title: Transcriptome-wide analysis of the role of HTLV-1 Tax PBM in T-Cells from infected humanized-mice (hu-Mice)

city: Lyon

first: Emiliano

middle: P

last: Ricci

address: 46 allée d'Italie

department: Centre International de Recherche en Infectiologie

institute: INSERM

summary: Human T-lymphotropic virus type 1 (HTLV-1) is associated with the development of Adult T-cell Leukemia, an aggressive CD4+ T-cells malignancy. Here, we have developed a new procedure to infect humanized mice with proviruses displaying specific mutations, such as one leading to the loss of the PDZ domain-binding motif (PBM) of Tax. In order to specifically analyze the in vivo role of the PBM of Tax, a comparative study of infected hu-mice was performed. We used next-generation sequencing to perform genome-wide transcriptomic analysis of T-cells infected with wild-type HTLV-1 virus or with virus bearing a mutated form of Tax lacking the PBM. Our results suggest that Tax PBM might be involved in the regulation of genes implicated in proliferation, apoptosis and cytoskeleton organization.

overall_design: mRNA profiles of T-cells obtained from hu-Mice infected with wild-type or Tax-PBM HTLV-1 were generated by deep-sequencing in triplicates using Illumina’s Hiseq3000 platform.

first: Madeleine

last: Duc-Dodon

first: Eléonore

last: Perès

first: Juliana

last: Blin


title: Regulation of posterior body and ectodermal morphogenesis in zebrafish by localized Yap1 and  Wwtr1

status: Public on Feb 14 2018

city: Bad Nauheim

first: Jason

last: Lai

state: Hessen

address: Ludwigstrasse 43

department: Developmental Genetics

country: Germany

institute: Max Planck Institute For Heart and Lung Research

type: Expression profiling by high throughput sequencing

summary: The vertebrate embryo undergoes a series of dramatic morphological changes as the body extends to form the complete anterior-posterior  axis during the somite-forming stages. The molecular mechanisms regulating these complex processes are still largely unknown. We show that  the Hippo pathway transcriptional coactivators Yap1 and Wwtr1 are specifically localized to the ectoderm and notochord, and play a critical and  unexpected role in posterior body extension by regulating the assembly of Fibronectin underneath the ectoderm and surrounding the notochord.  We also find that Yap1/Wwtr1, also acting through Fibronectin, have an essential role in the ectodermal morphogenesis necessary to form the  initial dorsal and ventral fins, a process that had been thought to involve bending of an epithelial sheet, but which we now show involves active  cell migration. Our results reveal how the Hippo pathway transcriptional program, localized to two specific tissues, acts to control essential  morphological events in the vertebrate embryo.

overall_design: two biological replicates of tails of yap1/wwtr1 double homozygous mutants and siblings (24 each at 16-18 somite stage) were collected for RNAseq.  Tails are tissues of the posterior end until the third newest somite (S-III).

first: David

last: Kimelman

first: Natalie

middle: L

last: Smith

middle: K

first: Didier

middle: Y

last: Stainier


title: Expression regulation by Pcgf3 and Pcgf5 in mouse embryonic stem cells

city: Nanjing

first: Wukui

last: Zhao

state: Jiangsu

address: 12 Xuefu Road

department: Model Animal Research Center

country: China

institute: Nanjing University

summary: Polycomb group (PcG) proteins are epigenetic transcriptional repressors that orchestrate numerous developmental processes and have been implicated in the maintenance of embryonic stem (ES) cell state. More recently emerging evidence suggests a subset of PcG proteins engage in transcriptional activation in some cellular contexts. But how this property is exerted remains largely unknown. Here, we generated ES cells with single or combined disruption of Pcgf3 (Polycomb group RING finger protein 3) and Pcgf5 by CRISPR-Cas9 technology. We showed that although these mutant cells maintained their self-renewal and colony-formation capacity, they displayed severe defects in mesoderm differentiation in vitro. To gain a better understanding of the role of Pcgf3/5 in transcriptional control of differentiation, we analyzed transcriptional profiles of ES cells with single or combined Pcgf3/5 deficiency using RNA-seq. In contrast to the canonical role of PRC1 in gene repression, we found that Pcgf3/5 mainly functioned as a transcriptional activator to drive expression of many genes involved in mesoderm differentiation. Proteomic approaches and promoter occupancy analyses allowed us to establish an extended Pcgf3/5 interactome and identify several novel interactors including Tex10, which may directly contribute to transcription activation by cooperating with transcriptional co-activator p300. Furthermore, Pcgf3/5 deletion substantially reduces the occupancy of Tex10 and p300 at target genes. Finally, we demonstrated an essential role for Pcgf3/5 in regulating global H2AK119ub1 levels in ES cells. Collectively, our studies establish Pcgf3/5 as a transcriptional activator in ES cells by cooperating with Tex10 and p300, and point to a redundant mode of action for Pcgf3/5 in pluripotency maintenance.

overall_design: Pcgf3 KO, Pcgf5 KO, Pcgf3/5 DKO and wildtype mESCs

first: Yikai

last: Huang

first: Jinzhong

last: Qin


title: Copy Number Profiles of Paired Primary and Metastatic Colorectal Cancer to Investigate Clonal Tumour Changes

city: Brisbane

first: Katia

last: Nones

state: QLD

address: 300 Herston Road

country: Australia

institute: QIMR Berghofer MEdical Research Institute

summary: Background: Liver metastasis is the major cause of death following a diagnosis of colorectal cancer (CRC) and is a major health burden.  Most molecular studies of CRC have profiled primary tumor samples and not the metastasis samples.  In this study, we compared the copy number profiles of matched primary and liver metastatic CRC to better understand how the genomic structure of primary CRC differs from the metastasis.  This has important implications for whether it is justified to base therapeutic approaches solely on data from the primary tumour.  Methods: Paired primary and metastatic tumours from 16 patients and their adjacent normal tissue samples were analyzed using Single-Nucleotide-Polymorphism (SNP) arrays to determine copy number alterations.  Nine patients had a synchronous liver metastasis at the time of CRC diagnosis and 7 patients developed a liver metastasis metachronously. Genome-wide chromosomal copy number alterations were assessed, with particular attention to 189 genes known to be somatically altered in CRC and 25 genes that are clinically actionable in CRC.  These data were analyzed with respect to the timing of primary and metastatic tissue resection and with exposure to chemotherapy.   Results: The genomic divergence with the whole genome duplication correction applied the average percent copy number discordance across all pairs of samples was 22.02%.  The pairs of tumour samples collected prior to treatment revealed a significantly higher copy number differences compared to previously treated liver metastasis samples (P=0.024).  However, loss of heterozygosity (LOH) acquired in metastasis was significantly higher in previously treated liver metastasis samples compared to treatment naïve liver metastasis samples (P= 0.0064) and which included where KRAS mutation was present in the primary cancers but was not detectable in the metastatic sample following chemotherapy.    With regard to 25 genes that are clinically actionable in CRC, amplification of the genes ERBB2, FGFR1, CDK8 or PIK3CA was observed in the metastatic tissue of 4 patients but not in the matched primary CRC.  In these cases, knowledge of these metastatic specific alterations could have informed therapeutic decision making and may have improved patient outcome.  Conclusion: Intra-patient genomic discrepancies observed between primary and metastatic tissue

overall_design: Paired primary CRC and metastatic liver tumour DNA, and normal patient DNA was assayed with the Omni 2.5-8, V1.0 and V1.1 IlluminaBeadChips as per manufacturer’s instructions (Illumina).  SNP arrays were scanned on an iScan (Illumina), data was processed using the Genotyping module (v.1.9.4) in GenomeStudio v.2011.1 (Illumina) to calculate B-allele frequencies (BAF) and logR ratios.  GAP[36] software was used to segment the SNP array data and determine the level of copy number which was classified into one of 5 categories: homozygous deletion (copy number: 0), loss (copy number:1), copy neutral LOH (copy number:2), gain (copy number: 3-5) and amplification (copy number: 6-8).

first: Futoshi

last: Kawamata

first: Ann-Marie

last: Patch

first: Catherine

last: Bond

first: Diane

last: McKeone

first: Sally-Ann

last: Pearson

first: Shigenori

last: Homma

first: John

last: Liu

first: Lochlan

last: Fennell

first: Troy

last: Dumenil

first: Gunter

last: Hartel

first: Moto

last: Fukai

first: Hiroshi

last: Nishihara

first: Toshiya

last: Kamiyama

first: Akinobu

last: Taketomi

first: Barbara

last: Leggett

first: Nicola

last: Waddell

first: Vicki

last: Whitehall


title: Wild type and Neuregulin 4 (Nrg4) knockout (KO) mouse livers

city: Ann Arbor

first: Jiandie

last: Lin

state: Michigan

address: 210 Washtenaw Avenue

department: Life Sciences Institute and Department of Cell & Developmental Biology

country: USA

institute: University of Michigan

summary:
Nrg4 is a brown fat-enriched adipokine that binds to the liver and suppress the process of steatosis-to-NASH progression. Adipose tissue Nrg4 expression was reduced in mice under NASH diet feeding. Nrg4 homozygous knockout mice are prone to diet-induced steatohepatitis
We used microarrays to elucidate the pathogenic pathways that are regulated by Nrg4 deficiency in the livers of mice under NASH diet feeding.

overall_design: Wild type and Neuregulin 4 (Nrg4) knockout mice were fed NASH diet (Research Diets D09100301) for twenty weeks. Tissues were harvested under ad lib condition for RNA isolation and microarray hybridization using Mouse Gene ST 2.1 arrays. Two independent pools of WT and KO mouse liver RNA were included in the study.

first: Liang

last: Guo

first: Peng

last: Zhang

first: Zhimin

last: Chen

first: Houjun

last: Xia

first: Siming

last: Li

first: Yanqiao

first: Weiping

last: Zou

middle: D


title: Chromatin conformation regulates the coordination between DNA replication and transcription

city: Madrid

first: Maria

last: Gomez

address: Nicolas Cabrera, 1

country: Spain

institute: CBMSO(CSIC/UAM)

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

overall_design: Refer to individual Series


title: Expression data from 5azaC- or gallic acid-treated human lung cancer H1299 cell line

city: Zhunan Miaoli County

first: Chia

middle: Huei

last: Lee

address: 35, Keyan Rd.

department: National Institute of Cancer Research

country: Taiwan

institute: Taiwan National Health Research Institute

summary:
Gallic acid (also known as 3,4,5-trihydroxybenzoic acid, GA), a naturally occurring phenolic acid, is a major constituent of tea and red wine. It has been demonstrated that GA possess anti-cancer activities. We found the epigenetic effect of GA in tobacco-associated human cancer cell lines.
In this dataset, we include the expression array data from human lung cancer H1299 cell line with or without the treatment of 5azaC or GA. These data were used to obtain genes upregulated in both 5azaC- orGA-treated H1299 cells.

overall_design: In total, 8 samples were analyzed. We generated the following pairwise comparisons using Affymetrix Expression Console™ Software (version 1.4): 5azaC compared with Ctr-Z ; GA compared with Ctrl-G. Genes with a P value < 0.05 and a fold-change ≥2 were selected. To identify the potential epigenetic targets of gallic acid, we performed Venn diagram analysis with genes showing either up-regulated by 5azaC or GA treatment.

