title: Transcriptome analysis of purified T cells from chronic lymphocytic leukemia patients treated with avadomide alone or in combination with immune checkpoint blocking antibodies

city: San Diego

first: Rajkumar

last: Balakrishnan

state: California

address: 10300 Campus Point Drive, Suite 100,

department: Informatics & Predictive Sciences

institute: Bristol Myers Squibb

summary:
Cancer treatment has been transformed by checkpoint blockade therapies, with the highest anti-tumor activities of anti-programmed death 1 (PD-1) antibody (Ab) therapy seen in Hodgkin lymphoma. Disappointingly, response rates have been low in the non-Hodgkin lymphomas, with no activity seen in relapsed chronic lymphocytic leukemia (CLL) with anti-PD-1 Ab. Thus, identifying more powerful combination therapy is required for these patients. Here, we pre-clinically demonstrate enhanced T cell mediated anti-CLL activity following combinational therapy with anti-PD-1 or anti-PD-1 ligand (PD-L1) Ab and avadomide, a cereblon-modulating agent.
Next-generation RNA sequencing was performed on highly purified T cells from treatment naïve CLL patients treated for 18 hours with avadomide or anti-PD-1 (nivolumab) or PD-L1 (durvalumab) alone or in combinations. Patient samples were selected to represent extremes of prognosis (n=6 good and n=6 poor prognostic groups). Total RNA was extracted using the RNeasy isolation kit (Qiagen) while the library preparation of extracted mRNA was performed by utilizing the TruSeq stranded mRNA kit (Illumina) and the resulting library sequencing was performed on an Illumina HiSeq 2500 system. In all analyses the primary assembly of hg38 was used (ENCODE version) and the annotation from Gencode v24. Alignment was performed using a two-pass mode with STAR (v2.5.2b) on the full genome and counts were obtained using the quantmode GeneCounts option. Salmon (v 0.7) was used to obtain pseudoalignments on transcripts and genes on the trimmed fastq files. Differentially expressed genes were identified by application of the voom R package. Each treatment group was compared to vehicle to estimate the effect size and statistical significance of gene expression changes between treatment and control.
Differential expression pathway analysis revealed that the top functional gene categories common for all the avadomide and combination treated patient samples were related to the response to both type I and II interferon (IFN) signalling, as well as inflammatory, TNF-α signalling, IL-6/JAK/STAT3 and IL-2/STAT5 signalling responses. Pathway analysis revealed a strong enrichment of genes involved in T cell proliferation, cytokine and chemokine signalling, F-actin polymerization, T cell differentiation and co-stimulation. Notably, avadomide induced the expression of IFN type I inducible chemokines Cxcl9, Cxcl10 and Cxcl11 that have been associated with activation of Th1 immunity and favourable response to immunotherapy in solid cancer. In addition, genes associated with IFN-induced counter-regulatory pathways including Cd274 (PD-L1), Lag3 (lymphocyte-activation gene 3) and Ido1 (indoleamine 2,3 deoxygenase) were also upregulated by avadomide. Our analysis revealed that avadomide and the combination treatments induced IFN signaling in both good and poor prognostic disease subtypes, suggesting that therapies targeting patient T cells could be effective for all CLL patients. Thus, these results demonstrate the ability of avadomide to normalize dysfunctional IFN and chemokine responses in patient T cells that are linked to anti-tumor immunity.

overall_design: Differential gene expression analysis of CLL patients derived CD3+ T cells following treatment with avadomide (0.1 μM) and/or durvalumab (a-PD-L1) or nivolumab (a-PD-1) (10 μg/mL) (or vehicle treatments) for 18 h.

first: Nikolaos

last: Ioannou

first: Alan

last: Ramsay


title: Stimulation of oncogene-specific tumor infiltrating T-cells through combined vaccine and alpha-PD1 enable sustained anti-tumor responses against established HER2 breast cancer (BC) [WXS]

status: Public on Apr 11 2020

city: Durham

first: Zachary

middle: Conrad

last: Hartman

state: NC

address: Research Drive MSRB rm 414

department: Surgery

country: USA

institute: Duke University

type: Genome variation profiling by high throughput sequencing

summary: This study demonstrates two fundamental tenets of immunotherapy: vaccines targeting any tumor antigen will not be as effective as those targeting true oncogenic drivers and neither the stimulation of tumor-specific T-cells nor the blockade of a key immune checkpoint is enough to overcome the layers of immune suppression by itself. It provides single cell genetic evidence that vaccination alone generates a population of CD8 T-cells incapable of long-term tumor control due to the activation of numerous immune dysfunction pathways within the tumor. These promising studies have led to the initiation of a Phase II clinical trial testing a novel HER2 vaccine in combination with Pembrolizumab (NCT03632941) to determine if this combination can elicit effective anti-tumor immunity while minimizing off-target immune responses in patients with advanced HER2+ BC.

overall_design: This novel mouse model is driven by expression of an oncogenic isoform of HER2. To examine the mutation rate and neoepitope formation in these tumors, we performed paired bulk RNAseq/DNAseq of tumors to determine tumor mutational burden and neoepitope profiles in our mice.

first: Erika

middle: J

last: Crossby

first: Chaitanya

middle: R

last: Acharya

first: Ben

middle: K

last: Ashby


title: Stimulation of oncogene-specific tumor infiltrating T-cells through combined vaccine and alpha-PD1 enable sustained anti-tumor responses against established HER2 breast cancer (BC) [scRNA-Seq]

type: Expression profiling by high throughput sequencing

overall_design: A total of three treatment groups (anti-PD1, Her2 vaccine alone and combination of anti-PD1 and Her2 vaccine) along with control isotype group.


title: Stimulation of oncogene-specific tumor infiltrating T-cells through combined vaccine and alpha-PD1 enable sustained anti-tumor responses against established HER2 breast cancer (BC) [RNA-Seq]

overall_design: This novel mouse model is driven by expression of an oncogenic isoform of HER2. To ensure that the resulting cancer replicates the phenotype of both human HER2+ cancer and other HER2 driven mouse models, we performed bulk RNAseq of tumors to look at expression profiles in our mice.


title: Stimulation of oncogene-specific tumor infiltrating T-cells through combined vaccine and alpha-PD1 enable sustained anti-tumor responses against established HER2 breast cancer (BC)

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

overall_design: Refer to individual Series


title: Sin3A mutant pancreatic islets

city: Nashville

first: Ken

last: Lau

state: TN

address: 2215 Garland Ave. MRBIV10475

department: Cell and Developmental Biology

institute: Vanderbilt University

summary: Sin3A null islet cells compared with wild type

overall_design: Mutant vs WT (2 biological replicates)

last: Simmons

first: Guoqiang

last: Gu

first: Xiao-Dun

last: Yang


title: An optimized platform to generate human cerebral organoids

city: Toronto

first: Bibaswan

last: Ghoshal

address: 600 University Avenue

country: Canada

institute: Lunenfeld Tanenbaum Research Institute

summary: We established a protocol to generate morphologically uniform human cerebral organoids with similar cell type composition at various time points of maturation as determined by single cell sequencing.

overall_design: Examination of human cerebral organoids

first: Adam

last: Sivitilli

first: Jessica

last: Gosio

first: Alesya

last: Evstratova

first: Javier

last: Hernandez

first: Daniel

last: Trcka

first: Parisa

last: Ghiasighorveh

first: Martin

last: Beaulieu

first: Jeffrey

middle: L

last: Wrana

first: Liliana

last: Attisano


title: De novo assembly and characterization of Rhododendron hybridum Hort. (Ericaceae) global transcriptome using Illumina sequencing

city: pingdingshan

first: shiping

last: cheng

address: weilai road

country: China

institute: pingdingshan university

summary: Rhododendron hybridum Hort. (Ericaceae) is an important ornamental species with striking continuous flowering feature. However, few genomic resources are currently available in this species, and the breeding programs were handicapped by the lack of basic genetic information. Here, we established a transcriptomic profiling study from four different tissues using RNA-Seq to gain insight on the functional genes and to isolate EST-SSR markers for breeding and conservation purposes. In total 38,050,296 high-quality sequence reads were obtained, and 56,120 unigenes (with N50 = 1,236bp) were assembled. Of which, 32,580 (58.05 %) and 8,788 (15.66 %) were annotated to GO and KEGG database, respectively. Additionally, 38,775 (69.09 %) and 37,409 (66.66 %) R. hybridum unigenes were aligned to the Arabidopsis thaliana and Oryza sativa genome, respectively. A total of 21,103 simple sequence repeat (SSR) motifs were identified in 15,050 contigs. Among them, dinucleotide repeats account for the largest proportion for 49.27%, followed by mono- (35.94%) and trinucleotide (21.5%). This study represents the first transcriptome data of R. hybridum and confirms that the transcriptome assembly data are a useful resource for EST-SSR loci development. Such vast sequence data and markers will be robust tools for genomic research and breeding of R. hybridum and related species.

overall_design: Fresh roots, leaves, flowers and stem tissues were collected from one adult R. hybridum tree located at the Baotianman National Nature Reserve. All tissues were immediately frozen in liquid nitrogen and stored at -80°C until future use. Total RNA was extracted from four tissues using RNeasy Plant Mini Kit (QIAGEN, Hilden, Germany) and quantified with an Agilent 2100 Bioanalyzer RNA Nanochip Kit (QIAGEN, Hilden, Germany). An equal amount of RNA from each sample was pooled, and the mixed RNA (~10 μg) was subjected to Illumina HiSeq X TEN sequencing.

first: Shiping

last: Cheng

first: Minghui

last: Chen

first: Jiansheng

last: Wang

first: Yanyan

last: Li

first: Weishuang

last: Tong


title: RNA microarray of sorted dendritic epidermal T cells of aryl hydrocarbon receptor deficient mice

status: Public on Apr 10 2020

city: Düsseldorf

first: Katja

last: Merches

address: Auf'm Hennekamp 50

country: Germany

institute: Leibniz Institute for Environmental Medicine

summary: To assess the role of the aryl hydrocarbon receptor (AHR) receptor in dendritic epidermal T cells (DETC), we sorted DETC from 2 weeks old mice homozygous and heterozygous for AHR-knockout. While DETC are not maintained in the epidermis of mice with a homozygous AHR-knockout, those in heterozygous mice devellop normally. The age at 2 weeks is critical for the DETC establishment and the peak time of the so-called proliferation burst of DETC in wildtype mice. DETC were identified in epidermal cell suspension by expression of the gamma-delta T cell receptor. The DETC proportion of live epidermal cells was between 10-15 % in Ahr-het and 2-4 % in Ahr-ko mice.  After FACS-sorting to a purity of 90-98 %, DETC were lysed and their RNA was extracted. Three RNA samples for each genotype were generated, by pooling the RNA of 2-3 mice for each sample. RNA was processed and hybridized to Applied BiosystemsTM ClariomTM S Mouse Gene Expression Microarrays. Using the Software package R the data were normalized using the Robust Multichip Average algorithm (RMA) and significance of differentially regulated genes was assessed by the False Discovery Rate (FDR) using the Benjamini and Hochberg’s method.

