title: Single-cell RNA sequencing of primary mouse brown adipocytes

city: Duarte

first: Xiwei

last: Wu

state: CA

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

summary:
Purpose: To test if there is a heterogeneity within brown adipocytes, we performed single cell RNA-sequencing of primary brown adipocytes isolated from mouse brown adipose tissue.
Methods: Brown adipocytes from 10-week-old C57BL/6J male mice were freshly collected and resuspended in PBS containing 0.04% BSA at a concentration of 700~1200 cells/µl. Cell number and viability were measured using a TC20 Automated Cell Counter (BioRad). Single-cell RNA libraries were prepared according to the Chromium™ Single Cell 3' Reagent Kits v2 User Guide (10x Genomics). Approximately 10,000 cells were loaded on a Chromium single cell Controller instrument (10x Genomics) to generate single cell gel beads in emulsion (GEMs). The barcoded sequencing libraries were constructed using the Chromium Single-Cell 3′ Library Kit (10x Genomics) for enzymatic fragmentation, end-repair, A-tailing, adaptor ligation, ligation cleanup, sample index PCR, and PCR cleanup. Libraries were sequenced with a Hiseq 2500 instrument (Illumina) with a depth of 50k-100k reads per cell. Raw sequencing data were processed using the 10x Genomics Cell Ranger pipeline (version 2.0) to generate FASTQ files and aligned to mm10 genome to gene expression count. The subsequent data analysis was performed using “Seurat” package and R scripts. Cells with mitochondrial read rate > 50% and < 200 detectable genes were considered as low-quality and filtered out. Normalized and scaled data were clustered using the top significant principal components of highly variable genes. The t-distributed stochastic neighbor embedding (t-SNE) algorithm was used to visualize the resulting clusters. Cluster-specific markers were identified to generate heatmap and feature plots in the identified cell clusters. Genes were compared between different clusters using Bioconductor package “Limma” on normalized data. Gene Set Enrichment Analysis (GSEA) v3 was performed using genes ranked by the fold changes between different clusters to evaluate the significant activation of the C2 KEGG gene sets in MSigDb (http://software.broadinstitute.org/gsea/msigdb/collections.jsp).
Results: Two major brown adipocyte subpopulations were clustered as brown adipocytes with high thermogenic activity (BA-H, 2,352 cells) and brown adipocytes with low thermogenic activity (BA-L, 1,250 cells).
Conclusions: In summary, the brown adipocyte single cell transcriptomic reveals a unique subpopulation of brown adipocytes with low thermogenic activity. These cells hold a unique metabolic status, and the function of these cells is fundamentally different from the cells within the BA-H subpopulation.

overall_design: Brown adipocytes from wide type mice were freshly collected and single-cell sequencing was performed using the 10X genomics platform.

first: Qiong

last: Wang

first: Anying

last: Song


title: Applications of Next Generation Sequencing in intrahepatic cholangiocarcinoma

status: Public on Dec 10 2019

city: Shanghai

first: Guang

last: Zhou

address: No. 600, Yishan Road

country: China

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

type: Non-coding RNA profiling by high throughput sequencing

summary: We generated 100 M of high-quality sequencing reads (~10 M per sample) and catalogued the expression profiles of 1643 microRNA in each sample. The analysis showed differences of microRNAs between intrahepatic cholangiocarcinoma and normal bile duct tissues.

overall_design: The expression profiles of microRNA in intrahepatic cholangiocarcinoma tissues and normal bile duct tissues were generated by deep sequencing using Illumina HiSeq2500.

first: Guangwen


title: Intestinal IL-17R signaling controls liver inflammation by constraining microbiome-induced TLR9 signaling and IL-18 production

city: New Orleans

first: Jay

middle: K

last: Kolls

state: LA

address: 333 S. Liberty St, JBJ 375

department: Center for Translational Research in Infection and Inflammation

country: USA

institute: Tulane University School of Medicine

type: Expression profiling by high throughput sequencing

summary: IL-17 and IL-17R signaling in the intestinal epithelium regulate the intestinal microbiome. Given the reported links between intestinal dysbiosis, bacterial translocation, and liver disease, we hypothesized that intestinal IL-17R signaling plays a critical role in mitigating hepatic inflammation. To test this, we studied intestinal epithelial-specific IL-17RA deficient mice in a model of concanavalin A hepatitis. Absence of enteric IL-17RA signaling exacerbated hepatitis and hepatocyte cell death. These mice exhibited commensal dysbiosis, increased intestinal and liver Il18, and increased liver translocation of bacterial products, specifically CpG DNA. Mechanistically, CpG DNA induced hepatic IL-18, increasing IFNγ and FasL in hepatic T-cells to drive inflammation. Thus, intestinal IL-17R regulates translocation of TLR9 ligands and constrains susceptibility to hepatitis. These data connect enteric Th17 signaling and the microbiome in hepatitis, with broader implications on the effects of impaired intestinal immunity and subsequent release of microbial products seen in other extra-intestinal pathologies.

overall_design: Liver mRNA profiles of 6-week old Il17ra fl/fl mice and Il17ra fl/fl x villin cre+ mice at the naïve state and 90 minutes post concanavalin a injection (n=2 mice/genotype/timepoint)

first: Timothy

middle: W

last: Hand

first: Kong

last: Chen


title: Functional and evolutionary significance of human microRNA seed region mutations [miR-141]

city: Atlanta

first: Neda

last: Jabbari

state: GA

address: 315 Ferst Dr

department: Biology

institute: Georgia Institute of Technology

summary: MicroRNAs (miRNAs) are small non-coding RNAs that play a central role in the regulation of gene expression at the post transcriptional and/or translational level thus impacting various biological processes. Dysregulation of miRNAs could affect processes associated with progression of a variety of diseases including cancer.  Majority of miRNA targeting in animals involves a 7-nt “seed region” mapping to positions 2-8 at the molecule’s 5' end. The importance of this 7 nt sequence to miRNA function is evidenced by the fact that the seed region sequence of many miRNAs is highly conserved within and between species. In this study, we computationally and experimentally explore the functional significance of sequence variation within the seed region of human miRNAs. Our results indicate that change of a single nt within the 7-nt seed region changes the spectrum of targeted mRNAs significantly meanwhile further nt changes have little to no additional effect. This high functional cost of even a single nucleotide change within the seed region of miRNAs explains why the seed sequence is highly conserved among many miRNA families both within and between species and could help clarify the likely mechanisms underlying the evolution of miRNA regulatory control.

overall_design: mRNAs were collected from 3 miR-141 treated and 3 negative control miRNA treated HEY ovarian cancer cell samples. mRNA expression was captured on Affymetrix U133 Plus 2 chips. To compare mRNA expression pattern between the miR-141 treated cells and the negative control treated cells, present/absent calls were generated using MAS5, while signals were calculated using GCRMA and then log2 transformed. Expression of differentially expressed genes or down regulated miRanda-mirSVR predicted miRNA target genes was compared between miRNA treated samples.

first: C

middle: G

last: Hill

first: N

first: L

last: Matyunina

first: J

middle: F

last: McDonald


title: Functional and evolutionary significance of human microRNA seed region mutations [miR-205]

overall_design: mRNAs were collected from 3 miR-205 treated and 3 negative control miRNA treated HEY ovarian cancer cell samples. mRNA expression was captured on Affymetrix U133 Plus 2 chips. To compare mRNA expression pattern between the miR-205 treated cells and the negative control treated cells, present/absent calls were generated using MAS5, while signals were calculated using GCRMA and then log2 transformed. Expression of differentially expressed genes or down regulated miRanda-mirSVR predicted miRNA target genes was compared between miRNA treated samples.


title: Functional and evolutionary significance of human microRNA seed region mutations [miR-200b]

overall_design: mRNAs were collected from 3 miR-200b treated and 3 negative control miRNA treated HEY ovarian cancer cell samples. mRNA expression was captured on Affymetrix U133 Plus 2 chips. To compare mRNA expression pattern between the miR-200b treated cells and the negative control treated cells, present/absent calls were generated using MAS5, while signals were calculated using GCRMA and then log2 transformed. Expression of differentially expressed genes or down regulated miRanda-mirSVR predicted miRNA target genes was compared between miRNA treated samples.

first: Ll


title: The effect of WEE1 inhibition on the replication timing program

status: Public on Dec 09 2019

city: Pittsburgh

first: Hatice

middle: Ulku

last: Osmanbeyoglu

state: PA

address: 5117 Centre Ave

institute: University of Pittsburgh

summary: As a part of the project looking into the role of WEE1 in regulating replication initiation, we report the replication timing analysis of the U2OS cells treated with WEE1 kinase inhibitor AZD1775

overall_design: U2OS cells were treated with DMSO or 500nM AZD1775 for 30 minutes before labelling of the ongoing replication with 10uM BrdU.

first: Tatiana

middle: N

last: Moiseeva

first: Norie

last: Sugitani

first: Christopher

middle: J

last: Bakkenist

first: Chenao

last: Qian

middle: U


title: DNA  methylation analysis of BeWo  cells  stimulated  by tumor necrosis factor-alpha and  insulin-like growth factor-I

city: Mitaka

first: Kei

last: Tanaka

state: Tokyo

department: Medicine

country: Japan

institute: Kyorin University

summary: Cellular functions of trophoblasts are regulated by various cytokines and growth factors. We previously reported the synergistic effects of tumor necrosis factor-α (TNF-α) and insulin-like growth factor-I (IGF-I) on BeWo cells proliferation. We performed DNA methylation array to elucidate the epigenetic regulation involved in the cross-talk of TNF-α and IGF-I in BeWo cells. We identified general increase in DNA methylation by co-stimulation of TNF-α and IGF-I. Total of 83474 differentially methylated CpG sites were identified in BeWo cells stimulated by IGF-I and high TNF-α. By correlating with the results of expression array, NFKBIE, C3 and GP1BA were identified as differentially methylated genes with significant expression change.

overall_design: Bisulphite converted DNA from 12 samples of BeWo cells were hybridised to Illumina Infinium MethylationEPIC Beadchip

first: Tomoko

last: Kawai

first: Kazuhiko

last: Nakabayashi

first: Kenichiro

last: Hata


title: Altered 5-hydroxymethylcytosine landscape in primary gastric adenocarcinoma

first: Ying

last: Cheng

address: 615 Michael Street

department: Human Genetics

institute: Emory University

type: Methylation profiling by high throughput sequencing

summary: Multiple factors, including molecular, genetic, and epigenetic changes, have been linked to gastric cancer formation and progression. Cytosine methylation (5mC) has been well studied and recognized as a critical epigenetic mark in the mammalian genome. The recent novel discovery of 5-hydroxymethylcytosine (5hmC), which generated by ten-eleven translocation (TET) enzymes, provide new perspective to understand DNA methylation-related plasticity. Here we show that gastric tumors display significant loss of 5hmC. Using matched distant normal, peripheral and tumor primary tissues, we performed genome-wide profiling of 5hmC and identified differentially hydroxymethylated regions (DhMRs) specifically associated with gastric tumors. Gene Ontology (GO) analyses indicated that DhMRs (both loss-of-5hmC and gain-of-5hmC) were enriched among the genes involved in specific pathways. Interestingly the binding motif of hypoxia-inducible factor 1 (HIF1) is enriched among both peripheral and tumor DhMRs, while the Myc-binding motif is specifically enriched among only tumor DhMRs. Tumor progression analyses revealed a unique set of DhMRs that correlate with tumor progression. These data together suggest that the alteration of 5hmC could potentially contribute to the tumorigenesis of gastric tumors.