first: Chia-Huei

first: Yui-Ping

last: Weng


title: Chromatin conformation regulates the coordination between DNA replication and transcription [SNS-Seq]

summary: Chromatin is the template for the basic processes of replication and transcription, making the maintenance of chromosomal integrity critical for cell viability. To elucidate how dividing cells respond to alterations in chromatin structure we analysed the replication initiation landscape, elongation kinetics, and timing of primary cells with altered chromatin configuration caused by the genetic ablation of the HMGB1 gene, or triple-KO in three histone H1 genes. We found that loss of chromatin compaction in H1-depleted cells alters dramatically the initiation patterns triggering the accumulation of stalled forks and DNA damage as a consequence of transcription-replication conflicts, whereas reductions in nucleosome content due to the lack of HMGB1 causes faster fork progression without perturbing the initiation landscape or fork stability. Thus, perturbations in the integrity of the chromatin template elicit a range of responses in the dynamics of DNA replication and transcription, with different consequences on replicative stress. These findings have broad implications for our understanding of how defects in chromatin structure, such as those occurring during cellular aging or in some developmental disorders or cancer, contribute to genomic instability.

overall_design: Replication initiation landscape in two different chromatin mutants has been analyzed: MEF cells KO for the HMGB1 gene or mES cells tripl-KO for three somatic histone H1 genes

first: Ricardo

last: Almeida

first: José

last: Fernández-Justel

first: Cristina

last: Santa-María

first: Jean-Charles

last: Cadoret

first: Laura

last: Cano-Aroca

first: Rodrigo

last: Lombraña

first: Gonzalo

last: Herranz

first: Alessandra

last: Agresti

first: María

last: Gómez


title: Chromatin conformation regulates the coordination between DNA replication and transcription [array]

overall_design: Replication timing has been compared between two experimental conditions: WT (control) versus H1-TKO cells. Two replicates.


title: TrapSeq: An RNA Sequencing-based pipeline for the identification of genetrap insertions in mammalian cells

first: Oscar

last: Fernandez-Capetillo

address: MFA 3

department: Genomic Instability Group

institute: CNIO

summary: Current pipelines used to map genetrap insertion sites are based on inverse- or splinkerette-PCR methods, which despite their efficacy are prone to artifacts and do not provide information on the impact of the genetrap on the expression of the targeted gene. We developed a new method, which we named TrapSeq, for the mapping of genetrap insertions based on paired-end RNA sequencing. By recognizing chimeric mRNAs containing genetrap sequences spliced to an endogenous exon, our method identifies insertions that lead to productive trapping.

overall_design:
We conducted two independent screenings for sensitivity against 6-thioguanine (6TG) and an ATR inhibitor (ATRi). We applied our RNAseq-based  pipeline (TrapSeq) to identify mutations that provide resistance to these reagents. Importantly, and besides its use for screenings, when applied to individual clones our method provides a fast and cost-effective way that not only identifies the insertion site of the genetrap but also reveals the impact of the insertion on the expression of the trapped gene.
Please note that HAP1, haploid for all chromosomes, derives from near-haploid KBM7 parent line which was in turn obtained from a chronic myeloid leukemia patient in blast crisis phase (Carette et al. Nature 477:340-343, 2011).

last: Mayor-Ruiz

first: Orlando

last: Domínguez

first: Óscar

last: Fernández-Capetillo


title: Differential expression of oral cancer cell line UM1 cultured in different glucose concentration

city: Chicago

first: Xiaofeng

last: Zhou

state: Illinois

address: 801 S Paulina Street

institute: University of Illinois at Chicago

summary:
High glucose has a significant effect on cancer progression. We aim to investigate the effect of glucose on oral cancer cells at gene expression level.
We use microarray to identify differentially expressed gene in oral cancer cells (UM1) that cultured in different glucose concentration.

overall_design: UM1 cells was growed in medium containing 5.6 or 16.7 mM glucose for 7 days, and total RNA was isolated with Qiagen kit, and then hybridized to the Affymetirx arrays.

first: Anxun

last: Wang


title: Phased secondary small interfering RNAs in Panax notoginseng

city: Kunming

first: Yun

last: Zheng

state: Yunnan

address: 452 Fengyuan Road

institute: Yunnan Agricultural University

type: Non-coding RNA profiling by high throughput sequencing

summary: Recent results demonstrated that either non-coding or coding genes generate phased secondary small interfering RNAs (phasiRNAs) guided by specific miRNAs. Till now, there is no studies for phasiRNAs in Panax notoginseng (Burk.) F.H. Chen (P. notoginseng), an important traditional Chinese herbal medicinal plant species. Here we performed a genome-wide discovery of phasiRNAs and its host PHAS loci in P. notoginseng by analyzing small RNA sequencing profiles. Degradome sequencing profile was used to identify the trigger miRNAs of these phasiRNAs and potential targets of phasiRNAs. We also used RLM 5'-RACE to validate some of the identified phasiRNA targets. After analyzing 24 small RNA sequencing profiles of P. notoginseng, 204 and 90 PHAS loci that encoded 21 and 24 nucleotide (nt) phasiRNAs were identified. Furthermore, we found that phasiRNAs produced from some pentatricopeptide repeat-contain (PPR) genes target another layer of PPR genes as validated by both the degradome sequencing profile and RLM 5'-RACE analysis. We also find that miR171 with 21 nt triggers the 21 nt phasiRNAs from its conserved targets. We validated that some phasiRNAs generated from PPRs are functional by targeting other PPRs in trans. These results provide the first set of PHAS loci and phasiRNAs in P. notoginseng, and enhance our understanding of PHAS in plants.

overall_design: Identification of phased small inferfering RNAs in Panax notoginseng by analyzing small RNA sequencing profiles of root tutor or whole plant using Illumina HiSeq 2000 sequencer.


title: Gene expression profile in external auditory canal squamous cell carcinoma

city: Shanghai

first: Hong

last: Liu

state: Shanghai

address: 83 Fenyang Road

department: Department of Otology and Skull Base Surgery

institute: Eye & Ear Nose and Throat Hospital, Fudan University

summary:
External auditory canal squamous cell carcinoma (EACC) is very rare, only accounting for two thousandth of the head and neck cancer. However, the development mechanism of EACC remains unknown. By using gene expression microarray analysis, we aimed to find differentially expressed genes involved in ESCC development. We identified a wide spectrum of molecular signatures in EACC, including  mRNA and lncRNA.
The present study systematically analyzed the expression of mRNA and lncRNA in squamous cell carcinoma of the external auditory canal and normal external auditory canal tissues. We detect the transcriptomic changes between squamous cell carcinoma of the external auditory canal and normal external auditory canal tissues to identify potential tumor biomarkers in squamous cell carcinoma of the external auditory canal.

overall_design: We selected patients with external auditory canal squamous cell carcinoma (EACC) who received surgery. The fresh EACC and normal external auditory canal tissues were collected from patients during surgery. Total RNA was extracted. The transcriptomic expression of genes was analyzed on Affymetrix microarrays.

first: Chunfu

last: Dai


title: Genome-wide transcriptional profiling of M.TB–specific antigens stimulated peripheral blood mononuclear cells (PBMCs) for identification of potential signatures in discriminating active tuberculosis from latent infection

city: Beijing

first: Liping

last: Pan

address: 97 Machang Road, Tongzhou District

institute: Beijing Chest Hospital, Capital Medical Universtiy.

summary: To further understand the host immune factors involved in the progression from latent tuberculosis infection (LTBI) to active tuberculosis (TB) and identify the potential signatures for discriminating TB from LTBI, the genome-wide transcriptional profile of the Mycobacterium.Tuberculosis (M.TB)–specific antigens stimulated peripheral blood mononuclear cells (PBMCs) from active TB, LTBI and health controls (HCs) were performed. A total of 209- and 234- differentially expressed genes (Fold change > 4, P < 0.05) were detected in comparisons of TB vs. LTBI and TB vs. HCs, respectively. Nineteen differentially expressed genes with top fold change between TB and the other two groups were validated in the same RNA samples by real-time PCR, and showed 94.7% consistent expression pattern with microarray test.

overall_design: Genome-wide transcriptional profiling of M.TB–specific antigens stimulated PBMCs (ESAT-6/CFP-10, stimulated for 24h at 10ug/ml) from active TB, latent TB infection individuals and healthy controls, were simultaneously measured using Agilent microarray technique. Four independent samples were included in each group (TB, LTBI, and HCs).

first: Zongde

last: Zhang


title: Next Generation Sequencing Facilitates Quantitative Analysis of Thymic Transcriptomes from Wild Type and Mir-146a Transgenic Mice

first: Zinan

last: Li

address: #5 Dong Dan San Tiao

department: Immunology

institute: Institute of Basic Medical Sciences of the Chinese Academy of Medical Sciences

summary:
Purpose: To find out the global transcriptomic change induced by overexpression of miR-146a in thymus
Methods:Thymic mRNA profile of two pools from age (five to six-week old)- and gender (one male and one female for each pool)- matched wild-type (WT) and miR-146a transgenic (Tg) mice were generated by deep sequencing using Illumina HiSeq 2500. The clean reads that passed quality filters were mapped against Mus musculus genome using HotHap2, and the only uniquely mapped reads were used to calculate reads per kilobase of exon per million fragment (RPKM) values for each sample. The transcript isoform with a fold-change over 2 and q<0.001 were considered differentially expressed.
Conclusion: Our study identified 101 differently expressed transcripts in thymus from miR-146a Tg mice, including 56 down-regulated transcripts covering 49 genes which are the candidate targets of miR-146a

overall_design: Thymic mRNA profile of pools from WT and Tg mice were generated by deep sequencing using HiSeq 2500.

first: Weiqing

first: Huaishan


title: Transcriptome analysis of murine macrophages infected with different strains of Leptospira spp

status: Public on Feb 13 2018

city: Araçatuba

first: Flavia

middle: Lombardi

last: Lopes

state: São Paulo

address: Rua Clovis Pestana, 793

department: DAPSA

country: Brazil

institute: FMVA-UNESP

summary: Leptospirosis is a neglected zoonotic disease of global importance. Despite its prevalence, pathogenesis is still poorly understood. Our aim was to discover transcripts responsable for pathogenicity of leptospirosis. We compared the transcriptome profiles of saprophyte, attenuated and virulent strain of Leptospira spp.

overall_design: Four treatments were performed in triplicates in J774A.1 macrophages in vitro, as follows: non-infected control cells and cells infected with virulent, attenuated and saprophyte strains of Leptospira. Following 6h of infection, total RNA was extracted and 250 ng of total RNA (RIN 10) was used to evaluate the mRNA profile using the microarray Affymetrix®  Mouse Gene 2.1 ST Array Strips. Raw intensity values were background corrected, log2 transformed and then quantile normalized by the software Expression Console (Affymetrix) using the Robust Multi-array Average (RMA-Sketch) algorithm. Next, statistical analysis was performed in the TAC software (Affymetrix) by ANOVA (fold change ± 2,  FDR-corrected p<0.01).

first: Erivelto

middle: C

last: Júnior

first: Leandro

middle: E

last: Garcia

first: Juliana

middle: R

last: Peiró

first: Daniel

last: Arnold

first: Márcia

last: Marinho


title: RNA-sequencing of in vitro differentiated WT and Chi3l1 KO Th1 cell

city: Seoul

first: Do-Hyun

last: Kim

address: 222 Wangsimni-ro

country: South Korea

institute: Hanyang University

summary: We report the differential mRNA expressino of WT and Chi3l1 KO Th1 cells. We cultured WT and Chi3l1 KO naive CD4 T cells under Th1 skewing condition : plate-bound anti-CD3/28 antibody (2ug/mL), IL-12 0.2ng/mL, IL-2 50U/mL, anti-IL-4 neutralizing antibody 2ug/mL, for 3 days. We found different Th1 regulatory and tumoricidal-related gene expression in Chi3l1 KO T cells.

