title: Synergistic Anti-Leukemic Effect Of Trc105 And Decitabine In AML Xenografts

city: Minneapolis

first: Alessandro

last: Magli

state: MN

address: 2231 6th St SE

department: Medicine

institute: University of Minnesota

summary: Acute myeloid leukemia (AML) is an aggressive hematologic malignancy, often characterized by poor prognosis following standard induction therapy. The DNA methyltransferase inhibitor decitabine (DAC) is an alternative to intensive chemotherapy in elderly and relapsed/refractory AML patients. Despite some efficacy, DAC monotherapy does not promote complete remission and overall survival rates are very poor. Therefore, novel therapeutic regimens for AML are warranted. CD105 (endoglin), a receptor for the TGF-β superfamily, is expressed in various hematopoietic malignancies, including AML in which high expression correlates with poor prognosis. We have recently demonstrated that targeting CD105+ AML blasts with the TRC105 monoclonal antibody abrogates leukemogenesis in vivo. Based on these encouraging findings, here we investigated whether TRC105 in combination with DAC could represent a novel therapeutic option to treat relapsed/refractory AML. Treatment of leukemic mice with DAC in combination with TRC105 resulted in superior survival and significant reduction of leukemia burden in the bone marrow (BM) of AML xenografts compared to DAC monotherapy. To determine if TRC105 anti-leukemogenic effect is mediated by NK cells, we performed in vitro and in vivo studies. In the latter, we tested TRC105 in the context of NK depletion by injecting mice with an antibody to CD122. TRC105 treatment resulted in comparable reduction of leukemia burden in xenografts regardless of NK depletion, demonstrating that the anti-leukemogenic effect of TRC105 in AML is independent of NK cells. Altogether, our findings provide proof-of-principle for the clinical evaluation of TRC105 in combination with DAC in AML patients.

overall_design: Human CD45+ cells were isolated from the bone marrow of AML-xenografts models treated with TRC105 (anti-human CD105 antibody) or IgG control. Transcriptomic analysis was performed by isolating total RNAs followed by library generation and sequencing.

first: June

last: Baik

first: Rita

last: Perlingeiro


title: Transcriptomic response in gills of gilthead sea bream (Sparus aurata) fed garlic, carvacrol and thymol essential oils (EOs) additive

status: Public on Oct 27 2020

city: Santiago

first: Felipe

middle: E.

last: Reyes-López

state: Santiago

address: Av. Libertador Bernado O'Higgins 3363

country: Chile

institute: Universidad de Santiago de Chile

summary: Explore the underlying mechanisms-of-action of the essential oils diet in gills of gilthead seabream.

overall_design: Transcriptomic analysis was conducted in gilthead sea bream (S. aurata) gills fed control standard diet or an experimental diet containing 0.5% inclusion of a microencapsulated additive composed of a blend of garlic, carvacrol, and thymol synthetic essential oils during 65 days (n=8 per dietary treatment; N total=16 fish) in order to determine the differences on gene expression level between these two dietary strategies at gill-specific level. The experimental design included two conditions: (1) fish fed basal diet with no EOs added (control); (2) fish fed 0.5% inclusion of the EOs additive. Total RNA were extracted invidually and then total RNA samples were grouped into 3 pools of 4 fish for each condition. The transcriptomic analysis was done following a reference design using the control diet group as reference.

first: Joana

middle: P

last: Firmino

first: Eva

middle: C

last: Vallejos-Vidal

middle: E

first: Enric

last: Gisbert


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Diabetic db/db Mice Islets Transcriptomes

status: Public on Oct 28 2020

city: Guangzhou

first: Liting

last: Wu

address: Zhongshan Road 2

department: Department of Endocrinology and Metabolism

country: China

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

type: Expression profiling by high throughput sequencing

type: Non-coding RNA profiling by high throughput sequencing

summary: Circular RNAs constitute an extensive fraction of the mammalian transcriptome.In this study, circular RNAs dysregulated in the islets of diabetic db/db mice were identified by high-throughput RNA sequencing. More than 5000 circRNAs were detected using RNA sequencing, indicating that circular transcripts were abundant in islets. Among them, we found that circ-Tulp4 showed significant downregulation in diabetic mouse islet cells. Further experiments indicated that modulating the expression of circ-Tulp4 in β cell lines desensitized β-cells to lipotoxicity.

overall_design: Islet circRNAs and mRNA profiling in db/db and db/m control mice were generated  by deep sequencing, in triplicate, using Illumina Hiseq.

first: Li

last: Xiong


title: MiRNA-mediated regulation of Bmp2 during pathological calcification

city: Newark

first: Melissa

middle: B.

last: Rogers

state: NJ

address: 185 south orange ave.

department: Biochem. & Molec. Biology

country: USA

institute: Rutgers NJMS

summary:
Renal disease is a major risk factor for cardiovascular disease. BMP2 and its downstream effectors are strong implicators of pathological calcificatoin.
We profiled miRNAs from Klotho mutant mice and from health mice to determine any potential biomarkers for predicting the progression of pathological calcification through targeting of BMP2 and its downstream effectors.

overall_design: 1908 miRNA levels measured from 19 mice.  Klotho homozygotes (Klkl/kl) exhibited the full phenotype with aortic calcification.  Control mice with the wild type (Kl+/+) or heterozygous (Kl+/kl) Klotho genotypes were healthy and indistinguishable.

first: Tapan

middle: A

last: Shah

first: Ying

last: Tang

middle: B


title: Suitability of formalin-fixed paraffin-embedded tumor tissue for unbiased tumor-associated antigen identification

city: Bern

first: Diana

last: Solis

address: Länggassstrasse 120

department: Vetsuisse Faculty

country: Switzerland

institute: The University of Bern

summary:
For the effectiveness of targeted immunotherapy, which is currently one of the most promising treatments for brain tumors, it is necessary to know specific tumor-associated antigens (TAA). This project aimed to validate the suitability of formalin-fixed and paraffin-embedded (FFPE) material instead of fresh-frozen material for RNA sequencing and downstream TAA identification.
Purpose: Detect potential oligodendroglioma-associated antigens using both fresh-frozen and FFPE brain tissues; assess the suitability of the FFPE material for TAA identification.
Results: A comparative analysis based on the RNA-seq of canine oligodendroglioma showed that formalin fixation of the samples had a significant effect on the RNA-seq library in terms of quality. Read distribution analysis showed that the FFPE samples contained fewer reads mapping to exonic regions and were enriched with reads mapped to introns and intergenic regions, while the fresh-frozen samples were mostly enriched in reads mapping to exons. Mismatch profile and SNVs calling analyses revealed some substitution artefacts present in the FFPE samples and absent in the corresponding fresh-frozen samples. However, according to the Principal Component Analysis, 36% of the variance between the samples could be explained by the types of conservation, while 43% of the variance could still be attributed to different expression profiles between oligodendroglioma and control conditions. A differential expression analysis of fresh-frozen oligodendroglioma versus fresh-frozen control samples identified 62 potential TAA strongly up-regulated in tumor tissue. The same analysis using the FFPE samples showed 80% of these genes (49/62) also to be differentially expressed. Comparative analysis showed good agreement between FFPE and fresh-frozen RNA-seq libraries in terms of the accuracy of gene expression measurements indicating that archived FFPE tissue can be used for identification of TAA candidates by RNA-seq providing a wealthy source of clinical samples for research. The following 10 genes encoding cell surface proteins have been identified by both approaches as potential TAA candidates based on their strong overexpression in oligodendrogliomas: PDGFRA, NOTCH1, DLL1, GPER1, TNR, IQGAP3, CD44, ERBB3, BCAS1 and ROR2. Future projects still need to investigate their suitability as TAA for targeted immunotherapy.
Conclusion: Formalin fixation of the samples had a significant impact on the RNA-seq quality in terms of the accuracy of gene expression measurements, as well as the quality of the nucleotide sequences. Nevertheless, the comparative analysis showed good agreement between FFPE and fresh-frozen RNA-seq libraries.

overall_design: Differential expression analysis between canine oligodndroglioma and healthy brain tissue. Comparative analyses between FFPE RNA-seq and fresh-frozen RNA-seq.

first: Vidhya

last: Jagannathan

first: Anna

last: Oevermann


title: Examining Sex Differences in the Human Placental Transcriptome During the First Fetal Androgen Peak

city: Stanford

first: Amy

middle: Elizabeth

last: Braun

state: California

address: 300 Pasteur Dr., Grant Building, S365

department: OBGYN

institute: Stanford

summary: Sex differences in human placenta exist from early pregnancy to term. However, it is unclear whether these differences are driven solely by sex chromosome complement or are subject to differential sex hormonal regulation. Here, we survey the human chorionic villus (CV) transcriptome for sex-linked signatures from 11 to 16 gestational weeks, corresponding to the first window of increasing testis-derived androgen production in male fetuses.

overall_design: 12 male and 11 female chorionic villus biopsies

first: Braun

last: Amy E

first: Muench

last: Kristin L

first: Robinson

last: Beatriz G

first: Wang

last: Angela

first: Palmer

last: Theo D

first: Winn

last: Virginia D


title: Plasma microRNA levels in male and female children with cystic fibrosis

city: Dublin

first: Catherine

last: Mooney

address: Belfield

department: School of Computer Science

country: Ireland

institute: University College Dublin

summary: A gender gap exists in cystic fibrosis (CF). Here we investigate whether plasma microRNA expression profiles differ between the sexes in CF children. microRNA expression was quantified in paediatric CF plasma (n=12; six females; Age range:1-6; Median Age: 3; 9 Phe508del homo- or heterozygotes) using TaqMan OpenArray Human miRNA Panels. Principal component analysis indicated differences in male versus female miRNA profiles. The miRNA array analysis revealed two miRNAs which were significantly increased in the female samples (miR-885-5p; fold change (FC):5.07, adjusted p value: 0.026 and miR-193a-5p; FC:2.6, adjusted p value: 0.031), although only miR-885-5p was validated as increased in females using specific qPCR assay (p < 0.0001). Gene ontology analysis of miR-885-5p validated targets identified cell migration, motility and fibrosis as processes potentially affected, with RAC1-mediated signalling featuring significantly. There is a significant increase in miR-885-5p in plasma of females versus males with CF under six years of age.

first: C

first: P

middle: J

last: McKiernan

first: R

last: Raoof

first: D

last: Henshall

first: B

last: Linnane

last: McNally

first: A

middle: M

last: Glasgow

last: Greene


title: RING1B recruits EWSR1-FLI1 and cooperates in the remodelling of chromatin necessary for Ewing sarcoma tumorigenesis [ChIP-Seq]

city: Barcelona

first: Enrique

last: Blanco

address: Dr. Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

country: Spain

institute: Center for Genomic Regulation (CRG)

type: Genome binding/occupancy profiling by high throughput sequencing

summary: EWSR1-FLI1 genome reprogramming through remodeling of enhancers is determinant for Ewing sarcoma (ES) tumorigenesis. We describe a non-canonical function of RING1B, a PRC1 subunit highly expressed in primary ES tumors, co-localizing genome wide with EWSR1-FLI1 in active enhancers. While retaining its repressive canonical activity, we find RING1B as necessary for the expression of key EWSR1-FLI1 activated targets like NKX2-2, SOX2 or IGF1 where it mainly exerts a role in promoting oncogene recruitment to enhancers. Knockdown of RING1B is sufficient to impair growth of tumor xenografts and expression of EWSR1-FLI1 induced neomorphic enhancers in vivo. Restoration of RING1B ubiquitin ligase activity by the AURKB inhibitor AZD1152 decreases expression of RING1B/EWSR1-FLI1 common targets. Overall, our findings demonstrate RING1B as a critical modulator of EWSR1-FLI1 induced chromatin remodeling.