overall_design: To explore the role of 5hmC in GC, we collected six sets of fresh gastric tissues, including gastric tumor (Tumor/T), adjacent gastric tissue to the tumor (Peripheral/P) and distant normal gastric tissue (Normal/N).

first: Peng

last: Jin


title: miRNA profiling of murine mesenchymal stem cell (mMSC)-derived extracellular vesicles (EVs) before and after freeze-drying

city: Montpellier

first: Morille

last: Marie

address: 15 avenue Charles Flahault

department: UFR Sciences pharmaceutiques et biologiques, Bat C,

country: France

institute: ICGM UMR5253

summary:
Purpose: The goal of this study was to determine the microRNA (miRNA) content of extracellular vesicles (EVs) derived from murine mesenchymal stem cells (mMSC), and evaluate reproducibility among distinct EV productions. We also aimed at assessing the effect of freeze-drying on EV miRNA content, by performing sequencing on freeze-dried EVs and calculating statistical difference between unmodified and freeze-dried EVs.
Methods: mMSC-derived EVs were obtained from mMSC in culture in reduced serum medium Opti-MEM by differential centrifugation, with a final step at 100,000 g for 110 min at 4°C. EV pellets (freeze-dried (n=3) or not (n=2)) were resuspended in Qiazol lysis buffer and RNA was extracted following RNeasy Micro kit. cDNA libraries for sequencing were prepared using the TruSeq Small RNA Sample Preparation Kit. Amplified cDNA constructs were purified on 6 % PAGE gel and DNA molecules corresponding to 15–50 nucleotide transcripts were excised, eluted from gel, and concentrated. Image analyses and base calling were performed using the HiSeq Control Software and Real-Time Analysis component (Illumina). Before statistical analysis, genes with less than 15 reads (cumulating all the analysed samples) were filtered out. Differentially expressed miRNA were identified using three Bioconductor packages: edgeR, DESeq and DESeq2.
Results: Considering miRNAs detected with at least 5 counts (in terms of normalised counts), 339 miRNAs were identified and miRNA content was highly conserved among the two batches tested, with 237 miRNAs out of the 339 present in both batches (70%). Statistical analysis did not evidence statistical difference between unmodified EVs (n=2) and freeze-dried EVs (n=3) (DESeq2, p<0.05). No statistical difference was found using other Bioconductor packages DESeq and edgeR. These results indicated conservation of miRNA content following freeze-drying.
Conclusion: mMSC-EV miRNA content was comparable between the two EV productions analysed, indicating reproducibility. Some of the miRNAs identified were consistent with previously published results on MSC-derived EVs. Freeze-drying conserved miRNA content.

overall_design: Examination of miRNA content of mMSC-derived EVs, before and after freeze-drying, and comparison of miRNA content between the two conditions (freeze-dried vs. not freeze-dried).

first: Marie

last: Morille

first: Joel

last: Chopineau

first: Sarah

last: Le Saux


title: Probe-Seq enables transcriptional profiling of specific cell types from heterogeneous tissue by RNA-based isolation

city: Boston

first: Ryoji

last: Amamoto

state: Massachusetts

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

summary: Probe-Seq is a method that allows transcriptional profiling of specific cell types from heterogeneous tissue by labeling RNA. Briefly, we developed Probe-Seq, which allows deep transcriptional profiling of specific cell types isolated based on RNA abundance of defined markers. We applied Probe-Seq to purify and profile specific cell types from mouse, human, and chick retinas as well as the Drosophila gut. We also showed that Probe-Seq is compatible with frozen nuclei and that multiplexed Probe-Seq enables iterative isolation of multiple cell types from the same tissue sample. Provided that unique markers are available, this simple, novel method could potentially enable bulk RNA sequencing of any cell type from any organism.

sample_organism:
Drosophila melanogaster
Gallus gallus
Mus musculus

overall_design: Overall, RNA sequencing was peformed on mouse retina whole cell, mouse retina nuclei, Drosophila gut, and developing chick retina. For the mouse retina whole cell experiment, 3 populations, Vsx2-, Grik1-, and Grik1+ populations were isolated for RNA sequencing, with 2 biological replicates each. For the mouse retina nuclei experiment, 2 populations, Grik1+ and Grik1-, were isolated for RNA sequencing, with 3 biological replicates each. For the Drosophila gut, 2 populations, esg+ and esg-, were isolated for RNA sequencing, with 3 biological replicates each. For the chick retina, 2 populations, FGF8+ and FGF8-, were isolated for RNA sequencing, with 3 biological replicates each.

first: Connie

last: Cepko


title: Baseline expression profiles of human breast carcinomas

city: Tampa

first: Douglas

last: Marchion

state: Florida

address: 12902 Magnolia Drive

department: Clinical Science Lab

institute: Moffitt Cancer Center

summary: mRNA expression profiles for 106 primary breast carcinomas

overall_design: Samples included N=53 triple-negative breast carcinomas (TNBC) and N=53 non-TNBC (ER+/PR+) samples. Only breast cancer patients whose carcinomas did not express HER2 receptors were included. The non-TNBC and TNBC groups were well balanced with no significant differences in age (non-TNBC: mean = 49, range = 32-80 years; TNBC: mean = 52, range = 30-79 years) and stage.

middle: C


title: A critical but divergent role of PRDM14 in human primordial germ cell fate revealed by inducible degrons [ChIP-seq]

status: Public on Dec 08 2019

city: Cambridge

first: Walfred

last: Tang

address: Tennis Court Road

department: Gurdon Institute

country: United Kingdom

institute: University of Cambridge

type: Genome binding/occupancy profiling by high throughput sequencing

summary: PRDM14 is a crucial regulator of mouse primordial germ cells (mPGC), epigenetic reprogramming and pluripotency, but its role in the evolutionarily divergent regulatory network of human PGCs (hPGCs) remains unclear. Besides, a previous knockdown study indicated that PRDM14 might be dispensable for human germ cell fate. Here, we decided to use inducible degrons for a more rapid and comprehensive PRDM14 depletion. We show that PRDM14 loss results in significantly reduced specification efficiency and an aberrant transcriptome of human PGC-like cells (hPGCLCs) obtained in vitro from human embryonic stem cells (hESCs). Chromatin immunoprecipitation and transcriptomic analyses suggest that PRDM14 cooperates with TFAP2C and BLIMP1 to upregulate germ cell and pluripotency genes, while repressing WNT signalling and somatic markers. Notably, PRDM14 targets are not conserved between mouse and human, emphasising the divergent molecular mechanisms of PGC specification. The effectiveness of degrons for acute protein depletion is widely applicable in various developmental contexts.

overall_design: ChIPseq of PRDM14-Venus in hESC and hPGCLCs by an anti-GFP antibody (abcam ab290).

first: Anastasiya

last: Sybirna

first: M

middle: A

last: Surani


title: Src modulates its oncogenic signaling via regulation of miRNA-129-3p [microRNA]

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: To address the molecular mechanisms underlying c-Src-induced cell transformation, we previously developed a model system using Csk-deficient fibroblasts that can be transformed by wild-type c-Src. In this study, we applied this system for the analysis of the potential contribution of mRNA and miRNA to c-Src-induced cell transformation. We found miR-129-3p was downregulated in c-Src-induced cell transformation in a Dox-inducible expression system via c-Src, c-Yes, and Fer.

overall_design: CskKO (Csk-/-) MEFs were transfected with c-Src. Cells were induced c-Src for 0, 6, 24 and 72 hours. Each sample was run in duplicate.

first: Chitose

last: Oneyama


title: Analysis of gene expression from  ßTC3 cells of Rip-Tag2 PanNET mouse model upon miR-137 and miR-23b cluster doxycycline (DOX) induction

city: Lausanne

first: Nadine

last: Fournier

state: Vaud

address: Agora Cancer Research Center, Bugon 25A

country: Switzerland

institute: Agora Cancer Research Center & Swiss Institute of Bioinformatics

summary: Using cross-species analysis, we have previously shown that the miR-137 and the miR-23b microRNA cluster are upregulated in the more aggressive and metastatic, mouse and human, primary tumors, designated as met-like primary (MLP). In order to identify miRNA target genes, we overexpressed the miRNAs in an inducible manner in the insulinoma-like ßTC3 cells and performed RNA-seq.

overall_design: Comparison of samples between DOX ON and OFF conditions, as well as control cells treated or not with DOX

first: Iacovos

last: Michael

last: Zangger

last: Hanahan


title: Src modulates its oncogenic signaling via regulation of miRNA-129-3p

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

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

overall_design: Refer to individual Series


title: Screening of differentially expressed circulating microRNAs during osteoporosis

city: Xi'an

first: Yat

last: Handsome

address: Changle Road

institute: Tissue engineering center

summary: To explore the variation of serum microRNA expression during osteoporosis, we have employed microRNA microarray expression profiling as a discovery platform to identify microRNAs with the potential to diagnose osteoporosis from healthy and osteopenia individuals for clinical use. Whole blood from healthy, osteopenic and osteoporotic donors was collected, and the sera were separated. Twenty two microRNAs (miR-15a-5p, miR-29b-5p, miR-30c-2-3p, miR-145-5p, miR-199a-5p, miR-301a-3p, miR-424-5p, miR-497-5p, miR-526b-5p, miR-550a-5p, miR-575, miR-654-5p, miR-663a, miR-708-5p, miR-877-3p, miR-1246, miR-1260b, miR-1299, miR-1323, miR-4447, miR-4769-3p and miR-5685) were finally used for further detection of osteoporosis diagnosis.

overall_design: Gradually differed microRNAs were measured in healthy, osteopenic and osteoporotic participants. Three independent cohorts were performed to verify the diagnostic performance.

first: Yan

last: Jin

first: Yi

last: Shuai


title: Expression Profiling of Rhabdomyosarcoma patients and normal muscle samples

city: Shihezi,

first: Qianru

last: Li

address: North 2nd Road

institute: Shihezi University School of Medicine

type:
Expression profiling by array
Third-party reanalysis

summary: Genome-wide gene expression in 66 Rhabdomyosarcoma patients and 16 normal muscle samples were studied using Affymetrix Human Genome U133 Plus 2.0 Array.

relation:
Reanalysis of: GSM410968
Reanalysis of: GSM410982
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Reanalysis of: GSM441045
Reanalysis of: GSM441046
Reanalysis of: GSM441047
Reanalysis of: GSM441048
Reanalysis of: GSM941830
Reanalysis of: GSM941831
Reanalysis of: GSM941832
Reanalysis of: GSM941833
Reanalysis of: GSM941834
Reanalysis of: GSM941835

overall_design: 66 Rhabdomyosarcoma patients and 16 normal muscle samples obtained from GSE16382, GSE66533, GSE39454, GSE17674 and GSE38417.

