title: Peptidylarginine deiminases 2 and 4 modulate innate and adaptive immune responses in TLR-7 dependent lupus

status: Public on Jan 17 2019

city: Bethesda

first: Hong-wei

last: Sun

state: MD

address: 9000 Rockville Pile

department: Office of Science & Technology

institute: NIAMS

summary: Peptidylarginine deiminases (PADs) play critical roles in the development and progression of autoimmune diseases. PAD4 is involved in systemic lupus erythematosus (SLE) pathogenesis while the role of PAD2 in immune dysregulation in SLE is not clear. The differential roles of PAD2 and PAD4 in the progression of murine SLE and in modulation of innate and adaptive immunity were examined. The transcriptome of lymphoid organs from imiquimod-treated PAD2/4 and control mice was characterized and elucidated using RNASeq technology.

overall_design: This dataset includes a total of 30 individual samples. This study sought to characterize the differential transcriptomic profiles in lymphoid organ(SPLN and LN) in Pad2-/- and Pad4-/- mice in response to TLR7 agonist(IMIQU), as compared to the WT mice treated with IMIQU

first: Y

last: Liu

first: YL

last: Lightfoot

first: N

last: Seto

first: C

last: Carmona-Rivera

last: Moore

first: R

last: Goel

first: L

last: O'Neil

first: P

last: Mistry

last: Hoffmann

first: S

last: Mondal

middle: N

last: Premnath

first: K

last: Gribbons

last: Dell'Orso

last: Jiang

last: Thompson

first: H

last: Coonrod

last: Kaplan


title: RNA-Seq of testicular peritubular myoid cells, other testicular cells, and other tissue smooth muscle-like cells

status: Public on Jan 19 2019

city: Beijing

first: Su-Ren

last: Chen

address: 1Beichen West Road, Chaoyang District

department: State Key Laboratory of Stem Cell and Reproductive Biology

country: China

institute: Institute of Zoology, Chinese Academy of Sciences

type: Expression profiling by high throughput sequencing

summary: In addition to germ cell population, testes contain several types of somatic cells, including Sertoli cells, Leydig cells, and peritubular myoid (PTM) cells. PTM cells are a type of smooth muscle-like cells and have contraction ability. To identify a marker of PTM cells, we isolated primary cells and subsequently performed RNA-Seq of testicular peritubular myoid cells (PTM_1, PTM_2, PTM_3), testicular Sertoli cells (Sertoli_1, Sertoli_2, Sertoli_3), testicular Leydig cells (Leydig_1, Leydig_2, Leydig_3), testicular germ cells (Germ_1, Germ_2, Germ_3), vascular smooth muscle cells (VSMC_1, VSMC_2, VSMC_3), intestinal smooth muscle cells (ISMC_1, ISMC_2, ISMC_3), and tracheal smooth muscle cells (TSMC_1, TSMC_2, TSMC_3) using BGISEQ-500 platform (BGI, China).

overall_design: The mouse testicular cells were isolated as previously described (PMID: 23759306, 26995740, 30306767). Smooth muscle-like cells were obtaiend from Procell (Wuhan, China).


title: Combinatorial genetics reveals a scaling law for the effects of mutations on splicing

city: Barcelona

first: Pablo

last: Baeza

address: Dr. Aiguader, 88

department: Systems Biology

country: Spain

institute: Centre for Genomic Regulation

summary: Despite a wealth of molecular knowledge, quantitative laws for accurate prediction of biological phenomena remain rare. Alternative pre-mRNA splicing is an important regulated step in gene expression frequently perturbed in human disease. To understand the combined effects of mutations during evolution, we quantified the effects of all possible combinations of exonic mutations accumulated during the emergence of an alternatively spliced human exon. This revealed that mutation effects scale non-monotonically with the inclusion level of an exon, with each mutation having maximum effect at a predictable intermediate inclusion level. This scaling is observed genome-wide for cis and trans perturbations of splicing, including for natural and disease-associated variants. Mathematical modelling suggests that competition between alternative splice sites is sufficient to cause this non-linearity in the genotype-phenotype map. Combining the global scaling law with specific pairwise interactions between neighbouring mutations allows accurate prediction of the effects of complex genotype changes involving >10 mutations.

overall_design: Combinatorially complete genotype-phenotype landscape of a model human alternatively-spliced exon (FAS exon 6) by deep mutation scanning

last: Baeza-Centurion

first: Belén

last: Miñana

first: Jörn

last: Schmiedel

first: Juan

last: Valcárcel

first: Ben

last: Lehner


title: West Nile virus-inclusive single-cell RNA sequencing reveals heterogeneity in the type I interferon response within single cells

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

country: USA

institute: Yerkes National Primate Research Center

summary: West Nile virus (WNV) is a neurotropic mosquito-borne flavivirus of global importance. Neuroinvasive WNV infection results in encephalitis and can lead to prolonged neurological impairment or death. Type I interferon (IFN-I) is crucial for promoting antiviral defenses through the induction of antiviral effectors, which function to restrict viral replication and spread. However, our understanding of the antiviral response to WNV infection is mostly derived from analysis of bulk cell populations. It is becoming increasingly apparent that substantial heterogeneity in cellular processes exists among individual cells, even within a seemingly homogenous cell population. Here, we present WNV-inclusive single-cell RNA sequencing (scRNA-seq), an approach to examine the transcriptional variation and viral RNA burden across single cells. We observed that only a few cells within the bulk population displayed robust transcription of IFN-β mRNA, and this did not appear to depend on viral RNA abundance within the same cell. Furthermore, we observed considerable transcriptional heterogeneity in the IFN-I response, with genes displaying high unimodal and bimodal expression patterns. Broadly, IFN-stimulated genes negatively correlated with viral RNA abundance, corresponding with a precipitous decline in expression in cells with high viral RNA levels. Altogether, we demonstrated the feasibility and utility of WNV-inclusive scRNA-seq as a high-throughput technique for single-cell transcriptomics and WNV RNA detection. This approach can be implemented in other models to provide insights into the cellular features of protective immunity and identify novel therapeutic targets.

overall_design: Bulk RNA sequencing and WNV-inclusive single-cell RNA sequencing were performed for WNV-infected L929 cells with and without reduced in vitro spread

first: Justin

middle: T

last: O’Neal

first: Amit

middle: A

last: Upadhyay

first: Amber

last: Wolabaugh

first: Nirav

middle: B

last: Patel

first: Steven

middle: E

last: Bosinger

first: Mehul

middle: S

last: Suthara


title: Functional Characterisation of the Ubiquitin-like Core Autophagy Protein ATG12 in Dictyostelium discoideum

status: Public on Jan 15 2019

city: Cologne

first: Ludwig

last: Eichinger

state: NRW

address: Joseph-Stelzmann-Str. 52

department: Biochemistry Medical Faculty

country: Germany

institute: Centre for Biochemistry Medical Faculty University of Cologne

summary:
Purpose: First global survey of the transcriptome in autophagy-deficient strains of D. discoideum.
Results: Our RNAseq analysis of ATG12‾, ATG16‾ and ATG12‾/16‾ cells revealed major transcriptional changes in a large number of genes in comparison to AX2.
Conclusions: Our study represents the first detailed analysis of the transcriptome in autophagy-deficient strains of D. discoideum. The data were generated by RNA-seq technology. The optimised data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell. We conclude that RNA-seq based transcriptome characterisation would expedite genetic network analyses and permit the dissection of complex biologic functions.

overall_design: Total RNA from either vegetative or for 3 h starved D. discoideum cells (AX2 wild-type and ATG12‾, ATG16‾, ATG12‾/16‾ mutant strains) was isolated, n=3 or n=6, Illumina HiSeq 4000.

first: Sarah

last: Fischer

first: Ramesh

last: Rijal

first: Peter

last: Frommolt

first: Prerana

last: Wagle

first: Roman

last: Konertz

first: Jan

last: Faix

first: Susanne

last: Meßling


title: Effect of endothelin-1 (ET-1) on mouse testicular peritubular myoid cells

first: Su-Ren

last: Chen

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Effect of endothelin-1 (ET-1) on mouse testicular peritubular myoid cells [RNA-Seq]

summary: PTM cells can be induced to contract by endothelin 1 (ET1). We performed RNA-Seq of untreated testicular peritubular myoid cells (PTM_1, PTM_2, PTM_3) and ET1-treated peritubular myoid cells (ET1_1, ET1_2, ET1_3) using BGISEQ-500 platform (BGI, China).

overall_design: The mouse testicular peritubular myoid cells were isolated as our previously described (PMID: 30306767). PTM cells were treated with or without 50 nM ET1 in DMEM/F12 for 5 min at 37°C incubator.


title: Enhanced Reduced Representation Bisulfite Sequencing of 48hpf WT and tet2/3 DM dissected heart

first: Heng

last: Pan

address: 49 North Garden Rd., Haidian District

institute: Peking University Third Hospital

type: Methylation profiling by high throughput sequencing

summary: Ten-eleven translocation (Tet) enzymes (Tet1/2/3) mediate 5-methylcytosine (5mC) hydroxylation, which can facilitate DNA demethylation and thereby impact gene expression. Studied mostly for how mutant isoforms impact cancer, the normal roles for Tet enzymes during organogenesis are largely unknown. By analyzing compound mutant zebrafish, we discovered a requirement for Tet2/3 activity in embryonic heart for recruitment of epicardial progenitors, associated with defects in development of the atrial-ventricular canal (AVC). Through a combination of methylation, hydroxymethylation, and transcript profiling, the genes encoding the ActivinA subunit Inhbaa (in endocardium) and Sox9b (in myocardium) were implicated as demethylation targets of Tet2/3 and critical for organization of AVC-localized extracellular matrix (ECM), facilitating migration of epicardial progenitors onto the developing heart tube. This study elucidates essential DNA epigenetic modifications that govern gene expression changes during cardiac development with striking temporal and lineage specificities, highlighting complex interactions in multiple cell populations during development of the vertebrate heart.

overall_design: For reduced representation bisulfite sequencing genomic DNA was isolated from 48hpf WT and tet2/3 DM dissected hearts using the DNeasy Blood & Tissue Kit (Qiagen, 69504) following manufacturer’s guidelines. One replicate was done for each sample.

first: Lan

last: Yahui

first: Pan

last: Heng


title: TETs Regulate Proepicardial Cell Migration through Extracellular Matrix Organization during Zebrafish Cardiogenesis

type: Genome binding/occupancy profiling by high throughput sequencing


title: RNA Sequencing of  sibling and TET2/3 DKO zebrafish

overall_design: For RNA-Sequencing total RNA was isolated with the RNeasy Mini Kit (Qiagen, 74136) from 25hpf sibling and TET2/3 DKO zebrafish embryos (n=3 each) or 48hpf WT, sibling and TET2/3 DKO zebrafish dissected heart (n=2 each).


title: Effect of endothelin-1 (ET-1) on mouse testicular peritubular myoid cells [miRNA-Seq]

summary: PTM cells can be induced to contract by endothelin 1 (ET1). We performed miRNA-Seq of untreated testicular peritubular myoid cells (PTM_1, PTM_2, PTM_3) and ET1-treated peritubular myoid cells (ET1_1, ET1_2, ET1_3) using BGISEQ-500 platform (BGI, China).


title: Host cell gene expression profile in ectromelia virus infected mouse RAW cells at 2, 16 hours post infection

city: Singapore

first: Richard

middle: J

last: Sugrue

address: 60 Nanyang Drive

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

summary: The poxviruses are a family of  linear double-stranded DNA viruses about 130 to 230 kbp, that belong to the family Poxviridae. The poxviruses have an animal origin and have evolved to infect a wide host range. Variola virus (VARV), the causative agent of smallpox, is a poxvirus that infect only humans, but other poxviruses such monkey pox virus and cowpox virus have also across over from animals to infect humans. Therefor understanding the biology of poxviruses can help to devise antiviral strategies. In this study we used a system-based approach to examine the host responses to three different orthopoxviruses, CPXV, VACV and ECTV in the murine macrophage RAW 264.7 cell line.

