title: Human ZNF341 deficiency underlies a recessive form of hyper IgE syndrome by disrupting STAT3 transcription-dependent STAT3 activity

status: Public on Jun 04 2018

city: Doha

first: Tanwir

last: Habib

address: Al Luqta Street

country: Qatar

institute: Weill Cornell Medicine Qatar

summary: Heterozygosity for human STAT3 dominant-negative (DN) mutations underlies an autosomal dominant form of hyper-IgE syndrome (HIES). We describe patients with an autosomal recessive form of HIES due to loss-of-function mutations of a previously uncharacterized gene, ZNF341. ZNF341 is a transcription factor that resides in the nucleus, where it binds a specific DNA motif present in various genes, including, most notably the STAT3 promoter. The patients’ cells have low basal levels of STAT3 mRNA and protein. The auto-induction of STAT3 production, activation, and function by STAT3-activating cytokines is particularly strongly impaired. Like patients with STAT3 DN mutations, ZNF341-deficient patients lack Th17 cells, have an excess of Th2 cells, and low memory B cells, due to the tight dependence of STAT3 activity on ZNF341 in lymphocytes. Their milder extra-hematopoietic manifestations and stronger inflammatory responses reflect the lower ZNF341-dependence of STAT3 activity in other cell types. Human ZNF341 is essential for the STAT3 transcription-dependent auto-induction and sustained activity of STAT3.

overall_design: Total of 11 samples were analyzed from two micorarray platforms (Clariom S Human and HuGene2_0). Clariom S human array was used for 5 samples and HuGene was used for 6 T cell samples. Out of 5 samples from Clariom array, 3 were control samples with Beads with IL-6 stimulation, and 2 patients (P4 and P7) with Beads with IL-6 stimulation. Out of 6 samples from HuGene array, 4 were control samples and two patients (P4 and P7).

first: Vivien

last: Béziat

first: Juan

last: Li

first: Jian-Xin

last: Lin

first: Cindy

last: Ma

first: Peng

first: Aziz

last: Bousfiha

first: Isabelle

last: Pellier

first: Samaneh

last: Zoghi

first: Safa

last: Baris

first: Sevgi

last: Keles

first: Paul

last: Gray

first: Ning

last: Du

first: Yi

last: Wang

first: Yoann

last: Zerbib

first: Romain

last: Lévy

first: Thibaut

last: Leclercq

first: Frédégonde

last: About

first: Ai

middle: I

first: Geetha

last: Rao

first: Kathryn

last: Payne

first: Simon

last: Pelham

first: Danielle

middle: T

last: Avery

first: Elissa

middle: K

last: Deenick

first: Bethany

last: Pillay

first: Janet

last: Chou

last: Guery

last: Belkadi

first: Antoine

last: Guérin

first: Mélanie

last: Migaud

first: Vimel

last: Rattina

first: Fatima

last: Ailal

first: Ibtihal

last: Benhsaien

first: Mathieu

last: Bouaziz

first: Damien

last: Chaussabel

first: Nico

last: Marr

first: Jamel

last: Benna

first: Bodo

last: Grimbacher

first: Orli

last: Wargon

first: Jacinta

middle: C

last: Bustamante

first: Bertrand

last: Boisson

first: Ingrid

last: Müller-Fleckenstein

first: Bernhard

last: Fleckenstein

first: Marie-Olivia


title: Protein kinase A-mediated phosphorylation regulates STAT3 activation and oncogenic EZH2 activity

status: Public on Jun 05 2018

city: Bloomington

first: Kenneth

last: Nephew

state: IN

country: USA

institute: Indiana University

type: Expression profiling by high throughput sequencing

summary:
The effect of T372E-EZH2 and Wt-EZH2 overexpression on gene expression in TOV112D cells.
We found in this study that Protein Kinase A phosphorylates T372-EZH2 and wanted to determine the gene expression changes brought upon this phosphorylation. We made a point mutation (T372E) that mimicked phospho T372-EZH2. The objective was to observe transcriptional changes in TOV112D cells in response to ectopic expression of Wt-EZH2 and T372E-EZH2 point mutation in TOV112D cells.

overall_design: 8 total samples were analyzed 2 for vector control, 2 for Wt-EZH2, 2 for T372A, and 2 for T372E mutation.

first: Ali

middle: R

last: Ozes

first: Osman

first: Mustafa

middle: G

last: Ertosun

first: Ece

last: Copuroglu

first: Nick

last: Pulliam

first: Jessica

last: Tang

first: Daniela

last: Matei

first: Ozlem

last: Yilmaz


title: ChIP-Seq of H4K5acK8ac in GM12878, K562

city: TSURUMI WARD YOKOHAMA

first: Aki

last: Minoda

state: KANAGAWA

address: 230-0045, 1 CHOME-7-22 SUEHIROCHO

department: IMS

country: Japan

institute: RIKEN YOKOHAMA

type: Genome binding/occupancy profiling by high throughput sequencing

summary: From: "JQ1 affects BRD2-dependent and independent transcription regulation without disrupting H4-hyperacetylated chromatin states". The bromodomain and extra-terminal domain (BET) proteins are known as drug targets in diseases. However, the BET protein association profile to histone H4 hyperacetylation is not well understood and BET inhibition effects have been studied more in the context of BRD4 than BRD2. Here, by integrating chromatin and transcriptome analyses of ChIP-seq and Cap Analysis Gene Expression (CAGE) datasets, we show that di-acetylation at K5 and K8 of histone H4 (H4K5acK8ac) co-localizes with H3K27ac and BRD2 in the majority of active enhancers and promoters, where BRD2 has a stronger association with H4K5acK8ac than H3K27ac. Interestingly, although BET inhibition by JQ1 led to complete reduction of BRD2 binding, only local changes of H4K5acK8ac were observed and surprisingly a remarkable number of BRD2-bound genes including MYC and its target genes were upregulated. Using BRD2-enriched sites and transcriptional activity analysis, we identified candidate transcription factors (TFs) potentially involved in the JQ1 response in BRD2-dependent and independent manner.

overall_design: ChIP-Seq of H4K5acK8ac in GM12878, and  K562 cells

first: A

first: T

last: Umehara


title: Expression data from mouse spleens after experimental stroke (reanalysis of dataset GSE70841 with additional experimental)

status: Public on Jun 06 2018

city: Easter Bush Campus

first: Laura

last: McCulloch

state: Midlothian

address: The Roslin Institute

department: Neuropathology Division

country: United Kingdom

institute: The Roslin Institute, University of Edinburgh

summary:
Infection is a major complication and cause of mortality and morbidity after acute stroke however the mechanisms are poorly understood.    After experimental stroke the microarchitecture and cellular composition of the spleen are extensively disrupted resulting in deficits to immune function.
We used microarray to determine differentially expressed genes in the spleens of mice after experimental stroke to determine contributers to immunosuppression after stroke.

overall_design: We extracted RNA from spleens from mice 1d (n=3), 2d (n=3) and 5 d (n=4) after experimental stroke  and also from spleens from sham-operated control mice (n=2) for comparison.

first: Barry

middle: W

last: McColl


title: FGF2 induces migration of human bone marrow stromal cells by increasing core-fucosylations on N-glycans of integrins

city: Sacramento

first: Fernando

middle: A

last: Fierro

state: California

address: 2921 Stockton Blvd

department: Cell Biology and Human Anatomy

institute: UC Davis

summary:
RNAseq analysis of human bone marrow derived stromal cells (MSCs) treated for 24 hours with or wihout 10ng/ml Fibroblast Growth Factor 2 (FGF2)
MSCs were derived from 4 different healthy donors. Cells were expanded to passage 3-4. Then cells were treated with FGF-2. 24 hours later, total RNA was extracted (total 8 samples).

overall_design: RNA was submitted to BGI Americas for RNAseq. Here, QC was performed  using Agilent 2100. All samples had a RIN above 8.0. For preparation for library, mRNA was enriched by using the oligo (dT) magnetic beads. mRNA was enriched by using the oligo (dT) magnetic beads. mRNA was fragmented into short fragments (about 200bp) using a fragmentation buffer. Then the first strand of cDNA was synthesized by random hexamer-primer using the mRNA fragments as templates. Buffer, dNTSPs, RNase H and DNA polymerase I were added to synthesize the second strand. The double strand cDNA was purified with QiaQuick PCR extraction kit and washed with EB buffer for end repair and base A addition. Finally, sequencing adapters were ligated to the fragments. The fragments are purified by Agarose gel electrophoresis and enriched by PCR amplification. The library products are ready for sequencing analysis via 2 sE50 lanes in Illumina HiSeq™ 2000.


title: Pericyte-to-neuron reprogramming via unfolding of a neural stem cell-like program

city: Leipzig

first: Gray

last: Camp

address: Deutscher Pl. 6

department: Evolutionary Genetics

country: Germany

institute: Max Planck Institute for Evolutionary Anthropology

summary: Ectopic expression of defined transcription factors can force direct cell fate conversion from one lineage to another in the absence of cell division. Several transcription factor cocktails have enabled successful reprogramming of various somatic cell types into induced neurons (iNs) of distinct neurotransmitter phenotype. However, the nature of the intermediate states that drive the reprogramming trajectory towards distinct iN types is largely unknown. Here we show that successful direct reprogramming of adult human brain pericytes into functional iNs by Ascl1 and Sox2 (AS) encompasses transient activation of a neural stem cell-like gene expression program that precedes bifurcation into distinct neuronal lineages. Intriguingly, during this transient state key signaling components relevant for neural induction and neural stem cell maintenance are regulated and functionally contribute to iN reprogramming and maturation. Thus, AS-mediated reprogramming into a broad spectrum of iN types involves the unfolding of a developmental program via neural stem cell-like intermediates.

overall_design:
Single-cell transcriptomes from multiple time points and conditions during direct conversion of human pericytes into induced pericytes through the overexpression of defined factors.

Please note that [1] the *ctrl samples represent mock-transfected cells (analyzed along side of the transfected cells) [2] The cell type (for each sample) is provided as 'pericytes or pericyte-derived induced neuronal cells' (as they are in a differentiation continuum from pericytes to neurons due to the treatment protocol) with the combination of 'genotype/variation' and 'time point' information.

first: J

first: Barbara

last: Treutlein


title: Evaluation of the post-stroke transcriptome of the mouse cortex using genome-wide RNA-seq

city: Edison

first: Ashutosh

last: Dharap

state: NJ

address: 65 James st

department: Neuroscience

institute: HackensackMeridian Health JFK Medical Center

summary: RNA-sequencing was conducted to profile the transcriptome of the post-ischemic mouse cortex at multiple reperfusion time-points. RNA was isolated from sham and middle cerebral artery occlusion (MCAO)-operated mice at different reperfusion time points (6 h, 12 h or 24 h; three independent biological replicates per group), converted into cDNA libraries,  and used for Illumina deep sequencing on a NexSeq500 instrument. The sequencing reads that passed quality filters were analyzed at the transcript isoform level  based on the Tuxedo software package. On average 40.6 million reads were obtained from each sample and genome mapping was on average 82.9% for all samples. We detected 20,748 genes and 56,586 isoforms in the sham group; 22,192 genes and 60,023 isoforms in the 6 h group; 21,771 genes and 59,539 isoforms in the 12 h group; and 21,576 genes and 59,020 isoforms in the 24 h group. Our study represents the first detailed analysis of post-stroke mouse cortex transcriptomes generated using RNA-sequencing technology.

overall_design: Genome-wide transcriptomic profiles of healthy and post-ischemic mouse cortices at various reperfusion time-points (6 h, 12 h, or 24 h) were generated using Illumina sequencing.