overall_design: ChIPseq for RING1B (2 replicates), INPUT for RING1B (2 replicates), H2Aub1 (2 replicates) and INPUT for H2Aub1  (2 replicates). ChIPseq for BMI1, CBX7, EWSR1-FLI1 and INPUT (1 replicate). ChIPseq for RING1B, EWSR1-FLI1 and INPUT (shCTRL and shRING1B conditions).

first: Sara

last: Sanchez


title: RING1B recruits EWSR1-FLI1 and cooperates in the remodelling of chromatin necessary for Ewing sarcoma tumorigenesis

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

overall_design: Refer to individual Series


title: Transcriptional response of A. thaliana Root and Shoot tissue to light stress and presence of microbial communities in myc2-3 and MYC2-Flag lines

city: Cologne

first: Thorsten

last: Thiergart

address: Carl-con-Linne-Weg 40

country: Germany

institute: MPIPZ cologne

summary: MYC2 is a central node controlling the crosstalk between JA and other phytohormone signalling pathways and regulating responses to light and circadian clock. We hypothesized that this transcription factor might coordinate prioritization of microbiota-induced growth over defense under suboptimal light conditions

overall_design: Combination of two different conditions were tested (in myc2-3 plants and MYC2-Flag plants), a) absence/presnece of microbes and b) normal condition and low PAR condition. Respectively in plant Roots (n= 2x12 samples) and Shoots (n= 2x12 samples)

first: Shiji

last: Hou

first: Stephane

last: Hacquard


title: Gene expression analysis of adult lung ILC2s

city: Vancouver

first: Maryam

last: Ghaedi

state: BC

address: 675 West 10th Avenue

department: Terry Fox Laboratory

country: Canada

institute: BC Cancer Agency

summary: To fully characterize the heterogeneity and gene expression profile of mouse lung ILC2s, we generated RORα lineage tracer mice by crossing RoraIRES-Cre (Chou et al., 2013) and R26R-EYFP mice, which have a loxP-flanked stop sequence followed by the gene encoding yellow fluorescent protein (YFP) in the ROSA26 locus. In these RORα-YFP mice, cells expressing Rorα during their development should be irreversibly labeled by YFP. Flow cytometric analyses of lymphocytes in RORα-YFP mice showed that innate lymphoid cells type 2 (ILC2s) were marked by YFP expression. However, both adult and neonatal lung Lin−YFP+ cells were heterogeneous and included not only ILC2s (GATA-3+Thy1+) but also GATA-3−Thy1− and GATA-3lowThy1+ cells. In order to fully assess the lung ILC2 heterogeneity, we analyzed all CD45low/+Linlow cells from adult (6-week-old) and neonatal (12-day-old) RORα-YFP mouse lungs by droplet-based scRNA-seq. Unsupervised clustering of the cells revealed distinct clusters of stromal, B, T, NK cell, DC and ILC2 based on their expression of well-characterized marker genes. We then isolated the ILC2 cluster and performed a second round of unsupervised clustering to examine the existence of possible ILC2 subsets. In both adult and neonatal datasets, ILC2s were divided into subsets with each subset expressing a distinct set of ILC2-associated genes. We validated the existence of distinct ILC2 subsets in adult and neonatal lungs using flow cytometry. We also comprehensively assessed the genes that were specifically and/or differentially expressed by ILC2s compared to other immune and non-immune cell populations in our datasets. This analysis revealed the expression of well-characterized ILC2 genes such as Gata3, Rora, Areg and Il7r as well as other genes with potential immune regulatory functions.

overall_design: Examination of adult lung ILC2 heterogeneity specific gene expression profile.

first: Fumio

last: Takei


title: Transcriptome imformation of Nannochloropsis under phosphate deprivation

city: Beijing

first: Ying

last: Shi

address: Chengfu Road, Haidian District

department: College Of Engineering

institute: Peking University

summary: In our study, we modified the proportion of macroelements in f/2 medium, thus Nannochloropsis. oceanica can produce double total fatty acid (TFA) and septuple triacylglycerol (TAG) under phosphate deprivation (PD) with no significant changes in biomass, and no reduction in photosynthetic capacity during an earlier stage, to discover the molecular mechanisms of lipid product in Nannochloropsis. oceanica. IMET1 samples and study its relationship with other biochemical changes, the global gene expression of phosphate deprivation over time was determined by RNA sequence. Considering that the changes in gene expression after phosphate deprivation may be earlier than the changes in cellular compounds, 0, 6, 12, 24, and 48 hours were chosen as the time points for RNA-seq, and each time point was repeated three times.

overall_design: 15 samples are analyzed, each of them was paired with forward and reward sequence

first: Jin

last: Liu


title: Human Kupffer Cell Subsets Defined by CD32

city: Seattle

first: Xia

last: Wu

state: WA

address: 750 Republican St., E650

institute: University of Washington

summary: Human liver myeloid cells are imperfectly defined, but it is broadly agreed that cells of stellate appearance in situ, expressing the markers CD11b and CD68, are the liver’s resident macrophages, termed Kupffer cells. Recent investigations using single cell RNA sequencing and unsupervised clustering algorithms suggest there are two populations of cells with the characteristics of tissue macrophages in human liver. We therefore analyzed dissociated human liver tissue using the markers CD11b and CD68 to define Kupffer cells and found within this population two subsets that differ in their expression of multiple surface markers. These subsets were FACS-sorted based on CD32 expression, and gene expression analysis identified them with human liver myeloid cell subsets defined by two independent single cell RNA sequencing studies. These two subsets differed in the expression of genes associated with T cell activation and immunosuppression, suggesting distinct roles in T cell tolerance.

overall_design: TaqMan Real-time PCR Assays with fluidigm 48x48 array platform was used in gene expression profiling.  CD68+CD11b+CD32-mid or -high Kupffer cell subsets were purified from three separate human resected livers with purfusion techniques.  Genes enriched in CD68+CD11b+CD32-mid or -high Kupffer cell subsets were defined by two-fold or greater in abundance compared with the expression in total livers of the same subject.    Gene abundance was normalized with the arithmetic mean of ACTB, GAPDH and HPRT1.  Genes enriched in Kupffer cell subsets were further compared between CD32-mid and CD32-high subsets.

first: Ian

middle: N

last: Crispe


title: RING1B recruits EWSR1-FLI1 and cooperates in the remodeling of chromatin necessary for Ewing sarcoma tumorigenesis [RNA-seq]

summary: Analysis of differential expression profiles of tumors wild-type and RING1B knock-down

overall_design: SK-ES1 xenograft wild-type and knock-down for RING1B

last: Sánchez-Molina

first: Elisabet

last: Figuerola-Bou

first: María

last: Sánchez-Jiménez

first: Pablo

last: Taboas

first: Soledad

last: Gómez

first: Cecilia

last: Ballaré

first: Daniel

last: García-Domínguez

first: Estela

last: Prada

first: Lourdes

last: Hontecillas-Prieto

first: Ángel

last: Montero-Carcaboso

first: Óscar

last: Tirado

first: Inmaculada

last: Hernández-Muñoz

last: de Álava

first: Cinzia

last: Lavarino

first: Luciano

last: Di Croce

first: Jaume

last: Mora


title: Next Generation Sequencing Facilitates Quantitative Analysis of shNC/sh337/ and EV/337 Transcriptomes

city: Shanghai

first: Honggang

last: Xiang

address: No. 490, South Chuanhuan Road

department: Department of General Surgery

institute: Pudong New Area People’s Hospital affiliated to Shanghai University of Medicine & Health Sciences

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare PDAC cell  silencing or overexpressing linc00337 with control cells transcriptomse profiling (RNA-seq)
Methods: Retinal mRNA profiles of PANC1 stable cells(shNC and sh337) and AsPC1 stable cells (EV and 337) were generated by deep sequencing, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays
Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample and identified more than 20000 transcripts in each stable cell lines.
Conclusions: Our study illustrated the biological significance of linc00337 in PDAC progression.

overall_design: PDAC stable cell lines' mRNA profiles by deep sequencing, in triplicate, using Illumina Hiseq2000.

first: Huakai

last: Wang


title: Ileal gene expression signatures of piglets after PCV2 infection

first: Fengyang

last: Shi

address: No. 7 Beinong Road, Changping District

institute: Beijing University Of Agriculture

summary: To further study of pcv2-related diseases, we have employed whole genome microarray expression profiling as a discovery platform to identify ileal differentially expressed genes of piglets after pcv2 infection. Infected and uninfected piglets were sampled and analyzed by whole genome microarray expression profiling. The result showed 43603 differencially expressed genes in ileum after PCV2 infection. Expression of 11 genes (IL-1α, IL-1β, IL-6, IFNε, C5, C1QA, CCL4, CCL5, CCL25, CXCL9, CD163) from this signature was quantified in the same RNA samples by real-time PCR, confirming low variability between samples.

overall_design: The gene expressions of infection and control groups in induction and effector sites of ileum were measured at 21 days post infection. Three independent experiments were performed at each site of each group using different donors for each experiment.

first: Zhanming

last: Zou

first: Qiuming

last: Li

first: Huanrong


title: Effects of naloxone on NSC proliferation and differentiation

first: Lining

last: Liang

address: 190,Kaiyuan Ave.

institute: Guangzhou Institute of Biomedicine and Health,Chinese Academy of Sciences

summary: Naloxone is an opioid-receptor antagonist used to reverse the effects of opioid.In our study, we treated NSCs (neural stem cells) with naloxone and damgo (a selective μopioid receptor agonist), and examined their effects on NSCs proliferation and differentiation.Naloxone was found to promote NSCs  proliferation and  neural differentiation, while the effects of damgo was very week. The results suggested that naloxone may work indepedent of opioid receptors. To investigate the underlying mechanisms, RNA-seq was conducted. For proliferation analysis,p8 NSCs were cultured with or without naloxone or damgo for 3 days. For differentiation analysis,p8 NSCs was induced to differentiate with or without naloxone or damgo, samples on D2 were collected and analyzed.

overall_design: Samples cultured +/- naloxone (Nal) and damgo (Dam), and samples differentiated +/- naloxone and damgo on D2 were collected.

first: Jinlong

last: Chen

first: Hao

last: Sun

first: Hui

last: Zheng


title: RING1B recruits EWSR1-FLI1 and cooperates in the remodelling of chromatin necessary for Ewing sarcoma tumorigenesis [microarray]

first: Enrique

last: Blanco

overall_design: 8 samples were analyzed: A673_GI (n=2); A673_RI (n=2); ES_GI (n=2);  ES_RI (n=2);

first: Sara

last: Sanchez


title: Effect of LXR agonist T0901317 on the intestinal transcriptome in mice.

city: Groningen

first: vincent

last: bloks

department: Pediatrics

country: Netherlands

institute: UMCG

summary: Mice were treated for three days by oral gavage with the synthetic LXR ligand T0901317 (Cayman chemical, USA) using a dose of 50 mg/kg/day in vehicle (0.5% Carboxy-methylcellulose; 400 cPs (Sigma-Aldrich, USA); 0.2% Tween80 (Sigma-Aldrich, USA)) or solely the vehicle (control group). Mice were anesthetized with isoflurane and euthanized by cardiac puncture followed by cervical dislocation. Intestines were flushed with ice cold PBS and frozen in liquid nitrogen.

