title: IGF2 is an epi-driver and therapeutic target in hepatocellular carcinoma

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

institute: CIBEREHD

summary: Background & Aims: Hepatocellular carcinoma (HCC) is a major health problem. Most patients are diagnosed at advanced stages when the only approved therapy is sorafenib. Consequently, there is an urgent need to develop effective treatments. IGF-signaling is aberrantly activated in HCC, but there is no clear understanding on the molecular drivers and potential therapeutic targets within the pathway. Since IGF2-ligand is overexpressed in HCC, we aimed to elucidate its mechanism of overexpression, assess its oncogenic potential in vitro and in vivo and determine the antitumoral efficacy of molecular therapies against IGF2.  Methods: Expression profiling, miRNAs expression and methylation were analyzed in 228 HCCs focusing on IGF2. Stable HCC cell lines with knock-down and ectopic overexpression of IGF2 were generated. A chemically-induced mouse model of HCC, and genetically-engineered mouse models (GEMM) overexpressing IGF2 in the liver were generated to assess IGF2 oncogenicity. The therapeutic potential of the monoclonal antibody against IGF-ligands (IGF1/2-mAb) and its combination with sorafenib was tested in vitro and in a xenograft model.  Results: IGF2-overexpression occurred in 15% of HCC patients as a result of the epigenetic reactivation of IGF2-fetal promoters, mainly through loss of promoter methylation. Re-expression of IGF2 was associated with progenitor cell-like and poorly differentiated HCCs, and with poor prognosis (p<0.0001). In the GEMM model, IGF2-overexpression accelerated HCC progression and reduced survival (p=0.02). Conversely, IGF2-blockage using IGF1/2- mAbs delayed tumor growth and increased survival in vivo (p<0.0001), through antiproliferative and antiangiogenic mechanisms.  Conclusions: We propose IGF2 as the first actionable epi-driver in HCC, and IGF1/2-mAbs as a potential targeted therapy in a defined subset of HCC patients.  Keywords: IGF2, HCC, epidriver, IGF-pathway, monoclonal antibody, BI 836845.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
Transcriptomic study of six genetically-engineered mouse models (GEMM) overexpressing IGF2 referenced  to three GEMM control
Transcriptomic study of two cell lines: SNU449 and Hep3B. They are treated to overexpress IGF2 or knocked down. Wild type cell lines are also included

first: I

last: Martinez-Quetglas

first: R

last: Pinyol

first: J

last: Llovet


title: Baseline microbiota composition modulates antibiotic-mediated effects on the gut microbiota and host

status: Public on Aug 05 2019

city: Paris

first: Aonghus

last: Lavelle

address: Faculte de medecine, 27 Rue de Chaligny

country: France

institute: Centre de Recherche Saint-Antoine/Sorbonne Universite

summary: A study aiming to determine if mice humanized by different donors have different gut microbiota and colonic gene expression patterns in response to the administration of a commonly prescribed, broad-spectrum antibiotic (co-amoxiclav). Male, germ-free mice were humanized by one of two healthy, unrelated human donors. 56 days later, gut microbiota and colonic transcriptome samples were analyzed at baseline, by 454 pyrosequencing and Agilent microarray, respectively. Antibiotics were then administered for 7 days, following by repeated sampling of both the microbiota and colonic RNA at days 8, 11 and 18. Results of the microbiota analysis revealed marked shifts in the composition of one donor group in response to antibiotics and not the other donor group. Transcriptomics revealed a more conserved response, however the magnitude of the effect was greater in the donor group that had a greater shift in the microbiota.

overall_design: Humanization of germ-free mice by one of two unrelated human donors, (n=30; 15 mice per group) followed by antibiotic challenge and mapping of the microbiota and host response. 3 mice in each donor group at baseline and 4 mice in each group at the subsequent time points (days 8, 11 and 18).

first: Thomas

middle: W

last: Hoffmann

first: Hang

middle: P

last: Pham

first: Philippe

last: Langella

first: Eric

last: Guedon

first: Harry

last: Sokol


title: TCP5 controls leaf margin development by regulating the KNOX and BEL-like transcription factors in Arabidopsis

status: Public on Aug 03 2019

city: Shenzhen

first: Tengbo

last: Huang

state: Guangdong

address: 1066 Xuanyuan Avenue

department: College of Life Sciences and Oceanography

country: China

institute: Shenzhen university

type: Expression profiling by high throughput sequencing

summary: In this supplemental high-throughput data, we report TCP5 downstream genes in leaf marginal development by RNAseq, using 12-day old seedlings derived from the inducible over-expression lines (35S:GR-TCP5).

overall_design: comparison of DEX or MOCK treated 12-day old seedlings from  35S:GR-TCP5 lines

first: Hongyang

last: Yu

first: Peng

last: Tian


title: Transcriptional profiles of hASCs cultured on RCP

city: Tsukuba

first: Hitomi

last: Takada

state: Ibaraki

address: Higashi 1-1-1

country: Japan

institute: National Institute for Advanced Industrial Science and Technology

summary: Chronic tissue injury caused by localized radiotherapy alters the microenvironment including stem cell niches, and leads to wound healing inhibition. We precultured human adipose-derived stem cells (hASCs) on recombinant collagen peptide (RCP) scaffold, and the cells showed upregulation of cell proliferation genes and extracellular-matrix genes, compared with hASCs cultured on normal dish. Also, pathway analyses revealed hASC cultured on RCP had gene expression pattern of inflammatory suppression, cell growth promotion and activation of certain growth factors including VEGF, HGF and TGF-β1, suggesting biological activity of RCP scaffold. In chronic radiation mice models (a total of 20 Gy radiation 4 weeks in advance), treatment with hASCs and human umbilical vein endothelial cells (HUVECs) precultured on RCP achieved the best wound healing acceleration, compared with hASC on RCP group, RCP only group, and control group which showed better healing in this order. RCP scaffold, and combination use of hASCs and ECs, could be a safe, effective and practical therapeutic tool for a variety of stem cell-depleted conditions such as chronic postirradiation tissues.

overall_design: Human ASCs were cultured for 2 days on RCP scaffold or normal adhesive dish. Gene expression profiles of these two culture conditions were analyzed by microarray.

first: Takanobu

last: Mashiko


title: Identification of Soybean AGL62-like binding sites in soybean seeds during seed development

status: Public on Aug 02 2019

city: Los Angeles

first: Bob

last: Goldberg

state: CA

address: 610 Charles E Young Drive East

department: Molecular, Cell and Developmental Biology

country: USA

institute: University of California, Los Angeles

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To dissect the gene regulatory networks operating during soybean seed development, we identified the binding sites genome-wide for transcription factor in soybean seeds during seed  development using ChIP-seq

overall_design: Identification of soybean WOX9-like binding sites in soybean seeds during seed development. ChIP and total chromatin controls (input) were obtained for two replicates. Samples were sequenced using the Illumina HiSeq2500 platform.

first: Robert

middle: B

first: Nestor

last: Apuya

first: Min

last: Chen


overall_design: Identification of soybean YAB1-like binding sites in soybean seeds during seed development. ChIP and total chromatin controls (input) were obtained for two replicates. Samples were sequenced using the Illumina HiSeq2500 platform.


title: Calreticulin Ins5 and Del52 mutations impair unfolded protein and oxidative stress responses in K562 cells expressing CALR mutants.

status: Public on Aug 04 2019

city: Modena

first: Rossella

last: Manfredini

address: Via Gottardi 100

department: Life Sciences

country: Italy

institute: Centre for Regenerative Medicine

summary: Somatic mutations of calreticulin (CALR) have been described in approximately 30-40% of JAK2 and MPL unmutated Essential Thrombocythemia and Primary Myelofibrosis patients. CALR is an endoplasmic reticulum (ER) chaperone responsible for proper protein folding and calcium retention. Recent data demonstrated that the TPO receptor (MPL) is essential for the development of CALR mutant-driven Myeloproliferative Neoplasms (MPNs). However, the precise mechanism of action of CALR mutants haven't been fully unraveled. In this study, we showed that CALR mutants impair the ability to respond to the ER stress and reduce the activation of the pro-apoptotic pathway of the unfolded protein response (UPR). Moreover, our data demonstrated that CALR mutations induce increased sensitivity to oxidative stress, leading to increase oxidative DNA damage. We finally demonstrated that the downmodulation of OXR1 in CALR-mutated cells could be one of the molecular mechanisms responsible for the increased sensitivity to oxidative stress mediated by mutant CALR. Altogether, our data identify novel mechanisms collaborating with MPL activation in CALR-mediated cellular transformation. CALR mutants negatively impact on the capability of cells to respond to oxidative stress leading to genomic instability and on the ability to react to ER stress, causing resistance to UPR-induced apoptosis.

overall_design: Gene expression profile (GEP) was performed starting from total RNA of K562 cells transduced with the LCALRwtIDN (CALR wild-type, CALRwt), LCALRdel52IDN (CALRdel52), LCALRins5IDN (CALRins5) retroviral vectors. After NGFR-based purification, the transduced cells were cultured with/without Melittin (MEL, 5ug/ml) for 24 hours.

first: Simona

last: Salati

first: Elena

last: Genovese

first: Zelia

last: Prudente

first: Chiara

last: Carretta

first: Niccolo'

last: Bartalucci

first: Valentina

last: Pennucci

first: Samantha

last: Ruberti

last: Rossi

first: Sebastiano

last: Rontauroli

first: Carmela

last: Mannarelli

first: Roberta

last: Zini

first: Elisa

last: Bianchi

first: Paola

last: Guglielmelli

first: Enrico

last: Tagliafico

first: Alessandro

middle: M

last: Vannucchi


title: RRM Transcription Factors Interact with NLRs and Regulate Broad-Spectrum Blast Resistance in Rice

city: Shanghai

first: yiwen

last: Deng

state: Shanghai

address: 300 Fenglin Road

department: Institute of Plant Physiology and Ecology

institute: Shanghai Institute for Biological Sciences, Chinese Academy of Sciences

summary: Nucleotide-binding site leucine-rich repeat (NLR) receptors perceive pathogen effectors and trigger plant immunity. However, the mechanisms underlying NLR-triggered defense responses remain obscure. The recently discovered Pigm locus in rice encodes a cluster of NLRs, including PigmR, which confers broad-spectrum resistance to blast fungus. Here, we identify PIBP1 (PigmR-INTERACTING and BLAST RESISTANCE PROTEIN 1), an RRM (RNA-recognition motif) protein that specifically interacts with PigmR and other similar NLRs to trigger blast resistance. PigmR-promoted nuclear accumulation of PIBP1 ensures full blast resistance. We find that PIBP1 and a homolog, Os06 g02240, bind DNA and function as unconventional transcription factors at the promoters of the defense genes OsWAK14 and OsPAL1, activating their expression. Knockout of PIBP1 and Os06g02240 greatly attenuated blast resistance. Collectively, our study discovers previously unappreciated RRM transcription factors that directly interact with NLRs to activate plant defense, establishing a direct link between transcriptional activation of immune responses with NLR-mediated pathogen perception

overall_design: Refer to individual Series


title: Chronic mTOR Activation Induces a Degradative Smooth Muscle Cell Phenotype

city: New Haven

first: George

last: Tellides

state: CT- CONNECTICUT

address: 10 Amistad St, 337B

department: Surgery

institute: Yale University

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


title: Weight loss resulted in increased expression of the anti-inflammatory protein, CRISPLD2, in mouse adipose tissue

city: Oklahoma City

first: Jonathan

middle: D

last: Wren

state: OK

address: 825 N.E. 13th Street

department: Genes and Human Disease

institute: Oklahoma Medical Research Foundation

summary:
Purpose:  NGS was used to determine if a distinct transcriptomic profile is observed between lean, obese and weight loss fat
Methods: We carried out RNA-Seq analysis of epididymal adipose mice ad libitum fed for 10 weeks either a high fat diet (HFD) or a regular chow diet (RD), versus a cohort of mice fed HFD for the first 5 weeks before swapping to RD for the remainder (SWAP).
Results:  SWAP feeding resulted in weight loss with a parallel improvement in insulin sensitivity.  RNA-Seq revealed several transcriptomic signatures distinct to SWAP adipose, distinguished from both RD and HFD adipose.  We found a unique up-regulated mRNA encoding a secreted, LPS-binding glycoprotein, CRISPLD2, in SWAP adipose tissue.  While cellular CRISPLD2 protein levels were unchanged, plasma CRIPSLD2 levels increased in SWAP mice following weight loss, and can correlate with insulin sensitivity.
Conclusions: Taken together, our data demonstrate that CRISPLD2 is a circulating adipokine that may regulate adipocyte remodeling during weight loss.