overall_design: Comparison of RNA expressino in WT and Chi3l1 KO Th1 cells

first: Je-Min

last: Choi


title: Defense against territorial intrusion is associated with DNA methylation changes in the honey bee brain

city: Urbana

first: Brian

middle: R.

last: Herb

state: IL

address: 2500 IGB, MC-195, 1206 W Gregory Dr

department: Carl R. Woese Institute for Genomic Biology

institute: University of Illinois at Urbana-Champaign

type: Methylation profiling by high throughput sequencing

summary:
Background: Aggression is influenced by individual variation in temperament as well as behavioral plasticity in response to adversity. DNA methylation is stably maintained over time, but also reversible in response to specific environmental conditions, and may thus be a neuromolecular regulator of both of these processes. A previous study reported DNA methylation differences between aggressive Africanized and gentle European honey bees. We investigated whether threat-induced aggression altered DNA methylation profiles in the honey bee brain in response to a behavioral stimulus (aggression-provoking intruder bee or inert control). We sampled five minutes and two hours after stimulus exposure to examine the effect of time on epigenetic profiles of aggression.
Results: There were DNA methylation differences between aggressive and control bees for individual cytosine-guanine dinucleotides (CpGs) across the genome. Eighteen individual CpG sites showed significant difference between aggressive and control bees 120 minutes post stimulus. For clusters of CpGs, we report four genomic regions differentially methylated between aggressive and control bees at the 5-minute time point, and 50 regions differentially methylated at the120-minute time point following intruder exposure. Differential methylation occurred at genes involved in neural plasticity, chromatin remodeling and hormone signaling. Additionally, there was a significant overlap of differential methylation with previously published epigenetic differences that distinguish aggressive Africanized and gentle European honey bees, suggesting an evolutionarily conserved use of brain DNA methylation in the regulation of aggression. Lastly, we identified individually statistically suggestive CpGs that as a group were significantly associated with differentially expressed genes underlying aggressive behavior and also co-localize with binding sites of transcription factors involved in neuroplasticity or neurodevelopment.
Conclusions: There were DNA methylation differences in the brain associated with response to an intruder. These differences increased in number a few hours after the initial exposure and overlap with previously reported aggression-associated genes and neurobiologically relevant transcription factor binding sites. Many DNA methylation differences that occurred in association with the expression of aggression in real time also exist between Africanized bees and European bees, suggesting an evolutionarily conserved role for epigenetic regulation in aggressive behavior.

overall_design: Aggressive and control bees were collected 5 minutes and 120 minutes post interaction with either an intruder bee or inert object

first: Molly

middle: S

last: Shook

first: Gene

last: Robinson


city: Los Angeles

first: Galyna

last: Bondar

state: CA

address: 10833 Le Conte Ave, CHS 32-164

department: Medicine-Cardiology

institute: UCLA

summary: This data represents whole transcriptome total RNA gene expression profiles of peripheral blood mononuclear cells collected from 29 advanced heart failure patients on the day before undergoing mechanical circulatory support surgery. Keywords = Advanced Heart Failure. Keywords =  Mechanical Circulatory Support. Keywords = Biological Age. Keywords = PBMC. Keywords = Immune Response. Keywords = Peripheral Blood. Keywords =Organ Function. Keywords = Recovery. Organism: Homo sapiens. Type: Expression profiling by array. Platforms: Illumina HiSeq 2500.

overall_design: Heart failure patients' peripheral blood mononuclear cell gene expression profiles before mechanical circulatory support mechanical circulatory support surgery.

first: Ryan

last: Togashi

first: Martin

last: Cadeiras

first: Joanna

last: Schaenman

first: Richard

last: Cheng

first: Lindsay

last: Masukawa

first: Josephine

last: Hai

first: Amy

last: Le

first: Tra-Mi

last: Bao

first: Dan

last: Tran

first: Desai

last: Chu

first: Eleanor

last: Chang

first: Maral

last: Bakir

first: Sophie

last: Kupiec-Weglinski

first: Azadeh

last: Esmaeili

first: Giovanny

last: Godoy

first: Victoria

last: Groysberg

first: Tristan

last: Grogan

first: Joseph

last: Meltzer

first: Murray

last: Kwon

first: Maura

last: Rossetti

first: David

last: Elashoff

first: Elaine

last: Reed

first: Pei-Pei

last: Ping

first: Mario

last: Deng


title: Expression data from HUVECs infected with influenza A virus  PR8 and CA07

first: Wu

last: Ying

address: No. 11, Bei San Huan Dong Lu, Chaoyang District

department: Department of Microbiology and Immunology

institute: Beijing University of Chinese Medicine

summary:
Using human umbilical vein endothelial cells (HUVECs) as cell models, the present study aims to explore the differential miRNAs in influenza virus-infected ECs and analyze their target genes involved in EC permeability regulation. As the results showed, permeability increased and F-actin cytoskeleton reorganized after HUVECs infected with influenza A virus (CA07 or PR8) at 30 MOI.
most of these miRNAs were down-regulated after flu infection. It has been reported that PKC, Rho/ROCK, HRas/Raf/MEK/ERK, and Ca2+/CaM pathways are activated by flu infection and play important roles in permeability regulation.

overall_design: When grown to 90% confluency, HUVECs were removed from the culture medium and washed twice with PBS. Cells were infected with inﬂuenza A virus in serum-free media at a multiplicity of infection (MOI) of 20~40 and harvested at the indicated time points. The non-infected cells were used as normal control.

first: Ying

last: Wu

first: Zinan

last: Xuan

first: Shujing

last: Zhang

first: Xiaoming

last: Chen

first: Junjie

first: Dongyu

last: Ge

first: Xudan

last: Wang


title: Whole-genome IAP methylation data for mouse sperm and tail DNA.

city: Nagoya

first: Kenji

last: Ichiyanagi

address: Furo-cho, Chikusa-ku

department: Graduate School of Bioagricultural Sciences

country: Japan

institute: Nagoya University

summary: IAP is one of the most transpositinally active retrotransposons in the mouse. Its transcription starts from the 5' long terminal repeat (LTR), and the expression level varied between cell types. This variation is thought to arise from differences in the epigenetic states, such as DNA methylation, of some copies of the 5' LTR between the cells. However, due to the high copy number and high sequence similarity, it was difficult to comprehensively and individually analyze epigenetic state of the IAP LTRs. Here, we developed a method called TEPBAT (Target Enrichment after Post-Bisulfite Adaptor Tagging) to analyze DNA methylation of individual retrotransposon copies. Using the method, we determined DNA methylation levels of >8,500 copies of genomic IAP LTRs (>97% of the copies targeted by the PCR primer) in sperm and tail. This revealed that the vast majority of the LTRs were heavily methylated both in sperm and tail, but hypomethylated copies were more frequently found in sperm than in tail. Interestingly, most of these hypomethylated LTRs were solo-type, belonged to specific subfamilies, and carried binding sites for transcription factors (TFs) active in male germ cells. We discuss possible roles for these TF-binding sites and the IAP internal sequence in regulation of LTR methylation.

overall_design: To study DNA methylation levels of individual IAP LTR loci comprehensively, genomic DNA was treated with bisulfite and the complementary strands were synthesized by PBAT. IAP LTR loci were then selectively amplified by PCR. The PCR products were ligated to the Illumina adaptor, followed by HiSeq sequencing (a lane per sample).

first: Ken-ichi

last: Shimosuga

first: Kei

last: Fukuda

first: Hiroyuki

last: Sasaki


title: Genome-wide profiling of DNA hydroxymethylation patterns in iAs-transformed cells

city: Grand Rapids

first: Yvonne

middle: Nsokika

last: Fondufe-Mittendorf

state: MI

address: 333 Bostwick Ave NE

department: Epigenetics

institute: Van Andel Institute

summary: To examine the global impact of iAs on DNA hdroxymethylation patterns. Genomic DNA was glucosylated, digested and analyzed using Reduced Representation Hydroxymethylation Profiling.

overall_design: DNA from both NT and iAs-transformed cells were  glucosylated, digested and analyzed using Reduced Representation Hydroxymethylation Profiling.

first: Matthew

last: Rea


title: Gene expression profiling during active Lyme arthritis development (22 days post infection with B. burgdorferi) in CD45 negative cells isolated from joint tissue of highly genetically similar mouse strains: B6, ISRCL4, and ISRCL3

city: Salt Lake City

first: Jacqueline

last: Paquette

state: UT

address: 15 North Medical Drive #1100

department: Pathology

institute: University of Utah

summary: Previously, using a forward genetic approach we identified B. burgdorferi arthritis-associated locus 1 (Bbaa1), a quantitative trait locus on Chr4, which physically encompasses the type I IFN gene cluster and regulates Lyme arthritis through heightened type I IFN production. Reciprocal radiation chimeras between B6.C3-Bbaa1 and B6 mice revealed that arthritis is initiated by radiation-sensitive cells, but orchestrated by radiation-resistant components of joint tissue. Advanced congenic lines were developed to reduce the physical size of the Bbaa1 interval, and RNA-seq of resident CD45- joint cells from advanced interval specific recombinant congenic lines (ISRCL4 and ISRCL3) identified myostatin as uniquely upregulated in association with Bbaa1 arthritis development. Our manuscript further demonstrates that myostatin expression is linked to IFN-β production, and in vivo inhibition of myostatin suppresses Lyme arthritis in the reduced interval Bbaa1 congenic mice, formally implicating myostatin as a novel downstream mediator of joint-specific inflammatory response to B. burgdorferi.

overall_design: 22 days following infection with B. burgdorferi, mouse rear ankle joints were gently digested into single-cell suspensions and CD45 negative cells were isolated by magnetic bead separation. CD45 negative cells from both rear ankle joints of two mice were pooled for each n sample in order to increase RNA concentration for gene expression analysis (n=5 per genotype). Gene expression comparisons were made between B6 (control group) and ISRCL4/ISRCL3 congenic lines.

first: Jackie

first: Janis

middle: J

last: Weis

first: Brian

last: Dalley

first: Chris

last: Stubben


title: Staphylococcus aureus evades macrophage killing through NLRP3 dependent effects on mitochondrial trafficking

city: Gaithersburg

first: Taylor

last: Cohen

state: MD

address: One Medimmune Way

institute: MedImmune

summary: Respiratory innate immunity requires alveolar macrophages, which are specifically targeted by the S. aureus toxin alpha toxin. These data compare the response of alveolar macrophages to S. aureus with or without alpha toxin neutralization.

overall_design: We used microarrays to detail the response of alveolar macrophages to S. aureus with or without alpha toxin neutralization.

first: Michelle

last: Boland

first: Brandon

middle: B

first: Virginia

last: Takahashi

first: Andrey

last: Tovchigrechko

first: Aimee

last: Wilde

first: Young

last: Lee

first: Mark

last: Mazaitis

first: Omari

last: Jones-Nelson

first: Christine

last: Tkaczyk

first: Rajiv

last: Raja

first: C

last: Stover

first: Bret

last: Sellman


title: Increased metastatic capacity of breast cancer cells after interaction and hybrid formation with mesenchymal stroma/stem cells (MSC)

city: Hannover

first: Ralf

last: Hass

state: Germany

address: Carl-Neuberg-Str. 1

department: Gynecology

institute: Hannover Medical School

summary: Functional changes were investigated in vitro and in vivo following spontaneous fusion and hybrid cell formation in co-cultures of primary human mesenchymal stroma/stem-like cells (MSC) with human MDA-MB-231 breast cancer cells. Lentiviral fluorescence-labeled MSC with eGFP and breast cancer cells labeled with mcherry resulted in dual-fluorescing hybrid cells. Double FACS sorting and single cell cloning revealed two different aneuploid male hybrid populations (MDA-hyb1 and MDA-hyb2)

overall_design: A total of 4 different total RNA samples was subjected to microarray analysis according to a single-color design.