overall_design: We performed RNA-microarrays to assess the role of the aryl hydrocarbon receptor (AHR) receptor in dendritic epidermal T cells (DETC). Therefore, we sorted DETC from 2 weeks old mice homozygous and heterozygous for AHR-knockout. The DETC proportion of live epidermal cells was between 10-15 % in Ahr-het and 2-4 % in Ahr-ko mice. DETC were identified in epidermal cell suspension by expression of the gamma-delta T cell receptor, FACS-sorted to a purity of 90-98 %, lysed and their RNA was extracted. Three RNA samples for each genotype were generated, by pooling the RNA of 2-3 mice for each sample. Three RNA samples for each genotype were generated, by pooling the RNA of 2-3 mice for each sample. RNA was processed and hybridized to Applied BiosystemsTM ClariomTM S Mouse Gene Expression Microarrays. The data were normalized using the Robust Multichip Average algorithm (RMA) and significance of differentially regulated genes was assessed by the False Discovery Rate (FDR) using the Benjamini and Hochberg’s method.

first: Alfonso

last: Schiavi

first: Nadine

last: Teichweyde

first: Patrick

last: Petzsch

first: Karl

last: Köhrer

first: Charlotte

last: Esser


title: Single Cell RNA-sequencing of murine tail interfollicular epidermis basal cells at postnatal days 7, 30 and in adult

city: Brussel

first: Cédric

last: Blanpain

address: 808 route de Lennik

country: Belgium

institute: Université Libre de Bruxelles

summary: The purpose of this study was to define, at the single cell level, the transcriptionnal profile of murine tail epidermal basal cells during potsnatal growth and to compare with adult homeostatic basal cells.  The analysis was performed on Lgr5DTR-EGFP mice (Tian et al., 2011)(knockin mice containing an Enhanced Green Fluorescent Protein (EGFP) under the control of the Lgr5 regulatory region), allowing to identify and exclude Lgr5-expressing cells of the bulge and basal cells of the interfollicular epidermis were enriched using EGFP negative, CD34 negative, alpha6 integrin positive gating. Our single-cell RNA sequencing revealed that epidermal basal cells at P7 form a more uniform population compared to adult basal cells and that heterogeneity starts to appear around P30.

overall_design:
Mouse tail epidermis was collected on mice at postnatal day 7, 30 and 60. (3 samples)

The dermis and epidermis were removed from the tail bone of untreated Lgr5DTR-EGFP mice (Tian et al., Nature, 2011)(knockin mice containing an Enhanced Green Fluorescent Protein (EGFP) under the control of the Lgr5 regulatory region) using forceps. The samples were incubated in HBSS (Gibco) 0,25% trypsin  (Gibco) at 4°C overnight. The next day, the epidermis was separated from the dermis. Epidermis was then incubated on a rocking plate (100 rpm) at room temperature for 5 min. BCs were mechanically separated from the epidermis by flushing 10 times under the epidermis. Tissues were then cut in small pieces with a scalpel and trypsin was neutralized by adding DMEM medium (Gibco) supplemented with 2% Chelex Fetal Calf Serum (cFCS). Samples were filtrated on 70 and 40µm filter (Falcon). Cells were incubated in PBS 2% cFCS with primary antibodies for 30 min on ice, protected from the light, with shaking every 10 min. Basal IFE and upper hair follicle  cells were stained using PE-conjugated anti-a6-integrin (clone GoH3; 1:200, ebioscience) and bulge cells were stained with biotinylated CD34 (clone RAM34; 1:50, BD Biosciences). Primary antibodies were washed with PBS 2% cFCS and cells incubated for 30 min in APC-conjugated streptavidin (BD Biosciences), on ice, with shaking every 10 min. Secondary antibody was washed with PBS 2% FCS and cells were incubated in Hoechst solution (1:4000 in PBS 2%cFCS) prior FACS analysis. Living epidermal cells were gated by forward scatter, side scatter and negative staining for Hoechst dye. Cells from the bulge were excluded from the sort using EGFP negative and CD34 negative gating and basal cells of the interfollicular epidermis were enriched using α6 integrin positive gating. Analysis were performed on a FACS Fortessa (BD Bioscience) and using FACS Diva software. Cell sorting was performed using a BD Influx at KULeuven Core facility (Leuven, Belgium) (P7 and P60) or a FACS Aria I at the ULB Flow Cytometry platform (Brussels, Belgium) (P30). After sorting, 6000 cells were loaded onto each channel of the Chromium Single Cell 3’ microfluidic chips (V2-chemistry, PN-120232, 10X Genomics) and individually barcoded with a 10X Chromium controller according to the manufacturer’s recommendations (10X Genomics). RNA from the barcoded cells was reverse transcribed, followed by amplification, shearing 5′ adaptor and sample index attachment. The libraries were prepared using the Chromium Single Cell 3’ Library Kit (V2-chemistry, PN-120233, 10X Genomics), quantified using a low coverage Illumina NextSeq 550 run and sequenced on an Illumina NovaSeq generating 343M, 245M and 336M reads for the P7, P30 and P60 libraries respectively. 10.338, 948 and 10.920  cells were detected, with a mean number of 33.179, 245.972 and 30.857 reads per cell, detecting a median of 2.290, 5.050 and 2.309 of genes per cell.

first: Cedric

first: Sophie

last: Dekoninck

first: Mariaceleste

last: Aragona

first: Alejandro

last: Sifrim

first: Thierry

last: Voet


title: Procaspase 3-Cyclin D1 assembly rewires cancer cells from apoptosis to proliferation

city: Montpellier

first: Frederic

middle: Emile

last: Bienvenu

address: 141 rue de la Cardonille

department: Cancer Biology

country: France

institute: CNRS-Institute of Functinal Genomics

summary:
Purpose: To gain insights into the activity of Cyclin D1 in tumor maintenance, we developed a cancer cell-specific RNAi strategy to knock down its expression and analyze the outcome on gene expression profile of the entire tumor.
Method: RAS/DNP53-driven tumor mRNA profiles were generated by RNA-Sequencing. Reads from RNA-Seq samples were mapped to the Mus musculus reference genome (MGSCv37) using Bowtie and TopHat. Transcript abundance and differential expression were called by Cufflinks.
Results: Cyclin D1 knock down in RAS-G12V or MMTV-ErbB2-driven tumors leads to expression change of genes involved in developmental processes, but no significant change in apoptotic genes was recorded among the samples.

first: Benjamin

last: Maurel

first: Julien

last: Champagne

first: Emeric

last: Dubois


title: Primary alcohol-activated human and mouse Hepatic Stellate Cells (HSCs) share similarities in gene expression profiles

city: La Jolla

first: Tatiana

last: Kisseleva

address: 9500 Gilman Dr

department: School of Medicine

institute: UCSD

summary: Alcoholic liver disease (ALD) is a leading cause of cirrhosis in the United States, which is characterized by extensive deposition of extracellular matrix proteins (ECM) and formation of a fibrous scar. Hepatic Stellate Cells (HSCs) are the major source of Collagen Type I producing myofibroblasts in ALD fibrosis. However, the mechanism of alcohol-induced activation of human and mouse HSCs is not fully understood. We compared the gene expression profiles of primary cultured human HSCs (hHSCs) isolated from patients with ALD (n=3) or without underlying liver disease (n=4) using RNA-Seq analysis. Furthermore, the gene expression profile of ALD hHSCs was compared to that of alcohol-activated mHSCs (isolated from intragastric (IG) alcohol-fed mice), or carbon-tetrachloride (CCl4)-activated mouse HSCs (mHSCs). Comparative transcriptome analysis revealed that ALD hHSCs, and alcohol- and CCl4-activated mHSCs share the expression of common HSC activation (Col1a1, Acta1, PAI-1, TIMP1, LOXL2), indicating that a common mechanism underlies activation of human and mouse HSCs. Furthermore, alcohol-activated mHSCs most closely recapitulate the gene expression profile of ALD hHSCs. We identified the genes that are similarly and uniquely upregulated in primary cultured alcohol-activated hHSCs and freshly isolated mHSCs, which include CSF1R, PLEK, LAPTM5, CD74, CD53, MMP9, CD14, CTSS, TYROBP, ITGB2, and other genes (compared to CCl4-activated mHSCs). We identified genes in alcohol-activated mHSCs from IG alcohol-fed mice that are largely consistent with the gene expression profile of primary cultured hHSCs from ALD patients. These genes are unique to alcohol-induced HSC activation in two species, and therefore, may become new targets or readout for anti-fibrotic therapy in experimental models of ALD.

overall_design: Using RNA-seq characterize of human hepatic stellate cells.

first: Xiao

last: Liu

first: Sara

last: Rosenthal


title: Elimination of Teratogenic Human Induced Pluripotent Stem Cells by Bee Venom via calcium-calpain pathway

city: Daejeon

first: Bu-Yeo

last: Kim

address: 1672 Yuseongdae-ro, Yuseong-gu

department: Herbal Medicine Research Division

country: South Korea

institute: Korea Institute of Oriental Medicine

summary: Induced pluripotent stem cells (iPSCs) are regarded as a promising option for cell-based regenerative medicine. To obtain safe and efficient iPSC-based cell products, it is necessary to selectively eliminate the residual iPSCs prior to in vivo implantation to eliminate the risk of teratoma formation. Bee venom (BV) has long been used in traditional Chinese medicine to treat inflammatory diseases and relieve pain, and has been shown to exhibit anti-cancer, anti-mutagenic, anti-nociceptive, and radioprotective activities. However, the potential benefits of BV in iPSC therapy, particularly its anti-teratoma activity, have not been examined. In this study, we tried to measure the effects of BV on expression of genes in iPSCs.

overall_design: Induced pluripotent stem cells (iPSCs) established from human foreskin fibroblasts were treated with BV.

first: Sun-Ku

last: Chung


title: Metabolomic Landscape of African American Prostate Cancer: insights into the Biological Basis of racial disparity

city: Houston

first: Arun

last: Sreekumar

state: Texas

address: One Baylor Plaza

department: Molecular and Cell Biology

institute: Baylor College of Medicine

summary: RNA-Seq data of adenosine and inosine treated stroma cell lines

overall_design: stroma cells were starved for 24hours and treated with 100uM adenosine; 3 replicates for each condition (adenosine and control); control is the reference sample

first: Jie

last: Gohlke

first: Stacy

last: Lloyd

first: Sumanta

last: Basu

first: Vasanta

last: Putluri

first: Shaiju

last: Vareed

first: Uttam

last: Rasaily

first: Danthasinghe

middle: B

last: Piyarathna

first: Victoria

last: Findlay

first: Rebeca

last: San Martin

first: Dang

last: Truong

first: Thekkelnaycke

last: Rajendiran

first: Tiffany

last: Dorsey

first: Rajni

last: Sonavane

first: Balasubramanyam

last: Karanam

first: Salil

last: Bhowmik

first: David

last: Labbé

first: Rick

last: Kittles

first: Stefan

last: Ambs

first: Michael

last: Ittmann

last: Rowley

first: Nora

last: Navone

last: Turner

first: Ganesh

last: Palapattu

first: Nagireddy

first: George

last: Michailidis


title: Secreted microRNA data from the parasitic filarial nematode Acanthocheilonema viteae

city: Sainte-Anne-de-Bellevue

first: Lucienne

last: Tritten

state: QC

address: 21111 Lakeshore Road

department: Institute of Parasitology

institute: McGill University

type: Non-coding RNA profiling by high throughput sequencing

summary: The helminth Acanthocheilonema viteae serves as model organism for research on parasitic filarial nematodes. Total RNA secreted or excreted by 1500 adult female and male A. viteae over 3 weeks was isolated from culture media previously processed by differential ultracentrifugation, and subjected to miRNA sequencing.