overall_design: 7 male mice (C57BL/6J): 4 vehicle and 3 T09 treated, RNAseq analysis of the duodenum

first: Irene

last: Zwarts

first: Vincent

middle: W

last: Bloks

first: Janine

middle: K

last: Kruit

first: Johan

last: Jonker


title: Simultaneous silencing of Aurora-A and UHRF1 inhibits colorectal cancer cell growth by regulating the expression of DNMT1 and STAT1

status: Public on Oct 26 2020

city: Xuzhou

first: Jing

last: Yang

state: Jiangsu

address: Room 519, Building A, The Department of Immunology, Xuzhou Medical University

institute: Xuzhou Medical University

summary: Aurora-A has attracted a great deal of interest as a potential therapeutic target. However, the outcomes of inhibitors targeting Aurora-A are not as favorable as expected, and the basis of their ineffectiveness remains unknown. Here, we found that signal transducer and activator of transcription 1 (STAT1) was highly expressed in colorectal cancer (CRC) xenograft mouse models that were resistant to alisertib, an Aurora-A inhibitor, in an interferon/Janus kinase-independent manner, suggesting an unconventional mechanism regulating STAT1 expression. Unexpectedly, we found that alisertib disrupted Aurora-A binding with ubiquitin-like with plant homeodomain and ring finger domain 1 (UHRF1), leading to UHRF1-mediated ubiquitination and degradation of DNA methyltransferase 1 (DNMT1), which in turn resulted in demethylation of the CpG islands in the STAT1 promoter and STAT1 overexpression. Simultaneous silencing of Aurora-A and UHRF1 prevented STAT1 overexpression and effectively inhibited CRC growth. Hence, concomitant targeting of Aurora-A and UHRF1 can be a promising therapeutic strategy for cancer patients.

overall_design: Control-treated xenografts and alisertib-treated xenografts were assayed for changes in genome-wide expression by using the Affymetrix GeneChip microarray (901838).

last: Han

first: Xin

first: Laili

last: Chu

first: Chennan

first: Rongqing

first: Zhen

last: Jiang

first: Xing

last: Ge

first: Junnian

first: Takayuki

last: Ikezoe


title: Expression data from BAX/BAK double knockout mouse embryonic fibroblast at baseline and following exposure to genotoxic stress.

status: Public on Oct 25 2020

city: New York

first: Emily

last: Cheng

state: NY

institute: Memorial Sloan-Kettering Cancer Center

summary: The BCL-2 family proteins are central regulators of apoptosis. However, cells doubly deficient for BAX and BAK or overexpressing BCL-2 still succumb to oxidative stress upon DNA damage or loss of matrix attachment. Our studies indicate a central role for the transcription factor deltaNp63alpha (referred to as p63 from this point forward) in this form of non-apoptotic cell death. We used microarrays to investigate gene expression in apoptosis-incompetent cells expressing a control vector or p63, at baseline and following exposure to genotoxic stress, to further elucidate molecular mechanisms regulating this type of non-apoptotic death and the role of p63 in this context.

overall_design: SV40 transformed BAX/BAK double knockout (DKO) mouse embryonic fibroblasts were transduced with retrovirus expressing GFP or p63, then were mock-treated or treated with etoposide (10 micrograms/ul) for 6 hours prior to harvesting of mRNA for analysis with Affymetrix GeneChip Mouse Gene 1.0 ST. Four samples are included: DKO GFP mock treated, DKO GFP etoposide treated, DKO p63 mock treated, and DKO GFP etoposide treated

first: Wang

middle: X

last: Gary

first: Tu

last: Ho-Chou

first: Dong

last: Yiyu

first: Skanderup

last: Anders

last: Yufeng

first: Takeda

last: Shugaku

first: Ganesan

middle: T

last: Yogesh

first: Han

last: Song

first: Liu

first: Hsieh

last: James

first: Cheng

middle: H

last: Emily


title: Molecular atlas of fetal and adult human liver sinusoidal endothelial cells: a F8 secreting cell [methylation I]

city: Bonn

first: Muhammad Ahmer

last: Jamil

state: NRW

address: Sigmund-Freud Str. 25

department: Institute of experimental haematology and transfusion medicine

institute: University Clinic Bonn

type: Methylation profiling by genome tiling array

summary:
In human F8 deficiency leads to hemophilia A and is largely synthesized and secreted by the sinusoidal endothelial cells of the liver (LSECs). However, the specificity and characteristics of these cells is not well known. In this study, we performed genome wide expression and CpG methylation profiling of fetal and adult human LSECs together with other fetal endothelial cells, from lung (micro-vascular and arterial), and heart (micro-vascular). Our results reveal plenty of expression and methylation markers distinguishing LSECs at both fetal and adult stages. Differential gene expression of fetal LSECs in comparison to other fetal endothelial cells pointed to several differential regulated pathways and functions in fetal LSECs. We used targeted bisulfite re-sequencing to confirm selected top differentially methylated regions. We further designed an assay where we used the selected methylation markers to test the degree of similarity of in house iPSs generated vascular endothelial cells to fetal and adult LSECs; a higher similarity was found to the fetal than to adult LSECs. Our molecular profiling study provides a guide to test the effectiveness of production of in vitro differentiated LSECs that could be used in cellular therapies.
In-silico analysis to identify molecular signature of liver sinusoidal endothelial cells in comparison to other endohtelial cells

overall_design: Commercial endothelial cells were ordered from ScienCell research laboratories via Provitro GmbH. All molecular materials were isolated at passage one as stated by manufacturing certificate.

first: Osman

last: El-Maarri


title: Genome-wide Sequencing Facilitates Quantitative Analysis of Wild Type and CRAF-/- cells

city: Kunming

first: Tian-Rui

last: Xu

address: No.727 South Jingming Rd., Chenggong District

institute: Kunming university of science and technology

summary: We utilized C-Raf-knockout cell model and carried out RNA-seq analysis of the global transcriptomes in wild-type and C-Raf-knockout cells treated with EGF, a potent activator of MAPK (Mitogen-activated protein kinase) pathway, or vehicle control.

overall_design: Wild-type and C-Raf-knockout HEK293T cells treated with EGF or vehicle control.

first: Tian

middle: R

first: Ying

last: Huang


title: Dissecting the epigenomic dynamics of human fetal germ cell development at single-cell resolution

first: Lin

last: Li

address: Shatai South Road

department: Pathophysiology

institute: Southern Medical University

type: Methylation profiling by high throughput sequencing

summary: The proper development of fetal germ cells (FGCs) is vital for genetic and epigenetic information transmission in generations. We have depicted the transcriptional landscape of distinct phases FGCs and the interaction between FGCs and gonadal niche cells. However, the epigenetic dynamics of sequential phases FGCs still remains in dimness. Here applied with single cell sequencing techniques (scBS-seq and scCOO-seq), we analyzed the genome-wide DNA methylation and chromatin accessibility map of female mitosis, meiotic prophase, and oogenesis FGCs, as well as male mitosis and mitotic-arrest FGCs.

overall_design:
In total, we analyzed 461 scBS-seq libraries and 362 scCOOL-seq libraries (including 44 FGCs with or without LDN treatment) from male ande female embryos.

Submitter declares that the raw data are being submitted to GSA (https://bigd.big.ac.cn/gsa-human/) due to privacy concerns.

first: Li

first: Qingqing

first: Fuchou

last: Tang


title: Molecular Analysis of Fetal and Adult Primary Human Liver Sinusoidal Endothelial Cells: A Comparison to Other Endothelial Cells


title: Context-dependent compensation among phosphatidylserine-recognition receptors

city: Charlottesville

first: Stephen

last: Turner

state: VA

address: 1670 Discovery Drive

institute: Signature Science, LLC

summary: Analysis of gene expression in RPE from Mertk KO, Mertk WT, Bai1-Tg+, and Bai1-Tg- mice. The hypothesis was that gene expression profile would differ with Mertk expression and Bai1-Tg expression.

overall_design: total RNA obtained from isolated retinal pigmented epithelial cells at 2 hours post light-onset from p14 female mice

first: Penberthy

last: Kristen

first: Rival

last: Claudia

first: Shankman

last: Laura

first: Raymond

last: Michael

first: Zhang

last: Jianye

first: Perry

last: Justin

first: Lee

last: Chang Sup

first: Onengut-Gumuscu

last: Suna

first: Palczewski

last: Krzysztof

first: Lysiak

last: Jeff

first: Ravichandran

last: Kodi


title: The levels of  human PDAC microRNAs’ expression in 10 patients with longest survival and 10 with shortest survival were selected

city: Shenyang

first: CE

address: Nanjing Street

institute: China Medical University

summary: MicroRNAs can be used in the prognosis of malignancies; however, their regulatory mechanisms are unknown, especially in pancreatic ductal adenocarcinoma (PDAC).From the 120 PDAC patients who underwent surgical resection, 10 patients with longest survival and 10 with shortest survival were selected. We found that high miR-29b-2-5p expression was associated with good prognosis (p=0.02). The validation cohort confirmed miR-29b-2-5p as an independent prognostic factor in PDAC (n=100, 95%CI=0.305-0.756, p=0.002).

overall_design: Among the 120 cases, 20 cases with similar clinicopathologic features and treatment but considerable different outcomes, composed the initial screening cohort for the miRNA microarray. What’s more, half of the patients had anextremely poor prognosis dying within the first year of diagnosis and were classified as “poor prognosis”, and the other 10 cases survived more than 21 months, which were classified as “good prognosis”.

first: Ce

first: Yun

last: Liu


title: Using a Zebrafish Model to Identify Cellular Responses to Uropathogenic E. coli Bacteremia

city: Indianapolis

first: Andrew

last: Schwaderer

state: IN

address: 1044 West Walnut Street

department: Pediatric Nephrology

institute: Indiana University School of Medicine

summary: Urinary tract infections (UTIs) are the second most common infections encountered in the pediatric population, second only to respiratory tract infections. UTIs are also a major cause of morbidity and mortality. UTIs can often ascend causing infection in the upper urinary tract or even progress to bacteremia or urosepsis. Urosepsis accounts for 10-30% of septic shock cases and Uropathogenic E.coli (UPEC) is responsible for almost 75% of cases. Therefore, increased understanding of the effects of urosepsis at the cellular and organ specific level will provide the foundation for improvements in clinical care.

overall_design: Two zebrafish cohorts were injected with either sterile saline or UPEC and subjected to scRNA-seq. Cell clusters were identified and subjected to RNA velocity analysis. Selected clusters relevant to the innate immune system and bactericidal activity underwent canonical pathway analysis. RNA velocity analysis revealed several key changes in the transcriptional state of UPEC infected cells and pathway analysis provided key information regarding changes in innate immune pathways within the cell clusters.

first: Ashley

last: Rawson

first: Vijay

last: Saxena

first: Hongyu

last: Gao

first: Jenaya

last: Hooks

first: Xiaoling

last: Xuei

first: Patrick

last: McGuire

first: Takashi

last: Hato

first: David

middle: S

last: Hains

first: Ryan

last: Anderson

middle: L


title: Disrupted mitochondrial function in aged human dermal fibroblasts

city: Mason

first: Joe

last: Sherrill

state: Ohio

address: 8700 Mason-Montgomery Rd

institute: Procter and Gamble

summary: Skin undergoes changes in structure and function with age, including a shift in metabolic programs.  This is particularly evident relative to mitochondrial function in skin cells.  Dermal fibroblasts have been known to accumulate damage caused by both external and internal stressors, leading to altered bioenergetics that limits efficient synthesis of ATP and NAD+.  To better understand the changes in mitochondrial function with age, metabolic profiles and transcriptomic profiles of primary dermal fibroblasts from varying aged donors were analysed.

overall_design: Primary dermal fibroblasts from 5 “young” (median age 24 ± 4.8 SD) and 5 “old” (median age 70.4 ± 15.8) Caucasian male donors were subjected to microarray profiling on the GeneTitan U219 array platform.

