title: Broad-spectrum adaptive antibiotic resistance associated with Pseudomonas aeruginosa mucin-dependent surfing motility

status: Public on Jun 26 2018

city: Vancouver

first: Evelyn

last: Sun

state: BC

address: 2259 Lower Mall

country: Canada

institute: University of British Columbia

summary: Surfing motility is a novel form of surface adaptation exhibited by the nosocomial pathogen, Pseudomonas aeruginosa, in the presence of the glycoprotein mucin that is found in high abundance at mucosal surfaces especially the lungs of cystic fibrosis and bronchiectasis patients. Here we investigated the adaptive antibiotic resistance of P. aeruginosa under conditions in which surfing occurs compared to cells undergoing swimming. P. aeruginosa surfing cells were significantly more resistant to several classes of antibiotics including aminoglycosides, carbapenems, polymyxins, and fluroquinolones. This was confirmed by incorporation of antibiotics into growth medium, which revealed a concentration-dependent inhibition of surfing motility that occurred at concentrations much higher than those needed to inhibit swimming. To investigate the basis of resistance, RNA-Seq was performed and revealed that surfing influenced the expression of numerous genes. Included amongst genes dysregulated under surfing conditions were multiple genes from the Pseudomonas resistome, which are known to affect antibiotic resistance when mutated. Screening transposon mutants in these surfing-dysregulated resistome genes revealed that several of these mutants exhibited changes in susceptibility to one or more antibiotics under surfing conditions, consistent with a contribution to the observed adaptive resistance. In particular, several mutants in resistome genes, including armR, recG, atpB, clpS, nuoB, and certain hypothetical genes such as PA5130, PA3576 and PA4292, showed contributions to broad-spectrum resistance under surfing conditions and could be complemented by their respective cloned genes. Therefore, we propose that surfing adaption led to extensive multidrug adaptive resistance as a result of the collective dysregulation of diverse genes.

overall_design: RNA-Seq profiling of gene expression in Pseudomonas aeruginosa UCBPP-PA14 grown in three conditions

first: Erin

last: Gill

first: Reza

last: Falsafi

first: Amy

last: Yeung

first: Sijie

last: Liu

first: Robert

last: Hancock


title: Nicotiana attenuata transcriptome after oviposition and herbivory by S. exigua and M. sexta

status: Public on Jun 27 2018

city: Berlin

first: Tobias

last: Lortzing

state: Berlin

address: Haderslebener Str. 9

department: Biology

country: Germany

institute: Freie Universität Berlin

summary: Oviposition by lepidopteran herbivores on Nicotiana attenuata primes plant defence responses that are induced by the feeding larvae. While oviposition by both the generalist Spodoptera exigua and the specialist Manduca sexta primes the production of defensive phenylpropanoids, their larvae are differentially affected. We investigate here the impact of prior oviposition on the transcriptome and phytohormone levels of plants that were later attacked by larvae to find regulatory signals of this priming. In a full-factorial design, we evaluated the effects of oviposition and herbivory by both species. Oviposition alone had only subtle effects at the transcriptional level. Laval feeding alone induced species-specific plant responses. Larvae of the generalist regulated phytohormones and gene expression stronger than larvae of the specialist. A day after larvae started to feed, we detected no significant alterations of the plant's response to larval feeding due to prior oviposition by conspecific moths. Yet, oviposition by each of the species profoundly influenced the plant's transcriptional and phytohormonal response to feeding larvae of the other species. Remarkably, the species-specific plant responses to larval feeding shifted towards the response normally elicited by larvae of the ovipositing species. Thus, plants may already recognise an insect's identity upon its oviposition.

overall_design: The effect of feeding and oviposition by M. sexta and S.exigua was studied in a 3x3 full factorial design. Per treatments 11-12 plants were used, that were pooled into three samples for hybridization on the arrays. The feeding treatments followed insect oviposition at their natural developmental time (3 and 4 days after S. exiua and M. sexta oviposition, respectively) and were performed on a leaf systemic to the oviposited leaf. The leaves were harvested 1 day after feeding, respectively 5 and 6 days after oviposition.

first: Sylvia

last: Drok

first: Michele

last: Bandoly

last: Lorzing

first: Sandra

last: Stelzer

first: Anke

last: Steppuhn


title: Genes important for DNA damage response in Bacillus subtilis

city: Ann Arbor

first: Lyle

middle: A

last: Simmons

state: MI

address: 830 N University Ave

department: MCDB

country: USA

institute: University of Michigan

summary: The objective of the experiments was to identify non-essential genes required for mitigating the response DNA damage

overall_design: Bacillus subtilis transposon insertion library; Triplicate samples of control, mitomycin C treated, methyl methane sulfonate treated, and phleomycin treated cultures were grown over the course of three growth periods. A total of 57 samples are included.