overall_design: The ectromelia virus infected mouse RAW cells were harvested at 2 and 16 hpi and RNA extraction was performed using standard protocol as described by Affymetrix. The aim of this experiment is to analyze host cell response to ectromelia virus infection.

last: Sutejo

first: Hui

first: Boon-Huan

last: Tan


title: Host cell gene expression profile in vaccinia virus infected mouse RAW cells at 2, 16 hours post infection

overall_design: The vaccinia virus infected mouse RAW cells were harvested at 2 and 16 hpi and RNA extraction was performed using standard protocol as described by Affymetrix. The aim of this experiment is to analyze host cell response to vaccinia virus infection.


title: 5hmC (48hpf WT dissected heart) 5hMe-Bead-Integrated Click-seq (5hMe-BIC-seq)

overall_design: Genomic DNA was isolated from wildtype (n=2) dissected hearts using DNeasy Blood & Tissue Kits (Qiagen). At least 40 hearts were collected for each biological group.


title: Host cell gene expression profile in cowpox virus infected mouse RAW cells at 2, 16 hours post infection

overall_design: The cowpox virus infected mouse RAW cells were harvested at 2 and 16 hpi and RNA extraction was performed using standard protocol as described by Affymetrix. The aim of this experiment is to analyze host cell response to cowpox virus infection.


title: miRNA-Seq of testicular peritubular myoid cells, other testicular cells, and other tissue smooth muscle-like cells

summary: In addition to germ cell population, testes contain several types of somatic cells, including Sertoli cells, Leydig cells, and peritubular myoid (PTM) cells. PTM cells are a type of smooth muscle-like cells and have contraction ability. To identify a marker of PTM cells, we isolated primary cells and subsequently performed miRNA-Seq of testicular peritubular myoid cells (PTM_1, PTM_2, PTM_3), testicular Sertoli cells (Sertoli_1, Sertoli_2, Sertoli_3), testicular Leydig cells (Leydig_1, Leydig_2, Leydig_3), testicular germ cells (Germ_1, Germ_2, Germ_3), vascular smooth muscle cells (VSMC_1, VSMC_2, VSMC_3), intestinal smooth muscle cells (ISMC_1, ISMC_2, ISMC_3), and tracheal smooth muscle cells (TSMC_1, TSMC_2, TSMC_3) using BGISEQ-500 platform (BGI, China).


title: DNA methylation profile of  Tasmanian Devil facial tumor biopsies and matched healthy skin and spleen samples, as well as additional nerve tissue, and strain 1 tumor cell line.

status: Public on Jan 14 2019

city: Vienna

first: Andreas

last: Bergthaler

address: Lazarettgasse 14 AKH BT25.3

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

summary:
Purpose: Depict the landscape of epigenetic regulation in Tasmanian devil facial tumor biopsies.
Differential analysis of healthy versus tumor biopsies highlighted 166 candidate genes with different DNA methylation levels in their promoters, which included the tumor-specific hypermethylated promoters of Estrogen Receptor 1 (ESR1) and the transcription factor GATA3.

overall_design: We mapped DNA methylation by reduced representation bisulfite sequencing and analysed epigenetic heterogeneity between healthy and tumor biopsies.

first: Alexandra

last: Popa

first: Johanna

last: Klughammer

first: Lindsay

last: Kosack

first: Christoph

last: Bock


title: Host-responses to Poxvirus-infected macrophages


title: Effect of heat stress on mouse testicular peritubular myoid cells [RNA-seq]

summary: We performed RNA-Seq of untreated testicular peritubular myoid cells (NC_1, NC_2, NC_3), and peritubular myoid cells that were collected 1 hour (H1_1, H1_2, H1_3) and 6 hours (H6_1, H6_2, H6_3) after heat treatment using BGISEQ-500 platform (BGI, China).

overall_design: The mouse testicular peritubular myoid cells were isolated as our previously described (PMID: 30306767). Heat treatment was performed as our previously described (PMID: 23759306).

first: Xiang-Nan

last: Wu


title: DNA IP for 5hmC modified CpGs in the liver of control and HFD fed mouse liver.

status: Public on Jan 12 2019

city: Edinburgh

first: Marcus

middle: James

last: Lyall

state: Lothian

address: The Queen's Medical Research Institute, 47 Little France Crescent

department: University/British Heart Foundation Centre for Cardiovascular Science

country: United Kingdom

institute: University of Edinburgh

summary: We carry out 5-hydroxymethylation DNA immunoprecipitation (hmeDIP) prior to sequencing Ion Proton P1 to report on the genome-wide 5hmC patterns of hepatic in murine hepatic steatosis.

overall_design: C56BL/6 mice were fed control (11% calories by saturated fat, Research Diets Inc cat number D12329) or high fat (58% calories by saturated fat Research Diets Inc cat number D12331) diet for 17 weeks to induce obesity and hepatic steatosis.  DNA was extracted from fresh frozen liver.  We carry out 5-hydroxymethylation DNA immunoprecipitation (hmeDIP) prior to sequencing Ion Proton P1 to report locus specific changes in 5hmC induced by obesity.  We demonstrate enrichment of 5hmC within gene bodies of induced genes with reciprocal loss of genic 5hmC in downregulated genes.

first: John

middle: P

last: Thomson

first: Amanda

last: Drake

middle: R

last: Meehan


title: Gender susceptibility to ventilator-induced lung injury

city: Oviedo

first: Guillermo

middle: M

last: Albaiceta

address: Avenida de Roma s/n

institute: Instituto de Investigación Sanitaria del Principado de Asturias

summary: To assess the differences between male and female mice submitted to mechanical ventilation, RNA extracted from lung homogenates from mice was compared

overall_design: Male and female C57Bl/6 mice were sacrificed in baseline conditions or after mechanical ventilation (2.5 hour, peak pressure 15, ZEEP, rate 100/min, I:E 1:1)

first: Inés

last: López-Alonso


title: Transcriptomes of wild-type C. albicans treated with respiration inhibitors SNP, SHAM or SNP+SHAM

city: Canterbury

first: Lucian

last: Duvenage

address: Giles Lane

department: School of Biosciences

institute: University of Kent

summary: We examined the early gene expression profiles (30 min) of log-phase wild-type C. albicans growing in YPD at 30 °C in response to respiration inhbitors 1mM SNP,  0.5 mM SHAM, or 1 mM SNP+ 0.5 mM SHAM combination

overall_design: Treatment of C. albicans with respiration inhibitors in triplicate and high-throughput sequencing using Illumina NextSeq500


title: Multi-omics and genome-scale modeling reveal a metabolic shift during C. elegans ageing

status: Public on Jan 11 2019

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

summary: We conducted a time series of transcriptomics measurements during normal ageing in C. elegans in two non-reproductive strains (fem and gem) during normal ageing (days 1 to 10 of adulthood) and used this together with a multi-omics modelling pipeline to explore the changes that take place due to ageing.

overall_design: Two strains and several time points with three replicates per strain and time point.

first: Janna

last: Hastings

first: Abraham

last: Mains

first: Bhupinder

last: Virk

first: Nicolas

last: Rodriguez

first: Sharlene

last: Murdoch

first: Juliette

last: Pearce

first: Sven

last: Bergmann

last: Le Novère

first: Olivia

last: Casanueva


title: Innate mesenchymal TLR4/MyD88 signals promote spontaneous intestinal tumorigenesis

city: Vari, Athens

first: George

last: Kollias

address: 34 Fleming Street

department: Immunology

country: Greece

institute: BSRC "Alexander Fleming"

summary: This study shows that the TLR4/MyD88 pathway in intestinal mesenchymal cells promotes intestinal carcinogenesis in the APCmin mouse model.

overall_design: 3’ RNA-Seq (QuantSeq) profiling of ColVIcre+ wt and MyD88 knockout primary mouse intestinal mesenchymal cells before and after treatment with LPS for 6 hours. 3 replicates per group.

first: Vasiliki

last: Koliaraki

first: Niki

last: Chalkidi

first: Ana

last: Henriques

first: Christos

last: Tzaferis


title: Transcriptome profiling of Tasmanian Devil facial tumor (DFTD1) cell lines of 4 strains and the fibroblast cell line.

first: Andreas

last: Bergthaler

summary:
Purpose: To asses the transcriptome of 4 strains of the Tasmanian Devil facial tumor and one healthy fibroblast cell line.
Methods: DFTD cells were grown from primary cell cultures derived from fine needle aspirates that have been collected from the wild. Total RNA from devil facial tumor strains 1-4 and the fibroblast was isolated from approximately 1 x 10^6 cells using QIAzol lysis reagent according to the manufacturer’s instructions (Qiagen). RNA-seq libraries were prepared with TruSeq Stranded mRNA LT sample preparation kit (Illumina) using Sciclone and Zephyr liquid handling robotics (PerkinElmer). The 5 libraries were pooled, diluted and sequenced on Illumina HiSeq 3000/4000 using 75 bp paired-end chemistry. Base calls provided by the Illumina Realtime Analysis software were converted into BAM format using Illumina2bam and demultiplexed using BamIndexDecoder. Paired-end reads were trimmed for adaptor sequences and filtered with the trimmomatic tool. Trimmed reads were aligned on the version 7.0 of the Tasmanian Devil with the STAR aligner. Counting of reads on annotated transcripts (Sarcophilus_harrisii.DEVIL7.0.90.gtf from Ensembl) was performed with featurecounts on fragments. The DESeq2 Biconductor library has been used for counts normalization and differential analysis between the transcriptomes of the four DFTD and fibroblast cell lines

overall_design: High coverage paired-end mRNA sequencing of 4 DFTD strains and one healthy fibroblast (Sarcophilus harrisii) were generated on a Illumina HiSeq 3000/4000 sequencer.

first: Lindsay

last: Kosack

first: Alexander

last: Lercher

first: Alexandra

last: Popa


title: The Impact of Wheat Rht-B1b Semi-Dwarfing Allele on Photosynthesis and Seed Development under Field Conditions

city: Bozeman

first: Michael

last: Giroux

state: Montana

address: 119 Plant Bioscience Building

department: Plant Sciences

institute: Montana State University

summary: The Reduced Height (Rht) genes formed the basis for the green revolution in wheat by decreasing plant height and increasing productive tillers. There are two current widely used Rht mutant alleles, Rht-B1b and Rht-D1b. Both reduce plant height by 20% and increase seed yield by 5-10%. They are also associated with decreased seed size and protein content. Here we tested the degree to which Rht-B1b impacts flag leaf photosynthetic rates and carbon and nitrogen partitioning to the flag leaf and grain during grain fill under field conditions using near isogenic lines (NILs) that were either standard height (Rht-B1a) or semi-dwarf (Rht-B1b). The results demonstrate that at anthesis, Rht-B1b reduces flag leaf photosynthetic rate per unit area by 18% and chlorophyll A content by 23%. Rht-B1b significantly reduced grain protein beginning at 14 days post anthesis with the greatest difference seen at 21 days post anthesis (DPA) (12%). Rht-B1b also significantly decreased individual seed weight beginning at 21 DPA and by 15.2% at 28 DPA. Global expression analysis using RNA extracted from developing leaves and stems demonstrated that genes associated with carbon and nitrogen metabolism are not substantially altered by Rht-B1b. From this study, we conclude that Rht-B1b reduces flag leaf photosynthetic rate at flowering while changes in grain composition begin shortly after anthesis.

overall_design: Total RNA was collected from leaf and stem tissue from plants at 14 days past anthesis. Three samples were taken from plants carrying the semi-dwarfing allele Rht-B1b and three samples were taken from plants without the semi-dwarfing allele.