first: Catharina

last: Melzer


title: FOXO in mouse brain

city: New york

first: Jihye

last: Paik

state: NY

address: 1300 York Ave.

institute: Weill Cornell Medical College

summary: Gene expression in FOXO KO vs WT brain

overall_design: Total RNA was isolated and analyzed

first: Florian

last: Muller


title: Detection of viral double-stranded RNA from Vero cells infected with HSV-1-mCherry

city: Parkville

first: Alexandra

last: Garnham

state: Victoria

address: 1G Royal Parade

institute: Walter and Eliza Hall Institute of Medical Research

summary: The aim of this experiment was to determine whether viral double-stranded RNA from HSV-1 infected cells were detectable in non infected cells

sample_organism:
Chlorocebus aethiops
Human alphaherpesvirus 1

overall_design: Vero cells were infected with mCherry-tagged HSV-1 virus and sorted for mCherry in order to deliniate between infected and uninfected cells. Stranded RNAseq was subsequently performed in order to identify overlapping HSV-1 RNA derived from both strands of the viral genome which correspond to double-stranded RNA.

first: Tan

middle: A

last: Nguen

first: Ken

last: Pang


title: Transcriptome of Ustilago maydis during tumour formation in bundle sheath and mesophyll cells of Zea mays L.

city: Cologne

first: Corinna

last: Ernst

address: Kerpener Straße 34

department: University Hospital Cologne

institute: University of Cologne

summary: The biotrophic fungus Ustilago maydis causes smut disease on maize (Zea mays L.), which is characterized by immense plant tumours. To establish disease and reprogram organ primordia to tumours, U. maydis deploys effector proteins in an organ-specific manner. However, the cellular contribution to leaf tumours remains unknown. We investigated leaf tumour formation on the tissue- and cell type-specific level. Cytology and metabolite analysis were deployed to understand the cellular basis for tumourigenesis. Laser-capture microdissection was performed to gain a cell-type specific transcriptome of U. maydis during tumour formation. In-vivo visualization of plant DNA synthesis identified bundle sheath cells as the origin of hyperplasic tumour cells, while mesophyll cells become hypertrophic tumour cells. Cell type specific transcriptome profiling of U. maydis revealed tailored expression of fungal effector genes. Moreover, U. maydis See1 was identified the first cell type specific fungal effector, being required for induction of cell cycle reactivation in bundle sheath cells. Identification of distinct cellular mechanisms in two different leave cell types, and See1 as an effector for induction of proliferation of bundle-sheath cells, are major steps in understanding U. maydis-induced tumor formation. Moreover, the cell-type specific U. maydis transcriptome data is a valuable resource to the scientific community.

sample_organism:
Zea mays
Mycosarcoma maydis

platform_organism:
Zea mays
Mycosarcoma maydis

overall_design: To analyze the cell type specific transcriptome of U. maydis during the indcution of plant tumors, transcriptomic profiling of U. maydis from LCM-dissected tumour cells was done. At 4 dpi, SG200 infected HTT cells, bundle sheath-derived HPT cells, and SG200Δsee1 infected HTT cells (Δsee1 HTT) were isolated. As controls, mesophyll and bundle sheath cells from mock treated leaf tissue of the same age were isolated.

last: Matei

first: Gunther

last: Doehlemann


title: Primed primary metabolism in systemic leaves: a functional systems analysis

city: Potsdam

first: Joachim

last: Kopka

state: Brandenburg

address: Am Muehlenberg 1

department: Infrastructure Groups and Service Units

institute: Max Planck Institute For Molecular Plant Physiology

summary: During their co-evolution, plants have learned to counteract bacterial infection by preparing yet uninfected tissues for an enhanced defence response, the so-called systemic acquired resistance or priming response. Primed leaves express a wide range of genes that enhance the defence response once an infection takes place. While hormone-driven defence signalling and generation of defensive metabolites has been well studied, less focus has been set on the reorganization of primary metabolism in systemic leaves. Since primary metabolism plays an essential role for fuelling and optimizing defences in terms of providing energy and chemical building blocks, we investigated medium-term primed changes in primary metabolism at RNA and metabolite levels in systemic leaves of Arabidopsis thaliana plants that were locally infected with Pseudomonas syringae. While known defence genes were still activated 3-4 days after infection, we also found several parts of primary metabolism to be significantly altered. Nitrogen (N)-metabolism and content of amino acids and other N-containing metabolites were significantly reduced, whereas the organic acids fumarate and malate were strongly increased. We suggest that reduction of N-metabolites in systemic, yet non-infected leaves primes defence against bacterial infection by reducing the nutritional value of systemic tissue. The increased organic acids serve as a quickly available metabolic resource of energy and carbon-building blocks for the production of defence metabolites during subsequent secondary infections.

overall_design: Transcriptome profiling by RNA-sequencing of 18 systemic leaf samples from Arabidopsis thaliana Col-0 treated with P. syringae or mock.

first: Jens

last: Schwachtje

first: Axel

last: Fischer

first: Alexander

last: Erban


title: Beyond the polymerase-gamma theory: Respiratory chain inhibition and production of ROS as modes of NRTI induced mitochondrial toxicity

city: Amsterdam

first: Martijs

last: Jonker

address: Science Park 904

department: Microarray Department

country: Netherlands

institute: University of Amsterdam

summary: HIV-1 nucleoside reverse transcriptase inhibitor (NRTI) use is associated with severe adverse events. However, the exact mechanisms behind their toxicity has not been fully understood. Mitochondrial dysfunction after chronic exposure to NRTIs has predominantly been assigned to mitochondrial polymerase- inhibition by NRTIs. However, an increasing amount of data suggests that this is not the sole mechanism. Many NRTI induced adverse events have been linked to the incurrence of oxidative stress, although the causality of events leading to reactive oxygen species (ROS) production and their role in toxicity is unclear. In this study we show that short-term effects of these drugs, which are rarely discussed in the literature, include direct inhibition of the mitochondrial respiratory chain (MRC), decreased ATP levels and increased ROS production. Collectively these events affect fitness and longevity of C. elegans through mitohormetic signalling events. Furthermore, we demonstrate that these effects can be normalized by addition of the anti-oxidant N-acetylcysteine (NAC), which suggests that ROS likely influence the onset and severity of adverse events upon drug exposure.

overall_design: RNA-seq on Caenorhabditis elegans exposed to DMSO,  3'-azido-3'-deoxythymidine (zidovudine or AZT), 2',3'-didehydro-2',3'-deoxythymidine (stavudine or d4T), 3'-deoxy-3'-fluorothymidine (alovudine or FLT) or untreated control after 24 or 72 hours of exposure.

first: Reuben

last: Smith

first: Josephine

middle: M

last: Tan

first: Aldo

last: Jongejan

first: Thomas

last: Buissink

first: Steve

last: Veldhuijzen

first: Antoine

middle: H

last: van Kampen

first: Stanley

last: Brul

first: Hans

last: van der Spek


title: Single Cell RNA-Seq profiling human embryonic kidney cortex cells

first: Andrew

middle: P

last: McMahon

state: California

address: 1425 San Pablo St, BCC 312

department: Stem Cell Biol & Regen Med

institute: University of Southern California

summary: To characterize the cellular diversity in the human kidney cortical nephrogenic niche we dissociated cells from the cortex and performed 10X Genomics single-cell RNA sequencing.

overall_design: Identifying cell types and nephrogenic programs in the developing human kidney

last: Ransick

first: Albert

last: Kim

first: Guilherme

last: De Sena Brandine

first: Nils

middle: O

last: Lindstrom


title: Tet2 loss dysregulates the behavior of bone marrow derived mesenchymal stromal cells [hME-Seal]

city: Tianjin

first: Rong

last: Li

state: Tianjin

address: No.288, Nanjing Road,Heping District

department: Institute of Hematology and Blood Diseases Hospital

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

summary: Identification the genome-wide distribution of 5-hmC in WT-MSCs and Tet2-/--MSCs by Genome-wide 5hmc Profiling.

first: Yuan

last: Zhou

first: Feng-Chun

last: Yang

first: Zhigang

last: Zhao


title: Tet2 loss dysregulates the behavior of bone marrow derived mesenchymal stromal cells

summary:
TET2 plays an important role in regulating the behavior of bone marrow derived MSCs in addition to its intrinsic role in HSPCs to participate in aberrant hematopoiesis. Moreover, MSCs are the most important niche cell components in Tet2-/- mice that contribute to the progression of Tet2 deletion-driven myeloid malignancies.

This SuperSeries is composed of the SubSeries listed below.

overall_design:
TET2 plays an important role in regulating the behavior of bone marrow derived MSCs in addition to its intrinsic role in HSPCs to participate in aberrant hematopoiesis. Moreover, MSCs are the most important niche cell components in Tet2-/- mice that contribute to the progression of Tet2 deletion-driven myeloid malignancies.

Refer to individual Series


title: SUV420H2 knockdown in PANC-1

city: South San Francisco

first: Suchit

last: Jhunjhunwala

address: 1 DNA Way, MS-444A

institute: Genentech

summary: PANC-1 cells were treated with siRNA against SUV420H2 to monitor the progressive transition between epithelial/mesenchymal states. Controls were untreated. Genentech internal expressionplot project id is PRJ0007677

overall_design: SUV420H2 knockdown in PANC-1


title: Comparison of microarray expression data from 23 day mouse germ cells from control and Mgat1 conditional knockout mice

city: BRONX

first: PAMELA

last: STANLEY

address: 1300 MORRIS PARK AVE

department: CELL BIOLOGY

institute: ALBERT EINSTEIN COLLEG OF MEDICINE

summary:
Loss of Mgat1 in spermatogonia was investigated in germ cells from 23 day males. Gene expression changes induced by deletion of Mgat1 were determined using the Affymetrix GeneChip Mouse Gene 2.0 ST Array.
We include the expression data obtained from three replicate aliquots of pooled testis total RNA obtained from six control or six conditional knockout Mgat1 testis germ cells from 23 dpp males,  Three replicates of the respective control and Mgat1 cKO pools were used for microarray analysis using Affymetrix GeneChip Whole Transcript Plus Reagent Kit. We identified differential expressed genes with a significance level of ANOVA and FDR p < 0.05 and an absolute fold-change (linear)  less than -2, and greater than 2.0.

overall_design: RNA from 3 replicates of control and 3 replicates of mutant germ cell RNA pools were purified using Trizol and Rneasy minielute clean up kit (Qiagen), RNA integrity was measured and samples with RIN >9.0 were submitted for cDNA preparation and microarray analysis.

first: Pamela

last: Stanley

first: Barnali

last: Biswas


title: LAKTP_MTO orthotopic primary caecum tumours from Galunisertib-treated C57BL/6J mice

status: Public on Feb 12 2018

city: Sabadell

first: Antoni

last: Berenguer-LLergo

state: Barcelona

address: Parc del Taulí, 1

department: A8G2 Group - Rheumatology Service

institute: Parc Taulí Research and Innovation Institute (I3PT)

summary: Mouse tumour organoids (MTOs) derived from a compound mutant (LAKTP) intestinal cancer model were orthoptopically transplanted into syngeneic C57BL/6J mice. Tumour-bearing mice were treated with TGF-beta inhibitor Galunisertib or vehicle control. Whole tumour mRNA was extracted from primary tumours and expression profiling was performed with the objective to characterize the tumour microenvironment (TME). As a TGF-beta-activated TME has been associated to a poor prognosis and the CRC consensum molecular subtype CMS4, and the mouse model was found to have such an activated TME, we used the array data to classify these tumours in this mouse model system as CMS4-like. Furthermore, treatment with TGF-beta inhibitor reduced the fibroblast- and T cell-specific TGF-beta response signatures, also associated to poor prognosis in human CRC. This treatment was associated to a strong reduction/prevention of liver metastasis, as well as a reduction of primary tumour (and local carcinomatosis) size.