first: Peter

middle: E

last: Burby


title: Analysis of HERV transcriptome in PBMCs upon dose dependent LPS stimulations identifies HERVs and genes shared signaling pathways

status: Public on Jun 25 2018

city: Lyon

first: Julien

last: Textoris

address: Hôpital Edouard herriot - Pavillon P; 5 place d'Arsonval

department: Medical Diagnostic Discovery Department (MD3)

country: France

institute: bioMérieux

summary: Human endogenous retroviruses (HERVs/MaLRs) are distributed among our 24 chromosomes and their long terminal repeats (LTRs) constitute putative regulatory sequences. HERVs have received much attention for their implication in cancer, autoimmunity and placental development. Herein, we used a recently described high-density microarray allowing the exploration of the whole HERVs/MaLRs transcriptome including 353,994 HERVs/MaLRs loci and also 1559 genes related to immunity. We obtained a first view of the HERV transcriptome in peripheral blood mononuclear cells (PBMCs) by using a composite panel of unstimulated, low dose and high dose LPS-stimulated PBMCs from healthy volunteers to mimic inflammatory response or monocyte anergy. About 5.6% of the HERVs/MaLRs repertoire is transcribed in PBMCs. Roughly, one tenth [5.7%-13.1%] of LTRs present a constitutive promoter or polyA function and a quarter [19.5%-27.6%] of LTRs may shift from silent to active LTRs, LTRs being broadly subjected to operational determinism. We provide evidence that some HERVs/MaLRs and genes share similar control of regulation upon LPS stimulation conditions, e.g. presenting a low dose LPS-dependent “tolerizable” profile which can be reversed by INF-g stimulation. Similarly to tissue tropism observed in solid tumors, stimulus-dependent response confirm that the expression of HERVs is tightly regulated in PBMCs. Altogether, these observations allow to integrate 62 HERVs/MaLRs and 26 genes in 11 canonical pathways. We highlight HERVs close to OAS2/3 and IFI44/IFI44L genes. HERV incorporation at the crossroads of immune response pathways, paves the way for further functional studies and analyses of HERV transcriptome in altered immune responses in vivo such as in sepsis.

overall_design: Endotoxin tolerance model was carried out in triplicate from 5 healthy volunteers. Conditions: not stimulated (NS), LPS stimulation (LPS), or  Endotoxin tolerance (ET)

first: Marine

last: Mommert

first: Olivier

last: Tabone

first: Guy

last: Oriol

first: Elisabeth

last: Cerrato

first: Audrey

last: Guichard

first: Paola

last: Fournier

first: Alexandre

last: Pachot

first: Guillaume

last: Monneret

first: Fabienne

last: Venet

first: Karen

last: Brengel-Pesce

first: François

last: Mallet


title: Pitx2c regulates axis extension via mesendodermal cell migration

status: Public on Jun 22 2018

city: Bad Nauheim

first: Michelle

middle: M

last: Collins

state: Hessen

address: Ludwigstrasse 42

department: Developmental Genetics

institute: Max Planck Institute for Heart and Lung Research

summary: Pitx2c, a homeodomain transcription factor, is classically known for its left-right patterning role.  However, an early wave of pitx2 expression occurs at the onset of gastrulation in several species, indicating a possible earlier role that remains relatively unexplored.  Here, we show that in zebrafish, maternal-zygotic (MZ) pitx2c mutants exhibit a shortened body axis indicative of convergence and extension (CE) defects.  Live imaging reveals that MZpitx2c mutants display less persistent mesendodermal migration during later stages of gastrulation.  Transplant experiments indicate that Pitx2c functions cell non-autonomously to regulate this cell behavior by modulating cell shape and protrusive activity.  Using transcriptomic analyses and candidate gene approaches, we identify transcriptional changes in components of the chemokine-ECM-integrin dependent mesendodermal migration network.  Together, our results define pathways downstream of Pitx2 that are required during early embryogenesis and reveal novel functions for Pitx2 as a regulator of morphogenesis.

overall_design: MZpitx2c and WT embryos were collected at shield stage to assess the loss of Pitx2c function by microarray.  For gain-of-function analysis, embryos were injected at the 1-cell stage with mRNA encoding pitx2c and collected at dome stage for microarray.


title: Bacterial 16SrRNA

city: Yokohama

first: Keiichiro

last: Suzuki

state: Kanagawa

address: 1-7-22 Suehiro-cho. Tsurumi

department: IMS

country: Japan

institute: RIKEN

type: Expression profiling by high throughput sequencing

summary: The gut microbiota is essential for several aspects of host physiology such as metabolism, epithelial barrier function and immunity. Previous studies have revealed that host immune system as well as diet and other environmental factors have a strong impact on the composition and activity of gut microbiota, but the molecular requirements for such functional regulation remain unknown. We show that the bacteria belonging to phylum Bacteroidetes acquire their symbiotic activity in the colonic mucus, depending on a newly characterized molecular family encoded within the polysaccharide utilization loci (PUL), which we have named Mucus-Associated Functional Factor (MAFF).

overall_design: Specific pathogen free mice were treated with antibiotics (metronidazone and ciprofloxacin) and then colonized B.theta (WT or MAFF-deleted mutant) with or without backpack of 7-6IgA hybridoma cell line or P3U1 myeloma cells.

first: Akira

last: Nakajima

first: Alexis

last: Vogelzang

first: Mikako

last: Maruya

first: Michio

last: Miyajima

first: Megumi

last: Murata

first: Aoi

last: Son

first: Tomomi

last: Kuwahara

first: Tatsuaki

last: Tsuruyama

first: Satoshi

last: Yamada

first: Minoru

last: Matsuura

first: Hiroshi

last: Nakase

first: Daniel

last: Peterson

first: Sidonia

last: Fagarasan


title: Bacterial RNA-Seq

overall_design: Germ free mice were colonized with indicated bacterial strains. In the other set of experiment, specific pathogen free mice were treated with antibiotics (metronidazone and ciprofloxacin) and then colonized B.theta (WT or MAFF-deleted mutant) with or without backpack of 7-6IgA hybridoma cell line or P3U1 myeloma cells.