first: John

last: Oblong

first: Mark

last: Birch-Machin


title: Genome-wide expression profiling of nematode-trapping fungus Arthrobotrys oligospora ku70 and ste12 strains upon nematode exposure

status: Public on Oct 24 2020

city: Taipei

first: Yen-Ping

last: Hsueh

state: -- Select --

address: 128 Academia Road, Section 2, Nankang

department: Institute of Molecular Biology

country: Taiwan

institute: Academia Sinica

summary: We report the transcriptomic comparisions between ku70 control and ste12 mutant strains in nematode-trapping fungus Arthrobotrys oligospora when induced with nematodes. Fungal Ste12 transcription factor and the upstream MAPK cascade are highly conserved and plays a role in host sensing and pathogenesis in various fungal pathogens. Identification of Ste12-dependent in A. oligospora may provide further insights into the molecular mechanisms of nematode-sensing and trap morphogenesis. The reference assemly used for remapping is A. oligospora TWF154 (GenBank assembly accession: GCA_004768765.1)

overall_design: Examination of the transcriptional regulation controlled by Ste12 transcription factor upon nematode contact in Arthrobotrys oligospora

first: Sheng-An

last: Chen


title: RNA sequencing of NF-kB knockout (KO) U937 cells

city: Singapore

first: Vipin

last: Narang

address: Immunos #04-01, 8A Biomedical Grove, Singapore-138648

country: Singapore

institute: Singapore Immunology Network (SIgN)

summary: Transcription factors of NF-kB family play central roles in inflammatory responses. However, most of our current understanding on these factors are based on in vitro context specific studies and animal models, and human specific cellular and pathophysiological functions at molecular level are poorly understood. Here, we have designed a new oligomer based lentiviral pgRNAs-CRISPR-Cas9 knock-out (KO) approach and performed RNA-seq on 11 independent clones representing p50, p52, p65, c-REL and RELB KO cells to systematically study NF-kB family of transcription factors in monocytic cells U937, in steady and inflammatory state. Our analysis reveals factor-specific and common genes and pathways that are dysregulated in an inflammatory state. However, in a steady state respective KO clones showed specific transcriptional perturbations. Incorporating DNA-binding ChIP-ChIP information in the transcriptomic data uncovered enrichment of metabolic and leukemia associated pathways in p65-/- cells. Using acute myeloid leukemia (AML) patient’s data, metabolic, proliferation and xenograft models we showed an anti-leukemic functions of p65 which was mediated by metabolic plasticity and stemness.

overall_design: RNA sequencing was performed on a total of 28 samples representing untreated and LPS treated clones of U937 derived cells; Controls (CTR) (n=3) and NF-kB family of TFs knockout (KO), c-Rel-/- (n=2),  p50-/- (n=2), p52-/- (n=2), RELB-/- (n=2), p65-/- (n=3).

first: Dilip

last: Kumar

first: Amit

last: Singhal


title: MiRNA expression-based, individualized outcome prediction for surgically paired solitary and multiple leiomyoma with its corresponding myometrium

city: Chendu

first: Luqi

last: Xue

state: Sichuan

address: Renming road 3rd 20

institute: West China Second University Hospital

summary: MiRNA microarray analysis was performed on 12 tissues from surgical leiomyoma patients, including three pairs of solitary leiomyoma and its corresponding myometrium and three pairs of multiple leiomyomas and corresponding myometrium.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: MiRNA microarray analysis was performed on 12 tissues from surgical leiomyoma patients. Tissues of uterine leiomyomas and corresponding normal myometrium were collected from 6 women with symptomatic leiomyomas, who underwent operations at West China Second University Hospital (Chengdu, P.R. China), and were stored in liquid nitrogen immediately after surgeries. Among 6 patients, 3 were diagnosed with solitary leiomyoma and 3 were multiple according to surgical findings.Written informed consents were obtained from all patients, and the Institutional Review Board of West China Second University Hospital approved the study protocol.During tissue collection, eligible subjects and tissue specimens were defined as: 1) no GnRH-a or oral contraception used before surgery; 2) pathological diagnosis of leiomyoma; 3) no accompanying adenomyosis or endometriosis; 4) minimum number of leiomyomas involved in multiple leiomyomas was 5; and 5) leiomyomas intraoperatively revealed as multiple leiomyomas fused as one were excluded from solitary leiomyoma group. 6) SL was defined as one leiomyomas identified by both ultrasound and surgery findings. And the diameter of SL should be larger than 8cm.

first: Zhengyu

last: Li

first: Jia

last: Jia


title: Differences in loin tenderness of Iberian pigs explained through dissimilarities in their transcriptome expression profile

city: Zafra

first: María

middle: Muñoz

last: Muñoz

state: Badajoz

address: Centro I+D en Cerdo Ibérico, carretera Ex-101, km 4.7

institute: INIA

summary: Tenderness is one of the most important meat quality traits and it can be measured through shear force with Warner-Bratzler test. In the current study, we use RNA-seq technique to analyse the transcriptome of Longissimus dorsi (LD) muscle in two groups of Iberian pigs (Tough and Tender) divergent for shear force breeding values. We identified 200 annotated differentially expressed genes (DEGs) and 245 newly predicted isoforms. The RNAseq expression results of 10 genes were validated with qPCR. Functional analyses showed an enrichment of DE genes in biological processes related with proteolysis (CTSC, RHOD, MYH8, ACTC1, GADD45B, CASQ2, CHRNA9 and ANKRD1), skeletal muscle tissue development (ANKRD1, DMD, FOS and MSTN), lipid metabolism (FABP3 and PPARGC1A) and collagen metabolism (COL14A1). The upstream analysis revealed a total of 11 transcription regulatory factors that could regulate the expression of some DEGs. Among them, IGF1, VGLL3 and PPARG can be highlighted since they regulate the expression of genes involved in biological pathways that could affect tenderness. The experiment revealed a set of candidate genes and regulatory factors suggestive to search polymorphisms that could be incorporated in a breeding program for improving meat tenderness.

overall_design: Twelve Iberian individuals with divergent breeding values for tenderness were selected (six per group), samples of Longissimus dorsi were collected after the slaughter, RNA from these samples was extracted, pair-end libraries were constructed

first: Miguel

last: Fernández-Barroso

first: Carmen

last: Caraballo

first: Luis

last: Silió

last: Rodríguez

first: Yolanda

last: Núñez

first: Fernando

last: Sánchez-Esquiliche

first: Gema

last: Matos

first: Juan

last: García-Casco


title: Phospho-antibody microarray anayses for control and DG-LRG1 treated HUVEC cells.

city: Seoul

first: Yebin

last: Im

address: 504-302, 1, Gwanak-ro, Gwanak-gu,

department: Biological Sciences

country: South Korea

institute: Seoul National University

summary: Deglycosylated-leucine-rich α-2-glycoprotein1 (DG-LRG1) as well as LRG1 was discovered to promote angiogenesis under diabetes mellitus condition through TGF-β independent binding to endoglin. To examine the signaling pathways triggered by DG-LRG1, we subjected whole-cell protein lysates of control and DG-LRG1 treated HUVECs to a Phospho Explorer antibody array analysis using commercial antibody array assay kit (Full Moon Biosystems, Inc.). Samples were probed against 1318 site-specific and phospho-specific antibodies with two replicates per antibody printed on a coated glass microscope slide. Phospho Explorer antibody array experiments and analyses were performed as a custom service by E-Biogen (Ebiogen Inc., Seoul, Republic of Korea).

overall_design: HUVECs were serum-starved for 8 hours and then incubated with an anti-TGFβ1 antibody for 1 hour, after which HUVECs were stimulated with 1μg/ml DG-LRG1 for 30 minutes. Whole-cell lysates of control and DG-LRG1 treated HUVECs were prepared, and aliquots of lysates containing 50 μg of protein were used for Phospho Explorer antibody assays (Full Moon Biosystems, Inc.).

first: H

last: Kim


title: Targeting eIF4F Translation Initiation Complex with SBI-756 Sensitizes B Lymphoma Cells to Venetoclax

first: Robert

last: Schneider

address: 550 First Ave, MSB 238

department: Microbiology

institute: NYU School of Medicine

summary: Through the study of translation regulation, we identify the disruption of eIF4F assembly as a promising approach to enhance venetoclax efficacy in non-Hodgkin’s lymphoma.

overall_design: Examination of the translation effects of SBI-756 on a non-Hodgkin's lymphoma cell line.

first: Lee-or

last: Herzog

first: Beth

last: Walters

first: David

last: Fruman


title: IRAK1/4 and BET bromodomain inhibitions converge on NF-κB blockade and display synergistic antitumor activity in ABC-DLBCL with MYD88L265P mutation

city: Badalona

first: Gael

last: Roue

address: Ctra de Can Ruti, Camí de les Escoles s/n

department: Lymphoma Translational lab

institute: Josep Carreras Leukaemia Research Institute

summary:
Diffuse large B cell lymphoma cell lines of the activated B cell subtype (ABC-DLBCL) were treated for 6h with IRAK1/4 inhibitor (50µM) followed or not by a 18h exposure to 500 nM CPI203
We used microarrays to uncover the mechanisms underlying IRAKi+BETi activity in ABC-DLBCL

overall_design: Global RNA expression was done in three ABC-DLBCL cell lines treated in vitro with IRAKi (6h) +/- BETi (18h)

first: Yvan

last: Dlouhy

first: Gaël

last: Roué


title: The role of microglial lnc-U90926 in ischemic stroke

city: Nanjing

first: jian

last: chen

address: zhongshan road #321

department: Neurology

institute: Nanjing Drum Town hospital

summary: Dysregulated long non-coding RNAs (lncRNAs) have been shown to contribute to the pathogenesis of ischemic stroke. However, the potential role of lncRNAs in post-stroke microglial reactivation remains largely unknown. Here, we uncovered that lncRNA-U90926 was significantly increased in the microglia exposed to ischemia/reperfusion in vivo and in vitro. In addition, adenovirus associated virus (AAV)-mediated microglial U90926 silencing alleviated neurological deficits and reduced infarct volume in experimental stroke mice. Microglial U90926 knockdown could reduce the infiltration of neutrophils into ischemic lesion site, which might be attributed to the downregulation of C-X-C motif ligand 2 (CXCL2). Mechanistically, U90926 directly bound to malate dehydrogenase (MDH2) and competitively inhibited MDH2-mediated decay of CXCL2 mRNA. Taken together, our study demonstrated that microglial U90926 aggravated ischemic brain injury via facilitating neutrophil infiltration, suggesting that U90926 might be a potential biomarker and therapeutic target for ischemic stroke.

first: Jian

last: Chen


title: Analysis of sputum gene expression data in Asthma and COPD

city: Großhansdorf

first: Espen

middle: E

last: Groth

address: Wöhrendamm 80

department: Department of Pulmonology

institute: LungenClinic Grosshansdorf

summary: In addition to analyzing whole-genome methylation, we concomitantly evaluated sputum cell gene expression in the context of chronic inflammatory lung disease. Nucleic acids were purified from sputum samples of subjects with Asthma, COPD as well as healthy controls. Gene expression was analyzed on the Agilent Human GE 4x44k v2 platform.