first: Emma

last: Jobson

first: Rachel

last: Johnston

first: Alanna

last: Oiestad

first: John

last: Martin


title: Single Cell Sequencing Reveals Gene Expression Signatures Associated with Bone Marrow Stromal Cell Subpopulations and Time in Culture [microarray]

status: Public on Jan 10 2019

city: BETHESDA

first: Shutong

last: Liu

state: Maryland

address: 9000 Rockville Pike

department: Clinical Center

institute: National Institutes of Health

summary: Background Bone marrow stromal cells (BMSCs) are a heterogeneous population that participates in wound healing, immune modulation and tissue regeneration. Next generation sequencing was used to analyze transcripts from single BMSCs in order to better characterize BMSC subpopulations. Methods Cryopreserved passage 2 BMSCs from one healthy subject were cultured through passage 10. The transcriptomes of bulk BMSCs from designated passages were analyzed with microarrays and RNA sequencing (RNA-Seq). For some passages, single BMSCs were separated using microfluidics and their transcriptomes were analyzed by RNA-Seq. Results Transcriptome analysis microarray and RNA-Seq of unseparated BMSCs from passages 2, 4, 6, 8, 9 and 10 yielded similar results; both data sets grouped passages 4 and 6 and passages 9 and 10 together and genes differentially expressed among these early and late passage BMSCs were similar. 3D Diffusion map visualization of single BMSCs from passages 3, 4, 6, 8 and 9 clustered passage 3 and 9 into two distinct groups, but there was considerable overlap for passage 4, 6 and 8 cells. Markers for early passage, FGFR2, and late passage BMSCs, PLAT, were able to identify three subpopulations within passage 3 BMSCs; one that expressed high levels of FGFR2 and low levels of PLAT; one that expressed low levels of FGFR2 and high levels of PLAT and one that expressed intermediate levels of FGFR2 and low levels of PLAT. Conclusions Single BMSCs can be separated by microfluidics and their transcriptome analyzed by next generation sequencing. Single cell analysis of early passage BMSCs identified a subpopulation of cells expressing high levels of FGFR2 that might include skeletal stem cells.

first: David

middle: F

last: Stroncek

first: Yingdong

last: Zhao

first: Victoria

last: Chen

first: Rongye

last: Shi

first: Jinguo

first: Jiaqiang

last: Ren

first: Hui

first: Hee

last: Bae

first: Steven

middle: L

last: Highfill

first: Ping

last: Jin


title: Identification of novel diagnostic markers for fatal hypothermia by body temperature-dependent gene expression analysis in rats

city: Kitakyushu

first: Takahiro

last: Umehara

address: 1-1 Iseigaoka Yahatanishiku

country: Japan

institute: University of Occupational and Environmental Health

summary: Diagnosis of fatal hypothermia is considered to be difficult in forensic practice. In this study, in order to identify novel molecular markers of fatal hypothermia, we made rat models of mild, moderate and severe hypothermia, and performed body temperature-dependent gene expression analysis in illiopsoas muscle using next-generation sequencing.

overall_design: Twelve male wistar rats (Pathogen-free 9-week-old) were divided into 4 groups (control, mild, moderate and severe hypothermia), which were belonged 3 rats, and were anesthetized with intraperitoneal. After 30 minutes, they were treated at cold (ambient temperature: 4 °C), and chronologically measured rectal temperature (Ret). Control was euthanized by cervical dislocation at 30 minutes after anesthesia. Mild hypothermia was done by cervical dislocation when the Ret reached 30°C. Similarly, moderate and severe hypothermia also was done when the Ret did 22°C and 12°C, respectively. Total RNA from iliopsoas muscle was extracted using RNeasy Protect Mini kit (QIAGEN GmbH, Hilden, Germany) according to the manufacturer's instructions. RNA integrity was assessed by on-chip capillary electrophoresis using an Agilent RNA 6000 Nano kit and Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA, USA). NGS was performed using 2000 ng of total RNA. Three libraries were generated for each of the four conditions (Control, mild, moderate and severe hypothermia) (TruSeq Stranded mRNA LT Sample Prep Kit, Illumina, San Diego, California, USA), and sequenced on an Illumina Miseq.


title: Characterization of a novel microRNA, miR-188, elevated in serum of muscular dystrophy dog model

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: MicroRNAs (miRNAs) are non-coding small RNAs that regulate gene expression at the post-transcriptional level. Several miRNAs are exclusively expressed in skeletal muscle and participate in the regulation of muscle differentiation by interacting with myogenic factors. These miRNAs can be found at high levels in the serum of patients and animal models for Duchenne muscular dystrophy, and which is expected to be useful as biomarkers for their clinical conditions. By miRNA microarray analysis, we identified miR-188 as a novel miRNA that is elevated in the serum of the muscular dystrophy dog model, CXMDJ. miR-188 was not muscle-specific miRNA, but its expression was up-regulated in skeletal muscles associated with muscle regeneration induced by cardiotoxin-injection in normal dogs and mice. Manipulation of miR-188 expression using antisense oligo and mimic oligo RNAs alters the mRNA expression of the myogenic regulatory factors, MRF4 and MEF2C. Searching for the direct target of miR-188 suggested that it could be MEF2-interacting transcription repressor (MITR). Our results suggest that miR-188 regulates myogenic factors targeting MITR during muscle differentiation and that it may serve as a serum biomarker reflecting skeletal muscle regeneration.

overall_design: In this study, miRNAs were extracted from serum of 2-month-old dystrophic dog and age-matched normal dog, and applied to array analysis.

first: Hiroyuki

last: Shibasaki

first: Michihiro

last: Imamura

first: Sayuri

last: Arima

first: Jun

last: Tanihata

first: Mutsuki

last: Kuraoka

first: Yasunari

last: Matsuzaka

first: Fumiaki

last: Uchiumi

first: Sei-ichi

last: Tanuma

first: Shin’ichi

last: Takeda


title: The flow responsive transcription factor Klf2 is required for myocardial wall integrity by modulating Fgf signaling

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

institute: Max Planck Institute for Heart and Lung Research

summary: Complex interplay between cardiac tissues is crucial for their integrity.  The flow responsive transcription factor KLF2, which is expressed in the endocardium, is vital for cardiovascular development but its exact role remains to be defined.  To this end, we mutated both klf2 paralogues in zebrafish, and while single mutants exhibit no obvious phenotypes, double mutants display a novel phenotype of cardiomyocyte extrusion towards the abluminal side.  This extrusion requires cardiac contractility and correlates with the mislocalization of N-cadherin from the lateral to the apical side of cardiomyocytes.  Transgenic rescue data show that klf2 expression in endothelium, but not myocardium, can rescue this cardiomyocyte extrusion phenotype.  Transcriptome analysis of klf2 mutant hearts reveals that Fgf signaling is affected, and accordingly, we find that inhibition of Fgf signaling in wild-type animals leads to abluminal cardiomyocyte extrusion.  These studies provide new insights into how Klf2 regulates cardiovascular development and specifically myocardial wall integrity.

overall_design: Examination of transcriptional adaptation of klf2 mutants compared to wild type in zebrafish hearts (1 sample each).  To further understand how klf2 regulate cardiac wall integrity, we carried out transcriptomic analysis (using whole genome microarray expression profiling) of klf2 mutant hearts compared to WT.  96 hpf hearts were extracted from klf2 WT and mutant larvae (500 hearts from each genotype) as previously described (Burns & MacRae, 2006)

first: Seyed

last: Rasouli

first: Didier

last: Stainier


title: Leaf age dependent transcriptome analysis in response to abscisic acid

city: Köln

first: Matthias

middle: Leonhard

last: Berens

address: Carl-von-Linné-Weg 10

institute: Max Planck Institute for Plant Breeding Research

summary: Since development is an important regulator in hormonal responses we wanted to investigate to what extent responses to the phytohormone abscisic acid (ABA) are controlled by old and young leaves within a single plant. Our RNAseq analysis indicate that ABA treatment triggers as set of common and leaf age specific responses in both old and young leaves.

overall_design: 4-5 week old Arabidopsis thaliana Col-0 plats were sprayed with either control (0.5% EtOH + 0.05% Tween20) or ABA (500µM, 100 mM stock in EtOH, 0.05% Tween20) treated and old leaves (true leave 7) and young leaves (true leave 12) were harvested 48h after treatment. The experiment was repeated 3 times and in total 12 samples were used for statistical analysis.

first: Akira

last: Mine

first: Kenichi

last: Tsuda


title: Pvt1 silencing in C2C12 cell cultures

status: Public on Jan 07 2019

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

country: Italy

institute: University of Padova

summary: In order to understand the role of lncRNA Pvt1 in skeletal muscle physiopathology we silenced this transcript in-vitro, using C2C12 cell cultures, and in-vivo, in leg muscles of CD1 wild-type and denervated mice.

overall_design: In vitro Pvt1 silencing experiments were performed on proliferating C2C12 myoblasts using antisense LNA GapmeRs specific for Pvt1. Silencing efficiency was assessed by qRT-PCR.

first: Enrico

last: Alessio

first: Lisa

last: Buson

first: Francesco

last: Chemello

first: Francesca

last: Grespi

first: Paolo

last: Martini

first: Maria

last: Massimino

first: Beniamina

last: Pacchioni

first: Caterina

last: Millino

first: Chiara

last: Romualdi

first: Alessandro

last: Bertoli

first: Luca

last: Scorrano

first: Stefano

last: Cagnin


title: Gene Expression profiles of normal and inflamed colon tissues from Nik+/+, NikΔIE

status: Public on Jan 08 2019

city: Ann Arbor

first: XIANG

last: XUE

state: Michigan

address: 1301 E. Catherine Street

institute: Umich

summary: To investigate the detailed molecular mechanisms for the regulatory role of Nik in colitis, microarray gene expression analysis was performed on colon tissue RNA isolated from 3-month-old untreated control and DSS treated Nik+/+ and NikΔIE mice.

overall_design: Global gene expression profiling in colon tissue RNAs isolated from 3-month-old Nik+/+, (n=4; shah026, control; shah028, DSS) and  NikΔIE (n=4; shah027, Control; shah029, DSS).

first: Xiang

last: Xue

first: Yatrik

last: Shah


title: Gene expression profiling of 4T1 cells isolated from primary tumour or from spontaneous metastases sites

city: London

first: marjan

last: iravani

address: 237 Fulham Road

department: Breast Cancer Now

institute: Institute of Cancer research

summary: Differential gene expression in 4T1 mouse mammary tumour cells isolated from primary tumour or metastatic sites.

overall_design: Balb/c mice were inoculated orthotopically with 4T1 mouse mammary tumour cells. The 4T1 subclones were isolated from primary tumours, brains and lungs and cultured for 3-4 passages and subjected to gene expression profiling using Illumina platform.

first: Marjan

last: Iravani

first: Qiong

last: Gao


title: Transcriptomic Analysis of the Intracellular Pathogen Response (IPR)

city: La Jolla

first: Emily

last: Troemel

state: CA

department: Cell and Developmental Biology

institute: University of California, San Diego

summary: We used RNA-seq to identify gene expression changes in C. elegans pals-22 and pals-22 pals-25 mutants compared to wild-type animals, as well as in wild-type animals in response to bortezomib treatment.

overall_design: Total RNA was extracted from synchronized whole L4 C. elegans grown in biological triplicates

first: Kirthi

middle: C

last: Reddy

first: Tal

last: Dror

first: Ryan

last: Underwood

first: Guled

last: Osman

first: Christopher

last: Desjardins

first: Christina

last: Cuomo

first: Michalis

last: Barkoulas


title: Subcellular localization analysis of long non-non coding RNAs (lncRNAs) in skeletal muscle myofibers

first: Gerolamo

last: Lanfranchi

summary: In order to study the subcellular localization of lncRNAs in myofibers of skeletal muscle, single myofibers were isolated from Soleus, Extensor Digitorum Longus (EDL) and Tibialis Anterior (TA) of 9 mice. RNA was extracted from nuclei and cytoplasmic fractions of 5-10 isolated myofibers and than separately hybridized on microarrays. Preferential expression in nuclear or cytoplasmic compartment of each lncRNA was determined.