title: The mammalian decidual cell evolved from a cellular stress response

status: Public on Jun 21 2018

city: West Haven

first: Cong

last: Liang

address: 300 Heffernan Dr.

institute: Yale University

summary: Among animal species, cell types vary greatly in terms of number and kind. The broad range of number of cell types among species suggests that cell type origination is a significant source of evolutionary novelty. The molecular mechanisms giving rise to novel cell types, however, are poorly understood. Here we show that a novel cell type of eutherians mammals, the decidual stromal cell (DSC), evolved by rewiring an ancestral cellular stress response. We isolated the precursor cell type of DSCs, endometrial stromal fibroblasts (ESFs), from the opossum Monodelphis domestica. We show that, in opossum ESF, the majority of decidual core regulatory genes respond to decidualizing signals, but do not regulate decidual effector genes. Rather, in opossum ESF, decidual transcription factors function in apoptotic and oxidative stress response. We propose that the rewiring of cellular stress responses could be a general mechanism for the evolution of novel cell types.

overall_design: Examination of mRNA profiles of in vitro cultured opossum endometrial stromal fibroblasts and those exposed to: 1) eutherian differentiation media, containing cyclic AMP (cAMP) analogue 8-Br-cAMP and the progesterone (P4) analogue medroxyprogesterone acetate (MPA), 2) MPA, 3) PGE2, 4) PGE2 and MPA.

first: Eric

last: Erkenbrack

first: Jamie

middle: D

last: Maziarz

first: Gunter

middle: P

last: Wagner


title: The BCG Delta BCG1419c vaccine candidate reduces lung pathology, IL-6, TNFa, and IL-10 during chronic TB infection

status: Public on Jun 20 2018

city: Seattle

first: Eliza

state: WA

address: 401 Terry Ave N

institute: Institute for Systems Biology

summary: Comparison of  transcriptional differences (RNA-seq) between BCG delta1419c and wild-type BCG that might explain the pathological differences in vaccination studies.

sample_organism: Mycobacterium tuberculosis variant bovis BCG

overall_design: Cultures of wild-type (Wt) and Delta1419c were grown for 10 days and harvested for mRNA expression profiling by Illumina sequencing, in duplicate from two independent experiments. The sequence reads that passed quality filters were aligned to BCG reference genome using STAR, followed by read count collection by HTSeq and differential expression analysis with DESeq2.

middle: J

first: Mario

last: Flores-Valdez


title: Bid Expression Controls Neuronal Cell Fate During Avian Ciliary Ganglion Development

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

institute: University of Lübeck

summary: To elucidate molecular networks regulating important aspects of parasympathetic neuronal development, a genome-wide expression analysis was performed during multiple stages of avian ciliary ganglion (CG) development. The transcriptome data showed a well-defined sequence of events, starting from neuronal migration via neuronal fate cell determination, synaptic transmission, regulation of synaptic plasticity to growth factor associated signaling. Focusing on cell death-related changes in the transcriptome, we could characterize a series of events that starts with the activation of neuronal apoptotic processes at E7 via the cell death execution phase at E8 and E9 and ends with apoptotic cell clearance at E14. Moreover, we detected a transient up-regulation of the transcription factors TP53 and RARB that was linked to cell death. The expression of BID, a p53 target, was also found to be dynamically regulated. Using a virus-based RNAi knockdown approach, BID expression was shown to be crucial for the execution of ontogenetic programmed cell death (PCD). Therefore, this study for the first time provides a comprehensive analysis of CG neuron development on the transcriptome level, revealing a temporally well-controlled expression of genes regulating ontogenetic PCD, with BID being one of the most dynamically regulated genes during the cell death phase. The effect of BID silencing in vivo suggests an essential role of BID expression in neuronal development.

overall_design: Ciliary ganglia were dissected from chicken embryos at E6,E7, E8, E9, E10 and E14. For each analyzed time point, ganglia from at least 40 embryos were pooled for RNA extraction using the Qiagen RNeasy micro kit (Qiagen, Hilden, Germany) according to manufacturer's instructions. Four replicate sample of each time point were obtained.

first: Melanie

last: Boerries

first: Sophie

last: Koszinowski

first: Kerstin

last: Krieglstein


title: Affymetrix SNP array data for cell line and tumor genotype alignment

status: Public on Aug 31 2018

city: Cambridge

first: Elin

middle: S.

last: Agoston

state: Massachusetts

address: 675 West Kendall Street

institute: Cellaria Biosciences

type: Genome variation profiling by genome tiling array

summary:
When characterizing novel cell lines, we used SNP genotyping alignment to compare the tumor to the resulting cell line. In order to do this pairwise comparison as each cell model was developed, we added additional data from the GEO database during the normalization step. These data were either tumor DNA or cancer cell line DNA. These samples were not part of a matched pair and so genotype alignment was not reported for these samples.
The GEO Series and Sample numbers used for each sample grouping is as follows. Wood- Series: GSE21541; Samples: GSM533396, GSM533397, GSM533398, GSM533399, GSM533400, GSM533401, GSM533402, GSM533404, GSM533410.  Ferry- Series: GSE16125; Samples: GSM403493, GSM403494, GSM403495, GSM403496, GSM403497, GSM403498, GSM403499, GSM403500, GSM403501. Jacket series 1: GSE15126; samples: GSM385517, GSM385518, GSM385519, GSM385520, GSM385521, GSM385522, GSM385523, GSM385524, GSM385525, GSM385526. Jacket series 2: GSE62407; Samples: GSM1526628, GSM1526648, GSM1526668. DF Series GSE39130; Samples: GSM956523, GSM956524, GSM956525, GSM956526, GSM956527, GSM956528.