overall_design: Induced sputum samples were sourced from the German cohort studies ALLIANCE and COSYCONET. We selected a total of 9 samples from non-smoking subjects with controlled (as indicated by Asthma Control Test score, ACT), eosinophilic/Type-2 Asthma (based on blood/sputum eosinophil counts). A total of 10 samples from subjects with COPD (>12 months after smoking cessation) as well as 10 samples from healthy controls (w/o any pulmonary or systemic-inflammatory disorder) were included in the analysis. Intentionally, we selected sputum samples that were stored/preserved in two different ways in order to explore effects on downstream analysis and simulate challenges in larger-scale biobanking studies (mainly regarding RNA quality in downstream transcriptome analysis): 1) storage in RLT lysis buffer (Qiagen) at -80 °C following sputum processing. 2) storage in HOPE medium (HEPES-glutamic acid buffer-mediated organic solvent protection effect; DCS innovative diagnostic systems, Hamburg, Germany) after sputum processing, followed by paraffin-embedding and storage at 4°C. Total RNA was extracted from the samples, amplified, labeled and hybridized to the Agilent Human GE 4x44k v2 array. Additionally, methylome analysis was performed on extracted DNA. From the initial sample pool, gene expression analysis was successfully performed on all Asthma samples as well as 7/9 COPD and 9/10 control samples. Downstream in silico analysis focused on methylation/transcription differences between Asthma/COPD and healthy controls, respectively. Information availbale about sputum differential cell counts (consisting of alveolar macrophages, neutrophils, eosinophils, lymphocytes, monocytes, ciliated cells and squamous cells) was used to implement and evaluate an in silico model correcting for variation in cell counts across disease conditions.

first: Thomas

last: Bahmer

first: Henrik

last: Watz

first: Frauke

last: Pedersen

first: Klaus

middle: F

last: Rabe

first: Ole

last: Ammerpohl

first: Torsten

last: Goldmann


title: The histone modification H3K27me3 and transcription factor MoGti1 coordinately control expression of effector genes in rice blast fungus

city: Athens

first: Zachary

middle: A

last: Lewis

state: GA

address: 1000 Cedar St. Biosciences Bldg

institute: University of Georgia

summary: Effector gene regulation by H3K27me3 and MoGti1

overall_design: Mycelial cultures collected at 5 days. Cells lysed and subjected to RNA extraction or chromatin immunoprecipitation. 48 total samples, replicates vary by sample.

first: Jie

last: Zhu

first: Abigail

last: Ameri

first: Peng

last: Qi

first: Katrien

last: Devos

first: Chang-Hyun

last: Khang


title: Transcriptomic study of single mutant hns and hns2 from enteroaggregative E. coli 042 by RNA-seq

city: Barcelona

first: Mario

last: Huttener Queiroz

address: Av. Diagonal 643

institute: Universitat de Barcelona

summary: Bacterial genomes encode in many instances more than one copy of genes coding for global modulators. The enteroaggregative E. coli strain 042 encodes, in addition to the hns and stpA genes, an additional hns-like gene, hns2. We have previously determined the patterns of the H-NS2 regulation in cells grown at 37ºC by using RNA-seq (see https://doi.org/10.1128/mSystems.00220-17). In this work, we used RNA-seq to compare the transcriptome of the wt strain and its hns and hns2 derivatives grown at 25ºC in LB medium.

overall_design: E. coli 042 and derivative mutants hns and hns2 mRNA profiles were generated by Illumina RNA-seq. RNA extraction, DNase treatment, evaluation of RNA quality and cDNA libraries for Illumina sequencing were performed by Vertis Biotechnologie AG, Freising-Weihenstephan, Germany. Bacterial cells were grown until O.D.600 of 2,0 in LB medium at 25ºC with 200rpm of agitation. Three replicates were grown from each strain, 1 ml of each replicate was collected and bacterial pellets were maintained at -80ºC. Bacterial pellets were sent to Vertis Biotechnologie AG, Freising-Weihenstephan, Germany in dry ice. E. coli 042 wt was used as genome reference (NC_017626 for the chromosome and NC_017627 for the pAA plasmid) for analysis.

first: A

last: Prieto

first: M

last: Hüttener

last: Juárez


title: Molecular atlas of fetal and adult human liver sinusoidal endothelial cells: a F8 secreting cell [methylation II]

first: Muhammad Ahmer

last: Jamil

address: Sigmund-Freud Str. 25

institute: University Clinic Bonn

summary:
In human F8 deficiency leads to hemophilia A and is largely synthesized and secreted by the sinusoidal endothelial cells of the liver (LSECs). However, the specificity and characteristics of these cells is not well known. In this study, we performed genome wide expression and CpG methylation profiling of fetal and adult human LSECs together with other fetal endothelial cells, from lung (micro-vascular and arterial), and heart (micro-vascular). Our results reveal plenty of expression and methylation markers distinguishing LSECs at both fetal and adult stages. Differential gene expression of fetal LSECs in comparison to other fetal endothelial cells pointed to several differential regulated pathways and functions in fetal LSECs. We used targeted bisulfite re-sequencing to confirm selected top differentially methylated regions. We further designed an assay where we used the selected methylation markers to test the degree of similarity of in house iPSs generated vascular endothelial cells to fetal and adult LSECs; a higher similarity was found to the fetal than to adult LSECs. Our molecular profiling study provides a guide to test the effectiveness of production of in vitro differentiated LSECs that could be used in cellular therapies.
In-silico analysis to identify molecular signature of liver sinusoidal endothelial cells in comparison to other endohtelial cells

overall_design: Commercial endothelial cells were ordered from ScienCell research laboratories via Provitro GmbH. All molecular materials were isolated at passage one as stated by manufacturing certificate.

first: Osman

last: El-Maarri


title: RNA differential expression induced after miR-491-5p transfection in human ovarian carcinoma IGROV1-R10 cells

status: Public on Oct 23 2020

city: Paris

first: Loredana

last: Martignetti

address: 26, rue d'Ulm

country: France

institute: Insitut Curie/ INSERM U900 / Mines Paris Tech

summary:
We were interested in understanding the cytotoxic effects induced by miR-491-5p in IGROV1-R10 cells
IGROV1-R10 cells are chemoresistant ovarian cancer cells - chemoresistance being main cause of therapeutic failure in this disease.

overall_design: Cells were transfected either with control miRNA or miR491-5p

first: Christophe

last: Denoyelle

first: Jean-Paul

last: Issartel


title: Analysis of sputum methylation data in Asthma and COPD

first: Espen

last: Groth

summary: We evaluated the applicability and usability of whole-genome methylomics of sputum samples in molecular profiling of chronic inflammatory lung diseases. Genomic DNA was purified from sputum samples of subjects with Asthma, COPD as well as healthy controls and analyzed on the Illumina Infinium HumanMethylation 450k platform.

overall_design: Induced sputum samples were sourced from the German cohort studies ALLIANCE and COSYCONET. We selected a total of 9 samples from non-smoking subjects with controlled (as indicated by Asthma Control Test score, ACT), eosinophilic/Type-2 Asthma (based on blood/sputum eosinophil counts). A total of 10 samples from subjects with COPD (>12 months after smoking cessation) as well as 10 samples from healthy controls (w/o any pulmonary or systemic-inflammatory disorder) were included in the analysis. Intentionally, we selected sputum samples that were stored/preserved in two different ways in order to explore effects on downstream analysis and simulate challenges in larger-scale biobanking studies (mainly regarding RNA quality in concomitant transcriptome analysis): 1) storage in RLT lysis buffer (Qiagen) at -80 °C following sputum processing. 2) storage in HOPE medium (HEPES-glutamic acid buffer-mediated organic solvent protection effect; DCS innovative diagnostic systems, Hamburg, Germany) after sputum processing, followed by paraffin-embedding and storage at 4°C. Genomic DNA was extracted from the samples, bisulfite converted and hybridized to the Illumina Infinium HumanMethylation450 BeadChip. Parallel transcriptome analysis was performed on extracted RNA. From the initial sample pool, methylation analysis was successfully performed on all Asthma and COPD samples as well as 7/10 control samples. Downstream in silico analysis focused on methylation/transcription differences between Asthma/COPD and healthy controls, respectively. Information availbale about sputum differential cell counts (consisting of alveolar macrophages, neutrophils, eosinophils, lymphocytes, monocytes, ciliated cells and squamous cells) was used to implement and evaluate an in silico model correcting for variation in cell counts across disease conditions.

first: Thomas

last: Bahmer

first: Henrik

last: Watz

first: Frauke

last: Pedersen

first: Klaus

last: Rabe

last: Ammerpohl


title: Gene expression of HUC model cells

city: Los Angeles

first: weibo

last: yu

address: Los Angeles

institute: UCLA

summary: HUC model includes three cell lines: HUC-BC, HUC-PC, and MCT11. They were all originally derived from human uroepithelium. However, three cell lines have different malignant potential. We here performed micro array to examine the differences in gene expression among three cell lines.

overall_design: Gene expression of HUC-BC, HUC-PC, MCT11, 4ABP treated HUC-BC, 4ABP treated HUC-PC, and 4ABP treated MCT11 were compared.

first: Weibo

last: Yu


title: Molecular atlas of fetal and adult human liver sinusoidal endothelial cells: a F8 secreting cell [expression array]

city: Bonn


title: Identify the master regulator of ILT3.Fc induced perturbation in Jurkat cells

city: New York

first: Zheng

last: Xu

state: New York

address: 630W 168th Street

department: Pathology

institute: Columbia University

summary: Generate gene expression profile of ILT3.Fc treated Jurkat cells

overall_design: Obtain RNA-Seq profile of ILT3.Fc treated Jurkat cells

first: Nicole

last: Suciu-Foca

first: George

last: Vlad

first: Aristidis

last: Floratos


title: Effects of Particulate Matter10 on RNA Expression in Lung Tissue of a Murine Model

city: seoul

first: heejae

last: han

address: dogokdong 146-92

institute: yonsei gangnam severance

summary: Inhalation of PM10 changed RNA expression in extensive range, and it also induced increase inflammatory cytokines, cellular inflammation, and fibrosis, in murine model.

overall_design: Female BALB/c mice were treated with PM10, ovalbumin (OVA), or both (OVA/ PM10). PM10 was intranasally administered four times over 2 weeks, and OVA was intraperitoneally injected on days 0 and 14, and then intranasally administered on days 21, 22, and 23. After 2 days from the last challenges, mice were sacrificed. Full RNA sequencing using lung homogenates was conducted. We analyzed three of them (control, PM10 treated and OVA and PM10 treated).

first: Hye

last: Park

first: Heejae

last: Han


title: ROS amplification drives mouse spermatogonial stem cell self-renewal

city: Kyoto

first: Hiroko

last: Morimoto

state: Kyoto

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

department: Graduate School of Medicine

country: Japan

institute: Kyoto University

summary: Reactive oxygen species (ROS) play critical roles in self-renewal division for various stem cell types. However, it remains unclear how ROS signals are integrated with selfrenewal machinery. Here we report that the MAPK14/MAPK7/BCL6B pathway creates a positive feedback loop to drive spermatogonial stem cell (SSC) self-renewal via ROS amplification. The activation of MAPK14 induced MAPK7 phosphorylation in cultured SSCs, and targeted deletion of Mapk14 or Mapk7 resulted in significant SSC deficiency after spermatogonial transplantation. The activation of this signaling pathway not only induced Nox1 but also increased ROS levels. Chemical screening of MAPK7 targets revealed many ROS-dependent spermatogonial transcription factors, of which BCL6B was found to initiate ROS production by increasing Nox1 expression via ETV5-induced nuclear translocation. Because hydrogen peroxide or Nox1 transfection also induced BCL6B nuclear translocation, our results suggest that BCL6B initiates and amplifies ROS signals to activate ROS-dependent spermatogonial transcription factors by forming a positive feedback loop.

overall_design: WT mouse germline stem cells (GS cells) infected Bcl6b knock down (KD) vector or Nox1 KD vector.  Mapk7 (ERK5) knock out (KO) mouse GS cells or Mapk14 (p38) KO mouse GS cells.