overall_design: Subcellular localization experiments were replicated using different pools of fibers from the same muscle of nine wild-type CD1 mice. Fibers were extracted from Soleus, EDL and TA for a total of 18 samples.

first: Enrico

last: Alessio

first: Lisa

last: Buson

first: Francesco

last: Chemello

first: Francesca

last: Grespi

first: Paolo

last: Martini

first: Maria

last: Massimino

first: Beniamina

last: Pacchioni

first: Caterina

last: Millino

first: Chiara

last: Romualdi

first: Alessandro

last: Bertoli


title: RNA-seq analysis from epididymis and testis of ArKI mice

status: Public on Jan 09 2019

city: Kuopio

first: Einari

last: Niskanen

address: Yliopistonranta 8

department: School of Medicine

country: Finland

institute: University of Eastern Finland

summary: We generated a mouse model (ArKI) in which the two conserved SUMO acceptor lysines of androgen receptor (AR) were permanently abolished by converting them to arginines (ArK381R, K500R). RNA-seq was used to analyse how the lack of AR SUMOylation affects the gene expression pattern of selected tissues.

overall_design: Initial segment and caput epididymal and testicular mRNA profiles of adult wild type (WT) and ArKI (KI) mice were generated by deep sequencing using Illumina HiSeq 3000 system.

first: Petra

last: Sipilä

first: Jorma

last: Palvimo


title: Gene expression analysis of breast tumours from dormant and acquired resistant patients

status: Public on Jan 05 2019

first: Cigdem

last: Selli

address: Little France Crescent

department: Centre for Reproductive Health

institute: Queen's Medical Research Institute

summary:
Sequential patient-matched samples treated with extended neoadjuvant therapy were studied. Long-term treatment (letrozole) induced changes in dormant and resistant patients were determined.
Samples were classified as pre-treatment (timepoint1, <0 days), early-on treatment (timepoint2, 0-120 days) and long-term treatment (timepoint4, >120 days).

overall_design: A total of 101 samples from 39 patients were processed. Data was analysed with two previously generated datasets, GSE59515 (14 patients, 42 samples) and GSE55374 (9 patients, 24 samples) which were also processed on Illumina HT-12v4 BeadChips (GPL10558).

first: Andrew

middle: H

last: Sims

first: Arran

last: Turnbull


title: DNA methylation signature reliably distinguishes pulmonary enteric adenocarcinoma from metastatic colorectal cancer

status: Public on Jan 04 2019

city: München

first: Philipp

last: Jurmeister

address: Thalkirchner Straße 36

department: Institute of Pathology

institute: Ludwig Maximilians University Hospital Munich

type: Methylation profiling by genome tiling array

summary:
Pulmonary enteric adenocarcinoma (PEAD) is a rare non-small cell lung cancer subtype. It is poorly characterized and cannot be distinguished from metastatic colorectal or upper gastrointestinal adenocarcinomas (ADCs) by means of routine pathological methods. As DNA methylation patterns are known to be highly tissue specific, we aimed to develop a methylation-based algorithm to differentiate these entities. To this end, genome wide methylation profiles of 600 primary pulmonary, colorectal and upper gastrointestinal ADCs obtained from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) database were used as a reference cohort to train a machine learning algorithm. The resulting classifier correctly classified all samples from a validation cohort consisting of 680 primary pulmonary, colorectal and upper gastrointestinal ADCs from TCGA and the GEO database, demonstrating the ability of the algorithm to reliably distinguish these three entities. We then analyzed DNA methylation data of 15 PEADs as well as four pulmonary metastases and four primary colorectal ADCs with the algorithm. All 15 PEADs were reliably classified as primary pulmonary tumors and all four metastases as well as all four primary colorectal ADC samples were identified as primary colorectal ADCs. In a t-distributed stochastic neighbor embedding analysis, the PEAD samples did not form a separate methylation subclass but rather diffusely intermixed with other pulmonary ADCs. Additional characterization of the PEAD series using fluorescence in-situ hybridization, next generation sequencing and copy number analysis revealed KRAS mutations in nine of 15 samples (60%) and a high number of structural chromosomal changes. Except for an unusually high rate of chromosome 20 gain (66.7%) the molecular data was mostly reminiscent of standard pulmonary ADCs.
In conclusion, we provide sound evidence of the pulmonary origin of PEAD and in addition provide a publicly available machine learning based algorithm to reliably distinguish PEAD from metastatic colorectal cancer and upper gastrointestinal adenocarcinomas.

overall_design: 14 pulmonary enteric adenocarcinomas and four pulmonary metastases of colorectal cancer were analyzed using the Illumina Infinium MethylationEPIC BeadChip

first: David

last: Capper


title: Knockdown of Atoh8 in Neurog3-expressing mouse ductal cells mPAC results in altered expression of multiple cell cycle related genes

city: Genève

first: Jordi

last: Altirriba

address: Rue Michel-Servet 1

department: Dpts de Médecine Interne et de Physiologie cellulaire et Métabolisme

country: Switzerland

institute: Centre Médical Universitaire de Genève

summary: Atoh8 is a transcription factor of the basic-helix-loop-helix (bHLH) family that is expressed in multiple tissues during embryonic development but whose specific functions remain unknown.  The gene encoding Atoh8 is induced by various lineage- determining bHLH transcription factors in cell culture, suggesting a possible common role of this gene in multiple bHLH-driven differentiation programs. In the pancreas, the pro-endocrine bHLH factors Neurogenin3 (Neurog3) and NeuroD1 activate Atoh8 expression. Moreover, Atoh8 is expressed in the embryonic pancreas confirming its participation in the pancreatic transcriptional cascade. This work aims at gaining insight into the molecular function of Atoh8 during the endocrine differentiation program initiated by Neurog3 in the pancreas. To this aim, we have generated a recombinant adenovirus encoding an Atoh8-specific shRNA (Ad-shAtoh8) and used it to down-regulate expression of the Atoh8 gene in Neurog3-expressing pancreatic ductal cells (mPAC), a cellular model of endocrine cell differentiation. Thus, we have compared global changes in gene expression profiles between cells treated with Ad-Neurog3+shControl and cells treated with Ad-Neurog3+shAtoh8 using Affymetrix microarrays. Our results show that Atoh8 silencing significantly affects the expression of 293 genes in Neurog3-expressing mPAC cells. Gene Ontology analysis has revealed cell cycle as the biological function most significantly represented among the modified genes. These results uncover a potential function of Math6 as a regulator of cell cycle progression and provide novel insights into the link between Neurog3 and the regulation of the cell cycle.

overall_design: mPAC cells (mouse pancreatic duct cells) overexpressing Neurogenin3 were divided in 2 groups according to the shRNA encoded by the recombinant adenoviruses used: 1) Scramble shRNA (control for the infection effect), 2) Atonal Homolog 8-specific shRNA. Experiment was performed three independent times (3 independent biological replicates).

first: Miriam

last: Ejarque

first: Ramon

last: Gomis

first: Rosa

last: Gasa


title: Small RNA sequencing of C. elegans treated with enoxacin and vehicle

city: Campinas

first: Silas

middle: Pinto

last: Silva

state: Sao Paulo

address: Rua Monteiro Lobato 255

department: Biochemistry and Tissue Biology

country: Brazil

institute: University of Campinas

summary: To perform miRNA expression analysis through deep sequencing, RNA was isolated from pools of day 1 adult worms treated with enoxacin or vehicle for 12h in M9 medium.

overall_design: These worms were collected in a series of 3 independent experiments

first: S

last: Pinto

first: M

last: Mori


title: Long non-coding RNAs expressed in fast gycolytic and slow oxidative myofibers

first: Gerolamo

last: Lanfranchi

summary: Long non-coding RNAs (lncRNAs) are emerging as important players in the regulation of several aspects of cellular biology. For a better comprehension of their function it is fundamental to determine their tissue or cell specificity and to identify their subcellular localization. In fact, the activity of lncRNAs may vary according to cell-type specific expression and subcellular localization. Myofibers are motor units of skeletal muscles characterized by great metabolic plasticity. How lncRNAs are expressed in different myofibers, participate to metabolism regulation, and are compartmentalized within a single myofiber is still unknown. We compiled a complete and integrated catalogue of lncRNAs expressed in skeletal muscle, associating the fiber-type specificity and subcellular location to each of them, demonstrating that many are altered when muscles changes myofiber composition and metabolism according to specific stimuli. We demonstrated that the lncRNA Pvt1, activated early during muscle atrophy, impacts mitochondrial respiration and morphology and affects mito/autophagy and myofiber size in vivo by binding specific DNA regions. This work corroborates the importance of lncRNAs in the regulation of metabolism and neuromuscular pathologies and offers a valuable resource to study the metabolism in single cells characterized by pronounced plasticity.

overall_design: EDL and soleus mouse muscles were incubated with type I collagenase (Sigma-Aldrich) to dissociate intact myofibers that were separately collected under stereomicroscope. Isolated myofibers were divided in two parts: one was immersed in Laemmli buffer for fiber typing; the other was placed in TRIzol Reagent (Life Technologies) for RNA purification. Myofibers were classified according to their myosin heavy chain (MyHC) protein isoform in pure MyHC-1, and -2B. We analyzed the transcription profiles of 10 single isolated myofibers (biological replicas) for type 2B myofibers and 11 single isolated myofibers (biological replicates) for type 1 myofibers (total: 21 experiments). One-color hybridizations were performed on SurePrint G3 Mouse GE 8x60K Microarrays (Agilent Technologies). Microarray platform was re-annotated according transcripts in Ensembl 74. Only long non coding RNAs were considered for expression analyses.

first: Enrico

last: Alessio

first: Lisa

last: Buson

first: Francesco

last: Chemello

first: Francesca

last: Grespi

first: Paolo

last: Martini

first: Maria

last: Massimino

first: Beniamina

last: Pacchioni

first: Caterina

last: Millino

first: Chiara

last: Romualdi

first: Luca

last: Scorrano

first: Stefano

last: Cagnin


title: Genome wide map of H3K9me2 in fission yeast Schizosaccharomyces pombe.

status: Public on Jan 03 2019

city: Bethesda

first: Shiv

last: Grewal

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

summary: Genome wide map of H3K9me2 in 4 different strains of fission yeast Schizosaccharomyces pombe.

overall_design: H3K9me2 ChIP-seq profiling in 4 different strains of fission yeast Schizosaccharomyces pombe.

first: Guodong

last: Xie

first: Tommy

last: Vo

first: Gobi

last: Thillainadesan

first: Sahana

last: Holla

first: Beibei

last: Zhang

first: Yiyang

last: Jiang

first: Mengqi

last: Lv

first: Zhang

last: Xu

first: Chongyuan

last: Wang

first: Vanivilasini

last: Balachandran

first: Yunyu

last: Shi

first: Fudong

last: Li

middle: I


title: RNA polymerase I activators count and adjust ribosomal RNA gene copy number

city: Bunkyo-ku

first: Tetsushi

last: Iida

state: Tokyo

address: 1-1-1 Yayoi

department: Research Center for Biological Visualization

institute: The Institute for Quantitative Biosciences (IQB), The University of Tokyo

type: Genome variation profiling by high throughput sequencing

summary: Ribosome is the most abundant RNA-protein complex in a cell and many copies of the ribosomal RNA gene (rDNA) have to be maintained. However, arrays of tandemly repeated rDNA genes can lose the copies by intra-repeat recombination. Loss of the rDNA copies of Saccharomyces cerevisiae is counteracted by gene amplification whereby the number of rDNA repeats stabilizes around 150 copies, suggesting the presence of a monitoring mechanism that counts and adjusts the number. Here, we report that in response to rDNA copy loss, the upstream activating factor (UAF) for RNA polymerase I which transcribes the rDNA is released and directly bind to a RNA polymerase II transcribed gene, SIR2 to repress, whose gene products silence rDNA recombination. We show that the amount of UAF determines rDNA copies number that is stably maintained. UAF ensures rDNA production not only by rDNA transcription activation but also by its copy number maintenance.