first: Sunil

last: Bhattarai


title: Distinct macrophage populations upon physiological changes in adipose tissue [scRNA-seq]

city: Cincinnati

first: Hee-Woong

last: Lim

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

summary: We report that obese fat tissue of mice contain multiple distinct populations of adipose tissue macrophage (ATM) with unique transcriptomes and chromatin landscapes. Mouse Ly6c ATMs express genes that are adipogenic, while CD9 ATMs express pro-inflammatory genes under the control of activating transcription factors. Adoptive transfer of Ly6c ATMs into lean mice activates gene programs typical of normal adipocyte physiology. By contrast, adoptive transfer of CD9 ATMs drives gene expression that is characteristic of obesity.

overall_design: ATMs were sort-purified and subjected to single-cell RNA-seq.

first: David

last: Hill

first: Yong

middle: H

last: Kim

first: Wesley

middle: Y

last: Ho

first: Yee

last: Foong

first: Victoria

middle: L

last: Nelson

first: Hoang

last: Nguyen

first: Kavya

last: Chegireddy

first: Jihoon

first: Taku

last: Kambayashi

first: Kyoung-Jae

last: Won

first: Mitchell

last: Lazar


title: Early lineage segregation of multipotent embryonic mammary gland progenitors [RNA-seq I]

city: Bruxelles

first: Alexandra

last: Van Keymeulen

address: 808, route de Lennik CP602

department: IRIBHM

country: Belgium

institute: Université Libre de Bruxelles

summary: The mammary gland (MG) is composed of basal cells (BCs) and luminal cells (LCs). While it is generally believed that MG arises from embryonic multipotent progenitors (EMPs), it remains unclear when lineage restriction occurs and what are the mechanisms responsible for the switch from multipotency to unipotency during MG morphogenesis. Here, we performed multicolor lineage tracing and assessed the fate of single progenitors and demonstrated the existence of a developmental switch from multipotency to unipotency during embryonic MG development. Molecular profiling and single cell RNA-seq revealed that EMPs express a unique hybrid basal and luminal signature and the factors associated with the different lineages.  Sustained p63 expression in EMPs promotes unipotent BC fate and was sufficient to reprogram adult LCs into BCs by promoting an intermediate hybrid multipotent like state. Altogether, this study identifies the timing and the mechanisms mediating the early lineage segregation of multipotent progenitors during MG development.

overall_design: RNAsequencing of mouse mammary gland cells

first: Cédric

last: Blanpain

first: Audrey

last: Brisebarre


title: Early lineage segregation of multipotent embryonic mammary gland progenitors  [RNA-Seq II]

summary: We report single cell RNA-seq data that reveals that Embryonic Multipotent Progenitors (EMPs) in the mammary gland express a unique hybrid basal and luminal signature associated with the different adult lineages.

overall_design: scRNAseq of FACS sorted  Lgr5+ mouse mammary gland embryonal progenitors and basal and luminal adult lineages

first: Aline

last: Wuidart

first: Cedric

first: Thierrry

last: Voet

first: Alejandro

last: Sifrim


title: The influence of adolescent nicotine exposure on ethanol intake brain gene expression

status: Public on Jun 02 2018

city: State College

first: Aswathy

last: Sebastian

address: University Park

institute: PennState

summary:
Background: Nicotine and alcohol are often co-abused. Adolescence is a vulnerable period for the initiation of both nicotine and alcohol use, which can lead to subsequent neurodevelopmental and behavioral alterations.
Aim: The aim was to to determine the effect of nicotine exposure during adolescence on ethanol intake, and the effect of both substances on brain gene expression.
Methods: RNA was extracted from a randomly selected subset of mice (16 total; 4 samples from each experimental group). Whole brains (including cerebellum) were dissected. Total RNA was extracted with an RNeasy® Midi Kit (QIAGEN, Valencia, CA). RNA quality was assessed using an Agilent 2100 BioAnalyzer™. An Illumina TruSeq® Stranded mRNA Library Prep Kit (Illumina, San Diego, CA) was used for cDNA library preparation following the manufacturers’ protocol. Libraries were sequenced using an Illumina HiSeq 2500 (Illumina, San Diego, CA). Trimmomatic was used to remove sequencing adapters and low-quality ends. The cleaned dataset was analyzed with the Tuxedo pipeline. Subsequently, readings were mapped to the mouse reference genome (Ensembl GRCm38, mm10) using TopHat2 software (http://tophat.cbcb.umd.edu/). The ‘--library_type’ parameter was set to ‘fr-firststrand’. Default settings were preserved for all other TopHat2 parameters. The resulting alignments files from TopHat2 were used to generate a transcriptome assembly. Gene expression was calculated for each condition using the Cufflinks  and Cuffmerge utilities. Cuffdiff2 with default settings was used to identify transcripts that were differentially expressed between each treatment group compared to the water only control group.The significance threshold was set at q < 0.05 (FDR corrected). Finally, a Fisher’s exact test was performed using the GeneOverlap R package to test the significance of DEG overlaps. Gene co-expression networks were identified using the Weighted Gene Co-expression Network Analysis (WGCNA) package.
Results: RNA Integrity Number (RIN) was on average 8.23 ± 0.26 for all samples, suggesting high RNA integrity and quality. On average, 43 million, 150 base pair single end reads were generated for each sample and used in the analysis. The resulting alignments files from TopHat2 had an average mapping rate of 87.4%.

overall_design:
Nicotine Treatment: Mice were randomly assigned into four groups: Water-Water (WW), Water-Ethanol (WE), Nicotine-Water (NW), or Nicotine-Ethanol (NE). During the first six days of the experiment, mice were exposed to 3 glass drinking bottles filled with water or nicotine for 22 h a day, and a single water bottle for 2 h each day (Fig 1). For the WW and WE groups, all 3 bottles were filled with tap water. For the NW and NE groups, all 3 bottles were filled with 200 µg/ml (−)-nicotine freebase (Sigma–Aldrich, St. Louis, MO) dissolved in tap water. Bottles were placed on the cages at 1500 h and were removed and replaced with the single water bottle at 1300 h the next day. The three bottles were read and nicotine consumption (mg/kg) was calculated for each mouse. The 2 h single bottle was weighed and water consumption (ml) was calculated. Leakage/evaporation was accounted for by tubes on control cages handled using the same protocol, but with no animal present. We subtracted the volume lost in control tubes from individual drinking values. These procedures continued throughout the experiment. However, during the last 4 days (PND 42-45) mice were exposed to ethanol via the drinking-in-the-dark (DID) protocol.
Drinking-in-the-dark: During experimental days (7-10) nicotine exposure continued as detailed above (22 h/day), however, at 1300 h, all 3 bottles (nicotine or water) were removed and replaced with a single 10 ml serological pipette fitted with a ball bearing drinking spout containing either ethanol or water. Ethanol was prepared from ethyl alcohol (200 proof; Koptec 200) diluted in tap water to produce a 20% v/v solution. Mice had 2 h access to a single bottle of water or ethanol for three days (PND 42-44). On the final day (PND 45), mice had 4 h access to the ethanol bottle. Leakage/evaporation was accounted for by tubes on control cages as described above. At the end of the 4 h drinking session on the final day, blood samples were collected from the tail vein (10µl) and mice were sacrificed via cervical dislocation, whole brains including the cerebellum were dissected and placed into RNAlater® for subsequent RNA extraction.

first: Helen

middle: M

last: Kamens-Horton

first: Istvan

last: Albert

first: Constanza

middle: P

last: Silva

first: William

last: Horton

first: Michael

last: Caruso

first: Laura

last: Klein


title: Early lineage segregation of multipotent embryonic mammary gland progenitors

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

overall_design: Refer to individual Series


title: Time course analysis of gene expression during hypoxia in several S. cerevisiae mutant strains using RNA-Seq

status: Public on Jun 01 2018

city: Glassboro

first: Mark

last: Hickman

address: 201 Mullica Hill Road

department: Biological Sciences

institute: Rowan University

summary: We used RNA-seq to monitor mRNA levels of all genes in response to hypoxia in several mutant strains of the yeast, S. cerevisiae (S288C background with wildtype HAP1).  To gain insights into how gene expression changes over time, cells were subjected to 100% nitrogen gas and collected after 0,5,10,30,60,120,180, and 240 minutes.  Total RNA was extracted and mRNAs were enriched by polyA selection.  The cDNA was prepared into a sequencing library, multiplexed and single-end sequenced by an Illumina HiSeq 2500 sequencer.  After mapping with Tophat2, the number of reads per feature was calculated using HTSeq.

overall_design: RNA-seq analysis of eight time points of a yeast strain grown in hypoxia. The time course course is repeated in different mutant strains.

middle: J


title: Profiling of murine resident adipose tissue and aortic macrophages according to their expression status of LYVE-1

city: Singapore

first: Daniel

last: Carbajo

state: Singapore

address: 8A Biomedical Grove, Immunos Building levels 3 & 4

department: Bioinformatics

country: Singapore

institute: SIgN (A*STAR)

summary: Beside their role in conventional immune regulation, macrophages are now recognised as essential regulator of local tissue homeostasis depending on the tissue in which they reside. Using phenotyping, we found that LYVE-1+ macrophages are the major resident macrophage population in murine aorta and adipose tissues under steady state. Furthermore, imaging analysis revealed the exclusive association of adipose tissue LYVE-1+ macrophages with smooth muscle positive large blood vessels. Hence, we hypothesize that LYVE-1+ macrophages sustain large vessel functional homeostasis. The present experiment aims to better characterize resident LYVE-1+ vs LYVE-1- macrophages in aorta and adipose tissues.

overall_design: LYVE-1+ and LYVE-1- aortic macrophages were FACS sorted as DAPI-CD45+CD64+MerTK+CD11b+F4/80+LYVE-1+ and DAPI-CD45+CD64+MerTK+CD11b+F4/80+LYVE-1- respectively from 30 adult C57/BL6 mice (n =3) their RNA extracted for transcriptome profiling. Similarly, LYVE-1+ and LYVE-1- adipose tissue macrophages were FACS sorted as DAPI-CD45+CD64+MerTK+CD11b+F4/80+LYVE-1+ and DAPI-CD45+CD64+MerTK+CD11b+F4/80+LYVE-1- respectively from 20 adult C57/BL6 epididymal and subcutaneous adipose tissue (n =3) their RNA extracted for transcriptome profiling.

first: Lim

last: Ying

first: Josephine

last: Lum


title: RNA expression following TMPRSS11B overexpression or depletion

city: Dallas

first: Barrett

middle: Logan

last: Updegraff

state: TX

address: 5323 Harry Hines Blvd.

department: Molecular Biology

institute: Univ. of Texas Southwestern Medical Center at Dallas

summary: Purpose: We are analyzing differential gene expression in human bronchial epithelial cells with TMPRSS11B overexpression or control GFP, as well has human lung squamous cell cancer line HCC2814 with inducible knockdown of TMPRSS11B or control.

overall_design: Examination of total RNA expression in 4 cell lines.

first: Xiaorong

last: Zhou

first: Yabin

last: Guo

first: Pei-Hsuan

last: Chen

first: Chendong

last: Yang

first: Jessica

last: Sudderth

first: Carla

last: Rodriguez-Tirado

first: Luc

last: Girard

first: John

middle: D

last: Minna

first: Prashant

last: Mishra

first: Ralph

last: Deberardinis

first: Kathryn

last: O'Donnell


title: Comparing the Transcriptomes of Wild Type (WT) and Gdf9-Cre or Zp3-Cre mediated Mtor Oocyte-Conditional Knockout (referred to as MG and MZ, respectively) Mouse GV-stage fully-grown oocytes (FGO) by RNA-Seq Analysis

city: Nanjing

first: You-Qiang

last: Su

state: Jiangsu

address: 140 Hanzhong Road

department: State Key Laboratory of Reproductive Medicine

country: China

institute: Nanjing Medical University

summary: The goal of this study is to identify the differentially expressed genes in Gdf9-Cre and Zp3-Cre mediated Mtor oocyte-specific knockout (CKO) GV-stage fully-grown oocytes (FGO) by comparing their transcriptomes with that of the wild-type (WT) via RNA-Seq Analysis.

