title: Postmortem gene expression profiles in the habenulae of suicides:  Implication of endothelial dysfunction in the neurovascular system

city: Seoul

first: Hyeijung

last: Yoo

address: Goryeodaero 73

department: Department of anatomy

country: South Korea

institute: Korea University College of Medicine

summary: The habenula (Hb) is an epithalamic structure that links multiple forebrain areas with the mid/hindbrain monoaminergic systems. As an anti-reward center, it has been implicated in the etiology of various neuropsychiatric disorders, particularly those associated with dysregulated reward circuitry. In this regard, Hb has been proposed as a therapeutic target for treatment-resistant depression associated with a higher risk of suicide. Therefore, we aimed to gain insight into the molecular signatures of the Hb in association with suicide in individuals with major depression. Postmortem gene expression analysis identified 251 differentially expressed genes (DEGs) in the Hb tissue of suicides in comparison with Hb tissues from neurotypical individuals. Subsequent bioinformatic analyses using single-cell data from the mouse Hb  showed that the levels of a subset of endothelial cell-enriched genes encoding cell-cell junctional complex and plasma membrane-associated proteins, as well as the levels of their putative upstream transcriptional regulators, were significantly affected in suicides. Taken together, the present study suggests a potential association of endothelial dysfunction in the Hb with depression and suicidal behavior. although our findings are based on a limited sample of individuals.

overall_design: For this study, we obtained Hb tissues from 10 suicide subjects diagnosed with major depression and 10 control subjects. All subjects were male Caucasians, and groups (suicides and controls) were matched for age, pH, and postmortem interval (PMI). Using RNAs longer than approximately 200 nucleotides from habenula tissue, GeneChip Human Gene 2.0 ST arrays was done, and anlayzed for altered gene expression in suicides.

first: Hyun

middle: J

last: Kim

first: Ji

middle: Y

middle: W

last: Lee

first: Heon-Jeong

first: Gi

last: Son


title: RNA-seq data for Huh7 cells in spheroid culture and adherent culture

status: Public on Jun 01 2022

city: Guangzhou

first: Peng

last: Ye

state: Guangdong Province

address: Xinzao, Panyu District, Guangzhou, P.R.China

department: center for cancer and immunology research

country: China

institute: Guangzhou Medical University

type: Expression profiling by high throughput sequencing

summary: Anchorage-independent spheroid cells of HCC possess stemness properties. Huh7 cells are cultured in ultra-low attachment surface plates with serum-free medium. RNA-sequencing (RNA-seq) was applied in spheroid culture cells and adherent culture cells.

overall_design: Two culture condition of Huh7 cells: adherent culture and spheroid culture. Biological replicates: 3 spheroid cells, 3 adherent cells.

first: W

middle: H

last: Yang

first: P

first: X

last: Yan


title: Administration of glutaredoxin-1 attenuates liver fibrosis caused by aging and non-alcoholic steatohepatitis

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

country: USA

institute: Boston University

summary: Glutaredoxin-1 (Glrx) controls redox signaling and has an anti-apoptotic function. We evaluated the role of Glrx on hepatic cell damage and fibrosis induced by a high-fat diet. We fed mice a high-fat high-fructose diet to induce non-alcoholic steatohepatitis (NASH) and injected AAV-Glrx to express hepatocyte-specific Glrx in diet-induced NASH mice. AAV-Glrx suppressed fibrosis and improved liver function in the NASH liver. We used microarrays to profile gene expression in the NASH liver and find pathways that AAV-Glrx mediated to attenuate fibrosis and NASH progression.

overall_design: 10-week-old C57BL/6J mice were fed a high-fat high-fructose diet to induce non-alcoholic steatohepatitis (NASH). AAV-Cont or AAV-Glrx (1 × 1E12 vg) was administered by intraperitoneal injection after 20 weeks of NASH diet and maintained for another 12 weeks. RNA was isolated from mouse liver (n=5 or 6 each), pooled into three samples per group.

first: Yuko

last: Tsukahara

first: Reiko

last: Matsui


title: ASC-J9 blocks STAT3 signaling, cell proliferation, collagen synthesis, inflammation, and ROS generation in keloid fibroblasts

city: Tainan City

first: Yi-Kai

last: Hong

state: Please select an option below

address: No.1, Daxue Rd., East Dist.

country: Taiwan

institute: National Cheng Kung University

summary: The purified RNA from NFs (n=1) and KFs (n=1) treated with DMSO or ASC-J9 was used for the preparation of the sequencing library by the TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s recommendations. Briefly, mRNA was purified from total RNA (1 µg) by oligo(dT)-coupled magnetic beads and fragmented into small pieces under elevated temperature. The first-strand cDNA was synthesized using reverse transcriptase and random primers. After the generation of double-strand cDNA and adenylation on the 3’ ends of DNA fragments, the adaptors were ligated and purified with the AMPure XP system (Beckman Coulter, Beverly, USA). The quality of the libraries was assessed by the Agilent Bioanalyzer 2100 system and a real-time PCR system. The qualified libraries were then sequenced on an Illumina NovaSeq 6000 platform with 150-bp paired-end reads generated by Genomics BioSci & Tech Co., Ltd.

overall_design:
The effect of ASC-J9 on keloid fibroblasts

****RAW data not provided due to lost fastq files****

first: Chao-Kai

last: Hsu


title: Functional RNA dynamics are progressively governed by RNA destabilization during the adaptation to chronic hypoxia

city: Frankfurt

first: Tobias

last: Schmid

address: Theodor-Stern-Kai 7

department: Institute of Biochemistry I

country: Germany

institute: Goethe University Frankfurt

summary: Previous studies towards reduced oxygen availability mostly focused on changes in total mRNA expression neglecting underlying transcriptional and post-transcriptional events. Therefore, we generated a comprehensive overview of hypoxia-induced changes in total mRNA expression, global de novo transcription, and mRNA stability in monocytic THP-1 cells. Since hypoxic epi-sodes often persist for prolonged periods, we further compared adaptations to acute and chronic hypoxia. While total mRNA changes correlated well with enhanced transcription during short term hypoxia, mRNA destabilization gained importance under chronic conditions. Reduced mRNA stability not only added to compensatory attenuation of immune responses, but most no-tably to the reduction of nuclear-encoded mRNAs associated with various mitochondrial func-tions. These changes may prevent the futile production of new mitochondria under conditions where mitochondria cannot exert their full metabolic function and are indeed actively removed by mitophagy. The post-transcriptional mode of regulation might further allow for rapid recov-ery of mitochondrial capacities upon reoxygenation. Our results provide a comprehensive re-source of functional mRNA expression dynamics and underlying transcriptional and post-transcriptional regulatory principles during the adaptation to hypoxia. Furthermore, we specifically uncover mitochondrial functions controlled by RNA stability regulation in the con-text of hypoxia.

overall_design: Examination of changes in total mRNA level, mRNA de novo synthesis, and stability in the course of hypoxia in human monocytic THP-1 cells.

first: Rebekka

last: Bauer

first: Bernhard

last: Brüne


title: RNA sequencing of tumor educated platelets reveals a three-gene diagnostic signature in esophageal squamous cell carcinoma

city: Chaoyang District

first: Tiejun

last: Liu

state: Beijing

address: Panjiayuan

institute: Chinese Academy of Medical Science

summary: We aimed to investigate the diagnostic potential of tumor educated platelets in ESCC. In this study, seventy-one ESCC patients and eighty healthy individuals were enrolled and divided into training cohort (23 patients and 27 healthy individuals) and validation cohort (48 patients and 53 healthy individuals). Next-generation RNA sequencing was performed on platelets isolated from peripheral blood of all participants and a support vector machine/leave-one-out cross validation (SVM/LOOCV) approach was used for binary classification. A diagnostic signature composed of ARID1A, GTF2H2 and PRKRIR discriminated ESCC patients from healthy individuals with 91.3% sensitivity and 85.2% specificity in the training cohort and 87.5% sensitivity and 81.1% specificity in the validation cohort. The AUC was 0.924 (95% CI, 0.845–0.956) and 0.893 (95% CI, 0.821–0.966), respectively, in the training cohort and validation cohort. This 3-gene platelet RNA signature could effectively discriminate ESCC from healthy control. Our data highlighted the potential of tumor educated platelets for the noninvasive diagnosis of ESCC. Moreover, we found keratin and collagen protein families, and ECM-related pathways might be involved in tumor progression and metastasis of ESCC, which might provide insights to understand ESCC pathobiology and advance novel therapeutics.

overall_design: RNA sequencing of periphral blood platelets in 71 esophagus  squemous cell carcinoma patients and 25 healthy controls.

first: Xin

last: Wang

first: Yibo

last: Gao

first: Jie

last: He


title: RNAseq analysis of Arabidopsis thaliana apices of Col-0, ap2-12 and rAP2-VENUS plants at 1-cm bolting stage

city: Cologne

first: Alice

last: Vayssieres

address: Carl-von-Linne-Weg 10

institute: Max Planck Institute for Plant Breeding Research

summary: The APETALA2 (AP2) transcription factor regulates flower development, floral transition and shoot apical meristem (SAM) maintenance in Arabidopsis. AP2 is also regulated at the post-transcriptional level by microRNA172 (miR172), but the contribution of this to SAM maintenance is poorly understood. We generated transgenic plants carrying a form of AP2 that is resistant to miR172 (rAP2) or carrying a wild-type AP2 susceptible to miR172. Phenotypic and genetic analyses were performed on these lines and mir172 mutants to study the role of AP2 regulation by miR172 on meristem size and the rate of flower production. We found that rAP2 enlarges the inflorescence meristem by increasing cell size and cell number. Misexpression of rAP2 from heterologous promoters showed that AP2 acts in the central zone (CZ) and organizing center (OC) to increase SAM size. Furthermore, we found that AP2 is negatively regulated by AUXIN RESPONSE FACTOR 3 (ARF3). However, genetic analyses indicated that ARF3 also influences SAM size and flower production rate independently of AP2. The study identifies miR172/AP2 as a regulatory module controlling inflorescence meristem size and suggests that transcriptional regulation of AP2 by ARF3 fine tunes SAM size determination.

overall_design: 12 samples, 4 biological replicates per condition.

last: Vayssières

first: Qing

last: Sang

first: Enric

last: Bertran Garcia de Olalla

first: George

last: Coupland


title: Expression data from 5 colorectal cancer patients neoadjuvantly treated with Imatinib (ImPACCT study)

city: Utrecht

first: Onno

last: Kranenburg

address: Heidelberglaan 100

country: Netherlands

institute: UMC Utrecht

summary: Gene expression profiling of CMS4 colon cancer treated with Imatinib in the ImPACCT study. Fresh-frozen biopsies were taken during diagnostic colonoscopy for CMS4 identification. Five patients gave informed consent for two week of neoadjuvant Imatinib therapy prior to removal of the primary tumor. Fresh-frozen samples were taken from surgically resected colon cancer specimens.

overall_design: Molecular subtyping of colon cancer has identified four Consensus Molecular Subtypes (CMS1-4). The mesenchymal subtype CMS4 is associated with poor prognosis and therapy resistance. In this proof-of-concept study, we assessed whether a rationally chosen drug (Imatinib) could mitigate the distinguishing molecular features of primary CMS4 colon cancer. In the ImPACCT trial, informed consent was obtained for molecular subtyping at initial diagnosis of colon cancer using a validated RT-qPCR CMS4-test on three colonoscopy biopsies per tumor (Phase-1, n=69 patients), and for neoadjuvant CMS4-targeting therapy with imatinib (Phase-2, n=5). Multiple biopsies were taken to account for intra-tumoral heterogeneity. Five patients consented to imatinib treatment prior to surgery. Three biopsies were taken from the surgical resection specimen per patient, yielding 15 pre- and 15 post-treatment samples from 5 patients for molecular analysis.