overall_design: ChIP-seq analyses of exponentially growing S. cerevisiae strains were performed for fine mapping of UAF30, an RNA polymerase I activator. 16 samples for UAF30-MN3HA ChIP-seq analyses. Whole genome sequencing was used for identification of SIR2-derepressed mutations in S. cerevisiae. 9 samples of whole genome sequencing for mutation identification.

first: Takehiko

last: Kobayashi


title: Glucose-dependent insulinotropic polypeptide ameliorates obesity and insulin resistance by attenuating S100A8/9 in myeloid cells

status: Public on Jan 02 2019

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

country: Israel

institute: Tel Aviv University

summary:
Our data mark GIP as a beneficial immunoregulator during obesity and suggest a novel untapped therapeutic potential for specific targeted GIP analogs.
Emerging studies suggest that glucose-dependent insulin tropic polypeptide (GIP) affect obesity-associated inflammation. Yet, whether GIP can directly regulate immune cell activity and the respective metabolic consequences remained unknown.  Here, we targeted GIP-receptor-deficiency to immune cells using bone marrow (BM) chimerism approach and the reconstituted chimeric mice were subjected to a high fat diet (HFD) regimen.  Mice reconstituted with Gipr-/- BM gained significantly more weight, despite similar food consumption. This was accompanied by increased epididymal adipose tissue (epiWAT) mass, adipocyte hypertrophy, enhanced hepatic steatosis, insulin resistance and significant myelopoiesis in the circulation, epiWAT and inguinal adipose tissue (ingWAT). In accordance these mice also exhibited reduced energy expenditure and ingWAT beiging. Mechanistically, impaired GIP-governed regulation of S100A8/9 in myeloid cells was responsible for the perturbed energy homeostasis, increased insulin resistance and intensified inflammatory response under nutrient overload.  Collectively, our results outline a beneficial immunoregulatory role for GIP in immune cells during obesity.

overall_design: 22 Samples (arrays) were performed.

first: Fernanda

middle: D

last: Mantelmacher

first: Isabel

last: Zvibel

first: Keren

last: Cohen

first: Thomas

last: Vogl

first: Yael

last: Kuperman

last: Pewjner-Jung

first: Shai

last: Weiss

first: Daniel

last: Drucker

first: Chen

last: Varol

first: Sigal

last: Fishman


title: Expression profilings of fission yeast strains

first: Shiv

last: Grewal

summary: We report gene expression profiling in the fission yeast Schizosaccharomyces pombe. We performed high-throughput sequencing of RNA isolated from wild-type, mmi1(W112A) mutant, erh1∆, and mmi1∆ strains. We find that mmi1(W112A) and erh1∆ derepress a shared subset of mmi1-repressed genes during vegetative growth.

overall_design: RNA sequencing in wild-type, mmi1(W112A), erh1∆ and mmi1∆ strains. Two biological replicates for all strains.

first: Guodong

last: Xie

first: Tommy

last: Vo

first: Gobi

last: Thillainadesan

first: Sahana

last: Holla

first: Beibei

last: Zhang

first: Yiyang

last: Jiang

first: Mengqi

last: Lv

first: Zhang

last: Xu

last: Wang


title: Enhancer associated long non-coding RNA transcription and immune gene regulation in experimental models of rickettsial infection

status: Public on Jan 01 2019

city: GALVESTON

first: Kamil

last: Khanipov

state: TX

address: 301 University Blvd

institute: University of Texas Medical Branch

summary: Recent discovery that much of the mammalian genome does not encode protein-coding genes (PCGs) has brought widespread  attention to long noncoding RNAs (lncRNAs) as a novel layer of biological regulation. Enhancer lnc (elnc) RNAs from the enhancer  regions of the genome carry the capacity to regulate PCGs in cis or in trans. Spotted fever rickettsioses represent the  consequence of host infection with Gram-negative, obligate intracellular bacteria in the Genus Rickettsia. Despite being implicated  in the pathways of infection and inflammation, the roles of lncRNAs in host response to Rickettsia species have remained a  mystery. We have profiled the expression of host lncRNAs during infection of susceptible mice with R. conorii as a model closely  mimicking the pathogenesis of human spotted fever rickettsioses. RNA sequencing on the lungs of infected hosts yielded reads  mapping to 74,964 non-coding RNAs, 206 and 277 of which were determined to be significantly up- and down-regulated in  comparison to uninfected controls. Following removal of short non-coding RNAs and ambiguous transcripts, remaining transcripts  underwent in-depth analysis of mouse lung epigenetic signatures H3K4Me1 and H3K4Me3, active transcript markers (POLR2A, p300,  CTCF), and DNaseI hypersensitivity sites to identify two potentially active and highly up-regulated elncRNAs NONMMUT013718 and  NONMMUT024103. Using Hi-3C sequencing resource, we further determined that genomic loci of NONMMUT013718 and  NONMMUT024103 might interact with and regulate the expression of nearby PCGs, namely Id2 (inhibitor of DNA binding 2) and  Apol10b (apolipoprotein 10b), respectively. Heterologous reporter assays confirmed the activity of elncRNAs as the inducers of  their predicted PCGs. In the lungs of infected mice, expression of both elncRNAs and their targets was significantly higher than  mock-infected controls. Induced expression of NONMMUT013718/Id2 in murine macrophages and NONMMUT024103/Apol10b in  endothelial cells was also clearly evident during R. conorii infection in vitro. Finally, shRNA mediated knock-down of  NONMMUT013718 and NONMMUT024103 elncRNAs resulted in reduced expression of endogenous Id2 and Apl10b, demonstrating the  regulatory roles of these elncRNAs on their target PCGs. Our results provide very first experimental evidence suggesting altered  expression of pulmonary lncRNAs and elncRNA-mediated regulation of PCGs involved in immunity and during host interactions with  pathogenic rickettsiae.

overall_design: Examination of expression of long non coding RNA's in mice infected with R. conorii in comparison to non infected mice.

first: Imran

last: Chowdhury

first: Hema

last: Narra

first: Abha

last: Sahni

first: Yuriy

last: Fofanov

first: Sanjeev

middle: K


title: CD56dim NK cell gene signature in melanoma patients with better and worse clinical outcomes

city: Pittsburgh

first: Lazar

last: Vujanovic

state: PA

address: L1.33 Hillman Cancer Center, 5117 Centre Ave

department: Medicine

institute: University of Pittsburgh

summary:
Natural killer (NK) cells are innate cytotoxic and immunoregulatory lymphocytes that have a central role in anti-tumor immunity and play a critical role in mediating cellular immunity in advanced cancer immunotherapies, such as dendritic cell (DC) vaccines. Our group recently tested a novel recombinant adenovirus-transduced autologous DC-based vaccine that simultaneously induces T cell responses against three melanoma-associated antigens for advanced melanoma patients. We examined the impact of this vaccine on the NK cell profile in melanoma patients.
Relative immune cell population abundance was evaluated as previously described (Danaher et al. JITC, 2017). The abundance of the CD56dim NK cell gene signature was compared between pattients with better and worse outcome.

overall_design:
41 lesions from 19 patients were excised at three different time-points during this trial and total RNA was extracted.
Samples were profiled on the nCounter® MAX platform with the PanCancer Immune Profiling Panel

first: Afshin

last: Mashadi-Hossein

first: Sarah

last: Warren

first: Andy

last: White

first: Alan

last: Huang

first: John

last: Kirkwood

first: Lisa

last: Butterfield


title: Genome-wide analysis of LY294002 effect on the glucocorticoid receptor function in human keratinocytes

city: Tempe

first: Ben

last: Readhead

state: AZ

address: 797 E. Tyler Street

institute: ASU-Banner Neurodegenerative Disease Research Center

summary: LY294002 increased negative effect of glucocorticoid fluocinolone acetonide (FA) on gene expression and blunted activation of some GR-target genes by glucocorticoid FA.

overall_design: HaCat cells grown in Phenol free DMEM supplemented with 10 % Charcoal stripped Fetal Bovine Serum and 1 X Pen/Strep a day prior to the experiment were either pre-treated with 50 μM LY294002 for 6 h followed by 1 μM of FA for additional 24 h (IB4 and IB8) or were treated with 1 μM of FA alone for 24 h (IB2 and IB6). Control cells used for comparison were either treated with DMSO (vehicle control. IB1 and IB5) or 1 μM of LY294002 alone (IB3 and IB7). The experiments were performed in duplicates.

first: Irina

last: Budunova

first: Shivani

last: Agarwal


title: RNA-seq for prostate cancer cell lines under oxidative stress with or without PAGE4 overexpression

city: Shenyang

first: Chengcheng

last: Lv

state: Liaoning

address: 44. Xiaoheyan Road

department: Department of Urology Surgery

institute: Liaoning Cancer Hospital and Institute

summary: RNA-seq for prostate cancer cell lines DU145 and 22RV1 with or without PAGE4 overexpression with hydrogen peroxide or PBS treatment

overall_design: 2 conditions with overexpressed PAGE4 or empty vector cells in two prostate cancer cell lines, using Illumina

last: LV

first: Fei

last: Li

first: Qingzhuo

last: Dong

first: Zi

last: Yu

first: Gejun

last: Zhang

first: Yu

last: Zeng


title: The chronological changes of transcriptomic profiles of hepatic macrophages after partial portal vein ligation

city: New Haven

first: Masatake

last: Tanaka

state: CT

address: 300 Cedar Street

department: Internal Medicine

institute: Yale School of Medicine

summary: We compared transcriptomic profiles of hepatic macrophages between sham operated rats, rats 3 days and 10 days after partial portal vein ligation (PPVL) surgery (n=3). The number of genes with a significant change was most numerous in Sham vs 3 days, followed by Sham vs 10 days and 3 days vs 10 days.

overall_design: Transcriptomic profile in hepatic macrophages from three male Sprague–Dawley rats three or ten days after partial portal vein ligation (PPVL) surgery and from the three sham rats.

first: Guilin

last: Wang

first: Junji

last: Saruwatari

first: Yasuko

last: Iwakiri


title: Co-chaperone Mzb1 is a key effector of Blimp1 in plasma cell differentiation and b1 integrin function

city: Freiburg

first: Senthilkumar

last: Ramamoorthy

address: Stübeweg 51

department: Cellular & Molecular Immunology

institute: Max Planck Institute of Immunobiology and Epigenetics

summary: Plasma cell differentiation involves coordinated changes in gene expression and functional properties of B cells. Here, we study the role of Mzb1, a Grp94 co-chaperone that is expressed in marginal zone (MZ) B cells and during the terminal differentiation of B cells to antibody-secreting cells (ASCs). By analyzing Mzb1 -/- Prdm1 +/gfp mice, we find that Mzb1 is specifically required for the differentiation and function of ASCs in a T cell-independent immune response. We find that Mzb1-deficiency mimics, in part, the phenotype of Blimp1 deficiency, including the impaired secretion of IgM and the deregulation of Blimp1 target genes. In addition, we find that Mzb1 -/- plasmablasts show a reduced activation of b1 integrin, which contributes to the impaired plasmablast differentiation and migration of ASCs to the bone marrow. Thus, Mzb1 function is required for multiple aspects of plasma cell differentiation.