first: Chunxia

last: Liu


title: ESAM KO


title: Src modulates its oncogenic signaling via regulation of miRNA-129-3p [mRNA]


title: Expression data of HEL cells with or without LY2784544 and GRN163L

status: Public on Dec 07 2019

city: Stockholm

first: Jenny

last: Dahlström

address: Solnavägen 1

country: Sweden

institute: Karolinska Institutet

summary: The mutant JAK2v617F is a driver of myeloproliferative neoplasms(MPNs). Consequently, several JAK2 inhibitors are currently being studied in clinical trials. The most investigated JAK2 inhibitor, Ruxolitinib, provides significant and sustained improvements in spleen related and constitutional symptoms secondary to the disease and represents a milestone in the treatment of myelofibrosis. However, JAK2 inhibitors are non-curative and murine experiments have shown that JAK2 inhibitors don?t eradicate MPN stem cells. In the present study, we determined the effect of the specific JAK2V617F inhibitor LY2784544 on leukemic stem (CD34+) cells (LSCs) using the JAK2V617F-bearing erythroleukemia cell line HEL. The LY2784544 treatment caused a transient proliferation inhibition and apoptosis of HEL cells, but a recovery occurred within a week. Thereafter, the continuous exposure of HEL cells to LY2784544 induced the accumulation of CD34+ LSCs, and the CD34+ cell fraction increased from 8% to over 90% by week 9, which was accompanied by substantially increased clonogenic potentials. A whole-transcript expression analysis revealed a significantly enhanced expression of the stem cell factor KLF4 in LY2784544 treated HEL cells. Inhibiting KLF4 expression attenuated LY2784544-mediated accumulation of CD34+ LSCs. Moreover, we further identified that the telomerase inhibitor GRN163L abolished the LY2784544-mediated CD34+ cell enrichment. Our findings collectively suggest that JAK2 inhibitors may cause enrichment of LSCs and are therefore unlikely to cure MPN as a monotherapy. Moreover, simultaneously targeting JAk2V617F and KLF4 or telomerase may be a novel strategy for MPN treatment.

overall_design: We detected the  expression file of HEL cell line after treated with JAK2 inhibitor LY2784544, telomerase inhibitor GRN163L, combination of LY2784544 and GRN163L, experiment were conducted twice seperately

first: Dawei

last: Xu

first: Magnus

last: Björkholm

first: Chuanyou

last: Xia

first: Xiaotian

last: Yuan

first: Xiangling

last: Xing


title: Single cell RNAseq analysis of mouse lung after irradiation

city: Paris

first: Charles

last: Fouillade

address: 25 rue d'Ulm

institute: Institut Curie

summary: Thoracic radiation therapy is limited by the development of acute (i.e. pneumonitis) and late (i.e. pulmonary fibrosis) side-effects. The goal of this study is to analyze, at the single cell level, the molecular impact of two radiation treatments : a conventional/clinical (CONV) modality vs. FLASH, a new radiation method that spares healthy tissue from late radiation-induced toxicities (Science Translational Medicine 6: 245ra293, 2014). We analyzed by single cell RNA sequencing (scRNAseq) dissociated lung cells from a non-irradiated control mouse (NI), a mouse 4 days after CONV thoracic irradiation (CONV) and a mouse 4 days after FLASH irradiation (FLASH). We identify transcriptional alterations induced in the distinct lung cell types after irradiation and show that FLASH irradiated lung cells present a reduced pro-inflammatory phenotype as well as a diminished activation of epithelial lung progenitor cells. In line with previous report (Radiother Oncol 124: 365-9, 2017), this study indicates that FLASH radiation therapy limits inflammation and preserves the regenerative capcity of the lung.

overall_design: Single-cell suspensions were prepared from 10-12 weeks C57Bl/6 mice and single cell RNA-seq libraries were generated using 3' V2 chemistry kit on Chromium Single cell controller (10x Genomics).


title: Transcriptome analysis reveals differentially expressed genes associated with high rates of egg production in chicken hypothalamic-pituitary-ovarian axis

city: XICHANG

first: Binlong

last: chen

state: SICHUAN

address: XUEFU ROAD NO. 1, ANNING TOWN

institute: XiChang University

summary:
Purpose: To identify the key regulatory genes and pathways involved in chicken high egg productivon in HPG axis.
Methods: A total of 856 Chinese Luhua chicken was raised in poultry breeding farm of Sichuan Agricultural University, the highest two hundred and the lowest two hundred chicken egg production were considered as high egg production (HEP) and low egg production (LEP) according to the total egg number at 300 days of age, respectively, integrated with RNA-seq sequencing of samples of HPG axis (hypothalamus, pituitary gland and ovary) from three HEP and three LEP chickens at 300 days of age.
Results: A total 86.7 Gb RNA-seq sequences were generated, and with each library averaged 5.1 Gb.
Conclusions: These important data might improve our understanding of reproductive biology of Luhua chicken by providing comprehensive gene expression information at transcriptional level. We indicate that our approach will contribute to the isolation of effective molecular markers that can be used in genetic breeding programs in Chinese domestic Luhua chicken.

overall_design: samples of HPG axis (hypothalamus, pituitary gland and ovary) from three HEP and three LEP chickens at 300 days of age were sequenced by Illumina HiSeq 2500.

first: Diyan


title: Transcriptome Profiling of bending fruit and Functional Analysis of an ERF/AP2 Family Gene CsERF025 Involved in bending fruit development in cucumber (Cucumis sativus L.)

city: harbin

first: chunhua

last: wang

state: Heilongjaing

address: Mucai Street 59

department: Horticulture

institute: Notheast Agriculture Unversity

summary: To identify the differentially expressed genes(DEGs) in the ventral and dorsal of cucumber bending fruits，cucumber bending  fruit mRNA profiles of 2-day-old ventral  and dorsal were generated by deep sequencing. After removing the low quality reads, the total number of clean reads in two library were 27.07 million and16.52 million, accounted for 85.21% and 80.71% of total reads .We identified a total of 4313 sequences differentially expressed in ventral and dorsal  of bending fruit with a 2-fold or greater change and P < 0.01 ,  the Dorsal  (D2) served as a control, in which 2351 up-regulated genes and 1962 down-regulated genes.For up-regulated genes, protein kinase activity, ethylene mediated signaling pathway, regulation of cell shape, auxin polar transport were significantly enriched, whereas down-regulated genes, the functional classes photosynthesis, oxidation reduction, response to auxin stimulus were significantly enriched. Moreover, among DEGs related to ethylene, we identified an ERF/AP2 gene CsERF025  that was significant difference in the dorsal and ventral of cucumber. up-regulation of CsERF025 in cucumber promoted fruit bendng and Increased the fruit bending angle, suggesting that CsERF025 plays an important role in cucumber bending fruit.

overall_design: Cucumber bending  fruit mRNA profiles of 2-day-old ventral  and dorsal were generated by deep sequencing.

first: Chunhua

last: Wang

first: Zhiwei

last: Qin


title: Identification of Lenalidomide resistance pathways in Myeloma and targeted re-sensitization using Cereblon replacement, inhibition of STAT3 or targeting of IRF4

city: Rochester

first: Xuewei

address: 200 1st street

institute: Mayo Clinic

summary: In the present study, we established four lenalidomide resistant HMCLs by culturing IMiD responsive HMCLs in the presence of lenalidomide for an extended time. Those resistant cell lines were studied along with their isogenic-sensitive lines to identify the genetic pathways underlying changes associated with resistance.  Here mRNAseq was performed to detect the gene expression changes in XG1LenRes compared with its IMiDs sensitive parental cell line XG1.

overall_design: We collected XG1 and XG1res ( XG1LenRes ) at different culture time (day 3 or 24 hours) and prepared total RNA for mRNAseq analysis

first: Yuan

middle: X

last: Zhu

first: Chang-Xin

last: Shi

first: Laura

last: Bruins

first: Esteban

last: Braggio

first: A

last: Stewart


title: Neuronal and glial DNA methylation and gene expression changes in early epileptogenesis

status: Public on Dec 06 2019

city: Oslo

middle: D.

last: Vigeland

address: Kirkeveien 166

department: Medical Genetics

country: Norway

institute: University of Oslo

summary: Mesial Temporal Lobe Epilepsy is characterized by progressive changes of both neurons and glia, also referred to as epileptogenesis. No curative treatment options, apart from surgery, are available. DNA methylation (DNAm) is a potential upstream mechanism in epileptogenesis and may serve as a novel therapeutic target. To our knowledge, this is the first study to investigate epilepsy-related DNAm, gene expression (GE) and their relationship, in neurons and glia. We used the intracortical kainic acid injection model to elicit status epilepticus. At 24 hours post injection, hippocampi from eight kainic acid- (KA) and eight saline-injected (SH) mice were extracted and shock frozen. Separation into neurons and glial nuclei was performed by flow cytometry. Changes in DNAm and gene expression were measured with reduced representation bisulfite sequencing (RRBS) and mRNA-sequencing (mRNAseq). Statistical analyses were performed in R with the edgeR package. We observed fulminant DNAm- and GE changes in both neurons and glia at 24 hours after initiation of status epilepticus. The vast majority of these changes were specific for either neurons or glia. At several epilepsy-related genes, like HDAC11, SPP1, GAL, DRD1 and SV2C, significant differential methylation and differential gene expression coincided. We found neuron- and glia-specific changes in DNAm and gene expression in early epileptogenesis. We detected single genetic loci in several epilepsy-related genes, where DNAm and GE changes coincide, worth further investigation. Further, our results may serve as an information source for neuronal and glial alterations in both DNAm and GE in early epileptogenesis.

overall_design: DNA methylation (RRBS) and gene expression (mRNA-seq) changes in neurons and glia; Right hippocampus of kainic acid injected mice (numbner of mice=8, number of samples=3);  vs saline injected mice(numbner of mice=8, number of samples=3) at 24 hrs post injection.

first: Hanne

middle: S

last: Hjorthaug

middle: D

first: Cecilie

last: Nome

first: Toni

last: Berger

first: Lars

last: Etholm

first: Erik

last: Taubøll

first: Kjell

last: Heuser

first: Kaja

last: Selmer


title: 6 Gy gamma-irradiation of mouse small intestinal organoids at 24h, 48h and 96h after irradiation

city: Amsterdam

first: Sander

last: Meisner

state: NH

address: Meibergdreef 69-71

department: Tytgat institute

country: Netherlands

institute: AMC

summary:
The intact intestinal epithelial barrier protects our body from a range of immune mediated diseases. The epithelial layer has an impressive ability to reconstitute and repair upon damage and this process of repair is increasingly seen as a therapeutic target. In vitro models to study this process in primary intestinal cells are lacking. Therefore we established and characterized an in vitro model of intestinal damage and repair by applying γ-radiation on small intestinal organoids. We then used this model to identify novel regulators of intestinal regeneration.
Small intestinal single crypts were isolated from C57BL/6 mice and cultured in matrigel. We treated the organoid cultures, 3 days after seeding, with 6 Gy of gamma-irradiation. RNA was isolated at 24, 48 and 96 hours after irradiation. Non-irradiated controls were collected per time point.

overall_design: 4 replicates per condition. Each time point has its own control.

first: Vanesa

last: Muncan

first: Gijs

middle: R

last: van den Brink

first: Paula

last: Montenegro-Miranda


title: ChIP-seq data from roots of the uri complementation line exposed to either Fe sufficient or Fe deficient conditions for 72 hours

city: Hanover

first: Mary Lou

last: Guerinot

address: 78 College St

department: Biological Sciences

institute: Dartmouth College

summary: We compared the URI binding to the chromosome in roots between +Fe and -Fe conditions.