overall_design: Five statistically independent RNA samples were sequenced for lean and obese mice.  Four independent samples were sequenced for weight loss mice.

first: Willlard

last: Freeman

first: Robert

last: Jackson

first: Ann

middle: L

last: Olson


title: Bulk RNAseq Analysis of Murine Thoracic Aortas with Tsc1+/+ and Tsc1-/- Smooth Muscle Cells

summary: We characterized the transcriptomic effects of chronic mTOR activation in aortic SMCs using a conditional genetic model to delete Tsc1 under control of a smooth muscle-specific Myh11 promoter

overall_design: Myh11-CreERT2.mT/mG (Tsc1+/+) and Tsc1fl/fl.Myh11-CreERT2.mT/mG (Tsc1−/−) male mice were treated with tamoxifen at 1.5 wk and the thoracic aortas were analyzed by bulk RNAseq at 24 wk.

first: Guangxin

last: Li


title: Proline 152 mutation in p53 abolishes cognate DNA binding, induces gain of function tumorigenesis

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

summary: We have identified a relatively rare mutation in p53 in an Indian oral cancer patient sample at the fade end of its DNA binding domain [P152L]. Although P152L p53 DBD potentially binds to DNA, the full length protein is completely devoid of cognate site DNA binding ability. Also the mutant protein can efficiently tetramerize. Significantly, this mutant was found to induce cell mobility and proliferation with greater tumorigenic potential in nude mice, the mechanistic details of which is also investigated upon. These data establish P152L as a new gain of function p53 mutation

overall_design: In order to gain the mechanistic insights of the gain-of-function effects elicited by P152L p53, RNA sequencing was performed for RNA from the tumor obtained (pCMV10 Ctrl and P152L p53) from xenograft experiment

first: S

last: Singh

first: M

last: Kumar

first: T

middle: K

last: Kundu

last: Naveen


title: Lmx1b is required at multiple stages to build expansive serotonergic axon architectures

city: Cleveland

first: Evan

last: Deneris

state: OH

address: 2109 Adelbert Rd.

department: Neurosciences

institute: Case Western Reserve University

summary: Formation of long-range axons occurs over multiple stages of morphological maturation. However, the intrinsic transcriptional mechanisms that temporally control different stages of axon projection development are unknown. Here, we addressed this question by studying the formation of mouse serotonin (5-HT) axons, the exemplar of long-range profusely arborized axon architectures. We report that LIM homeodomain factor 1b (Lmx1b)-deficient 5-HT neurons fail to generate axonal projections to the forebrain and spinal cord. Stage-specific targeting demonstrates that Lmx1b is required at successive stages to control 5-HT axon primary outgrowth, selective routing, and terminal arborization. We show a Lmx1b→Pet1 regulatory cascade is temporally required for 5-HT arborization and upregulation of the 5-HT axon arborization gene, Protocadherin-alphac2, during postnatal development of forebrain 5-HT axons. Our findings identify a temporal regulatory mechanism in which a single continuously expressed transcription factor functions at successive stages to orchestrate the progressive development of long-range axon architectures enabling expansive neuromodulation.

overall_design: 5-HT neuron RNA profiles of control (CON), Lmx1bCKO, and Pet1CKO (at E17.5 and P2 (Lmx1bCKO only at P2)) mice were generated by deep sequencing, in triplicate, using Illumina HiSeq 500/550. The sequence reads that passed quality filters were analyzed at the gene level with TopHat2 followed by Cufflinks.

first: Lauren

middle: J

last: Donovan

first: William

middle: C

last: Spencer

first: Meagan

last: Kitt

first: Brent

last: Eastman

first: Katherine

last: Lobur

first: Jerry

last: Silver

first: Kexin

last: Jiao

middle: S


title: Fibroblast activation protein restrains adipogenic differentiation and regulates matrix-mediated mTOR signaling

city: Philadelphia

first: Ellen

last: Pure

state: PA

address: 380 S University Ave

institute: University of Pennsylvania

summary: Obesity is a risk factor for multiple diseases, including diabetes, cardiovascular disease, and cancer. Within obese adipose tissue, multiple factors contribute to creating a disease-promoting environment, including metabolic dysfunction, inflammation, and fibrosis. Recent evidence points to fibrotic responses, particularly extracellular matrix remodeling, in playing a highly functional role in the pathogenesis of obesity. Fibroblast activation protein plays an essential role in remodeling collagen-rich matrices in the context of fibrosis and cancer. We observed that FAP-null mice have increased weight compared to wild-type controls, and so investigated the role of FAP in regulating diet-induced obesity. Using genetically engineered mouse models and in-vitro cell-derived matrices, we demonstrate that FAP expression by preadipocytes restrains adipogenic differentiation. FAP-mediated matrix remodeling also alters lipid metabolism in part by regulating mTOR signaling. Together, via these mechanisms, FAP confers resistance to diet-induced obesity. The critical role of ECM remodeling in regulating obesity offers new potential targets for therapy.

overall_design: Two or three biological replicates were analyzed for each of 4 conditions (two genotypes; two diets per genotype)

first: Rachel

last: Blomberg

first: Daniel

last: Beiting

first: Martin

last: Wabitsch

last: Puré


title: ATAC-seq of P2 mouse epithelial and non-epithelial cochlear cells

city: Baltimore

first: yang

last: song

state: MD

address: HSF-3, 3rd Floor; 670 W Baltimore St.

department: Department: Institute for Genome Sciences

institute: University of Maryland in Baltimore

summary: To identify gene regulatory regions in the cochlea, we FACS-sorted biological duplicates of epithelial cells (CD326+; including hair cells and supporting cells) and non-epithelial cells (CD326-; predominantly mesenchymal cells) from mouse cochlea at postnatal day 2 and performed ATAC-seq to identify open chromatin regions in each cell type. CD-1 timed-pregnant females were purchased from Charles River (Maryland). At postnatal day 2, the mice were euthanized and their temporal bone removed. Cochlear ducts from 20 mice were harvested, pooled and processed for Fluorescence-activated cell sorting (FACS). Briefly, single-cell suspensions were obtained and incubated with an APC-conjugated anti-CD326 (1:2000, BioLegend) to label epithelial cells. Cells were sorted into cochlear CD326 (+) cells (epithelial) and cochlear CD326 (-) cells (non-epithelial) by FACS using a BD FACS Aria II Cell Sorter (BD Biosciences) at the Flow Cytometry Facility, Center for Innovative Biomedical Resources (University of Maryland School of Medicine). 50,000 cells or 100,000 cells from each sample were further processed for ATAC-seq as described (Buenrostro et al. 2015. Curr. Prot. Mol. Med.) with the following modification: following the transposition reaction and purification step, a right side size selection (ratio 0.6) using SPRIselect (Beckman-Coulter, Indiana) was added before proceeding to the PCR amplification. This extra step resulted in the selection of DNA fragments between 150 bp to 700 bp.

overall_design: ATAC-seq data were generated from a total of four samples: two biological replicates from epithelial cells and two from non-epithelial cells.

first: Beatrice

last: Milon

first: Ronna

last: Hertzano


title: Affymetrix SNP6 array data for 56 breast cancer cell lines

city: Rotterdam

first: Marcel

last: Smid

address: Dr. Molewaterplein 50

department: Medical Oncology

country: Netherlands

institute: Erasmus MC

summary: Breast cancer is a genetically and phenotypically complex disease. To understand the role of microRNAs in this molecular complexity, we performed miRNA expression analysis in a cohort of molecularly well-characterized human breast cancer (BC) cell lines to discover miRNAs associated with the most common molecular subtypes and the most frequent genetic aberrations.Using a microarray carrying LNA™ modified oligonucleotide capture probes (Exiqon), expression levels of 725 human miRNAs were measured in 51 BC cell lines. MiRNA expression was explored by unsupervised cluster analysis and then associated with the molecular subtypes and genetic aberrations commonly present in breast cancer. Unsupervised cluster analysis using the most variably expressed miRNAs divided the 51 BC cell lines into a major and a minor cluster predominantly mirroring the luminal and basal intrinsic subdivision of BC cell lines. One hundred and thirteen miRNAs were differentially expressed between these two main clusters of which half were related to the ER-status of the cell lines. Forty miRNAs were differentially expressed between basal-like and normal-like/claudin-low cell lines. Within the luminal-group of cell lines, 39 miRNAs were associated with ERBB2 overexpression and 24 miRNAs with E-cadherin gene mutations, which are frequent in this subtype of BC cell lines. In contrast, 31 different miRNAs were associated with E-cadherin promoter hypermethylation, which, contrary to E-cadherin mutation, is exclusively observed in BC cell lines that are not of luminal origin. The differential expression of 30 miRNAs were associated with p16INK4 status while only a few differentially expressed miRNAs were associated with BRCA1, or PIK3CA/PTEN, TP53 mutation status of the cell lines (P-value < 0.05). Twelve miRNAs were associated with DNA copy number variation of the respective locus. Luminal-basal and epithelial-mesenchymal associated miRNAs determine the overall subdivision of miRNA transcriptome of BC cell lines. Specific sets of miRNAs were associated with ERBB2 overexpression, p16INK4aor E-cadherin mutation or E-cadherin methylation status, which implies that these miRNAs may contribute to the driver role of the genetic aberrations. Additionally, miRNAs, which are located in a genomic region showing recurrent genetic aberrations, may themselves play a driver role in breast carcinogenesis or contribute to a driver gene in their vicinity. In short, our study provides detailed molecular miRNA portraits of BC cell lines, which can be exploited for functional studies of clinically important miRNAs.

overall_design:
Affymetrix SNP arrays were performed according to the manufacturer's procedure on DNA extracted from cultured breast cancer cell lines
log2ratio copy number data of Affymetrix SNP6 arrays were calculated of 56 breast cancer cell lines which were associated with diverse characteristics.
This submission represents the copy number component of the study only

first: John

last: Martens


title: Long non-coding RNA SMILR regulates genes involved in cytokinesis in human vascular smooth muscle cell

city: Edinburgh

first: Julie

last: Rodor

address: 47 Little France Crescent

department: Centre for Cardiovascular Science

country: United Kingdom

institute: UNIVERSITY OF EDINBURGH

summary: In response to blood vessel wall injury, aberrant proliferation of vascular smooth muscle cells causes pathological remodelling. The controlling mechanisms involved are, however, not completely understood. We recently showed that the intergenic human, poorly-conserved long non-coding RNA, SMILR, promotes vSMC proliferation. Here, using deep RNA-sequencing of vSMCs with SMILR knockdown or overexpression, we identified an interconnected cell cycle network controlled by SMILR. SMILR inhibition led to vSMC binucleation and mitotic arrest.