overall_design: Methods: mRNA profiles of 3 sets of GV-stage FGOs collected from the large antral follicles of 23-day old WT-, MG-, and MZ- CKO female mice were generated by deep sequencing using HiSeq X Ten platform with 150bp pair-end reads. All reads passed filter were trimmed to remove low-quality bases and adaptor sequences. Reads were then aligned to the mm10 reference genome using tophat2 (v2.0.13), and FPKMs were calculated and normalized using cufflinks (v2.2.1). The differentially expressed genes were calculated using default parameter of cuffdiff (v2.2.1). Hierarchical clustering was carried on log2(FPKM+1) across samples. Genes used for clustering were selected by maximum FPKM≥1 and with top 10% standard deviation of log2(FPKM+1).


title: In-Vivo Expansion of Cancer Stemness Affords Novel Cancer Stem Cell Targets: Malignant Rhabdoid Tumor as an Example

city: Ramat-Gan

first: Tomer

last: Kalisky

address: Faculty of Engineering

department: Bioengineering

country: Israel

institute: Bar-Ilan University

summary: Cancer stem cell (CSC) identification relies on transplantation assays of cell sub-populations sorted from fresh tumor samples. Herein, we attempt to bypass limitations of abundant tumor source and predetermined immune selection by in-vivo propagating patient derived xenografts (PDX) from human malignant rhabdoid tumor (MRT), a rare and lethal pediatric neoplasm, to an advanced state in which most cells behave as CSCs. Stemness is then probed by comparative transcriptomics of serial PDXs generating a gene signature of EMT, invasion/motility, metastasis and self-renewal, pinpointing putative MRT CSC markers. The relevance of these putative CSC molecules is analyzed by sorting tumorigenic fractions from early-passaged PDX according to one such molecule, deciphering expression in archived primary tumors and testing the effects of CSC molecule inhibition on MRT growth. Using this platform, we identify ALDH1 and lysyl oxidase (LOX) as relevant targets and provide a larger framework for target and drug discovery in rare pediatric cancers.

overall_design: Tumorigenic fractions from early-passaged PDX

first: Itamar

last: Kanter


title: CAGE profiling after treatment with JQ1 BET inhibitor in lung cancer cell line.

first: Aki

last: Minoda

summary: The bromodomain and extra-terminal domain (BET) proteins are promising drug targets for cancer and immune diseases. However, BET inhibition effects have been studied more in the context of bromodomain-containing protein 4 (BRD4) than BRD2, and the BET protein association to histone H4-hyperacetylated chromatin is not understood at the genome-wide level. Here, we report transcription start site (TSS)-resolution integrative analyses of ChIP-seq and transcriptome profiles in human non-small cell lung cancer (NSCLC) cell line H23. We show that di-acetylation at K5 and K8 of histone H4 (H4K5acK8ac) co-localizes with H3K27ac and BRD2 in the majority of active enhancers and promoters, where BRD2 has a stronger association with H4K5acK8ac than H3K27ac. Although BET inhibition by JQ1 led to complete reduction of BRD2 binding to chromatin, only local changes of H4K5acK8ac levels were observed, suggesting that recruitment of BRD2 does not influence global histone H4 hyperacetylation levels. This finding supports a model in which recruitment of BET proteins via histone H4 hyperacetylation is predominant over hyperacetylation of histone H4 by BET protein-associated acetyltransferases. In addition, we found a remarkable number of BRD2-bound genes, including MYC and its downstream target genes, were transcriptionally upregulated upon JQ1 treatment. Using BRD2-enriched sites and transcriptional activity analysis, we identified candidate transcription factors potentially involved in the JQ1 response in BRD2-dependent and independent manner.

overall_design:
Lung cancer cell line H23 was treated with JQ1 BET inhibitor.
Gene expression profiling by CAGE was performed after 0h, 3h, 6h, 12h and 24h.

first: A

first: T

last: Umehara


title: Next Generation Sequencing Facilitates Quantitative Analysis of ALDH+ E-BCSC, CD24-CD44+ M-BCSC and Bulk tumor cell Transcriptomes from MC1 and Vari068 PDX models of TNBC

city: Ann Arbor

first: Ming

last: Luo

state: MI

address: 2800 Plymouth Rd

department: Internal Medicine

institute: University of Michigan

summary: We report the application of single-molecule-based sequencing technology for high-throughput profiling of genes in E-, M-BCSCs and bulk tumor cells in two PDX models of triple negative breast cancer .

overall_design: Examination of global gene expression in  E and M-BCSCs and Bulk tumor cells in 2 PDXs. Total RNA was extracted from E- (H2Kd-ALDH+), M- (H2Kd-CD44+/CD24-) BCSC-enriched and bulk (H2Kd-ALDH-CD44-/CD24+) cell populations freshly sorted from dissociated tumor cells of Vari068 and MC1 PDXs. Total RNA was extracted with RNeasy Mini Kit (Qiagen) according to manufacturer's instructions, and 500 ng was then taken out from each of them and subjected to mRNA isolation using NEBNext Poly (A) mRNA Magnetic Isolation Module (NEB, Ipswich, MA, USA). The mRNA library was constructed using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, Ipswich, MA) according to the instruction manual, which includes sequential RNA fragmentation, reverse transcription using random primers, second strand cDNA synthesis, end repair, dA-tailing, adapter ligation, U excision, and PCR enrichment. mRNA libraries were sequenced on an Illumina HiSeq X Ten platform with 150bp pair-end reads. All reads passed filter were trimmed to remove low-quality bases and adaptor sequences. Reads were then aligned to the mm10 reference genome using tophat2 (v2.0.13), and FPKMs were calculated.

first: Max

last: Wicha


title: Mitochondrial Fission 1 (FIS1) knockdown effect on the transcriptome of primary human acute myeloid leukemia (AML) cells

city: Aurora

first: Shanshan

last: Pei

state: CO

institute: University of Colorado

summary: To explore the function of Mitochondrial Fission 1 (FIS1) in acute myeloid leukemia (AML), we used shRNA to knock down the expression of FIS1 in primary human AML cells and performed RNA-seq experiments to profile global gene expression changes upon FIS1 depletion.

overall_design: Expression of FIS1 is knocked down using two indepedent shRNA sequences in three independent primary human AML patient specimens. Total RNA is isolated and subjected to RNA-seq analysis.

first: Craig

last: Jordan


title: Thymic tuft cell single-cell mRNA analysis

status: Public on Jun 03 2018

city: Stanford

first: Aparna

middle: Rajiv

last: Rajpurkar

state: CA

address: 279 Campus Drive

department: Genetics

institute: Stanford University

summary: The goal of the study was to sequence mRNA from tuft cells (identified as CD11c-;CD45-;EpCAM+;IL-25+ using Flare25 reporter mice) in C57BL/6 and Aire-/- mice. The data were used to investigate thymic tuft cell heterogeneity with and without AIRE protein expression.

overall_design: Single cells prepared from pooled, digested, thymi were stained for flow cytometry and individual cells were sorted into wells of a 96 well plate containg 5 ul of lysis buffer. As controls, several wells were left blank (0 cells) or 100 cells were sorted.

first: Corey

middle: N

last: Miller

first: Kristen

last: Wells

first: Lars

last: Steinmetz

first: Mark

middle: S

last: Anderson


title: Mitochondrial Fission 1 (FIS1) knockdown effect on the H3K27Ac status of leukemia cell line MOLM-13 cells

summary: To examine if loss of FIS1 would alter the H3K27Ac status of leukemic cells, we used shRNA to knock down the expression of FIS1 in leukemic cell line MOLM-13 cells and performed H3K27Ac CHIP-seq to characterize any changes in the H3K27Ac marks upon loss of FIS1.

overall_design: Expressin of FIS1 is knocked down by shRNA in leukemic cell line MOLM-13 cells, technical triplicates are performed. Control and knock-down cells are harvested and subjected to H3K27Ac CHIP-seq analysis.

middle: T

first: Stephen

last: Mack

first: Sisi

last: Lai

first: Jeremy

last: Rich


title: Distinct macrophage populations upon physiological changes in adipose tissue [ATAC-seq]

first: Hee-Woong

last: Lim

overall_design: ATM populations were sort-purified from murine obese eWAT and subjected to ATAC-seq analysis.

first: David

last: Hill

first: Yong

last: Kim

first: Wesley

last: Ho

first: Yee

last: Foong

first: Victoria

last: Nelson

first: Hoang

middle: C

last: Nguyen

first: Kavya

last: Chegireddy

first: Jihoon

first: Taku

last: Kambayashi

first: Kyoung-Jae

last: Won

first: Mitchell

last: Lazar


title: ChIP-Seq of H4K5acK8ac and BRD2 in H23 NSCLC cell line treated with 500 nM JQ1 for 24h

first: Aki

last: Minoda

summary: Changes in acetylation of histone H4 are a common hallmark of cancer cells. In leukemia cells, histone H4 is characterized by loss of K16 mono-acetylation. Bromodomain proteins specifically recognize acetylated lysines and have been used as a target for anti cancer drug, JQ1 and iBET. Although acetylation and de-acetylation of histone H4 have been shown to have big impact in cancer cells, little attention has been focused on histone H4-acetylation at a genome level. To uncover potential epigenetic role of hyper-acetylated histone H4 at a genome-wide level in cancer cell, we generated a novel monoclonal antibody specifically recognizing histone H4 with at least two acetylated lysine residues (H4K5ac+K8ac).  At the genome-wide level, hyper-acetylated histone H4 is associated with promoter and regulatory element (active enhancer, eRNA and super enhancer). We show that diacetylation at K5 and K8 of histone H4 co-localizes H3K27ac and BRD2 in the majority of active enhancer and promoters. However BRD2 has a stronger association with H4K5acK8ac. Furthermore we identified two specific chromatin states, which separately contain either H3K27ac or acetylated histone H4.  Although JQ1 led to global reduction of BRD2 binding on the chromatin, only local changes of histone H4 multi-acetylation were observed upon BET inhibition by JQ1


title: Oncogenic properties of NEAT1 in prostate cancer cells depend on the CDC5L-AGRN transcriptional regulation circuit

city: Beijing

first: Xuerui

last: Yang

address: Haidian District

department: School of Life Sciences

institute: Tsinghua University

summary: Silencing NEAT1 in prostate cancer cells repressed the transcriptional activity of CDC5L, and RNA-seq and  further analyses revealed a handful of potential targets of CDC5L regulated by NEAT1 expression. We have established the requirement of the CDC5L-AGRN circuit for the essential oncogenic role of NEAT1 in prostate cancer cells. Here we provide processed raw counts files.

overall_design: siNEAT1 and control(siNC) experiments with 2 replicates respectively.

first: Xin

last: Li

first: Zhengtao

last: Xiao

first: Rongyao

last: Huang


title: RNA-seq from HNSCC and melanoma populations

first: Andrew

last: Gentles

address: 1201 Welch Road

summary: Populations were sorted from tumor speciments via flow cytometry using EPCAM, FAP, CD45, and CD31 surface markers

overall_design: RNA-seq profiling from sorted populations from head and neck squamous carcinomas and melanomas


title: A Muscle-Specific Enhancer RNA Mediates Cohesin Recruitment and Regulates Transcription in Trans

city: Bethsda

first: Vittorio

last: Sartorelli

state: MD

address: 50 South Dr.