overall_design: Male and female excretory/secretory miRNAs were profiled and compared

first: Julien

last: Soichot

first: Yvette

last: Endriss

first: Hanspeter

last: Marti


title: Molecular and cellular signature of perirenal adipose tissue

city: Marseille

first: Paul

last: Pascale

address: 27 Bd Jean Moulin

department: Faculté de Pharmacie

summary:
We investigated whether the features of donor-derived stromal vascular fraction of perirenal adipose tissue (PRAT-SVF) could be indicative of the deleterious impact of the ECD microenvironment on renal transplants.
A comparative analysis of cellular components, transcriptomic and vasculogenic profiles was performed in PRAT-SVF obtained from deceased donors (non ECD) and expanded criteria donors (ECD)
The global RNA sequencing approach indicated a differential molecular signature in the PRAT-SVF of ECD donors characterized by the overexpression of inflammatory transcripts (CXCL1, CCL4, IL1-β,INF-ϒ).

overall_design: stromal vascular fraction  mRNA profiles of non-ECD and ECD donors were generated  using Illumina Nextseq sequencer.

first: Romain

last: Boissier

first: Pauline

last: François

first: Stéphanie

last: Simoncini

first: Pascale

last: Paul


title: Exogenous Melatonin Attenuates Post-harvest Decay by Increasing the Antioxidant Activity of Wax Apple (Syzygium samarangense)

city: xuzhou

first: yao

last: chen

address: Shanghai Road 101

institute: Jiangsu normal university

summary: Our experiments show that exogenous MT treatment can effectively delay the decay and water loss rate of post-harvest wax apples, which may be related to reducing the degree of membrane lipid peroxidation and inhibiting enzymatic browning. MT treatment also maintains the quality of post-harvest wax apple by enhancing the activity of antioxidant enzymes. At the same time, it can reduce the incidence of post-harvest diseases of wax apple by increasing the JA and SA contents. MT can down-regulate the expression of genes related to oxidation, and up-regulate the expression of related genes in antioxidant enzymes and non-enzymatic antioxidant pathways, suggesting that exogenous melatonin can reduce the production of excess ROS and maintain the redox homeostasis of post-harvest wax apple. Therefore, melatonin, as a strong and effective free radical scavenger and antioxidant, plays an important role in delaying the decay of post-harvest wax apples and prolonging the shelf life.

overall_design: Using IlluminaHiseq4000, de novo transcriptome sequencing was performed on the 5th day of wax apple samples, including control group and 800µM melatonin (MT) treatment group, including 3 biological repeats.

first: Yao

last: Chen


title: Comparative transcriptome analysis between two tomato materials under salt stress

city: Harbin

first: Jian

last: Wang

address: 600 Changjiang Road

institute: Northeast Agricultural University

summary: RNA sequencing was performed to investigate the the response mechanism of tomato response to salt stress.

overall_design: mRNA profiles of different tomato leaf samples were generated by deep sequencing. The sequence reads that passed quality filters were analyzed at the transcript .

first: Tingting

last: Zhao

first: Xiangyang

last: Xu


title: Gene expression profiling of primary hepatocytes stimulated with TGF-β  in the presence/absence of Caveolin-1

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

summary: Primary murine hepatocytes were transfected with siRNA targeting Caveolin-1 directly after attachment (o/n). Next day, cells were treated with TGF-beta for 48 h. Experiment was performed in triplicate using primary cells from 3  donor mice.

overall_design: RNA was isolated from primary hepatocytes treated with TGF-β  and siRNA targeting Caveolin-1.

first: Mei

last: Han

first: Christoph

last: Meyer


title: Epigenetic requirements for triggering heterochromatinization and Piwi-interacting RNA production from transgenes in the Drosophila germline

city: Moscow

first: Pavel

last: Komarov

address: Kurchatov sq. 2

country: Russia

institute: Institute of Molecular Genetics of the Russian Academy of Sciences

summary: Transgenes containing a fragment of I transposon represent a powerful model of piRNA cluster de novo formation in the Drosophila germline. We revealed that the same transgenes located at different genomic loci form piRNA clusters with various capacity of small RNA production. Transgenic piRNA clusters are not established in piRNA pathway mutants. However, in wild-type context, the endogenous ancestral I-related piRNAs are sufficient to heterochromatinize and convert the I-containing transgenes into piRNA-producing loci. Here, we address how the quantitative level of piRNAs influences the heterochromatinization and piRNA production. We show that neither the piRNAs mediated by active I-element copies nor inheritance of abundant maternal I-derived piRNAs enable to stimulate additional changes of transgenes chromatin state or piRNA production from them. Therefore, chromatin changes and piRNA production are initiated by a minimum threshold level of complementary piRNAs suggesting a selective advantage of prompt cell response to the lowest level of piRNAs. Noteworthy, the weak piRNA clusters do not transform into strong ones after being targeted by a larger amount of I-specific piRNAs, indicating the importance of the genomic context for piRNA cluster establishment. Analysis of ovarian transcription profiles suggests that regions facilitating convergent transcription favor formation of transgenic piRNA clusters .

overall_design: This study aims at understanding the quantitative level of small RNAs required for heterochromatinization and piRNA production from trangenes in the Drosphila germline using small RNA-seq and GRO-seq in adult ovaries of transgenic Drosophila strains.

middle: A

first: Olesya

last: Sokolova

first: Natalia

last: Akulenko

first: Emilie

last: Brasset

first: Silke

last: Jensen

first: Alla

last: Kalmykova


title: Endophytic and rhizophytic prokaryotic communities in S. alterniflora and petroleum degradation

first: Claudia

last: Gunsch

address: 100 Science Dr

summary: The experiment was designed to test the interactions of Spartina alterniflora, its microbiome, and the interaction of the plant-microbe relationship with oil from the Deepwater Horizon oil spill (DWH). Total RNA was extracted from leaf and root microbiome of S. alterniflora in soils that were oiled in DWH oil spill with or without added oil, as well as those grown in unoiled soil with or without added oil. The work in its entirety characterizes the transport, fate and catabolic activities of bacterial communities in petroleum-polluted soils and within plant tissues.

sample_organism:
synthetic construct
uncultured bacterium

platform_organism: Bacteria Archaea Eukaryota Viruses

overall_design: Total RNA was extracted from leaf and root of Spartina alterniflora and converted immediately into cDNA, which was used for GeoChip 5.0S analysis. S. alterniflora was grown in one of the four conditions: DWH-impacted soil with added oil, DWH-impacted soil without added oil, previously unoiled soil with added oil, and previously unoiled soil without added oil (control). Triplicates of leaf and root samples were collected from each S. alterniflora, and thus a total of 24 samples were analyzed on GeoChip.

first: Yeon

last: Kim

first: Stephen

last: Formel

first: Sunshine

last: Van Bael

first: Paige

last: Varner


title: KDM3B suppresses APL Progression by restricting chromatin accessibility and facilitating the ATRA-mediated degradation of PML/RARα (RNA-seq data set)

city: Shanghai

first: Xinrui

last: Wang

address: 197 Ruijin Rd II

institute: Rui-Jin Hospital affiliated to Shanghai Jiao Tong University School of Medicine

summary: Histone demethylase KDM3B is considered to play a critical role in leukemogenesis. To the best of our knowledge, this study is the first attempt to probe the detailed genetic and epigenetic mechanisms underlying the regulation of KDM3B in the development of APL from the perspectives of multi-layer omics. Results of the present study demonstrate that KDM3B exerts anti-APL effect by directly modulating H3K9me1/me2 levels to maintain compact chromatin status, but also indicate the interaction between KDM3B and PML/RARα regulates degradation of PML/RARα.

overall_design: RNA-seq in the NB4 cell line (undifferentiated/differentiated) before and after knockdown of KDM3B

first: Wang

last: Xinrui

first: Zhang

last: Ji


title: KDM3B suppresses APL Progression by restricting chromatin accessibility and facilitating the ATRA-mediated degradation of PML/RARα (ChIP-seq data set)

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Examination of the genome-wide binding of H3K9me1/me2/me3 in the NB4 cell line before and after knockdown of KDM3B


title: KDM3B suppresses APL Progression by restricting chromatin accessibility and facilitating the ATRA-mediated degradation of PML/RARα

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

overall_design: Refer to individual Series


title: TaqMan mouse miRNA array profile of LY6CHigh and LY6Clow monocyte

first: Isabelle

last: DUROUX-RICHARD

address: 80 av Augustin Fliche

summary: mouse Freshly isolated monocyte (LY6C high) and (LY6C low) were purified from WT DBA/1 mice blood, and sorted by FACS.  We used Taqman miRNA TLDA arrays to performed miRNA profiling

overall_design: qPCR miRNAexpression profiling.  Monocytes from three DBA/1 mices were used and treated separately as indicated in the summary.

last: Duroux-Richard

first: Florence

last: Apparailly


title: Unravelling the transcriptome and metabolite modulation of superficial scald development in pear fruit (cv. ‘Blanquilla’)

city: San Michele all'Adige

first: Fabrizio

last: Costa

state: N/A = Not Applicable

address: Via Mach 1

department: Center Agriculture Food Environment

country: Italy

institute: University of Trento

summary: The harveting of the fruit of a single cultivar are technically harvested over a period of time and the progression of the on-tree fruit maturity lead to important physiological modification and transcriptional signature able to impact the final quality of fruit and the management of the postharvest phase.

overall_design: Nine samples have been totally analyzed, representing three replicates of three different treatments carried out of pear fruit. In particular the first sample was represented by controlled untreated fruit, while the other two sub-samples have been treated with Lovastatine and 1-methylcyclopropene in order to prevent the development of superficial scald.

first: Jordi

last: Giné-Bordonaba

first: Nicola

last: Busatto

first: Christian

last: Larrigaudière

first: Violeta

last: Lindo-Garcìa

first: Gemma

last: Echeverria

first: Urska

last: Vrhovsek

first: Brian

last: Farneti

first: Franco

last: Biasioli

first: Marzia

last: Rossato

first: Massimo

last: Delledonne


title: TaqMan Human miRNA array profile of CD14++CD16- and CD14+CD16++ monocyte subsets

summary: Human Freshly isolated monocyte (CD14++CD16-) and (CD14+ CD16++) were purified from healthy volunteers' blood, and sorted by FAC.  We used Taqman miRNA TLDA arrays to performed miRNA profiling

overall_design: qPCR miRNAexpression profiling.  Monocytes from three donors were used and treated separately as indicated in the summary.


title: mRNAs microarray from 5 fresh lung cancer tissues and 5 fresh non-tumor tissues.

city: Guangzhou

first: neng

last: jiang

state: Guangdong

address: No. 58, ZhongShan Second Road

department: Department of Pathology

institute: The First Affiliated Hospital, Sun Yat-sen University

summary: We performed mRNAss microarray to analyze the differential mRNAs expression profiles according to the recommended protocols.

overall_design: In the study presented here, fresh lung cancer tissue specimens and non-tumor lung tissue specimens were collected immediately after surgical resection. mRNAs microarray was performed according to the manufacturer’s guideline.

first: Neng

last: Jiang

first: Zunfu

last: Ke


title: Prdx1,a RNA binding protein,regulate inflammatory injury in intracerebral hemorrhage by targeting RNA stability