overall_design: RNA sequencing was performed on primary Human Saphenous Vein Smooth Muscle Cells (HSVSMCs), stimulated with IL1a (10 ng/mL) and PDGF-ββ (20 ng/mL), exposed to either SMILR depletion via siRNA (siSMILR) or overexpression via lentivirus (SMILR_LV). Respective control corresponds to siCONTROL or empty lentivirus. Each treatment was done in triplicates.

first: Amira

last: Mahmoud

first: Margaret

last: Ballantyne

first: Andrew

middle: H

last: Baker


title: RNA-seq of stable and unstable section of human atherosclerotic plaques

summary: Atherosclerosis is a serious and very common condition where plaque builds up inside arteries and that can lead to heart attack or stroke. The development and rupture of the plaque is a complex process, involving the interplay of many cell types and the extracellular environment. We performed RNAseq on stable and unstable regions dissected from fresh human carotid plaques obtained at carotid endarterectomy in symptomatic patients. The dissection of the plaques into stable and unstable regions was based on macroscopic appearance, with unstable regions characterised as the visible zone of plaque rupture.

overall_design: Plaques were obtained from 4 patients and dissected in stable and unstable regions. RNAs were extracted from the two sections and sent for RNAseq (Genewiz).

first: Vladislav

last: Miscianinov

first: Karine

last: Pinel

last: Hung

first: Jakub

last: Kazynski

first: Adriana

last: Tavares

first: Angela

last: Bradshaw

first: David

middle: E

last: Newby

first: Andrea

last: Caporali

first: Gwyn

last: Gould

first: Sarah

last: George

first: Igor

last: Ulitsky

first: Judith

last: Sluimer


title: DNA copy number measurement of genome replication dynamics by high-throughput sequencing – the sort-seq, sync-seq and MFA-seq family

status: Public on Aug 01 2019

city: Norwich

first: Conrad

middle: A

last: Nieduszynski

address: Norwich Research Park

institute: Earlham Institute

type: Genome variation profiling by high throughput sequencing

summary: Genome replication follows a defined temporal programme that can change during cellular differentiation and disease onset. DNA replication results in an increase in DNA copy number that can be measured by high-throughput sequencing (HTS). Here we present a protocol to determine genome replication dynamics using DNA copy number measurements. Cell populations can be obtained in three variants of the method. First, sort-seq uses fluorescence activated cell sorting (FACS) to isolate replicating and non-replicating subpopulations from asynchronous cells. Second, sync-seq uses cell synchronisation to obtain samples before and during DNA replication. Third, marker frequency analysis (MFA-seq) assesses copy number differences in rapidly replicating asynchronous cells. These approaches have been used to reveal genome replication dynamics in prokaryotes, archaea, and a wide range of eukaryotes, including mammalian cells. The whole protocol can be performed in 7-10 days.

overall_design: S. cerevisiae strains from mid-log phase were sorted based on DNA content, enriching for S phase cells. Extracted DNA from the cells was sequenced on NextSeq 500 and unique reads were counted in genomic bins of 1 kb. Examples of aneuploidy (RWY012, chrXI and chrXII) and segmental duplication (RWY109, region of chrIV).

first: Dzmitry

middle: G

last: Batrakou

first: Carolin

last: Müller

first: Rosemary

last: Wilson


title: Single-Cell RNAseq Analysis of Murine Fate-Mapped Tsc1+/+ and Tsc1-/- Aortic Smooth Muscle Cells

first: George

last: Tellides

summary: We characterized the transcriptomic effects at the single cell level of chronic mTOR activation in aortic SMCs using a conditional genetic model to delete Tsc1 under control of a smooth muscle-specific Myh11 promoter

overall_design: Myh11-CreERT2.mT/mG (Tsc1+/+) and Tsc1fl/fl.Myh11-CreERT2.mT/mG (Tsc1−/−) male mice were treated with tamoxifen at 1.5 wk, the thoracic aortas were procured and enzyme digested at 24 wk, single, viable, GFP+ SMCs were isolated by FACS, and analyzed by single-cell RNAseq using the 10x system.

first: Guangxin

last: Li


title: Expression data from wild-type single muscle fibers

city: San Francisco

first: Andrew

last: Brack

address: 35 Medical Center Way

department: Orthopaedic Surgery

institute: University of California San Francisco

summary:
The muscle stem cells (or satellite cells (SC)) reside on the muscle fibers tightly wedged between the plasma membrane of the muscle fibers and the basal lamina. The muscle fibers represent a functional niche providing paracrine signals to maintain the tissue resident stem cells.
We performed microarrays to depict the global transcriptional profile of single muscle fibers at different time points

overall_design: We isolated purified single muscle fibers from the Extensor Digitorum Longus (EDL) muscle of Mus Musculus at different time points. The muscle fibers were isolated from postnatal pups (P3 and P7), adult mice (3-4 months old) and aged mice (24-25 months old).

first: Susan

last: Eliazer


title: Gene expression of cervical cells and immortalized keratinocytes transfected with whole genomes of HPV16 and HPV18

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

summary: Human ectocervical and endocervical cells immortalized by HPV16 E6/E7 (designated as Ect and End, respectively) and normal human immortalized keratinocytes (NIKS), were transfected with whole genomes of HPV16 or HPV18, and were subsequently grown in standard monolayer culture until passage 2. Total RNAs were extracted and subjected to TORAY 3D-gene analysis service using the 3D-Gene Human Oligo chip 25K (TORAY, Tokyo, Japan).

overall_design: Ect, End and NIKS cells with or without HPV16/18 genome (total nine cell samples) were analized.

first: Yoshiyuki

last: Ishii

first: Ayumi

last: Taguchi

first: Iwao

last: Kukimoto


title: Extended amygdala prepronociceptin neurons encode rapid changes in arousal state

city: Chapel Hill

first: Marcus

middle: Luis

last: Basiri

state: NC

address: 115 Mason Farm Road

institute: UNC Chapel Hill

summary: Transcriptional profiling of bed nucleus of stria terminalis (BNST) cell types.

overall_design: High-throughput single-cell RNA sequencing of BNST in male mice using Drop-seq. 6 mice were pooled per batch.

first: Garret

last: Stuber


title: The RNA hairpin binder TRIM71 modulates alternative splicing by repressing Mbnl1 [RNA-seq]

city: Basel

first: Panagiotis

last: Papasaikas

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute

summary: We demonstrate that TRIM71 alters stem cell splicing patterns through modulation of MBNL1 levels.

overall_design: RNA-seq of WT (2 replicates), TRIM71 KO (2 replicates), MBNL1 3'UTR(mut) (2 replicates), MBNL1 overexpression (2 replicates).

first: Thomas

last: Welte

first: Alex

last: Tuck

first: Sarah

last: Carl

first: Matyas

last: Flemr

first: Philip

last: Knuckles

first: Aneliya

last: Rankova

first: Marc

last: Bühler

first: Helge

last: Großhans


title: NURR1 activation in skeletal muscle controls systemic energy homeostasis (ChIP-seq)

city: Dallas

first: Eric

middle: N

last: Olson

state: TX

address: 6000 Harry Hines Blvd.

department: Molecular Biology

institute: University of Texas Southwestern Medical Center at Dallas

summary: Skeletal muscle plays a central role in the control of metabolism and exercise tolerance. Analysis of muscle enhancers activated after exercise in mice revealed the orphan nuclear receptor NURR1/NR4A2 as a prominent component of exercise-responsive enhancers. We show that exercise enhances the expression of NURR1 and transgenic overexpression of NURR1 in skeletal muscle confers an endurance phenotype in mice. NURR1 expression in skeletal muscle is also sufficient to prevent hyperglycemia and hepatic steatosis by enhancing muscle glucose uptake and storage as glycogen. Furthermore, treatment of obese mice with putative NURR1 agonists increases energy expenditure, improves glucose tolerance, and confers a lean phenotype, mimicking the effects of exercise. These findings identify a key role for NURR1 in governance of skeletal muscle glucose metabolism and reveal a transcriptional link between exercise and metabolism. Our findings also identify NURR1 agonists as possible exercise mimetics with the potential to ameliorate obesity and other metabolic abnormalities.

overall_design: H3K27Ac ChIP-seq analysis between sedentary and exercised mice.

first: Leonela

last: Amoasii


title: NURR1 activation in skeletal muscle controls systemic energy homeostasis (RNA-seq)

overall_design: RNA-seq experiment between 6 different conditions in mice.


title: NURR1 activation in skeletal muscle controls systemic energy homeostasis

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

overall_design: Refer to individual Series


title: The RNA hairpin binder TRIM71 modulates alternative splicing by repressing MBNL1


title: The RNA hairpin binder TRIM71 modulates alternative splicing by repressing Mbnl1 [RNA-seq & Ribo-seq]

summary: We demonstrate that global effects of TRIM71 on the cellular transcriptome of mouse embryonic stem cells (mESCs) are largely attributable to its RNA binding activity. We observe that target repression by TRIM71 in mESCs occurs predominantly through transcript degradation. We identify a core set of targets consistently regulated by TRIM71 in different human and mouse cell lines.

overall_design: RNA-seq of WT (10 replicates), TRIM71 KO (10 replicates), TRIM71 RING_mut (TRIM71RING; 5 replicates), and TRIM71 NHL_mut(TRIM71NHL, 5 replicates) mESC cells. RNA-seq of WT (8 replicates) and TRIM71 KO (8 replicates) Ne4C cells. RNA-seq of WT (3 replicates) and TRIM71 KO (3 replicates) Huh-7 cells. Ribosome profiling of WT (4 replicates), and TRIM71 KO (4 replicates) mES cells.


title: The RNA hairpin binder TRIM71 modulates alternative splicing by repressing Mbnl1

middle: Charles

address: Maulbeerstrasse 66

institute: Friedrich Miescher Institute for Biomedical Research

summary: We demonstrate that global effects of TRIM71 on the cellular transcriptome of mouse embryonic stem cells (mESCs) are largely attributable to its RNA binding activity, and map the transcriptome-wide targets of wild-type TRIM71, NHL domain mutant TRIM71, and RING domain mutant TRIM71.

overall_design: CRAC (crosslinking and analysis of cDNAs) analysis of Trim71 wild-type, NHL mutant and RING mutant in mouse embryonic stem cells.


title: Targeted deletion of Tcf7l2 in adipocytes promotes adipocyte hypertrophy and impaired gluose metabolism [preadipocytes]

city: Salt Lake City

first: Chris

last: Stubben

state: Utah

address: 2000 Cir of Hope Dr

department: University of Utah

institute: Huntsman Cancer Institute

summary:
We generated a Tcf7l2 F/F mouse and harvested preadipocytes rom these mice, immortalized them, and then transduced them with a retroviral vector containing CreERT2 and , differentiated them, performed ChIP-seq, and RNA-seq. We also generated and adipsoe specific knockout mouse where we crossed our Tcf7 F/Fmouse with an Adiponectin-Cre mice and performed RNA-seq on the inguimal white adipose tissue after 16 weeks of high fat diet, 65%
Conclusions: Our study shows that knocking of Tcf7l2 results in enhanced adipocyte differentiation

overall_design: RNA-seq on WT and Tcf7l2 immortalized differentiated preadipocytes.

first: Claudio

last: Villanueva

first: Gisela

last: Geoghegan


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Hrd1-/- T regulatory cells

city: Chicago

first: Matthew

middle: J.