first: Mito

last: Kanatsu-Shinohara

first: Narumi

last: Ogonuki

first: Satoshi

last: Kamimura

first: Atsuo

last: Ogura

first: Chihiro

last: Yabe-Nishimura

first: Yoshifumi

last: Mori

first: Kinya

last: Otsu

first: Takshi

last: Shinohara


title: Gene expression changes of intraperitoneal tumor microenvironment after STING activation

city: Seongnam-si

first: Hannah

last: Yang

address: CHA Bundang Medical Center

institute: CHA Bundang Medical Center

summary: The results revealed dramatic differences between the STING-activated and Control tumors

overall_design: To elucidate the transcriptional changes upon STING activation, we used the Nanostring PanCancer panel to compare 750 immune microenvironment-related genes in RR-CDA-treated tumors in WT mice bearing periotneal tumors

first: Seung-Joon

last: Lee

first: Woo-Ram

last: Kim

first: Chan

first: Hong-Jae

last: Chon


title: Melanoma cell intrinsic GABAA receptor enhancement potentiates radiation and immune checkpoint inhibitor response by promoting direct and T cell-mediated anti-tumor activity

city: Cincinnati

first: Soma

last: Sengupta

state: OH

address: 3125 Eden Avenue

institute: University of Cincinnati

summary: Most metastatic melanoma patients show variable responses to radiotherapy and do not benefit from immune checkpoint inhibitors (ICIs). Improved strategies for combination therapy that leverage potential benefits from radiotherapy and ICI are critical. Genes coding for subunits of GABAARs express functional GABAARs in melanoma cells. By enhancing GABAAR mediated anion transport, benzodiazepines depolarize melanoma cells and impair their viability. In vivo, benzodiazepine alone reduces tumor growth and potentiates radiotherapy and α-PD-L1 anti-tumor activity. Combination of benzodiazepine, radiotherapy, and α-PD-L1 results in near complete regression of treated tumors and a potent abscopal effect, mediated by increased infiltration of polyfunctional CD8+ T cells. Treated tumors show expression of cytokine:cytokine receptor interactions and overrepresentation of p53 signaling. This study identifies an anti-tumor strategy combining radiation and/or immune checkpoint inhibitor with modulation of GABAARs in melanoma using a benzodiazepine.

overall_design: B16F10-GP mice were treated with radiation and/or Drug (QH-II-066). Mice receiving rdiation (5 Gy once) were irradiated on right flank only. Mice receiving Drug, QH-II-066 was delivered ip. Mice receiving 5 Gy and Drug were irradiated first and then received drug ip.

first: Daniel

middle: P

last: Krummel

first: Maxwell

last: Xu

first: Mario

last: Medvedovic


title: A FOXO-dependent replication checkpoint restricts proliferation of damaged cells

city: Leiden

first: Marten

last: Hornsveld

address: Einthovenweg 20

institute: Leiden University Medical Center

summary: DNA damage results in the activation of a transcriptional program that promotes DNA repair and stalls cell cycle progression. To determine which transcriptional programs are induced by replication stress, we determined the transcriptome of aphidicolin-treated RPE-1 cells.

overall_design: mRNA expression profile of RPE-1 cells treated with aphidicolin

first: Jern

last: van den Berg


title: LncRNA Mrhl orchestrates differentiation programs in mouse embryonic stem cells through chromatin mediated regulation

city: Bangalore

first: Manchanahalli

middle: Rangaswamy

last: Satyanarayana Rao

state: Karnataka

address: Jakkur, Bengaluru, Karnataka

department: Molecular Biology and Genetics Unit (MBGU)

country: India

institute: Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR)

summary: Earlier studies from our lab have characterized lncRNA Mrhl extensively in the context of male germ cell meiotic commitment and spermatogenesis, unraveling a negative feedback loop between Mrhl and a highly conserved context-dependant developmental pathway such as the WNT pathway. LncRNAs have been implicated for their functional roles in diverse developmental phenomena, cell fate specification events and differentiation of stem cells into various lineages. In purview of these, we aimed towards exploring lncRNA Mrhl and its functional relevance in mouse embryonic stem cells (mESCs) to understand its role in development and differentiation. Towards this end, we have addressed the targets of Mrhl in mouse embryonic stem cells. Our studies have revealed developmental processes, lineage specific transcription factors and lineage specific cell adhesion and receptor pathway genes to be majorly dysregulated upon Mrhl knockdown in mESCs with no perturbation in pluripotency status of the cells. This study has revealed context-dependant regulation of target genes by lncRNA Mrhl and implicated its role in regulating differentiation events in mESCs.

overall_design: Mouse ES cells were transiently transfected with either scrambled or sh-RNA against Mrhl and total RNA isolation was performed (DNase treated). Library preparation was done using TruSeq RNA sample prep kits (Illumina) as per the kit protocol. Control and shRNA samples were sequenced and analyzed in duplicates.

first: Debosree

last: Pal

first: Neha

middle: C

last: Venkata

first: Utsa

last: Bhaduri

first: C

last: Subbulakshmi

first: Satyanarayana

last: Rao


title: White adipose tissue resident macrophages are required for adipogenesis and energy storage.

city: La Jolla,

first: Inge

last: Holtman

state: California

address: 9500 Gilman Drive

department: CMM

institute: UCSD

summary: White adipose tissue (WAT) stores energy in the form of lipids. WAT macrophages cause adipose tissue inflammation and insulin resistance when intake exceeds expenditures, but their contribution to homeostasis remain poorly understood. Here, we show that two populations, ã and ä, of TNF-producing bone marrow-derived monocytic cells are transiently recruited to damaged adipocytes and mediate insulin resistance. In contrast, we identify α/β yolk-sac derived resident macrophages that produce adipogenic growth factors, and form a niche required for adipogenesis as white adipocytes do not differentiate in their absence. Production of adipogenic growth factors by α/β macrophages increases with lipid storage, but they do not contribute to inflammation. Thus the molecular identities and functions of resident macrophages and BM-derived cells are specified by their lineage rather than diet variation. These results identify an essential function of WAT resident macrophages in adipogenesis and energy homeostasis, separate from inflammation mediated by the recruitment of inflammatory leukocytes.

overall_design: 5 immune populations were isolated from mice that were on 10 % and 45 % fat diets

first: Lucile

last: Crozet

first: Christian

last: Jacome-Galarza

first: Elvira

last: Mass

first: Christopher

last: Glass

first: Frederic

last: Geissmann


title: MicroRNAs differential expression under submergence, drought and alternated stress in maize and teosinte

city: Tuxtepec

first: Blanca

middle: Estela

last: Barrera-Figueroa

state: Oaxaca

address: Av. Circuito Central 200

department: Instituto de Biotecnología

country: Mexico

institute: Universidad del Papaloapan

summary: In this work, we performed high throughput sequencing of small RNA libraries in maize (Zea mays ssp. mays) and teosinte (Zea mays ssp. parviglumis) to investigate the response mediated by miRNAs in these plants under control conditions, submergence, drought and alternated drought-submergence or submergence-drought stress. After Illumina sequencing of 8 small RNA libraries, we obtained from 16,139,354 to 46,522,229 raw reads across the libraries. Bioinformatic analysis identified 88 maize miRNAs and 76 miRNAs from other plants differentially expressed in maize and/or in teosinte in response to at least one of the treatments, and revealed that a larger set of miRNAs were regulated in maize than in teosinte in response to submergence and drought stress.

sample_organism:
Zea mays subsp. parviglumis
Zea mays subsp. mays

overall_design: MicroRNA expression profiling in the response to submergence, drought and alternated stress in maize and teosinte

first: E

middle: B

last: Sepúlveda-García

first: J

last: Pulido-Barajas

first: A

last: Huerta-Heredia

middle: M

last: Peña-Castro

first: R

last: Liu

first: B


title: S100A9 from tumor-associated macrophage enhances cancer stem cell-like properties of hepatocellular carcinoma

city: Guangzhou

first: Ran

last: Wei

state: Guangdong

address: Dongfengdong Road 651, Guangzhou

institute: Sun Yat-sen University Cancer Center

summary: Tumor-associated macrophages (TAMs) are crucial components of the tumor microenvironment (TME). They play vital roles in hepatocellular carcinoma (HCC) progression. However, the interactions between TAMs and HCC cells have not been fully characterized. In this study, TAMs were induced using human monocytic cell line THP-1 cells in vitro to investigate their functions in HCC progression. S100 calcium binding protein A9 (S100A9), an inflammatory microenvironment-related secreted protein, was identified to be significantly upregulated in TAMs. S100A9 expression in tumor tissues was associated with poor survival of HCC patients. It could enhance the stem cell-like properties of HepG2 and MHCC-97H cells by activating nuclear factor-kappa B (NF-κB) signaling pathway through advanced glycosylation end-product specific receptor (AGER) in a Ca2+-dependent manner. Furthermore, we found that, after treatment with S100A9, HepG2 and MHCC-97H cells recruited more macrophages via chemokine (C-C Motif) ligand 2 (CCL2), which suggests a positive feedback between TAMs and HCC cells. Taken together, our findings reveal that TAMs could upregulate secreted protein S100A9 and enhance the stem cell-like properties of HCC cells, and provide a potential therapeutic target for combating HCC.

overall_design: THP-1 cells were polarized into macrophages using PMA (Sigma, 100ng/ml) treatment for 24 hours. As for THP-1 derived TAM, THP-1 cells (2×106 cells) treated with PMA were placed on the lower chamber of a 6-well transwell plate. Meanwhile, HepG2 or MHCC-97H cells were placed on the 0.4μm porous membrane of upper chamber. After 24 hours, we co-cultured HepG2 or MHCC-97H cells with THP-1 derived macrophages. Then 48 hours later, macrophages were collected for RNA extraction. Next, we analyzed the differentially expressed genes in THP-1 cells-derived TAMs using whole genome expression profile analysis compared with THP-1 derived macrophages.

first: Xiu

last: Qin

first: Yang

middle: G

last: Yu


title: Identification of translational microRNA biomarker candidates for ketoconazole-induced liver injury using next-generation sequencing

city: Jefferson

first: Dongying

last: Li

state: AR

address: 3900 NCTR Rd

department: NCTR

institute: FDA

summary: Drug induced liver injury (DILI) is a leading cause of acute liver failure. Reliable and translational biomarkers are needed for early detection of DILI. microRNAs (miRNAs) have received wide attention as a novel class of potential DILI biomarkers. However, it is unclear how DILI drugs other than acetaminophen may influence miRNA expression or which miRNAs could serve as useful biomarkers in humans. We selected ketoconazole (KCZ), a classic hepatotoxin, to study miRNA biomarkers for DILI as a proof-of-concept for a workflow that integrated in vivo, in vitro, and bioinformatics analyses. We examined hepatic miRNA expression in KCZ-treated rats at multiple doses and durations using miRNA-sequencing and correlated our results with conventional DILI biomarkers such as liver histology. Significant dysregulation of rno-miR-34a-5p, rno-miR-331-3p, rno-miR-15b-3p, and rno-miR-676 was associated with cytoplasmic vacuolization, a phenotype in rat livers with KCZ-induced injury, which preceded the elevation of serum liver transaminases (ALT and AST). Between rats and humans, miR-34a-5p, miR-331-3p, and miR-15b-3p were evolutionarily conserved with identical sequences, whereas miR-676 showed 73% sequence similarity. Using quantitative PCR, we found that the levels of hsa-miR-34a-5p, hsa-miR-331-3p, and hsa-miR-15b-3p were significantly elevated in the culture media of HepaRG cells treated with 100 mM KCZ (a concentration that could induce cytotoxicity). Additionally, we computationally characterized the miRNA candidates for their gene targeting, target functions, and miRNA/target evolutionary conservation. In conclusion, we identified miR-34a-5p, miR-331-3p, and miR-15b-3p as translational biomarker candidates for early detection of KCZ-induced liver injury with a workflow applicable to computational toxicology studies.