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.


title: MiRNA microarray analysis of 5 fresh lung cancer tissues and 5 fresh non-tumor lung tissues

summary: We performed miRNAs microarray to analyze the differential miRNAs expression profiles according to the recommended protocols.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: In the study presented here, fresh lung cancer tissue specimens and non-tumor lung tissue specimens were collected immediately after surgical resection. MiRNAs microarray was performed according to the manufacturer’s guideline.


title: Prdx1,a RNA binding protein,regulate inflammatory injury in intracerebral hemorrhage by targeting RNA stability (PRDX1_OE_RNA-seq)

summary: We overexpressed Prdx1 in HeLa cells to study Prdx1-regulated genes using RNA-seq technology, followed by bioinformatic analysis of target genes of Prdx1-regulated.

overall_design: transcrptional analysis of Prdx1 overexpression and control in Hela cells

first: Qingwu

last: Yang


title: Prdx1,a RNA binding protein,regulate inflammatory injury in intracerebral hemorrhage by targeting RNA stability (PRDX1_iRIP-seq)

summary: We overexpressed Prdx1 in HeLa cells to study Prdx1-regulated genes using RNA-seq technology, followed by bioinformatic analysis of target genes of Prdx1-regulated.In order to find the precise regulatory mechanisms,we performed iRIP-seq experiment in HeLa cell.

overall_design: RIP-seq analysis of Prdx1 versus input in Hela cells


title: hsa_circ_0007841: A novel potential biomarker and drug resistance for multiple myeloma

city: CHANG SHA

first: FU

middle: YUN

last: FENG

state: HUNAN

address: No. 138 Tonglu Road, Yuelu District, Hexi Distric

department: Blood

institute: The Third Xiangya Hospital of Central South University

summary: Purpose:It has been shown that circular RNA (circRNA) is a key regulatory factor in development and progression of human tumors.  However, the working mechanism and clinical significance of most circRNAs remain unknown in human cancer, including multiple  myeloma (MM), a hematologic malignancy.  Patients and methods:In the present study, high-throughput circRNA microarray was combined with bioinformatics to identify  differentially expressed circRNAs in MM. The hsa_circ_0007841 expressions were shown in MM tissues of 86 patients and  drug-resistant cell lines and pathological features were detected. Further, the relationship between hsa_circ_0007841 expressions  in the MM tissues and pathological features of MM patients were discussed. The role of hsa_circ_0007841 as a potential biomarker  and therapeutic target was analyzed.  Results:Our results indicated that in MM tissues collected from patients, MM cell lines and drug-resistant cell lines, the  hsa_circ_0007841 expression was significantly upregulated. A close connection with prognosis was observed. That is,  hsa_circ_0007841 upregulation was correlated with chromosomal aberrations, such as gain 1q21, t(4:14) and mutations in ATR and  IRF4 genes. This finding was further verified in large samples. Finally, bioinformatics analysis indicated interaction that 8  differentially expressed miRNAs and 10 candidate mRNAs interacted with hsa_circ_0007841. These results sheds new light on the  basic functional research in the future.  Conclusion:It was reported for the first time that hsa_circ_0007841 was significantly upregulated in MM. Our study indicated that  hsa_circ_0007841 may be a novel biomarker for MM and involved in the progression of MM.

overall_design: the bone marrow samples from 3 MM patients were sorted by magnetic activated cell sorting (MACS) using anti-CD138 MicroBeads, and the plasma cells were enriched.

first: Meng

last: Gao

first: Han

last: Xiao

last: Hang

first: Siyi

first: Yunfeng

last: Fu

first: Liying

last: Gong


title: Deficiency of C3a receptor attenuates the development of diabetic nephropathy

city: Zhengzhou

first: Xiao-Qian

last: Li

state: Henan

address: No. 1, East of Jianshe Street, Erqi District

department: Nephrology Hospital

institute: the First Affiliated Hospital of Zhengzhou University


title: Deficiency of C3a receptor attenuates the development of diabetic nephropathy (Control Group)

summary: Diabetic nephropathy (DN) is the leading cause of chronic kidney disease and end-stage renal disease. Emerging evidence suggests that complement activation is involved in the pathogenesis of DN. The aim of this study was to investigate the pathogenic role of C3a and C3a receptor (C3aR) in DN. The expression of C3aR was examined in the renal specimen of DN patients. Using a C3aR gene knockout mice (C3aR-/-), we evaluated kidney injury in diabetic mice. The mouse gene expression microarray was performed to further explore the pathogenic role of C3aR. Then the underlying mechanism was investigated in vitro with macrophage treated with C3a. Compared with normal controls, the renal expression of C3aR was significantly increased in DN patients. C3aR-/- diabetic mice developed less severe diabetic renal damage compared with WT diabetic mice, exhibiting significantly lower level of albuminuria and milder renal pathological injury. Microarray profiling uncovered significantly suppressed inflammatory responses and T cell adaptive immunity in C3aR-/- diabetic mice compared with WT diabetic mice and this result was further verified by immunohistochemical staining of renal CD4+, CD8+ T cells and macrophages infiltration. In vitro study demonstrated C3a can enhance macrophages secreted cytokines which could induce inflammatory responses and differentiation of T cell lineage. In conclusion, C3aR deficiency could attenuate diabetic renal damage through suppressing inflammatory responses and T cell adaptive immunity, possibly by influencing macrophages secreted cytokines. Thus, C3aR may be a promising therapeutic target for DN.

overall_design:
There were four groups including WT control group, C3aR-/- control group, WT diabetic group, C3aR-/- diabetic group. Total RNA was extracted from three replicate samples per group
This series includes the control samples.

first: Xiao-qian

first: Dong-yuan

last: Chang

first: Min

first: Ming-hui

last: Zhao


title: Deficiency of C3a receptor attenuates the development of diabetic nephropathy (Diabetic Group)

overall_design:
There were four groups including WT control group, C3aR-/- control group, WT diabetic group, C3aR-/- diabetic group. Total RNA was extracted from three replicate samples per group.
This series includes the diabetic samples.


title: Spinal cord stimulation prevents paclitaxel-induced mechanical and cold hypersensitivity and modulates spinal gene expression in rats

city: Baltimore

first: Yun

last: Guan

state: Maryland

address: Ross 350, 720 Rutland Ave

department: Anesthesiology and Critical Care Medicine

institute: Johns Hopkins University

summary: Introduction: Paclitaxel-induced peripheral neuropathy (PIPN) is a common dose-limiting side effect of this cancer treatment drug. Spinal cord stimulation (SCS) has demonstrated efficacy for attenuating some neuropathic pain conditions. Objective: We aim to examine the inhibitory effect of SCS for the development of PIPN pain in rats. Methods: We examined whether traditional SCS administered during paclitaxel treatment  attenuates PIPN-related pain behavior. After SCS, we carried out RNA-seq of the lumbar spinal cord to examine which genes are differentially expressed after PIPN with and without SCS. Results: Compared to rats treated with paclitaxel alone (n=7) or sham SCS (n=6), SCS treatment (n= 11) significantly inhibited the development of paclitaxel-induced mechanical and cold hypersensitivity, without altering open-field exploratory behavior. RNA-seq showed that SCS induced upregulation of 836 genes and downregulation of 230 genes in the spinal cord of paclitaxel-treated rats (n=3), as compared to sham SCS (n=5). SCS upregulated immune responses in paclitaxel-treated rats, including transcription of astrocyte- and microglial-related genes, but repressed transcription of multiple gene networks associated with synaptic plasticity, neuron projection development, g-aminobutyric acid reuptake, and long-term potentiation. Conclusion: Our findings suggest that traditional SCS may attenuate the development of pain-related behaviors in PIPN, partially by causing aggregate inhibition of synaptic plasticity through up- and down-regulation of gene networks in the spinal cord.

overall_design: RNAseq of 3 study groups: Naïve rats, rats after paclitaxel and SCS electrode placement (sham control), rats after paclitaxel, SCS electrode placement and SCS

first: Eellan

last: Sivanesan

first: Kimberly

middle: E

last: Stephens

first: Qian

last: Huang

first: Zhiyong

first: Neil

middle: C

last: Ford

first: Wanru

last: Duan

first: Shao-qui

last: He

first: Xinyan

first: Bengt

last: Linderoth

first: Srinivasa

middle: N

last: Raja


title: Contrasting gene expression profiles of monocytes and lymphocytes from Peste-des-petits-ruminants virus infected goats

city: Karnal

first: Ravi Kumar

last: Gandham

state: Haryana

address: Makrampur

country: India

institute: ICAR-NBAGR

summary: We have used RNA-Seq to examine lymphocytes and monocytes expression profiles in goats infected with  PPRV (Izatnagar94), suggesting its important functions in immune response during virus infection.

overall_design: In this study, transcriptome analysis of PPRV infected PBMCs subsets - T helper cells, T cytotoxic cells, monocytes and B lymphocytes was done to delineate their role in host response at 9 days post infection.

first: Sajad

last: Ahmad Wani

first: Amit

last: Ranjan Sahu

first: Aruna

last: Pandey

first: Raja

last: ishaq

first: Shikha

last: Saxena

first: Bina

last: Mishra

first: B

middle: P

first: A

last: Tiwari

first: Ravi

last: Kumar Gandham


title: Ampli-seq of iPSC-CMs cultured until day 30 and long-term until day 90 and day 200

city: Stanford

first: Joseph

last: Wu

state: Carlifornia

address: Stanford University School of Medicine

institute: Stanford University School of Medicine

summary: Two healthy control iPSC lines were differentiated into iPSC-CMs

overall_design: Ampli-seq of iPSC-CMs cultured until day 30, day 90, day 200

first: Ning-Yi

last: Shao

first: Antje

last: Ebert

first: Haodong

last: Chen


title: Epigenetic initiation of the Th17 differentiation programme is promoted by Cxxc finger protein 1

city: hangzhou

first: lie

last: wang

state: zhejiang

address: Zijingang Campus, Zhejiang University，Yuhangtang Road 866

department: immunology

institute: zhejiang universiry

summary: IL-6/STAT3 signalling is known to initiate the Th17 differentiation programme, but the upstream regulatory mechanisms remain minimally explored. Here, we show that Cxxc finger protein 1 (Cxxc1) promoted the generation and stability of Th17 cells as an epigenetic regulator and prevented their differentiation into Treg cells. Mice with a T cell-specific deletion of Cxxc1 were protected from experimental autoimmune encephalomyelitis and were more susceptible to Citrobacter rodentium infection. Cxxc1-deficient T cells acquired a Treg cell-biased programme that dominantly suppressed Th17 cell generation via IL-6Rα production. Cxxc1 deficiency decreased IL-6Rα expression and impeded IL-6/STAT3 signalling, whereas the overexpression of IL-6Rα could reverse the defects seen in Cxxc1-deficient Th17 cells in vitro and in vivo. Genome-wide occupancy analysis revealed that Cxxc1 bound to Il6rα gene loci in the Th17 programme by maintaining the appropriate H3K4me3 modification of its promoter. Therefore, these data highlight that Cxxc1 as a key regulator governs the balance between Th17 and Treg cells by controlling the expression of IL-6Rα, which subsequently affects IL-6/STAT3 signalling and has a direct impact on Th17-related autoimmune diseases.

overall_design: TH17 CHIP-SEQ

first: Wang

last: Lie

first: Feng

last: Lin


title: Co-expression Analysis Reveals Dysregulated miRNAs and miRNA-mRNA Interactions in the Development of Contrast-induced Acute Kidney Injury [mRNA]

city: Fuzhou

first: Zhiqing

last: Wang

state: Fujian

address: NO. 156, North Xierhuan Road

department: Department of Cardiology

institute: 900 Hospital of the Joint Logistics Team

summary:
Purpose:The pathogenesis of contrast-induced acute kidney injury (CI-AKI) has not yet been clearly understood. miRNAs are important mediators which normally work by post-transcriptional degradation of target mRNAs. Emerging evidence indicated a number of differentially expressed miRNAs in CI-AKI following intravenous contrast medium injection. However, there exist differences in the pathological mechanisms and incidences of CI-AKI between intravenous and intra-arterial contrast administration. We aimed to investigate the critical roles of dysregulated miRNAs and the correlated mRNAs in the kidney injury following intra-arterial contrast exposure.