department: NIAMS

institute: NIH

summary: The enhancer regions of the myogenic master regulator MyoD give rise to at least two enhancer RNAs. CEeRNA regulates transcription of the adjacent MyoD gene while DRReRNA affects expression of Myogenin in trans. We found that DRReRNA is recruited at the Myogenin locus where it colocalizes with Myogenin nascent transcripts. DRReRNA associates with the Cohesin complex and such association correlates with its transactivating properties. Despite being expressed in undifferentiated cells, Cohesin is not loaded on Myogenin until the cells start expressing DRReRNA, which is then required for Cohesin chromatin recruitment and maintenance. Functionally, depletion of either Cohesin or DRReRNA reduces chromatin accessibility, prevents Myogenin activation, and hinders muscle cell differentiation. Thus, DRReRNA ensures spatially appropriate Cohesin loading in trans to regulate gene expression.

overall_design: Examination of genome-wide distribution of DRReRNA, SMC3 and chromatin accessibility in mouse C2C12 myoblast cells.

first: Pei-Fang

last: Tsai

first: Stefania

last: Dell’Orso

first: Joseph

last: Rodriguez

first: Karinna

middle: O

last: Vivanco

first: Kyung-Dae

last: Ko

first: Kan

last: Jiang

first: Aster

last: Juan

first: Aishe

last: Sarshad

first: Laura

last: Vian

first: Michelle

last: Tran

first: Dara

last: Wang

first: A

first: Jelena

last: Perovanovic

first: Dimitros

last: Anastasakis

first: Evelyn

last: Ralston

first: Thomas

last: Ried

first: Hong-Wei

last: Sun

first: Markus

last: Hafner

first: Daniel

middle: R

last: Larson


title: Efficient and precise editing of endogenous transcripts with SNAP-tagged ADARs

city: STANFORD

first: Jin

middle: Billy

last: Li

address: 300 Pasteur Dr.

summary: Molecular tools to target RNA site‐specifically allow recoding of RNA information and processing. SNAP‐tagged deaminases, guided by a chemically stabilized guideRNA, enable the simultaneous editing of targeted adenosine to inosine in several endogenous transcripts, with high efficiency (up to 90%), high potency, sufficient duration, and high precision. We applied SNAP‐ADARs for the efficient and concurrent editing of two disease‐relevant signaling transcripts, KRAS and STAT1. We also show improved performance compared to the recently described Cas13b-ADAR.

overall_design: Identification of off-target editing events in SNAP-ADAR cell lines by RNA-Seq, 7 samples, 2 biologically independent experiments

first: Paul

last: Vogel

first: Matin

last: Moschref

first: Qin

first: Tobias

last: Merkle

first: Karthika

last: Selvasaravanan

middle: B

first: Thorsten

last: Stafforst


title: Inhibition of microRNA-138 enhances bone formation in multiple myeloma bone marrow niche

city: Boston

first: Irene

last: Ghobrial

state: MA

address: 4 Blackfan Circle, 2nd Floor, Suite 240

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: Myeloma bone disease is a devastating complication of multiple myeloma (MM) and is caused by dysregulation of bone remodeling processes in the bone marrow microenvironment. Previous studies showed that microRNA-138 (miR-138) is a negative regulator of osteogenic differentiation of mesenchymal stromal cells (MSCs) and that inhibiting its function enhances bone formation in vitro. In this study, we explored the role of miR-138 in myeloma bone disease and evaluated the potential of systemically delivered locked nucleic acid (LNA)-modified anti-miR-138 oligonucleotides in suppressing myeloma bone disease. We showed that expression of miR-138 was significantly increased in MSCs from MM patients (MM-MSCs) and myeloma cells compared to those from healthy subjects. Furthermore, inhibition of miR-138 resulted in enhanced osteogenic differentiation of MM-MSCs in vitro and increased number of endosteal osteoblastic lineage cells (OBCs) and bone formation rate in mouse models of myeloma bone disease. RNA sequencing of the OBCs identified TRPS1 and SULF2 as potential miR-138 targets that were de-repressed in anti-miR-138 treated mice. In summary, these data indicate that inhibition of miR-138 enhances bone formation in MM and that pharmacological inhibition of miR-138 could represent a new therapeutic strategy for treatment of myeloma bone disease.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNA sequencing of endosteal osteoblastic lineage cells (OBCs) from 4 C57BL/KaLwRij (KaLwRij) mice treated with anti-miR-138 LNA-modified antisense oligonucleotide and 4 KaLwRij mice treated with scramble control and RNA sequencing of primary human BM–derived MSCs obtained from normal healthy donors (ND-MSCs) co-cultured with myeloma cells (OPM2) and treated with anti-miR-138 LNA-modified antisense oligonucleotide (N=3) or scramble control (N=3)

first: Shokichi

last: Tsukamoto

first: Marianne

last: Løvendorf

first: Sakari

last: Kauppinen


title: Blocking IFNRA1 inhibits Multiple Myeloma-driven regulatory T-cell expansion and immunosuppression

summary: Despite significant advances in the treatment of multiple myeloma (MM), most patients succumb to disease progression. One of the major immunosuppressive mechanisms that is believed to play a role in myeloma progression, is the expansion of regulatory T-cells (Tregs). In this study, we demonstrate that myeloma cells drive Treg expansion and activation by secreting type-1 interferon (IFN). Blocking IFNAR1 (interferon alpha and beta receptor 1) on Tregs significantly decreases both, myeloma-associated Treg immunosupporessive function and myeloma progression. Using syngeneic transplantable murine myeloma models and bone marrow (BM) aspirates of multiple myeloma patients, we found that Tregs were expanded and activated in the BM microenvironment at early stages of myeloma development. Selective depletion of Tregs led to a complete remission and prolonged survival in mice injected with myeloma cells. Further analysis of the interaction between myeloma cells and Tregs using gene sequencing and enrichment analysis uncovered a feedback loop, wherein myeloma-cell-secreted type-1 IFN induced proliferation and expansion of Tregs. By using IFNAR1-blocking antibody treatment and IFNAR1 knockout Tregs, we demonstrated a significant decrease in myeloma-associated Treg proliferation, which was associated with longer survival of myeloma-injected mice. Our results thus suggest that blocking type-1 IFN signaling represents a potential strategy to target immunosuppressive Trage function in MM.

overall_design: RNA sequencing of 3 BM of Vk*MYC-injected and 3 BM of control mice

first: Yawara

last: Kawano

first: Oksana

last: Zavidij


title: Gene expression analysis of a human thymic cell line model of AIRE molecular function

city: Sheffield

first: Thomas

middle: Richard

last: Lovewell

address: Beech Hill

department: Infection and Immunity

institute: University of Sheffield

summary:
Microarray analysis of AIRE regulated gene expression has been performed extensively in studies using the thymi of different mouse strains, but to date, has only been rarely performed using human model systems, and critically, not yet with a human thymic model.  We have generated a Flp-In host cell line variant of the TEC 1A3 human thymic epithelial cell line and subsequently used site-specific recombination to generate a variant that stably expresses recombinant AIRE.  We used microarray analysis to determine the transcription expression profiles of these two variants and determine the repertoire of AIRE regulated gene expression in a human thymic model system.
The aim of the present study is to use microarray analysis to identify the repertoire of AIRE regulated genes within a human model system, and to validate this model as an appropriate human model system for the study of the molecular function of AIRE

overall_design: Site-specific recombination was used to generate a recombinant AIRE expression variant of the TEC 1A3 human thymic epithelial cell line. The transcription expression profile was determined for both the cell line prior to this modification, and the recombinant AIRE expression variant cell line.

first: Rachid

last: Tazi-Ahnini


title: Mitochondrial Fission 1 (FIS1) knockdown effect on the transcriptome of leukemia cell line MOLM-13 cells

first: Shanshan

last: Pei

summary: To explore the function of Mitochondrial Fission 1 (FIS1) in acute myeloid leukemia (AML), we used shRNA to knock down the expression of FIS1 in leukemia cell line MOLM-13 cells and performed RNA-seq experiments to profile transcriptional changes upon FIS1 depletion.

overall_design: Expression of FIS1 is knocked down using two indepedent shRNA sequences in leukemia cell line MOLM-13 cells. Technical triplicates are performed. Total RNA is isolated and subjected to RNA-seq analysis.

first: Craig

last: Jordan


title: Predicting Neuroblastoma Using Developmental Signals and a Logic-Based Model

status: Public on May 31 2018

city: Kansas City

first: Madelaine

last: Gogol

state: MO

address: 1000 E. 50th Street

department: Computational Biology Core

institute: Stowers Institute

summary: Genomic information from human patient samples of pediatric neuroblastoma cancers and known outcomes have led to specific gene lists put forward as high risk for disease progression. However, the reliance on gene expression correlations rather than mechanistic insight has shown limited potential and suggests a critical need for molecular network models that better predict neuroblastoma progression. In this study, we construct and simulate a molecular network of developmental genes and downstream signals in a 6-gene input logic model that predicts a favorable/unfavorable outcome based on the outcome of the four cell states including cell differentiation, proliferation, apoptosis, and angiogenesis. We simulate the mis-expression of the tyrosine receptor kinases, trkA and trkB, two prognostic indicators of neuroblastoma, and find differences in the number and probability distribution of steady state outcomes. We validate the mechanistic model assumptions using RNAseq of the SHSY5Y human neuroblastoma cell line to define the input states and confirm the predicted outcome with antibody staining. Lastly, we apply input gene signatures from 77 published human patient samples and show that our model makes more accurate disease outcome predictions for early stage disease than any current neuroblastoma gene list. These findings highlight the predictive strength of a logic-based model based on developmental genes and offer a better understanding of the molecular network interactions during neuroblastoma disease progression.

overall_design: The human SHSY5Y neuroblastoma cell line was obtained from ATCC (CRL-2266) and maintained in 1:1 mixture of Eagles’s Minimum Essential Medium (ATCC, 30-2003) supplemented with 10% FBS (VWR, 97068-085). Cells were plated in 8-well chamber slides (ThermoFisher, 177402) for Immunohistochemistry. All cultures were determined to be free of mycoplasma contamination using a polymerase chain reaction-based detection system (Roche, 0518424001). Total RNA was isolated from three, separate T25 flasks of adherent SHSY5Y cells at approximately 60% confluency using Sigma’s GenElute mammalian Total RNA miniprep kit (Millipore Sigma, RTN70) per the manufacturer’s recommendations. Total RNA was quantified on an Agilent Bioanalyzer 2100 using a Eukaryote Total RNA Nano chip (Agilent, 5067-1511) as well as a Nanodrop spectrophotometer (ThermoFisher Scientific, ND-1000). Libraries were made from 500ng of total RNA according to the manufacturer’s directions for the TruSeq Stranded mRNA LT– set A and B (Illumina,  Cat. No. RS-122-2101 and RS-122-2102) kit. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer High Sensitivity DNA assay (Agilent; 5067-4626) and Qubit Fluorometer (Life Technologies). Libraries were pooled, re-quantified and sequenced as 50 base pair, single reads on the Illumina HiSeq 2500 instrument to a depth of at least 20 million reads per sample using HiSeq Control Software 2.2.58.

first: Jennifer

last: Kasemeier-Kulesa

last: Kulesa


title: Transcriptome sequencing of differentially expressed genes in mouse and human skin with and without NCSTN mutation

first: Yanyan

last: He

address: Jiangwangmiao Street

department: Institute of Dermatology

institute: hinese Academy of Medical Sciences and Peking Union Medical College

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

overall_design: Refer to individual Series


title: Transcriptome sequencing of differentially expressed genes in acne inversa (AI) patients with NCSTN mutation and healthy individuals

summary: To elucidate the relationship between NCSTN mutations and familial AI pathogenesis by investigating differential gene expression, we have employed transcriptome sequencing profiling as a discovery platform to identify genes with the potential to be involved in familial AI pathogenesis. Skin biopsies were obtained from the lesions of AI patients with NCSTN mutations . Control skin tissues were obtained from healthy individuals undergoing cosmetic surgery procedures

overall_design: Two groups, AI patients with NCSTN mutations vs. healthy individuals. Each group contains 4 samples.