first: Inne

last: Borel Rinkes

first: Niek

middle: A

last: Peters


title: A novel mRNA decay inhibitor abolish pathophysiological cellular transition

city: Kyoto

first: Satoshi

last: Gojo

address: 465 Kajii-cho, Kamigyo-ku

country: Japan

institute: Kyoto Prefectural University of Medicine

summary: The synthesis and decay of mRNA in cells are carried out by influencing each other, and their balance is altered by either external or internal cues, resulting in changes in the dynamics of the cell. We have previously reported that it is indispensable that an array of mRNAs which shape a phenotype should be degraded before cellular transitions, such as cellular reprogramming and differentiation. In adipogenesis, the interaction between DDX6 and 4E-T had a definitive impact on the pathway in the processing body (PB). We screened a library of α-helix analog with an alkaloid backbone to determine a compound inhibiting the binding between DDX6 and 4E-T proteins, because the interaction is executed between α-helix of structured and internally disordered protein, respectively, and identified IAMC-00192 as a lead compound. The compound showed a direct inhibition in the interaction between DDX6 and 4E-T by using WAVE system with a KD of 774.3 nM. The compound inhibited PB formation that temporally increases during adipogenesis and epithelial-mesenchymal transition (EMT), and significantly suppressed their cellular transition. We also found that in the EMT model, the half-life of pre-existing mRNAs in PBs was extended twofold by the compound. The novel inhibitor of RNA decay will be not only a tool to analyze in detail what pathological conditions RNA decay affects and how it regulates the state, but also lead to drug discovery of the first in class as RNA decay inhibitor.

overall_design: We established a cell line (A549EGFP-DDX6) in which a protein fused with EGFP and DDX6 was introduced into A549 using a retrovirus. In A549 EGFP-DDX6, the processing body (PB) is fluorescent to EGFP. The cells were stimulated with TGFB2 (Tb2, 5 ng/ml) for 2 days, and PB fractions were isolated from epithelial-mesenchymal transition (EMT)-induced cells by FACS. The isolated PB fractions were subjected to RNA extraction and compared with cytoplasmic fractions. Each RNA-seq result was normalized by FPKM, and the gene with higher expression level than the average expression level of all genes was considered as the expressed gene and compared with each sample.

first: Gojo

last: Satoshi


title: Identification and characterization of BEND2 as a novel and key regulator of meiosis during mouse spermatogenesis [RNA-Seq II]

city: Beijing

first: Chunsheng

last: Han

address: 1-5 Beichen West Road, Chaoyang District

department: Institute of Zoology

institute: Chinese Academy of Sciences

summary: To describe the changes of transcriptome in Bend2 knockout mice, we conducted RNA-seq analyses by using spermatocytes from d12 (12-days after birth) Bend2 WT and KO mice. We found BEND2 contributed to inhibiting the expression of genes involved in spermatogonia differentiation and meiosis initiation.

overall_design: Spermatocytes isolated by FACS from d12 Bend2 WT and KO mice were performed in each experiment. RNA-seq data analyses were based on four independent replications.

first: Longfei

last: Ma

first: Dan

last: Xie

first: Xiwen

last: Lin


title: Muscle mRNA profiles from subjects enrolled in the ATLAS clinical study (NCT03464500)

city: Ecublens

first: Chris

last: Rinsch

address: EPFL Innovation Park, Building C

country: Switzerland

institute: Amazentis SA

summary:
Purpose: muscle transcriptomics of subjects supplemented with Urolithin A at different doses or placebo for 4 month.
Method: RNA-seq was performed  using Illumina HiSeq 4000 sequencing; single read 1 x 50 bp . The quantification of mRNA from the RNA-seq FASTQ files was performed using Salmon. Sample-wise quant.sf files containing raw transcript-level read estimates were read into R, v. 4.0.3 and were combined into a data matrix. Transcripts with very low total counts (< 10) across all samples were filtered out. The data was transformed using the variance stabilizing transformation (VST) method of R package DESeq2, v. 1.30.0. Top 10,000 transcripts with the highest variance across all samples were used for principal component analysis (PCA) using DESeq2. Data transformation and PCA was also done separately for each treatment group. Based on the PCAs, probable outlier samples were excluded and new PCAs were plotted without these samples. The raw transcript-level read count estimates were read in R and summarized to gene-level counts based on the provided transcript and gene ID annotations using summarizeToGene function of R package tximport, v. 1.18.0. DESeqDataSetFromTximport function of DESeq2 was then used for constructing a DESeqDataSet object for DE analysis. Pre-filtering was applied before the DE analysis by excluding genes with < 10 total counts across samples. Subset DE analysis was performed, contrasting Visit time D120 with baseline (BL) and by adjusting for the subject effect. The normalization and DE analysis was done separately for the three different treatment groups. Independent filtering option of DESeq2 was enabled (default), filtering out genes with very low counts and thus unlikely to show significant evidence. R package biomaRt. v. 2.46.0 was used for annotating the results with HGNC gene symbols, gene descriptions and gene biotypes. DESeq2-normalised expression values of all the samples in the given comparison were added to the result tables. Non-adjusted p-value 0.05 was used to filter the results by statistical significance. Results were also generated using DESeq2 function lfcShrink that allows for the shrinkage of the log2 fold change (LFC) estimates toward zero when the information for a gene is low (such as in those cases with low counts or high dispersion values) but has little effect on genes with high counts. The shrinked log2FC values were subsequently used for visualisation and ranking the genes.

first: Davide

last: D'Amico

first: Anurag

last: Singh


title: Genome-wide maps of hnRNP UL1 binding on DNA during the inflammatory process.

first: Zhongfei

address: 5, DongDan SanTiao, Dongcheng district

department: Department of Immunology

institute: Chinese Academy of Medical Sciences

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We performed ChIP-seq with antibody targeting hnRNP UL1 at 0, 4h and 10h following LPS stimulation in RAW 264.7 cells. NGS and data analysis were done by Novogen China Co. Ltd. We found that hnRNP UL1 binds to chromatin DNA broadly and dynamically during inflammatory response. hnRNP UL1 binds to genes' promoter mainly. And NF-κB binding sites (κB sites) were significantly enriched in the motifs bound by hnRNP UL1.

overall_design: RAW 264.7 cells were stimulated by LPS for 0, 4h and 10h. Then protein-DNA complexes were sellectively immunoprecipitated using hnRNP UL1 antibody. Purified input DNA fragments and ChIP-derived DNA fragments were undergone NGS.

first: Xuetao

last: Cao


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type Vibrio harveyi 345 and hfq mutant 345∆hfq Transcriptomes

first: Yiqin

last: Deng

state: Guangdong

address: 231 Xingang West Road, Haizhu District, Guangzhou, Guangdong, China

institute: South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare the gene (including sRNA) expression of the Wild Type Vibrio harveyi 345 and hfq mutant 345∆hfq, thus to figure out the effect of hfq on the gene expression of V. harveyi
Methods:The mid-log bacterial cells (OD600 = 3.5) of wild type strain V. harveyi 345 and the hfq mutant strain 345∆hfq were collected to extract the total RNA.  TruSeqTM RNA sample preparation Kit (Illumina, San Diego, CA)) was used to prepare RNA-seq transcriptome library using 2μg of total RNA. The Illumina HiSeq×TEN was performed to sequence the paired-end RNA-seq sequencing library (2 × 150bp read length). A Perl program was written to remove low-quality sequences, reads with more than 5% of N bases (unknown bases) and reads containing adaptor sequences, obtaining clean reads. The high quality reads in each sample were mapped to the referent V. harveyi (PRJNA418027) genome by Bowtie2 (Langmead and Salzberg, 2012). Transcript per million (TPM) mapped reads was calculated by RSEM (Dewey and Li, 2011) to assessment the gene expression. The different expressed genes (DEGs) were identified by using the edgeR, DESeq2, or DESeq packages (Anders, 2010; Love et al., 2014; Smyth, 2020).  The cluster Profiler software KOBAS 2.0 (Chen et al., 2011) was used to perform KEGG pathway enrichment analysis of DGEs. The adjusted P-value (padj) ≤ 0.05 was the threshold for significant enrichment.The software Rockhopper (Ryan et al., 2013) was used to predict sRNAs basing on base sequencing coverage. Then the sRNAs were annotated by Blast, sRNAMap, sRNATarBase, SIPHT, and Rfam (Hsi-Yuan et al., 2008; Cao et al., 2010). RNAfold (Denman, 1993) was performed to predicted sRNAs second structure. RNAphybrid and RNAplex were used to predicted sRNAs targets (Jan and Marc, 2006; Tafer and Hofacker, 2008).
Results: There were total 883 genes significantly differential expressed in 345Δhfq compared with the wild type strain V. harveyi 345, accounting for 16.39% of the total genes on V. harveyi 345 with 538 were up-regulated and 345 were down-regulated. The up-regulated genes were enriched mainly in the pathways those involved into metabolism, including biosynthesis of siderophore group nonribosomal peptides, phosphotransferase system (PTS), starch and sucrose metabolism, amino sugar and nucleotide sugar metabolism, fructose and mannose metabolism, naphthalene degradation, chloroalkane and chloroalkene degradation, ascorbate and aldarate metabolism, fatty acid degradation, retinol metabolism, and histidine metabolism. The down-regulated genes were mainly enriched in shigellosis (fliC), NOD-like receptor signaling pathway (fliC), Salmonella infection (gapA, fliC), legionellosis (fliC), plant-pathogen interaction (fliC), apoptosis, flagellar assembly (flgI, fliD, fliS, motY, and fliC), bacterial chemotaxis (malE, cheV, cheW, and mcp), and microRNAs in cancer (dcm) which were involved into bacterial virulence. In addition, a total of 434 sRNAs were obtained in the transcriptome data, and 11 sRNAs were significantly down-regulated (padjust>0.05, fold change >8, and at least one the strains Transcripts Per Million reads tpm >50) without hfq. The RNAfold indicated that all the sRNAs were stem-loop structures.
Conclusions: Our study represents the first detailed analysis of the effect of hfq on gene expression of Vibrio harveyi by RNA-seq technology.  We conclude that Hfq played variable roles in bacterial metabolism, cell mobility, bacterial chemotaxis, biofilm formation, and secretion which are associated with bacterial virulence.

first: Ziyang

first: Changhong

last: Cheng

first: Hongling

first: Guangxin

last: Liu

first: Juan

last: Feng


title: Transcriptome-wide analysis of U2AF2 RNA binding in a human hematopoietic cell line.