last: Schipma

state: IL

address: 750 N. Lake Shore Drive

department: Biochemistry and Molecular Genetics

institute: Northwestern University

summary:
Purpose: Natural T regulatory cells (nTreg) and induced Tregs (iTreg) were isolated from hrd1 WT and knockout mice. The purpose of this project is to look  at the transcriptional profiles changes of genes specifically involved in T cell receptor signaling, TGF-beta signaling, and metabolic genes in Hrd1 deficient Tregs.
Methods: natural Tregs were sorted according to CD4+GFP+, and RNA was harvested using QIAGEN Rneasy Mini Kit. For induced iTreg, CD4 T cells were isolated and polarized with IL2/TGFbeta for 5 days to induce FoxP3 induction. Day 5, GFP positive cells were isolated and RNA were harvested using QIAGEN RNeasy mini Kit.
Results and Conclusions: Our study represents the first detailed analysis of transcriptional profiles in Hrd1 deficient T regulatory cells, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles.

overall_design: natural and induced T regulatory cells mRNA profiles of 8 weeks old wild type (WT) and Treg specific deletion of Hrd1 mice were generated by deep sequencing, in triplicate, using Illumina NextSeq 500

first: Yuanming

last: Xu


title: Illumina 450K Methylation Data of Alzheimer's Disease: Middle Temporal Gyrus and Cerebellum

city: Tempe

first: Danielle

middle: Lisa

last: Brokaw

state: AZ

address: Biodesign Institute Building C, 1001 S McAllister Ave

department: Center for Neurodegeneration, Biodesign

institute: Arizona State University

type: Methylation profiling by genome tiling array

summary: Methylation analysis of 404 samples (Alzheimer's disease = 225; controls = 179) from two brain regions, the middle temporal gyrus (MTG) and the cerebellum (CBL), using the Illumina 450K methylation array.

overall_design: Banner Sun Health Research Institute Brain and Tissue Bank provided 404 samples from the middle temporal gyrus (area 21) consisting of 225 cases with Alzheimer’s disease (AD) and 179 non-demented (ND) cases. The tissue was collected within hours of death (average postmortem delay = 2.6 hours) and stored at -80ºC after autopsy. The cognitive ability of all cases was assessed prior to death by a board-certified neurologist using NIH AD Center criteria for Alzheimer’s disease. The diagnosis of clinical Alzheimer’s disease was confirmed postmortem via neuropathological assessment. DNA was extracted from each sample and hybridized to one of nine randomly assigned Illumina 450K methylation arrays. Data was normalized using the R packages minfi (version 1.23.4) and SVA (version 3.26.0). NOOB and functional normalization were performed through the minfi package, followed by SVA and ComBat correction of confounding variables and batch effects. Differentially methylated positions (DMPs) and regions (DMRs) related to Alzheimer’s were identified using the minfi dmpfinder and bumphunter algorithms, respectively. All results were filtered at an adjusted FDR of 0.05.

first: Daniel

last: Weisenberger

first: Ignazio

last: Piras

first: Diego

last: Mastroeni

first: Jennifer

last: Nolz

first: Elaine

last: Delvaux

first: Geidy

last: Serrano

last: Beach

first: Peter

middle: W

last: Laird

last: Huentelman

first: Paul

last: Coleman


title: Novel epoxy-tiglianes stimulate keratinocyte wound healing responses and re-epithelialization via protein kinase C activation

city: Brisbane

first: Glen

middle: M

last: Boyle

state: Queensland

address: 300 Herston Road Herston

department: Department of Cell and Molecular Biology, Cancer Program

country: Australia

institute: QIMR Berghofer Medical Research Insitute

summary: Impaired re-epithelialization is a hallmark of non-healing, chronic skin wounds. These represent major causes of patient morbidity, particularly amongst ever-increasing ageing and diabetic populations, posing significant challenges to healthcare providers worldwide. Despite many treatment options being available, these often offer limited benefits to healing outcomes. We address the need for more efficacious treatments through evaluation of novel epoxy-tigliane compounds as chronic wound pharmaceuticals, based on their effectiveness in promoting keratinocyte healing responses and re-epithelialization in vivo. Here, we identify that prototype epoxy-tigliane (EBC-46) and analogue (EBC-211), accelerate G1/S and S/G2 cell cycle transitions and proliferation in a normal human keratinocyte cell line of skin origin (HaCaTs). EBC-46 and EBC-211 further induce HaCaT migration/wound repopulation, even with mitomycin C treatment, suggesting epoxy-tiglianes can promote migration/repopulation independently of proliferation. Epoxy-tiglianes modulate keratin, DNA synthesis/replication, cell cycle/proliferation, motility/migration, differentiation, proteinase; and cytokine/chemokine gene expression, to facilitate enhanced responses. Although epoxy-tiglianes down-regulate cytokine/chemokine agonists of keratinocyte proliferation/migration, we demonstrate that enhanced HaCaT responses are mediated through protein kinase C (PKC) phosphorylation and abrogated by inhibition of PKC activation with bisindolylmaleimide-1 (BIM-1). By identifying how epoxy-tiglianes stimulate keratinocyte healing responses, we highlight their potential as novel therapeutics for impaired re-epithelialization associated with non-healing, chronic wounds.

overall_design: Single colour, Illumina Human HT12v4 Beadarrays.

first: Rachael

last: Moses

first: Rachel

last: Howard-Jones

last: Errington

first: Victoria

last: Gordon

last: Reddell

first: Robert

last: Steadman

first: Ryan

last: Moseley


title: Targeted deletion of Tcf7l2 in adipocytes promotes adipocyte hypertrophy and impaired gluose metabolism [HFD]

first: Chris

last: Stubben

summary:
We generated a Tcf7l2 F/F mouse and harvested preadipocytes from these mice, immortalized them, and then transduced them with a retroviral vector containing CreERT2 and , differentiated them, performed ChIP-seq, and RNA-seq. We also generated an adipose specific knockout mouse where we crossed our Tcf7 F/Fmouse with an Adiponectin-Cre mice and performed RNA-seq on the inguinal white adipose tissue after 16 weeks of high fat diet, 65%
Conclusions: Adipsose selective deletion of Tcf7l2 led to hypertrophic inguinal white adipose tissue and impaired glucose metabolsim with transcripts involved in lipid and glucose metabolsim being altered.

overall_design: RNA-seq of WT or Tcf7l2 KO inguinal white adipose tissue from mice fed high fat diet for 16 weeks.

first: Claudio

last: Villanueva

first: Gisela

last: Geoghegan


title: Targeted deletion of Tcf7l2 in adipocytes promotes adipocyte hypertrophy and impaired gluose metabolism


title: Single-cell parallel sequencing on human oocytes reveals essential targets and cis-regulatory for oocyte development maintenance

first: Thomas

last: Chan

address: Room623, Area 39, CUHK, Shatin

department: School of Biomedical Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

type: Methylation profiling by high throughput sequencing

summary: Oocyte quality declines dramatically after the age of 35 in females. Multiple cellular and molecular mechanisms have been revealed in the oocyte development and maintenance. However, the majority studies were performed on bulk oocyte samples. On the other hand, cis-regulatory mechanisms have been reported to be critical in cell biology. In this study, we employed the novel single-cell parallel sequencing technology to successfully generate the transcriptome and methylome profiles on two human oocytes. We demonstrated the high similarity in transcriptome and methylome between two oocytes and firstly showed the global regulation of DNA methylation and gene expression in single oocyte level. More importantly, we identified the potential enhancer-promoter networks and found two novel genes, DCP1A and THE1B, critical for oocyte development maintenance, were involved in the regulation networks. These discoveries offer a novel direction to explore the mechanism of oocyte development and maintenance and make it possible to identify associated screening or therapy targets for further study and clinic treatment.

overall_design: Performing single-cell parallel sequencing on two human oocytes.

first: Yan

last: QIAN

first: Qin

last: CAO

first: Jinyue

last: LIAO

first: Hoi

last: SUEN

first: Wing

middle: T

last: LEE

last: CHUNG

first: Leung

last: TANG

first: King

last: CHOW

first: Yuk

last: YIP

first: Tak

middle: Y

last: LEUNG

first: Wai-Yee

last: CHAN

first: Yiu

first: Tin

last: LI

first: Tin-Lap


title: Pathways Underlying Impaired Cardiac Preconditioning Potential   in Subjects with the Metabolic Syndrome, and its Restoration by ACE-inhibition

city: Leuven

first: Alvaro

last: Cortés Calabuig

address: Herestraat 49 PO box 602

country: Belgium

institute: Genomics Core Leuven

summary:
Aims. The goal of the study was to identify the possible transcriptional alterations responsible for the restoration of the second window preconditioning in the metabolic syndrome heart.
Methods. LDLR-/-;ob/ob (DKO) and C57Bl6/J (WT) mice were injected with ACE-inhibitor, captopril (10 mg/kg/day) or NaCl 0.9% as controls. Preconditioning (HPC) was induced by five 6-min cycles at 6% oxygen interposed with 6 min at 21% oxygen. Non-preconditioned mice underwent a sham procedure without hypoxia. Transcriptome analysis (RNA-seq) from the whole heart RNA samples, differential gene expression with Cufdiff, pathway and network analysis with Ingenuity Pathway Analysis (IPA), qRT-PCR, and transcription factor motif enrichment analysis with i-cisTarget were performed. In separate groups, the infarct size was determined histologically after a 30-min occlusion of LAD, followed by 60-min reperfusion.
Results. Preconditioning could not reduce infarct size in the untreated DKO mice (1+2%, p>.05). Preconditioning reduced infarct size to 28+2% in WT-HPC and to 23+1% in WTACE-I-HPC, both p<.05. In DKOACE-I hearts, preconditioning potential was partially restored with a reduction of infarct size by 16%. Preconditioning induced low number of differentially expressed genes (DEG) in DKO hearts (29 genes, p<.05) when compared WT and WTACE-I hearts (1634 and 2215 genes respectively, p<.05). In DKOACE-I, the number of DEG after preconditioning increased to 59, p<.05.   In the three groups that could phenotypically be protected, preconditioning triggered shared pathways associated with the cell cycle quiescence, such as mTORC2 signaling, eIF2 signaling, regulation of eIF4 and p70S6K signaling, and actin cytoskeleton pathway signaling. The model-specific pathways and transcription factors differed between the groups. In the WT hearts, preconditioning enriched the pathways of mitochondrial biogenesis, oxidative phosphorylation, and anti-apoptotic signalling. In the WTACE-I hearts, preconditioning enriched the pathways of immune system signaling, metabolism, and cell cycle regulation. In the DKOACE-I hearts, pathways associated with negative inotropic effect and inhibition of myocyte growth were enriched after preconditioning.
Conclusion. Our findings explain the molecular mechanism behind preconditioning in the healthy and the metabolic syndrome hearts. The phenotypically cardioprotective effect of HPC was absent in the metabolic syndrome hearts and was partially reinstated after ACE-I therapy. Transcriptional response to preconditioning differs between DKO and WT hearts and is model-specific with some degree of overlap.

overall_design: Experimental animal models: DKO; LDLR-/- and ob/ob)18. C57BL/6 (WT); RNA Extraction and Sequencing; RNA-Seq Data Analysis; Pathway and Regulatory Network Analysis; Ethical committee approval.

