed. The 19 total-RNA samples were used for RNA-SEQ sequencing.

first: Elise

last: Loisel

first: Nathalie

last: Poussereau

last: Simon

first: Muriel

last: Viaud


title: Microarray analysis of mouse TRAF3-/- premalignant splenic B cells

city: Piscataway

first: Ronald

middle: P.

last: Hart

state: NJ

address: 604 Allison Rd Rm B430

department: Cell Biology & Neuroscience

institute: Rutgers University

summary: Specific deletion of the tumor suppressor gene TRAF3 from B lymphocytes (B-TRAF3-/-) in mice leads to prolonged survival of mature B cells and expanded B cell compartment in secondary lymphoid organs. To understand the metabolic basis of the prolonged survival of TRAF3-/- B cells, we performed LC-MS-based metabolome and lipidome screening with resting splenic B cells of young adult B-TRAF3-/- and littermate control (LMC) mice. Our metabolome screening data showed that phosphocholine (P-Cho) and phosphoethanolamine, two small metabolites and precursors of phospholipids, were significantly increased in TRAF3-/- B cells. Consistently, our lipidome screening revealed markedly elevated levels of multiple species of phosphatidylcholine (PC) and phosphatidylethanolamine in TRAF3-/- B cells. Interestingly, our transcriptome profiling identified Chka, the rate-limiting enzyme of choline metabolism, as a significantly up-regulated gene in TRAF3-/- B cells. To investigate the functional importance of elevated choline metabolism, we examined the effects of two Chka inhibitors, MN58B and RSM932A. We found that both MN58B and RSM932A potently induced cell apoptosis in TRAF3-/- mouse B lymphoma and human multiple myeloma cell lines in vitro.  Furthermore, in vivo administration of MN58B and RSM932A partially decreased the spleen size and B cell compartment in B-TRAF3-/- mice. Together, our results indicate that TRAF3 specifically re-engineers the P-Cho-PC-PE metabolic pathways to regulate mature B cell survival. Our findings also suggest that the P-Cho-PC-PE metabolic pathways have diagnostic and therapeutic value for B cell malignancies with TRAF3 deletion or relevant mutations.

overall_design: Three control (normal splenic B cells) and three TRAF3-/- (premalignant splenic B cells) samples were collected to identify mechanisms altered in the absence of TRAF3.

first: Sining

last: Zhu

first: Yingying

last: Liu

first: Samantha

last: Gokhale

first: Shanique

last: Edwards

first: Ping

last: Xie


title: Circadian clock genes and the vitamin A pathway regulate seasonal photoperiodic responsiveness in an insect

city: College Station

first: Christine

last: Merlin

address: 3258 TAMU

department: Biology

institute: Texas A&M University

summary: Seasonal adaptation to changes in light:dark regimes (i.e., photoperiod) allows organisms living at temperate latitudes to anticipate environmental change and adjust their physiology and behavior accordingly. The circadian system has been implicated in measurement and response to changes in photoperiod in nearly all animals studied so far (Saunders, 2011). The use of both traditional and non-traditional model insects with robust seasonal responses has recently genetically demonstrated the central role that clock genes play in photoperiodic response. Yet, the molecular pathways involved in insect photoperiodic responses remain largely unknown. Here, using the Eastern North American monarch butterfly (Reppert et al, 2016; Denlinger et al, 2017), we identified the vitamin A pathway as a novel pathway downstream of the circadian clock mediating insect photoperiod responsiveness. We found that interrupting clock function by disrupting circadian activation and repression abolishes photoperiodic responses in reproductive output, providing a functional link between clock genes and photoperiodic responsiveness in the monarch. Through transcriptomic approaches, we identified a molecular signature of seasonal-specific rhythmic gene expression in the brain, the organ known to function in photoperiodic reception in both Lepidoptera and some flies (Bowen et al, 1984; Saunders & Cymborowski, 1996). Among genes differentially expressed between both long and short photoperiods and between seasonal forms, several were belonging to the vitamin A pathway. The rhythmic expression of all of these genes was abolished in clock-deficient mutants. We also showed that a CRISPR/Cas9-mediated loss-of-function mutation in the pathway’s rate-limiting enzyme, ninaB1, impaired the monarch ability to respond to the photoperiod independently of visual function in the compound eye and without affecting circadian rhythms. Our finding that the vitamin A pathway is a key mediator of photoperiodic responses in insects could have broad implications for understanding the molecular mechanisms underlying photoperiodism.

overall_design: Determine the identify of rhythmic genes underlying photoperiodic responses in monarch butterfly brains using RNA-seq.

last: Iiams

first: Aldrin

middle: B

last: Lugena

first: Ying

last: Zhang

first: Ashley

last: Hayden


title: Microarray analysis of SEMA5A downstream pathways on A549 cells

city: Taipei

first: Liang-Chuan

last: Lai

state: Taiwan

address: 1 Jen-Ai Road, Sec 1

department: Physiology

country: Taiwan

institute: National Taiwan University

summary: A549 cell line shows low endogenous SEMA5A expression and is an ideal platform of screening the dowstream pathways of SEMA5A.

overall_design: Total RNA obtained from cultured A549 cells 24 hours after transfection of SEMA5A in vitro.

first: Pin-Hao

last: Ko


title: Integrated transcriptomic analyses identify altered nerve triglycerides in mouse models of prediabetes and type 2 diabetes

status: Public on Nov 12 2019

city: Grand Forks

first: Junguk

last: Hur

state: ND

address: 1301 N. Columbia Rd. Stop 9037

institute: University of North Dakota

summary: We employed high-fat diet (HFD)-induced prediabetes and HFD/streptozotocin (STZ)-induced type 2 diabetes mouse models that develop PN, which we compared to control mice maintained on standard diet (SD) and to HFD and HFD/STZ mice that were subject to SD dietary reversal (DR) half-way through the study. We performed gene expression profiling on sciatic nerves from SD, HFD, HFD-STZ, HFD-DR, and HFD-STZ-DR animal cohorts. Nerve transcriptomic profiles were integrated using complex correlation analyses, and biological meaning was inferred from known lipid-gene interactions in the literature

overall_design: mRNA profiles of sciatic nerve (SCN) tissue was isolated from 16-week and 24-week old C57BL/6J mice that were under . Our prediabetic model consisted of BL/6J mice fed a HFD (60% kcal fat) from 5 weeks of age. Our T2D diabetic model consisted of 12-week old HFD mice injected with low dose streptozotocin (STZ; 75mg/kg followed by a 50mg/kg dose 3 days later (i.p. injection)). At 16 weeks, subgroups of HFD and HFD-STZ mice were switched to a control diet (13% kcal fat) for 8 weeks to mimic dietary reversal. RNA-seq of SCN was performed on SCN tissue at the 16 week and 24 week timepoints.