Methods:Based on a reliable CI-AKI rat model, we sought to investigate the roles of miRNA-mRNA interactions in the kidney injury following intra-arterial contrast exposure using the Illumina Genome Analyzer IIx.

Results:In the study, 36 differentially expressed mature miRNAs were identified ( fold change > 1.5 and p value < 0.05) in the kidney of CI-AKI rats (n = 3) compared with controls  (n = 3), consisting of 23 up-regulated and 13 down-regulated ones. Bioinformatics analysis revealed that Wnt, TGF-β, and AMPK signaling pathways were most likely to be modulated by these dysregulated miRNAs. Around 453 dysregulated genes ( fold change > 2.0 and p value < 0.05) were identified. Integrated analysis revealed 2037 putative miRNA-mRNA pairs with negative correlations. Of which, 6 differential miRNAs and 13 genes were selected for further quantitative real-time polymerase chain reaction validation (n = 6 for each group), and a well correspondence between the 2 techniques was observed.

Conclusions:In conclusion, our present study contributes to the first evidence of miRNA-mRNA regulations in the development of kidney injury following an intra-arterial contrast injection route. These novel findings provide insights into the underlying mechanisms of CI-AKI.

overall_design: Three-month-old male Sprague-Dawley rats were used in this study. Kidney mRNA and miRNA profiles of CI-AKI rats and controls were generated by deep sequencing, in triplicate, using Illumina Illumina Genome Analyzer IIx.

first: Mingfang

last: Huang

first: Weiwei

last: Bao


title: Identifying the Transcriptome Signature of Calcium Channel Blocker in Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes

first: Lei

last: Tian

state: CA

address: 1215 Welch Rd

institute: Stanford's Postdoctoral Scholar programs

summary: This study aimed to simulate chronic CCB treatment and to examine both the functional and transcriptomic changes in human cardiomyocytes. We differentiated cardiomyocytes from three human induced pluripotent stem cell (iPSC) lines and exposed them to four different CCBs—nifedipine, amlodipine, diltiazem, and verapamil—at their physiological serum concentrations for two weeks. Without inducing cell death and damage to myofilament structure, CCBs elicited line specific inhibition on calcium kinetics and contractility. While all four CCBs exerted similar inhibition on calcium kinetics, verapamil applied the strongest inhibition on cardiomyocyte contractile function. By profiling cardiomyocyte transcriptome after CCB treatment, we identified little overlap in their transcriptome signatures. Verapamil is the only inhibitor that reduced the expression of contraction related genes, such as myosin heavy chain and troponin I, consistent with its depressive effects on contractile function.   This is the first study to identify the transcriptome signatures of different CCBs in human cardiomyocytes. The distinct gene expression patterns suggest that although the four inhibitors act on the same target, they may have distinct effects on normal cardiac cell physiology.

overall_design: RNA profiling of 15 samples of calcium channel blocker- and vehicle (DMSO)-treated human iPSC-CMs

first: Chi

last: Lam

first: Nadjet

last: Belbachir


title: Analysis of a long noncoding RNAs that modulate neurotransmitter release

city: Deutschland

first: Raza

middle: Ur

last: Rahman

address: Falkenried, 94

institute: Systembiologie Bonnlab

summary: We report the application of a novel integrated screening strategy to identify lncRNAs that regulate synaptic vesicle release. We identified one of these lncRNAs, which is conserved across mammals, neuron-specific and strictly nuclear. Modulations of this lncRNA influence synaptic vesicle release, presynaptic calcium influx, neurite elongation and neuronal migration. We have characterized the DNA, RNA and protein inteactors of this lncRNA and clarified its involvement in the stabilization of mRNAs for synaptic vesicle proteins.

overall_design: Examination of DNA and RNA interactors of the lncRNA from mouse brain ex vivo

first: Eugenio

middle: F

last: Fornasiero

first: Vikas

last: Bansal

first: Raza-Ur


title: Transcriptomic Signature of Celiac show induced epithelial proliferation coupled with suppressed metabolic functions

city: Ramat Gan

first: Tzipi

last: Braun

address: Derech Sheba 2

country: Israel

institute: Sheba Medical Center at Tel Hashomer

summary: Background and aims: Celiac disease is provoked by gluten exposure, but the resultant pathogenic process in the duodenum is not well understood. We aimed to define the core celiac transcriptomic signature and pathologic pathways in pre-treatment diagnostic duodenum biopsies. Methods: We use mRNAseq to define pre-treatment diagnostic duodenum gene expression in 54 pediatric celiac patients and non-celiac controls, and we validate our key findings in an independent cohort of 40 participants. We further define similar and divergent genes and pathways in 177 Crohn disease patients and controls. Results: We observe a marked suppression of mature epithelial metabolic functions in celiac patients, overlapping substantially with the Crohn signature. A marked adaptive immune response was noted for the up-regulated signature including interferon response, alpha-beta, and gamma-delta T-cells that overlapped to some extant with the Crohn signature. However, we identified a celiac specific signature linked to increased cell proliferation, nuclear division, and cell cycle activity that was localized primarily to the epithelia as noted by CCNB1 and Ki67 staining. Lastly, we demonstrate the utility of the transcriptomic date to correctly classify disease or healthy states in the discovery and validation cohorts. Conclusion: Our data provide insights into celiac pathogenesis and can stimulate new approaches to address this highly prevalent condition.

first: Nurit

last: Loberman-Nachum

first: Katya

last: Sosnovski

first: Ayelet

last: Di Segni

first: Gilat

last: Efroni

first: Marina

last: BenShoshan

first: Lait

last: Anafi

first: Camila

last: Avivi

first: Iris

last: Barshack

first: Dror

middle: S

last: Shouval

first: Lee

last: Denson

first: Amnon

last: Amir

first: Ron

last: Unger

first: Batia

last: Weiss

first: Yael

last: Haberman


title: Co-expression Analysis Reveals Dysregulated miRNAs and miRNA-mRNA Interactions in the Development of Contrast-induced Acute Kidney Injury

first: Zhiqing

last: Wang

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

overall_design: Refer to individual Series


title: A Novel Role for the Tumor Suppressor Gene ITF2 in Tumorigenesis and Chemotherapy Response

city: Madrid

first: Carlos

last: Rodriguez Antolin

address: Paseo de la Castellana

department: Genetics

country: Spain

institute: Hospital La Paz Institute for Health Research

type: Genome variation profiling by genome tiling array


title: Co-expression Analysis Reveals Dysregulated miRNAs and miRNA-mRNA Interactions in the Development of Contrast-induced Acute Kidney Injury [miRNA]

summary:
Purpose: The pathogenesis of contrast-induced acute kidney injury (CI-AKI) has not yet been clearly understood. miRNAs are important mediators which normally work by post-transcriptional degradation of target mRNAs. Emerging evidence indicated a number of differentially expressed miRNAs in CI-AKI following intravenous contrast medium injection. However, there exist differences in the pathological mechanisms and incidences of CI-AKI between intravenous and intra-arterial contrast administration. We aimed to investigate the critical roles of dysregulated miRNAs and the correlated mRNAs in the kidney injury following intra-arterial contrast exposure.

Methods: Based on a reliable CI-AKI rat model, we sought to investigate the roles of miRNA-mRNA interactions in the kidney injury following intra-arterial contrast exposure using the Illumina Genome Analyzer IIx.

Results: In the study, 36 differentially expressed mature miRNAs were identified ( fold change > 1.5 and p value < 0.05) in the kidney of CI-AKI rats (n = 3) compared with controls  (n = 3), consisting of 23 up-regulated and 13 down-regulated ones. Bioinformatics analysis revealed that Wnt, TGF-β, and AMPK signaling pathways were most likely to be modulated by these dysregulated miRNAs. Around 453 dysregulated genes ( fold change > 2.0 and p value < 0.05) were identified. Integrated analysis revealed 2037 putative miRNA-mRNA pairs with negative correlations. Of which, 6 differential miRNAs and 13 genes were selected for further quantitative real-time polymerase chain reaction validation (n = 6 for each group), and a well correspondence between the 2 techniques was observed.

Conclusions: In conclusion, our present study contributes to the first evidence of miRNA-mRNA regulations in the development of kidney injury following an intra-arterial contrast injection route. These novel findings provide insights into the underlying mechanisms of CI-AKI.

first: Mingfang

last: Huang

first: Weiwei

last: Bao


title: A Novel Role for the Tumor Suppressor Gene ITF2 in Tumorigenesis and Chemotherapy Response [CGH]

summary: Despite often leading to platinum resistance, platinum-based chemotherapy continues to be the standard treatment for many epithelial tumors. In this study we analyzed and validated the cytogenetic alterations that arise after treatment in four lung and ovarian paired cisplatin-sensitive/resistant cell lines by 1-million microarray-based comparative genomic hybridization (array-CGH) and qRT-PCR methodologies. RNA-sequencing, functional transfection assays, and gene-pathway activity analysis were used to identify genes with a potential role in the development of this malignancy. The results were further explored in 55 lung and ovarian primary tumors and control samples, and in two extensive in silico databases. Long-term cell exposure to platinum induces the frequent deletion of ITF2 gene. Its expression re-sensitized tumor cells to platinum and recovered the levels of Wnt/β-catenin transcriptional activity. ITF2 expression was also frequently downregulated in epithelial tumors, predicting a worse overall survival. We also identified an inverse correlation between ITF2 and HOXD9 expression, revealing that Non-small cell lung cancer (NSCLC) patients with lower expression of HOXD9 had a better overall survival rate. We defined the implication of ITF2 as a molecular mechanism behind the development of cisplatin resistance probably through the activation of the Wnt-signaling pathway. This data highlights the possible role of ITF2 and HOXD9 as novel therapeutic targets for platinum resistant tumors.

overall_design: DNA from paired cisplatin-sensitive/resistant cell lines was used to analyze copy number variations by the Array-CGH SurePrint G3 Human CGH Microarray 1x1M (Agilent, USA).