city: New Haven

first: Giulia

last: Biancon

state: Connecticut

address: 300 George Street

department: Internal Medicine - Yale Cancer Center

institute: Yale University

summary:
The essential pre-mRNA splicing factor U2AF2 (also called U2AF65) identifies polypyrimidine (Py) tract signals of nascent transcripts, despite length and sequence variations. Previous studies have shown that the U2AF2 RNA recognition motifs (RRM1 and RRM2) preferentially bind uridine-rich RNAs. Nonetheless, the specificity of the RRM1/RRM2 interface for the central Py tract nucleotide has yet to be investigated.  Enhanced crosslinking and immunoprecipitation of endogenous U2AF2 in human erythroleukemia cells showed uridine-sensitive binding sites with lower sequence conservation at the central nucleotide positions of otherwise uridine-rich, U2AF2-bound splice sites. Altogether, these results highlight the importance of RNA flexibility for protein recognition and take a step towards relating splice site motifs to pre-mRNA splicing efficiencies.
Keywords: splicing, RNA binding, U2AF2, U2AF65, 3'SS, 3' splice site, eCLIP, polypyrimidine tract, RNA recognition motif, RRM, U-rich, Py-tract

overall_design: In this study, we performed high-throughput sequencing of RNA isolated by enhanced crosslinking immunoprecipitation (eCLIP-seq) to determine U2AF2-RNA binding in the context of a human hematopoietic cell line (HEL). Experiments were performed in biological duplicate.

first: Toma

last: Tebaldi

first: Stephanie

last: Halene


title: DLX1 and the NuRD complex cooperate in enhancer decommissioning and transcriptional repression

city: San Francisco

first: James

middle: D

last: Price

state: CA

address: 1550 4th Street

department: Psychiatry

institute: UC San Francisco

summary: In the developing subpallium, the fate decision between neurons and glia is driven by expression of Dlx1/2 or Olig1/2 respectively, two sets of transcription factors (TFs) with a mutually repressive relationship. The mechanism by which Dlx1/2 repress progenitor and oligodendrocyte fate, while promoting transcription of genes needed for differentiation, is not fully understood. We identified a motif within DLX1 that binds RBBP4, a NuRD complex subunit. ChIP-seq studies of genomic occupancy of DLX1 and six different members of the NuRD complex show that DLX1 and NuRD colocalize to putative regulatory elements (pREs) enriched near other transcription factor genes. Loss of Dlx1/2 leads to dysregulation of genome accessibility at pREs near genes repressed by Dlx1/2, including Olig2. Consequently, heterozygosity of Dlx1/2 and Rbbp4 leads to an increase in the production of OLIG2+ cells. These findings highlight the importance of the interplay between TFs and chromatin remodelers in regulating cell fate decisions.

overall_design: Examination of genomic occupancy profiles of six NuRD complex proteins from ganglionic emninences of E13.5 mice and comparison of genomic accessibility measured via ATAC of VZ (Ftag+) and SVZ/MZ cells (Ftag-) from ganglionic eminences of WT and Dlx1/2 -/- E12.5 mice

first: Susan

last: Lindtner

first: Athena

last: Ypsilanti

first: Fadya

last: Binyameen

first: Jeffrey

middle: R

last: Johnson

first: Billy

last: Newton

first: Nevan

last: Krogan

first: John

middle: L

last: Rubenstein


title: Comparative transcriptome profiles of human dental pulp cells from maxillary and mandibular teeth

city: Bangkok

first: Sermporn

last: Thaweesapphithak

address: 34 Thanon Henri Dunant Wang Mai, Khet Pathum Wan

country: Thailand

institute: Chulalongkorn University

summary: PITX1 had a significantly higher expression in the lower teeth compared to the upper teeth and this difference in PITX1 level was more evident in the molars compared to premolars, consistent with data in mouse developing teeth. These show that the differential gene expression during odontogenesis can continue to exist in mature teeth. We suggest that an in vitro study of dental pulp cells should take the differential gene profiles between the mandibular and maxillary teeth into consideration. The knowledge about gene profiling and pathways in mature teeth paves a way to explore a more precise treatment approach in regenerative dentistry.

overall_design: The upper and lower premolar and molar teeth obtained from the same participant were employed. Ten participants (four subjects for RNA-Sequencing and six for quantitative real-time PCR) were recruited. The pulp cells from two pairs of opposing premolars and two pairs of opposing molars were cultured and subjected for RNA-Seq. RNA-Seq alignment and differential expression analyses were used to analyze gene expression profile. The cells from three pairs of premolars and three pairs of molars were subjected for qRT-PCR to confirm the RNA-Seq results.

first: Thira

last: Faruangsaeng

last: Thaweesapphitak

first: Chompak

last: Khamwachirapitak

first: Thantrira

last: Porntaveetus

first: Vorasuk

last: Shotelersuk


title: Transcriptional profiling in neurons of C. elegans : comparison between ahr-1 mutant and wild-type animals.

city: PARIS

first: LINH CHI

last: BUI

address: 45 rue des Saints-Pères

department: INSERM

country: France

institute: Université de Paris

summary: The Aryl hydrocarbon Receptor (AhR) is a transcription factor well known in vertebrate to play an essential role as xenobiotic sensor. On the contrary, no ligand has been identified to date for invertebrate AhR. In some model organisms such as D. melanogaster and C. elegans, AhR orthologs have physiological functions and their inability to bind prototypical ligands of vertebrate AhR such as tetrachlorodibenzo-p-dioxin (TCDD) suggests that the detoxification role of the receptor could be an adaptation acquired during evolution. To better understand the physiological roles of AhR, we studied AhR-1, the C. elegans ortholog and performed transcriptomic and metabolomic analysis respectively in neuronal cells expressing AhR-1 and in whole animals. Next, we designed a reporter system in order to investigate if the transcriptional activity of AhR-1 could be modulated. Cos-7 cells were transfected with AhR-1, its dimerization partner AhA-1 (C. elegans ARNT ortholog) and a Firefly luciferase gene under the control of the human cytochrome P450 1A1 promotor. The luciferase bioluminescence measurement allows the identification of C. elegans AhR-1 modulators. Transcriptional profiling in neurons expressing AhR-1 revealed 95 genes down-regulated, and 76 genes up-regulated in AhR-1 KO animals. These genes are associated with nervous system function (depleted) and fatty acid process, oxidative phosphorylation and glycolysis (enriched). Metabolomic profiling results indicate a role for AhR-1 in regulating several endogenous metabolic pathways: amino-acid metabolism, carbohydrate metabolism as well as fatty acid metabolism Then, with the COS-7 in vitro screening model, we identified positive and negative modulators such as bacterial, dietary or environmental compounds. Considering C. elegans environment, these results could be used to highlight the role of invertebrate AhR and identified new features in vertebrate AhR.

overall_design: Two transgenic strains expressing the green fluorescent protein (GFP) under the transcriptional control of mec3 (Pmec3:GFP), a direct regulator of AhR-1were used : one strain was the wild-type strain (expressing GFP in mec3-active cells, which will subsequently express AhR-1), while the other strain was the result of a cross with ahr-1(ia03), a AhR-1 knockout strain.   Enriched population of AhR-1 expressing neurons in both wild-type GFP and mutant AhR-1:GFP were generated using fluorescence activated cell sorting (FACS).  RNA from both cell types were extracted, amplified and analyzed  using a C. elegans array from Agilent

first: L

middle: C

last: Bui

first: C

last: Tourette

last: Ottolenghi

first: S

last: Imbeaud

last: Tomkiewicz

last: Coudouel

first: H

last: Delacroix

first: J

last: Ichanté

first: X

last: Coumoul


title: Identification and characterization of BEND2 as a novel and key regulator of meiosis during mouse spermatogenesis

first: Chunsheng

last: Han

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

overall_design: Refer to individual Series


title: The effect of hyperthermia on nasopharyngeal carcinoma cells

city: zhengzhou

first: le

middle: xiao

last: li

address: wulibao street

institute: the First Affiliated Hospital of Zhengzhou

summary: Hyperthermia has shown unique advantages in tumor treatment as an anti-cancer treatment method, which combined with radiotherapy and/or chemotherapy reduces the side effects. However, its specific mechanism is unknown.

overall_design: The CNE2 cells were divided into two groups, the control group and the hyperthermia group. The hyperthermia group cells were treated in a hot water bath at 43 degrees for 30 minutes, and samples were collected 24 hours later.

first: Leli

last: Xiao

first: Daoke

last: Yang


title: Next Generation Sequencing of Wild Type and Hnrnpul1-/- RAW 264.7 Cells Transcriptomes

first: Zhongfei

last: Ma

summary:
Purpose: The goal of this study is to compare NGS-derived wild type and Hnrnpul1 knockout (Hnrnpul1-/-) RAW 264.7 cells transcriptomes with or without LPS stimulation.
Methods: Sequancing was performed by Novogene China Co. Ltd. RNA profiles of wild type and Hnrnpul1-/- RAW 264.7 cells as well as LPS stimulated (10 h) wild type and Hnrnpul1-/- RAW 264.7 cells were generated by deep sequencing using Illumina Novaseq 6000. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. Method of TMM was used to normalize the readcount. Negative binomial distribution model was used to calculate the P value, and FDR was calculated by the method of Benjaminiand Hochberg.
Results: Using an optimized data analysis workflow, we mapped about 40 million sequence reads per sample to the mouse genome (GRCm38/mm10). Comparing to wild type RAW 264.7 cells, 237 genes were up-regulated and 181 genes were down-regulated in Hnrnpul1-/- cells. At 10 h following LPS stimulation, 341 genes were up-regulated and 288 genes were down-regulated in Hnrnpul1-/- cells. Genes were pre-ranked according to log2FoldChange(KO/WT) followed by GSEA and 6 gene sets were significantly enriched. Significantly differential genes were undergone GO analysis (biological process) and biological process including cell-cell adhesion, positive regulation of cell activation and regulation of response to external stimulus were enriched.
Conclusions: Lacking Hnrnpul1 promotes the expression of inflammatory cytokines in LPS stimulated RAW 264.7 cells.

overall_design: mRNA profiles of wild type and Hnrnpul1-/- RAW 264.7 cells with or without LPS stimulation.

first: Xuetao

last: Cao


title: Wild Type and Hnrnpul1-/- RAW 264.7 Cells


title: Characterization of zebrafish melanoma-derived interstitial EVs and their ncRNA content

city: Trento

first: Maria Caterina

last: Mione

address: Via Sommarive 9

department: CIBIO

country: Italy

institute: University of Trento

summary: Extracellular vesicles (EVs) are membranous particles released by all cell types. Their role as functional carriers of bioactive molecules is boosted in cancer where they can be either secreted in biological fluids or found in the intercellular space (interstitial EVs, iEVs). Here we have opti-mised a method for the isolation and characterization of zebrafish iEVs from whole melanoma tissues. Zebrafish melanoma iEVs are in the range of ~ 140 nm by nanoparticle tracking analysis (NTA) and TEM analysis. Western blot revealed enrichment for CD63 and Alix in the iEV frac-tion, but not in melanoma cell lysates. Super resolution and confocal microscopy revealed that purified zebrafish iEVs were GFP+ indicating that they integrate the oncogene, GFP-HRASV12G within their vesicular membrane.  Analysis of RNA-Seq data revealed that 118 ncRNAs are differentially distributed between zebrafish melanoma and their iEVs, with only 18 of them be-ing selectively enriched in iEVs. Among these, the RNA components of RNAses MRP and P, which process ribosomal RNA precursors, mitochondrial RNAs and some mRNAs, were enriched in iEVs. We found that melanoma iEVs induce an inflammatory response when injected in larval blood stream with increase of macrophage and induction of Interferon Responsive Genes. To clarify whether MRP and P contribute to the inflammation induced by melanoma iEVs we inject-ed larvae with MRP or P RNAs and found an inflammatory response similar to that induced by melanoma iEVs. This suggests that zebrafish melanoma iEVs are a source of MRP and P RNAs that can trigger inflammation in cells of the tumor-microenvironment.