first: Kai

last: Guo

first: Eva

last: Feldman


title: Ptpn6 inhibits caspase-8- and Ripk3/Mlkl-dependent inflammation

city: La Jolla

first: Nathan

last: Lewis

state: California

address: 9500 Gilman Dr

department: Pediatrics

institute: UCSD

summary: Ptpn6 is a cytoplasmic phosphatase that functions to prevent autoimmune disease and IL-1R-dependent caspase-1-independent inflammatory disease. Conditional deletion of Ptpn6 in neutrophils (Ptpn6∆PMN) is sufficient to initiate IL-1R-dependent cutaneous inflammatory disease, but the source of IL-1 and the mechanisms behind IL-1 release remain unclear. Here, we investigated the mechanisms controlling IL-1α/β release from neutrophils by inhibiting caspase-8-dependent apoptosis and Ripk1/Ripk3/Mlkl-regulated necroptosis. Loss of Ripk1 accelerated disease onset, whereas combined deletion of caspase-8 and either Ripk3 or Mlkl strongly protected Ptpn6∆PMN mice. Ptpn6∆PMN neutrophils displayed increased p38-dependent Ripk1-independent IL-1 and TNF production, and were prone to cell death. Together, these data emphasize dual functions for Ptpn6 in the negative regulation of p38 MAP kinase activation to control TNF and IL-1α/β transcription, and in maintaining Ripk1 function to prevent caspase-8- and Ripk3/Mlkl-dependent cell death and concomitant IL-1α/β release.

overall_design: RNA-seq for murine neutrophils with different genotypes show transciptional differences in SHP1 knockouts related to immune pathways. Age-related transcriptional differences are seen as well.

first: Mary

last: Speir

first: Ben

last: Croker

first: Isaac

last: Shamie


title: ERα over-expression does not accelerate development of p53-deficient mammary tumors in mice

first: Lisette

last: Cornelissen


title: Sperm DNA Methylation Epimutation Biomarkers for Male Infertility and FSH Therapeutic Responsiveness

status: Public on Nov 11 2019

city: Pullman

first: Michael

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

summary: Male factor infertility is increasing and recognized as playing a key role in reproductive health and disease. The current primary diagnostic approach is to assess sperm quality associated with reduced sperm number and motility, which has been historically of limited success in separating fertile from infertile males. The current study was designed to develop a molecular analysis to identify male infertility using genome wide alterations in sperm DNA methylation. A signature of differential DNA methylation regions (DMRs) was identified to be associated with male infertility patients. A promising therapeutic treatment of male infertility is the use of follicle stimulating hormone (FSH) analogs which improved sperm numbers and motility in a sub-population of infertility patients. The current study also identified genome-wide DMRs that were associated with the patients that were responsive to FSH therapy versus those that were non-responsive.

overall_design: Twenty-two patients were enrolled which included nine patients in the fertile control group and thirteen in the infertility treatment group. Initial semen analysis and basal hormone determination to assess eligibility criteria were performed. Sperm samples were processed and stored for the subsequent epigenetic analysis. The infertility group received 150 IU of urinary or recombinant FSH three times per week for 12 weeks and the fertile control group did not received treatment. After three months of treatment, semen analysis and hormone profiles were retested in both groups. MeDIP-seq was performed on the pre treatment samples. An additional eighteen patients were enrolled and contributed samples that were not used for the DMR analysis. Samples from these patients were processed in an identical manner as the samples in the treatment groups and were used as a validation dataset.

first: Satur

last: Luján

first: Ettore

last: Caroppo

first: Craig

last: Niederberger

first: Joan-Carles

last: Arce

first: Ingrid

last: Sadler-Riggleman

first: Daniel

last: Beck

first: Eric

last: Nilsson


title: Dysregulation of different classes of tRNA fragments in chronic lymphocytic leukemia

city: Columbus

first: Carlo

middle: Maria

last: Croce

state: OHIO

address: 460 West 12TH Avenue

department: Cancer Biology & Genetics

institute: The Ohio State University

summary:
We analyzed small RNA sequencing data from CD5+/CD19+ B cells of a cohort of indolent and aggressive CLL patients compared with CD19+ B-cells of healthy donors.
We identified tsRNA signatures in indolent and aggressive CLL vs. normal B-cells; we also found a drastic dysregulation of the expression of mature tRFs in CLL.

overall_design: A total of 20 whole blood samples provided by the CLL Research Consortium and grouped into the following two categories: 10 indolent CLL and 10 aggressive CLL. A third category of 8 CD19+ B-cell control samples (courtesy of J. Byrd MD, IRB approved protocol) was also considered in the study.

first: Y

last: Perkarsky

first: C


title: Transcription factor T-bet in B cells controls germinal centre polarization and antibody affinity maturation in response to malaria (ATAC-seq)

city: Clayton

first: Wei

last: Shi

state: VIC

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology

country: Australia

institute: Monash University

summary: Despite the key role that antibodies play in protection against malaria, the cellular processes modulating the acquisition of immunity are not fully understood. Using an infection model of severe malaria, we found that GC B cells strongly upregulate the transcription factor T-bet in response to infection. Expression of T-bet in B cells was required for IgG2c switching but reduced the magnitude of GC B cell responses. RNA-sequencing and flow cytometry analysis revealed that T-bet supports a transcriptional program resulting in a substantial enrichment of the GC dark zone (DZ), thereby significantly influencing DZ/light zone (LZ) polarization. Mice deficient in T-bet in their B cells displayed significantly reduced affinity mutation frequencies in their IghV genes and lower antibody avidity than controls, indicating that T-bet modulates affinity maturation. These results demonstrate that T-bet promotes appropriate GC dynamics, thereby leading to the differentiation of B cells with increased affinity for antigen.

overall_design: ATACeq data were generated from murine GC B cells to investigate the chromatin accessibility between wild-type and T-bet-deficient GC B cells.

first: Ann

last: Ly

first: Yang

last: Liao

first: Halina

last: Pietrzak

first: Lisa

middle: J

last: Ioannidis

first: Tom

last: Sidwell

first: Renee

last: Gloury

first: Anthony

last: Triglia

first: Kim

last: Good-Jacobson

first: Axel

last: Kallies

first: Diana

middle: S

last: Hansen


title: A potent and selective small-molecule degrader of STAT3 achieves complete tumor regression in vivo

city: Memphis

first: Chao-Yie

last: Yang

state: Tennessee

address: 881 Madison Avenue, Rm559

department: Pharmaceutical Sciences

institute: University of Tennessee HSC

summary: Signal transducer and activator of transcription 3 (STAT3) is an attractive cancer therapeutic target. We report herein the discovery of SD-36, a small-molecule degrader of STAT3. SD-36 potently induces the degradation of STAT3 protein in vitro and in vivo and demonstrates high selectivity over other STAT members. Induced degradation of STAT3 results in a strong suppression of its transcription network in leukemia and lymphoma cells. SD-36 inhibits the growth of a subset of acute myeloid leukemia and anaplastic large cell lymphoma cell lines by inducing cell cycle arrest and/or apoptosis. SD-36 achieves complete and long-lasting tumor regression in multiple xenograft mouse models at well tolerated dose schedules. Degradation of STAT3 protein therefore represents a promising cancer therapeutic strategy.