overall_design: For every MTO, two biological replicates were included: every strip was set up with 2 control samples vs 2 treated samples

first: Daniele

middle: V

last: Tauriello


title: Comparison of microarray expression data from 22 day mouse germ cells from control and Mgat1 conditional knockout mice

summary:
Mechanistic insights into MGAT1 loss during spermatogenesis were  investigated in germ cells from 22 day males. Gene expression changes induced by deletion of Mgat 1in spermatogonia were determined using the Affymetrix  GeneChip Whole Transcript Plus Reagent Kit.
We include the expression data obtained from control and conditional knock out Mgat1 mutant mouse testis germ cells . We identified the  genes that were differentially expressed (DEGs) in 22 day Mgat1 mutant versus control germ cells, with a significance level of ANOVA p < 0.05 and an absolute fold-change (linear) less than -2 and greater than 2.0.

overall_design: RNA from 3 control and 3 mutant germ cell preparations was purified using RNeasy mini kit and Rneasy Minielute clean up kit (Qiagen), RNA integrity was measured and samples with RIN >9.0 were submitted for cDNA preparation and microarray analysis.


title: RNA-Seq analysis of maize lines resistant and susceptible to Cercospora zeina, causal organism of Grey leafspot disease

city: Cape Town

first: Shane

last: Murray

address: University Avenue North

department: Dept of Molecular and Cell Biology

country: South Africa

institute: University of Cape Town

summary:
Purpose: The aim was to compare the transcriptome (using RNASeq) of a Cercospora zeina-resistant line (RIL387) and a Cercospora zeina susceptible line (RIL165), following inoculation by Cercospora zeina, in order to identify the defense responses associated with each line.

Methods: Plants were grown in rows in three randomised blocks.  Natural infection with Cercospora zeina was allowed to take place.  Infected leves were harvested at the R5-early dent stage.  Three leaves (one per plant) were harvested per block and pooled to make up one biological rep.  One biological rep was harvested per block for each line.  RNA was extracted and sequenced using Illumina.  Sequencing reads were mapped to the B73 reference genome and were analysed using the Tuxedo suite of tools (Top hat, Cufflinks, Cuffmerge and Cuffdiff).

Results: 5349 genes were differentially expressed between RIL165 and RIL387.  In order to dissect responses specific to RIL165 and RIL387, 2394 genes with Log2FC ≤-1 were defined as having higher expression in RIL165 compared to RIL387 and 1393 genes with a Log2FC ≥1 as having increased expression in RIL387 compared to RIL165.  Nine genes were validated using RT-qPCR.  Four reference genes were included in the RT-qPCR analysis.  Differentially expressed genes were further analysed for GO enrichment and pathway representation.

Conclusions: Our RNA-Seq results show that a resistant and susceptible line repond differently to infection with Cercospora zeina, as differentially expressed genes were identified between the two lines.

overall_design: A total of 6 biological replicates were analysed.  Cercospora zeina inoculated leaves were harvested from field grown plants.  Three biological replicates came from the susceptible RIL line 165 and three biological replicates came from the resistant RIL line 387

first: Jacqueline

last: Meyer

middle: L

first: Dave

middle: K

last: Berger


title: Kinome and transcriptome profiling reveal broad and distinct activities of erlotinib, sunitinib, and sorafenib in the mouse heart and suggest cardiotoxicity from combined STAT and EGFR inhibition

city: Chapel Hill

first: Brian

middle: Colwell

last: Jensen

state: NC

address: 6012 Burnett-Womack Building, CB 7075

department: Cardiology

institute: UNC School of Medicine

summary: We administered clinically relevant doses of sorafenib, sunitinib (cardiotoxic multi-targeted kinase inhibitors) or erlotinib (a cardiosafe EGFR inhibitor) to mice daily for two weeks. We then compared the effects of these three kinase inhibitors on the cardiac transcriptome using RNAseq and the cardiac kinome using multiplexed inhibitor beads coupled with mass spectrometry.  We found unexpectedly broad molecular effects of all three kinase inhibitors, suggesting that target kinase selectivity does not define either the molecular response or the potential for cardiotoxicity. Using in vivo drug administration and primary cardiomyocyte culture, we also show that the cardiosafety of erlotinib treatment may result from upregulation of the cardioprotective STAT3 pathway, as co-treatment with erlotinib and a STAT inhibitor decreases cardiac contractile function and cardiomyocyte fatty acid oxidation.

overall_design: 12 total murine heart samples: (3) water control, (3) 14 day sunitinib treatment, (3) 14 day sorafenib treatment, (3) 14 day erlotinib treatment


title: Comparison of microarray expression data from 22 and 23 day mouse germ cells from control and Mgat1 conditional knockout mice

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

overall_design: Refer to individual Series


title: Changes in relative transcript amounts caused by treatment of streptozotocin and floxuridine in S.aureus USA300

city: Bloomington

first: Ram

last: Podicheti

state: IN

institute: Indiana University

summary: Staphylococcus aureus is an important human pathogen causing skin infection and many serious diseases such as pneumonia, sepsis, and toxic shock syndrome. We identified two anti-cancer drugs, streptozotocin (STZ) and floxuridine (FU), as promising lead compounds for further optimization into effective anti-virulence drugs against S. aureus infections.   To understand the molecular mechanism of the in vivo efficacy of STZ and FU, we carried out RNA-seq. S. aureus USA300 was treated with 1 ug/mL (= 3.8 uM for STZ, 4 uM for FU) for 3 h. STZ treatment altered transcription of 829 genes (382 up-regulated; 447 down-regulated) whereas FU affected the transcription of 1192 genes (580 up-regulated; 612 down-regulated). Importantly, both compounds inhibited the transcription of the other virulence-regulatory systems such as Agr, Arl, and SarA.  Therefore, the results indicate that the high in vivo efficacy of STZ and FU might be due to their repression of multiple virulence regulatory systems.

overall_design: RNA was prepared from cultures of strains USA300_P23 (control), streptozotocin treated and floxuridine treated cells in TSB media at 37°C. Three independent biological replicates of RNA were prepared for each strain or condition. cDNA libraries were sequenced and the sequencing results were used as the data base for differential expression analysis.

first: Bae

last: Taeok

first: Yeo

last: Won-Sik

first: Douglas

last: Rusch


title: Spatial and single-cell transcriptional profiling identifies functionally distinct human dermal fibroblast subpopulations

city: San Francisco

first: Angela

last: Oliveira Pisco

address: 499 Illinois St

department: Data Science

institute: Chan Zuckerberg Biohub

summary:
Expression data from P2 mouse fibroblasts sorted for CD26, Sca1 and Dlk1. We have sorted mouse fibroblasts using the different lineages markers
In this dataset, we include 3 biological replicates for CD26+, Sca1+Dlk1-, Sca1+Dlk1+ and Sca1-Dlk1+, a total of 12 samples

overall_design: 12 samples were analysed and performed all the pairwise comparisons

first: S

last: Telerman

first: A

last: Pisco

first: F

last: Watt


title: Loss of ASXL1 in the bone marrow niche dysregulates hematopoietic stem cell fates

city: Miami

first: Feng-Chun

last: Yang

state: FL

address: 1011 NW 15th Street

institute: University of Miami Miller School of Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Identification of ASXL1 binding profile in WT MSPCs and examination of PolII in WT and Asxl1-/- MSPCs.

overall_design: Identification of ASXL1 binding profile in WT BMSCs and examination of PolII in WT and Asxl1-/- BMSCs.

first: Peng

last: Zhang

first: Zizhen

last: Chen


title: Expression profile analysis of long noncoding RNA in acute myeloid leukemia versus iron-deficiency anemia

city: Xi'an City

first: Aili

last: He

address: NO.157 Xiwu Rd

department: Hematology

institute: The Second Affiliated Hospital of Xi'an Jiao Tong University

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: To determine whether lncRNAs are involved in acute myeloid leukemia (AML), we analyzed the expression profile of lncRNAs and mRNAs in AML.

overall_design: In the study presented here, 5 pairs of AML patients and iron deficiency anemia (IDA) controls were screening by microarray.


title: Neutrophils in systemic onset Juvenile Idiopathic Arthritis display sepsis-like features which can be reverted by IL-1 blockade

city: Utrecht

first: Michal

last: Mokry

address: Lundlaan 6

institute: Wilhelmina Children's Hospital, University Medical Center Utrecht

summary: This study investigated neutrophils in systemic onset Juvenile Idiopathic Arthritis (sJIA), one of the most common multifactorial autoinflammatory diseases, characterized by arthritis and severe systemic inflammatory manifestations like fever, rash, hepatosplenomegaly and serositis. Neutrophil counts were markedly increased at disease onset, correlated to levels of inflammatory mediators and normalized within days after initiation of therapy with recombinant IL-1 receptor antagonist (rIL-1RA). Neutrophils isolated from 3 sJIA patients with active disease, before initiation of therapy (2 disease onset, 1 systemic flare) and 3 healthy controls were compared. A clear separation between the transcriptome of sJIA patients and HCs was observed. In total, 1068 genes were significantly upregulated and 625 genes were downregulated in sJIA; GO-analyses indicated upregulation of inflammatory processes in sJIA neutrophils compared to HCs. GSEA analyses revealed a significant enrichment with the transcriptome of neutrophils in sepsis patients. Correspondingly, neutrophils from sJIA patients during active disease displayed a primed phenotype characterized by an increased respiratory burst, CD62L shedding and degranulation of secretory vesicles. This phenotype was completely reversed in sJIA patients in remission on rIL-1RA. Our data show an important role for neutrophils in the early inflammatory phase of sJIA and a strong susceptibility of neutrophil numbers and inflammatory activity to IL-1 signaling blockade.

overall_design: Transcriptomes from peripheral blood neutrophils of 3 systemic JIA patients and 3 healthy controls


title: Ageing-related bladder dysfunctions and their gender differences in mice: in vitro and in vivo functional and gene expression changes

city: Toyohashi

first: Toshio

last: Kojima

address: 1-1 Hibarigaoka Tenpaku-cho

department: Health Care Center

institute: Toyohashi University of Technology

summary:
Objective
To investigate aging-related changes and their sex differences in in vivo and in vitro functions and gene expression in the bladder of mice.
Materials and Methods
Mature (12-month old) and aged (27–30-month old) mice of both sexes were studied. In in vivo experiments, frequency, volume, and conscious free-moving cystometry measurements were investigated. In in vitro experiments, organ bath studies using detrusor strips were performed to observe functional changes, and serum sex hormone levels and mRNA expression of muscarinic, purinergic, and β-adrenergic receptors in the bladder using a cDNA microarray were evaluated.
Results
Although few differences were detected in the frequency/volume measurements between the two groups in either sex, aged mice showed a lower mean flow rate and higher number of non-voiding contractions in both sexes and lower maximum pressure and smaller voided volume and bladder capacity was observed in males according to cystometry measurements. Detrusor strips from aged mice showed weaker contractile responses to carbachol and electrical field stimulation, particularly in the cholinergic component, and relaxant responses to isoproterenol, which were accompanied by a decreased mRNA expression of M3 muscarinic receptors in aged males and β2-adrenoceptors in aged females. This aging-related bladder dysfunction was more severe in males, and the serum testosterone level in aged males was significantly decreased. Gene expression changes in the bladder with aging were different between sexes: 469 and 544 genes in males, 392 and 75 in females, and 8 and 37 in both sexes were significantly upregulated and downregulated, respectively, with aging.
Conclusions
Aged mice of both sexes demonstrated both voiding and storage dysfunctions, which were more pronounced in males. Sex hormone and genomic changes associated with aging may contribute to this functional deterioration in mice.