first: Aziza

last: Yakubova

first: Lieven

last: Thorrez

first: Dmitry

last: Svetlichnyy

first: Liesbeth

last: Zwarts

first: Griet

last: Laenen

first: Wouter

last: Oosterlinck

first: Álvaro

last: Cortés-Calabuig

first: Yves

last: Moreau

first: Luc

last: Dehaspe

first: Jeroen

last: Van Houdt

first: Bart

last: De Moor

first: Patrick

last: Callaert

first: Paul

last: Herijger


title: Targeted deletion of Tcf7l2 in adipocytes promotes adipocyte hypertrophy and impaired gluose metabolism [ChIP-seq]

first: Chris

last: Stubben

summary: We generated a Tcf7l2 F/F mouse and harvested preadipocytes rom these mice, immortalized them, and then transduced them with a retroviral vector containing CreERT2 and , differentiated them, performed ChIP-seq, and RNA-seq. We also generated and adipsoe specific knockout mouse where we crossed our Tcf7 F/Fmouse with an Adiponectin-Cre mice and performed RNA-seq on the inguimal white adipose tissue after 16 weeks of high fat diet, 65%

overall_design: Examination of genome-wide TCF7L2 occupancy in wt and TCF7L2 deficient diiferentiated immortalized preadipocytes

first: Claudio

last: Villanueva

first: Gisela

last: Geoghegan


title: Genome-wide analysis of coding and non-coding RNAs in ovary of honey bee workers

city: Beijing

first: Xiao

last: Chen

state: Beijing

address: Haidian Xiangshan Beigou No.1

institute: Institute of Apicultural Research, Chinese Academy of Agricultural Sciences

type: Non-coding RNA profiling by high throughput sequencing

summary: The present study is the first study to identify the involvement of mRNA, lncRNAs, circRNAs and miRNA in the ovary of honey-bee workers.We predicted 10271 mRNAs, 7235 lncRNAs, 11794 circRNAs and 164 miRNAs in the ovary of honey bee workers.

overall_design: To identify the involvement of mRNAs, lncRNAs, circRNAs and miRNAs in the ovary of honey-bee workers,  Pools of honey bee workers’ ovaries were used in this study (N=3). Ovaries of worker bees sampling were carried out according to the procedure of Macedo, with minor modifications (Macedo et al. 2016). Briefly, 5 colonies with sister queens were reared using standard beekeeping techniques (Harbo 1986). The frames with emerging broods from these colonies were placed in an incubator (34 ℃ and 80% relative humidity). Newly emerged workers were paint marked and returned to their original colony. After 4 days, the marked workers were collected. Their ovaries were dissected, snap frozen in liquid nitrogen and stored at -80 ℃. For each biological sample, 40 ovary pairs were dissected from workers of one single colony. Totally, three samples were used for RNAseq.


title: Hormesis underlies the adaptive response in methylmalonic acidemia (MMA)

city: BETHESDA

first: abdel

last: Elkahloun

address: 50, SOUTH DRIVE

institute: NHGRI-NIH

summary: Methylmalonic acidemia (MMA), an organic acidemia characterized by metabolic instability and multiorgan complications, is most frequently caused by mutations in methylmalonyl-CoA mutase (MUT). To define the metabolic adaptations in MMA, in the chronic and acute settings, we studied a mouse model generated by transgenic expression of Mut in the muscle. Mut-/-;TgINS-MCK-Mut mice accurately replicate the hepato-renal mitochondriopathy and growth failure seen in severely affected patients, and were used to characterize the response to fasting. The hepatic transcriptome in MMA mice was characterized by the chronic activation of stress-related pathways and responded abberrantly to fasting when compared to controls.

overall_design: RNA expression was studied in livers from the following 4 conditions: heterozygote Mut +/-;TgINS-MCK-Mut mice at baseline and after 12 hrs of fasting, mutant Mut -/- ;TgINS-MCK-Mut mice at baseline and after 8-12 hrs of fasting. Four mice in each genotype group and fed or fasting state were sacrificed for liver and RNA extraction. All the mice used in this study were males, at 4 months of age. After organ removal, livers were snap frozen in liquid nitrogen.

first: Irini

last: Manoli

first: Abdel

first: Charles

middle: P

last: Venditti


title: From gene networks to network motif dynamics: how the presense of positive feed-back and -forward loops between PERIANTHIA, WUSCHEL-RELATED HOMEOBOX5 and GRF-INTERACTING FACTOR 1 modulates gene expression and function in the Arabidopsis roots.

city: Raleigh

first: Adam

last: Fisher

state: North Carolina

address: 112 Derieux Place

institute: North Carolina State University

summary: We isolated QC and CEI cells and obtained their cell-type specific transcriptional profiles in a WT and in a wox5 mutant background by sorting GFP+ cells marked with pWOX5::GFP and pCYCD6::GFP.

overall_design: Seedlings were grown for 5 days. Cells expressing WOX5::GFP and CYCD6::GUS-GFP were collected by FACS. RNA was extracted from the collected cells.

first: Natalie

last: Clark

first: Rosangela

last: Sozzani


title: Unr is a potential post-transcriptional master regulator of protein expression

city: Coventry

first: Nigel

middle: Paul

last: Dyer

address: Gibbet Hill Road

institute: University of Warwick

summary: Ribonucleoprotein immunoprecipitation followed by mass spectrometry and RNA-Seq was used to investigate the ‘Upstream of N-RAS’ (UNR) protein interactome across three cancer cell lines. A number of novel UNR-interacting proteins and transcripts were discovered, including the ubiquitin E3 ligase, HUWE1; the nucleolar protein, NARR; the multifunctional protein, SQSTM1; and the erythropoiesis-related protein, LDB1 . GO-term analysis of putative UNR interactors suggested that UNR interacts with both proteins and mRNAs encoding proteins that are involved in RNA binding

overall_design: Examination of UNR binding to RNA by RIP-RNA-Seq using three replicates of three cell types,

first: Pól

last: Ó Catnaigh

first: Swagat

last: Ray

first: Keith

last: Leppard

first: Sascha

last: Ott

first: Emma

last: Anderson


title: Gene expression analysis of Arabidopsis thaliana inoculated with fungal endophyte Mucor sp. 10 days after inoculation

city: Kraków

first: Piotr

last: Rozpądek

address: Gronostajowa 7a

department: Małopolska Centre of Biotechnology

country: Poland

institute: Jagiellonian University

summary: To investigate the mechanisms Mucor sp. induced plant growth acceleration whole genome microarray profiling was employed.

overall_design: Gene expression profiles of  of A. thaliana shoots inoculated at 2 leaf seedling stage (15 days after germination), cultivated in vitro in MSR

first: Rafał

last: Ważny

first: Agnieszka

last: Domka


title: Next generation sequencing facilitates quantitative analysis of transcriptomes of wild type and overexpression of PuHSFA4a transgenic lines

city: Harbin City

first: Chenghao

last: Li

state: HeiLongJiang Province

address: No. 51 HeXing Road,Xiangfang District

department: College of Forestry

institute: Northeast Forestry University

summary:
Purpose:  we performed comparative RNA-seq analyses to identify differentially expressed genes between overexpression of PuHSFA4a transgenic lines and Wild Type with or without excess Zn stress

Methods: Illumina HiSeq technology was used to generate mRNA profiles from PuHSFA4a transgenic roots compared to wild type roots.overexpression of PuHSFA4a and wild type material was obtained from root of Populus ussuriensis grown for 7 days in 1/2 MS medium only then exposed to 1/2 MS medium supplemented with 1.2mM ZnSO4 for two weeks. The control was plant grown for three weeks in 1/2 MS medium. Reads of 150bp were generated and aligned to the Populus trichocarpa reference genome (https://phytozome.jgi.doe.gov/pz/portal.html). qRT–PCR validation was performed using TransStart 1 Top Green qPCR SuperMix

Results: By pairwise comparisons of the RNA-seq data, 33 genes were showed significant expression differences between PuHSFA4a-OE and WT (FDR adjusted P value < 0.01 including 17 genes under normal condition, 19 genes under excess Zn treatment. Altered expression of 17 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method.

Conclusions: Our study represents the detailed analysis of excess Zn response transcriptomes , with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that next generation sequencing offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

overall_design: With or without excess Zn stress, roots mRNA profiles of 21-day old wild type (WT) and PuHSFA4a transgenesis Populus ussuriensis  were generated by deep sequencing, in triplicate, using Illumina HiSeq 4000.

first: Jingli

last: Yang

first: Haizhen

last: Zhang


title: Cadmium chloride-induced gene expression changes in D. melanogaster

city: Boston

first: Katherine

last: Silkaitis

state: MA

address: 655 Huntington Ave, 2-237

department: Environmental Health

institute: Harvard T.H. Chan School of Public Health

summary: Heavy metals and organic compounds, such as pesticides and plasticizers, exert toxicity through their ability to perturb molecular mechanisms. We investigated the ability of 18 compounds to modify the epigenetic state of the white locus in a Drosophila model of position-effect variegation (PEV). Our data indicate that cadmium chloride (CdCl2) is a potent enhancers of variegation. We demonstrate that genes differentially expressed upon CdCl2 exposure are enriched for genes that have heterochromatic states associated with them.

overall_design: Two genotypes (isogenic except for the Y chromosome) were either treated with CdCl2 or were raised on control food. Two-channel microarrays were used with balanced dye-swaps and the expression signal from each treatment/genotype combination was collected from four distinct slides.

first: Bernardo

last: Lemos


title: Effect of Fumonisin B1 on hepatic transcriptome in WT and LXR KO female mice

city: Toulouse

first: Hervé

last: Guillou

address: 180 Chemin de Tournefeuille

department: ToxAlim

institute: INRAE

summary: Adult (8 week old) female mice from mixed genetic background (Sv129/C57Bl6J) were either treated with water or with FB1 for one month prior to liver gene expression analysis.

overall_design: 6 mice per group (control or FB1 treated) and per genotype (WT and KO)

first: Marion

last: Régnier

first: Arnaud

last: Polizzi

first: Claire

last: Naylies

first: Isabelle

last: Oswald

first: Nicolas

last: Loiseau

first: Yannick

last: Lippi


title: Transcriptome-Wide Identification of Differentially Expressed Genes and Long Non-coding RNAs in Nitroglycerin Tolerant Rat Aorta

city: Huaihua

first: Wei-hua

last: Wu

state: Hunan

address: Jingxi South Street, 492

department: School of Pharmaceutical Sciences

institute: Hunan University of Medicine

summary: We investigated comprehensive transcriptomic change in rat aorta tolerant to nitroglycerin (GTN) with a focus on lncRNAs. We employed RNA sequencing (RNA-seq) technique and identified 22788 genes (RPKM > 0.1, 14720 protein coding and 4408 lncRNA). And 115 differentially expressed (DE) mRNAs (65 upregulated and 50 downregulated) and 104 DE lncRNAs (56 upregulated and 48 downregulated) were found in GTN-tolerant aortas. Many DE mRNAs and cis-target genes of DE lncRNAs have been implicated in regulation of blood pressure or cell contraction. Collectively, these results suggested that dysregulated mRNAs and lncRNAs contribute to the development of GTN tolerance and might be used as novel potential targets to prevent and reverse GTN tolerance.

overall_design: Aorta mRNA and lncRNA profiles of 12-week rats treated with nitroglycerin and solvent for 3 d were generated by deep sequencing, in quadruple, using Illumina Hiseq 4000.


title: Gene expression analysis of Arabidopsis thaliana inoculated with fungal endophyte Mucor sp. 5 days after inoculation

overall_design: Gene expression profiles of  of A. thaliana shoots inoculated at 2 leaf seedling stage (10 days after germination), cultivated in vitro in MSR


title: Chromatin accessibility and transcriptomic profiling in NMe Gata-site double mutant mouse DN3 Thymocytes

city: New York

first: Stuart

middle: Aidan

last: Quinn

state: NY

address: 1130 St Nicholas Ave

department: Institute for Cancer Genetics

institute: Columbia University

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

overall_design: Refer to individual Series


title: ATACseq in NMe wild type and NMe GATA site 1 and 2 homozygous mutant DN3 thymocytes

summary: The NOTCH1-driven MYC enhancer (NMe) is essential for T cell development, transformation and the development of acute lymphoblastic leukemia. Here we analyze chromatin accessibility by ATACseq in DN3 thymocytes and Notch-induced TALL blasts from NMe wild type and NMe GATA site 1 and 2 (GS1+2) homozygous mutant mice.