overall_design: Global gene transcription profiling was performed in MOLM-16 and SU-DHL-1 cell lines treated with DMSO, SD36 (1000 nmol/L) or SD36Me (1000 nmol/L) for 8 and 24 hours. Independent biological replicates (such as DMSO_8h and DMSO_24h) were analyzed for each cell line under each condition. DMSO-treated samples were used as controls.

first: Chao

middle: Y

first: Longchuan

last: Bai

first: Hui

last: Jiang

first: Shaomeng

last: Wang


title: RNA sequencing of keratinocytes with or without LRG1 addition

city: Shanghai

first: Gao

last: Ya

state: Shanghai

address: Zhizaoju road No.639

department: School of medicine

institute: Shanghai Jiao Tong University

summary: Leucine-rich-alpha-2-glycoprotein1 (LRG1), a highly conserved member of the leucine-rich repeat family of proteins, has been reported to be involved in several tumors. Previous studies showed that it has great importance in epithelial–mesenchymal transition in colorectal cancer and could promote glioma cell lines invasion and migration. Despite the intimate relationships between LRG1 and migration in cancer research, its role in wound repair or re-epithelialization has not been uncovered. So we dicided using keratinocytes to see its transcriptomes changing after LRG1 addition.

overall_design: Examination of keratinocytes RNA sequencing comparing the LRG1 addition(500ng/ml, 12h) group and control group

first: Ya

last: Gao

first: Yifan

last: Zhang

first: Qingfeng

last: Li


title: RNA sequencing of Tregs from skin of neonatal mice colonized with Staphlyococcus epidermidis versus Staphylococcus aureus

city: San Francisco

first: Tiffany

last: Scharschmidt

address: 513 Parnassus Ave, 1201B

department: Dermatology

institute: University of California, San Francisco

overall_design: Mice were colonized every other day from birth with either S. epi or S. aureus. Mice were sacrificed on day 21 of life and Tregs isolated from skin by FACS prior to bulk RNA sequencing.

last: Crawford Scharschmidt

first: Johnathon

last: Leech


title: Transcription factor T-bet in B cells controls germinal centre polarization and antibody affinity maturation in response to malaria

first: Wei

last: Shi

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

overall_design: Refer to individual Series


title: Next Generation Sequencing analysis to examine the transcriptional responses of the nematode-trapping fungus Duddingtonia flagrans with the treatment of extraction of Caenorhabditis elegans

city: Hohhot

state: Inner Mongolia

address: Zhaowuda Road

institute: Inner Mongolia Agricultural University

summary:
Purpose: To identify the putative high pathogenicity for fungal infection of nematodes of the nematode-trapping fungus Duddingtonia flagrans, RNA-seq was used to  examine the transcriptional responses in three stages with the treatment of extraction of Caenorhabditis elegans.
Methods:mRNA of three interaction stages (0h, 12h, 48h) were generated by deep sequencing, in triplicate, using Illumina Hiseq platforme,and 125 bp paired-end reads were generated.Then raw reads were firstly processed by in-house perl scripts and clean reads were obtained by removing reads containing adapter,poly-N and low quality reads. Clean reads were aligned to the reference genome using TopHat V2.0.12 (Duddingtonia flagrans genome with the accession number of MDKD00000000).Then HTSeq and DESeq were used to analyse the gene expression level.
Results: After sequencing, 81.8% of the genes predicted in genome of Duddingtonia flagrans were expressed (FPKM>1) in the samples free of treatment of extraction of Caenorhabditis elegans (0h). After treatment with nematode extracts for 12 h , 40.7% of predicted genes, including 1,752 up-regulated genes and 2,072 down-regulated genes, were found to be differentially expressed (padj<0.05, DESeq) compared to the genes at 0 h. Similarly, after treatment with nematode extracts for 48 h, 13.8% of predicted genes, including 673 up-regulated genes and 628 down-regulated genes, were found to be differentially expressed compared to the genes at 12 h.

overall_design: Examination of 9 transcriptomes in different predation periods to find their different gene expression style.

first: Rui

first: Xiaoye


title: Transcription factor T-bet in B cells controls germinal centre polarization and antibody affinity maturation in response to malaria (RNA-seq)

overall_design: RNASeq data were generated from murine GC B cells to investigate the different gene signatures between wild-type and T-bet-deficient GC B cells.

first: Ann

last: Ly

first: Yang

last: Liao

first: Halina

last: Pietrzak

first: Lisa

last: Ioannidis

first: Tom

last: Sidwell

first: Renee

last: Gloury

first: Anthony

first: Kim


title: Gene expression profile of human neuroblastoma cell line SHSY-5Y after LMO1 knockdown

status: Public on Nov 10 2019

city: Singapore

first: Tze King

last: Tan

address: 14 Medical Drive

department: Cancer Science Institute

institute: National University of Singapore

summary: To dissect molecular pathways regulated by LMO1 in neuroblastoma, we performed microarray gene expression profiling in a neuroblastoma cells (SHSY-5Y) after LMO1 knockdown.

overall_design: A human neuroblastoma cell line SHSY-5Y cells was transduced with LMO1 (shLMO1#2) or control GFP shRNA (shGFP).  Experiment was done in biological duplicate (dup1 and dup2). A total of 4 RNA samples (2 control and 2 LMO1 knockdown) were used for microarray gene expression analysis.

first: Lu

first: Tze

middle: K

first: Thomas

last: Look

first: Takaomi

last: Sanda


title: Human muscle-derived CLEC14A-positive cells regenerate muscle independent of PAX7

city: Berlin

first: Nikos

last: Karaiskos

address: Hannoversche Str. 28

institute: Max Delbrück Center for Molecular Medicine

summary: Skeletal muscle stem cells, called satellite cells, are responsible for postnatal muscle growth, homeostasis and regeneration. Attempts to utilize the regenerative potential of muscle stem cells for therapeutic purposes so far failed. The transcription factor Pax7 defines satellite cells across species 1-4 . We previously established human PAX7-positive cell colonies with high regenerative potential 5 . We now identified PAX7-negative human muscle-derived cell colonies (PAX7neg) also positive for the myogenic markers desmin and MYF5. These included cells from a unique myopathic patient with rigid spine and respiratory insufficiency due to a homozygous PAX7 c.86-1G>A mutation (PAX7null). Single cell and bulk transcriptome analysis showed high intra- and inter-donor heterogeneity and revealed the endothelial cell marker CLEC14A to be highly expressed in PAX7null cells. All PAX7neg cell populations, including PAX7null, formed myofibers after transplantation into mice, and regenerated muscle after reinjury. Transplanted PAX7neg cells repopulated the satellite cell niche where they re-expressed PAX7. Strikingly, PAX7null cells expressing CLEC14A were also identified below the basal lamina. In summary, transplanted human cells do not depend on PAX7 for muscle regeneration. Thus, Pax7 is not a suitable marker for selection of optimal cells for muscle regenerative therapies.