title: Effect of nuclear IL-33 on gene expression

city: Cincinnati

first: Mark

last: Rochman

state: OH

address: 3333 Burnett Ave

department: Allergy and Immunology

institute: CCHMC

summary: The aim of this study was to examine the transcriptional regulatory activity of nuclear IL-33 independent of its well-described extracellular cytokine activity mediated by its receptor, ST2.

overall_design: Single-cell clones of Human TE-7 esophageal epithelial cells, which lack expression of the ST2 receptor, and with lentiviral-mediated, Dox-inducible overexpression of full-length IL-33, a non-chromatin binding form of IL-33 (amino acids 112-270), or empty vector (pINDUCER20) were treated with 100 ng/mL of doxycycline (Clontech) or control media for 48 hours. Expression of wild-type and truncated IL-33 was verified by Western blot. RNA was isolated using Tripure reagent and subjected to genome-wide RNA-sequencing through the Cincinnati Children’s Hospital Medical Center Gene Expression Core.

first: Jared

last: Travers

first: Marc

middle: E

last: Rothenberg


title: Transcriptional profile from peripheral blood in patients infected with avian influenza H7N9 virus

city: La Jolla

first: Nicholas

last: Wu

address: Beckman Build, BCC206, 10650 North Torrey Pines Road

institute: The Scripps Research Institute

summary: Avian influenza A (H7N9) viruses have emerged in China in 2013 and caused zoonotic disease associated with a case-fatality ratio of over 30%. Transcriptional profile from peripheral blood has been shown to reflect host responses against a specific respiratory pathogen and can be used to understand the disease. Methods: We correlated the clinical data and blood transcriptomic profile of patients with avian influenza A (H7N9) disease and determined the biological significance of the infection from the analysis.

overall_design: Eight patients diagnosed with laboratory-confirmed avian influenza A (H7N9) virus infection at the First Affiliated Hospital of Guangzhou Medical University from 2014 to 2016 were included in this study. The peripheral whole blood samples was collected at multiple time-points for each patient post-infection.

first: Wenda

last: Guan

first: Horace

middle: Y

last: Lee

first: Yimin

last: Li

first: Wenxin

last: Jiang

first: Lihan

last: Shen

first: Douglas

first: Rongchang

last: Chen

first: Nanshan

last: Zhong

first: Ian

middle: A

last: Wilson

first: Malik

last: Peiris

first: Zifeng

last: Yang

first: Chris

last: Mok


title: Protein Kinase AMP-Activated Catalytic Subunit Alpha 1 (PRKAA1) knockdown effect on the transcriptome of primary human acute myeloid leukemia (AML) cells

first: Shanshan

last: Pei

summary: To explore the function of AMPK signaling in acute myeloid leukemia (AML), we used shRNA to knock down the expression of PRKAA1, the catalytic subunit of the 5'-prime-AMP-activated protein kinase (AMPK), in primary human AML cells and performed RNA-seq experiment to profile transcriptional changes upon AMPK inactivation.

overall_design: Expression of PRKAA1 is knocked down in three independent primary human AML patient specimens. Total RNA is isolated and subjected to RNA-seq analysis.

first: Mohammad

last: Minhajuddin

first: Craig

last: Jordan


title: Differences in molecular expression in cases of non-viable ectopic and intrauterine pregnancies

city: Reno

first: Nicole

last: Ortogero

state: Nevada

address: 1664 N. Virginia St

department: Physiology and Cell Biology

institute: University of Nevada, Reno

summary:
Ectopic pregnancy is the leading cause of morbidity and mortality among women in the first trimester. A reliable diagnostic test for the detection of ectopic pregnancy in cases of non-viable pregnancy of unknown location (NV-PUL) is needed.  The objective of the current study is to define differences in molecular expression profiles in ectopic and abnormal intrauterine pregnancies toward discovery of biologically plausible ectopic classifier candidate. These samples come from a prospective cohort study comparing transcriptome profiles from women with ectopic pregnancy (ECT) or non-viable intrauterine pregnancy (NV-IUP). Samples were analyzed with the Affymetrix Human Gene 2.0 ST Array.
The views expressed are those of the author(s) and do not reflect the official policy of the Department of the Army, the Department of Defense or the U.S. Government.
The investigators have adhered to the policies for protection of human subjects as prescribed in 45 CFR 46.

overall_design: 17 endometrial biopsies taken from women with non-viable intrauterine (n=9) and ectopic (n=8) pregnancies

first: Jessica

last: Lentscher

first: Laurel

last: Gillette

first: Richard

last: Burney

first: Gregory

last: Chow


title: Multi-axial self-organisation properties of mouse embryonic stem cells into gastruloids [E6.5 to E9.5]

city: Geneva

first: Leonardo

last: Beccari

address: 30 Quai Ernest Ansermet

department: Genetics and Evolution

country: Switzerland

institute: University of Geneva

summary: Gastruloids are small aggregates of murine Embryonic Stem (ES) cells stimulated to undergo gastrulation-like symmetry breaking events in vitro (van den Brink, S. C. et al. 2014, Simunovic, M. & Brivanlou, A. H 2017). We analyzed the transcriptomic profiles of gastruloids at different time-points after aggregation (AA) and compared them with those of mouse embryo at different stages, raging from e6 to e9.5. We show that gastruloids are capable of organizing a post-occipital pattern of neural, mesodermal and endodermal derivatives that mimics that of the embryo in terms of gene expression.

overall_design: RNA-seq analysis of wild type ouse embryos at different developmental stages ranging from E6.5 to E9.5

first: L

first: N

last: Moris


title: Single-cell RNA-seq analysis of human tumor ascites dendritic cells and macrophages

status: Public on May 30 2018

city: Paris

first: Paul

last: Gueguen

address: 26 rue D'Ulm

department: Inserm U932

country: France

institute: Institut Curie

summary: We performed single-cell RNA-seq on dendritic cells and macrophages isolated from the tumor ascites of one cancer patient. We used the 10x chromium technology. The expression matrix provided in supplementary is the result Cellranger aggregate method on : GSE115007, GSE115006 and GSE103544.

overall_design: Ascites phagocytes were prepared by centrifugation on a Ficoll gradient. Dendritic cells and macrophages were enriched by negative selection using magnetic beads. Cell populations were further isolated by cell sorting. Cellular suspensions (3500 cells) were loaded on a 10X Chromium instrument (10X Genomics) according to manufacturer’s protocol.

first: Elodie

last: Segura

first: Tsing-Lee

last: Tang-Huau

first: Mylène

last: Bohec

first: Christel

last: Goudot


title: Transcriptomes and methylomes from naïve CD4+ T-cells from infants and children with and without food allergy

city: NEDLANDS

first: David

last: Martino

state: Western Australia

address: Perth Childrens Hospital, 15 Hospital Avenue

country: Australia

institute: Telethon Kids Institute


title: A central extended amygdala circuit that modulates anxiety

city: Cold Spring Harbor

last: Tollkuhn

address: 1 Bungtown Rd

institute: Cold Spring Harbor Laboratory

summary: Both the amygdala and the bed nucleus of the stria terminalis (BNST) have been implicated in maladaptive anxiety characteristic of anxiety disorders. However, the underlying circuit and cellular mechanisms have remained elusive. Here we show that mice with Erbb4 gene deficiency in somatostatin-expressing (SOM+) neurons exhibit heightened anxiety as measured in the elevated plus maze test and the open field test, two assays commonly used to assess anxiety-related behaviors in rodents. Using a combination of electrophysiological, molecular, genetic and pharmacological techniques we demonstrate that the abnormal anxiety in the mutant mice is caused by enhanced excitatory synaptic inputs onto SOM+ neurons in the central amygdala (CeA), and the resulting reduction in inhibition onto downstream SOM+ neurons in the BNST. Notably, our results indicate that an increase in dynorphin signaling in SOM+ CeA neurons mediates the paradoxical reduction in inhibition onto SOM+ BNST neurons, and that the consequent enhanced activity of SOM+ BNST neurons is both necessary for and sufficient to drive the elevated anxiety. Finally, we show that the elevated anxiety and the associated synaptic dysfunctions and increased dynorphin signaling in the CeA-BNST circuit of the Erbb4 mutant mice can be recapitulated by stress in wild-type mice. Together, our results unravel previously unknown circuit and cellular processes in the central extended amygdala that can cause maladaptive anxiety.

overall_design: Analysis of differential expression between 10 IP (SOM+ neurons) & 4 input replicates from CeL tissue in 8-12 pooled mice for each replicate

first: Bo

last: Li


title: Single cell transcriptomic analysis (InDrops) of mouse FoxP3+ regulatory CD4+ T cells isolated from spleen and muscle after injury

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

overall_design: Single cells were sorted by flow cytometry for single cell RNAseq library preparation (InDrops)

last: Zemmour

first: Christophe

last: Benoist


title: A recessive form of hyper-IgE syndrome by disruption of ZNF341-dependent STAT3 transcription and activity

city: Bethesda

first: Peng

address: 9000 Rockville Pike

department: NHLBI

summary: Heterozygosity for human STAT3 dominant-negative (DN) mutations underlies an autosomal dominant form of hyper-IgE syndrome (HIES). We describe patients with an autosomal recessive form of HIES due to loss-of-function mutations of a previously uncharacterized gene, ZNF341. ZNF341 is a transcription factor that resides in the nucleus, where it binds a specific DNA motif present in various genes, including, most notably the STAT3 promoter. The patients’ cells have low basal levels of STAT3 mRNA and protein. The auto-induction of STAT3 production, activation, and function by STAT3-activating cytokines is particularly strongly impaired. Like patients with STAT3 DN mutations, ZNF341-deficient patients lack Th17 cells, have an excess of Th2 cells, and low memory B cells, due to the tight dependence of STAT3 activity on ZNF341 in lymphocytes. Their milder extra-hematopoietic manifestations and stronger inflammatory responses reflect the lower ZNF341-dependence of STAT3 activity in other cell types. Human ZNF341 is essential for the STAT3 transcription-dependent auto-induction and sustained activity of STAT3.

overall_design: RNA-Seq and ChIP-Seq analyses using freshly isolated CD3+ T cells or EBV-B cells transduced with ZNF341 WT isoform 1 (NM_001282933) or 2 (NM_032819) or an empty vector (EV) from the same patient (P4).

first: Vivien

last: Beziat

first: Juan

first: Jian-Xin

last: Lin

first: Cindy

last: Ma

first: Aziz

last: Bousfiha

first: Isabelle

last: Pellier

first: Samaneh

last: Zoghi

first: Safa

last: Baris

first: Sevgi

last: Keles

last: Gray

first: Ning

last: Du

first: Yi

last: Yang

first: Yoann

last: Zerbib

first: Romain

last: Levy

first: Thibaut

last: Leclercq

first: Fredegonde

last: About

first: Ai-Ing

last: Lim

first: Geetha

last: Rao

first: Kathryn

last: Payne

first: Simon

last: Pelham

first: Danielle

last: Avery

first: Elissa

middle: K

last: Deenick

first: Bethany

last: Pillay

first: Janet

last: Chou

last: Guery

last: Belkadi

first: Antoine

last: Guerin

first: Melanie

last: Migaud

first: Vimel

last: Rattina

first: Fatima

last: Ailal

first: Ibtihal

last: Benhsaien

first: Mathieu

last: Bouaziz

first: Habib

last: Tanwir

first: Damien

last: Chaussabel

first: Nico

last: Marr

first: Jamel

last: El Benna

first: Bomo

last: Grimbacher

first: Orli

last: Wargon

first: Jacinta

last: Bustamante

first: Bertran

last: Boisson

first: Ingrid

last: Muller-Fleckenstein

first: Bernhard

last: Fleckenstein


title: Single-cell RNA-seq analysis of human tonsil dendritic cells

first: Paul

last: Gueguen

summary: We performed single-cell RNA-seq on dendritic cells isolated from the tonsils of one healthy donor. We used the 10x chromium technology.The expression matrix provided in supplementary is the result of Cellranger aggregate method on : GSE115007, GSE115006 and GSE103544.