overall_design: In order to identify small RNAs preferentially accumulated in extracellular vesicles derived from zebrafish melanoma,  we performed RNA sequencing analysis (RNA-Seq), of small RNAs isolated from EVs and melanoma samples.

first: Maria

first: Valentina

last: Biagini

first: Viviana

last: Anelli

first: Emanuela

last: Kerschbamer

first: Marta

last: Baghini

first: Federica

last: Busi

first: Elena

last: Gurrieri

first: Michela

last: Notarangelo

first: Silvano

last: Piazza

first: Guillaume

last: Van Niel

first: Vito

last: D'Agostino


title: Jasmonic acid and dark induced leaf senescence in tomato was alleviated by knock-out of SlWRKY37

first: Wang

middle: Zhi

last: rong

address: 2#, Yuanmingyuan West Road,100193 Beijing, China

institute: China Agricultural University

summary: Leaf senescence can be triggered by jasmonic acid (JA) and darkness. There are scattered reports about JA and dark-induced senescence, respectively. While the precise regulatory mechanisms that integrate these two factors to initiate and regulate leaf senescence have not been identified. Here, we report a transcriptional regulating module centered on novel WRKY transcription factor that is responsible for both JA and dark-induced leaf senescence in tomato. The expression levels of SlWRKY37 together with the master transcription factor in JA signaling SlMYC2 could be significantly induced by both MeJA and dark treatments. SlMYC2 directly binds to the promoter of SlWRKY37 to active its expression. Knock out of SlWRKY37 inhibited JA and dark-induced leaf senescence. Transcriptome analysis revealed 1312 differentially expressed genes between slwrky37-CR and SlWRKY37-OE, including genes involved in JA synthesis as well as several senescence-associated genes (SAGs). We characterized SlWRKY53 and SlSGR1 as direct transcriptional targets of SlWRKY37 to regulate leaf senescence. Moreover, SlWRKY37 interacts with SlVQ7 protein in vivo and the interaction enhances its binding ability to the promoters and transcriptional activation to downstream target genes. In addition, SlWRKY37 is phosphorylated at the post-translational level. Phosphorylation of SlWRKY37 is essential for its protein interaction and transcriptional activation, indicating phosphorylation modification has a great effect on the function of SlWRKY37 protein. Our study reveals the physiological and molecular functions of SlWRKY37 in leaf senescence and offered a target gene to retard leaf yellowing by reducing the sensitivity to internal and external senescence signal such as JA and darkness.

overall_design: Leaf mRNA profiles of 21-day old wild type (Micro Tom), slwrky37 and SlWRKY37-OE

first: Zhirong

last: Wang

first: Ming

last: Gao

first: Hui

last: Su

first: Yafei

last: Li


title: Mmp-13 deletion in cells of the mesenchymal lineage increases bone mass, decreases endocortical osteoclast number and attenuates the cortical bone loss caused by estrogen deficiency in mice

city: Little Rock

first: Intawat

last: Nookaew

address: 4301 W Markham St

department: Department of Biomedical Informatics

institute: University of Arkansas for Medical Sciences

summary: We generated mice with conditional Mmp-13 deletion in Prrx1 expressing cells (Mmp-13dPrrx1) and compared the effect of estrogen deficiency on their bone phenotype to that of control littermates (Mmp-13f/f)

overall_design: We compare transcriptome of calvaria cells between Mmp13 knock out mice with wildtype

first: Filipa

last: Ponte

last: Almeida


title: Altered mRNA profile in testis of patients with“secondary idiopathic non-obstructive azoospermia”

city: Hefei

first: Kuokuo

institute: Anhui Medical University

summary: Background: Non-obstructive azoospermia (NOA) is the most severe form of male infertility. Currently known causative factors, including congenital and several acquired causes can only account for approximately 30% of NOA cases. Causes for most patients with NOA remains unclear, which were known as idiopathic NOA (iNOA). However, whether iNOA is congenital defects or acquired abnormalities is a confusing problem due to the delayed diagnosis of this frustrating situation until childbearing age.   Materials and Methods: In this study, several patients who were diagnosed as iNOA at this stage, but with a history of natural conceptions with female before were enrolled and defined as “secondary idiopathic NOA”. As little was known about these cases, we performed the mRNA expression profiling by Next-generation sequencing (NGS) in this three patients and other three patients with obstructive azoospermia (OA) as controls.   Results: A series of mRNAs were found to be altered in testicular tissues between “secondary idiopathic NOA” and controls, including 6028 downregulated and 3402 upregulated mRNAs. GO analysis and KEGG analysis revealed a range of GO and KEGG terms, such as cellular process involved in reproduction, protein digestion and absorption, etc.   Conclusion: Overall, this study introduces a novel classification called “secondary idiopathic NOA” in iNOA. We provide a global view of the altered mRNAs involved in spermatogenetic failure in these cases.

overall_design: Examination of  different different gene expression between NOA and control

first: Dongdong

last: Tang

first: Mingrong

last: Lv

first: Xiaojin

last: He

first: Yunxia

last: Cao


title: Detection of transcriptome changes caused by knockdown of Ptbp1 in U251 GBM cells

city: wenzhou

first: kankai

last: wang

address: wenzhou medical university

institute: wenzhou medical university

summary: We demonstrated that knocking down Ptbp1 can reprogram GBM cells into neuron-like cells. In order to further explore the mechanism of Ptbp1 causing this phenomenon, we performed mRNA sequencing on U251 cells infected with sh-Luci-3d, sh-Ptbp1-3d and sh-Ptbp1-7d.

overall_design: The mRNA changes of U251 cells infected with sh-Luci-3d, sh-Ptbp1-3d and sh-Ptbp1-7d were detected.

first: Kankai


title: Identification and characterization of BEND2 as a novel and key regulator of meiosis during mouse spermatogenesis [ATAC_seq]

first: Chunsheng

last: Han

summary: To describe the changes of chromatin accessibility in Bend2 knockout mice, we conducted ATAC-seq analyses by using zygotene spermatocytes from Bend2 WT and KO mice. We found the chromatin state were opened in the proximal promoter of Bend2 up-regulated genes.

overall_design: Zygotene spermatocytes isolated by FACS from Bend2 WT and KO mice were performed in each experiment. ATAC-seq data analyses were based on two independent replications.

first: Longfei

last: Ma

first: Dan

last: Xie

first: Xiwen

last: Lin


title: Identification and characterization of BEND2 as a novel and key regulator of meiosis during mouse spermatogenesis [Histone_CUTRUN]

summary: To describe the changes of histone modifications in Bend2 knockout mice, we conducted CUT&RUN analyses by using zygotene spermatocytes from Bend2 WT and KO mice with H3K4me3 and H3K27me3 antibodies. We found the enrichment of these histone modifications in the proximal promoter of Bend2 down-regulated genes were disrupted in Bend2 KO mice.

overall_design: Zygotene spermatocytes isolated by FACS from Bend2 WT and KO mice were performed in each experiment. CUT&RUN data analyses were based on two independent replications.


title: Exposure to contaminated river water is associated with early hatching and dysregulation of gene expression in early life stages of the endangered copper redhorse

city: Ste-Anne-de-Bellevue

first: Jessica

last: Head

state: Quebec

address: 21111 Lakeshore

department: Natural Resource Sciences

country: Canada

institute: McGill University

summary: The copper redhorse (Moxostoma hubbsi) is an endangered fish endemic to Quebec, Canada that is only known to spawn in two locations within the Richelieu River, a waterway draining a significant area of agricultural land. Accordingly, concerns have been raised over the impacts that agricultural pesticide contamination of spawning grounds and nursery habitats within the Richelieu River may have on early life stage copper redhorse. We assessed the effects of contaminants on early life stages of copper redhorse and river redhorse (Moxostoma carinatum), a closely related fish that shares the copper redhorse’s habitat and spawning grounds but is distributed more widely and is not yet listed as endangered. Copper and river redhorse embryos (1000 each) were exposed to either Richelieu River water in an in-situ flow-through system or to laboratory water used as a control. We assessed embryos hatching time, incidence of deformities and survival in copper and river redhorses. We then performed RNA sequencing on copper redhorse larvae to better understand changes due to river water exposure. We identified 341 compounds in the river water that were absent from lab water. Pesticide concentrations in the river peaked following rainfall during the spawning season. Embryos exposed to river water hatched prematurely at 63.0 and 59.2 cumulative degree days (CDD) compared to 65.4 and 69.9 CDD in laboratory water for river and copper redhorse, respectively. Copper redhorse exposed to river water also had a significantly lower survival rate than laboratory water (73% vs. 93%). RNA sequencing of copper redhorse revealed 18 differentially expressed genes (DEGs) following river water exposure. Eight of the upregulated DEGs (cd44, il1b, lamb3, lamc2, tgm5, orm1, saa, acod1) are linked to immune function and injury response and 7 of the downregulated DEGs (cpa2, ctrb, cela2a, ctrl, cpa1, prss1, cel) are involved with digestion and nutrient absorption. This study provided valuable data on the effects of anthropogenic contaminants present in the Richelieu River and increased our knowledge on the individual and mixture effects they have on an endangered fish.

overall_design: Whole larvae mRNA profile of 14 day old copper redhorse (Moxostoma hubbsi) raised in either laboratory or river water

first: Hugo

last: Marchand

first: Benjamin

last: Barst

first: Emily

last: Boulanger

first: Nathalie

last: Vachon

first: Magali

last: Houde

first: Jeff

last: Xia

first: Peng

last: Liu

last: Ewald

first: Stephane

last: Bayen

first: Lan


title: Identification of the effect of AhR antagonists on the physiology of human HSPC.

city: Seoul

first: Dong-Yeop

last: Shin

address: 101 Daehak-ro, Jongno-gu

department: College of Medicine

institute: Seoul National University

summary: We demonstrated to examine the effect of AhR antagonists on the specific lineage-biased differentiation of HSPC. To confirm this, CD34+ cells isolated from cord blood were cultured with two antagonists (CH223191 and StemRegenin 1) for 14 days to monitor their phenotype, and chromatin immunoprecipitation DNA was extracted from cultured cells on the 14th day of culture. We sought to explain the relationship between the action of AhR-antagonist complex and the megakaryocyte lineage-biased differentiation of HSPC with these ChIP-seq results.

overall_design: Examination of 2 different Ary hydrocarbon receptor antagonists in cord blood (CB)-HSPCs (DMSO control vs. CH223191-treated vs. StemRegenin1-treated).

first: Dongchan

last: Kim


title: Identification and characterization of BEND2 as a novel and key regulator of meiosis during mouse spermatogenesis [RNA-seq]

summary: To describe the changes of transcriptome in Bend2 knockout mice, we conducted RNA-seq analyses by using leptotene and zygotene spermatocytes from Bend2 WT and KO mice. We found BEND2 contributes to shutting down the mitotic program and to activating or enhancing the meiotic and post-meiotic program of spermatogenic cells.

overall_design: Leptotene and zygotene spermatocytes isolated by FACS from Bend2 WT and KO mice were performed in each experiment. RNA-seq data analyses were based on three independent replications.