overall_design: C57BL/6 male and female mice were divided into two groups: matured mice (12 months-old; male: N = 4, female: N = 4, respectively) and aged mice (27-30 months-old; male: N = 4, female: N = 4, respectively). Mice were maintained under standard laboratory conditions with a 12:12 h light (9:00 a.m. to 9:00 p.m.) and dark (9:00 p.m. to 9:00 a.m.) cycles, and free access to food pellets and tap water. Experimental protocols were approved by the Animal Ethics Committee, The University of Tokyo Graduate School of Medicine, Tokyo, Japan, and were in line with NIH guidelines for the care and use of experimental animals. Mice were obtained from the Tokyo Metropolitan Institute of Gerontology, and after 1-week adaptation period, they were used for measurements.

first: Jun

last: Kamei

first: Hiroki

last: Ito

first: Naoki

last: Aizawa

first: Harumi

last: Hotta

first: Yasunori

last: Fujita

first: Masafumi

first: Yukio

last: Homma

first: Yasuhiko

last: Igawa


title: Determine the ADAR1 editome during IFN response.

status: Public on Feb 09 2018

city: New York

first: Jorg

last: Calis

state: NEW YORK

address: 1230 York Avenue

institute: The Rockefeller University

summary: ADAR1 is an interferon (IFN) inducible RNA editing enzyme that converts adenosine (A) to inosine (I). Here we identified ADAR1 and ADAR1p150 specific editing events by conducting RNA-seq on WT, ADAR1 KO, and ADAR1p150 KO cells.

overall_design: Mock or IFNb (1nM) treat WT, ADAR1 KO, and ADAR1p150 KO cell lines. For each genotype, three independent cell clones were used.

first: Charles

last: Rice

first: Hachung

last: Chung

first: Brad

last: Rosenberg


title: Mammary tumors of xenograft mice with the treatment of nicotine and JMY117 as well as CHRNA9 and SLC19A7 knockdown in MDA-MB-231, A549 and Hep3B cells

status: Public on Feb 10 2018

city: Hsinchu

first: Jinn-Moon

last: Yang

address: 75 Po-Ai Street

institute: National Chiao Tung University

summary: First, we want to know whether JMY117 (Bupropion) would act as a blockade to attenuate nicotine induced cancer metastatic effect. With two months observations, we discovered that nicotine treatment (10 µg/ml) via drinking water significantly increased tumor distant metastasis. Furthermore, using 100 and 200 µg/kg JMY117 three times per week significantly suppressed the numbers of lung metastasis nodules on both with or without nicotine treatment, indicating JMY117 not only block the signals from nicotine but also inhibits the signals from other endogenous nAChR agonists. In addition, we also investigated the roles of CHRNA9 and SLC16A7 in breast cancer (MDA-MB-231), lung cancer (A549) and liver cancer (Hep3B) cell lines

overall_design: The experiment of mammary tumors of xenograft mice with the treatment of nicotine and JMY117 includes six groups: Control (no treatment), JMY117 100 µg/kg addition, JMY117 200 µg/kg addition, nicotine exposure, JMY117 100 µg/kg addition with nicotine exposure, and JMY117 200 µg/kg addition with nicotine exposure. Nicotine was added in the drinking water of 10 µg/ml. The experiment of CHRNA9/SLC19A7 knockdown in MDA-MB-231 cells contains three groups: Control (no knockdown), CHRNA9 knockdown, and SLC16A7 knockdown. The experiment of CHRNA9/SLC19A7 knockdown in A549 cells contains three groups: Control (no knockdown), CHRNA9 knockdown, and SLC16A7 knockdown. The experiment of CHRNA9 knockdown in Hep3B cells contains three groups: Control (no knockdown), CHRNA9 knockdown 1, and CHRNA9 knockdown 2. RNA was prepared from treated cells and analyzed by microarray.

first: Chun

middle: Y

last: Lin

first: Chia

last: Lee

first: Jung

first: Yuan

last: Ho

first: Jinn


title: Expression profiles of Arabidopsis thaliana Col-0 seedlings and seedlings of a mutant impaired in cytoplasmic calcium elevation in response to cellotriose treatment (Johnson et al., 2017)

city: Jena

first: Doreen

last: Meichsner

address: Dornburger Strasse 159

department: General Botany and Plant Physiology

institute: FSU Jena

summary:
The endophytic fungus Piriformospora indica is a member of Sebacinales. It colonizes the roots of many plant species including the model plant Arabidospis thaliana (Peskan-Berghofer et al. 2004). P. indica promotes plant growth (Peskan-Berghofer et al. 2004), seed production (Shahollari et al. 2007) and confers resistance to biotic (Camehl et al. 2011) and abiotic stresses (Sherameti et al., 2008, Matsuo et al., 2015). Vadassery et al. (2009) have shown that a cell wall extract from P. indica induces cytoplasmic calcium elevation in Arabidopsis Col-0 roots. Johnson et al. (2017) isolated an ethylmethane-induced mutant cycam (cytoplasmic calcium elevation mutant) which fails to induce cytoplasmic calcium elevation in response to the cell wall preparation. The active compound was identified as cellotriose (CT) (Johnson et al., 2017). The cycam mutant shows a wild-type response to treatment with chitin. The expression profiles compare the response of WT and cycam roots to treatments with CT and chitin.
References: Camehl I, Drzewiecki C, Vadassery J, Shahollari B, Sherameti I, Forzani C, Munnik T, Hirt H, Oelmüller R. (2011) The OXI1 kinase pathway mediates Piriformospora indica-induced growth promotion in Arabidopsis. PLoS Pathog. 7(5):e1002051.   Johnson JM, Thürich J, Petutschnig EK, Altschmied L, Meichsner D, Sherameti I, Dindas J, Mrozinska A, Paetz C, Scholz S, Furch A, Lipka V, Hedrich R, Schneider B,  Svatoš S, Oelmüller R. (2017) Cellotriose-induced cytoplasmic calcium elevation is controlled by a poly(A) ribonuclease in Arabidopsis root. (submitted to elife).  Matsuo M, Johnson JM, Hieno A, Tokizawa M, Nomoto M, Tada Y, Godfrey R, Obokata J, Sherameti I, Yamamoto YY, Böhmer FD, Oelmüller R. (2015) High REDOX RESPONSIVE TRANSCRIPTION FACTOR1 Levels Result in Accumulation of Reactive Oxygen Species in Arabidopsis thaliana Shoots and Roots. Mol Plant. 8(8):1253-73.  Peškan-Berghöfer T, Shahollari B, Giang PH, Hehl S, Markert C, Blanke V, Varma AK, Oelmüller R. (2004) Association of Piriformospora indica with Arabidopsis thaliana roots represents a novel system to study beneficial plant–microbe interactions and involves early plant protein modifications in the endoplasmatic reticulum and at the plasma membrane. Physiol. Plant. 122: 465–477.   Shahollari B, Vadassery J, Varma A, Oelmüller R. (2007) A leucine-rich repeat protein is required for growth promotion and enhanced seed production mediated by the endophytic fungus Piriformospora indica in Arabidopsis thaliana. Plant J. 50(1):1-13.  Sherameti, I., Tripathi, S., Varma, A., and Oelmüller, R. (2008). The root-colonizing endophyte Pirifomospora indica confers drought tolerance in Arabidopsis by stimulating the expression of drought stress-related genes in leaves. Mol. Plant Microbe Interact. 21: 799-807.  Vadassery, J., Ranf, S., Drzewiecki, C., Mithöfer, A., Mazars, C., Scheel, D., Lee, J., and Oelmüller, R. (2009) A cell wall extract from the endophytic fungus Piriformospora indica promotes growth of Arabidopsis seedlings and induces intracellular calcium elevation in roots. Plant J. 59: 193-206.

overall_design: 13 day-old Arabidopsis seedlings, Col-0 and the cycam mutant, were grown under long day conditions and light (60-70 µM m-2 sec-1, 16 h light/8 h dark) at 22°C. For CT and chitin (chitohexaose) treatments (10 µM), the roots of 13-day old seedlings were soaked in a solution containing either CT or chitin; autoclaved H2O (control) was used as control. The seedlings were then transferred to long day conditions before the roots were harvested at 0 h, 4 h and 8 h after the treatments. The roots were then frozen in liquid nitrogen before RNA extraction. Data are based on 3 independent biological replicates. For additional experimental information, cf. Johnson et al. (2017).

first: Ralf

last: Oelmüller


title: Expression data from normal weight/obese and sham/injured female C57BL/6J mice

city: Ulm

first: Jens-Uwe

last: Werner

address: Albert-Einstein-Allee 23

institute: Ulm University Hospital

summary:
Injury of skeletal muscle is a common occurence affecting millions worldwide. Injuries usually are not major incisions into daily life, however, the underlying health varies e. g. due to obesity. Obesity is usually accompanied by excessive and dysfunctional lipid depots, chronic low-grade inflammation as well as several co-morbidities, which are able to impair the regeneration of skeletal muscle.
A blunt injury approach was used to damage mouse skeletal muscle of the extensor iliotibialis anticus in both obese and normal weight C57BL/6J mice. Microarray analysis was used to assess the molecular fingerprint in different stages of muscle regeneration while observing different health conditions.

overall_design: Muscle tissue from extensor iliotibialis anticus of normal weight and obese female mice, control and injury (n = 3). Harvesting time points were 1h, 6h, 24h, 3d and 8d to cover the early and middle stage regeneration process. Isolation of total RNA with subsequent microarray analysis performed with the Affymetrix system. 100 ng RNA per sample were used as described in the GeneChip® WT PLUS Reagent Kit from Affymetrix. Mouse Gene 1.0 ST Array GeneChip was used. Analysis of arrays was carried out with Affymetrix GeneChip Scanner 3000 and evaluated using Affymetrix Expression Console™. Evaluation of the CEL files was designed in R with RStudio. Briefly, injured versus control animals were normalized by RMA fit for time and diet, respectively. Pval function was used to determine p-values. Regulation of genes was first assessed without consideration for significance or expression levels to develop an unbiased time lapse heatmap. Significance level p ≤ 0.05 was introduced to screen for differentially expressed genes (DEG).

first: Uwe

last: Knippschild

first: Martin

last: Wabitsch

first: Pengfei

last: Xu

first: Annette

last: Schürmann

first: Markus

last: Jähnert

first: Pascal

last: Gottmann


title: Reprogramming of Schwann Cells by LATS1/2-TAZ/YAP Signaling Drives Malignant Peripheral Nerve Sheath Tumorigenesis

city: Cincinnati

first: Richard

last: Lu

state: OH

address: 3333 Burnet Ave

department: CBDI

institute: Cincinnati Children's Hospital Medical Center

summary: Malignant peripheral nerve sheath tumors (MPNSTs) are highly aggressive Schwann cell (SC)-lineage derived sarcomas with poor prognosis. The molecular events underlying SC lineage cells-to-MPNST transformation remain elusive. Here, we show that human MPNSTs exhibit elevated HIPPO-TAZ/YAP expression, and that TAZ/YAP hyperactivity in SCs caused by Lats1/2 loss potently induces high-grade nerve-associated tumors with full penetrance. Lats1/2 deficiency reprograms SCs to a cancerous, progenitor-like phenotype and promotes hyper-proliferation. Conversely, disruption of TAZ/YAP activity alleviates tumor burden in Lats1/2-deficient mice and inhibits human MPNST cell proliferation. Moreover, genome-wide target profiling reveals that TAZ/YAP-TEAD1 directly activates a set of oncogenic programs in SCs including PDGFR/RAF signaling. Co-targeting TAZ/YAP and PDGFR/RAF signaling efficaciously reduces tumorigenicity in Lats1/2-deficient tumors. Thus, our findings establish a previously unrecognized convergence between LATS1/2-TAZ/YAP pathway and MPNST pathogenesis, suggesting that combined inhibition of TAZ/YAP-PDGFR/RAF signaling may be beneficial in MPNSTs.