first: Olga

last: Pernía

first: Ana

last: Sastre-Perona

last: Rodriguez-Antolín

first: Alvaro

last: García-Guede

first: María

last: Palomares-Bralo

first: Rocío

last: Rosas

first: Darío

last: Sanchez-Cabrero

first: Carmen

last: Rodriguez

first: Rubén

last: Martín-Arenas

first: Verónica

last: Pulido

first: Javier

last: de Castro

first: Pilar

last: Santisteban

last: Vera

first: Inmaculada

last: Ibáñez de Cáceres


title: RNA-Seq of LEF1 overexpression ECA109 cells

first: Yue

last: Zhao

address: 168 Changhai Road, Shanghai 200433, China

department: Department of Thoracic Surgery

institute: Changhai Hospital

summary: RNA-seq was performed on three biological replicates. Total RNA from ECA109 LV-GFP/LV-LEF1.Differentially expression genes were considered to be significant between groups when the P-value was <0.05 and the fold change of expression was ≥2-fold or ≤0.5-fold.  By this way, the RNA-Seq data showed the differential expression genes in LEF1 overexpression ECA109 cells compared with NC cells. Furthermore, Gene ontology (GO) analysis was performed to facilitate elucidating the biological implications of the differentially expressed genes in the experiment. Pathway analysis was used to find out the significant pathway of the differentially expressed genes according to KEGG database.  In conclusion, our study represents the first detailed analysis of LEF1 transcriptomes in esophageal squamous cell carcinoma cells.

overall_design: Exploring changes of transcriptome in in LEF1 overexpression ECA109 cells compared with control ECA109 cells


title: A Novel Role for the Tumor Suppressor Gene ITF2 in Tumorigenesis and Chemotherapy Response [RNA-seq]

last: Rodriguez Antolin

overall_design: RNA-seq from NSCLC patients were analyzed.


title: Integrated application of multi-omics provides insights into cold stress responses in pufferfish Takifugu fasciatus

city: Nanjing

first: Shaowu

last: Yin

state: jiangsu

address: College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road,  210023, China.

institute: Nanjing Normal University

summary: we used next-generation sequencing technology to characterise mRNA-seq of control- and hypoxia-treated T. fasciatus livers to elucidate the molecular mechanisms of cold adaptation. We were able to find mRNA pairs using bioinformatics analysis.

overall_design: Examination of 2 different temperature-treated in Takifugu fasciatus (Repeat each treatment has three biology).

first: Xin

last: Wen


title: RNA sequencing of mouse carotid arteries after sacubitril/valsartan treatment

city: Rochester

first: Vyacheslav

last: Korshunov

address: 601 Elmwood Ave

institute: University of Rochester

summary:
Purpose: To get insight into mouse strain-dependent differences in vascular remodeling, we analyzed gene expression profiles of the ligated carotid arteries after interventions in C57BL/6J and 129X1/SvJ mice
Methods: mRNA isolations from snap-frozen single carotids (n=3 per group) were conducted. Tissue homogenization by Next Advance Bullet Blender with zirconium oxide beads and Trizol. Total RNA isolation using Trizol and Qiagen RNeasy Micro kit.
Results: Multiple quality controls showed a reliable RNAseq of mRNAs from the ligated carotid arteries. Specifically, there was less than 2.6% drop in reads that ranged between 26.5 to 37.7 million reads. We found a good alignment and mapping to a mouse genome (82.4 - 91.0%) in this RNAseq study. A differential gene expression analysis was done by DESeq2-1.16.1 within R-3.4.1 for data normalization and differential expression analysis with an adjusted p-value threshold of 0.05 on each set of raw expression measures.
Conclusions: Our study shows significant differences in gene expression signatures in carotid arteries from two inbred mouse strains after sacubitril/valsartan treatment. We conclude that genetic background determines efficacy of the sacubitril/valsartan in mice.

overall_design: Mouse carotid artery mRNA profiles of C57BL/6J and 129X1/SvJ mice after two treatment regimen of vehicle, valsartan or sacubitril/valsartan were generated by deep sequencing, in triplicate, using Illumina HiSeq2500v4 high-throughput DNA sequencer.

first: Breandan

last: Quinn

first: Abrar

last: Faiyaz

first: Rifat

last: Ahmed

first: Mark

last: Sowden

first: Marvin

middle: M

last: Doyley

first: Bradford

last: Berk


title: Worker antennal gene expression in Solenopsis invicta identifies candidate genes for queen discrimination (Nugen_lib_RNA-seq-2)

city: Taipei

first: John

last: WANG

address: Academia Rd sec 2

department: Biodiversity Research Center

country: Taiwan

institute: Academia Sinica

summary: Queen discrimination behavior in the red imported fire ant Solenopsis invicta maintains its two types of societies: colonies with one (monogyne) or many (polygyne) queens, yet the underlying genetic mechanism is poorly understood. This behavior is controlled by two supergene alleles, SB and Sb, with ~600 genes. Polygyne workers, having either the SB/SB or SB/Sb genotype, accept additional SB/Sb queens into their colonies but kill SB/SB queens. While monogyne workers, all SB/SB, reject all additional queens regardless of genotype. Because the SB and Sb alleles do not recombine, it is difficult to determine which genes within the supergene mediate this differential worker behavior. We hypothesized that the alternate worker genotypes sense queens differently because of different patterns of gene expression in their main sensory organ, the antennae. To identify such differentially expressed genes, we sequenced RNA from four biological replicates of pooled antennae from three groups of workers: monogyne SB/SB, polygyne SB/SB, and polygyne SB/Sb. We identified 81 differentially expressed protein coding genes with 14 encoding potential odor metabolism and perception proteins. We focused on the two differentially expressed odorant perception genes: an odorant binding protein SiOBP12 and an odorant receptor SiOR463. We found that the SiOR463 was lost in the Sb-genome. In contrast, the SiOBP12 has an Sb-specific duplication SiOBP12b’, which was expressed in the SB/Sb worker antennae, while both paralogs SiOBP12 and SiOBP12b’ were expressed in the body. This result indicates that SiOBP12b’ has gained an antennal promoter or enhancer and suggests neofunctionalization, perhaps for queen discrimination behavior.

overall_design: Extracted total mRNA of antennae of three worker types: monogyne SB/SB, polygyne SB/SB and polygyne SB/Sb. Four biorelicates were conducted (total 12 samples). RNA samples were amplified using Nugen Ovation v.2 kit independently (12 samples). Four samples of the same genotype were mixed to make one representative sample for sequencing on the Illumina HiSeq platform with a 150 paired-end protocol.

first: Viet-Dai

last: Dang

first: Amir

last: Cohanim

first: Silvia

last: Fontana

first: Eyal

last: Privman

last: Wang


title: Unique microglia expression profile in developing white matter.

city: Freiburg

first: Ori

last: Staszewski

address: Breisacher Str. 64

department: Institute of Neuropathology

institute: University Medical Center Freiburg

summary: Recently we demonstrated that amoeboid microglia in white matter regions are essential for proper oligodendrocyte homeostasis and myelinogenesis in the first postnatal week of mice. Amoeboid microglia in the corpus callosum change their activation profile already within few days after postnatal day (P)7 and microglia of the cerebellum show similar features to callosal microglia. Here we expanded our previous transcriptional analysis and performed bulk RNA sequencing of microglia during development in a detailed way in P7, P10 and P42 microglia from corpus callosum, cortex and cerebellum. The goal of this study was to identify a specific gene profile for both, white matter and grey matter microglia during development.

overall_design: We used FACS sorted microglia cells from C57BL6 animals at postnatal days 7, 10 and 42 isolated from different brain regions (cerebellum, corpus callosum andcerebral cortex).

first: Nora

last: Hagemeyer


title: Worker antennal gene expression in Solenopsis invicta identifies candidate genes for queen discrimination (Clontech_lib_RNA-seq)

overall_design: Extracted total mRNA of antennae of three worker types: monogyne SB/SB, polygyne SB/SB and polygyne SB/Sb. Four biorelicates were conducted (total 12 samples). Three of the four bioreplicates of the same genotype were mixed to make three RNA samples. These RNA samples were subjected to polyA-RNA selection and amplified with SMARTer Stranded RNA-seq kit. Amplified cDNA samples were sequenced on the Illumina HiSeq platform with a 150 paired-end protocol.


title: Worker antennal gene expression in Solenopsis invicta identifies candidate genes for queen discrimination


title: Worker antennal gene expression in Solenopsis invicta identifies candidate genes for queen discrimination (Nugen_lib_RNA-seq-1)

overall_design: Extracted total mRNA of antennae of three worker types: monogyne SB/SB, polygyne SB/SB and polygyne SB/Sb. Four biorelicates were conducted (total 12 samples). RNA samples were amplified using Nugen Ovation v.2 kit and sequenced on the Illumina HiSeq platform with a 150 paired-end protocol. The 12 samples were run on 2 lanes.

first: Viet

middle: D


title: Enhanced immunomodulation in inflammatory environments favors human cardiac mesenchymal stromal-like cells for allogeneic cell therapies

city: Berlin

first: Karsten

last: Jürchott

address: Luisenstraße

department: Rahel Hirsch Center

institute: BIH at Charité

summary:
Rising numbers of patients with cardiovascular diseases and limited availability of donor hearts require new and improved therapy strategies. Human atrial appendage-derived cells (hAACs) are promising candidates for an allogeneic cell-based treatment. In this study, their inductive and modulatory capacity regarding immune responses and underlying key mechanisms were evaluated in vitro. For this, cryopreserved hAACs were analyzed either unstimulated or after stimulation with interferon-gamma by flow cytometry. This revealed the expression of characteristic mesenchymal stromal cell markers (CD29, CD44, CD73, CD166), but also highlighted a predominant negativity for CD90. A low immunogenic phenotype in an inflammatory milieu was shown by lacking expression of co-stimulatory molecules and upregulation of the inhibitory ligands PD-L1 and PD-L2, despite of de novo expression of HLA-DR. Co-cultures of hAACs with allogeneic peripheral blood mononuclear cells, proved the low immunogenic state by absence of induced CD4+ and CD8+ T cell proliferation and activation. However, elevated levels of IL-1β, IL-33 and IL-10 were detectable in those cell culture supernatants. In a second step, the immunomodulatory potential of hAACs was assessed in co-cultures with αCD3/αCD28-activated peripheral blood mononuclear cells. A strong inhibition of T cell proliferation and lowering of pro-inflammatory cytokines (IFNγ, TNFα, TNFβ, IL-17A, IL-2) were observable after pre-stimulation of hAACs with interferon-gamma.
Transwell experiments confirmed that mostly soluble factors are responsible for these suppressive effects. We were able to identify indolamin-2,3-dioxygenase (IDO) as a potential key player through a genome-wide gene expression analysis and could demonstrate its involvement in lowered proliferation and induction of apoptosis in T cells. While the application of blocking antibodies against both PD-1 ligands did not affect the immunomodulation by hAACs, 1-Methyl-L-Tryptophan as specific inhibitor of IDO was able to restore proliferation and to lower apoptosis of T cells. In conclusion, hAACs represent a cardiac-derived mesenchymal stromal-like cell type with a high potential for application in allogeneic settings, since they do not trigger T cell responses and even increase their immunomodulatory potential in inflammatory environments.

overall_design: Human atrial appendage-derived cells (hAACs) from three different donor were analyzed either untreated or stimulated with IFNγ.

first: Martina

last: Seifert

first: Falk

last: Diedrichs


title: Exercise reverses dysregulation of T cell-related function in blood leukocytes of patients with PD

city: Shanghai

first: Kunshan

last: Zhang

address: 389 Xincun Rd.

department: Tongji Hospital

institute: Tongji University

summary: Parkinson’s disease (PD) is a common neurodegenerative disease with movement and balance impairments. It has been shown that physical exercise could ameliorate balance impairments and improve life quality of PD patients. However, the related mechanisms of benefit of exercise are still poorly understood, especially in the peripheral immune system. The present study aimed to utilize sensitive high-throughput transcriptome analyses to investigate potentially favorable effects of physical exercise in leukocytes.