title: METTL3 Regulates LPS-Induced Inflammatory Response via the NOD1 Signaling Pathway

city: Guangzhou

first: Yongjie

last: Cai

address: 56 Ling Yuan Xi Road

institute: SUN YAT-SEN UNIVERSITY

summary: Inflammation is normally a protective response to defend and restore homeostasis; nonresolving inflammation is a major driver of immune disorders. N6-methyladenosine (m6A) is a prevalent mRNA modification that plays a crucial function in multiple biological processes. The effect of m6A on the immune response has recently been reported. However, the effect is unclear, and the results are contradictory. In this study, the expression of total m6A and the methyltransferase METTL3 decreased in LPS-stimulated macrophages. METTL3 knockdown significantly upregulated expression of proinflammatory cytokines, including TNF-α, IL-6 and NO. RNA sequencing analysis showed that the upregulated genes were enriched in inflammation-related signaling pathways and that the NOD-like receptor signaling pathway might be the target molecules of METTL3. METTL3 depletion resulted in upregulation of the NOD1 pathway without impacting NOD2. Moreover, the increase in proinflammatory cytokines induced by METTL3 knockdown was reversed by blocking the NOD1 pathway using the NOD-IN-1 and ML130 specific inhibitors. Mechanistically, METTL3 knockdown promoted the mRNA expression and stability of NOD1 and RIPK2, and the same results were detected in m6A-binding protein YTHDF1- or YTHDF2-silenced cells. All findings suggested that METTL3 depletion inhibits the degradation of NOD1 and RIPK2 mRNA mediated by YTHDF1 and YTHDF2, which upregulate the NOD1 pathway and subsequently promote the LPS-induced inflammatory response in macrophages.

overall_design: two repeates of mRNA from shControl RAW264.7 cells and two repeates of mRNA from shMETTL3 RAW264.7 cells


title: Characterization of bronchoalveolar lavage samples from two Be-exposed subjects

city: NEW YORK

first: RUI

last: FU

state: NY

address: 101 6th Ave

department: Computational Biology

institute: New York Genome Center

summary: Chronic beryllium disease (CBD) is a metal-induced hypersensitivity disorder characterized by CD4+ T cell alveolitis. Single-cell gene expression profiling of bronchoalveolar lavage (BAL) cells focused on T cells may provide insight into unique subsets of CD4+ T cells, functional pathways, and/or molecules that could potentially be developed into novel therapeutics for treating CBD and other granulomatous lung diseases. To understand the unbiased cellular composition of airway associated CD4+ T cells in subjects with beryllium exposure, we used BAL cells from one beryllium-exposed (BeS) and one CBD subject diagnosed using previously defined criteria, and these two samples comprised the disease cohort.

overall_design: Cells were thawed and rested in culture overnight in complete medium. Single cells were flow-sorted using propidium iodide to exclude dead cells. The sorted cells were resuspended in PBS buffer, recounted, and processed for 10X Genomics 3’v2 Kit as specified by the manufacturer’s protocol for each patient sample. Approximately 5000 cells were loaded in the wells of a 10X Genomics Chromium controller to create GEM emulsions, targeting a recovery of 3000 cells. Reverse transcription, cDNA amplification and RNA- sequencing library preparation were performed using the GEM emulsion. Libraries were sequenced on the Illumina Hi-Seq 4000 platform, using 75 bp paired end reads.

first: Rui

last: Fu

first: Shaikh

middle: M

last: Atif


title: Identification and characterization of BEND2 as a novel and key regulator of meiosis during mouse spermatogenesis [BEND2_ChIPseq]

first: Chunsheng

last: Han

address: 1-5 Beichen West Road, Chaoyang District

institute: Chinese Academy of Sciences

summary: To characterize BEND2-binding sites on the genome, we conducted ChIP-seq analyses by using testicular lysates from FLAG-BEND2 KI mice. We found BEND2 preferentially binds to simple sequence repeats.

overall_design: Ttesticular tissues from 15 dpp or 40 dpp FLAG-BEND2 mice were performed in each experiment. ChIP-seq data analyses were based on six independent replications.

first: Longfei

last: Ma

first: Dan

last: Xie

first: Xiwen

last: Lin


title: Effect of berberine on global modulation of lncRNA and mRNA expression profiles in patients with stable coronary heart disease

first: Jinghua

last: Yang

address: 32 North Third Ring Road West, Haidian District, Beijing

institute: Beijing Zhiyun data technology co. LTD

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

summary: To identify long non-coding RNA and mRNA expression profiles in plasma of myocardial infarction patients before and after Berberine administration and to predict the potential role of differentially expressed lncRNAs and mRNAs in the improvement of MI disease by BBR.

overall_design: Whole blood was collected and plasma was separated from 5 MI patients before and after Berberine administration（BBR and Ctrl group，n=5）, frozen in liquid nitrogen for 1-2 minutes, and then stored at -80°C.

first: Ye-Chen

first: Hong-Zhi

first: Bo

last: Lu

first: Ruo-Lan

last: Xiang

first: Jing-Yi

last: Li

first: Hao

last: Qian

first: Shu-Yang

last: Zhang


title: Comparison with gene expression profile of young and aged muscle progenitor cells

city: Osaka-Sayama

first: Toshiyuki

last: Takehara

state: Osaka

address: 377-2, Ohno-Higashi

department: Faculty of Medicine

institute: Kindai Universty Hospital

summary: Frailty of the locomotory organs has become a widespread problem in the geriatric population. The major factor leading to frailty is an age-associated decrease in muscular mass and a reduced number of muscular cells and myofibers. To understand why decrease self-renew at he gene expression profile the diffeerences between aged and young Muscle progenitor cells(MPSCs). In aged muscular tissues, muscle progenitor cells(MPSCs) are reduced due to abnormalities in their self-renewal and the induction of apoptosis. However, the molecular mechanisms connecting aging-associated physiological changes and the reduction of MPSCs are largely unknown. In this study, we compared the gene expression profile of young and aged MPSCs to identify genes involved in the reduction of MPSCs.

overall_design: Muscle progenitor cells( MPSCs) (CD29+/ITGA7+) were isolated from young (5 weeks old) and aged (2 years old) C57Bl/6 mice.

first: Yuta

last: Onodera

first: Takeshi

last: Teramura


title: Transcriptomic Analysis of Trigeminal Ganglia and Spinal Trigeminal Nucleus Caudalis in Mice with Chronic Inflammatory Temporomandibular Joint Pain

city: Zhengzhou

first: Qian

last: Bai

address: JING BA ROAD

institute: The second affiliated hospital of Zhengzhou University

summary: Purpose: In this study, we aimed to analyze lncRNA expression in the whole transcriptome of trigeminal ganglia (TG) and spinal trigeminal nucleus caudalis (Sp5C) in a chronic inflammatory TMJ pain mouse model. Chronic inflammatory TMJ pain was induced by intra-TMJ injection of complete Freund's adjuvant (CFA). The lncRNA expression patterns in the whole transcriptome of TG and Sp5C were profiled with RNA sequencing.

overall_design: long non-coding RNA profiles of trigeminal ganglia (TG) and spinal trigeminal nucleus caudalis (Sp5C) of 56-day old wild type (WT)  mice were generated by deep sequencing, in triplicate, using Illumina GAIIx.

first: Tieli

last: Dong


title: RNA-seq analysis of NRF2 silenced human skin fibroblasts

city: Lyon

first: Florence

last: Ruggiero

address: 32 avenue Tony Garnier

institute: ENS de Lyon - IGFL

summary: This RNA-seq analysis was the beginning of our study, to have a first global unbiased approach to analyze the effect of NRF2 silencing on the mRNA profile of human skin fibroblasts. We demonstrated that besides NRF2 conventional antioxidant and metabolic target genes, tissue skeleton and especially matrisome genes were affected by NRF2 silencing. We further confirmed that NRF2 silencing some collagen genes, impacting collagen fibrillogenesis.

overall_design: We used primary papillary fibroblasts from 3 young donors, that we transfected either with a scramble siRNA or 3 different siRNA targeting NRF2, which is encoded by the NFE2L2 gene.

first: Mélanie

last: Salamito


title: AhR antagonist

first: Dong-Yeop

last: Shin

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

overall_design: Refer to individual Series


title: EVI1 promotes proliferation and invasive properties of head and neck squamous cell carcinoma cells

city: Vienna

first: Rotraud

last: Wieser

address: Waehringer Guertel 18-20

department: Department of Medicine I

country: Austria

institute: Medical University of Vienna

summary: Head and neck squamous cell carcinoma (HNSCC) is the tenth most common cancer worldwide. Alcohol and tobacco consumption are the predominant risk factors. Despite a multidisciplinary approach, the 5-year overall survival ranges only from 25% to 60%, depending on the site of origin. EVI1 expression increases with higher grading of HNSC tumors and over-expression was linked to a higher rate of lymph node metastasis. In lung cancer, its expression correlated negatively with patient survival. EVI1 was retrovirally over-expressed in CAL-33 and SCC-25 cells. Over-expression promoted proliferation, migration, and invasion of the cells. In CAL-33 cells, 1690 and 1684 genes were up- and down-regulated, respectively, at an FDR <0.1 in response to expression of EVI1. In SCC-25 cells, 334 significantly up- and 417 significantly down-regulated genes were identified. 71 and 181 genes were up- and down-regulated, respectively, in response to EVI1 expression in both cell lines. Gene ontology analysis revealed, among others, the terms epithelium development, extracellular matrix organisationorganization, cell adhesion, response to growth factor, and epithelial cell proliferation to be significantly enriched among the 252 genes that were regulated by EVI1 in a consistent manner in both cell lines.

overall_design: Gene expression profiles of CAL-33 EVI1 over-expression and CAL-33 control cell lines, and of SCC-25 EVI1 over-expression and SCC-25 control cell lines, in quadruplicates, using Illumina HiSeq 2500.

first: Alexander

last: Grandits

first: Gerwin

last: Heller


title: ChIP-seq of Pol II in glioblastoma stem cells

city: Shanghai

first: Zhixin

last: Qiu

address: Dongan Road

institute: Fudan University

summary: NOT PROVIDED; REQUESTED

overall_design: ChIP-seq analysis of Pol II binding in glioblastoma stem cells after YY1 knockdown

first: Qiu

last: Zhixin

first: Rich

last: Jeremy


title: The murine liver x receptor is selectively modulated by different ligands to differentially alter tumor-associated myeloid cells.

city: Urbana

first: Erik

last: Nelson

state: Illinois

address: 407 S Goodwin Ave

department: Molecular and Integrative Physiology

institute: University of Illinois at Urbana Champaign


title: Analysis of RNA expression under AhR antagonist treatment in human HSPCs

summary: To examine the changes in RNA expression profile under AhR antagonist treatment in human hematopoietic stem progenitor cells (HSPCs), CD34+cells were isolated from umbilical cord blood (UCB) unit. CD34+cells were cultured with two different AhR antagonists CH223191 and StemRegenin1 (SR1) ex vivo for 7 days. cultured cells were used to perform RNA sequencing and analyze the changes in RNA expression profile by treatment.

overall_design: Examination of 2 different Ary hydrocarbon receptor antagonists in cord blood (CB)-HSPCs (DMSO control vs. CH223191-treated vs. StemRegenin1-treated). Three biological replication of each group from identical individuals

first: Dongchan

last: Kim


title: Exosomal microRNA sequencing in Tongxinluo pretreated and non-treated MSC-derived exosomes

city: beijing

first: yuyan

last: xiong

address: No.167 North Lishi Road, Xicheng District

institute: fuwai hospital

type: Non-coding RNA profiling by high throughput sequencing

summary: In order to investigate the specific mechanisms underlying the cardioprotective effects of Tongxinluo pretreated MSC-derived exosomes (MSCTXL-Exo) in cardiac repair, we performed microRNA sequencing on exosomes secreted from Tongxinluo pretreated MSCs and non-treated MSCs to identify differentially expressed miRNA. We found that 18 miRNAs were identified to be upregulated and 25 miRNAs downregulated (over 2-fold change) in MSCTXL-Exo compared to MSC-Exo.