first: Sun

last: Kim

first: Mary

middle: L


title: A critical but divergent role of PRDM14 in human primordial germ cell fate revealed by inducible degrons [RNA-seq]

first: Walfred

last: Tang

overall_design: RNAseq of hESC and hPGCLCs derived from parental line and 2 PRDM14-AID clones with or without Auxin (2 replicates each).

first: Anastasiya

last: Sybirna

first: M

last: Surani


title: NK cells expressing CD27 and CD11b are mature NK intermediates with organ specific distribution in cynomolgus macaque

city: Singapore

first: Sarah

last: Daud

address: 1E Kent Ridge Road,NUHS Tower Blk,Lvl 12,

country: Singapore

institute: National University of Singapore

summary: In this study, we aim to establish the means to characterize macaque natural killer (NK) cells, and to investigate whether the CD27/CD11b NK maturation model proposed in human and murine models is applicable to Macaca fascicularis (cynomolgus macaque) NK cells. The NK development studies performed in mice models have demonstrated four functionally distinct subsets defined by CD27 and CD11b, however this has not yet been established in nonhuman primates. The expression data of these macaque NK subsets will be associated with the antibody-dependent cellular cytotoxicity and missing-self responses produce by each subset.

overall_design: Unstimulated NK cell subsets were profiled for gene expression after 10-colour flow cytometry cell sorting, based on CD27 and CD11b surface expression. The expression profile of selected mafa-KIR genes based on published cynomolgus macaque KIR haplotypes will be studied for a subset of cynomolgus macaque NK cells using this customized microarray.

first: S

last: Yawata


title: Dysregulated mesenchymal PDGFR-β drives kidney fibrosis

city: Aachen

first: Bernd

last: Denecke

state: NRW

address: Pauwelsstrasse 30

department: IZKF Aachen

country: Germany

institute: RWTH Aachen University

summary: Kidney fibrosis is characterized by expansion and activation of platelet-derived growth factor receptor-β (PDGFR-β) positive mesenchymal cells. To study the consequences of PDGFR-ß activation, we developed a model of primary renal fibrosis using transgenic mice with PDGFR-β activation specifically in renal mesenchymal cells, driving their pathological proliferation and phenotypic switch towards myofibroblasts. This resulted in progressive mesangioproliferative glomerulonephritis, mesangial sclerosis and interstitial fibrosis with progressive anemia due to loss of erythropoietin production by fibroblasts. We used microarrays to compare wildtype animals (Foxd1_wt Pdgfrb_wt) to animals with constitutive mesenchymal PDGFR-β activation (Foxd1_mt Pdgfrb V536A) in the kidney to identify target genes of PDGFR-β signaling.

overall_design: To generate mice with a renal mesenchymal cell-specific, constitutively active PDGFR-β (Foxd1_mt Pdgfrb V536A), we used mice in which one wt Pdgfrb allele was substituted by a conditional knock-in of Pdgfrb with an activating point mutation (V536A) in the juxtamembrane domain of PDGFR-β, behind a floxed STOP cassette. Expression of the mutated Receptor occurs after Cre-recombinase excision. Cre-recombinase expression occurs under the FoxD1-promoter, which is active in renal mesenchymal precursors during development. Foxd1_mt Pdgfrb V536A mice were compared to wildtype littermates Foxd1_wt Pdgfrb_wt.

first: Peter

last: Boor

first: Eva

middle: M

last: Buhl


title: A critical but divergent role of PRDM14 in human primordial germ cell fate revealed by inducible degrons


title: Compensatory Csf2-driven macrophage activation blunts long-term efficacy of therapeutic Csf1r inhibition in breast-to-brain metastasis

first: Florian

last: Klemm

address: Ch. des Boveresses 155

department: DOF

institute: University of Lausanne, Ludwig Center for Cancer Research

summary: Tumor microenvironment-targeted therapies are emerging as promising treatment options for different tumor types. Tumor-associated macrophages/microglia (TAMs) represent the most abundant non-malignant cell type in brain metastasis and are known to support metastatic colonization and outgrowth. We used the colony-stimulating factor 1 receptor (Csf1r) inhibitor BLZ945 to target TAMs at distinct stages of the metastatic cascade in experimental breast-to-brain metastasis and demonstrate that Csf1r inhibition leads to anti-tumor responses in prevention and intervention trails. However, compensatory Csf2-mediated pro-inflammatory TAM activation blunts long-term efficacy of Csf1r inhibition by inducing signatures associated with neuroinflammation followed by wound repair responses that foster tumor recurrence. Combined blockade of Csf1r and Csf2rb-Stat5 signaling leads to sustained tumor control and a normalization of microglial activation states.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Microglia (MG), monocyte-derived macrophages (MDM) and MDA brain metastasis (BrM) GFP+ tumor cells were FAC-sorted from mice under the following conditions: healthy animals (n=3), BrM bearing, vehicle treated mice (n=5) and BrM bearing, BLZ945 treated mice (n=4). RNA was isolated and subjected to RNA-sequencing to investigate the education of MG and MDM in BrM and the consequences of Csf1r-targeted therapy.

first: F

first: L

last: Sevenich

first: J

last: Joyce


title: Functional characterization of Arabidopsis ARGONAUTE 3 in reproductive tissue

city: Bern

first: Pauline

middle: Emilie

last: Jullien

address: Altenbergrain 21

department: Institute of Plant Biology

institute: University of Bern

summary: Arabidopsis encodes ten ARGONAUTE (AGO) effectors of RNA silencing, canonically loaded with either 21-22nt small RNAs (sRNA) to mediate post-transcriptional-gene-silencing (PTGS) or 24nt sRNAs to promote RNA-directed-DNA-methylation. Using full-locus constructs, we characterized the expression, biochemical properties, and possible modes of action of AGO3. Although AGO3 arose from a recent duplication at the AGO2 locus, their expression differs drastically, with AGO3 prevailing in aerial vascular terminations and specifically in chalazal seed integuments; accordingly, AGO3 down-regulation alters gene expression in siliques. Similar to AGO2, AGO3 binds sRNAs with a strong 5’-adenosine bias, but unlike most Arabidopsis AGOs - AGO2 included - it binds efficiently both 24nt and 21nt sRNAs. AGO3 immuno precipitation experiments in siliques revealed that these sRNAs mostly associate to genes and intergenic regions and not to canonical AGO targets, such as transposable elements. AGO3 localizes to the cytoplasm and co-fractionates with polysomes to possibly mediate PTGS via translation inhibition.

overall_design: For mRNA sequencing, 2 biological samples per genotype were assessed. Samples were: ago3-3 homozygous, ago3-3 heterozygous, and Columbia 0 wilt-type samples. For sRNA sequencing, no replication was done. Three samples were analyzed: Total sRNA extracted from Arabidopsis siliques (TOTAL_smRNA), sRNA fraction which was collected from immunoprecipitated AGO3:FLAG protein (IP_AGO3), and sRNA from a control Immunoprecipitation experiment, conducted in wild-type siliques using a FLAG antibody.

middle: E

first: Stefan

last: Grob

first: Antonin

last: Marchais

first: Nathan

last: Pumplin

first: Clement

last: Chevalier

first: Caroline

last: Otto

first: Gregory

last: Schott

first: Olivier

last: Voinnet


title: RNA-Seq of Arabidopsis Col-0  seedlings treated with L-Glu, urea, SA, and distilled water, and Col-0 and sid2 seedlings treated with L-Glu and urea

city: Yokohama

first: Yukihisa

last: Goto

address: 1-7-22 Suehiro-cho

institute: RIKEN


title: RNA-Seq of Arabidopsis Col-0 and sid2 seedlings treated with L-Glu and urea

summary: Plant resistance inducers (PRIs) are compounds that protect crops from diseases by activating plant immunity. The exogenous treatment with glutamate (Glu), an important amino acid for living organisms, was shown to induce resistance against fungal pathogen in rice and tomato. To understand the molecular mechanism of Glu-induced immunity, we developed a model system using Arabidopsis thaliana. Here, we found that exogenous treatment with Glu to Arabidopsis enhances resistance against Pseudomonas syringae pv. tomato DC3000 and Colletotrichum higginsianum. Consistently, transcriptome analyses of Arabidopsis seedlings treated with Glu showed that Glu significantly induces the expression of wound, defense, and stress related genes. Interestingly, Glu activates the expression of pathogen or damage associated molecular patterns (PAMP or DAMP)–inducible genes at much later time points than PAMP/DAMPs normally do. Moreover, expression of Glu-inducible genes does not require known components of PAMP receptor complex, glutamate receptors, salicylic acid-biosynthesis enzyme, or glutamate decarboxylase. In addition, Glu also enhances PAMP-inducible immune responses, such as production of reactive oxygen species and mitogen-activated protein kinase activation. These results show that Glu activates PAMP/DAMP-triggered immunity signaling pathway in a novel manner.

overall_design: Examination of L-Glu-inducible genes in Arabidopsis Col-0 and sid2 seedlings after 48h treatment.

first: Yasunori

last: Ichihashi

first: Yasuhiro

last: Kadota

first: Ken

last: Shirasu


title: Transient epigenetic reprogramming during adult zebrafish muscle regeneration

city: Ann Arbor

first: Brian

last: Magnuson

state: MI

address: 1500 East Medical Center Drive

institute: University of Michigan

summary: Genomic reprogramming and cellular dedifferentiation are critical to the success of de novo tissue regeneration in lower vertebrates such as zebrafish and axolotl. ChIP-seq of the histone modifications H3K27Ac, H3K27me3, and H3K4me3 was used to characterize early epigenetic changes in a zebrafish in vivo model of adult muscle regeneration.

overall_design: Histone H3 modification in Danio rerio lateral rectus muscle before and after injury. This study consists of 9 ChIP-seq samples and 1 input sample. Chromatin from control, 9 hours post-injury (hpi), and 18 hpi tissue from multiple wild-type specimens was assayed by ChIP-seq for H3K27Ac, H3K27me3, and H3K4me3 modification.

first: Christina

last: Tingle

first: Alon

last: Kahana


title: Effect of Astragalus Polysaccharide Combined with Metformin on Liver mRNA expression profile in aging type 2 diabetic mice and functional analysis

city: 兰州

first: 佳佳

last: 刘

state: 甘肃

address: 城关区定西东路35号

institute: 甘肃中医药大学

summary:
Objective: To study the effect of astragalus polysaccharide combined with metformin on mRNA expression profile of type 2 diabetic mice, and to explore the molecular mechanism of astragalus polysaccharide combined with metformin in the treatment of type 2 aging diabetes.

Methods: Natural aging mice were induced by high-sugar and high-fat diet combined with streptozotocin to prepare aging diabetes model. The experimental mice were divided into aging control group, aging diabetes model group, metformin treatment group, astragalus polysaccharide and metformin. The treatment group was treated with gavage for 60 consecutive days. Immunohistochemical detection of insulin levels in pancreatic tissue of each group of mice, serum insulin levels were measured by mouse insulin kit to observe the treatment of aging diabetes and astragalus polysaccharide combined with metformin; using Agilent mouse whole gene expression profile chip The mRNA expression changes of liver tissues in each group were analyzed, and the differential genes were screened by bioinformatics tools and the differential genes and signal pathways were enriched and analyzed.