overall_design: Male Sprague-Dawley rats (6-week old) were orally administered with ketoconazole (KCZ) at the low (10 mg/kg), middle (30 mg/kg), or high dose (100 mg/kg) per day for 3, 7, and 14 days, respectively. Rats treated with 0.5% methylcellulose (a vehicle for KCZ) for each of the three durations served as a corresponding control for that timepoint. Each treatment condition indicated a unique combination of a dose (control, low, middle, or high) and a timepoint (3, 7, or 14 days), totaling 12 conditions in this study. Rats were sacrificed and livers were collected 24 h after the final dosing.

first: Bridgett

last: Knox

first: Binsheng

last: Gong

first: Si

last: Chen

first: Lei

last: Guo

first: Zhichao

first: Weida

last: Tong

first: Baitang

last: Ning


first: Ivette

last: Zelaya

state: CA

address: 695 Young Drive South, Rm 1524 Gonda

institute: University of California, Los Angeles

summary: The objective of the study was to compare gene expression across SMA cases and postnatal controls in spinal cord, diaphragm and iliopsoas tissues. This dataset was used in the testing of the GENDULF algorithm.

overall_design: SMA cases and postnatal controls from spinal cord, diaphragm and iliopsoas tissues. A total of 5 SMA spinal cord cases, 4 spinal cord postnatal controls, 6 diaphramg SMA cases, 3 diaphragm postnatal controls, 5 iliopsoas SMA cases and 3 iliopsoas postnatal controls.

first: Charlotte

middle: J

last: Sumner

first: Daniel

last: Ramos


title: S100A9 from tumor-associated macrophage enhances cancer stem cell-like properties of hepatocellular carcinoma (RNA-Seq)

summary: Tumor-associated macrophages (TAMs) are crucial components of the tumor microenvironment (TME). They play vital roles in hepatocellular carcinoma (HCC) progression. However, the interactions between TAMs and HCC cells have not been fully characterized. In this study, TAMs were induced using human monocytic cell line THP-1 cells in vitro to investigate their functions in HCC progression. S100 calcium binding protein A9 (S100A9), an inflammatory microenvironment-related secreted protein, was identified to be significantly upregulated in TAMs. S100A9 expression in tumor tissues was associated with poor survival of HCC patients. It could enhance the stem cell-like properties of HepG2 and MHCC-97H cells by activating nuclear factor-kappa B (NF-κB) signaling pathway through advanced glycosylation end-product specific receptor (AGER) in a Ca2+-dependent manner. Furthermore, we found that, after treatment with S100A9, HepG2 and MHCC-97H cells recruited more macrophages infiltration via chemokine (C-C Motif) ligand 2 (CCL2), which suggests a positive feedback between TAMs and HCC cells. Taken together, our findings reveal that TAMs could upregulate S100A9 and enhance the stem cell-like properties of HCC cells, and provide a potential therapeutic target for combating HCC.

overall_design: we used a THP-1 cells-derived TAMs induction experiment system to induce TAMs(co-cultured with HepG2/MHCC-97H cells). The expression levels of TAM markers, IL-10 and CD206, were significantly increased in THP-1 cells-derived macrophages after co-culture with HepG2 cells or MHCC-97H cells. These indicate the successful induction of TAMs. Next, we analyzed the differentially expressed genes in THP-1 cells-derived TAMs using RNA-sequencing (RNA-seq) analysis.

first: Lun-Xiu

first: Wen-Wei

last: Zhu

first: Guang-Yang


title: Expression data between migrating keratinocytes in diabetic mice against normal mice during re-epithelialization 3 days post wounding

city: SINGAPORE

first: Mark

last: Tan

address: BLK 652 YISHUN AVE 4

institute: NTU

summary:
During re-epithelialization, keratinocytes have to undergo specific gene expression changes that grant them increased motility. Diabetic keratinocytes have been observed to portray an impairment in this aspect.
We used microarrays to identify the changes in the expression patterns of both normal and diabetic migrating keratinocytes during re-epithelialization.

overall_design: Wounds were harvested 3 days post wounding in diabetic and normal mice. Laser capture microdissection and microarray analysis was carried out on migrating keratinocytes as depicted by immunohistological staining of E-cadherin.

middle: W

first: Nguan


title: Analysis of putative transcription factor binding regions during natural aging in C. elegans

city: Seoul

first: Tae-Young

last: Roh

state: --- Select One ---

address: 52 Ewhayeodae-gil, Seodaemun-gu

department: Life Sciences

institute: Ewha Womans University

summary: To exmine the role of comibination of transcription factors in natural aging in C. elegans, we sequenced mRNA of CF512 adult worms at day 1, 5, 9, 13.

overall_design: Examination of mRNA levels in CF512 adult worms at day 1, 5, 9, 13 by deep sequencing

first: Seokjin

last: Ham

first: Mihwa

last: Seo

first: Chang-Pyo

last: Hong

first: Seonhye

first: Seongjae

middle: V

last: Lee


title: RNA sequencing results of dipyridamole treatment in SLC29A2-expressing SK-hep1 cells

city: Taipei

first: Roger

last: Shen

address: 128 Sec. 2, Academia Rd. Nankang

institute: Academia Sinica

summary: We observed an increasing trend of nuclear SLC29A2 expression associated with high histological de-differentiation grades, metastasis and poor patient prognosis by immunohistochemical analysis of HCC tumors. Treatments of dipyridamole to SLC29A2 expressing SK-hep1 cells reduced cell viability and cell migration. To examine the anticancer activities of dipyridamole, transcriptome analysis was performed to detect the modulations of oncogenic SLC29A2 and the downstream signaling pathways.

overall_design: Gene expression profiles of dipyridamole and/or sorafenib treatment in SLC29A2-expressing Sk-hep1 cells were generated by Illumina RNA sequencing and compared to profiles derived from mock control cells.

first: Yuh-shan

last: Jou


title: Nascent-seq data from DRB-treated/untreated human U2OS cell line

city: Beijing

first: huanwei

last: huang

address: 7 Science Park Rd., ZGC life science park

institute: NIBS

summary: Confluent U2OS cells were released to serum-free medium, and continued to grow for 36 h (Per2-dLuc peak) or 48 h (Per2-dLuc trough), then added DRB (10uM) treatment for 0.5, 1.5, 3.5 h, then added BrU (250uM) for 0.5 h, harvested total RNA, captured with anti-BrU antibody, and conduced hi-seq.

overall_design: To determine the global effect of low-dose DRB on gene transcription in human cells

first: Dapeng

last: Ju

first: Huanwei

last: Huang

first: Eric

last: Zhang


title: Critical Role for a Subset of Intestinal Macrophages in Shaping Gut Microbiota in Adult Zebrafish

city: Chapel Hill

first: Celia

last: Shiau

state: NC

address: 4344 Genome Sciences Building

institute: UNC Chapel Hill

summary: We conducted a whole genome transcriptome analysis to examine significant gene expression changes in the gut tissue of macrophage-deficient irf8 mutants compared with their heterozygous sibling guts.

overall_design: RNAseq dataset of mRNA libraries made from whole gut total RNA isolated from adult zebrafish: two irf8 heterozyous animals and two irf8 homozygous mutants.


title: Measuring gene expression in serially-evolved E. coli BW25113 strains in M9+glucose and M9+glucose+rifampicin

city: East Lansing

first: Sean

last: Crosson

state: Michigan

address: 567 Wilson Rd

department: Dept. Microbiology and Molecular Genetics

institute: Michigan State University

summary: We measured steady-state E. coli transcript levels in 1) a pykF(C8Y) mutant, 2) a rpoB(T1037P) mutant, and 3) five rifampicin-resistant rpoB mutant strains selected from each of these single mutants, in the presence and absence of rifampicin.

overall_design: E. coli strains were grown to mid-log phase (OD600 ~0.2) in M9 defined medium containing 0.4% glucose or 0.4% glucose + 7.5 micrograms/ml rifampicin. Cells were rapidly pelleted and resuspended in Trizol for RNA purification and subsequent RNA sequencing.

first: Thomas

last: Wytock

first: Manjing

first: Aetha

last: Fiebig

first: Adilson

last: Motter


title: An optimized protocol for retina single-cell RNA sequencing

city: Bethesda

first: Zachary

last: Batz

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

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

overall_design: Refer to individual Series


title: An optimized protocol for retina single-cell RNA sequencing [scRNA-Seq]

summary: In this work, we compared different protocols to prepare single-cell suspensions used for scRNAseq and suggest an optimized dissociation protocol for mouse retina, which preserves cell morphology to a higher level leading to an overall increase of gene number per cell. We compared scRNAseq libraries generated with our optimized protocol to publicly available scRNAseq data of mouse retina. We further demonstrate a pipeline to reduce noise in scRNAseq caused by multiplets and ambient RNA.

overall_design: Mouse retina were disected and dissociated using different protocols. Libraries were generated using 10x Genomics' "Chromium Single Cell Gene Expression" system. We compared cell suspensions, gene number per cell, level of ambient RNA and the overall gene detection rate within accross cell types and protocols.

first: Benjamin

last: Fadl

first: Anand

last: Swaroop

first: Laura

last: Campello


title: An optimized protocol for retina single-cell RNA sequencing [snRNA-Seq]


title: β-arrestin 2 as an activator of cGAS-STING signaling and target of viral immune evasion

status: Public on Oct 22 2020

city: Shanghai

first: Yihua

state: Shanghai

address: Fudan University

institute: Fudan University

summary: Virus infection may induce excessive interferon (IFN) responses that can lead to host tissue injury or even death. β-arrestin 2 regulates multiple cellular events through the G protein-coupled receptor (GPCR) signaling pathways. Here we demonstrate that β-arrestin 2 also promotes virus-induced production of IFN-β and clearance of viruses in macrophages. β-arrestin 2 interacts with cyclic GMP-AMP synthase (cGAS) and increases the binding of dsDNA to cGAS to enhance cyclic GMP-AMP (cGAMP) production  and the downstreatm stimulator of interferon genes (STING) and innate immune responses. Mechanistically, deacetylation of β-arrestin 2 at Lys171 facilitates the activation of the cGAS–STING signaling and the production of IFN-β. In vitro, viral infection induces the degradation of β-arrestin 2 to facilitate immune evasion, while a β-blocker, carvedilol, rescues β-arrestin 2 expression to maintain the antiviral immune response. Our results thus identify a viral immune-evasion pathway via the degradation of β-arrestin 2, and also hint that carvedilol, approved for treating heart failure, can potentially be repurposed as an antiviral drug candidate.

overall_design: Wild-type and Arrb2-/- peritoneal macrophages treated for 16 h with HSV-1 before they were lysed with RNAiso Plus according to the manufacturers’ instructions. The lysates were sent to Personalbio for cDNA library construction and sequencing by Illumina NovaSeq 6000.


title: Regulatory landscape of human stem cell-derived sinoatrial node-like pacemaker cells and ventricle-like cells

city: Amsterdam

first: Vincent

middle: M.