overall_design: Three samples were processed for each kind of exosomes that derived from normal MSCs and TXL pretreating MSCs (MSC-Exo and MSCTXL-Exo). MSCTXL-Exo was isolated from conditioned medium of MSCs pretreated by 400 μg/mL of TXL for 24 hours. RNA isolated from exosomes were analyzed using Illumina Hiseq X Ten platform.

first: Y

last: Xiong

last: Yang


title: Obstructive cholestasis compromises balance and alters brain lipid composition in neonatal piglets

city: Frederiksberg

first: Xiaoyu

last: Pan

address: Dyrlægevej 68

department: Department of Veterinary and Animal Sciences

country: Denmark

institute: University of Copenhagen

summary: Infants with neonatal cholestasis are prone to neurodevelopmental deficits including neuromotor function. Accumulation of potentially neurotoxic molecules in the bloodstream including ammonia and bile acids and malabsorption of lipids may affect neurodevelopment in these patients. This study examined neuromotor function and bile acid and lipid composition of the brain in a piglet model of obstructive neonatal cholestasis via bile duct ligation (BDL) surgery. Results showed that BDL piglets had compromised balance and increased liver enzyme levels, liver fibrosis and bile duct proliferation compared to SHAM piglets. Plasma and cerebellum bile acid profiles differed between BDL and SHAM piglets with hyocholic acid and conjugated bile acid forms dominating in the BDL group. In the cerebellum there were different lipid profiles, but similar gene expression profiles between the two groups.

overall_design: Eight-day old piglets underwent bile duct ligation (BDL) or sham surgery (SHAM) and were followed for three weeks during which neuromotor functional tests (balance beam, open field, neuromotor score, gait analysis) were conducted. Samples were collected for liver histopathology, RNA sequencing and qPCR analysis of the cerebellum, and bile acid and lipid profiling of the plasma and/or cerebellum.

first: Nicole

last: Henriksen

first: Svend

last: Hansen

first: Matthew

last: Lycas

first: Thomas

last: Eriksen

first: Lars

middle: S

last: Johansen

first: Christer

last: Ejsing

first: Douglas

middle: G

last: Burrin

first: Vibeke

middle: B

last: Christensen

last: Thymann

first: Stanislava

last: Pankratova


title: RBFOX2/GOLIM4 Splicing Axis Activates Vesicular Transport Pathway to Promote Nasopharyngeal Carcinogenesis

first: Jin-Xin

last: Bei

address: 651 Dongfeng Road East, Yuexiu District, Guanzhou, P.R. China

institute: Sun Yat-sen University Cancer Center

summary: ABSTRACT  20-30% of patients with nasopharyngeal carcinoma (NPC) develop distant metastasis or recurrence leading to poor survival, of which the underlying key molecular events have yet to be addressed. Here we profiled alternative splicing events in 85 NPC samples using transcriptome analysis and revealed that the long isoform of GOLIM4 (-L) with exon-7 was highly expressed in NPC and associated with poor prognosis. Lines of evidence demonstrated the pro-tumorigenic function of GOLIM4-L in NPC cells. We further revealed that RBFOX2 binds to a GGAA motif in exon-7 and promotes its inclusion forming GOLIM4-L. RBFOX2 knockdown suppressed the tumorigenesis of NPC cells, phenocopying GOLIM4-L knockdown, which was significantly rescued by GOLIM4-L overexpression. Moreover, high expression of RBFOX2 was correlated with the exon-7 inclusion of GOLIM4 in NPC biopsies and associated with worse prognosis. Furthermore, we observed that RBFOX2 and GOLIM4 could influence vesicle-mediated transport through maintaining the organization of Golgi apparatus. Finally, we revealed that RAB26 interacted with GOLIM4 and mediated its tumorigenic potentials in NPC cells. Taken together, our findings provide insights into how alternative splicing contributes to NPC development, by highlighting a functional link between GOLIM4-L and its splicing regulator RBFOX2 activating vesicle-mediated transport involving RAB26.    Keywords: GOLIM4, RBFOX2, Nasopharyngeal carcinoma (NPC), Alternative splicing, RAB26

overall_design: We performed transcriptome sequencing of NPC cells to identify RBFOX2 and GOLIM4-L-regulated genes and alternative splicing events.

first: Chunling

last: Luo

first: Xiaochen

last: Xu

first: Chujun

last: Liu

first: Shuai

last: He

first: Jierong

last: Chen

first: Yanchun

last: Feng

first: Shuqiang

first: Wan

last: Peng

first: Yaqing

last: Zhou

first: Panpan

last: Wei

first: Yuxiang

first: Bo

last: Li

first: Haiqiang

last: Mai

first: Xiaojun

last: Xia


title: RNAseq analysis of CRISPR/Cas9-based perturbation of DNMT1 in FXS induced pluripotent stem cells

city: Jerusalem

first: Dan

last: Vershkov

address: The Edmond J. Safra Campus

country: Israel

institute: Hebrew University of Jerusalem

summary: The primary mechanism causing Fragile X syndrome (FXS) is the expansion and silencing of a repetitive CGG sequence in the 5’-UTR of the FMR1 gene. Previous work has demonstrated that chemical disruption of DNA methylation induces FMR1 expression in FXS-iPSCs. To further explore the maintenance of DNA methylation in the FMR1 locus, and to test the possibility of FMR1 reactivation using gene targeting of a single epigenetic factor, we performed a global transcriptional analysis of FXS-iPSCs infected with a lentiviral construct containing Cas9 and sgRNA targeting DNMT1.

overall_design: To overcome the sensitivity of human PSCs to the loss of DNMT1, we infected FXS-iPSCs with a lentiviral vector containing sgRNA targeting DNMT1 and collected the culture 7-14 days following the initiation of selection.

first: Atilgan

last: Yilmaz

first: Ofra

last: Yanuka

first: Nissim

last: Benvenisty


title: RNA-binding Motif Protein RBM47 Promotes Tumorigenesis in Nasopharyngeal Carcinoma through Multiple Pathways

first: Jin-Xin

last: Bei

summary: ABSTRACT  RNA binding motif proteins (RBMs) have been widely implicated in the tumorigenesis of multiple human cancers, but scarcely studied in nasopharyngeal carcinoma (NPC). Here, we compare the mRNA levels of 29 RBMs between 87 NPC and 10 control samples. We find that RBM47 is frequently upregulated in NPC specimens and its high expression is associated with poor prognosis of patients with NPC. Biological experiments show that RBM47 plays an oncogenic role in NPC cells. Mechanically, RBM47 binds to the promoter and regulates the transcription of BCAT1 and its overexpression partially rescues the inhibitory effects of RBM47-knockdown on NPC cells. Moreover, transcriptome analysis reveals that RBM47 regulates alternative splicing of pre-mRNA, including those cancer-related, to a large extent in NPC cells. Furthermore, RBM47 binds to hnRNPM and cooperativelyjointly regulates multiple splicing events in NPC cells. In addition, we find that knockdown of hnRNPM inhibits proliferation and migration of NPC cells. Taken together, our study shows that RBM47 promotes the progression of NPC through multiple pathways, acting as a transcriptional factor and a modulator of alternative splicing in cooperation with hnRNPM. Our study also highlights that RBM47 and hnRNPM could be prognostic factors and potential therapeutic targets for NPC.     Keywords  RBM47, BCAT1, Alternative splicing, hnRNPM, Nasopharyngeal Carcinoma (NPC)

overall_design: We performed transcriptome sequencing of NPC cells to identify RBM47-regulated genes and alternative splicing events.

first: Xiaochen

first: Jinxin

first: Chunling


title: Spatial transcriptomics reveals increased energetic requirements underpinning age-dependent declines in digit regeneration rescued through administration of OAA

city: Dallas

first: Robert

last: Tower

address: 5323 Harry Hines Blvd

institute: UTSW

summary: De novo limb regeneration after amputation is restricted in mammals to the distal digit tip. Central to this regenerative process is the blastema, a heterogeneous population of lineage-restricted, dedifferentiated cells that ultimately orchestrates the regeneration of the amputated bone and surrounding soft tissue. To investigate skeletal regeneration, we made use of spatial transcriptomics to characterize the transcriptional profile specifically within the blastema. Using this technique, we generated a gene signature with high specificity for the blastema in both our spatial data, as well as other previously published single-cell RNA-sequencing transcriptomic studies. To elucidate potential mechanisms distinguishing regenerative from non-regenerative healing, we applied spatial transcriptomics to an aging model. Consistent with other forms of repair, our digit amputation mouse model showed a significant impairment in regeneration in aged mice. Contrasting young and aged mice, spatial analysis revealed a metabolic shift in aged blastema associated with an increased bioenergetic requirement. This enhanced metabolic turnover was associated with increased hypoxia and angiogenic signaling, leading to excessive vascularization and altered regenerated bone architecture in aged mice. Restoration of this metabolic deficiency using the metabolite oxaloacetate enhanced in vivo bone regeneration. Thus, targeting cell metabolism may be a promising strategy to mitigate aging-induced declines in tissue regeneration.

overall_design: Digits from young (age 6 months) and aged (age 18 months) mice were harvested 10 days after amputation of the distal 1/3 of the P3 phalangeal element. For OAA treatment, aged mice were treated with OAA daily starting at day 10 post amputation and sacrificed at day 21.

first: Mimi

last: Sammarco


title: DNAseq analysis of a genome-wide loss-of-function CRISPR/Cas9 library in haploid human embryonic stem cells transfected with a methylated construct containing the FXS-related mutation upstream to an EGFP reporter gene

summary: The primary mechanism causing Fragile X syndrome (FXS) is the expansion and silencing of a repetitive CGG sequence in the 5’-UTR of the FMR1 gene. To identify novel epigenetic pathways involved in FXS pathogenesis, we have established a model system for FMR1 silencing using a construct containing the FXS-related FMR1 CGG expansion upstream to an EGFP reporter gene. This construct was methylated in vitro and introduced into a genome-wide loss-of-function (LOF) library established in haploid human pluripotent stem cells. Library cells were then sorted to GFP-positive and GFP-negative populations. The analysis of the changes in abundance of mutants between the GFP-positive and GFP-negative populations has yielded a list of candidate genes whose functional loss reversed the methylation-induced silencing of the expanded FMR1 5'-UTR sequence.

overall_design: For the genome-wide screen, we used a CRISPR/Cas9 based genome-wide loss-of-function library of haploid hESCs, which contains 178,896 different gRNA constructs, targeting 18,166 genes. Library cells were transfected with the in-vitro methylated pFMR1-CGG(240)-EGFP constuct. 48 hours following transfection with methylated pFMR1-(240)CGG-EGFP construct, library cells were harvested and sorted to GFP-positive and GFP-negative populations. The abundance of different gRNAs represented in both populations was assessed by the amplification of the sgRNA-containing genomic DNA segment and high throughput sequencing. Following the mapping of the reads to the sgRNA sequences, an enrichment score was assigned to each gene by calculating the log2 fold change of its sgRNA counts between GFP-positive populations (n=4) and the GFP-negative population (n=3) using the EdgeR software.