overall_design: Eleven human primary myoblasts cell lines with and without PAX7 expression were analysed using single- cell or bulk RNA-seq. For single-cell experiments we analysed myoblast subpopulations with and without PAX7 expression from the same donor as well as myoblasts from a patient with PAX7 deficiency. Bulk RNA-seq included a PAX7-positive and a PAX7-negative myoblast cell line and myoblasts from the patient with PAX7 deficiency.

first: Andreas

last: Marg

first: Stefanie

last: Grunwald

first: Sascha

last: Sauer

first: Christine

last: Kocks

first: Nikolaus

last: Rajewsky

first: Simone

last: Spuler


title: RNA-seq analysis after knockdown of ASCL1 gene in Kelly cells

summary: RNA-seq analysis was performed in Kelly neuroblastoma cell line to analyze gene expression changes after ASCL1 knockdown.

overall_design: Lentiviral shRNA transduction was carried out in Kelly cells to knockdown control GFP or ASCL1. One shRNA was used to target each gene. Experiments were done in biological duplicates. Total RNA was harvested 3 days after knockdown and RNA-seq analysis was performed.

last: Wang


title: Transcriptional profile Lactobacillus plantarum WCFS1 : Resveratrol treated cells

city: Madrid

first: Felix

last: Lopez de Felipe

address: Jose Antonio Novais

country: Spain

institute: ICTAN-CSIC

summary: Whole genome transcriptional profiling was used to characterize the response of Lactobacillus plantarum WCFS1 human isolate during challenge with resveratrol. Twelve independent experiments were performed and mixed at random in groups of four for total of three RNA samples. The transcriptional profile reveals  a large reshape of nitrogen metabolism whic affects, among others, the pyridine and purine metabolisms as well as the metabolism of aminoacids related to thiol-specific oxidative stress response in this microorganism. Genes involved in the general stress response and carbon metabolism were also affected. A distinctive feature of the response to resveratrol identified in the transcriptomic analysis was a marked modulation of genes coding for certain ABC-type transporters.

overall_design: Biological triplicates: untreated cells: Control vs. Resveratrol treated cells: Experimental

first: Inés

last: Reverón

first: Laura

last: Plaza

first: Blanca

last: de las Rivas

first: Rosario

last: Muñoz

first: Félix

middle: L

last: de Felipe


title: Downregulation of polycomb repressive complex 2 mediates cisplatin acquired resistant in testicular germ cell tumors

city: Urbana

first: Michael

last: Spinella

state: IL

address: 2001 S Lincoln Ave

department: Comparative Biosciences

institute: University of Illinois at Urbana-Champaign

summary: A greater understanding of the hypersensitivity and curability of testicular germ cell tumors (TGCTs) has the potential to inform strategies to sensitize other solid tumors to conventional chemotherapies.  More than 80% of metastatic TGCT patients are cured with cisplatin-based chemotherapy. However, resistance can occur, which results in poor outcomes. The mechanisms of cisplatin hypersensitivity and resistance in these tumors and embryonal carcinoma (EC), the stem cells of TGCTs, remain largely undefined. To study the mechanisms of cisplatin acquired resistance we generated a large panel of independently derived, acquired resistant clones from three distinct parental EC models employing a protocol designed to match standard of care regimens of TGCT patients.  Transcriptomics revealed highly significant alterations shared between resistant cells regardless of their parental origin. This included a highly significant enrichment of genes normally repressed by H3K27 methylation and the polycomb repressive complex 2 (PRC2) which correlated with a substantial decrease in global H3K27me3, H2AK119 ubiquitination and expression of BMI1.  Importantly repression of H3K27 methylation with the EZH2 inhibitor GSK-126 conferred cisplatin resistance to parental cells while induction of H3K27 methylation with the histone lysine demethylase inhibitor GSK-J4 resulted in increased cisplatin sensitivity to resistant cells. A gene signature based on H3K27me gene enrichment was associated with an increased rate of recurrent/progressive disease in testicular cancer patients.  Our data indicates that repression of H3K27 methylation may be a mechanism of cisplatin acquired resistance in TGCTs and that restoration of PRC2 complex function could be a viable approach to overcome treatment failure.

overall_design: gene expression of parental and cisplatin resistant cell lines in biological triplicate were analysed


title: A rare subpopulation of melanoma cells with low expression of metastasis suppressor NME1 has a neural crest-like phenotype and is highly metastatic in vivo

status: Public on Nov 09 2019

city: Baltimore

first: David

last: Kaetzel

state: MD

address: 108 N Greene St

department: Biochemistry and Molecular Biology

institute: University of Maryland, Baltimore

summary: Examination of heterogeneous cell populations found within WM9 melanoma cell lines, which express high or low levels of NME1 protein

first: Devin

last: Snyder

first: Ying


title: Two distinct colonic CD14+ subsets characterized by single-cell RNA profiling in Crohn's disease

city: Montreal

first: Marika

last: Sarfati

state: Quebec

address: 900 rue St Denis

institute: CRCHUM

summary: Inflammatory bowel diseases are associated with dysregulated immune responses in the intestinal tissue. Four molecularly identified macrophage subsets control immune homeostasis in healthy gut. However, the specific roles and transcriptomic profiles of the phenotypically heterogeneous CD14+ macrophage-like population in inflamed gut remain to be investigated in Crohn’s disease (CD). Here we identified two phenotypically, morphologically and functionally distinct colonic HLADR+SIRPα+CD14+ subpopulations that were further characterized using single-cell RNA-sequencing (scRNAseq) in CD. Frequencies of CD64hiCD163−/dim cells selectively augmented in inflamed colon and correlated with endoscopic score of disease severity. IL-1β and IL-23-producing CD64hiCD163−/dim cells predominated over TNF-α-producing CD64hiCD163hi cells in lesions. Purified “inflammatory monocyte-like” CD163−, but not “macrophage-like” CD163hi cells, through IL-1β, promoted Th17/Th1 but not Th1 responses in tissue memory CD4+T cells. Unsupervised scRNAseq analysis that captures the entire HLADR+SIRPα+ population revealed six clusters, two of which were enriched in either CD163− or CD163hi cells, and best defined by TREM1/FCAR/FCN1/IL1RN or CD209/MERTK/MRCI/CD163L1 genes, respectively. Selected newly identified discriminating markers were used beyond CD163 to isolate cells that shared pro-Th17/Th1 function with CD163− cells. In conclusion, a molecularly distinct pro-inflammatory CD14+ subpopulation accumulates in inflamed colon, drives intestinal inflammatory T-cell responses, and thus, might contribute to CD disease severity.