overall_design: Splenic B cells were purified from Mzb1 +/+ Prdm1 +/gfp and Mzb1 -/- Prdm1 +/gfp mice using anti-B220 magnetic beads and cultured in the presence of 25ug/ml LPS. After 4 days, undifferentiated CD138 - Blimp - B cell blasts (Activated B Cells), CD138 - Blimp + (Pre-PB cells), and CD138 + Blimp + (PB cells) were isolated with FACSAria (Becton Dickinson) sort.

first: Virginia

last: Andreani

first: Rudolf

last: Grosschedl


title: Chromatin state in activated neural stem cells

city: New york

first: Jihye

last: Paik

state: NY

address: 1300 York Ave.

department: Pathology

institute: Weill Cornell Medical College

summary: We report distribution of H3K4m3 marks in activated neural stem cells

overall_design: Examination of H3K4m3 distribution in neural stem cells

first: Inah

last: Hwang


title: Gene expression changes in neural stem cells under different redox potential

overall_design: Cultured neural stem/progenitor cells were treated for 48 hrs to induce different intraceullar redox potential and ensuing gene expression changes were determined.


title: Global expression data from mouse dorsal, ventral and central suprachiasmatic nuclei sub-regions following phase advance inducing light exposure.

city: Rotterdam

first: Karl

last: Brand

address: Dr Molewaterplein 50

department: Bioinformatics

country: Netherlands

institute: Erasmus Medical Center

summary:
In mice and other mammals the suprachiasmatic nuclei (SCN) within the brain, synchronises daily rhythms in metabolism, physiology and behaviour to the Earth's local time. Whilst much is known about the SCN's time keeping mechanism, less is known about how it adjusts or resets timing to changes in local time beyond the induction of CRE regulated genes and the differential response of dorsal and ventral sub-regions of the SCN after light exposure known to advance rhythms.
As transcription of several clock genes is required for maintaining daily rhythms, we assayed global transcription levels in the dorsal, ventral and central SCN following phase advance inducing light exposure to expand understanding of how the SCN adjusts to new local times.

overall_design: Adult C57BL/6 mice were maintained under conditions devoid of timing cues with constant dim red light for at least seven days before receiving a 30m phase advance light pulse (P) or sham (S) treatment. 3.5hrs later mice were sacrificed and brains quickly removed, snap frozen and cryosectioned for subsequent isolation of dorsal, ventral and central SCN by laser catapult microdissection (LCM).

first: Mino

last: Belle

first: Hugh

last: Piggins

first: Gijsbertus

last: van der Horst

first: Edwin

last: Jacobs


title: Single Cell RNA Sequencing Facilitates Quantitative Analysis of CD31+ endothelial cells at day4 of hESC hematopoietic differentiation

status: Public on Dec 27 2018

city: Tianjin

first: Jiaxi

last: Zhou

state: Tianjin

address: 288# Nanjing Road, He ping district

institute: PUMC

summary:
Purpose: The goals of this study are to investigate the cell fate desicion and molecular mechanism in CD31+ endothelial cells at the day4 of hematopoietic differentiation.
Methods: mRNA profiles of Single CD31+ endothelial cell at day4 of hESC hematopoietic differentiation, were generated by deep sequencing using Illumina GAIIx. The sequence reads that passed quality filters were analyzed with CellRanger pipeline to align reads, generate feature-barcode matrices.
Conclusions: We found that the fate of HE and Non-HE has been decided and separated at the emergence of endothelial precursor population during hPSC hematopoiesis.

first: Hongtao


title: Effect of Fbxo22 on ER and SRC-3 recruitment to the genomic loci

status: Public on Dec 26 2018

city: Tokyo

first: Yoshikazu

last: Johmura

address: 4-6-1 Shirokanedai, Minato-ku

department: Institute of Medical Science

institute: University of Tokyo

summary:
The agonistic/antagonistic bio-character of selective estrogen receptor modulators (SERMs) can have therapeutic advantages, particularly in the case of premenopausal breast cancers. Although the contradictory effects of these modulators have been studied in terms of cross-talk between estrogen receptor (ER)-coactivator dynamics and growth factor signaling, the molecular basis of these mechanisms is still obscure. We demonstrate here an unidentified series of regulatory mechanisms controlling cofactor dynamics on ER and SERM function whose activities require F-box protein 22 (Fbxo22). Skp, Cullin, F-box containing complex (SCF)Fbxo22 ubiquitylates lysine demethylase 4B (KDM4B) complexed with tamoxifen-bound ER, whose degradation releases steroid receptor coactivator (SRC) from ER. Depletion of Fbxo22 results in ER-dependent transcriptional activation via transactivation function 1 (AF1) function even in the presence of SERMs. In living cells, tamoxifen releases SRC and KDM4B from ER in a Fbxo22-dependent manner. SRC release by tamoxifen requires Fbxo22 on almost all ER-SRC-bound enhancer/promoters. Tamoxifen fails to prevent growth of Fbxo22-depleted ER-positive breast cancers both in vitro and in vivo. Clinically, a low level of Fbxo22 in tumor tissues predicts a poorer outcome in ER-positive/Human Epidermal Growth Factor Receptor Type 2 (HER-2)-negative breast cancers with high hazard ratios independently of other markers such as Ki-67 and node status. We propose that the level of Fbxo22 in tumor tissues defines a new subclass of ER-positive breast cancers for which patients SCFFbxo22-mediated KDM4B degradation can be a therapeutic target by the next generation of SERMs.
We carried out the analysis using MCF-7 and Fbxo22-depleted MCF-7 cells. Cells were estrogen-starved for 72 hrs and subsequently stimulated for 2 hrs by E2 (10 nM) or E2 plus TAM. As a result, we identified a total of 12,645 and 23,216 enriched ER peaks in MCF-7 and Fbxo22-depleted MCF-7cells, respectively, in cells treated with E2, and 26,751 and 19,924 enriched ER peaks in MCF-7 and Fbxo22-depleted MCF-7cells, respectively, in cells treated with E2 plus 4-OHT.

overall_design: Examination of ER and SRC-3 in control or shFbxo22 MCF7 cells

first: Makoto

last: Nakanishi


title: glioblastoma(GBM) tissues: Tumor tissues(C) vs. Normal tissues(N)

first: Renjie

state: State...

address: No 220, Chenglin Road, Hedong strict.

institute: Pingjin Hospital

summary: To identify ceRNA network associated with GBM, a hybridization-based microarray assay was used to analyze three paired GBM tissues with lower expression of miR-422a.

overall_design: Three GBM tissues vs. three Adjacent normal tissues.

first: Haiqian

last: Liang


title: RNA-sequencing of whole lungs from mice with activating Kras mutations and epithelial Stat3 deletion

city: Houston

first: Humam

last: Kadara

address: 2130 W. Holcombe Blvd

institute: University of Texas MD Anderson Cancer Center

summary: We have previously shown that Kras mutant-induced lung tumors in CCSPCre/LSL-K-rasG12D mice (CC-LR) exhibited Stat3 activation. Here we sought to study the role of epithelial Stat3 in Kras-mutant lung tumor oncogenesis through derivation of a lung epithelial specific CC-LR/Stat3 conditional knockout (LR/Stat3D/D or LRDD) model. Analysis of tumor burdens revealed marked gender disparity following epithelial Stat3 deletion, LRDD males exhibited increased tumor burdens compared to male CC-LR animals whereas female LRDD mice displayed attenuated tumor development when compared to female CC-LR littermates. We then performed RNA-sequencing of whole lungs from the mice in order to understand global expression programs that may underlie this gender-specific effect of epithelial Stat3 deletion.

overall_design: Frozen whole lungs from 14 weeks old male and female CC-LR and LRDD mice (n= 3 in each subgroup by gender and genotype; n = 12 total) were excised and total RNA isolated. Total RNA was sequenced using the Ion Torrent Proton and analyzed for differential gene expression that are modulated by gender, genotype and both.

first: Seyed

last: Moghaddam


title: Transcriptomic analysis of normal mouse retinal and conditional medium cultured retinal progenitor cells

city: Shanghai

first: Qingjian

last: Ou

address: Siping Rd

department: Medical

institute: Tongji University

summary: We reported that bFGF increases the cell proliferation by stimulating the G1/S and G2/M  phase transitions.

overall_design: Mouse retinal progenitor cells mRNA profiles of different treatments at various time points were generated by deep sequencing using BGISEQ-500.

first: Caixia

last: Jin


title: Expression data from human lung cancer cancer treated with  TXA1.Hcl

status: Public on Dec 24 2018

city: Porto

first: Rune

last: Matthiesen

address: Rua Dr. Roberto Frias s/n

country: Portugal

institute: IPATIMUP

summary:
The antitumour activity of a hit tioxanthone is associated with alterations in cholesterol localization
We used microarrays to detail the global programme of gene expression underlying treatment of lung cancer  with TXA1.Hcl

overall_design: We analyzed three control biological replicas and three treated biological replicas

first: Raquel

middle: T

last: Lima

first: Diana

last: Sousa

first: Ana

last: Gomes

first: Nuno

last: Mendes

first: Madalena

last: Pedro

last: Pinto

first: Emília

first: Helena

last: Vasconcelos


title: Nuclear FOXO1 promotes lymphomagenesis in germinal center B cells

status: Public on Dec 21 2018

city: Berlin

first: Lars

last: Bullinger

address: Augustenburger Platz 1

department: Hematology, Oncology and Tumorimmunology

institute: Charité

summary: FOXO1 acts as a tumor suppressor in solid tumors. The oncogenic PI3K pathway suppresses FOXO1 transcriptional activity by enforcing its nuclear exclusion upon AKT-mediated phosphorylation. We show here abundant nuclear expression of FOXO1 in Burkitt lymphoma (BL), a germinal center (GC) B cell derived lymphoma whose pathogenesis is linked to PI3K activation. Recurrent FOXO1 mutations which prevent AKT targeting and lock the transcription factor in the nucleus are used by BL to circumvent mutual exclusivity between PI3K and FOXO1 activation. Using genome editing in human and mouse lymphomas in which MYC and PI3K cooperate synergistically in tumor development we demonstrate pro-proliferative and anti-apoptotic activity of FOXO1 in BL and identify its nuclear localization as an oncogenic event in GC B cell derived lymphomagenesis.

overall_design:
Isogenic murine BL cell line modified by CRISPR/Cas9 genome editing

Genotype definitions:
wt+: wild type FOXO1 (mouse)
mt+: T24P FOXO1 (mouse)
wt-: knockout of wild type FOXO1 (mouse)
mt-: knockout of T24P FOXO1 (mouse)

first: Sandrine

last: Sander

first: Klaus

last: Rajewsky


title: Gene expression profiles in epididymal white adipose tissue of lysophosphatidic acid receptor 4-KO mice

status: Public on Dec 23 2018

city: Aomori

first: Yuji

last: Nakai

state: Aomori

address: 2-1-1, Yanagawa

department: Institute of Regional Innovation

institute: Hirosaki University

summary: White adipose tissue (WAT) is a highly active metabolic and endocrine organ, and its dysfunction links obesity to a variety of diseases, ranging from type 2 diabetes to cancer. The function of WAT is under the control of multiple cell signaling systems, including that of G protein-coupled receptors (GPCRs). Gαs- and Gαi-coupled receptors have been reported to regulate lipolysis, and Gαq-coupled receptors stimulate glucose uptake in adipocytes. However, the roles of Gα12/13-coupled receptors in WAT are totally unknown. Here we show that lysophosphatidic acid receptor 4 (LPA4), an adipose cluster GPCR, selectively activates Gα12/13 proteins in adipocytes, and limits continuous remodeling and healthy expansion of WAT in mice. Under standard diet conditions, LPA4-knockout mice showed higher expression levels of mitochondrial biogenesis-related genes in WAT, along with higher production of adiponectin than control mice. In vitro studies have consistently demonstrated that the LPA4/Rho/Rho-kinase signaling pathway suppresses mRNA expression of mitochondrial biogenesis-related genes in adipocytes. In a diet-induced obesity model, LPA4-deficient mice showed “metabolically healthy obese” phenotypes, with continuous WAT expansion, and protection from WAT inflammation, hepatosteatosis, and insulin resistance. Given that GPCRs comprise the most successful class of drug targets, LPA4 would be a promising therapeutic target for obesity-related metabolic disorders.