title: Integrative Pharmacology Powers the Active Components Detection and Mechanism Exploration of Wang Bi Granules Acting on Rheumatoid Arthritis

city: Beijing

last: Wu

address: No. 16, Nei Nanxiao Street, Dongzhimen, Dongcheng District

institute: Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences

summary: Wang Bi Granule (WBG), composed of 16 botanical drugs and 1 animal drug, is clinically used to treat “Wang Bi” syndrome, which mainly refers to later rheumatoid arthritis (RA) in modern medicine, as well as ankylosing spondylitis, tuberculous arthritis, and Kashin-Beck disease characterized by joint pain and swelling deformation. However, its chemical composition and pharmacological mechanisms have not been clarified. Therefore, in the present study we aimed to characterize the chemical components of WBG and explore its mechanism in treating RA using integrative pharmacology, including chemical composition detection, efficacy evaluation, and mechanism exploration. We employed UPLC-QTOF-MS/MS to describe the chemical profile of WBG, TNF-α-stimulated RAW264.7 cells to simulate inflammatory process of RA and evaluate the anti-inflammatory effect of WBG, and network pharmacology to mine the mechanism of WBG acting on RA. As a result, a total of 278 chemical components were identified or tentatively characterized and the water extract of WBG improved the imbalance of inflammation by regulating 179 differential genes in RAW264.7 cells induced by TNF-α. 55 key active constituents were obtained based on the interactions among “components’ targets, RA-related genes, and differential genes (WBG vs TNF-α group)”, which may ameliorate RA conditions by regulating 161 hub genes that mainly involved in inflammation-immune related pathways. The present study, for the first time, employed integrative pharmacology to characterize the chemical profile of WBG and reveal its mechanism against RA through inflammation-immune regulation system.

overall_design: Based on RAW264.7 cells (mouse origin), blank group, induction group (inflammatory factors), WBG group and and want to obtain differentially expressed genes among each group, and further analyze the mechanism of drug efficacy

first: Jia

last: XU

first: Hong

last: CHEN

first: Xiaofang

last: Deng

first: Ping

last: WANG


title: Analysis of gastrocnemius muscle from chow-fed control and UCP1 knockout rats at room temperature and after exposure to 4 degrees Celsius

city: Baton Rouge

first: Jaycob

last: Warfel

state: Louisiana

address: 6400 Perkins Road

department: RNA Homeostasis

institute: PBRC

summary: To determine the transcriptomic effects of cold exposure on skeletal muscle gene expression in rats with and without UCP1, we assessed gastrocnemius muscle in chow-fed control and whole body UCP1 knockout rats using RNA-seq.

overall_design: Gastrocnemius muscles were dissected from 7 male control and 9 male UCP1 knockout rats. Total RNA was prepared using Trizol, RNA concentration was determined usign a nanodrop UV spectrophotometer, and 500ng RNA per sample was given for sequencing library construction.

first: Bolormaa

last: Vandanmagsar

last: Noland

first: Randall

last: Mynatt

first: Sujoy

last: Ghosh

first: Susan

last: Newman

first: Richard

last: Carmouche

first: Claudia

last: Kruger

first: J

last: Salbaum


title: Plasmodium-specific atypical memory B cells upregulate markers of activation and co-stimulatory molecules indicative of cellular interaction with T cells in response to a febrile malaria infection in children and adults.

city: Hamilton

first: Sarah

last: Anzick

state: MT

address: 903 South 4th Street

department: Research Technologies Branch

institute: National Institute of Allergy and Infectious Diseases

summary: In naturally acquired immunity to malaria, antibodies that reliably protect are only acquired after years of repeated Plasmodium falciparum (Pf) infections. We have shown in Mali that this inefficiency in humoral immunity to malaria is associated with a large expansion of CD21loCD27- ‘atypical’ B cells (atBCs). The function of atBCs remains elusive, as they exhibit altered B cell receptor (BCR) signaling and when activated fail to secrete cytokines and antibodies. We set out to study the participation and function of malaria-specific atBCs during the immune response to a febrile malaria infection. Here, we show in a Mali cohort spanning infants to adults, that atBCs frequencies within the malaria and influenza-specific MBC compartment are comparable to the overall atBC frequency, showing that atBCs are not predominantly expanded within Pf-specific B cells.  We performed a transcriptional analysis of Pf- and influenza-specific atBCs, actBC and MBCs and show that CXCL16, IL-6, IL-10, TNFα, IL12R and IL12R are uniquely upregulated in Pf-specific atBCs. Comparative transcriptomic and flow cytometric analysis before and after an acute malaria infection showed that after malaria, Pf-specific atBCs are transcriptionally most like the actBC subset, sharing many common features, such as activation of intracellular signaling pathways and expression of high levels of T-bet, FcRL5, Ki67 and CD86.  Unique to Pf-specific atBCs was an upregulation of IL-5RA, CD38, CXCR3, TLR7, 9 and 10 after a febrile malaria episode. Our data shows that atBCs exhibit a surface marker profile that could facilitate cellular interaction with T cells in secondary lymphoid tissues.

overall_design: Using B cell probes as previously described (Hopp et al., 2021), malaria- and influenza-specific B cells were detected in ex vivo flow cytometry of cryopreserved PBMCs obtained from children residing in the malaria endemic village of Kalifabougou, Mali, a study site that has previously been described in detail (Tran et al., 2013).  Malaria transmission in Mali is highly seasonal and PBMCs were collected at the end of the 6-month dry season in May (healthy baseline) and one week after treatment (convalescence) of the first febrile malaria episode in the ensuing 6-month malaria season. To glean insight into the function of the atypical B cell lineage, we performed a transcriptomic analysis of antigen-specific B cell subsets. Pf- and HA- specific IgD- CD10- B cells were bulk sorted from 16 Malian malaria-exposed individuals, into atBC, actBC and MBC subsets at healthy baseline from malaria.  Transcriptome libraries were generated from a total of 73 samples using the SMART-Seq v4 Ultra low Input RNA kit (Takara).  To understand how atBCs functionally respond to an acute febrile malaria episode, we performed transcriptomic analysis of antigen-specific B cell subsets obtained from the same 16 donors after their first acute febrile malaria episode that followed the healthy baseline timepoint of the previous analysis. Transcriptome libraries were generated from 91 samples.

first: Christine

last: Hopp

first: Jeff

last: Skinner

first: Chris

last: Tipton

first: Shanping

last: Li

first: Safiatou

last: Doumbo

first: Kassoum

last: Kayentao

first: Aissata

last: Ongoiba

first: Boubacar

last: Traore

first: Craig

last: Martens

first: Peter

last: Crompton


title: Mouse gut and human gut xenograft - PBS control vs Lipopolysaccharide (LPS) treated raw sequence reads

city: Coventry

first: Nigel

middle: Paul

last: Dyer

address: Gibbet Hill Road

country: United Kingdom

institute: University of Warwick

summary:
Background: Gastrointestinal symptoms in COVID-19 patients suggests that the gut may present a viral target organ. Disease development and severity is dependent on viral interaction with two cell surface human proteins, ACE2 and TMPRSS2, and on antiviral response which may lead to systemic hyperinflammatory syndrome and multiorgan dysfunction
Understanding the host response to SARS-CoV-2 infection and the pathology of the disease will be greatly enhanced by the development of appropriate animal models. However, the virus does not grow in wild type mice and only induced mild disease in transgenic animals expressing human ACE2.
Results: As there are known differences between immune response in laboratory mice and humans, the response of human gut developed as xenografts and host mouse gut following systemic LPS injections as a hyperinflammation model system was evaluated. Gene set enrichment analysis of significantly upregulated human and mouse genes revealed that a number of inflammatory and immune response pathways are commonly regulated in the two species. However, species differences were also observed.
The analysis shows that the intestinal immune response to inflammation in humans and mice are generally very similar. However, certain human-specific diseases, such as COVID-19, can only be successfully studied in an experimental model of human tissue, such as the gut xenograft

overall_design: mRNA expression profiles of mouse gut with human gut xenografts after varying LPS treatments

first: Lorna

last: Morris

first: Einat

last: Nisim-Eliraz

first: Iftach

last: Schouten

first: François

last: Bergey

first: Hiroshi

last: Momiji

first: Eilam

last: Nir

first: Noga

last: Marsiano

first: Raheleh

last: Tezerji

first: Simcha

last: Yagel

first: Philip

last: Rosenstiel

first: David

last: Rand

first: Vitor

last: Martins dos Santos

first: Nahum

last: Shpigel


title: Single cell RNA sequencing reveals myeloid-biased hematopoiesis and pro-inflammatory state in TLR9-/- bone marrow

first: Peng

last: Ding

address: No.600, Yishan Road

department: Orthopaedics

institute: Shanghai Jiao Tong University Affiliated Sixth People’s Hospital

summary: The TLR9-/- mice had more myeloid cells and progenitors and fewer B cells in the bone marrow. Activity of Fos and Cebpb, important mediator of myelopoiesis, in the cluster of HSPCs were increased. PU.1 and Fos, critical transcription factors mediating osteoclastogenesis, were upregulated in monocyte progenitors. In addition to myeloid biased hematopoiesis in TLR9-/- mice, there were upregulated levels of inflammatory cytokines in the TLR9-/- bone marrow.

overall_design: Bone marrow mononuclear cells from 2 wildtypes and 2 TLR9-/- mice were profiled in two independent experiments (each experiment included samples from 1 wildtype and 1 TLR9-/- mice).

first: Yao

last: Chen

first: Ding

last: Peng


title: Differentiated expression of ceRNA (circRNA, lncRNA, and mRNA) in PBMCs (peripheral blood mononuclear cells) of healthy controls and AD (atopic dermatitis) patients

first: Lan

last: Yang

address: 1838 North Guangzhou Street

department: Department of Plastic and Aesthetic Surgery

institute: Nanfang Hospital of Southern Medical University

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

summary: The changed ceRNA expression in PBMCs of healthy controls and AD patients.

overall_design: To determine ceRNA transcribed in PBMCs of healthy controls and AD patients, respectively, and analyze the differences between the groups, we have employed a ceRNA microarray (Agilent) as a discovery platform. Four subjects for each group (Normal, AD).

first: Yufeng

last: Zhou


title: Ecdysoneless protein regulates viral and cellular mRNA splicing to promote cervical oncogenesis

city: Omaha

first: Jordan

last: Rowley

state: NE

address: 3828 Jones St, Apt 202

institute: University of Nebraska Medical Center

summary: The high-risk subgroup of Human papilloma viruses (HPVs), exemplified by HPV16/18, are causally linked to human cancers of the anogenital tract, skin, and upper aerodigestive tract.  The high-risk HPV oncoproteins E6 and E7 are expressed from a polycistronic transcript that can potentially give rise to alternatively spliced E6 mRNAs, a process important for E6 and E7  expression and oncogenic transformation. Previously, we identified ECD, the human homologue of the Drosophila ecdysoneless gene, as a novel HPV16 E6-interacting protein using Yeast two-hybrid system. Here, we show that the C-terminal region of ECD selectively binds to high-risk but not to low-risk HPV E6 proteins. We demonstrate that ECD is overexpressed in HPV+ as well as HPV- cervical and head and neck patient tumor samples. Using the TCGA dataset, we show that ECD mRNA overexpression predicts shorter survival in these cancer patients.  Recent work from our laboratory showed that ECD associates with several components of RNA biogenesis/splicing machinery and are involved in mRNA export. Here, we show that ECD is an RNA binding protein and regulates mRNA splicing. RNAseq analyses of SiHa cells upon ECD knockdown (KD) revealed alterations of many cellular pathways with prominent downregulation of components of the mRNA splicing machinery. Further investigation revealed that ECD KD resulted in dysregulation of E6 RNA splicing, resulting in decreased E7 and increased RB protein. Furthermore, ECD KD dysregulated several cellular mRNAs known to be critical for HPV oncogenesis. Finally, we demonstrate that while ECD KD in cervical cancer cell lines led to a reduction in oncogenic traits, ECD overexpression together with E7 led to the immortalization of keratinocytes. Taken together, our results support a novel role of ECD in transcription and in viral and cellular mRNA splicing to support HPV-driven oncogenesis.