Results:  Compared with the aging group, the insulin and insulin antibody levels in the model group were significantly decreased (P<0.05). Compared with the model group, the insulin and insulin antibody levels in the two treatment groups increased (P<0.05), and jaundice The level of polysaccharide in combination with metformin was significantly higher than that in metformin group (P<0.05). The differential gene analysis of the chip showed that there were 5617 differential genes in the aging diabetes model group, 3131 were up-regulated, and 2486 were down-regulated; the Astragalus polysaccharide combined with metformin treatment group had 4767 differential genes, compared with the aging diabetes model group. 2143 up-regulated, 2624 down-regulated, genes with significant differences were mainly involved in protease activity and drug metabolism, and significantly enriched into 33 signaling pathways (P<0.01).

Conclusion: The gene regulatory network plays an important role in the intervention of Astragalus polysaccharides and metformin in the treatment of aging type 2 diabetes.

overall_design: Analysis of 4 samples, no repetition

first: Jiajia

last: Liu

first: Dandan

last: Li

first: Yi

last: Zhao

first: Yuhong

last: Wu

first: Jing

last: Wang


title: RNA-Seq of Arabidopsis Col-0  seedlings treated with L-Glu, urea, SA, and distilled water.

overall_design: Examination of Glu-inducible genes in Arabidopsis Col-0 seedlings after  6 h, 12 h, 24 h, and 48 h treatment


title: TuxNet: A simple interface to process RNA sequencing data and infer gene regulatory networks [XVE:PAN]

city: Raleigh

first: Maria

middle: Angels

last: de Luis Balaguer

state: NC

address: 2115 Gardner Hall, Box 7612

department: Plant and Microbial Biology

institute: North Carolina State University

summary: We obtained transcriptional profiles of roots from an XVE:PAN transgenic line under the control of the β-estradiol-inducible promoter, at times 0, 6, and 24 hours after induction of PAN expression.

overall_design: XVE:PAN seeds were first grown on 1X MS supplemented with 1% sucrose plates, and then were transferred to 1X MS supplemented with 1% sucrose and 10 uM β-estradiol for 0, 6, or 24 hour PAN induction. RNA was then exctracted from the roots. All XVE:PAN seeds were grown for a total of 5 days.

first: Adam

middle: P

last: Fisher

first: Rosangela

last: Sozzani


title: RNA-Seq of human PDA cell lines transfected with control siRNA or Pdx1 siRNA

city: San Francisco

first: Nilotpal

last: Roy

address: 513 Parnassus Ave.

department: Diabetes Center

institute: UCSF

summary: We compared the transcriptome of four human PDA lines: HPAF-II, Panc.05.04, Panc.8 and Panc.10.05 transfected with control siRNA or Pdx1 siRNA.

overall_design: HPAF-II, Panc.05.04, panc.8 and Panc.10.05 cells were transfected with control or Pdx1 si RNA. 3 days after transfection, cells were harvested and RNA-Seq was performed.

first: Matthias

last: Hebrok


title: TuxNet: A simple interface to process RNA sequencing data and infer gene regulatory networks

summary: We obtained the transcriptional profiles from Arabidopsis WT and hb13 mutant roots

overall_design: Seedlings were grown for 5 days.  Roots were dissected at approximately 0.5 cm from the root tip for RNA extraction.


title: Small intestinal tissue 96h after 14 Gy whole body gamma-irradiation of VillinCreERT2 Hnf4a knockout mice

first: Sander

last: Meisner

summary: This experiment was performed to assess the effect of loss of Hnf4a in the intestinal epithelium on the regeneration process after irradiation. Intestinal epithelium specific knockout was obtained by oral adminstration of tamoxifen to VillinCreERT2+-Hnf4afl/fl mice and VillinCreERT2--Hnf4afl/fl mice (which served as controls). 3 weeks after the tamoxifen administration, mice received 14 Gy whole-body gamma-irradiation. RNA was extracted from small intestinal tissue 96 hours after irradiation.

overall_design: 8 Hnf4a knockout versus 8 Hnf4a wildtype mice

first: Vanesa

last: Muncan

first: Gijs

last: van den Brink

first: Paula

last: Montenegro-Miranda


title: Genetic deletion of Pax2 and Pax8 in adult mice

status: Public on Dec 05 2019

first: Greg

last: Dressler

address: 109 Zina Pitcher Drive

department: Pathology

summary:
Background: The mammalian kidneys maintain salt and water homeostasis for proper electrolyte balance and hydration.  As the glomerular filtrate passes through the nephron and into the renal medulla, electrolytes, water, and urea are reabsorbed through the concerted actions of solute carrier channels and aquaporins located at various positions along the nephron and in the outer and inner medulla.  Renal epithelial cells develop from Pax2 positive proliferating stem cells that suppress Pax2 expression once differentiated into mature proximal and distal tubules, but continue to express the related Pax8 protein.  The collecting tubules and renal medulla are derived from a Pax2 positive ureteric bud epithelia that continue to express Pax2 and Pax8 in adult kidneys.  Despite the necessity for Pax2 in renal development, functions for Pax2 or Pax8 in adult renal epithelia have not been established.

Methods: In this report, we deleted either Pax2, Pax8, or both genes in adult mice and examined the phenotypes and changes in gene expression patterns.  The mechanism of Pax8 mediated activation of potential target genes was described in inner medullary collecting duct cells.

Results: Mice with induced deletions of both Pax2 and Pax8 exhibit severe polyuria that can be attributed to significant changes in the expression of solute carriers, such as the urea transporter UTA1, and aquaporins within the inner and outer medulla.  Furthermore, Pax8 expression is induced by high salt in collecting duct cells and activates the UTA1 gene by recruiting a histone methyltransferase complex to the promoter.

Conclusions: These data uncover novel functions for Pax proteins, in adult renal epithelia, that are essential for retaining water and concentrating urine.

overall_design:
Changes in gene expression due to the loss of Pax2 and Pax8 were estimated based on RNA transcript levels in the adult kidney.

Mice homozygous for conditonal (floxed) Pax2 and Pax8 alleles were bred to Rosa26CreER mice for tamoxifen inducible activion of Cre recombinase. Adult mice were given tamoxifen and tissues were harvested 14 days post last injection.
Total RNA from Pax2/8 knockouts and controls were isolated from kidney halves. RNAs were compared by Affymetrix Mouse Gene 2.1 ST Arrays. Controls were Cre negative and given tamoxifen.

first: Gregory

first: Atsuko

middle: Y

last: Higashi


title: Small RNA sequencing from transgenic Arabidopsis 35S:GUS (lines 6b4 and L1) and 35S:SUG (line SUG6)

city: Castanet

last: Zytnicki

address: 24, Chemin de Borde-Rouge

department: Applied Mathematics and Informatics

institute: INRA

summary: Transgene loci were transfered in different Arabidopsis thaliana mutant backgrounds by crossing. Small RNA molecules were extracted and sequenced to survey the influence of mutations on transgene small RNA biogenesis.

overall_design: Whole plants were grown in vitro, harvested 11 days after germination and grinded to extract total RNA with phenol/chloroform and ethanol precipitated. RNA samples were sent to GATC Biotech for size-selection, cloning and sequencing on HiSeq2000 platform.

first: Jean-Sébastien

last: Parent

first: Hervé

last: Vaucheret


title: Expression data from roots of WT and uri plants exposed to either Fe sufficient or Fe deficient conditions for 72 hours

first: Mary Lou

last: Guerinot

summary: We compared the gene expression in roots between WT and uri mutant under +Fe and -Fe conditions using ATH1 microarray analysis to explore which genes are affected by the loss of URI function.

overall_design: RNA was harvested from root tissues from WT and uri plants grown on half-strength B5 for 2 weeks and then transferred to either +Fe or -Fe conditions for 3 days. Two biological replicates were prepared per genotype and per condition.

first: Sun

last: Kim

first: Mary


title: Transcriptional profiling of neurons in the cerebral cortex and dentate gyrus in an Rbp4-Cre (KL100) mouse line

status: Public on Dec 14 2019

city: New York

first: Laura

last: Kus

state: NY

address: 1230 York Avenue # 260

department: Heintz Laboratory

institute: The Rockefeller University

summary: TRAP translational profiling is a method that allows investigators to genetically characterize specific cell types in complex tissues such as mouse brain.  Using this technique we obtained RNA-Seq data from actively translating transcripts present in neurons in the cerebral cortex and dentate gyrus of adult Rbp4-Cre (KL100) mice x Rosa26-LSL-EGFP/Rpl10a mice.

overall_design: TRAP-Seq of neurons in the cerebral cortex and dentate gyrus of adult Rbp4-Cre (KL100)::Rosa26-LSL-EGFP/Rpl10a mice

first: Cuidong

last: Wang


title: CNOT1 and Transcriptomic Landscape of a HeLa Cell Line

city: Birmingham

first: Nafiseh

last: Chalabi

state: West Midland

address: Vincent Drive

department: Cancer and Genomic Sciences

institute: University of Birmingham

summary: Purpose: The goals of this study are to compare NGS-derived total transcriptome profiling (RNA-seq) of CNOT1-depleted cells (using siRNA) with control HeLa cells before and after DNA damage to examine quantitative gene expression.

overall_design: Methods: 72 hours post siRNA transfection control and CNOT1-depleted HeLa cells were mock-treated or treated with HU 0.25m, DRB 100µm or MMC 1µm. Cells were collected at indicated timepoints for each treatment. Total RNA was extracted from control and CNOT1-depleted HeLa cells using RNeasy Plus Mini (Qiagen). The quality and quantity of extracted RNA were measured using a Qubit 2.0 Fluorometer (Life Technologies) and an Agilent 2200 TapeStation system, respectively. Dual-indexed, strand-specific RNA-Seq library was prepared from submitted total RNA, using RiboZero (Illumina) rRNA depletion and the NEBNext Ultra Directional RNA library preparation kit (NEB). RNA-Seq was performed on 2 lanes of HiSeq4000 (paired-end, 2x150bp) platform to generate ~80M reads per sample. The raw data files were generated in binary base call (BCL) format and converted to FASTQ format using bcl2fastq Conversion Software (Illumina). FASTQ format readings were transferred to BaseSpace® Sequence Hub (Illumina). The assay was run in 4 lanes in paired-end and 76-cycle mode. The FASTQ files were aligned using HISAT2 (Kim, Langmead et al. 2015), and the resulting mRNA transcripts were assembled using StringTie (Pertea, Pertea et al. 2015) as described in (Pertea, Kim et al. 2016).

first: Chalabi

middle: H

last: Nafiseh

last: Morteza

first: John

middle: G

last: Roger


title: Using single-cell RNA-Seq for unbiased analysis of developmental hierarchies (scRNA-Seq of BM lineage-negative Sca1+ CD117+ CD150+CD48-cells)