overall_design: 3 Control and 6 Mutant for RNA-seq, ChIP-seq and ATAC-seq

first: Lai

last: Wu

first: Qing


title: Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain

city: Philadelphia

first: Bushra

last: Raj

state: PA

address: 421 Curie Boulevard

institute: University of Pennsylvania

summary: The lineage relationships among the hundreds of cell types generated during development are difficult to reconstruct. A recent method, GESTALT, used CRISPR–Cas9 barcode editing for large-scale lineage tracing, but was restricted to early development and did not identify cell types. Here we present scGESTALT, which combines the lineage recording capabilities of GESTALT with cell-type identification by single-cell RNA sequencing. The method relies on an inducible system that enables barcodes to be edited at multiple time points, capturing lineage information from later stages of development. Sequencing of ∼60,000 transcriptomes from the juvenile zebrafish brain identified >100 cell types and marker genes. Using these data, we generate lineage trees with hundreds of branches that help uncover restrictions at the level of cell types, brain regions, and gene expression cascades during differentiation. scGESTALT can be applied to other multicellular organisms to simultaneously characterize molecular identities and lineage histories of thousands of cells during development and disease.

overall_design: inDrops libraries of single-cell transcriptomes and scGESTALT barcodes, and genomic DNA GESTALT libraries


title: Expression analysis of BMP7 responsive P2RY1/ALK3 expressing progenitor like cells within the human exocrine pancreas

status: Public on Feb 08 2018

first: Juan

last: Domínguez-Bendala

address: 1450 NW 10th Ave Miami

department: Department of Surgery

institute: Diabetes Research Institute, University of Miami, Miller School of Medicine

summary:
Purpose: Here we demonstrate ALK3Bright/PDX1+ cells residing within the human pancreatic ducts have progenitor like characteristics. Using flow cytometery, live-cell sorting of ALK3bright/PDX1+ cells is possible using a surrogate surface marker for PDX1 (P2RY1). Treating ALK3bright/P2RY1+ cells with BMP7 results in their expansion. Later removal of BMP7 results in the differentiation of these cells to β-like cells. Here we compare the mRNA expression profiles of these three different cell types (in triplicate).
Methods: mRNA profiles of ALK3Bright/P2RY1+ cells isolated from human non-endocrine pancreatic tissue, ALK3Bright/P2RY1+ cells treated with BMP7 and ALK3Bright/P2RY1+ cells differentiated to β-like cells after BMP7 removal were generated by deep sequencing, in triplicate, using Illumina HiSeq PE Cluster Kit v4 and Illumina HiSeq Flow Cell v4 with 50 nt paired end reads plus dual index reads using the Illumina HiSeq SBS kit v4. Sequence reads that passed quality filters were analyzed at the transcript isoform level following alignment using TopHat v2.1.0 followed by exon and gene level counting using Bioconductor easyRNASeq v 2.4.7.
Conclusions: Our study represents the first detailed analysis of ALK3Bright/P2RY1+ sorted cells with biological replicates. We demonstrate ALK3Bright/P2RY1+ cells were shown to form progenitor-like epithelial colonies characterized by NKX6.1 and PDX1 expression. Unlike the negative fraction controls, these colonies responded to BMP-7 by generating new β-like cells as well as cells from other pancreatic lineages. The transcriptional profile of these cells and their BMP7 treated counterparts suggest a mitotic and progenitor like state. Our studies confirm the progenitor-like nature of ALK3Bright/PDX1+ cells within the human pancreas and suggest a specific anatomical location within the ductal network.

overall_design: Comparison of transcriptional expression in Alk3Bright/P2RY1+ cells, Alk3Bright/P2RY1+ cells treated with BMP7 and Alk3Bright/P2RY1+ cells allowed to differentiate after BMP7 removal. Human islets, isolated from the same donors were included as a control.

first: Mirza

last: Fahd Qadir

last: Dominguez-Bendala

first: Ricardo

last: Pastori


title: Transcriptome analysis of IMR90 fibroblasts expressing OSKM or control vector and OSKM-induced senescent IMR90 fibroblasts upon p21CIP or mTOR knockdown

city: London

first: Gopuraja

last: Dharmalingam

address: Faculty of Medicine, Imperial College, Hammersmith Hospital Campus

department: Epigenetics section

country: United Kingdom

institute: MRC London Institute of Medical Sciences

summary: Ectopic expression of the transcription factors Oct4, Sox2, Klf4 and c-Myc (OSKM) can reprogram somatic cells into induced pluripotent stem cells (iPSCs). These iPSCs are highly similar to embryonic stem cells and can be used for regenerative medicine, drug screening and disease modelling. Despite recent advances, reprogramming is a slow and inefficient process. This suggests that there are several safeguarding mechanisms to counteract cell fate conversion. Cellular senescence is one of these barriers, which is mediated through activation of the tumour suppressors p53/p21CIP1, p15INK4b and p16INK4a. In this study, we have screened for shRNAs blunting reprogramming-induced senescence. To investigate the effects of OSKM expression on the transcriptome of human primary IMR90 fibroblasts, we performed RNA-sequencing (RNA-Seq). Cells were transduced with OSKM expression or control vector and RNA was extracted after 14 or 20 days. In addition, to study the transcriptome of cells bypassing OSKM-induced senescence due to p21 or mTOR depletion, we performed RNA-seq of cells transduced with OSKM and shRNA expressing vectors targeting p21 or mTOR for 14 or 20 days.

overall_design: 8 samples in triplicate: IMR90 + OSKM + shRNA targeting p21CIP1 for 20 days (O211_1) or 14 days (O211_2), IMR90 + OSKM + different shRNA targeting p21CIP1 for 20 days (O212_1) or 14 days (O212_2), IMR90 + OSKM + shRNA targeting mTOR for 20 days (OmT2_1) or 14 days (OmT2_2), IMR90 + OSKM + different shRNA targeting mTOR for 20 days (OmT3_1) or 14 days (OmT3_2), IMR90 + control vector for 20 days (EV_1), IMR90 + control vector for 14 days (EV_2), IMR90 + OSKM for 20 days (OSKM_1),  IMR90 + OSKM for 14 days (OSKM_2)

first: Marieke

last: Aarts

first: Jesus

last: Gil

first: Thomas

last: Carroll


title: Differentially expressed microRNAs in the aqueous humor of patients with exfoliation glaucoma or primary open-angle glaucoma

city: Augusta

first: Yutao

last: Liu

state: GA

address: 1120 15th Street

department: Cell Biology and Anatomy

institute: Medical College of Georgia

summary: To better understand the molecular changes in the aqueous humor (AH) content with glaucoma, we analyzed the microRNA (miRNA) profiles of AH samples from patients with Primary Open Angle Glaucoma (POAG) and Exfoliation Glaucoma (XFG) compared to non-glaucoma controls.

overall_design: This study profiled the expression of miRNAs in AH from patients with POAG (n = 12), XFG (n = 12), and cataract controls (n = 11).

first: Michelle

middle: D

last: Drewry


title: p38-MK2 signaling axis regulates RNA metabolism  after UV light-induced DNA damage

city: Mainz

first: Petra

last: Beli

address: Ackermannweg 4

institute: Institute of Molecular Biology (IMB)

summary: Ultraviolet (UV) light radiation induces the formation of bulky photoproducts in the DNA that globally affect transcription and splicing. However, the signaling pathways and mechanisms that link UV light-induced DNA damage to changes in RNA metabolism remain poorly understood. Here, we employ quantitative phosphoproteomics and protein kinase inhibition to provide a systems view on protein phosphorylation patterns induced by UV light, and uncover the dependencies of phosphorylation events on the canonical DNA damage signaling by ATM/ATR and the p38 MAP kinase pathway. We identify RNA binding proteins as primary substrates and 14-3-3 as direct readers of p38-MK2-dependent phosphorylation induced by UV light. Mechanistically, we show that MK2 phosphorylates the RNA binding subunit of the NELF complex NELFE on Serine 115. NELFE phosphorylation promotes the recruitment of 14-3-3 and rapid dissociation of the NELF complex from chromatin, which is accompanied by RNA polymerase II elongation.

overall_design: Analysis of RNA pol II occupancy genome-wide in mock-treated U2OS cells and cells exposed to UV light (40 J/m2, 1 hour recovery).


title: Transcripts within Rod Photoreceptors of the Zebrafish Retina

city: Moscow

first: Deborah

middle: Lynn

last: Stenkamp

state: Idaho

address: 875 Perimeter Drive, MS 3051

department: Biological Sciences

institute: University of Idaho

summary: Purpose: The purpose of this study was to identify transcripts of rod photoreceptors of the zebrafish, an important animal model for vision science. Methods: Zebrafish rods, and non-rod retinal cells of the XOPS:eGFP transgenic line, were separated by cell dissociation and fluorescence-activated cell sorting (FACS), followed by RNA-seq. Validation studies used qPCR and in situ hybridization. Some transcripts were examined in sorted retinal cell populations of larval and juvenile retinas and regenerated adult retinas, and in a zebrafish model for rod degeneration. Results: At a false discovery rate of <0.01, 597 transcripts were upregulated in rods vs. non-rod retinal cells, and 1032 were downregulated. 13,324 total transcripts were detected in rods, including many not previously known to be expressed by rods. Transcripts enriched in rods from adult retinas were also enriched in rods from larval and juvenile retinas, and were also enriched in regenerated rods. Many transcripts enriched in rods were upregulated in retinas of wildtype retinas vs. those of a zebrafish model for rod degeneration. Conclusions: We report the generation of an RNA-seq dataset describing the rod transcriptome of the zebrafish, which is now available as a resource for further studies of rod photoreceptor biology and comparative transcriptomics.

overall_design: 8 samples analyzed: 4 GFP+ (FACS-sorted rods), 4 GFP- (FACS-sorted non-rods from retina); the two retinas from each of four fish contributed to each sample.

first: Chi

last: Sun


title: Coupling shRNA screens with single-cell RNA-Seq identifies mechanisms regulating senescence during reprogramming

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

overall_design: Refer to individual Series


title: Gene  expression profiles of ibrutinib-responsive and ibrutinib non-responsive cells in ERBB4 expressing cancer cell lines

status: Public on Feb 07 2018

city: Tempe

first: Joshua

last: LaBaer

state: AZ

address: 1001 S McAllister Ave

department: Biodesign Institute

institute: ASU

summary: By  using a unique functional protein microarray platform, we found that the FDA approved drug ibrutinib can inhibits ERBB4 activity in the same nM range as its canonical target, BTK. Cell-based assays revealed that ibrutinib treatment inhibited cell growth in some ERBB4 expressing cancer cells whereas no response was observed in other cells. Therefore, to identify global gene expression differences between ibrutinib responsive and non-responsive cancer cells, we performed RNA-Seq, and identified a signature featuring the WNT pathway that predicts growth responsiveness to ibrutinib in ERBB4 expressing cancers.