overall_design: ECD role in viral and cellular splicing

first: Sameer

last: Mirza

first: Achyuth

last: Kalluchi

first: Mohsin

last: Raza

first: Irfana

last: Saleem

first: Bhopal

last: Mohapatra

first: Aniruddha

last: Sarkar

first: Kishor

middle: K

last: Bhakat

first: Shrabasti

last: Roychoudhury

first: Dhananjaya

last: Pal

first: Subodh

last: Lele

first: Michel

last: Ouellette

first: Fang

last: Qiu

first: Lulu

last: Yu

first: Alexis

last: Lobanov

first: Zhi-Ming

last: Zheng

first: Ying

last: Zhang

first: Mansour

last: Alsaleem

first: Emad

last: Rakha

first: Hamid

last: Band

first: Vimla


title: Multi-omics analysis of myelodysplastic syndromes resistance to epigenetics threrary reveals PI3K/Akt activation mediated by epigenetic silencing of PTEN and epi-transcriptional silencing of MDM2 [transcriptome]

city: Pokfulam

first: Rita

middle: Lok Hay

last: Yim

address: Room 311, 3rd Floor, Professorial Block, Queen Mary Hospital,

department: Department of Medicine

country: Hong Kong

institute: Hong Kong University

summary: Myelodysplastic syndrome (MDS) is a clonal myeloid neoplasm characterized by ineffective haematopoiesis and cytopenia with frequent epigenetic modifications. Hypomethylating agents (HMA) such as azacitidine (AZA) and decitabine (DEC) are standard therapeutic options in MDS, but drug resistance is not uncommon. Herein, multi-omic analysis is used to identify signaling pathways during MDS HMA resistance using MDS cell line P39 and validated in P39 and Kasumi-1. The Illumina Infinium Methylation EPIC BeadChip (850k) was used for comparison of P39-AZA-S and P39-DEC-S (control group) and P39-AZA-R and P39-DEC-R (resistant group). Sampple was prepared following the manufacturer protocol and final chip imaging was performed on Illumina iScan System (Illumina). Bioinformatic analysis of Methylation EPIC data utilized the Illumina GenomeStudio Methylation module V2011. Only CpG sites passed quality controls were filtered and normalized for differential methylation calculation.

overall_design: Resistant cell line of MDS and AML was derived from HMA Azacytidine or Decitabine.

first: Paul

last: Lee

first: Harinder

last: Singh Gill


title: CRISPR Knockout Screen to Identify Mechanisms of Rescue of DDX41-deficient Hematopoietic Progenitors

city: Cincinnati

first: Kwangmin

last: Choi

state: Ohio

address: 333 Burnet Avenue

department: Experimental Hematology & Cancer Biology

institute: Cincinnati Children's Hospital Medical Center

summary: DDX41 is essential for the survival and proliferation of mouse hematopoietic progenitor cells (HPC). To identify mechanisms to rescue the survival of DDX41-deficient HPC, we conducted a genome-wide CRISPR Knockout Screen in DDX41-deficient and wild-type mouse bone marrow lineage-negative cells.

overall_design: Lineage-negative BM were harvested from wildtype or Ddx41-floxed mice expressing Cas9 from one Rosa locus and Cre-ERT from the other Rosa locus. The cells were transduced with the Brie lentiviral CRISPR library and allowed to proliferate in liquid culture for 5 days. The surviving cells were harvested and their DNA was isolated in order to identify the gRNA that were over and under-represented in DDX41-deficient cells compared to control cells.

first: Daniel

middle: T

last: Starczynowski

first: Timothy

last: Chlon


title: Multi-omics analysis of myelodysplastic syndromes resistance to epigenetics threrary reveals PI3K/Akt activation mediated by epigenetic silencing of PTEN and epi-transcriptional silencing of MDM2

type: Methylation profiling by high throughput sequencing

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Multi-omics analysis of myelodysplastic syndromes resistance to epigenetics threrary reveals PI3K/Akt activation mediated by epigenetic silencing of PTEN and epi-transcriptional silencing of MDM2 [methylome]


title: Multi-omics analysis of myelodysplastic syndromes resistance to epigenetics threrary reveals PI3K/Akt activation mediated by epigenetic silencing of PTEN and epi-transcriptional silencing of MDM2 [epitranscriptome]

summary: Myelodysplastic syndrome (MDS) is a clonal myeloid neoplasm characterized by ineffective haematopoiesis and cytopenia with frequent epigenetic modifications. Hypomethylating agents (HMA) such as azacitidine (AZA) and decitabine (DEC) are standard therapeutic options in MDS, but drug resistance is not uncommon.To study RNA modification in particular M6A, P39-AZA-S and P39-AZA-R native RNA libraries were prepared using the direct RNA sequencing kit (Oxford Nanopore) following the manufacturer’s protocol (SQK-RNA002). Differential methylated RNA signal called from raw fast5 files were used as input for basecalling and downstream mapping and methylated transcript detection.


title: Single Cell RNA sequencing of the Dendritic Cells from controls and pulmonary arterial hypertension (PAH) patients

city: Sunnyvale

first: Xin

last: Zhou

state: CA - California

address: 3165 Porter Drive

department: Department of Genetics

institute: Stanford University

summary: We report the application of single cell RNA sequencing on human dendritic cells. By using the negative selecting kit, we enriched theconventional DC from human PBMCs. The seven samples are sequenced as biological replications (4 control and 3 patients), and pooled at the analysis stage. The library was prepared using the Chromium Single Cell 3' v2 Reagent Kit, and sample processing was under bcl2fastq2/2.20.0 and cellranger/2.2.0. We report a increased cDC1 to cDC2 ratio, and an increased inflammatory DC in PAH patient, with the major changes of CXCR4 expression which are experimentally confirmed. This study provide a reference for studying the DC related abonormalties in PAH and other inflammatory diseases.

overall_design: Four control samples and three patient samples are barcoded for sequencing in the same flowcell on Illumina HiSeq-4000 platform. For each sample, 2000 alive cells are used as input.

first: Marlene

last: Rabinovitch

first: Michael

last: Snyder

first: Toshie

last: Saito


title: HyperTRIBE Analysis for DDX41 in human leukemia cells

summary: In HyperTRIBE analysis, a hyperactive mutant of the catalytic domain of ADAR enzyme is fused to an RNA-binding protein of interest in order to identify RNAs that are bound by the protein interest through RNA-sequencing (Rahman et al Nat Protoc. 2018). By discovery of RNAs where adenosines have been edited to iosines, the RNAs that were bound by the protein of interest and then edited by ADAR are identified genome-wide.  We conducted this analyis for DDX41, an RNA Helicase protein with multiple described cellular functions, including RNA splicing and innate immune sensing. Because DDX41 mutations have been discovered in leukemia patients, this analysis was conducted in the human lyeloid leukemia cell line THP-1.

overall_design: DDX41 was fused to the hyperactive catalytic domain of ADAR by cloning and this fusion protein was expressed from the pGK-GFP retrovirus in THP-1 cells. Cells transduced with empty retrovirus or retrovirus containing the ADAR hyperactive catalytic domain alone were used as  controls. The cells were allowed to grow for one week post-transduction and then were harvested for total RNA.

last: Starczynwoski


title: Gene expression profiling of newly diagnosed plasma cell leukemia patients included in the HOVON129 clinical trial

city: Rotterdam

first: Mark

last: van Duin

address: Wytemaweg 80

institute: Erasmus MC

summary:
This gene expression set contains data from patients included in the HOVON129 clinical trial. Using this data the relation between a signature identifying patients with aggressive biology and clinical parameters was studied in newly diagnosed plasma cell leukemia patients.
This dataset was used to identify the relationship between a signature for aggressive disease and clinical parameters in plasma cell leukemia.

overall_design: 57 samples were analysed, which were taken from 29 individual patients. Samples were derived from bone marrow aspirates and peripheral blood samples, which were subjected to enrichment of PCL cells using CD138 specific beads.  RNA sample workup was performed according to the instructions for use of the MMprofilers at the SkylineDx reference lab (SkylineDx, Rotterdam, The Netherlands). Samples were hybridized to Affymetrix HG-U133 plus2 chips, using Affymetrix Inc. (Santa Clara, CA)  3' IVT PLUS reagents. All samples passed wet lab and data QC acceptance criteria. Gene expressions were MAS5.0 normalized (values below 30 were truncated) with a target value of 1500.

first: Rowan

last: Kuiper

first: Davine

last: Hofste op Bruinink

first: Annemiek

last: Broijl

first: Tom

last: Cupedo

first: Niels

last: van de Donk

first: Pieter

last: Sonneveld


title: Next generation sequencing  of  human cholangiocarcinoma cells and associated stem-like component

city: Firenze

first: Matteo

last: Ramazzotti

address: viale Morgagni 50

department: Experimental and Clinical Biomedical Sciences

institute: University of Florence

summary: The goal of this study is to provide a global transcriptome profiling (RNA-seq) of stem-like subset in human cholangiocarcinoma (CCA).   Functional enrichment of CCA stem-like subset was performed by 3D sphere culture (SPH) in CCA cell lines. Comparison to parental CCA cells grown as 2D monolayer is provided.

overall_design: mRNA profile of 3D cholangio-spheres (SPH) compared to parental 2D monolayer (MON) cells of 4 different cholangiocarcinoma cell lines

first: Fabio

last: Marra

first: Chiara

last: Raggi

first: Clelia

last: Peano

first: Margherita

last: Correnti


title: Gene expression profiling by RNA-seq of newly diagnosed multiple myeloma patients included in the HOVON95 clinical trial

summary: This gene expression set contains data from patients included in the HOVON95 clinical trial. Using this data the technical comparison between microarray and RNAseq was made.

overall_design:
Circulating tumor cells are a known prognostic factor in multiple myeloma. However, the causes of high circulating tumor cells have been insufficiently characterised. This study aimed to identify factors involved in high circulating tumor cell count, using a model to correct for important contributing factors to this phenotype, which is closely associated with aggressive disease. To validate that the gene expression patterns identified in microarray data were similar in RNAseq data, the current set of RNAseq data was used. In addition, this RNAseq dataset is part of the Horizon2020 MMpredict study, and was in part funded using European funding from MMpredict.
Raw data not provided due to patient privacy concerns.

last: Hofste Op Bruinink

first: Jasper

last: Koenders


title: Gene expression profiling by RNA-seq of newly diagnosed multiple myeloma patients included in the HOVON143 clinical trial

summary: This gene expression set contains data from patients included in the HOVON143 clinical trial. Using this data the relation between circulating tumor cells and gene expression patterns was studied in newly diagnosed multiple myeloma patients.

overall_design:
Circulating tumor cells are a known prognostic factor in multiple myeloma. However, the causes of high circulating tumor cells have been insufficiently characterised. This study aimed to identify factors involved in high circulating tumor cell count, using a model to correct for important contributing factors to this phenotype, which is closely associated with aggressive disease. This set was used to validate the relation between circulating tumor cells and gene expression patterns.

*** Submitter states that raw data cannot be deposited in GEO due to patient privacy issues ***

first: Sonja

last: Zweegman