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

summary: Hematopoietic stem cell metabolic requirements change with their cell cycle activity. However, the underlying role of mitochondria remain ill-defined. The goal of our study is to investigate how hematopoietic stem cells use mitochondria during cell division to control their fate and self-renewal activity. We found that after mitochondrial activation with replication, HSC irreversibly remodel the mitochondrial network and this network is not repaired after HSC re-entry into quiescence. HSC keep and accumulate dysfunctional mitochondria through asymmetric segregation during active division. Single cell RNA seq and bioinformatic analysis are used to characterize hematopoietic stem cell functions before and after replicative stress to uncover novel key drivers that limit hematopoietic stem cell self-renewal after replicative stress.

overall_design: Single cell RNA seq  hematopoietic stem cell populations; all 305 samples represent the 'scRNA-Seq of BM lineage-negative Sca1+ CD117+ CD150+CD48-cells'

first: Ashwini

last: Hinge

first: Jingyi

last: He

first: James

last: Bartram

first: Juying

last: Xu

first: jose

last: Javier

first: Ellen

last: Fjellman

first: Hiromi

last: Sesaki

first: Tingyu

last: Li

first: Jie

last: Yu

first: Mark

last: Wunbderlich

last: Mulloy

first: Matthew

last: Kofron

first: H

last: Grimes

first: Marie-Dominique

last: Filippi


title: Type II but not type I interferon signaling is indispensable for TLR7-promoted development of autoreactive B cells and systemic autoimmunity

city: Hershey

first: Yuka

last: Imamura Kawasawa

address: 500 University Dr.

department: College of Medicine, Pharmacology

institute: Penn State University

summary: The gene transcripts in splenic tissues derived from imiquimod treated B6.Sle1b and B6.Sle1b.IFNgR-/- mice were analyzed by RNA sequencing.

overall_design: To investigate how IFNg may promote autoreactive B cell development into the AFC and GC pathways in TLR7-accelerated SLE, we analyzed the gene transcripts in spleens of IMQ-treated B6.Sle1b and Sle1b.IFNgR-/- mice by RNA sequencing.

first: S

middle: B

last: Chodisetti

first: A

middle: J

last: Fike

first: P

last: Domeier

last: Singh

first: N

last: Choi

first: C

last: Corradetti

first: Y

middle: I

last: Kawasawa

first: T

middle: K

last: Cooper

first: R

last: Caricchio

first: Z

last: Rahman


title: Expression data from human myocardial cells, AC16

city: Beijing

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

summary:
This study aimed to provide new compelling clues in the PM2.5-induced toxicity and mechanism which order the meaningful bioinformatics evidences for further study on human cardiovascular system.
We used microarrays to detail the global programme of gene expression underlying cellularization and identified distinct classes of up-regulated genes after treated with chemical substance

overall_design: Human myocardial cells AC16 were exposed to PM2.5 for 24h, and collected for RNA extraction and hybridization on Affymetrix microarrays. After that, we tested the expression data of human myocardial cells.

first: Junchao

last: Duan

first: Zhiwei

last: Sun


title: Expression data from Kidney of DBA/2 Ahsg -/- and WT mice

city: Wuerzburg

first: Marietta

last: Herrmann

address: Roentgenring 11

department: IZKF Group Tissue Regeneration in Musculoskeletal Diseases

institute: University Hospital Wuerzburg

summary:
DBA/2N Ahsg -/- mice suffer from sever soft tissue calcification. Gene expression in whole kidney of 5-6 week old mice were analyzed, at this stage calcification is not yet macroscopically detectable.
Evaluation of the gene expression pattern was performed to provide insights into the mechanisms preceding the formation of mineralized lesions.

overall_design: Animals were perfused with 20 ml ice-cold PBS to rinse blood from the circulation unless otherwise stated. RNA was extracted from whole kidneys.

first: Anne

last: Babler

first: Irina

last: Moshkova

first: Felix

last: Gremse

first: Frank

last: Kiessling

first: Ulrike

last: Kusebauch

first: Valentin

last: Nelea

first: Rafael

last: Kramann

first: Robert

last: Moritz

first: Marc

last: McKee

first: Willi

last: Jahnen-Dechent


title: Expression data from brown adipose tissue of DBA/2 Ahsg -/- and WT mice

summary:
DBA/2N Ahsg -/- mice suffer from sever soft tissue calcification. Gene expression in brown adipose tissue isolated from the pelvic region of 6 week old mice was analyzed, representing early stage calcification.
Evaluation of the gene expression pattern was performed to provide insights into the mechanisms associated with soft tissue calcification.

overall_design: Animals were perfused with 20 ml ice-cold PBS to rinse blood from the circulation unless otherwise stated. RNA was extracted from pelvic brown adipose tissue.


title: Expression data from Kidney and brown adipose of DBA/2 Ahsg -/- and WT mice

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

overall_design: Refer to individual Series


title: Neutrophil-derived microvesicle induced dysfunction of the blood-brain barrier in vitro

city: Sheffield

first: Paul

middle: Roy

last: Heath

state: S. Yorks

address: SITraN, 385a Glossop Road

department: Academic Neurology Unit

institute: University of Sheffield

summary: The aim of this study is to understand how NMV can affect the vascular integrity of the blood-brain barrier using a cell line- hCMEC/D3. Recent studies have reported that NMV can affect other endothelial barriers in the body contributing to inflammation and pathogenesis of diseases such as atherosclerosis. The transcriptomic profile of NMV-treated hCMEC/D3 cells was compared to that of cells without treatment to understand whether functional groupings and pathways are differentially expressed, which can contribute to changes in blood-brain barrier.

overall_design:
This study is to understand how NMV interact with hCMEC/D3 cells and can alter the transcriptomic profile of these cells after NMV treatment for 24h.
Changes in the transcriptomic profile of  the brain endothelial cell line, hCMEC/D3, after treating with neutrophil-derived microvesicles (NMV) were compared to control cells receiving no treatment, to identify differentially expressed genes and pathways.

first: Anjana

last: Ajikumar

first: Merete

last: Long

first: Stephen

last: Wharton

last: Ince

first: Victoria

middle: C

last: Ridger

first: Julie

last: Simpson


title: Genome-wide expression analysis of memory-like inflammatory responses in murine micoglial cells (BV-2 immortalized microglial cell line)

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

institute: Leibniz Institute on Aging - FLI

summary: Trained immunity and immune tolerance have been identified as long-term response patterns of the innate immune system. The causes of these opposing reactions remain elusive. Here we report about differential inflammatory responses of microglial cells derived from neonatal mouse brain to increasing doses of the endotoxin LPS. Prolonged priming with ultra-low LPS doses provokes trained immunity, i.e. increased production of pro-inflammatory mediators in comparison to the unprimed control. In contrast, priming with high doses of LPS induces immune tolerance implying decreased production of inflammatory mediators and pronounced release of anti-inflammatory cytokines. Investigation of the signaling processes and cell functions involved in these memory-like immune responses reveals essential role of phosphoinositide 3-kinase γ (PI3Kγ), one of the phosphoinositide 3-kinase species highly expressed in innate immune cells. Together, our data suggest profound influence of preceding contacts with pathogens on the immune response of microglia. The impact of these interactions – trained immunity or immune tolerance - appears to be shaped by pathogen dose.

overall_design: Samples of murin microglial cells were analysed after one or two time treatment with LPS (12 samples: 3 treated once with LPS, 3 treated twice with LPS (high-dose), 3 treated twice with LPS (low-dose))

first: Trim

last: Lajqi


title: RNA-seq and Term-seq of Methanococcus maripaludis wild-type strain S2 and aCPSF1 depletion strain ▽aCPSF1

first: Lei

last: Yue

address: NO.1 Beichen West Road, Chaoyang District

department: Institute if Microbiology

institute: Chinese academy of science

summary:
Using the high-throughput strand-specific RNA-seq, we performed differential transcriptome analysis between strains S2 and ▽aCPSF1
Using the Term-seq method, we meatured the RNA 3'-end of strains S2 and ▽aCPSF1

overall_design:
Triplicates for RNA-seq and duplicates for Term-seq on each strain.
contributor: Novegene

first: Jie

last: Li


title: Inter-α-trypsin inhibitor heavy chain 5 (ITIH5) is a natural stabilizer of hyaluronan that modulates biological processes in the skin

first: Sebastian

last: Huth

address: Pauwelsstr. 30

institute: Uniklinik RWTH Aachen

summary: Hyaluronan (HA) is a major component of the skin that exerts a variety of biological functions. Inter-α-trypsin inhibitor heavy chain (ITIH) proteins comprise a family of hyaladherins of which ITIH5 was recently described in skin, playing a functional role in skin morphology and inflammatory skin diseases including allergic contact dermatitis (ACD). The current study focused on the ITIH5-HA interaction and its potential clinical and functional impact in extracellular matrix (ECM) stabilization.  Using murine skin models, ITIH5 knockdown fibroblasts and a reactive oxygen species (ROS)-mediated HA degradation assay we proved that ITIH5 binds to HA thereby acting as a stabilizer of HA. Moreover, micro-array profiling revealed the impact of ITIH5 on biological processes such as skin development and ECM homeostasis. To understand more precisely the role of ITIH5 in inflammatory skin diseases such as ACD we generated ITIH5 knockout cells of the KeratinoSens cell line. Performing the in vitro KeratinoSens skin sensitization assay, we detected that ITIH5 decreases the sensitizing potential of moderate and strong contact sensitizers.     Taken together, our experiments revealed that ITIH5 forms complexes with HA, thereby on the one hand stabilizing HA and facilitating the formation of ECM structures and on the other hand modulating inflammatory responses.

overall_design: Two samples were analyzed: Comparison between a murine 3D skin model of an Itih5 knockout mouse vs. a wildtype control.

first: Laura

first: Yvonne

last: Marquardt

first: Katharina

last: Fietkau

first: Edgar

last: Dahl

first: Philipp

last: Esser

first: Stefan

middle: F

last: Martin

first: Ruth

last: Heise

first: Hans

last: Merk

first: Jens

last: Baron


title: Histone 3 Lysine 9 Dimethylation Attenuates the Vascular Smooth Muscle Cell Inflammatory Response

city: Cambridge

first: Steven

middle: William

last: Wingett

state: Cambs

address: Francis Crick Avenue, Cambridge Biomedical Campus

department: Cell Biology

institute: MRC Laboratory of Molecular Biology

summary: Vascular inflammation underlies cardiovascular disease. Vascular smooth muscle cells (VSMCs) upregulate selective genes, including matrix metalloproteinases (MMPs) and pro-inflammatory cytokines in response to local inflammation, which directly contribute to vascular disease and adverse clinical outcome. Identification of factors controlling VSMC responses to inflammation is therefore of considerable therapeutic importance. Here, we determine the role of H3K9me2, a repressive epigenetic mark that is reduced in atherosclerotic lesions, in regulating the VSMC inflammatory response. We used VSMC-lineage tracing to detect reduced H3K9me2 levels in VSMCs of arteries after injury and in atherosclerosis. Intriguingly, chromatin immunoprecipitation revealed H3K9me2 enrichment at a subset of inflammation-responsive gene promoters, including MMP3, MMP9, MMP12 and IL6, in mouse and human VSMCs. Inhibition of G9A/GLP, the primary enzymes responsible for H3K9me2, significantly potentiated inflammation-induced gene induction in vitro and in vivo without altering NFkB and MAPK signalling. Rather, reduced G9A/GLP activity enhanced inflammation-induced binding of transcription factors NFkB-p65 and cJUN to H3K9me2 target gene promoters MMP3 and IL6. Taken together, these results suggest that promoter-associated H3K9me2 directly attenuates the induction of target genes in response to inflammation in human VSMCs. This study implicates H3K9me2 in regulating the pro-inflammatory VSMC phenotype. Our findings suggest that reduced H3K9me2 in disease allows complete binding of NFkB and AP-1 transcription factors at specific inflammation-responsive genes to augment pro-inflammatory stimuli in VSMC. Since increased MMP and IL6 activity are features of vascular disease, H3K9me2-regulation may be a novel target for clinical intervention.