overall_design: Examination of gene expression profiles of 4 ibrutinib responsive and 4 ibrutinib non-responsive ERBB4 expressing cancer cell lines

first: Jin

middle: G

last: Park

first: Femina

last: Rauf

first: Fernanda

last: Festa


title: CD157 positive endothleilal stem cells in the liver

city: Mitaka

first: Jun-ichi

last: Suehiro

state: Tokyo

address: 6-20-2, Shinkawa

department: Department of Pharmacology and Toxicology

institute: Kyorin University School of Medicine

summary: Analysis of primary liver endothelial cells (ECs) isolated from WT mice. Results provide insight into the heterogeniety of liver ECs.

overall_design: To explore endothelial stem cell marker, DNA microarray analysis was performed to compare the gene expression profiles between EC-SP cells and EC-MP cells, and among CD157+CD200+ ECs, CD157-CD200+ ECs, and CD157-CD200- ECs from adult liver. Three independent samples were collected.

first: Taku

last: Wakabayashi

first: Hisamichi

last: Naito


title: Transcription factor Hoxb5 reprograms B cells into functional T lymphocytes

city: chengdu

first: Yong

last: Dong

state: sichuan

address: Xindu road 783, Xindu district

department: Immunology

institute: Chengdu medical college


title: Tacrolimus-induced nephrotoxicity in mice is associated with microRNA deregulation

status: Public on Feb 06 2018

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

summary:
Although Tacrolimus is an immunosuppressive drug widely used in renal transplantation, its chronic use paradoxically induces nephrotoxic effects, in particular renal fibrosis, which is responsible for chronic allograft dysfunction and represents a major prognostic factor of allograft survival. As molecular pathways and mechanisms involved in Tacrolimus-induced fibrogenic response are poorly elucidated, we assessed whether miRNAs are involved in the nephrotoxic effects mediated by Tacrolimus. Treatment of CD-1 mice with Tacrolimus (1mg/kg/d for 28 days) resulted in kidney injury and was associated with alteration of a gene expression signature associated with cellular stress, fibrosis and inflammation. Tacrolimus also affected renal miRNA expression, including miRNAs previously involved in fibrotic and inflammatory processes including “fibromirs” such as miR-21-5p. Specifically, Renal Proximal Tubular Epithelial cells exposed to tacrolimus showed up-regulation of miR-21-5p and the concomitant induction of epithelial phenotypic changes, inflammation and oxidative stress. In conclusion, this study suggests for the first time that miRNAs, especially fibromiRs, mediate Tacrolimus-induced nephrotoxic effects.

This SuperSeries is composed of the SubSeries listed below.

first: C

last: Cauffiez

first: G

last: Savary

first: N

last: Nottet

last: Pottier

first: B

last: Mari


title: Tacrolimus-induced nephrotoxicity in mice is associated with microRNA deregulation (miRNome analysis)

summary: Although Tacrolimus is an immunosuppressive drug widely used in renal transplantation, its chronic use paradoxically induces nephrotoxic effects, in particular renal fibrosis, which is responsible for chronic allograft dysfunction and represents a major prognostic factor of allograft survival. As molecular pathways and mechanisms involved in Tacrolimus-induced fibrogenic response are poorly elucidated, we assessed whether miRNAs are involved in the nephrotoxic effects mediated by Tacrolimus. Treatment of CD-1 mice with Tacrolimus (1mg/kg/d for 28 days) resulted in kidney injury and was associated with alteration of a gene expression signature associated with cellular stress, fibrosis and inflammation. Tacrolimus also affected renal miRNA expression, including miRNAs previously involved in fibrotic and inflammatory processes including “fibromirs” such as miR-21-5p. Specifically, Renal Proximal Tubular Epithelial cells exposed to tacrolimus showed up-regulation of miR-21-5p and the concomitant induction of epithelial phenotypic changes, inflammation and oxidative stress. In conclusion, this study suggests for the first time that miRNAs, especially fibromiRs, mediate Tacrolimus-induced nephrotoxic effects.

overall_design: CD-1 mice were treated with Tacrolimus (1mg/kg/d for 28 days) or physiological serum as control (n=4) and total RNA was prepared from kidneys. Experiment performed in a one color design, corresponding to 2 conditions (Control: CTL and Tacrolimus: TAC) for a total of 8 samples.


title: pre-B cells from normal control, preleukemic, fully leukemic and fully leukemic, nilotinib-treated P190 BCR/ABL transgenic mice

status: Public on Feb 05 2018

city: Monrovia

first: Nora

last: Heisterkamp

state: CA

address: 1218 S Fifth Avenue

department: Department of Systems Biology

institute: Beckman Research Institute City of Hope

summary:
Precursor B-lineage acute lymphoblastic leukemia (pre-B ALL) can be subdivided into different categories based on genetic abnormalities.
One type of pre-B ALL is characterized by the presence of the Philadelphia (Ph) chromosome, the derivative chromosome 22 that is one product of a reciprocal translocation between chromosomes 22 and 9. The 22/9 translocation fuses the 5’ part of the BCR gene to the 3’ end of the c-ABL gene. The resulting BCR/ABL fusion encodes a Bcr/Abl protein with deregulated Abl kinase activity. Two major fusion proteins are found in Ph-positive leukemias which differ in molecular weight and the size of the Bcr moiety. The P190 Bcr/Abl protein is common in Ph-positive ALL. Targeted tyrosine kinase inhibitors such as nilotinib are used therapeutically to treat this type of leukemia.
The 22/9 translocation fuses the 5’ part of the BCR gene to the 3’ end of the c-ABL gene.
The resulting BCR/ABL fusion encodes a Bcr/Abl protein with deregulated Abl kinase activity. Two major fusion proteins are found in Ph-positive leukemias which differ in molecular weight and the size of the Bcr moiety.
The P190 Bcr/Abl protein is common in Ph-positive ALL. Targeted tyrosine kinase inhibitors such as nilotinib are used therapeutically to treat this type of leukemia.

overall_design: Mice transgenic for the human P190 form of Bcr/Abl (Jackson Labs strain 017833) develop precursor B-lineage (pre-B) acute lymphoblastic leukemia, on average within 3 months of birth, when on a C57Bl/6J background. Bone marrows were isolated from control C57BLl/6J mice and from transgenic Bcr/Abl mice when they had not yet developed full-blown leukemia (<60 days of age), from Bcr/Abl transgenic mice with overt leukemia and packed bone marrows (>90 days of age), and from fully leukemic mice that had received a seven-day treatment with 75 mg/kg AMN107 (nilotinib). Three mice were used per condition, and cells from each mouse were processed separately. Pre-B cells from these twelve bone marrows were flow-sorted using CD19 and AA4.1 as markers. Total RNA from CD19+ AA4.1+cells used for microarray analysis was isolated by RNeasy (QIAGEN) purification. Double-strand complementary DNA was generated from 5 µg of total RNA using a poly(dT) oligonucleotide that contains a T7 RNA polymerase initiation site and the SuperScript III reverse transcription (Invitrogen). Biotinylated cRNA was generated and fragmented according to the Affymetrix protocol and hybridized to 430 mouse microarrays (Affymetrix).

middle: C

first: P

last: Kaur

first: D

last: Trageser

first: L

last: Klemm

first: M

last: Muschen


title: Next Generation Sequencing Facilitates Quantitative Analysis of Health donors and SLE patients' PBMC Transcriptomes

city: 上海

first: Junli

last: Liu

address: New Research Buliding,320 Yue Yang Road Shanghai, P.R.China

institute: Institute of Health Sciences   Shanghai Institutes for Biological Sciences   Chinese Academy of Sciences

summary: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare SLE patients to Health donors PBMCs-derived transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to discovery the potential pathway which can be used as a therapeutic target.

overall_design: Methods: Peripheral blood from Health donors and SLE patients with high or low peli1 expression was collected，PBMCs was processed to RNA-sequencing.

first: Yichuan

last: Xiao


title: Expression analysis of melanocyte stem cells from Mitfmi-vga9/+ mice reveals a role for MITF in the transcriptional regulation of innate immune gene expression

status: Public on Feb 04 2018

city: Bethesda

first: Derek

last: Gildea

state: MD

address: 12 South Drive Rm 4009-24

institute: NHGRI/NIH

summary: Melanocyte stem cells (McSCs) and mouse models of hair graying serve as useful systems to uncover mechanisms involved in stem cell self-renewal and the maintenance of regenerating tissues. Interested in assessing genetic variants of hair graying, we found that the Mitfmi-vga9/+ strain of mice is susceptible to loss of McSC maintenance via ectopic McSC differentiation. Based on transcriptome and molecular analyses of Mitfmi-vga9/+ mice we report a novel role for MITF in the regulation of systemic innate immune gene expression. We also demonstrate that viral mimic (poly I:C) is sufficient to expose genetic susceptibility to hair graying. These observations point to a critical suppressor of innate immunity and the consequences of its dysregulation, and for melanocytes, both may have particular implications for the autoimmune, depigmenting disease vitiligo.

overall_design: RNA-seq gene expression analysis was performed on melanocyte stem cells isolated from wildtype and Mitfmi-vga9/+ animals. These melanocyte stem cells were isolated from 8-week-old mice using flow cytometry. Melanocyte stem cells from approximately 10, 8-week-old animals were pooled to generate enough RNA to serve as one biological replicate. RNA-seq analysis was performed in biologial triplicate for each genotype.

first: Melissa

last: Harris

first: Temesgen

last: Fufa

first: Sandeep

middle: S

last: Joshi

first: Denise

last: Larson

first: Arturo

last: Incao

middle: E

first: Niraj

last: Trivedi

first: Joseph

middle: W

last: Palmer

first: Autumne

middle: N

last: Lee

first: Thomas

last: Hornyak

first: William

last: Pavan


title: PARP14 controls the nuclear accumulation of a subset of type I Interferon-inducible proteins [ChIP-seq]

city: Milano

first: Viviana

last: Piccolo

state: Milano

address: Via Adamello 16

department: Department of Experimental Oncology

country: Italy

institute: European Institute of Oncology (IEO)

summary: The enzymes of the poly-ADP-ribose polymerase (PARP) super-family control many relevant cellular processes, but a precise understanding of their activities in different physiological or disease contexts is largely incomplete. We found that transcription of several PARP genes was dynamically regulated upon macrophage activation by several inflammatory stimuli. Specifically, PARP14 was strongly induced by endotoxin stimulation and translocated to the nucleus in stimulated cells. Quantitative mass spectrometry analysis showed that PARP14 bound to a group of interferon-stimulated gene (ISG)-encoded proteins, most with an unknown function, and it was required for their nuclear accumulation. Moreover, PARP14 depletion attenuated transcription of primary antiviral response genes regulated by the transcription factor IRF3, including Ifnb1, thus reducing IFNβ production and activation of ISGs involved in the secondary antiviral response. Overall, these data hint at a role of PARP14 in the control of antimicrobial responses and specifically in nuclear activities of a subgroup of ISG-encoded proteins.

overall_design: H3K27ac genomic peaks counts in PARP14 knock out RAW 264.7 macrophages relative to wild type cells

first: Greta

last: Caprara

first: Elena

last: Prosperini

first: Gianluca

last: Sigismondo

first: Alessia

last: Melacarne

first: Alessandro

last: Cuomo

first: Mark

last: Boothby

first: Maria

last: Rescigno

first: Tiziana

last: Bonaldi

first: Gioacchino

last: Natoli