overall_design: Tonsil phagocytes were prepared by centrifugation on a Ficoll gradient. Dendritic cells were enriched by negative selection using magnetic beads. Cell populations were further isolated by cell sorting. Cellular suspensions (3500 cells) were loaded on a 10X Chromium instrument (10X Genomics) according to manufacturer’s protocol.

first: Elodie

last: Segura

first: Mélanie

last: Durand

first: Mylène

last: Bohec


title: PTHrP overexpression in MCF7 cells

city: Nashville

first: Rachelle

last: Johnson

address: 2215B Garland Ave

institute: Vanderbilt University Medical Center

summary: A PTHrP construct expressing full-length secreted PTHrP (-36-139aa) was stably expressed in MCF7 cells. The goal of the study was to determine the gene targets of PTHrP in human MCF7 breast cancer cells.

overall_design: There are three biological replicates of the control MCF7 cells containing a pcDNA construct, and three biological replicates of the MCF7 cells expressing the PTHrP construct. Each biological replicate was collected from independent experiments.

middle: W


title: RNA-seq of strains grown under the control of  native galactose regulon or synthetic xylose regulon vs constitutive expression of galactose and xylose metabolic genes

city: Medford

first: Nikhil

middle: Unni

last: Nair

state: Massachusetts

address: 4 Colby St, STC 276

department: Chemical & Biological Engineering

institute: Tufts University

summary: In this study, we first assess the role of the GAL regulon in enabling efficient galactose utilization for cell growth by decoupling its regulatory responses from sugar catabolism. We provide evidence that regulon-controlled galactose assimilation is more efficient than constitutive expression of the catabolic genes in supporting fast growth rates to higher cell densities. Next, we assessed whether a regulon could enable more complete and efficient utilization of a nutrient that is non-native to this yeast – xylose. We first adapt the GAL regulon to respond to xylose through directed evolution of Gal3p, enabling coupling of nutrient stimulus with sensing, computation, and regulatory actuation. Next, by using a rational, model-guided approach, we test two different positive feedback signal transduction loop designs for the regulon and demonstrate their individual merits and weaknesses. We also show that implementation of a GAL-type xylose-responsive regulon can regulate multiple genes across the yeast genome and enable more homogeneous population-wide gene expression. By integrating a minimal set of heterologous catabolic genes into the synthetic regulon we demonstrate high cellular growth rates and high final cell densities on xylose as well as better growth in non-inducing carbon sources. Finally, we compare the genome-wide expression profiles of strains grown with regulon assistance and conventionally engineered strains to identify mechanistic reasons that account for the different phenotypes observed. We posit that this study strongly supports the need to re-evaluate how nutrient assimilation systems are currently implemented and introduces a new and unexplored paradigm of adapting a native regulon for efficient non-native sugar assimilation.

overall_design: Four different samples with biological triplicates were analyzed in the study. The strains include, A) Wildtype yeast strain with intact GAL regulon grown in galactose B) Yeast strain with GAL4 knock out, but GAL1, GAL10 and GAL7 genes expressed under constitutive TEF1p, TPI1p and GPM1p promoters, grown in galactose, C) A GAL-adapted xylose regulon with XYLA*3, XKS1, TAL1 and GAL2-2.1, necessary for growth in xylose and grown in xylose and D) Strain without xylose regulon but constitutively expressing XYL*3, XKS1, TAL1 and GAL2-2.1, and grown in xylose.

first: Venkatesh

last: Endalur Gopinarayanan

middle: U


title: Downregulation of Endothelin Receptor B Contributes to Defective B Cell Lymphopoiesis in Trisomy 21 Pluripotent Cells

first: Jialiang

last: Huang

address: 450 Brookline Avenue

summary: Individuals with Trisomy 21 (T21) exhibit numerous hematological abnormalities, including reductions in numbers of circulating B and T lymphocytes.  To elucidate molecular mechanisms underlying these phenotypes, we differentiated human isogenic disomic and trisomic pluripotent cells, and observed that trisomic cells showed defects in B cell, but not T, cell differentiation.  Global gene expression of differentiated, trisomic B cells revealed reduced expression of genes encoding endothelin signaling components, namely the Endothelin Receptor B (Ednrb), and its ligand Endothelin1 (Edn1).. Depletion of Ednrb mRNA in cord blood CD34+ cells led to defective B cell differentiation, supporting an hypothesis that low expression of Ednrb in T21 contributes to intrinsic lymphoid defects.  Further evidence for the role of the Ednrb pathway in B cell differentiation was obtained through CRISPR/Cas9 gene targeting in disomic and trisomic iPS cells.  Knockout of Ednrb in both cell backgrounds reduced the capacity for B cell differentiation.  Collectively, this work identifies downregulation of Ednrb as a causative factor for impaired B lymphocyte generation in trisomic cells, which may contribute to defects in immune function associated with T21.  Furthermore, a novel role for endothelin signaling in regulation of B cell development has been identified.

overall_design: Disomic and trisomic isogenic iPS cells were differentiated in parallel, and after co-culture with MS5 cells, CD45+ CD34- CD19+ cells were isolated by FACS. RNA was extracted using Trizol.  Global gene expression analysis by microarray was performed on the Human HG U133 Plus 2.0 platform. Each group contains three biological replicates.

first: Glenn

last: MacLean


title: Gene expression data of iPSCs reprogrammed and/or maintenanced with 3i

city: Shinjuku-ku, Tokyo

first: Koji

last: Nishihara

state: -- Please Select --

address: 35 Shinanomachi

department: physiology

institute: Keio University school of medicine

summary: RNA exracted from 3i (-)/(+) and (+)/(+) iPSCs was hybridized to Affymetrix microarray.

first: Wado

last: Akamatsu


title: Mouse E14.5 Ret+ mechanoreceptors vs. laser captured spinal cord dorsal column midline cells

city: Philadelphia

first: Kim

last: Kridsada

state: PA

address: 3610 Hamilton Walk 145 Johnson Pavilion UNIVERSITY OF PA/CLINICAL

department: Neuroscience

institute: University of Pennsylvania

summary: Our study examined a population of radial glial-like cells (RGLCs) in the dorsal spinal cord midline that we showed provide long-distance growth support for longitudinal rapidly adapting (RA) mechanoreceptor axons during development of spinal cord dorsal column. To evaluate potential molecular markers of these cells, we isolated the RGLCs using hematoxylin and eosin staining to visualize the cell bodies in the dorsal column midline from E14.5 mouse embryos, and used laser capture microdissection for each sample ("LCM"). To compare transcript expression to the adjacent RA mechanoreceptive axons, we performed FACS of dorsal root ganglion of E14.5 Ret-Tdtomato+ RA mechanoreceptors. Our analyses revealed a high enrichment of radial glial-specific markers in the LCM replicates compared to Ret-Tdt samples. In contrast, neuronal-specific markers were more highly enriched in the Ret-Tdt samples, as expected. These data suggest the midline RGLCs are of radial glial identity. Others may find these data helpful in determining potential RGLC-mechanoreceptor molecular interactions in subsequent studies.

overall_design: mRNA transcript levels to compare E14.5 mouse Ret+ mechanoreceptors vs. laser captured dorsal column spinal cord midline cells, deep sequencing, analyzed in triplicates for each cell type,  using Illumina (HiSeq 2500)

first: Jingwen

last: Niu

first: Wenqin

last: Luo


title: Next Generation Sequencing Facilitates Quantitative Analysis of Ter cells Transcriptomes

city: shang hai

first: Qian

last: Zhang

address: xiangyin road 800

institute: Second military medical university

summary: Purpose:The purpose of this study is to detect genes Ter-119+CD45−Lin− cells sorted from spleen of tumor-bearing mice and the control cells. Gene expression differences between seven samples could be found using transcriptome profiling (RNA-seq) analysis. Methods: The seven cell subsets were isolated from spleen of tumor-bearing mice, embryonic liver (E14.5) and bone marrow of wild type mice by cell sorter respectively. Cells with purity >98% were used for subsequent experiments. The cell subsets RNA profiles were generated by deep sequencing,using Illumina. Results: Genes with FPKM values above 10.0 in the cell groups were used for subsequent analysis. Single linkage clustering analysis between the groups and prcomp function-based PCA analysis on the expression matrix were performed by R software. We found that the tumor-induced Ter-119+CD45−Lin− cells expressed the transcriptional factors and functional genes associated with erythrocyte and megakaryocyte development, but not myeloid cells differentiation.

overall_design: Ter-119+CD45−Lin− cells mRNA profiles of tumor-bearing mice were generated by deep sequencing.

first: Yanmei

last: Han

first: Xuetao

last: Cao


title: ATAC-seq reveals GATA-1- and heme-dependent chromatin targeting in erythroid cells.

city: Madison

first: Emery

middle: H.

last: Bresnick

state: WI

address: 4009 WIMR 1111 Highland Ave

department: Cell and Regenerative Biology

institute: University of Wisconsin Madison

summary: CRISPR/Cas9-mediated ablation of two Alas2 intronic cis-elements in G1E-ER-GATA1 cells strongly reduced GATA-1-induced Alas2 transcription, heme biosynthesis, and GATA-1 regulation of other vital constituents of the erythroid cell transcriptome. Bypassing Alas2 function in Alas2 cis-element-mutant (double mutant) cells by providing its catalytic product 5-aminolevulinic acid (5-ALA) rescued heme biosynthesis and a subset of GATA-1-dependent genetic network. Using the same system, we discovered a GATA-1- and heme-dependent circuit that regulates chromatin accessibility during erythroid maturation.

overall_design: G1E-ER-GATA1 WT and double mutant cells were examined. Untreated WT, beta-estradiol-treated WT, untreated double mutant, beta-estradiol-treated double mutant and beta-estradiol/5-ALA-treated double mutant cells were subject to ATAC-seq.

first: Ruiqi

last: Liao

first: Nobuyuki

last: Tanimura

first: Xin

last: Liu

first: Jian

last: Xu

middle: H


title: Transcriptome sequencing of differentially expressed genes of the skin tissue of Ncstn ΔKC mice and normal mice

city: Nanjing

first: Yanyan

last: He

address: Jiangwangmiao Street

summary: We constructed keratinocyte-specific Ncstn-knockout mice to investigate the role of NCSTN in the pathogenesis of human AI.

overall_design: Two groups, NcstnΔKC mice vs. normal mice. Each group contains 4 samples.