overall_design:
Single cell RNA sequencing of FACS-sorted HLADR+SIRPa+ cells  from colonic inflamed mucosa  of 3 CD patients
The raw data files have not been included due to privacy concerns.

first: Laurence

last: Chapuy

first: Bsat

last: Marwa

first: Sarkizova

last: Siranush

first: Alexandra-Chloé

last: Villani

first: Nir

last: Hacohen


title: Neogenin-1 distinguishes between myeloid-biased and balanced Hoxb5+ mouse long-term hematopoietic stem cells

city: Palo Alto

first: Gunsagar

middle: Singh

last: Gulati

state: CA

address: 265 Campus Drive

department: Institute for Stem Cell Biology and Regenerative Medicine

institute: Stanford University

summary: Hematopoietic stem cells (HSCs) self-renew and generate all blood cells. Recent studies with single-cell transplants and lineage tracing suggest that adult HSCs are diverse in their reconstitution and lineage potentials. However, prospective isolation of these subpopulations has remained challenging. Here, we identify Neogenin-1 (NEO1) as a unique surface marker on a fraction of mouse HSCs labeled with Hoxb5, a specific reporter of long-term HSCs (LT-HSCs). We show that NEO1+Hoxb5+ LT-HSCs expand with age and respond to myeloablative stress in young mice, while NEO1–Hoxb5+ LT-HSCs exhibit no significant change in number. Furthermore, NEO1+Hoxb5+ LT-HSCs are more often in the G2/S cell cycle phase compared to NEO1–Hoxb5+ LT-HSCs in both young and old bone marrow. Upon serial transplantation, NEO1+Hoxb5+ LT-HSCs exhibit myeloid-biased differentiation and reduced reconstitution, while NEO1–Hoxb5+ LT-HSCs are lineage-balanced and stably reconstitute recipients. Gene expression analysis reveals erythroid and myeloid priming in the NEO1+ fraction and association of quiescence and self-renewal-related transcription factors with NEO1− LT-HSCs. Finally, transplanted NEO1+Hoxb5+ LT-HSCs rarely generate NEO1–Hoxb5+ LT-HSCs, while NEO1–Hoxb5+ LT-HSCs repopulate both LT-HSC fractions. This supports a model in which dormant, balanced, NEO1–Hoxb5+ LT-HSCs can hierarchically precede active, myeloid-biased NEO1+Hoxb5+ LT-HSCs.

overall_design: Bulk RNA-sequencing profiles of NEO1+Hoxb5+ (n = 5) and NEO1–Hoxb5+ (n = 5) LT-HSCs from the bone marrow of 2- to 3-month-old Hoxb5-mCherry mice.

first: Krzysztof

last: Szade

first: Rahul

last: Sinha

first: Irving

last: Weissman


title: ASCL1 is a MYCN- and LMO1-dependent member of the adrenergic neuroblastoma core regulatory circuitry

first: Tze King

last: Tan


title: RNA-seq analysis after LMO1 or MYCN knockdown in Kelly cells

summary: RNA-seq analysis was performed in Kelly neuroblastoma cell line to analyze gene expression changes after LMO1 or MYCN knockdown.

overall_design: Lentiviral shRNA transduction was carried out in Kelly cells to knockdown control GFP, LMO1 or MYCN. One shRNA was used to target each gene. Experiments were done in biological duplicates. Total RNA was harvested 3 days after knockdown and RNA-seq analysis was performed.

first: Lu

last: Wang

first: Takaomi

last: Sanda


title: cAMP/EPAC signaling enables ETV2 to induce endothelial cells with high angiogenesis potential

city: Seoul

first: JaeJun

last: Kim

address: 1 Gwanak-ro, Gwanak-gu

department: Veterinary Medicine

country: South Korea

institute: Seoul National University


title: cAMP/EPAC signaling enables ETV2 to induce endothelial cells with high angiogenesis potential [RNA-seq]

summary: Although the generation of ETV2-induced endothelial cells (iECs) from human fibroblasts serves as a novel therapeutic strategy in regenerative medicine, the process is inefficient, resulting in incomplete iEC angiogenesis. Therefore, we employed ChIP-sequencing and identified molecular mechanisms underlying ETV2-mediated endothelial transdifferentiation to efficiently produce iECs retaining appropriate functionality in long-term culture. We revealed that the majority of ETV2 targets in human fibroblasts are related to vasculature development and signaling transduction pathways including Rap1 signaling. From a screening of signaling pathway modulators, we confirmed that forskolin facilitated efficient and rapid iEC reprogramming via activation of cAMP/EPAC/RAP1 axis. The iECs obtained via cAMP signaling activation showed superior angiogenesis in vivo as well as in vitro. Moreover, these cells could form aligned endothelium along the vascular lumen ex vivo when seeded into decellularized liver scaffold. Overall, our study provided evidence that cAMP/EPAC/RAP1 axis is required for the efficient generation of iECs with angiogenesis potential.

overall_design: For RNA-seq, 4 samples are uploaded.  hDFs transduced with rtTA and tet-HA-ETV2 were administered with or without doxycycline for 7 days. HUVEC was used for control.

first: Jae-Jun

first: Da-Hyun

first: Kyung-Sun

last: Kang


title: Serum exosome microRNAs predict multiple sclerosis disease activity after fingolimod treatment

status: Public on Nov 08 2019

city: Sydney

first: Fatemeh

last: Vafaee

state: UNSW

address: Gate 11 Botany Street, UNSW Sydney, School of BABS

department: School of Biotechnology and Biomolecular Sciences

institute: University of New South Wales

summary:
Background: We and others have previously demonstrated the potential for circulating exosome microRNAs to aid in disease diagnosis. In this study, we sought the possible utility of serum exosome microRNAs as biomarkers for disease activity in multiple sclerosis patients in response to fingolimod therapy. We studied patients with relapsing-remitting multiple sclerosis prior to and 6 months after treatment with fingolimod.
Methods: Disease activity was determined using gadolinium-enhanced magnetic resonance imaging. Serum exosome microRNAs were profiled using next-generation sequencing. Data were analysed using univariate/multivariate modelling and machine learning to determine microRNA signatures with predictive utility.
Results: we identified 15 individual miRNAs that were differentially expressed in serum exosomes from post-treatment patients with active versus quiescent disease. The targets of these microRNAs clustered in ontologies related to the immune and nervous systems, and signal transduction. While the power of individual microRNAs to predict disease status post-fingolimod was modest (average 77%, range 65 to 91%), several combinations of 2 or 3 miRNAs were able to distinguish active from quiescent disease with greater than 90% accuracy. Further stratification of patients identified additional microRNAs associated with stable remission, and a positive response to fingolimod in patients with active disease prior to treatment.
Conclusions: Overall, these data underscore the value of serum exosome microRNA signatures as non-invasive biomarkers of disease in multiple sclerosis and suggest they may be used to predict response to fingolimod in future clinical practice. Additionally, these data suggest that fingolimod may have mechanisms of action beyond its known functions.