overall_design: ATACseq analysis of DN3 thymocytes and Notch-driven T cell leukemia blasts with and without mutations in the GATA sites within Notch-Myc enhancer

first: Laura

last: Belver

first: Aidan

first: R

last: Albero

first: Adolfo

last: Ferrando


title: Transcriptional response of M. tuberculosis to quinazoline-11626252 treatment

city: Bern

first: Andrej

last: Benjak

address: Murtenstrasse 24-28

department: Department for BioMedical Research

institute: University of Bern

summary: We report here lead optimisation efforts of a new series of cytochrome bc1 oxidase inhibitors, the quinazoline derivatives. Four derivatives showed mild to no cytotoxicity as potent in vitro and ex vivo activity in infected THP-1 macrophages against M. tuberculosis. Isolation of resistant mutants to one of the derivatives in M. tuberculosis revealed mutations in both QcrA and QcrB of the cytochrome bc1 oxidase, one of two terminal oxidases of the mycobacterial electron transport chain. Cross-resistance studies, transcriptomic analyses and bioenergetics flux assays provide further evidence of the cytochrome bc1 as the target of the quinazolines compounds. The transcriptomic and bioenergetic profiles obtained when M. tuberculosis was treated with 11626252 are similar to transcriptomic and respiratory signatures of other cytochrome bc1 oxidase inhibitors.

overall_design: To gain insight into the initial adaptive response of M. tuberculosis to quinazoline-11626252, the transcriptomes of wild-type H37Rv exposed to quinazoline-11626252 at 10x and 30x MIC for a duration of four hours were examined. Two biological replicates were used for each condition. The control samples (which were part of the same experiment) are available under accession GSM3111057 and GSM3111058.

first: Andreanne

last: Lupien

first: Stewart

last: Cole


title: RNAseq in NMe wild type and NMe GATA site 1 and 2 homozygous mutant DN3 thymocytes

summary: The NOTCH1-driven MYC enhancer (NMe) is essential for T cell development, transformation and the development of acute lymphoblastic leukemia. Here we analyze by RNAseq the gene expression profile of DN3 thymocytes from NMe wild type and NMe GATA site 1 and 2 (GS1+2) homozygous mutant mice. GSEA analysis show a significant enrichment of MYC signature genes, consistent with a deficient function of NMe in GATA site 1 and 2 homozygous mutant thymocytes.

overall_design: RNAseq analysis of DN3 thymocytes in two genotypes and three samples per genotype

last: Belver Miguel


title: Transgenerational effects of thyroid hormone in the hypothalamus of the F2 generation

city: Scarborough

first: Arturo

last: Hernandez

state: ME

address: 81 Research Drive

department: Center for Molecular Medicine

institute: Maine Medical Center Research Institute

summary: Genetic factors do not fully account for the relatively high heritability of neurodevelopmental conditions, suggesting that non-genetic heritable factors contribute to their etiology. To evaluate the potential contribution of aberrant thyroid hormone status to the epigenetic inheritance of neurological phenotypes, we examined genetically normal mice with paternal grandparents that were developmentally overexposed to thyroid hormone due to a Dio3 mutation. Hypothalamic gene expression profiling in postnatal day 15 mice with control ancestry (Control), with a Dio3KO paternal grandmother (PGM), with Dio3KO paternal grandfather (PGF), with a heterozygous DIo3KO mother (HM) and with a heterozygous DIO3KO father (HF).

overall_design: 15 samples were analyzed representing 5 experimental groups in biological triplicates


title: Histone acetylation recruits the SWR1 complex to regulate active DNA demethylation in Arabidopsis

city: West Lafayette

first: Jian-Kang

last: Zhu

state: IN

address: 625 Agriculture Mall Dr.

department: Department of Horticulture and Landscape Architecture

institute: Purdue University

summary: The eukaryotic genome is divided into regions of heterochromatin and euchromatin. The histone variant H2A.Z specifically localizes at euchromatin and displays a genome-wide anti-correlation with DNA methylation. DNA methylation plays a central role in the epigenetic regulation of many eukaryotic genomes. Active DNA demethylation is critical for controlling the epigenome in plants and mammals. Yet, little is known about how DNA demethylases are recruited to target loci. Here we report that SWR1, a conserved histone H2A.Z deposition complex, regulates DNA demethylation in Arabidopsis thaliana by recruiting the plant DNA demethylase ROS1. A forward genetic screen for anti-silencing mutants identified two SWR1 components, PIE1 and ARP6, as cellular factors required for ROS1-mediated DNA demethylation. We further discovered two bromodomain-containing proteins, the methyl-DNA-binding protein AtMBD9, and NPX1, a plant homolog of ScBDF1 in yeast, as components of the SWR1 complex in Arabidopsis. AtMBD9 and NPX1 function redundantly in preventing DNA hypermethylation and transcriptional gene silencing by recognizing histone acetylation marks established by IDM1, a known regulator of DNA demethylation. We show that IDM1 is required for H2A.Z deposition in many genomic regions targeted for active DNA demethylation. We found that H2A.Z interacts with ROS1 and is required for locus-specific DNA demethylation and antisilencing. Our results reveal a role of H2A.Z in active DNA demethylation, and a mechanism through which DNA demethylases can be recruited to target regions by specific histone acetylation marks.

overall_design: MethylC-Seq: 18 samples examined: 35S:SUC2 WT (6 replicates); mutants: h2a.z-2, arp6-4, idm1-9, pie1-6, ros1-14, and atmbd9-4npx1-4 (each mutant has 2 replicates). H2A.Z ChIP-Seq: 35S:SUC2 WT, arp6-4, pie1-6, idm1-9, ros1-14 (each genotype has 2 ChIP replicates and one Input control). H3K18Ac/H3K23Ac ChIP-Seq: 35S:SUC2 WT, arp6-4, idm1-9, atmbd9-4npx1-4 (each genotype has 2 ChIP replicates for H3K18Ac and H3K23Ac and one Input control)

first: Wen-Feng

last: Nie

first: Mingguang

last: Lei

first: Kai

last: Tang


title: Effect of chronic DDG exposure on transcriptome in the testes and brain of male zebrafish

city: Guangzhou

first: Wenjun

last: Shi

address: South China Normal University, Guangzhou 510006, China

institute: The Environmental Research Institute, MOE Key Laboratory of Environmental Theoretical Chemistry

summary: Synthetic progestins are widely used in human and veterinary medicine. They can enter aquatic environments mainly via wastewater discharge and agricultural runoff, thus affecting fish populations in receiving waters. Here we investigated the chronic effects of dydrogesterone (DDG) on zebrafish from 21 days post fertilization (dpf) to 140 dpf at 5, 50 and 500 ng L-1.

overall_design: In total, 16 microarrays were analyzed for testis (SC, L, M, and H treatments, 4 biological replicates per treatment) and 16 microarrays were analyzed for brain (SC, L, M, and H treatments, 4 biological replicates per treatment).

first: Yuxia

last: Jiang


title: Thyroid hormone regulated genes in the neonatal testis

summary: An excess in thyroid hormone during rodent neonatal life causes abnormal prolifration and maturation of testicular cells, leading to reduced testis size and  impairments in steroidogenesis, Sertoli cell function, spermatogenesis and fertility. The high expression of type 3 deiodinase in the neonatal testis protects this tissue from premature exposure to thyroid hormones, since this gene (Dio3) function is to degrade thyroid hormones. DIO3-deficient mice (Dio3KO) exhibit a marked reduction in Sertoli cell proliferation and testis size, abnormalities in the reproductive axis and impaired fertility (Martinez et al. 2016, Endocrinology157:1276). To identify genes that are untimely regulated by thyroid hormone in the developing testes, we have performed RNAseq in testis total RNA from wild type and DIO3KO mouse neonates.

overall_design: 8 samples were analyzed representing 2 experimental groups in biological cuadruplicates


title: RNA-seq in transgenic cells

first: Yiming

address: No 38 Xueyuan Road

department: Chemical Bilogy

institute: Peking University Health Science Center

summary: To investigate the effects of natural TAG encoding in transgenic cells, RNA-seq was performed to compared the expression profiles of these genes

overall_design: Examine the mRNA abundance in transgenic cells either in the present or absent of NAEK

first: Huan

last: Xu


title: Ribosome profiling in transgenic and HEK293T cells

last: Wu

summary: To investigate whether natural TAG can be decoded by stably transfected pyltRNA, whole cell lysate of transgenic cells was collected 48h after the addition of NAEK and subjected to ribosome profiling, examining the physical locations of ribosomes along 15662 TAG terminated transcripts. And HEK293T cells were taken as control.

overall_design: Examine the physical locations of ribosomes along 15662 TAG terminated transcripts in both transgenic and HEK293T cells


title: miR394 and its target gene modulate BR signaling to regulate hypocotyls elongation in Arabidopsis

city: Jinan

first: Fengning

last: Xiang

state: Shandong

address: 27, Shandanan Road

department: School of life science

institute: Shandong University

summary: MicroRNAs and phytophormes are all small molecular signals that play important roles in regulating development and environmental responses in plants. The interplay between them allow the plants to better converge multiple inner and outer signals to optimizing their survival strategy. So far, the knowledge of how miRNAs are involved in brassinosteroid (BR) signaling is lacking. Here, we report the finding of miR394 and its target gene LEAF CURLING RESPONSENESS (LCR), which were transcriptionally responsive to BR, participate in BR signaling in regulating hypocotyls elongation in Arabidopsis. By phenotypic analyzing of a set of transgenic and mutants, miR394 was found to act as a negative regulator in BR signaling in hypocotyls elongation, while its target gene on the contrary. Genetically, miR394 functions upstream of BIN2 and BZR1/BES1, but partially downstream or independent with BRI1 and BSU1. RNA-seq analysis further supports that miR394 inhibits BR signaling through BIN2 because miR394 co-regulate significant number of genes together with BIN2. Additionally, miR394 improved the accumulation of BIN2 but decreased the protein amount of BZR1 and BES1, which can be phosphorylated by BIN2. miR394 also repressed the transcription of PRE1/5/6 and EXP8, the key hypocotyls elongation regulating genes, which had been reported to be BZR1/BES1 targets. These findings revealed a new pathway that miRNA involved in BR signaling in Arabidopsis.

overall_design: Col-0, MIR394A OE and bin2-1, 5-day-old light-grown seedlings, 2 replicates for MIR394A OE, 3 replicates for Col-0 and bin2-1

first: Shuo

last: Li


title: Genome-wide RNA sequencing of D. vulgaris respond to CuO nanoparticles exposure

city: Brisbane

first: Zhaoyu

last: Chen

address: Research Road | St. Lucia campus |

department: Advanced Water Management Centre

institute: The University of Queensland

summary:
Purpose: The objective of this study is to reveal the potential effects of CuO nanoparicles (NPs) on Desulfovibrio vulgaris Hildenborough (D. vulgaris) via genome-wide RNA sequencing
Methods: RNA was harvested from D. vulgaris cultures in the presence and absence of CuO NPs (0, 1, 50, 250 mg CuO NPs/L) 8 h after cultivation.

overall_design: Examination of 4 samples with diffferent CuO NPs exposure

first: Jianhua

last: Guo

first: Shuhong

last: Gao


title: Gene expression analysis of lung adenocarcinoma cancer cell line with ADAR knockdown

first: Jeffrey

last: Zhao

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

summary: In this experiment, we analyzed and compared gene expression in H358 lung adenocarcinoma cell lines with or without ADAR knockdown.

overall_design: The lung adenocarcinoma cell line H358 was transfected with ADAR shRNA or scrambled sequences. Total RNA was isolated from two biologically replicates. Samples for each group in duplicate were processed for Illumina BeadChip (Illumina HT-12) by the MSKCC genomics core facility according to the specifications of the manufacturer.