overall_design: LPA4-knockout (LPA4-KO) and wild type (WT) mice were housed on a 12-h light dark cycle and fed standard chow (MF [Oriental Yeast Co., Tokyo, Japan]) diet. All experiments in this study were conducted on male littermates. The animal care and experimental procedures used in this study were approved by Animal Care Committee of the University of Tokyo.

first: Keisuke

last: Yanagida

first: Hidemitsu

last: Igarashi

first: Takayo

last: Ohto

first: Daisuke

last: Yasuda

first: Noriyuki

last: Akahoshi

first: Atsushi

last: Sekiba

first: Tsudoi

last: Toyoda

first: Tomoko

last: Ishijima

first: Naoto

last: Kubota

first: Keiko

last: Abe

first: Takashi

last: Kadowaki

first: Satoshi

last: Ishii

first: Takao

last: Shimizu


title: GPCR19 agonist increases in number of immune-regulatory myeloid cells and their expression of immune checkpoint molecule

city: Seoul

first: Seung-yong

last: Seong

address: 28 Yongon-dong, Jongno-gu

department: Microbiology and Immunology

country: South Korea

institute: Wide River Institute of Immunology, Seoul National University College of Medicine

summary:
GPCR19 pathway has been implicated in regulating various inflammation. However, the exact mechanism of immune regulation by GPCR19 pathway has not been elucidated in detail.
Here, we report that intravenous infusion of a GPCR19 agonist, sodium taurodeoxycholate (STDC), decreases serum pro-inflammatory cytokines, normalizes hypotension, protects against renal injury and prolongs mice survival during sepsis.

overall_design: Eight- to 12-week-old female mice were used for the experiments. Gr1- cells and Gr1+ cells were purified by MACS (Miltenyi Biotec). Total RNA was extracted from the cells using an RNeasy Mini kit according to the manufacturer’s instructions (QIAGEN).

first: Sooghee

last: Chang

first: Youn-Hee

last: Kim

first: Young-Joo

first: Sungyoon

last: Moon

first: Yong

middle: Y

last: Lee

first: Jin

last: Jung

first: Youngsoo

first: Hi-Eun

first: Tae-Joo

first: Taek-Chin

last: Cheong

first: Hye-Jung

first: Jung-A

last: Cho

first: Hang-Rae

first: Dohyun

last: Han

first: Yirang

first: Seung-Hyeok

last: Seok

first: Nam-Hyuk

first: Hyosuk

first: Nagahiro

last: Minato

first: Seung-Yong


title: Characterization of myocardial B cells in naïve hearts, acutely injured hearts and acutely injured hearts of mice treated with Pirfenidone

status: Public on Dec 25 2018

city: Indianapolis

first: Scot

last: Matkovich

state: IN

address: Lilly Corporate Center

institute: Eli Lilly and Company

summary: Myocardial CD19+CD11b+ and CD19+CD11b- cells were FACS sorted from transgenic mice expressing the Diphtheria Toxin (DT) receptor under the myocardial specific MLC2v promoter. Cells were sorted from hearts of mice not exposed to DT (naïve hearts), from the hearts of animals treated with DT 4 days prior to the experiment (DTR) and from the hearts of mice exposed to DT and fed chow enriched with the anti-inflammatory/anti-fibrotic drug Pirfenidone (0.5% in powdered chow, PFD)

overall_design: Cells sorted from naïve hearts were compared to cells sorted from DTR injured hearts and to cells sorted from the hearts of DTR injured animals treated with Pirfenidone

first: Luigi

last: Adamo

first: Douglas

last: Mann


title: Gene expression profiles in white adipose tissues of lysophosphatidic acid receptor 4-KO mice

first: Yuji

last: Nakai

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

overall_design: Refer to individual Series


title: Gene expression profiles in inguinal white adipose tissue of lysophosphatidic acid receptor 4-KO mice

first: Keisuke

last: Yanagida

first: Hidemitsu

last: Igarashi

first: Takayo

last: Ohto

first: Daisuke

last: Yasuda

first: Noriyuki

last: Akahoshi

first: Atsushi

last: Sekiba

first: Tsudoi

last: Toyoda

first: Tomoko

last: Ishijima

first: Naoto

last: Kubota

first: Keiko

last: Abe

first: Takashi

last: Kadowaki

first: Satoshi

last: Ishii

first: Takao


title: Role of Sympathic Nervous System and RGM-A in the Resolution of Inflammation

status: Public on Dec 19 2018

city: Tuebingen

first: Andreas

last: Körner

address: Hoppe-Seyler-Straße 3

department: Clinic of Anesthesiology and Intensive Care Medicine

institute: University of Tuebingen

summary: Protein and phosphorylation (Phospho Explorer Antibody Array, FullMoonBioscience, #PEX100) profiling of peritoneal monocytes (pooled lavages from 3-4 mice / condition) was carried out according to the manufacturer’s instructions.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Peritoneal monocytes/macrophages from C57BL/6 mice treated with RGM-A +/- β2 ADR agonist were used following 12 h of ZyA-induced peritonitis.

first: Valbona

last: Mirakaj


title: Gene expression of murine repeatedly activated Th1 cells after miR-31 knock down

first: Pawel

last: Durek

address: Charitéplatz 1

institute: Deutsches Rheuma-Forschungszentrum

summary: Gene expression of murine repeatedly activated Th1 cells 36h, 48h and 72h after miR-31 inhibition using a specific antagomir (Antagomir-31) compared to a scrambled controll (Antagomir-SCR).

overall_design: CD4+CD62Lhi (naϊve) from spleens and lymph nodes of 6- to 10-weeks old OTII mice were isolated and labeled with αCD4-FITC (GK1.5, DRFZ) followed by Magnetic Cell Sorting (MACS) with αFITC microbeads (Miltenyi Biotec). Subsequent purification of CD4+CD62Lhi cells was achieved using αCD62L microbeads (Miltenyi Biotec). Cells were cultured (1:5) with irradiated (30 Gy), CD90.2 depleted APCs in the presence of OVA323-339 (0.5 mM) in RPMI supplemented with 10% fetal calf serum (FCS), 100 units/ml penicillin, 0.1 mg/ml streptomycin and 10 μM β-mercaptoethanol, IL-12 (5 ng/ml, R&D Systems) and αIL-4 (10 µg/ml, 11B11). Viable cells were separated by density gradient centrifugation using Histopaque 1083 (Sigma Aldrich) and reactivated  with freshly isolated APCs every six days for three times consecutively. IL-2 (10 ng/ml, R&D Systems) was added  from the second stimulation on. After the fourth round of stimulation, viable cells were separated by density gradient centrifugation using Histopaque 1083 (Sigma Aldrich) and treated (5 x 10^6 cells/ml) in serum-free siRNA delivery medium (ACCELL, Dharmacon) containing antagomir-31 or antagomir-SCR (1 µM) for 1.5h at 37°C and 5% CO2. Cell suspension was diluted (1:5) with RPMI supplemented with 10% fetal calf serum (FCS), 100 units/ml penicillin, 0.1 mg/ml streptomycin and 10 μM β-mercaptoethanol, IL-12 (5 ng/ml, R&D Systems), αIL-4 (10 µg/ml, 11B11) and IL-2 (10 ng/ml, R&D Systems) and reactivated with plate-bound αCD3 and αCD28 (3 µg/ml, BD). 36h, 48h, and 72h after the treatment, cells were harvested and total RNA was isolated using ZR RNA MiniPrepTM kit (Zymo Research) according to the manufacturer’s recommendations. RNA Quality control was performed with a bioanalyzer using the RNA 600 Pico Kit and 10µg RNA with a RIN > 8 was hybridized to Mouse 430_2 (Affymetrix) according to the manufacturer's recommendations.

first: Markus

last: Bardua

first: Claudia

last: Haftmann

first: Kerstin

last: Westendorf

first: Antje

last: Buttgereit

first: Cam

last: Tran

first: Mairi

last: McGrath

first: Melanie

last: Weber

first: Katrin

last: Lehmann

first: Richard

last: Addo

first: Gitta

middle: A

last: Heinz

first: Anna-Barbara

last: Stittrich

first: Patrick

last: Maschmeyer

first: Helena

last: Radbruch

first: Michael

last: Lohoff

first: Hyun-Dong

last: Chang

first: Mir-Farzin

last: Mashreghi


title: Circulating miRNAs in the regulation of epithelial mesenchymal transition and their potential role as possible diagnostic biomarkers in areca nut associated oral submucous fibrosis in South Indian population

city: Kanchipuram

first: Subramaniam

last: Sivakumar

state: TamilNadu

address: Enathur

department: Biochemistry

country: India

institute: Sri Sankara Arts and Science College

summary: Expression of miRNA analysis in human lecukocytes was analysed using Next-generation sequencing (NGS) method in Oral Submucosis Firbrosis condition.

overall_design: Examination of 2 different samples of control and diseased in leukocytes.

first: K

last: Rakheerathnam

first: S

last: NiranjaliDevaraj


title: Rat Schwann cell gene expression analysis after Sox2 overexpression

status: Public on Dec 18 2018

city: Plymouth

first: Xinpeng

last: Dun

state: Devon

address: John Bull Building, Research Way

institute: University of Plymouth

summary:
In this dataset, we include the expression data obtained from rat Schwann cells overepressing GFP (control) or Sox2/GFP to identfiy Sox2 tragets in Schwann cells.
An in vitro microarray analysis of GFP (control) and Sox2/GFP overexpressing Schwann cells

overall_design: Schwann cells were infected with GFP (control) or Sox2/GFP adenovirus for 24 hours in defined medium (DM) and then changed to DM without virus. After 48 hours of adenovirus infection, total RNA was purified with miRNeasy mini kit (Qiagen, 217004) and on-column DNase digestion was also performed. mRNA samples purified from GFP or Sox2/GFP adenovirus infected Schwann cells were analysed on an Affymetrix 1.0 ST Rat Exon array by the Patterson Institute for Cancer Research (Manchester, UK)

first: Xin-peng

first: David

middle: B

last: Parkinson


title: DksA controls the response of the Lyme disease spirochete Borrelia burgdorferi to starvation

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

summary: The pathogenic spirochete Borrelia burgdorferi senses and responds to diverse environmental challenges, including changes in nutrient availability, throughout its natural infectious cycle in Ixodes spp. ticks and mammalian hosts. This study examined the role of the putative DnaK suppressor protein (DksA) in the transcriptional response of B. burgdorferi to starvation. Wild-type and dksA-deficient B. burgdorferi strains were subjected to starvation by shifting mid-logarithmic cultures grown in BSK-II medium to serum-free RPMI medium for six hours under microaerobic conditions (5% CO2, 3% O2). Microarray analyses of wild-type B. burgdorferi revealed that genes encoding flagellar components, ribosomal proteins, and DNA replication machinery were downregulated in response to starvation. DksA mediated transcriptomic responses to starvation in B. burgdorferi as the dksA-deficient B. burgdorferi strain differentially expressed only 47 genes in response to starvation compared to the 500 genes differentially expressed by wild-type strains. Consistent with a role for DksA in the starvation response of B. burgdorferi, fewer CFUs were observed for dksA-deficient spirochetes after prolonged starvation in RPMI medium compared to wild-type B. burgdorferi. Transcriptomic analyses revealed a partial overlap between the DksA regulon and the regulon of the guanosine tetraphosphate and guanosine pentaphosphate [(p)ppGpp] synthase RelBbu, while the DksA regulon also included many plasmid-borne genes. Corresponding to a DksA-(p)ppGpp regulatory relationship, (p)ppGpp levels were constitutively elevated in the dksA-deficient strain compared to the wild-type strain. Together, these data indicate that DksA directs the stringent response with a regulatory interplay with (p)ppGpp that is fundamental to B. burgdorferi responses to the environment.