overall_design: DNA was extracted from cell lines at several passages and the tumor tissue samples from which they were derived. Genotype was determined by SNP 250K Nsp.

middle: S

first: Ronny

middle: I

last: Drapkin


title: Next Generation Sequencing Analysis of S. aureus cultured in the presence/absence of V12CBD

city: Wuhan

first: Hang

last: Yang

state: Hubei

address: 44 Xiaohongshan

country: China

institute: Wuhan Institute of Virology, Chinese Academy of Sciences

summary: We reported the application of NGS technology for high-throughput transcription profiling of S. aureus in the presence of V12CBD, the binding domain from bacteriophage lysin PlyV12. In summary, a total of 225 differentially expressed genes (DEGs) were identified (at least 2-fold change, with a p-value <0.05) after V12CBD treatment. Of those, transcripts of 111 genes were found upregulated and 114 downregulated in response to V12CBD. Predominantly genes involved in translation (76.9%), nucleotide metabolism (80%), cell division (100%), as well as replication and repair (82%), were repressed in S. aureus treated with V12CBD. The GO enrichment analysis showed that the DEGs were scattered in 34 GO terms, specifically, a total of 3 items related to cellular components, 25 items for biological processes, and 6 items for molecular functions. Functional classification of the DEGs using KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment analysis, revealed that a large group of S. aureus genes expressed differentially in response to V12CBD belonged to the membrane transport pathway, the environmental information processing category. Several genes encoding important virulence factors, such as surface protein encoding gene sdrC, protein arginine kinase encoding gene mcsB, persistent infection associated genes (putP and oppF2), and the genes involved in capsular polysaccharide biosynthesis (tarI and SAOUHSC_00125), were downregulated in the presence of V12CBD. Finally, two two-component systems (TCSs), WalKR, SrrAB, were also found downregulated in the presence of V12CBD. The transcription levels of these genes were also confirmed by primer-specific qRT-PCR. This study showed that V12CBD could suppress multiple important virulence factors expression in S. aureus.

overall_design: S. aureus T23 was cultured in the presence and absence of 25 μg/ml V12CBD for 4 h at 37°C, and the mRNA profiles were generated by deep sequencing using Illumina NextSeq.

first: Hongping

last: Wei


title: miRNA expression data from multilineage differentiation of hiPSC

status: Public on Jun 18 2018

city: Los Angeles

first: Lu

last: Li

state: CA

address: Room 706, 1985 Zonal Ave

department: School of Pharmacy

institute: University of Southern California

summary: We built a comprehensive miRNA expression atlas for multilineage comparison by differentiating induced PSC (iPSC) into three lineages representatively derived from the three germ layers and profiling the dynamic miRNA expression by microarray.

overall_design: The hiPSC line iBC 1.2 was induced to differentiate into representative lineages of the three germ layers, namely, hepatocytes for endoderm (HD), nephron progenitors for mesoderm (KD), and neural progenitors for ectoderm (ND), respectively. miRNA expression profiling was performed using small RNA microarrays. Each lineage differentiation including eight samples with replicates for four time-points (day 0, 3, 6, 10) were collected and profiled.

first: Wai

middle: Y

last: Chan

first: Hoi

middle: H

last: Cheung


title: Real-time quantitative PCR analysis of induced pluripotent derived endothelial cells

status: Public on Jun 16 2018

city: Baltimore

first: Sharon

last: Gerecht

state: Maryland

address: 3400 N. Charles Street

institute: Johns Hopkins University

summary: CD31+/VECad+ hiPSC-ECs were purified through magnetic activated cell sorting.  Expanded endothelial cells were then subjected to serum starvation conditions for 24 hours by culturing in DMEM.  After serum starvation, total RNA was extracted.  We used a custom Thermo Fisher Scientific PCR assay panel to quantify gene expression relevant to ciliogenesis, cytoskeletal integrity, Wnt signaling, pluripotency and endothelial phenotype.

overall_design: Biological Replicates: BC1-ECs (n=3); C12-ECs (n=2); hiPSC-ECs (n=3). Technical triplicates were performed for each gene analyzed.

first: Quinton

last: Smith


title: Transcriptome Profiling in KY1005-treated NHP HCT-recipients

city: Pittsburgh

first: Warren

middle: David

last: Shlomchik

state: PA

address: 3550 Terrace Street

department: Medicine

institute: University of Pittsburgh

summary: Graft versus host disease (GVHD) is the most common complication of hematopoietic stem cell transplant (HCT). However, our understanding of the molecular pathways that cause this disease remains incomplete, leading to inadequate treatment strategies. To address this, we measured the gene expression profile of non-human primate (NHP) T cells during acute GVHD.  In this study we specifically interrogated the transcriptional signatures of animals treated with FR104 monotherapy and FR104/Sirolimus combination therapy

overall_design: Series of n=108 arrays taken from animal from the post transplant period including arrays from n=56 untransplanted healthy controls

first: Victor

last: Tkachev

first: Leslie

last: Kean


title: Role of DmSTING in fly

status: Public on Jun 19 2018

city: Pullman

first: Alan

middle: G.