first: Elianna

last: Amin

first: David

middle: R

last: Jones


title: miRNAs related to silique development in Brassica napus

city: Wuhan

first: li

last: chen

address: Huazhong Agricultural University

institute: National Key Laboratory of Crop Genetic Improvement

summary: MicroRNAs (miRNAs) are a class of non-coding small RNAs (sRNAs) that play crucial regulatory roles in various developmental processes. Silique length indirectly influences seed yield in rapeseed (Brassica napus); however, the molecular roles of miRNAs in silique length are largely unknown. Here, backcross progenies of rapeseed with long siliques (LS) and short siliques (SS) were used to elucidate this role. Four small RNA libraries from early developing siliques were sequenced, and a total of 814 non-redundant miRNA precursors were identified, representing 65 known miRNAs, and 394 novel miRNAs. Expression analyses revealed 12 known miRNAs and 5 novel miRNAs that were differentially expressed in LS and SS lines. Furthermore, though two degradome sequencing, we annotated 522 cleavage events. An analysis of correlated expression between differentially expressed miRNAs and their targets demonstrated that some transcription factors might repress cell proliferation or auxin signal transduction to control silique length, and that a Pi/Cu deficiency might also restrict silique development. More significantly, the overexpression of miR160 in rapeseed may repress auxin response factors and result in increased silique length, illustrating that silique length could be regulated via an auxin-response pathway. These results will serve as a foundation for future research in B. napus.

overall_design: The aim of the present study was to systematically identify miRNAs that may be involved in early silique development.

first: Li

first: Jinxiong

last: Shen


title: HNF4A functions as an HCC oncogene or tumor suppressor depending upon the AMPK pathway activity status

city: Shanghai

last: Qin

address: Room 815, Mingdao Building, 131 Dong'an Road

department: Institutes of Biomedical Sciences

institute: Fudan University

summary:
Background & Aims: Hepatocyte nuclear factor 4A (HNF4A) is a master transcription factor (TF) in hepatocytes that regulates metabolism and differentiation. The mechanism of HNF4A in cancer progression remains unclear due to conflicting results observed in numerous studies. We aimed to address the roles of HNF4A in hepatocellular carcinoma (HCC).
Methods: We established the HNF4A overexpression and knocking-down stable cells in HCCLM3 and Huh7, and compared the effects of HNF4A on HCC cells in different glucose supply conditions in vitro and in vivo. Pathway inhibitors treatment and phosphatase activity comparisons were performed for signaling pathway analysis. Gene levels in HCC tissues and the clinical information were collected from TCGA for survival analysis. Multiomics approaches including proteomics, TFRE and ChIP-seq were applied to identify HNF4A target genes. Rescue experiments were performed to verify the functions of the potential target genes.
Results: We found HNF4A exhibited tumor-suppressive effects on proliferation and migration of HCC cells in glucose-sufficient conditions but tumor-promotive effects in glucose-insufficient conditions. This diverse functionality of HNF4A was dependent upon the AMPK pathway activity. Similarly, the prognosis predicted by HNF4A was also correlated with AMPKa expression level in HCC patients. The potential HNF4A target genes, including NEDD4 and RPS6KA2, are involved in the diverse functionality of HNF4A in response to AMPK activity status.
Conclusions: The glucose supply status could be the potential decisive factor to determine functions of HNF4A on HCC cells. The switch of HNF4A between oncogene and tumor suppressor was determined by AMPK activation status, which was correlated with glucose levels.

overall_design: To analyze the target genes of HNF4A under different glucose conditions.

first: Yihe

last: Bai


title: H3K36me3 protects the mouse epigenome from single nucleotide variations [ChIP-Seq]

city: shanghai

first: Jin

last: Sun

department: life science and technology

institute: Tongji University

summary: We analyze high-throughput profiling of histone H3K36me3 in mouse embryonic stem cells from chromatin immunoprecipitated DNA captured by H3K36me3-specific antibody. We find that H3K36me3 distribution is like expected and enriched at transcribing gene bodies especially with enrichment at 3’-terminal of gene body, which is identical with findings observed in other mammalian cells.

overall_design: Examination of histone H3K36me3 modification in mouse embryonic stem cell with histone H3.1WT overexpression, we analyzed two replicates.

first: FangLin

first: Xuan

last: Kang

first: Jianfeng

last: Chang


title: Genome-wide maps of acetylated histone 3 lysine 4 in human head and neck squamous cell carcinoma cells  under normoxia and hypoxia

city: Hangzhou

first: Jian-Qiu

last: Wang

state: Zhejiang

address: No. 16 Xuelin Street

department: Basic Medical Science

institute: Hangzhou Normal University

summary: Hypoxia-induced EMT involves the interplay between chromatin modifiers histone deacetylase 3 (HDAC3) and WDR5. The histone mark acetylation of histone 3 lysine 4 (H3K4Ac) is observed in the promoter regions of various EMT marker genes (e.g. E-cadherin, vimentin). However, there are only a limited number of EMT marker genes whose promoters were shown to be labeled with H3K4Ac. To further define the genome wide location of H3K4Ac, a chromatin immunoprecipitation followed by massively parallel DNA sequencing (ChIP-seq) analysis was performed using a head and neck squamous cell carcinoma (HNSCC) FADU cell line under normoxia and hypoxia. H3K4Ac was found to be located mainly around the transcription start site (TSS), and was partially removed from transcribed genes under hypoxia, indicating that H3K4Ac is responsible for regulation of gene expression during normoxia and hypoxia. 779 H3K4Ac-labeled genes whose H3K4Ac peaks were decreased under hypoxia were obtained by screening with a FDR< 0.05 and a distance to TSS of -5000~1000 bp.

overall_design: Examination of the histone modification H3K4Ac in FADU cells under normoxia and hypoxia

first: Kou-Juey


title: Expression analysis of the TAF1 syndrome

city: Kensington

first: Sara

last: Ballouz

state: NSW

address: High St

institute: UNSW

summary: The goal of this study was to perform a transcriptomic analysis on individuals from the TAF1 syndrome cohort to discover rare expression variants.

overall_design: We used RNA-seq to measure counts and expression levels for a family style DE analysis.

first: Max

last: Doerfel

first: Gholson

last: Lyon

first: Jesse

last: Gillis


title: RNA-SEQ of humna lung and breast cancer cell lines

status: Public on Jul 31 2019

city: Spokane

first: Bin

last: Shan

state: Washington

address: 412 E Spokane Falls Blvd

department: Biomedical Sciences

institute: Washington State University

summary: We cultured human lung and breast cancer cell lines, A549, H23, MDA-MB-231, MCF-7-TNR, and T47D cells. Total RNA was extracted and processed for RNA-SEQ.

overall_design: Total cell RNA was extracted from the treated cells at 48 hrs after transfection using TRIZOL. Libraries were constructed using the Illumina TruSeq Stranded Total RNA Library Prep Kit/Ribo-Zero Gold kit.

first: Simon

last: Alsager


title: SETD2-mediated loss of a panel of miRNAs determines MAPK/JNK signaling pathway activation and multidrug resistance in renal cell carcinoma

first: Libin

last: Yan

state: Hubei

address: No.1095, Jiefang Avenue

department: Urology

institute: Tongji Hospital,Tongji Medical College, Huazhong University of Science Technology

summary:
Finding the downstream miRNAs of SETD2 in the renal cell carcinoma cell line
the coordinated expression of SETD2-miRNAs-MAPK/JNK may be predictive of poor prognostic in patients with RCC. Our findings also emphasize the therapeutic potential of MAP4K4 in RCC therapy and support the development of an effective therapeutic strategy to target MAP4K4 by molecularly targeted approaches

overall_design: six samples. Including three siSETD2 samples and three control samples

first: Haoran

last: Liu


title: Genome-wide analysis of Ctr and OPA1 knock-down transcriptomes

city: Rotterdam

first: Qiuwei

last: Pan

address: Wytemaweg 80

institute: Erasmus University Medical Center

summary: Through the genome-wide analysis of Ctr and OPA1 knock-down group, we reveal the transcriptome changes with OPA1 down-regulation

overall_design: To observe the function of OPA1 in HCC, we knocked down the expression of OPA1 in Huh7 cell line and prepared RNA-sequencing

first: Meng

last: Li

first: Shaoshi

last: Zhang


title: Let-7 and induced autophagy

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

summary: Macroautophagy (hereafter autophagy) is the major pathway by which macromolecules and organelles are degraded. Autophagy is regulated by the mTOR signaling pathway, which is the focal point for integration of metabolic information, with mTORC1 playing a central role in balancing biosynthesis and catabolism. Of the various inputs to mTORC1, the amino acid sensing pathway is among the most potent. Based upon transcriptome analysis of neurons subjected to nutrient deprivation, we identified let-7 as a microRNA capable of promoting neuronal autophagy. We found that let-7 activates autophagy by coordinately down-regulating the amino acid sensing pathway to prevent mTORC1 activation. Let-7 induced autophagy in the brain and greatly reduced protein aggregates in a lentivirus model of polyglutamine disease, establishing the physiological relevance of let-7 for in vivo autophagy modulation. Moreover, peripheral delivery of let-7 anti-miR repressed autophagy in muscle and white fat, suggesting that let-7 autophagy regulation extends beyond the CNS. Hence, let-7 plays a central role in nutrient homeostasis and proteostasis regulation in higher organisms.

overall_design: anti-let7 treated cortices and hippocampi

first: Richard

last: Beyer

first: Amy

last: Dubinsky


title: Expression data from murine intrahepatic biliary organoids

city: Tokyo

first: Hiroaki

last: Fujiwara

address: 2-2-6, Bakurocho

department: Gastroenterology

institute: The Institute of Adult Disease, Asahi Life Foundation

summary:
Mutations of isocitrate dehydrogenase (IDH) 1 or 2 occur in 10-30% of intrahepatic cholangiocarcinomas (ICCs). However, their functional roles in biliary carcinogenesis are still unknown.
We used microarrays to investigate how mutant IDH1 affect the gene expression of intrahepatic biliary organoids generated from normal murine liver.

overall_design: By lentiviral techniques, we established murine intrahepatic biliary organoids stably expressing wild-type human IDH1 (IDH1-WT) and mutant human IDH1 (IDH1-MT). Each of them was selected for RNA extraction and hybridization on Affymetrix microarrays.

first: Keisuke

last: Tateishi


title: Androgen receptor is a back-door inhibitor of Androgen Receptor is a Backdoor Inhibitor of Wildtype and Mutant Estrogen Receptors in Refractory Hormone Receptor-Positive Breast Cancers

city: Memphis

first: Daniel

middle: Lee

last: Johnson

state: Tennessee

address: 71 S Manassas

department: Molecular Informatics Core

institute: UTHSC

summary:
HCI-13 patient-derived xenograft was treated with vehicle or a tissue-selective androgen receptor modulator (SARM), enobosarm. RNA was extracted from the tumors and microarray was performed.
Objective: The objective of the study is to determine the effect of an androgen receptor (AR) agonist or a selective AR modulator (SARM) on hormone receptor-positive breast cancer growth in preclinical models and to determine the underlying mechanism of action.