overall_design: PD patients attended 1-hour exercise classes of tai chi or multimodal exercise training (MET) twice a week for 12 weeks. Before and after the training, the PBMC were separated from whole blood and applied to RNA-Seq.

first: Yong

last: Hu

first: Lingjin

last: Jin


title: GATA factor-mediated gene regulation in human erythropoiesis

city: Padova

first: Oriana

last: Romano

address: Via U. Bassi 58/B

department: Molecular Medicine

institute: University of Padova


title: Analysis of transcriptome profiling of somatic and reproductive cells under UV-B irradiation in the green alga Volvox carteri

city: Tabriz

first: Soulmaz

last: Ekhtari

address: 29 Bahman Blvd

country: Iran

institute: Tabriz university

summary:
Purpose: Light is one of the most important environmental signal that affects the physiology and action of Volvox carteri. However, there are limited reports about the effects of UV-B irradiation on genome-wide transcriptional regulation in this organism. We surveyed the overall transcriptional responses of somatic and reproductive cells to UV-B irradiation using RNA-seq data.
Methods: The somatic and reproductive cells were separated. The cell-types were treated for one hour by low-doses UV-B irradiation. Three biological replicates per cell-types (totally 12 samples) were used for RNA extraction. High-throughput RNA sequencing performed with separated-cells samples. Sequencing runs were performed on an Illumina HiSeq-2500. Transcriptome analysis was carried out in order to elucidate the effect of UV-B irradiation on whole transcriptional modification of physiological mechanisms.
Results: In total, 264 and 272 million clean reads were produced in somatic and reproductive cells, respectively. The results showed that, as compared to control group, there were no differentially expressed genes in reproductive cells under treatment. However, treating the somatic cells with UV-B irradiation resulted in 126 differential genes as compared to untreated control group. Our results showed that there is light-specific transcriptional regulation in this organism. So that, different pathways were co-regulated by UV-B irradiation via the transcriptional regulation of genes encoding key enzymes in these pathways.
Conclusions: Our findings showed that low UV-B irradiation influence on the cell-type specific gene expression. The findings of this study may present new insights to understand responsive mechanisms to UV-B irradiation by modulating expression of cell-type specific in the V. carteri.

overall_design: Investigation of directed effects of UV-B irradiation on transcriptomic profiling of V. carteri.

first: Arash

last: Kianianmomeni

first: Jafar

last: Razeghi

first: Karim

last: Hasanpur


title: GATA factor-mediated gene regulation in human erythropoiesis (ChIP-Seq)

summary: Human erythropoiesis is a stepwise process in which multipotent hematopoietic stem/progenitor cells (HSPC) are initially committed towards the erythroid lineage and then differentiated into mature erythroid precursors. Commitment and differentiation are tightly regulated by the coordinated action of a host of transcription factors, including GATA2 and GATA1. Although the role of GATA factors in erythropoiesis has been extensively studied, how they regulate transcription from early to late stages of human erythropoiesis still remains underinvestigated. Here, we investigated GATA-mediated transcriptional regulation along erythroid development through the integrative analysis of gene expression, chromatin modifications, and GATA factors’ binding in human HSPC, early erythroid progenitors, and late precursors. A progressive loss of H3K27 acetylation, a mark of active regulatory elements, and diminished usage of active enhancers and super-enhancers was observed during erythroid lineage commitment and differentiation. We found that GATA factors mediate the transcriptional changes occurring during erythropoiesis through a stage-specific interplay with regulatory elements. In particular, GATA1 binds different sets of regulatory elements in early progenitors and late precursors, and controls the transcription of distinct genes in commitment and differentiation. By Chromosome Conformation Capture and CRISPR/Cas9-mediated genome editing, we demonstrated that the binding of GATA1 to a stage-specific super-enhancer sustains the expression of the stem cell factor receptor KIT in human erythroid progenitors. This study provides insights into the dynamics of epigenetic and transcriptional interactions during erythroid development and highlights a new layer of GATA1-mediated regulation in erythropoiesis.

overall_design: ChIP-seq of H3K4me3, H3K4me1, H3K27ac, H3K27me3, GATA2 and GATA1 in erythroid progenitors (E-Prog) and erythroid precursors (E-Prec).

first: Luca

last: Petiti

first: Tristan

last: Felix

first: Vasco

last: Meneghini

first: Silvio

last: Bicciato

first: Clelia

last: Peano

first: Annarita

last: Miccio


title: GATA factor-mediated gene regulation in human erythropoiesis (RNA-Seq)

overall_design: RNA-seq of human hematopoietic stem/progenitor cells (HSPC), erythroid progenitors (E-Prog) and erythroid precursors (E-Prec). For each cell type, 3 biological replicates were analyzed.


title: Identification and integrative analysis of microRNAs and mRNAs involved in proliferation and invasion in mechanical pressure-treated human hepatocellular carcinoma cell lines

first: Shen

last: si

address: No. 500 Chengdu North Road

institute: Shanghai Changzheng hospital

summary: The pressure changes in hepatic microenvironment may be involved in the regulation of proliferation and invasion of hepatocellular carcinoma, but the mechanism is unknown. This project simulates the mechanical microenvironmental conditions of liver cirrhosis, exerts the static water pressure on human hepatoma cell lines and observes the changes of proliferation and invasion of hepatoma cells under different pressure loading conditions. Then screens the differential expression mechanic-responsive miRNAs under the optimal loading condition and carry out biological verification. Bioinformatics analysis was used to explore the related pathways. This study provides a theoretical basis for the prevention and treatment of liver cancer and provides a direction for finding effective drugs for clinical treatment of liver cancer.

overall_design: 6 samples are analysised, of which 3 are of control group which cultured without pressure, and 3 are of case group which cultured under pressure (15mmHg, 24h).

first: Si

last: Shen

first: Liang

last: Zhu


title: Identification and integrative analysis of microRNAs and mRNAs involved in proliferation and invasion in mechanical pressure-treated human hepatocellular carcinoma cell lines (mRNA)

summary: The pressure changes in hepatic microenvironment may be involved in the regulation of proliferation and invasion of hepatocellular carcinoma, but the mechanism is unknown. This project simulates the mechanical microenvironmental conditions of liver cirrhosis, exerts the static water pressure on human hepatoma cell lines，and observes the changes of proliferation and invasion of hepatoma cells under different pressure loading conditions. Then screens the differential expression mechanic-responsive mRNAs under the optimal loading condition and carry out biological verification. Bioinformatics analysis was used to explore the related pathways. This study provides a theoretical basis for the prevention and treatment of liver cancer and provides a direction for finding effective drugs for clinical treatment of liver cancer.

overall_design: 4 samples are analysised, of which 2 are of control group which cultured without pressure, and 2 are of case group which cultured under pressure (15mmHg, 24h).


title: Liver tissues of 12h after brain death donor liver transplantation and matched non-brain death donor liver transplantation.

city: Zhengzhou

first: chen

last: sanyang

state: erqi

address: No.1, East Jian She Road

department: Department of Hepatobiliary and Pancreatic Surgery

institute: The First Affiliated Hospital of Zhengzhou University

summary: To determine the circRNA expression profile in hepar tissues of 12h after brain death donor liver transplantation and matched non-brain death donor liver transplantation, we uesed circRNA microArray analysis form Arraystar to examine the expression of circRNAs and circRNAs in hepar tissues of 12h after brain death donor liver transplantation and matched non-brain death donor liver transplantation.

overall_design: Hepar tissues from 12h after liver transplantation were distributed into two experimental groups: brain death donor liver transplantation group and matched non-brain death donor liver transplantation group, then perform circRNAs chips by Arraystar Rat circRNAs chip (Arraystar)


title: SFRP1-regulated gene expression in premalignant breast lesions

city: Amherst

first: D.

middle: Joseph

last: Jerry

state: MA

address: 661 North Pleasant St

department: Veterinary and Animal Sciences

institute: University of Massachusetts

summary: • Atypical hyperplasias (AH) provide insights into early changes that may predispose breast epithelial cells to oncogenic transformation.  • Of genes associated with premalignancy in prior studies, only mRNA levels of ESR1 and SFRP1 were detected in the present study.   • Transcriptional profiling defined signatures distinguishing atypical hyperplasias. The patterns of expression were similar among hyperplastic lesions of lobular and ductal phenotype suggesting a common set of alterations underlying both lesions. Pathway analyses identified elevated expression of estrogen receptor alpha, androgen receptor and EGFR receptors and Rho signaling as central events nodes in the pathways altered in AH.   • A set of 43 genes were identified as common targets using 2 different algorithms to detect signatures associated with AH. Knockdown of SFRP1 in a TERT immortalized breast epithelial cell line resulted in 14 genes from this signature being either up-regulated or down-regulated as observed in the expression profiles from AH.   • The results demonstrate a signature of genes representing alterations that are common to the development of hyperplasias in both ductal and lobular epithelium. Loss of SFRP1 expression is a key player underlying the transcriptional changes in AH that directs a module of genes that can be used to improve reproducibility of diagnosis of AH.

overall_design: In the present study, patients with atypical hyperplasia (AH) but no history of breast cancer were selected. Laser capture microdissection was used to collect both histologically normal benign epithelium (HNB) as well as AH tissues from each patient. The complete transcriptome was evaluated using microarrays and used to define signatures that distinguish AH lesions from the HNB tissues.

first: Kelly

last: Gregory

first: Amy

last: Roberts

first: Jacob

last: Mayfield

first: Erin

last: Conlon

first: Giovanna

last: Crisi

first: Grace

last: Makari-Judson

first: Holly

last: Mason

first: Jun

last: Wang

first: Ben

last: Schneider

first: Julie

first: Karl

last: Simin

first: Sallie

first: D

middle: J


title: RNA-sequencing expression of MMTV-Neu mouse mammary tumors

city: Durham

first: Zachary

middle: Conrad

last: Hartman

state: NC

address: Research Drive MSRB rm 414

department: Surgery

institute: Duke University

summary: We use RNA-seq to measure gene expression from mammary tumors from untreated MMTV-Neu mice.

first: Charles

last: Perou

first: Jerry

last: Usary


title: Effects of hemocyte ablation on fat body gene expression

city: Ames

first: Andrew

last: Severin

email: severin@iastate.edu, csiva@iastate.edu

state: IA

address: 2200 Osborn Drive

department: Office of Biotechnology

institute: Iowa State University

summary: To test the contributions of phagocytic immune cells to mosquito immunity, we depleted mosquito phagocytes using clodronate liposomes and then challenged mosquitoes with malaria parasites. Observing a large increase in infection intensity, the purpose of the RNA-seq experiment is to determine their effects of phagocyte depletion on mosquito immunity.

overall_design: Control and experimental samples were collected ~24hrs after infection with the rodent malaria parasite, P. berghei.