last: Goodman

state: WASHINGTON

address: 100 Dairy Rd., BLS 202

department: School of Molecular Biosciences

institute: Washington State University

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

overall_design: Refer to individual Series


title: Molecular mechanism of repression of meiotic recombination around centromeres

status: Public on Jun 14 2018

first: Gerald

middle: R

state: Washington

address: 1100 Fairview Ave. N.

department: Basic Sciences Division

institute: Fred Hutchinson Cancer Research Center

type: Genome binding/occupancy profiling by genome tiling array

summary: In most eukaryotes, meiotic crossovers are essential for error-free chromosome segregation but are specifically repressed near centromeres to prevent missegregation. Recognized for >85 years, the molecular mechanism of this repression has remained unknown. Meiotic chromosomes contain two distinct cohesin complexes: pericentric complex (for segregation) and chromosomal arm complex (for crossing-over). We show that the pericentric-specific complex also actively represses pericentric meiotic double-strand break (DSB) formation and, consequently, crossovers. The fission yeast pericentric regions contain heterochromatin, removal of which can result in derepression in double-strand break formation and recombination during meiosis. We uncover the mechanism by which fission yeast heterochromatin protein Swi6 (mammalian HP1-homolog) prevents recruitment of activators of meiotic DSB formation such as Rec10. Localizing these missing activators to wild-type pericentromeres bypasses repression and generates abundant crossovers but reduces gamete viability.The molecular mechanism elucidated here likely extends to other species including humans, where pericentric crossovers can result in disorders such as Down syndrome. These mechanistic insights provide new clues to understand the roles played by multiple cohesin complexes, especially in human infertility and birth defects.

overall_design: ChIP-chip arrays for the meiotic protein Rec10 at 0h and 3.5h during meiosis in wild type and the H3K9 methyltransferase mutant (Clr4Δ) cells. Dyes were swapped in these experiments. The centromere-specific probes were separated from the other probes and analyzed after dye swap correction and genome-median normalization.

first: Mridula

last: Nambiar


title: An epigenomic approach to identifying differential overlapping and cis-acting lncRNAs in cisplatin-resistant cancer cells

city: Madrid

first: Carlos

last: Rodriguez Antolin

address: Paseo de la Castellana

department: Genetics

country: Spain

institute: Hospital La Paz Institute for Health Research

summary: Long noncoding RNAs are newly discovered regulators that play a critical role in cell biology, crucial to the correct functioning of the cell. Alterations in lncRNAs can lead to the development of diseases such as cancer. However, the role of lncRNAs in resistance to platinum chemotherapy is largely unknown. To screen for epigenetic changes involved in the development of resistance, we combined lncRNA and mRNA expression microarrays with whole genome bisulfite sequencing (WGBS) in four paired cisplatin-sensitive/resistant cells from non-small cell lung cancer and ovarian cancer. We found low levels of expression changes in lncRNAs (1.5%) and mRNAs (2%) when comparing resistant vs. sensitive cells. The correlation between lncRNA/mRNA arrays and WGBS identified two groups of lncRNAs, classified according to their relationship with the gene they have in silico complementarity or with their possible epigenetic regulation at the DNA methylation level. Validation of the results of expression and methylation levels allowed us to characterize lncRNAs in cisplatin-resistant phenotypes. In this study, we characterized lncRNAs that change in cisplatin-resistant cells due to epigenetic regulation at the DNA methylation level and the associated changes in expression levels. We have identified two groups of differentially expressed and methylated lncRNAs, indicating a new approach to the study of the mechanisms involved in the development of acquired resistance to cisplatin in cancer cells.

overall_design: A total of four cell lines were purchased from ATCC and ECACC (Sigma-Aldrich) and cultured as recommended. To analyze the changes in the transcriptome as a result of CDDP treatment, we established the CDDP-resistant variants of H23-R, H460-R, A2780-R and OVCAR3-R from the parental-sensitive variants H23, H460, A2780 and OVCAR3, after exposure to increasing doses of CDDP treatment in a time period of 6–18 months. Labelled cDNA from the 8 cell lines was hybridized by duplicate into the Human LncRNA Array v3.0 (8 x 60K, Arraystar).

first: Olga

last: Vera

last: Rodriguez-Antolin

first: Javier

last: de Castro

first: Florian

last: Karreth

first: Thomas

last: Sellers

first: Inmaculada

last: Ibañez de Caceres


title: Transcriptome analysis of wildtype and rb1-/- zebrafish larval head tissue by RNA-Seq

status: Public on Jun 13 2018

city: Ames

first: Maura

last: McGrail

state: IA

address: 2310 Pammel Dr

department: GDCB

institute: Iowa State University

summary: The wild type and rb1 mutant transcriptomes were used to identify molecular pathways and epigenetic regulators altered in rb1 mutant brain cells. The data was also used for comparative analysis with zebrafish rb1-embryonal brain tumor transcriptome, to identify molecular pathways that distinguish transformed rb1- tumor cells from non-transformed rb1-/- mutant cells.

overall_design: 3 pools of 5 zebrafish 5-day-old larval heads were used to prepare 3 wild type +/+ and 3 rb1-/- homozygous mutant barcoded indexed RNA-Seq libraries.