overall_design: Methods: Patient-derived xenograft (PDX) HCI-13 (a kind gift from Dr. Alana Whelm, University of Oklahoma) was implanted under the mammary fat pad in female NOD SCID Gamma mice. Once the tumors grew to 100-200 mm3, the animals were randomized and treated orally with vehicle or 10 mg/kg enobosarm. Tumor volume was measured thrice weekly. Thirty days after treatment initiation, the animals were sacrificed and the tumors were snap frozen. RNA was extracted from the tumors using Qiagen RNA isolation kit and its quality, integrity, and quantity were checked. The RNA was then subjected to microarray

first: Ramesh

last: Narayanan


title: circRNA expression profiles of fibroblasts: normal vs. NASH cirrhosis

city: guangzhou

first: jiayu

last: liu

address: NO.74 2nd Zhongshan Road

institute: Sun Yat-Sen University

summary: The progression from steatosis to nonalcoholic steatohepatitis (NASH) in nonalcoholic fatty liver disease (NAFLD) patients is one of the major causes of liver-related death worldwide and have limited effective therapies. We comparing the circular RNomics of liver fibroblasts isolated from patients with NAFLD-caused cirrhosis and the ones without NAFLD.

overall_design: 4 patients with NASH cirrhosis and 4 patients without NAFLD

first: Qiyi

last: Zhao

first: Jiayu

first: Ruiying

last: Ma


title: In vivo RNA-sequencing of Vibrio cholerae during intestinal colonization of infant rabbits

city: Boston

first: Fabian

last: Rivera

state: UNITED STATES

address: 77 Avenue Louis Pasteur, NRB 1039

department: Microbiology

institute: Harvard Medical School

summary: To understand how cholera toxin (CT) produced by Vibrio cholerae modulates gene expression of this organism within the intestine, RNA-seq analysis was performed on two samples each of WT and the ∆ctx mutant bacteria harvested from either the infant rabbit ileum or the cecum one-day post-intragastric infection. We found that 243 genes that were significantly up-regulated in the WT compared to the ∆ctx mutant and these included 101 genes in ileum samples, 118 in the cecum samples, and 24 in both samples. We found that genes known to be induced under low-iron growth conditions were up-regulated in WT relative to the ∆ctx mutant in both the ileum and in the cecum, with a marked up-regulation in the ileum relative to the cecum. We also found that genes involved in TCA cycle metabolism, L-Lactate utilization, and LCFA utilization were significantly up-regulated in the WT in the ileum relative to the ∆ctx mutant during infection. We conclude that CT-induced disease creates an iron-depleted metabolic niche in the gut that modulates the transcriptional profile of this pathogen during infection.

overall_design: RNA-seq analysis was performed on two samples each of WT and the ∆ctx mutant V. cholerae harvested from either the infant rabbit ileum or the cecum one-day post-intragastric infection.

last: Rivera-Chávez

first: John

middle: J

last: Mekalanos


title: Expression data from ovarian cancer cell line OVCAR3 following Knockdown or Knockout of BORIS (CTCFL)

city: Mexico City

first: Ernesto

last: Soto-Reyes

state: Mexico City

address: Av. Vasco de Quiroga

department: Departamento de Ciencias Naturales

country: Mexico

institute: Universidad Autónoma Metropolitana

summary:
The identification of prognostic biomarkers is a priority for patients suffering from high-grade serous ovarian cancer (SOC), which accounts for >70% of ovarian cancer (OC) deaths. Meanwhile borderline ovarian cancer (BOC) is a low malignancy tumor and usually patients undergo surgery with low probabilities of recurrence. However, SOC remains the most lethal neoplasm due to the lack of biomarkers for early diagnosis and prognosis. In this regard BORIS (CTCFL), a CTCF paralog, is a promising cancer biomarker that is overexpressed and controls transcription in several cancer types, mainly in OC. Studies suggest that BORIS has an important function in OC by altering gene expression, but the effect and extent to which BORIS influences transcription in OC from a genome-wide perspective is unclear.
Here we sought to identify BORIS target genes in an OC cell line (OVCAR3) with potential biomarker use in OC tumor samples. To achieve this, we performed in vitro knockout (KO) and knockdown (KD) experiments of BORIS in OVCAR3 cell line followed by expression microarrays and bioinformatics network enrichment analysis to identify relevant BORIS target genes.

overall_design: Expression profiles of OVCAR3 cell line following the Knockdown (KD) or Knockout (KO) of BORIS versus control cells were obtained with expression microarrays GeneChip Human Gene 2.1 ST oligonucleotide arrays (Affymetrix, Santa Clara, California, United States) . Three biological replicates of BORIS KD, three biological replicates of BORIS KO and two biological controls (WT) were used.

first: Marisol

last: Salgado-Albarrán


title: Germ Granules Govern Small RNA Inheritance

city: Tel Aviv

first: Itai

middle: Antoine

last: Toker

address: Haim levanon St.

department: Neurobiology

country: Israel

institute: Tel Aviv University

summary: In C. elegans nematodes, components of liquid-like germ granules were shown to be required for transgenerational small RNA inheritance. Surprisingly, we show here that mutants with defective germ granules can nevertheless inherit potent small RNA-based silencing responses, but some of the mutants lose this ability after many generations of homozygosity. Animals mutated in pptr-1, which is required for stabilization of P granules in the early embryo, display extraordinarily strong heritable RNAi responses, lasting for tens of generations. Intriguingly, the RNAi capacity of descendants derived from mutants defective in the core germ granules proteins MEG-3 and MEG-4 is determined by the genotype of the ancestors, and changes transgenerationally. Further, whether the meg-3/4 mutant alleles were present in the paternal or maternal lineages lead to different transgenerational consequences. Small RNA inheritance, rather than maternal contribution of the germ granules themselves, mediates the transgenerational defects in RNAi of meg-3/4 mutants and their progeny. Accordingly, germ granule defects lead to heritable genome-wide mis-expression of endogenous small RNAs. Upon disruption of germ granules, hrde-1 mutants can inherit RNAi although HRDE-1 was previously thought to be absolutely required for RNAi inheritance. We propose that germ granules sort and shape the RNA pool, and that small RNA inheritance maintains this activity for multiple generations.

overall_design: RNA was extracted from dissected gonads of wild-type or mutated young adult worms. All worms bore a Pmex-5::GFP transgene, driving GFP expression in the germline.

first: Itamar

last: Lev

middle: A

first: Yael

last: Mor

first: Anat

last: Nitzan

first: Guy

last: Weintraub

first: Olga

last: Antonova

first: Ornit

last: Bhonkar

first: Itay

last: Ben Shushan

first: Uri

last: Seroussi

first: Julie

last: Claycomb

first: Sarit

last: Anava

first: Hila

last: Gingold

first: Ronen

last: Zaidel-Bar

first: Oded

last: Rechavi


title: Reconstruction of the Human Blood-Brain Barrier in vitro reveals a Pathogenic Mechanism of APOE4 in Pericytes

city: Cambridge

first: Li-Huei

last: Tsai

state: Massachusetts

department: Picower Institute for Learning and Memory

institute: MIT

summary: The majority of Alzheimer’s disease patients and 20–40% of non-demented elderly experience amyloid deposits along their cerebral vasculature, a condition known as cerebral amyloid angiopathy (CAA). CAA impairs the function of the blood-brain barrier (BBB) leading to ischemia, hemorrhages, and accelerated cognitive dysfunction. The APOE4 allele is the strongest known genetic risk factor for CAA and sporadic AD, however the pathogenic mechanisms underlying this predisposition are unknown. Here, we recreate the human BBB in vitro by co-culturing the three cellular components of the BBB, endothelial cells, pericytes, and astrocytes in 3D scaffolding to construct a tractable model that recapitulates key anatomical and physiological properties of the BBB. Similar to the in vivo BBB, we find amyloid accumulates on our in vitro BBB (iBBB) and both APOE4 homozygous and heterozygous iBBBs exhibit significantly more amyloid accumulation than APOE3/3 iBBBs. Combinatorial experiments revealed that pericytes have a causal role in the development of CAA. We found that APOE expression is markedly up-regulated in APOE4 pericytes, but not in astrocytes or endothelial cells. Transcriptional profiling revealed that calcineurin/NFAT signaling is dysregulated in APOE4 pericytes. Pharmacologically inhibiting calcineurin led to downregulation of APOE and subsequently reduced amyloid deposition on the iBBB. These results demonstrate an unexpected role of pericytes in cerebral amyloid deposition and advocate for inhibiting calcineurin/NFAT-signaling as a therapeutic strategy to mitigate APOE4 predisposition to CAA and potentially AD.

overall_design: RNA-Seq of iPSC-derived pericytes

first: Joel

last: Blanchard

first: Hugh

last: Cam


title: Effect of dietary protein on gut gene expression in rat

city: Nanjing

first: Fan

last: Zhao

state: Jiangsu

address: Weigang 1#

department: Department of Food Science

institute: Nanjing Agricultural University

summary: A total of 49.88 Gb high quality reads of 6 samples (n=3) were obtained. The result of sample distance indicated that the cecal gene expression profiles of rats fed with diets composed of casein and chicken protein were clearly separated into two clusters. The variation of samples in casein protein fed group was higher than that in chicken protein fed group. There were 2524 differential expressed genes between the two groups, of which 871 genes were up regulated in chicken protein diet group compared with casein diet group.

overall_design: A 7-day short term effect of dietary protein on gene expression of large intestine in mice

first: Chunbao

last: Li


title: Enhanced plasmid mediated bioaugmentation of RDX contaminated matrices in column studies using donor strain Gordonia sp. KTR9

city: Vicksburg

first: Karl

last: Indest

address: 3909 Halls Ferry Road

institute: US Army Engineer Research and Development Center

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

sample_organism:
Rhodococcus jostii RHA1
Gordonia sp. KTR9

overall_design: Refer to individual Series


title: Enhanced plasmid mediated bioaugmentation of RDX contaminated matrices in column studies using donor strain Gordonia sp. KTR9 [exp 2]

summary:
To further explore potential molecular mechanisms and pathways by which the presence or absence of the pGKT2 plasmid may be affecting the overall fitness cost in the native Gordonia sp KTR9 strain, transcriptome studies were performed.
Transcriptome experiments comparing KTR9 wild-type and mutant strains grown in rich media confirmed the loss of the pGKT2 plasmid and also indicated the loss of the 90 kb pGKT1 plasmid.

overall_design: An 8 x 15K array study using total RNA recovered from triplicate cultures of Gordonia sp KTR9 wild-type and a pGKT2 plasmid curred KTR9 mutant grown in Luria broth (LB) were performed.

first: Matthew

last: Carr

first: Carina

last: Jung

first: Gary

last: Blakeney


title: Expression analysis of C. elegans eat-2, eat-2; acs-22 and eat-2; pmk-1; acs-22 mutants

first: Lina

last: Zou

address: 12 Xue-Fu Road, Pukou District , Nanjing, Jiangsu

department: Model Animal Research Center

institute: Nanjing University

summary: Investigation of whole genome gene expression level changes in C. elegans eat-2; acs-22 and eat-2; pmk-1; acs-22 mutant compared to the eat-2 strain.

overall_design: RNA-Seq analysis of C. elegans eat-2 mutant (3 replicates),  eat-2; acs-22 mutant (3 replicates) and eat-2; pmk-1; acs-22 mutant (3 replicates).

first: Di

last: Chen

last: Wu


title: Enhanced plasmid mediated bioaugmentation of RDX contaminated matrices in column studies using donor strain Gordonia sp. KTR9 [exp1]

summary:
To further explore potential molecular mechanisms and pathways by which the presence or absence of the pGKT2 plasmid may be affecting the overall fitness cost in a transconjugant Rhodococcus jostii RHA1 strain, transcriptome studies were performed.
Transcriptome experiments comparing RHA1 wild-type and RHA1 transconjugant strains grown in rich media confirmed the presence of the pGKT2 plasmid.

platform_organism:
Rhodococcus jostii RHA1
Gordonia sp. KTR9

overall_design: An 8 x 15K array study using total RNA recovered from triplicate cultures of Rhodococcus jostii RHA1 wild-type strain and a RHA1 transconjugant strain that took up the pGKT2 plasmid were performed.