platform_organism:
Borreliella burgdorferi
Yersinia pestis
Coxiella burnetii
Chlamydia trachomatis
Staphylococcus aureus
Streptococcus pyogenes

overall_design: Borrelia burgdorferi mutant and media comparisons

first: William

last: Boyle

first: Ashley

last: Groshong

last: Drecktrah

first: Jon

middle: S

last: Blevins

first: D

last: Samuels

first: Frank

last: Gherardini

first: Travis

middle: J

last: Bourret


title: Expression analysis of lung miRNAs responding to ovine VM virus infection by RNAseq

city: Leioa

first: Begoña

last: Jugo

state: Basque Country

address: Sarriena auzoa s/n

department: Genetics, Physical Anthropology and Animal Physiology

country: Spain

institute: University of the Basque Country (UPV/EHU)

summary: MicroRNAs (miRNAs) are short endogenous, single-stranded, non-coding small RNA molecules of about 22 nucleotides in length. They regulate gene expression post-transcriptionally by silencing mRNA molecules and they regulate many physiological processes. Visna-Maedi virus (VMV) is a lentivirus that causes Visna-Maedi disease (VM) in sheep characterised by pneumonia, mastitis, arthritis and encephalitis; and affects cells of the monocyte/macrophage lineage. So far, there are no studies in the role of miRNAs in this viral disease. Using RNAseq technology and bioinformatics analysis the expression of miRNAs in different phases of the disease were studied. A total of 212 miRNAs were found, of which 46 were conserved sequences found for the first time in sheep and 12 were completely novel. Differential expression analysis showed changes in several miRNAs comparing uninfected and seropositive groups, but did not detect significant differences between seropositive asymptomatic and diseased sheep. The high increase in expression of oar-miR-21 agrees with the increase of the same miRNA detected in other viral diseases. In addition, the target prediction of dysregulated miRNAs revealed that they control genes involved in proliferation-related signalling pathways like PI3K-Akt, AMPK and ErbB.

overall_design: MicroRNA expression by RNA-seq in three phases of infection with Visna-Maedi virus in sheep: Seronegative, seropositive asymptomatic and seropositive with clinical lessions. 5 replicates for each group.

first: Martin

last: Bilbao-Arribas

first: Naiara

last: Abendaño

first: Endika

last: Varela-Martínez

first: Ramses

last: Reina

first: Damián

last: de Andrés


title: Quantitative mass spectrometry-based proteomics reveals the dynamic protein landscape during initiation of human Th17 cell polarization

status: Public on Dec 14 2018

city: Turku

first: Tommi

last: Välikangas

address: Huhkonmaantie 26 as.11

department: Turku Centre for Biotechnology

institute: University of Turku

summary: CD4+ T cells play a key role in the adaptive immune system. Their subset, Th17 cells contribute to pathogenesis of inflammatory and autoimmune diseases and cancer. To reveal the Th17 cell-specific proteomic signature regulating Th17 cell differentiation and function in human we used a label-free mass spectrometry-based approach. To determine the degree of similarities and differences between the transcript and the protein levels, we performed a comprehensive analysis of the transcript-protein relationships. Comparison of the proteomics and RNA-sequencing data generated in this study during human Th17 differentiation revealed a high degree of overlap between the datasets. However, we found very limited overlap between the proteins differentially regulated in response to Th17 differentiation in human and mouse. Of the 758 and 397 proteins differentially regulated at 72h during Th17 specification in human and in mouse, respectively, only 33 were detected as differentially regulated in a similar fashion in both species. We validated a panel of selected proteins with known and unknown functions. Finally, using RNA interference (RNAi), we showed that SATB1 negatively regulates of human Th17 cell differentiation. To our knowledge, this study is the first to illustrate a comprehensive picture of the global protein landscape during early human Th17 cell differentiation. Poor overlap with recently reported mouse data underlines the importance of human studies for translational research.

overall_design: In this study, the proteomic landscape of differentiating Th17 cells were compared to those of naive CD4+ T cells (Thp) and to those of only TCR-activated T cells (Th0) at 24 and 72h during Th17 polarization. Furthermore, transcriptomic analysis of Th17 and Th0 cells was performed at 72h post initiation of polarization and compared to the proteomic findings of the same timepoint. Finally, the proteomic dataset between Th17 and Th0 at 72h were compared to a mouse dataset (Mohammad, I., Nousiainen, K., Bhosale, S.D., Starskaia, I., Moulder, R., Rokka, A., Cheng, F., Mohanasundaram, P., Eriksson, J.E., Goodlett, D.R., et al. (2018). Quantitative proteomic characterization and comparison of T helper 17 and induced regulatory T cells. PLoS Biol. 2018 May 31;16(5):e2004194).

first: Subhash

last: Tripathi

first: Ankitha

last: Shetty

first: Mohd

last: Khan

first: Santosh

last: Bhosale

first: Robert

last: Moulder

first: Elina

last: Komsi

first: Verna

last: Salo

first: Rafael

last: De Albuquerque

first: Omid

last: Rasool

first: Sanjeev

last: Galande

first: Laura

middle: E

last: Elo

first: Riitta

last: Lahesmaa


title: Multi-brain-region transcriptional organization linking sleep and affective functions

city: Evanston

first: Peng

last: Jiang

state: IL

address: 2205 Tech Drive, Hogan 2-160

department: Center for Sleep and Circadian Biology

country: USA

institute: Northwestern University

summary: Sleep and affective behaviors are highly interrelated phenotypes, commonly altered in a variety of neuropsychiatric diseases, including major depressive disorder (MDD). To understand the transcriptomic organization underlying sleep and affective function, we studied a population of (C57BL/6J x 129S1/SvImJ) F2 mice by measuring 283 affective and sleep phenotypes and profiling gene expression across four brain regions, including the frontal cortex, hippocampus, thalamus, and hypothalamus. We identified converging molecular bases for sleep and affective phenotypes at both the single-gene and gene-network levels. Utilizing publicly available transcriptomic datasets collected from sleep-deprived mice and major depressive disorder (MDD) patients, we identified three cortical gene networks altered by sleep/wake changes and depression. The network-level actions of sleep loss and depression were opposite to each other, providing a mechanistic basis for the sleep disruptions commonly observed in depression as well as the reported acute antidepressant effects of sleep deprivation. We highlight one particular network composed of circadian rhythm regulators and neuronal activity-dependent immediate-early genes. The key upstream driver of this network, Arc, may act as a nexus linking sleep and depression. Our data provide mechanistic insights into the role of sleep in affective function and MDD.

overall_design: Integrated network modeling of genotypic, phenotypic, and transcriptomic data collected in a genetically diverse mouse population.

first: Joseph

middle: R

last: Scarpa

first: Vance

last: Gao

first: Martha

last: Vitaterna

first: Andrew

last: Kasarskis

first: Fred

middle: W

last: Turek


title: Competition for mitogens regulates spermatogenic stem cell homeostasis in an open niche

city: Okazaki

first: Yu

last: Kitadate

address: 5-1 Higashiyama, Myodaiji

institute: National Institute for Basic Biology

summary:
In many tissues, homeostasis is maintained by physical contact between stem cells and an anatomically-defined niche. However, how stem cell homeostasis is achieved in environments where cells are motile and dispersed among their progeny remains unknown. Using murine
spermatogenesis as a model, we find that spermatogenic stem cell density is tightly regulated by the supply of fibroblast growth factors (FGFs) from lymphatic endothelial cells. We propose that stem cell homeostasis is achieved through competition for a limited supply of FGFs. We show that the quantitative dependence of stem cell density on FGF dosage, the biased
localization of stem cells toward FGF sources, and stem cell dynamics during regeneration following injury can all be predicted and explained within the framework of a minimal theoretical model based on “mitogen competition”. We propose that this model provides a generic and robust mechanism to support stem cell homeostasis in open, or facultative, niche environments.

overall_design: To understand the impact of FGF5 for in vitro spermatogonia, the gene expression profiles on in vitro cultured spermatogonia with or without FGF5. Two independent experiments were performed using different biological samples. To understand the impact of Fgf5 for in vivo GFRα1+ spermatogonia, the gene expression profiles on GFRα1+ spermatogonia in wt and Fgf5–/– mice were measured. GFRα1+ spermatogonia were isolated by FACS from cell suspensions prepared from the testes of GFRα1-EGFP knock-in mice in wt and Fgf5–/– background. Three independent experiments were performed for wt and Fgf5–/–.


title: miRNA expression signatures in human alveolar macrophages after toll-like receptor activation

status: Public on Dec 13 2018

city: Saarbruecken

first: Jessica

last: Hoppstaedter

address: Campus C2 3

department: Pharmacy

country: Germany

institute: Saarland University

summary: We have employed miRNA microarray expression profiling to identify miRNAs that are differentially regulated by toll-like receptor activation in alveolar macrophages. Macrophages are strategically distributed all over the body and represent the first line of defense to invading pathogens. In response to bacterial or viral infections, these phagocytic cells engulf and destroy the infectious agent. Macrophages recognize a variety of microbial products, such as bacterial cell wall components and nucleic acids, via pathogen recognition receptors (PRRs), such as toll-like receptors (TLRs). TLR4 represents the receptor for bacterial lipopolysaccharide (LPS). The extracellular TLR1/2 heterodimer recognizes bacterial triacetylated lipopeptides and their mimic, the synthetic compound Pam3CSK4. In contrast, intracellular TLR3 detects double-stranded RNA, i.e., an intermediate in viral replication, as well as its synthetic analogon polyinosinic:polycytidylic acid (Poly(I:C)). TLRs differentially activate transcription factors due to the varying involvement of the adapter molecules. However, little is known about TLR-mediated miRNA induction in macrophages. In this study, several microRNAs were identified that were specifically associated with a certain treatment scheme, suggesting that macrophage responses highly depend on the nature of the stimulus.

overall_design: Human alveolar macrophages isolated from lung tissue of patients undergoing lung resection were either left untreated or treated as follows: 1 µg/mL LPS for 2 h; 1 µg/mL Pam3CSK4 for 2 h; 10 µg/mL Poly(I:C) for 2 h; 0.1 µg LPS for 24 h (chronic low-dose exposure to induce LPS tolerance); 0.1 µg LPS for 24 h followed by rechallenge with 1 µg/mL LPS for 2 h; 1 µg Poly(I:C) for 24 h (chronic low-dose exposure).

last: Hoppstädter

first: Christina

last: Backes

first: Petra

last: Leidinger

first: Eckart

last: Meese

first: Alexandra

last: Kiemer


title: Chemical reprogramming of human fibroblasts

status: Public on Dec 12 2018

city: Frankfurt am Main

first: Xinlai

last: Cheng

state: Hessen

address: Max-von-Laue-Strasse 15. R. 3.652

department: Chemical Biology

institute: Goethe Frankfurt University. BMLS

summary: The compound (O4I3) showed a remarkable OCT4 induction, which at least in part, is due to the inhibition of H3K4-specific lysine demethylase (KDM5, also known as JARID1). Experiments demonstrated that KDM5A, serves as a reprogramming barrier via interference with the enrichment of H3K4Me3 at the OCT4 promoter. Thus, our results introduce a new class of KDM5 chemical inhibitors and provide further insight into the pluripotency-related properties of KDM5-family members.

overall_design: RNA was obtained from treated and non-treated human fibroblast and fibroblast-derived induced Pluripotent Stem Cells and treated with an episomal constrcuts of Oct4, Sox2, Klf4 and c-Myc in addition to O4I3

first: Rodrigo

last: Gama-Brambila