overall_design: Serum exosomal miRNA profiles of MS patients before and after treatment with fingolimod were generated by deep sequencing, single end, using Illumina HiSeq. 2000 System at the Ramaciotti Centre for Genomics.

first: Saeideh

last: Ebrahimkhani

first: Heidi

middle: N

last: Beadnall

first: Chenyu

first: Catherine

last: Suter

first: Michael

middle: H

last: Barnett

last: Buckland


title: Transcriptional profiling of Usp22-WT and Usp22-KO pancreatic tumor cells

city: New York

first: Jinyang

last: Li

state: New York

address: 1230 York Ave

institute: The Rockefeller University

summary: RNA-seq analysis of sorted Usp22-WT and Usp22-KO tumor cells from subcutaneously implanted mouse pancreatic tumors

overall_design: Compare Usp22-WT vs Usp22-KO in one tumor cell clone

first: Ben

last: Stanger


title: RNASeq of Arg2 gRNA or scrambled gRNA CRISPR'd Tregs

first: Margaret

last: Lowe

address: 513 Parnassus Avenue, HSW1201B

institute: UCSF

summary: The aim of the study was to analyze the transcriptional profile of Tregs following CRISPR deletion of Arg2

overall_design: Expanded human Tregs either treated with Arg2 gRNA pool or scrambled gRNA were RNASequenced

middle: D

last: Rosenblum


title: Effects of ALK inhibitory treatment with alectinib in glioblastoma cells

city: Heidelberg

first: Anne

last: Berberich

address: Im Neuenheimer Feld 280

institute: German Cancer Research Center

summary: Anaplastic lymphoma kinase (ALK) is expressed in around 60% of glioblastomas and conveys tumorigenic function. Therefore, ALK inhibitory strategies with alectinib were investigated in glioblastoma cells. We demonstrated that alectinib inhibited proliferation and clonogenicity of ALK expressing glioblastoma initiating cells, whereas cells without ALK expression or after ALK depletion via knockdown showed primary resistance against alectinib. The aim of this analysis was to investigate molecular mechanisms of alectinib mediated treatment effects in the ALK expressing S24 cells, which represent a primary glioblastoma cell culture, and after knockdown of ALK.

overall_design: S24 cells were treated for 24h with 500nM alectinib or respective DMSO amounts as treatment control. Total mRNA was isolated from three replicates and were used for analysis of molecular mechanisms of alectinib mediated treatment effects. ALK knockdown was performed using commercial lentiviral small hairpin RNAs. ALK knockdown cells were treated with 500nM alectinib and respective DMSO amounts as treatment control. Total mRNA was isolated from three replicates and were used to analyze potential off-target treatment effects of alectinib.

first: Lara-Marie

last: Schmitt

first: Wolfgang

last: Wick


title: cAMP/EPAC signaling enables ETV2 to induce endothelial cells with high angiogenesis potential [ChIP-seq]

overall_design: For ChIP-seq, 4 samples are uploaded. hDFs transduced with rtTA and tet-HA-ETV2 were administered with or without doxycycline for 7 days.


title: ASCL1 is directly activated by the LMO1 and MYCN oncogenes and is a master regulator of the differentiation program in neuroblastoma

city: Cambridge

first: Richard

middle: A

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: Neuroblastoma is an embryonal tumor of the peripheral sympathetic nervous system.  Elevated expression of the transcription factor LMO1 and the polymorphisms within this gene are associated with the susceptibility to develop neuroblastoma.  LMO1 has been implicated as an oncogene in T-cell acute lymphoblastic leukemia; however, the transcriptional targets regulated by this protein in neuroblastoma cells are unknown.  Here, we identify the genes and molecular pathways controlled by LMO1 in neuroblastoma cells.  ChIP-seq analysis revealed that LMO1-bound regions are frequently co-occupied by GATA3 and MYCN proteins and are associated with active histone marks in neuroblastoma cells.  RNA-seq analysis demonstrated that LMO1 regulates gene expression in a tumor type-specific manner.  One high-confidence target gene directly regulated by LMO1 and MYCN is ASCL1, which is more highly expressed in adrenergic subtype of neuroblastoma cells as compared to normal neuronal cells.  High levels of ASCL1 expression are associated with inferior overall survival in primary human neuroblastoma cases.  ChIP-seq analysis identified a regulatory element controlling ASCL1 expression that is bound by LMO1, MYCN and the members of the core regulatory circuitry in neuroblastoma cells.  Furthermore, ASCL1 is required for neuroblastoma cell growth and regulates genes responsible for repression of neuronal cell differentiation.  Taken together, our results implicate ASCL1 as a critical downstream target of LMO1 in the molecular pathogenesis of neuroblastoma.

overall_design: ChIP-Seq for LMO1 in the Kelly neuroblastoma cell line

first: Lu

last: Wang

first: Tze

last: Tan

first: Adam

last: Durbin

first: Mark

middle: W

last: Zimmerman

first: Brian

last: Abraham

first: Shi

first: Nina

last: Weichert-Leahey

first: Koshi

last: Akahane

first: Jo

last: Harenza

first: John

last: Maris

first: A

middle: T

last: Look

first: Takaomi


title: RNASeq of Human Skin Tregs and CD4 Teffs from melanoma cutaneous tumors

first: Margaret

summary: The aim of the study was to analyze the transcriptional profile of Tregs and CD4 Teffectors present within melanoma cutaneous lesions

overall_design: Tregs and CD4 Teffectors from two samples of human cutaneous melanoma tumors were sort-purified and RNA-sequenced

middle: M

first: Kelly

last: Mahuron

first: Michael


title: Life-long epigenetic programming of cortical architecture by maternal Western diet during pregnancy

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

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

overall_design: Refer to individual Series


title: RNASeq of Healthy Human Skin Tregs and CD4 Teffs versus Psoriatic Human Skin Tregs and  CD4 Teffs

last: Lowe

summary: The aim of the study was to compare the transcriptional profile of healthy skin Tregs to Tregs isolated from psoriatic lesions and to compare these profiles to CD4 Teffectors isolated from the same patient.