title: Dietary fat, but not dietary protein or carbohydrate (sucrose), regulates energy intake and causes adiposity in mice

status: Public on May 29 2018

city: Beijing

first: John

last: Speakman

address: No. 1 West Beichen Road,

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

summary:
Purpose: Obesity is a global health issue. To investigate if protein and fat contents of the diets had effects on energy balance via the canonical hunger signaling pathways in the hypothalamus, RNAseq was performed on RNA extracted from the hypothalami of mice exposed to the different diets. A suggested mechanism by which animals may avoid obesity is by burning off excess energy via upregulation of white adipose tissue (WAT) browning. To investigate if protein and fat content of the diet had effects on energy balance via the browning related signaling pathways in the WAT, RNAseq was performed on RNA extracted from the subcutaneous WAT (sWAT) and epididymal WAT (eWAT) of mice exposed to the different diets.
Methods: C57BL/6 male mice were used in this work. All mice were fed a standard diet with 10% fat and 20% protein (D12450B, Research Diets Ltd) for 2 weeks as the baseline period. Following 2 weeks of baseline monitoring (at age 12 weeks), all mice were randomly allocated to different groups and switched to the experimental diets for 12 weeks. After 12 weeks all mice were sacrificed and dissected.
Methods: In total, mice were fed on 4 diet series, each series consisting of 6 different diets (total = 24 diets). In the first two series (Series 1: D14071601–D14071606 and series 2: D14071607 – D14071612) we fixed the level of fat by energy, and varied the protein content. The protein source was casein. The balance was made up by carbohydrate (roughly equal mix of corn starch and maltodextrose). The source of fat was a mix of cocoa butter, coconut oil, menhaden oil, palm oil and sunflower oil. This mix was designed to match the balance of saturated, mono-unsaturated and polyunsaturated fats (ratio 47.5: 36.8: 15.8) and the n-6: n-3 ratio (14.7: 1) in the typical western diet. The proportions of the different fat constituents and hence fatty acid distributions did not change as the total fat content changed. Sucrose and cellulose were both fixed 5% by energy and weight respectively, and all diets were supplemented with a standard vitamin and mineral mix. In the second two series of diets (series 3: D14071613 – D14071618 and series 4: D14071619 – D14071624) we fixed the level of protein by energy and then allowed the fat content to vary.  In these diets the sucrose, cellulose and vitamin and mineral contents were the same as the diets in series 1 and 2. All these diets can be ordered direct from research diets (www.researchdiets.com) using the diet codes provided.
Methods: From each diet group, the hypothalami of 8/20 individuals were collected. The left halves of two, and the right halves of another two, were pooled together as one sample, and the same was performed with the other 4 hypothalami, resulting in each diet group having 2 pooled samples of 4 hypothalami (n = 48 samples in total across 24 diets). From each diet group, the sWAT and eWAT of 12/20 individuals were also collected. A small piece from each of six sWAT collections were pooled together as one sample, and the same was performed with the other six eWAT collections. In this way each diet group had one pooled sWAT sample and one pooled eWAT sample (also n = 48 across 24 diets).
Methods: The total RNA of the hypothalamus and WAT was isolated using the RNeasy Mini Kit (QIAGEN, 74104) according to manufacturer's protocol. All sequencing was carried out using the Illumina NextSeq 500 sequencer. RNA fragments were sequenced by 75 bp long reads from paired ends (PE 2 x 75 bp, 150 bp per fragment). Quality control checks for raw data FASTQ files were done by using FASTQC (a quality control tool for high throughput sequence data; http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Paired-end reads were mapped to the Mus musculus genome (GRCm38) using Bowtie 2-2.1.0, TopHat-2.0.10, and Samtools-0.1.19; uniquely mapped reads for each gene were counted against the GTF file of GRCm38 provided by Ensembl (release 83) using HTSeq-0.6.1p1 using the strand = reverse; after read count data were obtained from the TopHat-HTSeq pipeline, counts per million (CPM) value for each gene was calculated by using the R package ‘edgeR’ (version 3.12.0, R version 3.2.2) to normalize the count data by the size of the library of each sample. Genes with the CPM value ≥ 1 in at least one of the 24 diets group were retained (Anders et al., 2013). Generalized Linear Modelling (GLM) was applied by R (version 3.2.2). The GLM model used here was: ~p+f+p:f, which regresses gene expression (CPM) against the protein (p) and fat contents (f) of diets, as well as their interaction (p:f). However, when the effect of the interaction was not significant (p value ≥ 0.05), the interaction term was dropped and a revised model (~p+f) was utilized.
Results: With TopHat-HTSeq pipeline, reads of each sample were mapped to 46,078 genes. In hypothalamus there were 15,371 genes with the counts per million (CPM) value ≥ 1 in at least one of the 24 diets group; in white adipose tissue there were 18,202 genes with the CPM value ≥ 1 in at least one of the 24 diets group. No major changes in hypothalamic gene expression levels were found in relation to different dietary protein levels at fixed fat contents, however hypothalamic gene expression showed increase in expression of genes in reward pathways in relation to dietary fat, while Agrp and Npy were both downregulated in relation to dietary fat levels. WAT gene expression showed decrease in expression of general thermogenic related genes and WAT browning related genes in relation to both dietary protein and dietary fat, while Tgfb1, Pdk4 and Fgf1 were all upregulated in relation to dietary fat levels.
Conclusions: Significant positive associations were evident between the fat levels of the diet and the main hedonic signaling systems linked to food intake. Significant negative associations were found between both protein and fat levels of the diet and WAT browning or general thermogenic signalings linked to energy expenditure.

overall_design: In total 96 samples are analyzed. From each diet group, the hypothalami of 8/20 individuals were collected. The left halves of two, and the right halves of another two, were pooled together as one sample, and the same was performed with the other 4 hypothalami, resulting in each diet group having 2 pooled samples of 4 hypothalami (n = 48 samples in total across 24 diets). From each diet group, the sWAT and eWAT of 12/20 individuals were also collected. A small piece from each of six sWAT collections were pooled together as one sample, and the same was performed with the other six eWAT collections. In this way each diet group had one pooled sWAT sample and one pooled eWAT sample (also n = 48 across 24 diets)

first: Sumei

last: Hu

first: Lu

last: Wang

first: Dengbao

last: Yang

first: Li

last: Li

first: Jacques

last: Togo

first: Yingga

last: Wu

first: Quansheng

first: Baoguo

first: Min

first: Guanlin

first: Xueying

first: Jianbo

first: Yanchao

first: Elspeth

last: Couper

first: Andrew

last: Whittington-Davies

first: Mohsen

last: Mazidi

first: Lijuan

first: Shengnan

first: Alex

last: Douglas


title: Methylomes from naïve CD4+ T-cells from infants and children with and without food allergy [methylation]

first: David

last: Martino

summary: Here we studied the epigenetic regulation of the naïve CD4+ T-cell activation response among children with IgE-mediated food allergy. Using integrated DNA methylation and transcriptomic profiling, we found that food allergy in infancy is associated with dysregulation of T-cell activation genes. Reduced expression of cell cycle related targets of the E2F and MYC transcription factor networks, and remodeling of DNA methylation at metabolic (RPTOR, PIK3D, MAPK1, FOXO1) and inflammatory genes (IL1R, IL18RAP, CD82) were associated with poorer T-lymphoproliferative responses in infancy after polyclonal activation of the T-cell receptor.

overall_design: Bisulphite converted gDNA from naïve CD4+ T-cells under two conditions (anti-CD3+CD28 activated, or quiescent) at two ages (baseline (12months) and followup (2 or 4 years)) in allergic and non-allergic children, were hybridized to Illumina EPIC arrays


title: Gene expression of human littoral cells and splenic vascular endothelial cells from the spleens of normal individuals and patients with myelofibrosis

city: New York

first: Jiajing

last: Qiu

state: NY

address: 1468 Madison Ave, ANBG bldg 24-10

department: Hematology/Oncology Department of Medicine

institute: Icahn School of Medicine at Mount Sinai

summary: The vascular lining cells in the human spleens include littoral cells (LCs) and other splenic vascular endothelial cells (SVECs). LCs that comprise about 30 percent of the splenic red pulp are specialzed endothelial cells distinct from SVECs. They line the splenic sinusoids and function as the filters and scavengers for senescent or altered red blood cells. Patients with advanced forms of myelofibrosis (MF) often develope extramedullary hematopoiesis in the spleen.Vascular lining cells within MF spleens are thought to serve as a supportive microenvironment for MF hematopoietic cells. In this study we isolated MF and normal LCs and SVECs from human spleens using immunostaining and flow cytometric sorting and used microarrays to analyze the underling mechanism of LCs' unique functions that distinguish them from SVECs, and the properties of MF LCs and SVECs and their contributions to the microenvironment of MF spleens.

overall_design: Normal human spleens were obtained from National Disease Research Interchange (NDRI) from healthy donors who required splenectomy for a traumatic injury. MF spleens were obtained from patients with advanced forms of MF who have marked splenomegaly and were undergoing therapeutic splenectomy. All patients signed an informed consent. CD34- CD8a+ CD31+ CD3- CD45- LCs and CD34+ CD8a- CD31+ CD3- CD45 SVECs were isolated from the normal and MF spleens and their gene expression profiles were compared.

first: Ronald

last: Hoffman


title: Mutant GNAS drives pancreatic tumorigenesis by inducing PKA-mediated SIK suppression and reprogramming lipid metabolism

city: Boston

first: Krushna

last: Patra

address: 185 Cambridge Street

department: Cancer Center

institute: MGH

summary:
Gain-of-function mutation of GNAS is frequently observed in pancreatic and other gastrointestinal cancers. Aim of this study was to delineate the oncogenic mechanisms downstream of mutant GNAS.
To gain insight into the expression of different transcripts, we perforemd RNA-sequencing (RNA-seq) studies. For this total RNA was isolated in duplicate from two independent KRAS,GNAS mutant lines (A and B) grown in 3D culture with doxycycline supplementation. RNA samples were prepared using Illumina TruSeq RNA Sample Preparation Kit v2 and sequenced using an Illumina HiSeq 2500 sequencer, generating 50-bp single-end reads. Data was processed using a standard RNA-seq pipeline that used Tophat2 to align the reads to mm9, and the Cufflinks suite to calculate FPKM values. Our results shows level of RNA expression in KRAS, GNAS mutant cells.

overall_design: RNA profiles of KGC 3D cultures were generated by deep sequencing, in duplicate in two different lines by Illumina HiSeq 2500 sequencer.

first: Nabeel

last: Bardeesy


title: Transcriptomes from naïve CD4+ T-cells from infants and children with and without food allergy [RNA-seq]

overall_design: mRNA sequencing of naïve CD4+ T-cells under two conditions (anti-CD3+CD28 activated, or quiescent) at two ages (baseline (12months) and followup (2 or 4 years)) in allergic and non-allergic children.


title: Foxd1 is required for terminal differentiation of anterior hypothalamic neuronal subtypes

city: Baltimore

first: Jie

state: Maryland

address: 400 N Broadway

institute: Johns Hopkins University

summary: Although the hypothalamus functions as a master homeostat for many behaviors, little is known about the transcriptional networks that control its development.  To investigate this question, we analyzed mice deficient for the Forkhead domain transcription factor Foxd1.  Foxd1 is selectively expressed in neuroepithelial cells of the prethalamus and hypothalamus prior to the onset of neurogenesis, and is later restricted to neural progenitors of the prethalamus and anterior hypothalamus.  During early stages of neurogenesis, we observed that Foxd1-deficient mice showed reduced expression of Six3 and Vax1 in anterior hypothalamus, but overall patterning of the prethalamus and hypothalamus is unaffected.  After neurogenesis is complete, however, a progressive reduction and eventual loss of expression of molecular markers of the suprachiasmatic, paraventricular and periventricular hypothalamic is observed.  These findings demonstrate that Foxd1 acts in hypothalamic progenitors to allow sustained expression of a subset of genes selectively expressed in mature neurons of the anterior hypothalamus.