first: Jeffrey

last: Haltom


title: Identification of differentially expressed genes and pathways in mice exposed to mixed field neutron/x-ray radiation

status: Public on Jun 15 2018

city: New York

first: Constantinos

last: Broustas

state: NY

address: 630 168th Street

department: Center for Radiological Research

institute: Columbia University

summary:
Background: Radiation exposure due to the detonation of an improvised nuclear device remains a major security concern. Radiation from such a device involves a combination of photons and neutrons. Although photons will make the greater contribution to the total dose, neutrons will certainly have an impact on the severity of the exposure as they have high relative biological effectiveness.
Results: We investigated the gene expression signatures in the blood of mice exposed to 3 Gy x-rays, 0.75 Gy of neutrons, or to mixed field photon/neutron with the neutron fraction contributing 5%, 15%, or 25% of a total 3 Gy radiation dose. Gene ontology and pathway analysis revealed that genes involved in protein ubiquitination pathways were significantly overrepresented in all radiation doses and qualities. On the other hand, eukaryotic initiation factor 2 (EIF2) signaling pathway was identified as one of the top 10 ranked canonical pathways in neutron, but not pure x-ray, exposures. In addition, the related mTOR and regulation of EIF4/p70S6K pathways were also significantly underrepresented in the exposures with a neutron component, but not in x-ray radiation. The majority of the changed genes in these pathways belonged to the ribosome biogenesis and translation machinery and included several translation initiation factors (e.g. Eif2ak4, Eif3f), as well as 40S and 60S ribosomal subunits (e.g. Rsp19, Rpl19, Rpl27). Many of the differentially downregulated ribosomal genes (e.g. RPS19, RPS28) have been causally associated with human bone marrow failure syndromes and hematologic malignancies. We also observed downregulation of transfer RNA processes, in the neutron-only exposure (p < 0.005). Ingenuity Pathway Analysis (p < 0.05) of differentially expressed genes predicted significantly suppressed activity of the upstream regulators c-Myc and Mycn, transcription factors known to control ribosome biogenesis.
Conclusions: We describe the gene expression profile of mouse blood following exposure to mixed field neutron/x-ray irradiation. We have discovered that pathways related to protein translation are significantly underrepresented in the exposures containing a neutron component. Our results highlight the significance of neutron exposures that even the smallest percentage can have profound biological effects that will affect medical management and treatment decisions in case of a radiological emergency.

overall_design: Radiation induced gene expression in mouse blood was measured at 7 days after 3 Gy and 0.75 Gy neutron exposure or after 3 Gy mixed-field irradiation of x-rays with neutrons contributing 5%, 15%, and 25% of the total dose. Six independent experiments were performed at each dose and time point.

middle: G

first: Sally

last: Amundson


title: Transcriptome analysis of zebrafish wildtype adult brain and rb1-embryonal brain tumors, and wildtype and rb1-/- zebrafish larval head tissue, by RNA-Seq


title: Transcriptome analysis of zebrafish wildtype adult brain and rb1-embryonal brain tumors by RNA-Seq

summary: Zebrafish wildtype adult brain and rb1-embryonal brain tumor transcriptomes were used to identify candidate rb1-interacting chromatin remodelers and epigenetic regulators altered in rb1- transformed brain tumor cells. The data was also used for comparative analysis with zebrafish rb1-/- mutant transcriptome, to identify molecular pathways that distinguish transformed rb1- tumor cells from non-transformed rb1-/- mutant cells.

overall_design: RNA-Seq libraries were prepared from 10 tumor biological replicates and two pools of three normal adult brains ages 6.5 to 10.5 months.


title: APOBEC3G-regulated host factors interfere with measles virus replication: role of REDD1 and KDELR2

city: Würzburg

first: Claus

middle: Juergen

last: Scholz

address: Josef-Schneider-Str. 2

department: Core Unit SysMed

institute: University Hospital Würzburg

summary: Classically, the cytidine deaminase APOBEC3G (A3G) exerts antiviral activity against transposable elements, retroviruses, and hepatitis B virus. However, we found earlier, that it also inhibits measles (MV), mumps (MuV) and respiratory syncytial virus (RSV), but the mechanism of inhibition remained unclear. Because A3G is present in RNA processing (P) bodies, where it is involved in the regulation of mRNA decay, we supposed that it may influence the expression of host cell factors, some of which may affect viral replication. Using a microarray we therefore assessed in Vero cells whether A3G expression influences the cellular gene expression. We found alterations indicating 844 up-regulated and 598 down-regulated transcripts (adjusted P values < 0.05). Of these trancripts 19 were up-regulated and 23 down-regulated by a factor of > 2. One of the down-regulated factors, MOSC2, appeared to support MV replication, since shRNA-mediated MOSC2 knock down reduced MV replication. In addition, two up-regulated factors, REDD1 and KDELR2, impaired MV replication when over-expressed in VeroREDD1 is a cellular inhibitor of mTORC1, a regulator of cellular homeostasis controlling cell growth and protein synthesis. Rapamycin also reduced MV replication confirming our findings with REDD1. The KDELR2 retains chaperons in the ER, which are required for proper folding and transport of MV glycoproteins to the cell surface, and thereby reduces MV glycoprotein expression at the cell surface, syncytium formation, and the formation of infectious virus.

overall_design: Comparison of transcript expression between Vero (Vero-023)  and A3G-expressing Vero (Vero-024-2) cells. The effects of altered gene expression on MV infection were evaluated.

first: Vishakha

last: Tiwarekar

first: Julia

last: Wohlfahrt

first: Markus

last: Fehrholz

first: Susanne

last: Kneitz

first: Jürgen

last: Schneider-Schaulies


title: Transcriptome profiling of alphaherpesvirus-infected cells treated with the HIV-integrase inhibitor raltegravir reveals profound and specific alterations in host transcription.