first: Ryan

last: Smith


title: FAM46C controls antibody production by the polyadenylation of Ig mRNAs and inhibits cell migration in multiple myeloma

city: Salamanca

first: Ana Belén

last: Herrero Hernández

state: Salamanca

address: Campus Universitario Miguel de Unamuno

department: Hematology

institute: Cancer Research Institute of Salamanca

summary: FAM46C, which is frequently mutated in multiple myeloma (MM), has recently been shown to encode a non-canonical poly(A) polymerase (ncPAP). However, its target mRNAs and its role in MM pathogenesis remain largely unknown. Using CRISPR-Cas9 technology and gene expression analysis we found that inactivation of FAM46C in MM downregulates immunoglobulins (Igs) and several mRNAs encoding ER-resident proteins, including some involved in unfolded protein responses (UPRs), such as PDIA6, ERP44 and EDEM2, and others that affect glycosylation, such as SSR4, AGA and DDOST. We show that FAM46C expression is induced during PC differentiation and that Ig mRNAs encoding heavy and light chains are direct substrates of the ncPAP, as revealed by poly(A) tail-length determination assays. The absence of the ncPAP results in Ig mRNA poly(A) tail-shortening, leading to a reduction in mRNA and protein abundance. On the other hand, loss of FAM46C upregulates metastasis-associated lncRNA MALAT1 and results in a sharp increase in the migration ability of MM cells. This phenotype depends mainly on the activation of PI3K/Rac1 signaling in FAM46C knockout cells since treatment with specific inhibitors substantially reduces cell mobility. This finding may have significant therapeutic implications.   In conclusion, our results identify Ig mRNAs as targets of FAM46C, reveal an important function of this protein during PC maturation to increase antibody production, and show that its inactivation in MM increases cell migration and invasion, which might explain the poor prognosis of MM patients with FAM46C alterations and its role as a tumor suppressor.

overall_design: The human multiple myeloma cell line (HMCL) JJN3 was obtained from DSMZ. Cells (1 × 10^6) were transfected with 5 μg of FAM46C CRISPR-Cas9 KO plasmids, or 5 μg of control CRISPR-Cas9 Plasmid (sc-418922), which contained a non-targeting 20 nt scramble guide gRNA. Transfections were carried out using the Amaxa Cell Line Nucleofector Kit V, the Amaxa Nucleofector device (Lonza, Allendale, NJ, USA) and programs T-016 for JJN3. Successful transfection of the CRISPR-Cas9 plasmids was visually confirmed by detection of the plasmid encoded-green fluorescent protein (GFP). Single GFP+ cells were sorted into 96-well plates 6 days after transfection using a Becton Dickinson (Mountain View, CA) FACSCalibur flow cytometer. Isolated clones were expanded in culture over a period of one month.

first: A

last: Herrero

last: Quwaider

first: L

last: Corchete

first: R

last: García-Sanz

first: N

last: Gutierrez


title: miR22 is a master regulator of genes predictive of patient survival in clear cell renal cell carcinoma

city: Stanford

first: James

middle: D.

last: Brooks

address: 300 Pasteur Drive

department: Department of Urology

institute: Stanford University

summary: RNA sequencing libraries were made for RLC cell line to detect the transcripts regulated by the miR22 mimic comparing mimic and the negative control.

overall_design: miR22 mimic and negative control were introduced to the cell line RLC. After 24 and 48 hours total RNA were extracted. Barcoded cDNA libraries were then prepared from total RNA using the Illumina TruSeq RNAseq kit, and sequenced (single-end 101-bp reads) on an Illumina HiSeq instrument.

first: Xue

last: Gong

first: Hongjuan

last: Zhao


title: Genome-wide maps of SOX2 binding sites in lung cancer cells

city: Hong Kong

first: Zhi-Jie

last: Xiao

state: Hong Kong

address: Pokfulam

department: Pathology

country: Hong Kong

institute: the University of Hong Kong

summary: Discovery of SOX2 binding sites in lung cancer cells by CHIPseq and validate the target genes in two lung cancer cells by CHIP-QPCR.

overall_design: Examination of SOX2 binding sites in lung cancer cells and validate the target genes in two lung cancer cells by CHIP-QPCR.

first: Yun

last: Zhu


title: Histone modification and nucleosome mapping in human liver cancer cells

city: Perth

first: Zhaoyu

last: Li

state: Western Australia

address: QE II, M block, 225C

department: School of Biomedical Sciences

country: Australia

institute: University of Western Australia

type: Methylation profiling by high throughput sequencing

summary: The nucleosome is a fundamental unit of chromatin architecture, but it has been under-evaluated during the analysis of histone modification using ChIP-Seq. Thus, we developed a novel approach for defining histone modification at single nucleosome resolution by synergistic analyses of histone modification data from ChIP-Seq and high-resolution nucleosome mapping data from native MNase-Seq using a PCR-free strategy. With this approach, we have generated histone modification data at the single nucleosome resolution in human embryonic stem cells, normal hepatocytes, and liver cancer cells of both genders, and performed quantitative analysis of epigenetic regulation in stem cell differentiation into hepatocytes and neoplastic transformation of liver cancer.

overall_design: We developed a novel algorithm to generate histone modification data at the single nucleosome resolution based on both histone modification data from ChIP-Seq and nucleosome mapping data from native MNase-Seq. We compared single nucleosome resolution of histone modification data between human embryonic stem cells and hepatocytes and between human hepatocytes and liver cancer cells for both genders to reveal quantitative epigenomic regulation in cell differentiation and transformation.


title: EXP_139_AC_ranscriptional changes observed in 94T778 cells subjected to different pharmacologic pressures.

status: Public on Apr 09 2020

city: Melbourne

first: David

last: Goode

state: Victoria

address: 305 Grattan Street

department: Research Division

institute: Peter MacCallum Cancer Centre

summary: 94T778 cells were exposed to nutlin-3a, palbociclib and tunicamycin. Cells were harvested during the early phase of the adaptive evolution in 94T778 cells exposed to palbociclib (P), nutlin-3a (N) and tunicamycin (T) sampled at 10 weeks for P and N and at 9 weeks post-bottleneck for T condition.

overall_design: The experiment was designed to study the impact of targeted anti-cancer therapies on the expression of genes involed in different DNA repair pathways

first: Arcadi

last: Cipponi

middle: L


title: EXP. 229_AC_RNAseq data of human cancer cell lines 94T778, SKBR3, AU565, SKMEL28 and A375 exposed to the selective MTOR inhibitor torkinib (PP242, Selleckchem, TX, USA) for 72 hours.

summary: Drug concentrations were selected to halt cell cycle progression without affecting cell viability: 94T778 10 µM, A375, SKMEL28 and AU565 4 µM, SKBR3 0.8 µM. The pharmacologic inhibition of MTOR repressed expression of the homologous recombination (HR) and Fanconi Anemia (FA) pathways, and selectively high-fidelity but not error-prone DNA polymerases  in all cancer cell lines sequenced

overall_design: The experiment has been designed to understand the impact of MTOR inhibition on the expression profile of different genes involved in DNA repair.


title: study the effect of environmental pH of Cronobacter sakazakii, transcriptome analysis of some muntants

city: wuxi

first: Hua

last: Jingjing

address: 1800 Lihu Road

institute: Jiangnan University

summary: Cronobacter sakazakii is a foodborne opportunistic pathogen that causes pneumonia, meningitis and bacteremia. To understand the acidic regulated and two component system PmrA/PmrB about strain pathogenesis, transcriptomics  analysis of C. sakazakii grown under acidic pH 5.0 was performed by using RNA-sequencing.

overall_design: There are five samples, Cronobacter sakazakii at pH 7.0, Cronobacter sakazakii at pH 5.0, eptA muntant, pmrA muntant, lpxM muntant

first: Jingjing

last: Hua

first: Yanyan


title: RNA Sequencing of si-Contol treated M010817 and siSMAD7 treated M010817 human melanoma cell line

city: Zurich

first: giancarlo

last: russo

state: Schweiz

address: winterthurerstrasse 190

department: Functional Genomics Center Zurich

country: Switzerland

institute: ETH/University of Zurich

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived retinal transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis
Methods:  mRNA profiles of si-Contol treated M010817 and  siSMAD7 treated M010817 human melanoma cell line were generated by deep sequencing, in triplicate, using Illumina HiSeq 2500. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays
Conclusions: Our study represents the first detailed analysis of si-Contol treated M010817 and siSMAD7 treated M010817 human melanoma cell line 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 NGS 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.


title: Translin KO mice display elevated adiposity

city: Baltimore

first: Jay

last: Baraban

state: MD

address: 725 North Wolfe Street

department: Neuroscience

country: USA

institute: The Johns Hopkins University School of Medicine

summary:
The high prevalence of obesity has focused attention on defining the pathophysiological processes that underlie susceptibility or resistance to its deleterious metabolic consequences. Mice lacking translin (Tsn), a gene implicated in a variety of biological functions from transcription to microRNA degradation, display extremely high levels of adiposity, comparable to those found in well-known genetic models of obesity, such as melanocortin 4 receptor or leptin knockout (KO) mice. Although translin KO mice display increased adiposity they retain normal glucose tolerance.
In contrast, wild-type (WT) mice placed on a high-fat diet until they match translin KO adiposity levels are glucose intolerant, as expected. Conversely, translin KO mice display prominent hepatic steatosis that is more severe than that of adiposity-matched WT mice. The ability of translin KO mice to retain normal glucose tolerance in the face of massive tissue expansion may be due to three factors: preferential accumulation of subcutaneous fat, reduced levels of TNF mRNA in both adipose and hepatic tissue, and elevated levels of plasma adiponectin. Further studies aimed at defining the molecular bases for these phenotypes may yield new approaches to limit the adverse metabolic consequences of obesity.

overall_design: Comparison between adipose tissue microRNA expression levels from adult, male translin KO mice and wildtype (WT) mice with six biological replicates per group.

first: Aparna

last: Shah

first: Xiuping

last: Fu

first: C

last: Talbot Jr


title: Transcriptional profiling and therapeutic targeting of oxidative stress in neuroinflammation (bulk RNA-seq dataset)

city: San Francisco, CA

first: Katerina

last: akassoglou

address: 1650 Owens st

institute: Gladstone Institutes

summary: Oxidative stress is a central part of innate-immune induced neurodegeneration. However, the transcriptomic landscape of the central nervous system (CNS) innate immune cells contributing to oxidative stress is unknown, and therapies to target their neurotoxic functions are not widely available. Here, we provide the oxidative stress innate immune cell atlas in neuroinflammatory disease, and report the discovery of new druggable pathways. Transcriptional profiling of oxidative stress-producing CNS innate immune cells (Tox-seq) identified a core oxidative stress gene signature coupled to coagulation and glutathione pathway genes shared between a microglia cluster and infiltrating macrophages. Tox-seq followed by a microglia high-throughput screen (HTS) and oxidative stress gene network analysis, identified the glutathione regulating compound acivicin with potent therapeutic effects decreasing oxidative stress and axonal damage in chronic and relapsing models of multiple sclerosis (MS). Thus, oxidative stress transcriptomics identified neurotoxic CNS innate immune populations and may enable the discovery of selective neuroprotective strategies.

overall_design: Bulk RNA-seq analysis of FACS isolated CD45loCD11b+ microglia and CD45hiCD11b+ infiltrating monocytes/macrophages from EAE (onset of disease) spinal cord tissue. Microglia and macrophage subpopulations were classified into four populations based on the expression of MHC II and ROS (MHC II+ ROS+, MHC II– ROS– (baseline), MHC II– ROS+ and MHC II+ROS–). Detailed methods of sample extraction and data analysis are provided.

first: Andrew

last: Mendiola

last: Akassoglou