overall_design: We measured gene expression profiles of wild-type and Foxd1-mutant hypothalamic tissues separately at E12.0, E12.5 and E17.5

first: Elizabeth

last: Newman

first: Jun

last: Wan

first: Jiang

last: Qian

first: Seth

last: Blackshaw


title: Small noncoding RNAs in FSHD2 muscle cells reveal both DUX4- and SMCHD1-specific signatures

city: Seattle

first: Stephen

last: Tapscott

state: WASHINGTON

address: 1100 Fairview N. Ave

department: Human Biology

institute: Fred Hutch Cancer Research Center

type: Non-coding RNA profiling by high throughput sequencing

summary: Facioscapulohumeral muscular dystrophy (FSHD) is caused by insufficient epigenetic repression of D4Z4 macrosatellite repeat where DUX4, an FSHD causing gene is embedded. There are two forms of FSHD, FSHD1 with contraction of D4Z4 repeat and FSHD2 with chromatin compaction defects mostly due to SMCHD1 mutation. Previous reports showed DUX4-induced gene expression changes as well as changes in microRNA expression in FSHD muscle cells. However, a genome wide analysis of small noncoding RNAs that might be regulated by DUX4 or by mutations in SMCHD1 has not been reported yet. Here, we identified several types of small noncoding RNAs including known microRNAs that are differentially expressed in FSHD2 muscle cells compared to control. Although fewer small RNAs were differentially expressed during muscle differentiation in FSHD2 cells compared to controls, most of the known myogenic microRNAs, such as miR1, miR133a, and miR206 were induced in both FSHD2 and control muscle cells during differentiation. Our small RNA sequencing data analysis also revealed both DUX4- and SMCHD1-specific changes in FSHD2 muscle cells. Six FSHD2 microRNAs were affected by DUX4 overexpression in control myoblasts, whereas increased expression of tRNAs and 5S rRNAs in FSHD2 muscle cells was largely recapitulated in SMCHD1-depleted control myoblasts. Altogether, our studies suggest that the small noncoding RNA transcriptome changes in FSHD2 might be different from those in FSHD1 and that these differences may provide new diagnostic and therapeutic tools specific to FSHD2.

overall_design: 2 control myoblast (MB) samples, 2 control myotube (MT) samples, 2 FSHD2 MB samples, and 2 FSHD2 MT samples

first: Jong-Won

last: Lim

first: Chao-Jen

last: Wong

first: Zizhen

last: Yao

first: Rabi

last: Tawil

first: Silvère

middle: M

last: van der Maarel

first: Daniel

middle: G

last: Miller

middle: J

first: Galina

middle: N

last: Filippova


title: Recurrent 8q24 rearrangement in BPDCN: association with immunoblastoid cytomorphology, MYC expression, and drug response (CAL1 vs PMDC05)

city: Koto

first: Kana

last: Sakamoto

state: Tokyo

institute: Japanese Foundation for Cancer Research

summary: Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is a rare skin-tropic hematological malignancy of uncertain pathogenesis and poor prognosis. We examined 118 BPDCN cases for cytomorphology, MYC locus rearrangement, and MYC expression. Sixty-two (53%) and 41 (35%) showed the classic and immunoblastoid cytomorphology, respectively. Forty-one (38%) MYC+BPDCN (positive for rearrangement and expression) and 59 (54%) MYC-BPDCN (both negative) cases were identified. Immunoblastoid cytomorphology was significantly associated with MYC+BPDCN. All examined MYC+BPDCNs were negative for MYB/MYBL1 rearrangement (0/36). Clinically, MYC+BPDCN showed older onset, poorer outcome, and localized skin tumors more commonly than MYC-BPDCN. MYC was demonstrated by expression profiling as one of the clearest discriminators between CAL-1 (MYC+BPDCN) and PMDC05 (MYC-BPDCN) cell lines, and its shRNA knockdown suppressed CAL-1 viability. Inhibitors for bromodomain and extraterminal protein (BETis) and aurora kinases (AKis) inhibited CAL-1 growth more effectively than PMDC05. We further showed that a BCL2 inhibitor was effective in both CAL-1 and PMDC05, indicating that this inhibitor can be used to treat MYC-BPDCN, to which BETis and AKis are probably less effective. Our data will provide a rationale for the development of new treatment strategies for patients with BPDCN in accordance with precision medicine.

overall_design: We compared the gene expression profiling of CAL-1 (n=3) and PMDC05 (n=3).

first: Kengo

last: Takeuchi


title: Recurrent 8q24 rearrangement in BPDCN: association with immunoblastoid cytomorphology, MYC expression, and drug response (CAL-1, JQ1 treatment)

overall_design: CAL-1 were treated with either DMSO or 400 nM JQ1 for 24 hours (n=3, each).


title: Analysis of changes in Dendritic cell (DC) gene expression upon exposition to T-cell Exosomes.

city: Madrid

first: Manuel

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

summary: Bone Marrow derived dendritic cells (BMDC) were cultured for 9 days. BMDC were treated with T cell exosomes for 6 hours and frozen for further analysis.

overall_design: RNA was extracted and RNAseq performed on 4 paired biological replicates of exosome-treated or untreated BMDC.

first: F

last: Sanchez-Madrid

first: D

last: Torralba


title: Whole Blood Transcriptome Profiling in Juvenile Idiopathic Arthritis and Inflammatory Bowel Disease

city: Atlanta

first: Angela

last: Mo

state: GA

address: 950 Atlantic Drive

department: School of Biological Sciences

institute: Georgia Institute of Technology

summary: We report whole blood gene expression of 12 healthy controls and 190 patients with either oligoarticular (n=43), polyarticular (n=46), or systemic JIA (n=26), or Crohn's disease (n=60) and ulcerative colitis (n=15). The subtypes of JIA are characterized by a gradient of differential gene expression ranging from controls to oligoJIA, polyJIA, sJIA, and IBD.

overall_design: Whole blood samples were obtained from JIA patients age <17 years. Transcriptome profiling was performed with RNA-Seq.

first: Urko

last: Marigorta

first: Subra

last: Kugathasan

first: Sampath

last: Prahalad

first: Greg

last: Gibson


title: CAR T cell related cytokine release syndrome mouse model

status: Public on May 28 2018

first: Bic

last: MSKCC

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

summary: Chimeric antigen receptor (CAR) therapy targeting CD19 is an effective treatment for refractory B cell malignancies, especially acute lymphoblastic leukemia (ALL). While a majority of patients will achieve a complete response following a single infusion of CD19 CAR T cells, the broad applicability of this treatment is hampered by severe cytokine release syndrome (CRS), which is characterised by fever, hypotension and respiratory insufficiency associated with elevated serum cytokines including interleukin-6 (IL-6). CRS usually occurs within days of T cell infusion at the peak of CAR T cell expansion. In ALL, it is most frequent and more severe in patients with high tumour burden CRS is often responsive to IL-6 receptor blockade, but may require intensive life support and further treatment with high dose corticosteroids to prevent potentially lethal severity. Improved therapeutic and preventive treatments require a better understanding of CRS physiopathology, which has so far remained elusive. We report here a murine model of CRS that develops within 2-3 days of CAR T cell infusion, may be lethal and is responsive to IL-6 receptor blockade. We show that its severity is mediated not by CAR T cell-derived cytokines but by IL-6, interleukin-1 (IL-1) and Nitric Oxide (NO) produced by recipient macrophages. This CRS mechanism enables novel therapeutic interventions.

overall_design: Tumor bearing mice were injected intraperitoneally with CAR T cells to elicit CRS or were left untreated. 18 hours after CAR T cell transfer peritoneal and splenic cells were harvested. Specific myeloid populations were purified by FACS sorting and were immediately processed for RNAseq analysis.

first: Theodoros

last: Giavridis

first: Michel

last: Sadelain


title: Recurrent 8q24 rearrangement in BPDCN: association with immunoblastoid cytomorphology, MYC expression, and drug response

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

overall_design: Refer to individual Series


title: Epigenetic control of innate and adaptive immune memory [ATAC-Seq]

city: Ithaca

first: Colleen

last: Lau

state: New York

address: 930 Campus Road

department: Microbiology & Immunology

institute: Cornell University

summary: Clonal expansion and immunological memory are hallmark features of the mammalian adaptive immune response and essential for prolonged host control of pathogens. Recent work demonstrated that natural killer (NK) cells of the innate immune system also exhibit these adaptive traits during infection. Here we demonstrate that differentiating and ‘memory’ NK cells possess distinct chromatin accessibility states, and that their epigenetic profiles reveal a ‘poised’ regulatory program at the memory stage. Furthermore, we elucidate how individual STAT proteins differentially control epigenetic and transcriptional states early during infection. Finally, concurrent chromatin profiling of the canonical CD8+ T cell response against the same infection demonstrated parallel and distinct epigenetic signatures defining NK cells and CD8+ T cells. Overall, our study reveals the dynamic nature of epigenetic imprinting during the generation of innate and adaptive lymphocyte memory.

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

first: Joseph

middle: C

last: Sun


title: Adipocyte-derived lipids mediate melanoma progression via FATP proteins

status: Public on May 26 2018

first: Maomao

last: Zhang

department: Cancer Biology & Genetics

institute: Memorial Sloan Kettering Cancer Center

summary: We performed RNA-seq on A375 melanoma cells in monoculture or after coculture with adipocytes and identified differentially expressed genes

overall_design: 6 samples

first: Richard

last: White


title: Enhancer and transcription factor dynamics within the granulocytic-monocytic lineage reveal an early differentiation block in Cebpa null progenitors

city: Copenhagen

first: Bo

middle: Torben

last: Porse

address: Ole Maaløes Vej 5, 4.

department: Finsen Laboratory and BRIC

country: Denmark

institute: University of Copenhagen

summary: Myeloid cells of the granulocytic-monocytic (GM) lineage develop in a process orchestrated mainly by the transcription factors PU.1 and CEBPA, but how these factors collaborate on a global scale during GM-lineage differentiation remains uncharacterized. To address this question we have combined epigenetic profiling, transcription factor binding and gene expression analyses of successive stages of murine GM-lineage differentiation and show that PU.1 and CEBPA binds to GM enhancers with distinct kinetics. Surprisingly, we find no evidence of a pioneering function of PU.1 during GM-lineage differentiation but instead delineate a set of GM enhancers that appears to open in a CEBPA-dependent manner. Analyses of Cebpa null bone marrow demonstrate that CEBPA controls PU.1 levels and, unexpectedly, that the loss of CEBPA results in a very early differentiation block. These data are consistent with a model involving an extensive functional interplay between PU.1 and CEBPA in driving GM-lineage differentiation.

overall_design:
Examined 2 replicates each of H3K4me1, H3K27ac histone marks, 2 replicates each of PU.1 and CEBPA transcription factors across four granulocytic-monocytic differentiation stages and CEBPA KO condition

Examined transcriptome from LSK, preGMs, GMP, CFU-G, CFU-M, granulocytes and monocytes in biological triplicates

middle: T

first: Felicia

last: Lauridsen

first: Mikkel

last: Schuster

first: Janus

middle: S

last: Jakobsen

first: Ying

last: Ge

first: Sachin

last: Pundhir


title: The effects of mutant ASXL1 and BAP1 expression on hematopoietic cells

status: Public on May 25 2018

city: Tokyo

first: Shuhei

last: Asada

address: 4-6-1 Shirokanedai, Minato-ku

department: Cellular Therapy

institute: Institute of Medical Science, The University of Tokyo

summary:
To identify target genes of mutant ASXL1 and BAP1 in hematopoietic cells, we performed RNA-seq using murine c-kit positive cells transduced with ASXL1-MT (MT) or ASXL1-MT-K351R (KR)  together with vector or BAP1.
Method：Murine c-kit positive bone marrow cells were transduced with ASXL1-MT (MT) or ASXL1-MT-K351R (KR)  (coexpressing blastcidin resistant gene) together with vector or BAP1 (coexpressing puromycin resistant gene).  After the selection with blasticidin and puromycin for three days, colony-forming cells were collected to extract RNA for RNA-seq analysis.

overall_design: Three biologically independent experiments were perfomed for each sample.

first: Susumu

last: Goyama

first: Shinya

last: Kojima

first: Masahito

last: Kawazu

first: Hiroyuki

last: Mano

first: Toshio

last: Kitamura