overall_design: Tregs and CD4 Teffectors from five samples of healthy human skin from psoriatic lesions were sort-purified and RNA-sequenced

last: Rosenblum


title: Differentially expressed genes by DMSO in mouse 2-cell embryos identified by RNA sequencing

first: Min-Hee

last: Kang

state: Seoul

address: 120 Neungdong-ro

department: Stem Cell and Regenerative Biotechnology

institute: Konkuk University

summary: Since discovery of dimethyl sulfoxide (DMSO), it has been applied to the multidisciplinary studies for basic and clinic research; yet its toxicity versus biocompatibility is poorly understood, leading to our inability to discover etiology behind its paradox. Here, we found that exposure of 2% DMSO to mouse zygotes caused developmental arrest at 2/4-cell embryos, and showed a decreased total acetylation levels. Besides, H3, H4, p53, H3K9, and H3K27 acetylation levels at DMSO-exposed 2-cell embryos are significantly increased. This affected the male pronucleus more than female. Further, RNA-sequence data demonstrates that DMSO alters approximately 16.26% transcripts of 2-cell embryos. Among them, maternal and minor zygotic gene activation (ZGA) transcripts are highly increased, whereas ubiquitin-proteasome system, major ZGA, embryonic gene activation, cell cycle, and ribosomal biogenesis transcripts are significantly down-regulated. These results suggest that DMSO caused developmental arrest by disrupting maternal-to-embryonic transition due to low proteasome activity and epigenetic alternations.

overall_design: We cultured 18 hours post hCG zygotes in KSOM media supplemented with or without 2% DMSO for 24 hours and then fifty of developed 2-cell embryos in each group were  subjected to low-put RNA sequencing.

first: Jin-Hoi

last: Kim


title: SHAPE and DMS probing of SLNCR1 lncRNA conserved region 403-780

status: Public on Nov 07 2019

city: Ann Arbor

first: Chase

middle: Andrew

last: Weidmann

state: MI

address: 1150 W. Medical Center Drive

department: Biological Chemistry

institute: University of Michigan

summary: The goal of this study was to understand the underlying structure of nucleotides 403-780 of the lncRNA SLNCR1, in-cell and when extracted from nuclear and cytoplasmic fractions. SHAPE and DMS probing revealed that the region is largely unstructured inside and outside of the cell, and appears protein-bound in primary melanoma cells.

overall_design: RNA from WM1976 (melanoma short-term culture) cells were treated with the SHAPE reagent 5-nitroisatoic anhydride (25 mM) or DMS (2%) either in-cell or after extraction from the cytoplasm or nuclei and removal of proteins. Purified RNA was used as templates in modified reverse transcription conditions (MaP RT), wherein sites of chemical adducts on the RNA were encoded into cDNA as non-templated sequences. MaP RT was initiated with primers specific to SLNCR1 region 403-780 or, as a control, the U1 small nuclear RNA. cDNAs were further amplified, sequenced, and aligned to respective targets. Nucleotide mutation rates were transformed into SHAPE reactivities, which informed RNA structure modeling.

first: Breanne

last: Hatfield

first: Kevin

last: Weeks


title: RNA-seq of lipid droplet-low and lipid droplet-rich microglia isolated from the hippocampi of Progranulin KO mice

city: Stanford

first: Julia

last: Marschallinger

address: 1201 Welch Road

department: Neurology

summary: Sequencing data related to the manuscript entitled, "Lipid droplet accumulating microglia represent a dysfunctional and pro-inflammatory state in the aging brain".

overall_design: 10-month old Progranulin knockout mice (GRN KO) were perfused and hippocampi were dissected (Hippocampi of 2 mice were pooled per sample). Primary microglia were isolated by gentle dounce homogenization of the brain, Percoll-based myelin removal, and FACS-purification of ~10,000 live CD11b+CD45lo cells. BODIPYlo (=lipid droplet-low) and BODIPYhi (=lipid droplet-high) microglia were sorted into RLT Plus buffer (Qiagen) containing beta-mercaptoethanol. RNA was extracted using a RNeasy Micro Plus kit (Qiagen) according to the manufacturer’s protocol. RNA integrity was assessed on a Bioanalyzer (Agilent), and high quality samples (RIN >9) were used for library preparation. cDNA synthesis and amplification was performed using the SmartSeq v4 Ultra-low input kit (Takara), and libraries were tagmented, adaptor ligated, and indexed using the Nextera XT kit (Illumina). Sequencing of isolated microglia was carried out with Illumina Novogene 6000, paired end, 2x 100 bp. The quality of fastq files was assessed using FASTQC (v 0.11.4). Reads were mapped to mouse mm10 reference genome using STAR (v 2.5.3a). Raw read counts were generated with STAR using the GeneCounts function. Differential expression analysis was performed using DESeq2 with standard settings.

first: Macy

last: Zardeneta


title: Genome-wide maps of chromatin H3K9ac state in control and mTORC2-suppressed glioblastoma cells

city: Shinjuku

first: Kenta

last: Masui

state: Tokyo

address: 8-1 Kawada-cho

department: Department of Pathology

country: Japan

institute: Tokyo Women's Medical University

summary: We herein demonstrate that mammalian target of rapamycin complex 2 (mTORC2), a critical core component of the growth factor signaling system, globally alters histone acetylation through metabolic reprogramming in the highly malignant brain tumor glioblastoma (GBM). Integrated analyses unravel that mTORC2 regulates iron trafficking via histone H3K9 acetylation of the ferritin promoter, facilitating GBM growth and survival. These findings nominate mTORC2 as a critical epigenetic regulator of iron metabolism in cancer.

overall_design: Examination of one histone modification in two cell types.

first: Masui

last: Kenta


city: Minneapolis

first: Douglas

middle: Gene

last: Mashek

state: Minnesota

address: Suite 6-155, 321 Church St. SE

department: Biochemistry, Molecular Biology and Biophysics

institute: University of Minnesota

summary: Hepatic perilipin 5 is required for fasting-induced autophagy to prevent fatty acid-induced inflammation.

overall_design: Mice were injected with Control/PLIN5 targeted ASOs twice a week for three weeks. Mice were fasted overnight, with half of them receiving a 4 hour re-feeding before sacrifice and liver harvest.

first: Enxiang

last: Zhang

first: Juan

middle: E

last: Abrahante


title: SDR9C7 catalyzes critical dehydrogenation of acylceramides for skin barrier formation

city: Tokyo

first: Tetsuya

last: Hirabayashi

address: 2-1-6 Kamikitazawa, Setagaya-ku

institute: Tokyo Metropolitan Institute of Medical Science

summary: SDR9C7 encodes an orphan short-chain dehydrogenase/reductase recently found mutated in ichthyosis. In a patient with SDR9C7 mutation and a mouse Sdr9c7 knockout model we show loss of covalent binding of epidermal ceramides to protein, a structural fault in the barrier.   For reasons unresolved, protein binding requires lipoxygenase-catalyzed transformations of linoleic acid (18:2) esterified in ω-O-acylceramides. In Sdr9c7-/- epidermis, quantitative LC-MS assays revealed almost complete loss of a species of ω-O-acylceramide esterified with linoleate-9,10-trans-epoxy-11E-13-ketone; other acylceramides related to the lipoxygenase pathway were in higher abundance. Recombinant SDR9C7 catalyzed NAD-dependent dehydrogenation of linoleate 9,10-trans-epoxy-11E-13-alcohol to the corresponding 13-ketone, while ichthyosis mutants were inactive. We propose, therefore, that the critical requirement for lipoxygenases and SDR9C7 is in producing acylceramide containing the 9,10-epoxy-11E-13-ketone, a reactive moiety known for its non-enzymatic coupling to protein. This suggests a novel mechanism for coupling of ceramide to protein and provides important insights into skin barrier formation and pathogenesis.