city: Ithaca

first: Jennifer

middle: K

last: Grenier

address: 526 Campus Rd

department: Biomedical Sciences

institute: Cornell University

summary: Purpose: To study the effects of raltegravir treatment for corneal cells on host gene expression during FHV-1 infection and in uninfected cells. Method: For examination of effects in infected cells, corneal cells were infected with FHV-1 for 2 hours and treated with raltegravir or DMSO for 2 h. For examination of effects in uninfected cells, corneal cells were infected with FHV-1 for 2 h. Data was analyzed using a standard pipeline. Follow up of results were done with SYBR green based qPCR and functional assays where relevant.  Results: In infected cells, we identifed 399 differentially expressed genes following raltegravir therapy. Many of these genes had functions as anti-angiogenic factors and in metabolic pathways. In contrast, in uninfected cells, only 27 genes were identified as differentially regulated by raltegravir, with little overlap with those modulated during infection and little shared biological functions. This indicates that raltegravir is unlikely to induce side effects in vivo. Conclusion: Our study represents the first, to our knowledge, use of RNAseq technology to study the effects of an antiviral on host gene expression during a virus infection. We conclude that such methodology will be useful in future studies to identify bystander effects of drug treatment.

overall_design: RNAseq analysis of gene expression of antiviral treated, FHV-1 infected or uninfected corneal cells. For each sample, 3 independent biological replicates were performed

first: Matthew

last: Pennington

first: Gerlinde

last: Van de Walle


title: NEDD9 promotes oncogenic signaling, a stem/mesenchymal gene signature, and aggressive ovarian cancer growth in mice

status: Public on Jun 12 2018

city: Philadelphia

first: Denise

middle: C

last: Connolly

address: 333 Cottman Avenue

institute: Fox Chase Cancer Center

summary: Neural precursor cell expressed, developmentally downregulated 9 (NEDD9) supports oncogenic signaling in a number of solid and hematologic tumors. Little is known about the role of NEDD9 in ovarian carcinoma (OC), but available data suggest elevated mRNA and protein expression in advanced stage high grade cancers. We used a transgenic MISIIR-TAg mouse OC model combined with genetic ablation of Nedd9 to investigate its action in the development and progression of OC. A Nedd9-/- genotype delayed tumor growth rate, reduced incidence of ascites, and reduced expression and activation of signaling proteins including SRC, STAT3, E-cadherin and AURKA. Cell lines established from MISIIR-TAg;Nedd9-/- and MISIIR-TAg;Nedd9+/+ mice exhibited altered migration and invasion. Growth of these cells in a syngeneic allograft model indicated that systemic Nedd9 loss in the microenvironment had little impact on tumor allograft growth, but in a Nedd9 wild type background Nedd9-/- allografts exhibited significantly reduced growth, dissemination and oncogenic signaling compared to Nedd9+/+ allografts. Gene expression analysis revealed that Nedd9+/+ tumors exhibited more mesenchymal ‘stem-like’ transcriptional program, including increased expression of Aldh1a1 and Aldh1a2. Conversely, loss of Nedd9 resulted in increased expression of differentiation genes, including fallopian tube markers Foxj1, Ovgp1 and Pax8. Collectively, these data suggest that tumor cell-intrinsic Nedd9 expression promotes OC development and progression by broad induction of oncogenic protein signaling and stem/mesenchymal gene expression.

overall_design: Spontaneous ovarian tumors from female C57BL/6JTgMISIIR-TAg;Nedd9-WT and  C57BL/6JTgMISIIR-TAg;Nedd9-null mice (n=4 per genotype) were used.  Overall tumor burden is less than 2000 mm^3. The mice were not treated with any drug.

first: Rashid

last: Gabbasov

first: Fang

last: Xiao

first: Caitlin

last: Howe

first: Laura

last: Bickel

first: Shane

middle: W

last: O'Brien

first: Daniel

last: Benrubi

first: Thuy-Vy

last: Do

first: Yan

last: Zhou

first: Emmanuelle

last: Nicolas

first: Kathy

middle: Q

last: Cai

first: Samuel

last: Litwin

first: Sachiko

last: Seo

first: Erica

middle: A

last: Golemis


title: RNA Framework: an all-in-one toolkit for the analysis of RNA structures and post-transcriptional modifications

status: Public on Jun 10 2018

city: Groningen

first: Danny

last: Incarnato

state: Netherlands

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: University of Groningen

summary: RNA is emerging as a key regulator of a plethora of biological processes. While its study has remained elusive for decades, the recent advent of high-throughput sequencing technologies provided the unique opportunity to develop novel techniques for the study of RNA structure and post-transcriptional modifications. Nonetheless, most of the required downstream bioinformatics analyses steps are not easily reproducible, thus making the application of these techniques a prerogative of few laboratories. Here we introduce RNA Framework, an all-in-one toolkit for the analysis of most NGS-based RNA structure probing and post-transcriptional modifications mapping experiments. To prove the extreme versatility of RNA Framework, we applied it to both an in-house generated DMS-MaPseq dataset, and to a series of literature available experiments. Notably, when starting from publicly available datasets, our software easily allows replicating authors' findings. Collectively, RNA Framework provides the most complete and versatile toolkit to date for a rapid and streamlined analysis of the RNA epistructurome. RNA Framework is available for download at: http://www.rnaframework.com.