last: Christoffels

state: N/A (NA)

address: Meibergdreef 15  K2-159

department: Medical Biology

institute: Amsterdam UMC

summary: ATAC-seq revealed multiple pacemaker cell-specific accessible regions in the genome of pacemaker-like cells

overall_design: ATAC-seq on cultured pacemaker and ventricle-like cells

last: van Eif

first: Stephanie

last: Protze

first: Karel

last: van Duijvenboden


title: Role of H1 and DNA methylation in selective regulation of transposable elements during heat stress

city: Uppsala

first: Minerva

middle: Susana

last: Trejo Arellano

state: Uppsala

address: Almas Allé 5

department: Plant Biology

country: Sweden

institute: SLU

summary: Heat stressed Arabidopsis plants release heterochromatin-associated transposable element (TE) silencing, which however is not accompanied by major reductions of epigenetic repressive modifications. In this study, we explored the functional role of histone H1 in repressing heterochromatic TEs in response to heat stress. Loss of H1 caused activation of pericentromeric GYPSY elements upon heat treatment, despite that these elements remained highly methylated. In contrast, non-pericentromeric COPIA elements became activated concomitantly with loss of DNA methylation. The same COPIA elements became activated in heat-treated chromomethylase2 (cmt2) mutants, indicating that H1 represses COPIA elements through maintaining DNA methylation under heat. We discovered that H1 is required for TE repression in response to heat stress, but its functional role differs depending on TE location. Strikingly, H1 deficient plants treated with the DNA methyltransferase inhibitor zebularine were highly tolerant to heat stress, suggesting that both, H1 and DNA methylation redundantly suppress the plant response to heat stress.

overall_design: We generated and analyzed RNA and bisulfite-sequencing data of wild-type, h1, and cmt2 mutant seedlings before and after heat stress.

first: Shujing

last: Liu

first: Jennifer

last: De Jonge

middle: S

last: Trejo-Arellano

first: Juan

last: Santos-González

first: Claudia

last: Köhler

first: Lars

last: Hennig


title: Transcriptomic profiling of canine osteosarcoma and non-malignant bone

city: Nottingham

first: Nigel

last: Mongan

address: University Park

department: Biodiscovery Institute

country: United Kingdom

institute: University of Nottingham

summary: Dogs develop osteosarcoma (OSA) and the disease process closely resembles that of human OSA. OSA has a poor prognosis in both species and disease free intervals and cure rates have not improved in recent years. Gene expression in canine OSAs was compared with non-tumor tissue utilising next generation RNA sequencing. The data provides novel insights into the molecular mechanisms of OSA in high risk breeds. This knowledge may inform development of prevention and treatment for OSA in dogs and supports the dog as a model of OSA in people.

overall_design: Canine OSA tumor and non-tumor tissue was obtained from veterinary surgeons following surgical amputation or immediately following euthanasia. Confirmation of OSA diagnosis was confirmed by qualified pathologists via histopathological examination. A 1cm3 piece of tumor was extracted along with a 1cm3 piece of adjacent non-tumor affected bone tissue. These samples were placed directly into RNAlater® and shipped at room temperature and stored at -20°C. OSA tumor and matched adjacent non-tumor bone tissue samples were homogenized. and RNA extracted using Qiagen RNeasy Mini Kit (Qiagen, Germany) according to manufacturer’s instructions. The extracted RNA was stored at -80°C. RNA was quantified using both a NanoDrop 8000 (Thermo Fisher Scientific, USA), and an Agilent 2100 Bioanalyzer (Agilent, USA). RNAseq was completed at Edinburgh Genomics using an Illumina HiSeq platform. In all cases ~20 million reads were obtained from all samples analysed.

first: Catrin

last: Rutland

first: Mark

last: Dunning


title: Next Generation Sequencing Facilitates Quantitative Analysis of Acinetobacter baylyi ADP1 Transcriptomes under heavy metal-based NPs and ions exposure

city: Brisbane

first: Jianhua

last: Guo

address: Research Road, Level 4 Gehrmann Building

department: Australian Centre for Water and Environmental Biotechnology

country: Australia

institute: University of Queensland

summary: The goals of this study are to use Next-generation sequencing (NGS)to detect bacterial mRNA profiles of   Acinetobacter baylyi ADP1 in response to 0, 1 mg/L AgNPs or Ag ions, 1 mg/L CuO NPs or Cu ions, 10 mg/L ZnO NPs or Zn ions for 2 h, in triplicate, using Illumina HiSeq 2500.The NGS QC toolkit (version 2.3.3) was used to treat the raw sequence reads to trim the 3’-end residual adaptors and primers, and the ambiguous characters in the reads were removed. Then, the sequence reads consisting of at least 85% bases were progressively trimmed at the 3’-ends until a quality value ≥ 20 were kept. Downstream analyses were performed using the generated clean reads of no shorter than 75 bp. The clean reads of each sample were aligned to the E. coli reference genome (NC_000913) using SeqAlto (version 0.5). Cufflinks (version 2.2.1) was used to calculate the strand-specific coverage for each gene, and to analyze the differential expression in triplicate bacterial cell cultures. The statistical analyses and visualization were conducted using CummeRbund package in R (http://compbio.mit.edu/cummeRbund/). Gene expression was calculated as fragments per kilobase of a gene per million mapped reads (FPKM, a normalized value generated from the frequency of detection and the length of a given gene.

overall_design: Bacterial mRNA profiles of  Acinetobacter baylyi ADP1 in response to  0, 1 mg/L AgNPs or Ag ions, 1 mg/L CuO NPs or Cu ions, 10 mg/L ZnO NPs or Zn ions for 2 h, in triplicate, using Illumina HiSeq 2500

first: Ji

last: Lu


title: IL-10 prevents pathological microglia hyperactivation following peripheral endotoxin challenge

city: Brussels

first: Daliya

last: Kancheva

address: Pleinlaan 2

country: Belgium

institute: Vrije Universiteit Brussel

summary: Microglia, the resident macrophages of the brain parenchyma, are central players in CNS development, homeostasis and disorders. Distinct brain pathologies seem associated with discrete microglia activation modules. How microglia regain their ground state following challenges remains much less understood. Here, we explored the role of the IL-10 axis in restoring murine microglia homeostasis following peripheral endotoxin challenge. Specifically, we show that lipopolysaccharide (LPS)-challenged mice harboring IL-10 receptor-deficient microglia display neuronal impairment and succumb to fatal sickness. Addition of a microglial TNF deficiency rescues these animals, suggesting a microglia-based circuit driving pathology. Single cell transcriptome analysis revealed various IL-10 producing resident and recruited immune cell in the CNS, including most prominently Ly49D+ NK cells and neutrophils, but not microglia. Collectively, we define the kinetics of the microglia response to peripheral endotoxin challenge, including their activation and robust silencing, and highlight the critical role of non-microglial IL-10 in preventing deleterious microglia hyperactivation.

overall_design: sample of LPS treated whole brain + dura, sample of LPS treated whole brain + dura, sample of WT whole brain + dura

first: Anat

last: Shemer

first: Isabelle

last: Scheyltjens

first: Gal

middle: R

last: Frumer

first: Jung-Seok

last: Kim

first: Jonathan

last: Grozovski

first: Serkalem

last: Ayanaw

first: Bareket

last: Dassa

first: Hannah

last: Van Hove

first: Louise

last: Chappell-Maor

first: Sigalit

last: Boura-Halfon

first: Dena

last: Leshkowitz

first: Werner

last: Mueller

first: Nicola

last: Maggio

first: Kiavash

last: Movahedi

first: Steffen

last: Jung


title: Comparative global gene expression of primary neural progenitors and MEFs transdfferentiated with OCT4 and SOD2

city: Bangalore

first: Genotypic

last: technology

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

institute: Genotypic Technology

summary: To further validate the extent of transdifferentiated cells resembling the primary neural progenitor cells, the global gene expression analysisi was perfmred. Our preliminary qPCR showed the enrichment of neural genes , but not the endoderm or mesoderm lineage genes.

overall_design: Agilent Mouse Whole Genome 8x60k Microarray: AMADID: 028005

first: Smitha

last: Bhaskar

first: Preethi

last: Sheshadri

first: Anujith

last: Kumar


title: Sequencing Facilitates Quantitative Analysis of Wild Type and d5rf mutant Transcriptomes

city: Wuhan

first: Shaojuan

last: Zhang

state: Hubei

address: Shizishan Street, Hongshan District

department: College of Life Sciences and Technology

country: China

institute: Huazhong Agricultural University

summary: To gain insight into the biological role of D5RF in plants, we conducted a comprehensive survey of global gene expression employing high throughput-RNA sequencing to quantify the variations in transcript abundance between wild-type Columbia-0 (Col-0) and d5rf.

overall_design: mRNA expression profiles of 10 day old wild type (WT) and mutant d5rf

first: Meizhong

last: Luo


title: Genotyping of Infinium OmniZhongHua BeadChip from Illumina for haplotype construction

city: Bangkok

first: Monnat

last: Pongpanich

address: Phayathai Road

country: Thailand

institute: Chulalongkorn University

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary: SNP array using HumanOmniZhongHua-8 BeadChip showed that Thai haplotype containing the (TTTCA)n insertion region was found to be shared among all Japanese Chinese and Thai pedigrees.

overall_design: To genotype the Thai BAFME1 family members for haplotype construction and compared with Japanese and Chinese families.

first: Vorasuk

last: Shotelersuk


title: Conservation of global DNA methylation patterns due to cell culture establishment from human melanoma tissue

city: Dunedin

first: Aniruddha

last: Chatterjee

state: Otago

address: 270 Great king Street

country: New Zealand

institute: University of Otago

summary: Cell lines are a critical in vitro model and heavily used to unravel mechanisms of cancer cell biology. However, limited data is available to assess whether DNA methylation patterns in tissues are retained when cell lines are established. Here, we provide the first genome-scale sequencing-based methylation map of metastatic melanoma tumour tissues and their derivative cell lines.

overall_design: Here we generated single-nucleotide resolution DNA methylation map of a total of 4 cell lines using Reduced Representation Bisulfite Sequencing (RRBS). We show that globally DNA methylation profiles are well conserved in vitro compared to their tissue of origin.

first: Euan

last: Rodger

first: Peter

last: Stockwell

first: Micheal

last: Eccles


title: Inhibition  of O-GlcNAc transferase activates tumor-suppressor gene expression in tamoxifen-resistant breast cancer cells

city: Helsinki

first: Harri

last: Itkonen

address: Haartmaninkatu

country: Finland

institute: University of Helsinki

summary: In this study, we probed the importance of OGT activity for the survival of Tamoxifen-sensitive (TamS) and Tamoxifen-resistant (TamR) breast cancer cells. Tamoxifen is an antagonist of estrogen receptor (ERα), a transcription factor expressed in over half of all breast cancers, and the defining characteristic of the ERα-positive disease. ERα-positive breast cancers are successfully treated with Tamoxifen; however, a significant number of patients develops Tamoxifen-resistant disease. We show here that in vitro development of Tamoxifen-resistance results in acquired sensitivity to OGT small molecule inhibitor OSMI-1. Global transcriptome profiling revealed that TamS cells adapt to OSMI-1 treatment by undergoing significant chromatin compaction.  In the TamR cells, however, OGT inhibition induces ERRFI1 tumor-suppressor gene expression. ERRFI1 is an endogenous inhibitor of ERBB-signaling, while activation of the ERBB-signaling is one of the best understood mechanism for Tamoxifen-resistance. We show that ERRFI1 is selectively downregulated in ERα-positive breast cancers and breast cancers driven by ERBB2, and provide data to support that this occurs through promoter methylation. Finally, we show that increased ERRFI1 expression is associated with extended survival in patients with ERα-positive tumors (p=9.2e-8). In summary, we show that Tamoxifen-resistance is associated with acquired sensitivity to OSMI-1, and propose that this is explained in part through an epigenetic activation of the tumor-suppressor ERRFI1 in response to OSMI-1 treatment.

overall_design: Total RNA was isolated from tamoxifen-sensitive MCF7 and tamoxifen-resistant TAMR cells following 24 hours of treatment with 40μM OGT inhibitors, or DMSO control.  To cell lines with the two different treatments  matched to respective controls with 3 replicate runs.

first: Anna

last: Barkovskaya

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