overall_design: We compared gene expression in Sdr9c7-/- (knockout) epidermis at P0 with Sdr9c7+/+ (wild type) controls. Individual array samples were generated by pooling equal amounts of total RNA derived from skins of 5 animals.

first: Yasumasa

last: Nishito

first: Takuya

last: Takeichi

first: Masashi

last: Akiyama


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Larp7 Knock-out Staged Male Germ Cells Transcriptomes

city: shanghai

first: Xin

last: Wang

state: shanghai

address: 320 Yue Yang Road, Shanghai 200031

institute: Shanghai Institute of Biochemistry and Cell Biology

summary: Analysis the difference in the transcriptomes (expression and alternative splicing) of either spermatocytes or round spermatids between Larp7 conditional knock-out and control mice

overall_design: Examination of mRNAs in spermatocytes and round spermatids isolated from Larp7 conditional knock-out and control mice.Two biological replicates of spermatocytes and round spermatids isolated from Larp7 conditional knock-out and control mice were analyzed.

first: Penghui

last: Lin


title: Nuclear exosome targeting complex core factor Zcchc8 regulates the degradation of LINE1 RNA in early embryos and embryonic stem cells

first: You

last: Wu

address: 1239 siping road

department: school of life science and technology

institute: tongji university

summary: The nuclear exosome targeting (NEXT) complex is responsible for recruiting RNA exosomes to degrade specific nuclear RNAs in mammalian cells. However, its function in mammalian development remains unknown. Here, we found that the depletion of a central factor of the NEXT complex, Zcchc8, resulted in mouse developmental defects, a shortened life span and infertility. Zcchc8-deficient embryonic stem cells (ESCs) exhibited proliferation abnormalities and reduced developmental potencies. Interestingly, we found that retrotransposon elements, especially LINE1 RNAs, are targeted and degraded by Zcchc8 in ESCs. We subsequently demonstrated that Zcchc8-depleted oocytes show defects in meiotic maturation and early embryo development. Moreover, the sustained expression of higher levels of LINE1 RNA was also detected in maternal Zcchc8-depleted oocytes and Zcchc8-deficient embryos, which can further increase chromatin accessibility. Collectively, our study uncovers the important role of Zcchc8 in the degradation of LINE1 transcripts in early embryos and ESCs at the posttranscriptional level.

overall_design: Nuclear RNA RIP seq of HA-Rbm7 and HA-Zcchc8 were done in ESCs using HA antibody, with 2 replicates for RIP and one for input. Small amount RNA seq of WT and Zcchc8 KO GV oocytes were done with 4 replicates respectively. Small amount RNA seq of WT and Zcchc8 knockdown embryos at 4 cell stage and blastocyst were done with 3 replicates for control and 2 replicates for knockdown embryos.Small amount RNA seq of WT and Zcchc8 knockout embryos at 4 cell stage and inner cell mass were done with 3-4 replicates for each sample. rRNA free total RNA seq were done for control, KO, overexpression of Zcchc8 in KO ESCs with 2 replicates each. Total RNA half-life test of control and Zcchc8 KO ESCs using Actinomycin D treatment, with 2 replicates each time point. ATAC-seq was done for WT and Zcchc8 KO ESCs with 2 replicates.

first: Yawei

last: Gao


title: Identify RNAs That are Bound by LARP7

summary: Anti-LARP7 RNA immunoprecipitation (RIP) coupled with RNA-seq  assays  showed significant enrichment of U6 snRNA, but not other 4 spliceosomal snRNAs, in LARP7 complexes in adult mouse testis.

overall_design: Examination of RNAs in LARP7 and IgG complexes from adult mouse testis.Two biological replicates of RIP-seq data were analyzed.


title: LSD1 mediates AKT activity in PIK3CA mutant colorectal cancer

status: Public on Nov 06 2019

city: Boston

first: Robert

last: Policastro

state: Massachusetts

address: 451 D St Unit #600

institute: Ensoma Inc.


title: RNA-seq of lipid droplet-low and lipid droplet-rich microglia isolated from the hippocampi of LPS-treated young mice

overall_design: 3-month old mice were given intraperitoneal injections of PBS or LPS (1 mg/kg BW) for four days. Mice were perfused 24 hours after the last LPS injection and hippocampi were dissected (Hippocampi of 2 mice were pooled per sample). Primary microglia were isolated by gentle dounce homogenization of the brain, Percoll-based myelin removal, and FACS-purification of ~10,000 live CD11b+CD45lo cells. BODIPYlo (=lipid droplet-low) and BODIPYhi (=lipid droplet-high) microglia were sorted into RLT Plus buffer (Qiagen) containing beta-mercaptoethanol. RNA was extracted using a RNeasy Micro Plus kit (Qiagen) according to the manufacturer’s protocol. RNA integrity was assessed on a Bioanalyzer (Agilent), and high quality samples (RIN >9) were used for library preparation. cDNA synthesis and amplification was performed using the SmartSeq v4 Ultra-low input kit (Takara), and libraries were tagmented, adaptor ligated, and indexed using the Nextera XT kit (Illumina). Sequencing of isolated microglia was carried out with Illumina Novogene 6000, paired end, 2x 100 bp. The quality of fastq files was assessed using FASTQC (v 0.11.4). Reads were mapped to mouse mm10 reference genome using STAR (v 2.5.3a). Raw read counts were generated with STAR using the GeneCounts function. Differential expression analysis was performed using DESeq2 with standard settings.


title: RNA sequencing of Sphk1fl/fl Sphk2-/-  and Sphk1-/- Sphk2-/- mESC clones.

first: Kelly

middle: Madigan

last: Banks

state: NY

address: 1300 York Ave, LC711

department: Surgery

institute: Weill Cornell Medicine

summary: We report a growth defect in sphingosine kinase null clones due to a cell cycle arrest in G2/M phase resulting in a growth defect. GSEA showed upregulation of the G2M checkpoint geneset. Further, telomere elongation factors are upregulated in kinase null cells.

overall_design: mESC clones derived from Sphk1fl/fl Sphk2-/-  mice were cultured in tamoxifen for 48 hours then sorted for Cre-GFP expression yielding GFP- Sphk1fl/fl Sphk2-/- cells and GFP+ Sphk1-/- Sphk2-/- (Kinase Null) cells. This was done for 2 separate clones resulting in 4 sample types: Clone 4 GFP-, Clone 4 GFP+, Clone 10 GFP- and Clone 10 GFP+.

first: Suveg

last: Pandey

first: Duancheng

last: Wen

first: Ritu

last: Kumar

first: Timothy

last: Hla

first: Todd

last: Evans