overall_design: This submission contains a total of four samples: two replicates of H3K9me2 ChIP from ex vivo vascular smooth muscle cells, and two corresponding input samples.

first: Jennifer

last: Harman

first: Lina

last: Dobnikar

first: Helle

last: Jørgensen


title: Genome-wide contacts of rDNA units detected by 4C procedure in human genome [old.hs]

city: Moscow

first: Nickolai

last: Tchurikov

address: 32, Vavilova str.

department: Department of Epigenetic Mechanisms of Gene Expression Regulation

country: Russia

institute: Engelhardt Institute of Molecular Biology

summary: 4C procedure was used for analysis of genomic contacts of rDNA units in HEK 293T cells.   The primers for 4C were selected downstream from EcoRI site at coordinate  30487 in rDNA sequence with Accession number U13369.1.

overall_design: Examination of rDNA genome-wide contacts in HEK 293T cells using 4C approach.

middle: A

first: Yuri

middle: V

last: Kravatsky

first: Olga

last: Kretova


title: Surviving climate change – the role of acclimatization in reef-building corals [MethylRAD]

city: University Park

first: Iliana

last: Baums

state: PA

address: 212 Mueller Laboratory, Penn State University

department: Biology

institute: The Pennsylvania State University

summary: Branching coral species like the Caribbean Acroporids are long lived and reproduce asexually via breakage of branches. Fragmentation is the dominant mode of local population maintenance for these corals across much of their range. Thus, large genets with many member ramets (colonies) are common. Each of the ramets experiences different microenvironments, especially with respect to light and water flow. Here, we investigate whether colonies that are members of the same genet have different epigenomes because of differences in their microenvironments. The Florida Keys experienced a large- scale coral bleaching event in 2014-2015 caused by high water temperatures. During the event, ramets of the same coral genet bleached differently. Previous work had shown that this was unlikely to be due to their eukaryotic algal symbionts (Symbiodinium ‘fitti’) because each genet of this coral species typically harbors a single strain of S. ‘fitti’. Characterization of the microbiome via 16S tag sequencing did not provide evidence for a central role of microbiome variation in determining bleaching response. Instead, epigenetic changes were significantly correlated with the host’s genetic background, the position of the sampled polyps within the colonies (e.g. tip versus base of colony), and differences in the colonies’ condition during the bleaching event. We conclude that microenvironmental differences in growing conditions led to long-term changes in the way the ramets methylated their genomes and thus to a differential bleaching response.

overall_design: The methylome of Acropora palmata from Florida with differential bleaching responses were analyzed.

first: Meghann

last: Devlin-Durante

first: Dusty

last: Kemp

first: Dana

last: Williams


title: Let-7 derived from endometrial extracellular vesicles is a master inducer of embryonic diapause in mice

status: Public on Dec 12 2019

city: Hong Kong

first: William Shu Biu

last: Yeung

address: Laboratory Block, 21 Sassoon Road

department: Obstetrics and Gynaecology

country: Hong Kong

institute: The University of Hong Kong

summary:
Embryonic diapause is a maternally controlled phenomenon enabling offspring to be born in a favorable environment. The molecule controlling onset of this phenomenon is unknown.
We used microarray to compare the transcriptomes between dormant and active mouse blastocysts

overall_design: GeneChip™ Mouse Gene 2.0 ST Array was used to determine the transcriptomes of D4-activated (D4-act-7g), in-vivo dormant (Dor-7g) and in-vitro let-7-induced dormant (DOX-7g) blastocysts from let7g-transgenic mice

first: William

first: Andy

last: Chen


title: Gene expression-based, identification of differential expression genes in MCF-7 cells with or without silencing of OR2T6 gene

city: Jinan

first: Peng

last: Gao

address: Wenhua Xi Road 44

department: Department of Pathology

institute: Shandong University School of Medicine

summary: Microarray was utilized to screen the differentially expressed mRNAs between MCF-7 cells with or without silencing of OR2T6 gene

overall_design: Differential expression analysis of global gene profiling were performed in MCF-7 cells with or without silencing of OR2T6 gene.

first: Ming

last: Li


title: The thyroid hormone receptor β inhibits self-renewal capacity of breast cancer stem cells (Adherent MCF7 cells)

city: Madrid

first: Cristian

last: Suarez Cabrera

state: Madrid

address: Av. Complutense 40

country: Spain

institute: CIEMAT

summary: Since the thyroid hormone receptor β (TRβ) appears to suppress breast tumor growth and metastasis, we have analyzed the possibility that this receptor could affect cancer stem cell biology using TRβ-expressing MCF-7 cells (MCF7-TRβ cells) treated with the thyroid hormone T3.

overall_design: Gene expression was compared among MCF7 control cells (transduced with a selector Neo gene), MCF7-TRβ cells and both of them treated with T3. Three replicates were analyzed per each group.

first: Irene

last: López-Mateo

first: Elvira

last: Alonso-Merino

last: Suárez-Cabrera

first: Shue-Ye

last: Cheng

first: Susana

last: Alemany

first: Jesús

middle: M

last: Paramio

first: Ana

last: Aranda


title: BET and Aurora Kinase A Inhibitors Synergize against MYCN-positive Human Glioblastoma Cells

city: Uppsala

first: Fredrik

middle: Johansson

last: Swartling

address: Dag Hammarskjölds väg 20

department: Immunology, Genetics and Pathology

institute: Uppsala University

summary: Glioblastoma multiforme (GBM) is the most common primary malignant brain tumor in adults. Patients usually undergo surgery followed by aggressive radio- and chemotherapy with the alkylating agent temozolomide (TMZ). Still, median survival is only 12-15 months after diagnosis. Many human cancers including GBMs demonstrate addiction to MYC transcription factor signaling and can become susceptible to inhibition of MYC downstream genes. JQ1 is an effective inhibitor of BET Bromodomains, a class of epigenetic readers regulating expression of downstream MYC targets. Here, we show that BET inhibition decreases viability of patient-derived GBM cell lines. We propose a distinct expression signature of MYCN-elevated GBM cells that correlates with significant sensitivity to BET inhibition. In tumors showing JQ1 sensitivity, we found enrichment of pathways regulating cell cycle, DNA damage response and repair. As DNA repair leads to acquired chemoresistance to TMZ, JQ1 treatment in combination with TMZ synergistically inhibited proliferation of sensitive cells. Bioinformatic analyses showed that JQ1-sensitive cells could also respond to Aurora Kinase A inhibition which indeed showed synergistic efficacy in combination with BET inhibition. Collectively, our data suggest that BET inhibition could potentiate the efficacy of TMZ or could be combined with Aurora Kinase inhibitors in MYCN-elevated GBM.

overall_design: A total of 24 samples were profiled for RNA expression; four tumor derived cell lines were pertubed in triplicates with either JQ1 drug or DMSO.

first: Matko

last: Čančer

first: Lisa

last: Drews

first: Johan

last: Bengtsson

first: Sara

last: Bolin

first: Gabriela

last: Rosén

first: Bengt

last: Westermark

first: Sven

last: Nelander

first: Karin

last: Forsberg-Nilsson

first: Lene

last: Uhrbom

first: Holger

last: Weishaupt


title: Exogenous pyruvate represses histone gene expression to inhibit cancer cell proliferation via the NAMPT-NAD + -SIRT1 pathway

city: Wuhan

first: Yinsheng

last: Wu

state: Hubei

address: No.368,Youyi Avenue

department: School of life science

institute: Hubei University

summary: Pyruvate is a glycolytic metabolite used for energy production and macromolecule biosynthesis. However, little is known about its potential functions in tumorigenesis. Here,we report that exogenous pyruvate inhibits the proliferation of different types of cancer cells. This inhibitory effect of pyruvate on cell growth is attributed to its function as a signal molecule to repress histone gene expression, which leads to less compact chromatin structure and misregulation of genome-wide gene expression. Pyruvate represses histone gene expression by inducing the expression of NAD + biosynthesis enzyme, nicotinamide phosphoribosyltransferase (NAMPT), which increases NAD + levels and NAD + /NADH ratio. This increase activates the histone deacetylase activity of SIRT1. Chromatin immunoprecipitation analysis indicates that pyruvate enhances SIRT1 binding at histone gene promoters where it reduces histone acetylation. Although pyruvate delays cell entry into S phase, pyruvate represses histone gene expression independent of cell cycle progression. Moreover, we find that administration of pyruvate significantly reduces histone expression and retards tumor growth in xenograft mice without significant side effects. Using tissues from cervical cancer patients, we find intracellular pyruvate concentrations inversely correlate with histone protein levels. Together, we uncover a previously unknown function of pyruvate in histone gene expression and characterize pyruvate as a potential anti-cancer agent.

overall_design: RNA Sequencing Analysis between no treatment and pyruvate treatment in HeLa cells.

first: Shanshan

last: Li


title: DNA Methylation Markers Predict Recurrence-free Interval in Triple-Negative Breast Cancer.

city: Baltimore

first: leslie

last: cope

state: MD

address: 550 N. Broadway

institute: leslie cope

summary: We lack tools to risk-stratify triple-negative breast cancer (TNBC). Our goal was to develop molecular tools to predict disease recurrence. Methylation array analysis was performed on 110 samples treated by locoregional therapy obtained from Institutional cohorts. Discovered marker sets were then tested by Kaplan Meier analyses in a prospectively collected TNBC cohort of 49 samples from the no chemotherapy arms of IBCSG trials VIII and IX, and by logistic regression in a chemotherapy-treated cohort of 121 TNBCs from combined IBCSG trials and Institutional repositories. High methylation was associated with shorter recurrence-free interval in the no chemotherapy arm of the IBCSG studies, as well as in the chemotherapy-treated patients within the combined Institutional and IBCSG chemotherapy cohorts (100 marker panel, P=0.002; 30 marker panel, P=0.05). Chromosome 19 sites were enriched among these loci. In conclusion, our hypermethylation signatures identify increased recurrence risk independent of whether patients receive chemotherapy.

overall_design: Three archival TNBC patient sample sets were analysed: An Institutional NoChemo Discovery set of 110 samples of convenience (49 cases & 61 controls) from collaborating institutional tissue archives; One validation NoChemo set of 49 samples from the IBCSG trialists (15 cases & 34 controls); and one combined Institutional and IBCSG Chemo validation set set of 120 samples (26 cases and 94 controls). Only the institutional datasets are available in this repository - access to IBCSG-derived datasets are contingent upon IBSCG review and approval. To request access to data, contact the IBCSG Statistical Center (stat_center@ibcsg.org).

first: MaryJo

last: Fackler

first: Soonweng

last: Cho

first: Leslie

last: Cope

first: Edward

last: Gabrielson

first: Kala

last: Visvanathan

first: Kathleen

last: Wilsbach

first: Danielle

last: Meir-Levi

first: Charles

last: F. Lynch

first: Jeffrey

last: Marks

first: Joseph

last: Geradts

first: Meredith

last: M. Regan

first: Giuseppe

last: Viale

first: Antonio

last: C. Wolff

first: Saraswati

last: Sukumar

first: Christopher

last: B. Umbricht


title: Comparison of gene expression profiles of uropathogenic Escherichia coli CFT073 after prolonged exposure to subinhibitory concentrations of different biocides

city: Lyngby

first: Malgorzata

last: Ligowska-Marzeta

address: Søltofts Plads 221

country: Denmark

institute: Technical University of Denmark

summary:
Biocides are chemical compounds widely used in hospital settings for a variety of purposes, but mainly for disinfection. The chemical properties of a biocide, as well as the biocide concentration, influence which cellular targets are affected. Exposure of bacteria to residual concentrations of biocides could lead to development of increased resistance towards the biocide in use, as well as cross-resistance towards other antimicrobials, including antibiotics. The aim of this study was to examine whether biocides could induce any potentially relevant genes that could affect pathogen's drug resistance or fitness.
By examining global gene expression of the uropathogenic Escherichia coli CFT073 after exposure to subinhibitory concentrations of four biocides (benzalkonium chloride - BAC, chlorhexidine - CHX, hydrogen peroxide - H2O2, triclosan - TSN), we found that each biocide changed expression of different groups of genes and that exposure to benzalkonum chloride caused changes in expression of the largest number of genes among all biocides. In general, the four biocides tested in this study at subinhibitory concentrations did not increase the resistance potential of the pathogen to other antimicrobials. We could, however, identify clusters of genes that could possibly help the strain to grow in the presence of a biocide in the medium.

overall_design: A culture of E. coli CFT073 without any biocide treatment served as the control sample. That culture was grown under the exact same conditions as the four biocide-treated samples. Each sample was collected in three biological replicates at the mid-exponential phase of growth.

first: Viktoria

last: Hancock

first: Hanne

last: Ingmer

first: Frank

last: Aarestrup


title: The thyroid hormone receptor β inhibits self-renewal capacity of breast cancer stem cells (mammospheres from MCF7 cells)

first: Cristian

last: Suarez Cabrera

summary: Since the thyroid hormone receptor β (TRβ) appears to suppress breast tumor growth and metastasis, we have analyzed the possibility that this receptor could affect cancer stem cell biology using mammospheres from TRβ-expressing MCF-7 cells (MCF7-TRβ cells) treated with the thyroid hormone T3.

overall_design: Gene expression was compared among mammospheres from MCF7 control cells (transduced with a selector Neo gene), MCF7-TRβ cells and both of them treated with T3. Three replicates were analyzed per each group.

first: Irene

last: López-Mateo

first: Elvira

last: Alonso-Merino

last: Suárez-Cabrera

first: Shue-Ye

last: Cheng

first: Susana

last: Alemany

first: Jesús

last: Paramio

first: Ana

last: Aranda


title: The thyroid hormone receptor β inhibits self-renewal capacity of breast cancer stem cells


title: Adipose derived stem cells (ASCs) methylation differences between lean and obese individuals

city: Tarragona

first: Miriam

last: Ejarque

address: c/Mallafré Guasch 4

institute: Institut d'Investigacions Sanitaries Pere Virgili

type: Methylation profiling by genome tiling array

summary: Pathological expansion of adipose tissue (AT) in obesity is supported by adipocyte precursors, termed adipose-derived stromal/stem cells (ASCs). Elucidation of mechanisms underlying ASC function may lead to therapeutic interventions to treat fat mass accumulation. Using epigenome-wide association studies, we explored the impact of obesity on the methylation signature of human ASCs.

overall_design: Genomic DNA was extracted from cells using the NucleoSpin® Tissue Kit (Macherery-Nagal GmbH). DNA methylation profiles were generated on the Infinium Human-Methylation450K BeadChip (Illumina). The BeadChip was developed to assay more than 480,000 CpG sites and selected CpG loci in parallel. DNA methylation data were processed using GenomeStudio software (Illumina) by applying the default settings.

first: Sonia

last: Fernández-Veledo

first: Joan

last: Vendrell

first: Carolina

last: Serena

first: Victoria

last: Ceperuelo-Mallafré


title: Development of gene expression signatures in colon tissues from wildtype and CARD9 knockout tumor mice

city: Nanjing

first: TINGTING

last: WANG

address: 22 Hankou Road

institute: Nanjing University

summary: We report the application of single-molecule-based sequencing technology for high-throughput profiling of mRNA expression profile for colon tissues from wildtype and CARD9 knockout mice treated with AOM/DSS

overall_design: WT and Card9-/- mice  were injected intraperitoneally with AOM (10 mg/kg) on day 1. After 5 days, 2% DSS (molecular weight, 36-50 kDa) was added to the drinking water for 7 consecutive days. Three cycles of DSS treatment were used, and mice were euthanized on day 100. Colon tissues were collected from mice. mRNA of the colon tissues were isolated with TRIZOL and subject to RNA-seq

first: T

last: Wang

first: X

last: Lin


title: CNOTshRNA or Melatonin treated samples

city: Seoul

first: Hyemin

last: Lee

address: Kyunghee-dae-ro 26

country: South Korea

institute: Kyunghee Univ

summary:
This microarray data was assessed in CNOT knockdown or non-treated non small lung cancer cells (A549 and H1299).
This microarray data was assessed in melatonin treated compared to non-treated glioblastoma stem like cells (XO1 and XO2).

overall_design: After treated with CNOT knockdown or melatonin hormone in each group, RNA of the cells were extracted. The RNA was evaluated using Agilent assay by company Bioneer.

first: Sung-Hoon

last: Kim

first: Ji-Hoon

last: Jung


title: Temporal changes of floral color and expression of carotenoids-related genes in flower petal of Osmanthus fragrans var. semperflorens : using de novo transcriptome sequencing

city: Chengdu

first: Rui

last: Chen

address: 20 Temple RD.Jingjiang District,Chengdu

institute: Horticulture Institute, Sichuan Academy of Agricultural Science

summary: Genes of carotenoids biosynthetic pathway were inspected in different flowering stages of two flowering rounds. And we found core genes are regulated under different patterns in the two flowering rounds.

overall_design: Genes of carotenoids biosynthesis at six flowering stages were analyzed. Finally, Five replicated were pooled into one sample for each stage

first: Xiaolin

last: Xian

first: Yuanzhi

last: Pan


title: ChAP-Seq analysis of CgpS in C. glutamicum

status: Public on Dec 04 2019

city: Juelich

first: Andrei

last: Filipchyk

address: Wilhelm-Johnen-Straße

institute: FZ-Juelich

summary: We evaluated how CgpS binds in the genome of C. glutamicum

overall_design: Examination of the CgpS binding profile under standard cultivation conditions

first: Eugen

last: Pfeifer

first: Max

last: Hünnefeld

first: Tino

last: Polen


title: Transcriptional profiling of neurons in the cerebral cortex of a Cbln1-TRAP (NIDA030) mouse line

city: New York

first: Laura

last: Kus

address: 1230 York Avenue # 260

institute: The Rockefeller University

summary: TRAP translational profiling is a method that allows investigators to genetically characterize specific cell types in complex tissues such as mouse brain.  Using this technique we obtained RNA-Seq data from actively translating transcripts present in pyramidal neurons in the cerebral cortex of adult Cbln1-EGFP/Rpl10a (NIDA030) mice.

overall_design: TRAP-Seq of neurons in the cerebral cortex of adult Cbln1-EGFP/Rpl10a (NIDA030) mice

first: Jim

last: Li

first: Nathaniel

last: Heintz


title: Loss of TSC complex enhances gluconeogenesis via upregulation of Dlk1-Dio3 locus miRNAs

city: Zurich

first: Andrzej

middle: Jerzy

last: Rzepiela

address: John-von-Neumann-Weg 9

department: ScopeM

institute: ETH

summary: Loss of the tumor suppressor tuberous sclerosis complex 1 (Tsc1) in the liver promotes gluconeogenesis and glucose intolerance.  We asked whether this could be attributed to aberrant expression of small RNAs.  We preformed small-RNA sequencing on liver of Tsc1 knock-out mice, and found that miRNAs of the delta like homolog 1 (Dlk1) – deiodinase iodothyronine type III (Dio3) locus are upregulated in an mTORC1-dependent manner.  Sustained mTORC1 signaling during development prevented CpG methylation and silencing of the Dlk1-Dio3 locus, thereby increasing miRNA transcription.  Deletion of miRNAs encoded by the Dlk1-Dio3 locus reduced gluconeogenesis, glucose intolerance and fasting blood glucose levels. Thus, miRNAs contribute to the metabolic effects observed upon loss of TSC1 and hyperactivation of mTORC1 in the liver.  Furthermore, we show that miRNA is a downstream effector of hyperactive mTORC1 signaling.

overall_design: MiRNA-Seq sample from mice liver is analyzed. There are 5 replicates for Tsc1 mutant ("M") and 5 for the control condition ("C").

first: Dritan

last: Liko


title: Driver gene alterations and activated signaling pathways toward malignant progression of gastrointestinal stromal tumors

city: Sunto-gun

first: Keiichi

last: Ohshima

state: Shizuoka

address: 1007 Shimonagakubo, Nagaizumi-cho

department: Medical Genetics Division

institute: Shizuoka Cancer Center Research Institute

summary: Mutually exclusive KIT and PDGFRA mutations are considered to be the earliest events in gastrointestinal stromal tumors (GISTs), but insufficient for their malignant progression. Here, we explored to identify driver genes and signaling pathways relevant to GIST progression. We investigated gene expression along with genetic profiles of 707 driver genes, including mutations, gene fusions, copy number gain or loss, for 65 clinical specimens of surgically dissected GISTs, consisting of 6 metastasis and 59 primary tumors from stomach, small intestine, rectum, and esophagus. Genetic alterations include oncogenic mutations and amplification-dependent expression enhancement for oncogenes (OGs), and loss of heterozygosity (LOH) and expression reduction for tumor suppressor genes (TSGs). We assigned activated OGs and inactivated TSGs to 27 signaling pathways, whose activation was compared between malignant GISTs (metastasis and high-risk GISTs) and less malignant GISTs (low- and very low-risk GISTs). Integrative molecular profiling indicated that higher incidence of genetic alterations of driver genes were detected more in malignant GISTs (96%, 22 of 23) than in less malignant GISTs (73%, 24 of 33). The malignant GIST samples showed mutations, LOH, and aberrant expression dominantly in driver genes associated with signaling pathways of PI3K (PIK3CA, AKT1, and PTEN) and cell cycle (RB1, CDK4, and CDKN1B). Additionally, we identified potential PI3K-related genes, whose expression was upregulated (SNAI1 and TPX2) or downregulated (BANK1) in malignant GISTs. Based on our observations, we propose that inhibition of PI3K pathway signals might potentially be an effective therapeutic strategy against malignant progression of GISTs.

overall_design: The mRNA expression profiles of 65 GIST tumors were determined using Agilent SurePrint G3 Human Gene Expression 8×60K v2 Microarray.

last: Hatakeyama