overall_design: RNA structure probing

first: Edoardo

last: Morandi

first: Lisa

middle: M

last: Simon

first: Salvatore

last: Oliviero


title: CBP/p300 transcriptome

city: Copenhagen

first: Brian

middle: Tate

last: Weinert

address: Blegdamsvej 3, 6b

country: Denmark

institute: University of Copenhagen

summary: Comparison of CBP/p300 gene knock-out, bromodomain inhibitor, and acetyltransferase inhibitors Cmpd-R and A-485 in the same cell line (MEF).

overall_design: 3-6 biological replicates per experiment and control condition

first: Chunaram

last: Choudhary

middle: T


title: Lkb1 interacts with a ciliopathy complex to regulate inflammation (array)

first: Hauke

last: Busch

summary: Ciliopathies comprise a spectrum of inherited disorders involving different organ systems such as the central nervous system, the skeleton, and the kidney1. The cilium is a hair-like organelle at the cell surface that acts as a sensor and signal transducer2. Many ciliopathy manifestations can be linked to deficient cilia function, yet it is unclear how a cilium defect results in nephronophthisis (NPHP), the most prevalent renal manifestation in children, characterized by inflammation, interstitial fibrosis, and renal cysts3. Here, we report that deletion of the serine threonine kinase Lkb1 in the mouse kidney results in cardinal features of nephronophthisis. An in-vivo proteomic interaction screen revealed ANKS3, a known interaction partner of the nephronophthisis protein NPHP1, and its interactor NEK7 as novel binding partners of LKB1. Lkb1 genetically interacts with Nphp1 in zebrafish. Unbiased transcriptional analysis in-vitro and in-vivo revealed that the chemokine CCL2 is upregulated in Lkb1 deficiency and is accompanied by recruitment of CCR2 expressing mononuclear cells in the kidney. CCL2 regulation requires NPHP1, ANKS3 and NEK7. These findings link LKB1 and ciliopathy proteins to immune regulation and explain how mutations in NPHP proteins result in fibrosis of the kidney.

overall_design: The transcriptomes of WT MDCK cells was compared Stk11 (Lkb1) KD MDCK cells

first: Melanie

last: Boerries

first: Amandine

last: Viau

first: Wolfgang

middle: E

last: Kuehn

first: Frank

last: Bienaimé


title: CREB Controls Cortical Circuit Plasticity and Functional Recovery after Stroke

status: Public on Jun 08 2018

first: Riki

last: Kawaguchi

address: 760 Westwood Plaza, Room 37-420

department: Department of Neurology and Department of Psychiatry

institute: University of California Los Angeles

summary: Treatments that stimulate neuronal excitability enhance motor performance after stroke.cAMP-response-element binding protein (CREB) is a transcription factor that plays a key rolein neuronal excitability. Increasing the levels of CREB with a viral vector in a small pool ofmotor neurons enhances motor recovery after stroke, while blocking CREB signaling preventsstroke recovery. Silencing CREB-transfected neurons in the peri-infarct region with thehM4di-DREADD blocks motor recovery. Reversing this inhibition allows recovery to continue,demonstrating that it is possible to turn off and on stroke recovery by manipulating theactivity of CREB-transfected neurons. CREB transfection enhances re-mapping of injuredsomatosensory and motor circuits, and induces the formation of new connections withinthese circuits. CREB is a central molecular node in the circuit responses after stroke that leadto recovery from motor deficits.

overall_design: Motor cortical neurons in adult C57 mice were transfected with tdTomato or tdTomato-Creb, and received either a stroke or no manipulation (control). 4 weeks after stroke, or 5 weeks after viral injection (control), tdTomato+ neurons were FACS-isolated, total RNA isolated and whole genome microarrays performed. This was done in duplicate. In the sample listing PT = photothrombotic stroke and is the same procedure as stroke.

first: L

last: Caracciolo

first: M

last: Marosi

first: J

last: Mazzitelli

first: S

last: Latifi

first: Y

last: Sano

last: Galvan

first: R

first: F

last: Gao

last: Holley

middle: S

last: Levine

first: G

last: Coppola

first: C

last: Portera-Cailliau

first: A

middle: J

last: Silva

last: Carmichael


title: A cancer avatar models prospectively guides therapy

city: Clevleand

first: Mohamed

middle: E.

last: Abazeed

state: OH

department: Radiation Oncology/Translational Hematology Oncology Research

institute: Cleveland Clinic

summary: Analysis of transcriptomic fidelity between primary and pdx tumor. The hypothesis tested in the present study was that pdx can serve as high fidelity models of human cancer and guide longitudinal care. Results provide important information on the response of preservation of gene expression changes between the primary tumor and the first generation pdx.

overall_design: Total RNA obtained from primary and patient derived xenografts (PDX)  tumor

first: Abazeed

last: Mohamed


title: Personal and transgenerational cues are nonadditive at the phenotypic and molecular level

city: Urbana

first: Alison

last: Bell

state: Illinois

address: Justin Smith Morrill Hall, 505 S Goodwin Ave #393

department: Animal Biology

institute: University of Illinois at Urbana Champaign

summary: Organisms can gain information about their environment from their ancestors, their parents, or their own personal experience. “Cue integration” models often start with the simplifying assumption that information from different sources is additive.  Here, we test key assumptions and predictions of cue integration theory at both the phenotypic and molecular level in threespined sticklebacks (Gasterosteus aculeatus). We show that regardless of whether cues about predation risk were provided by their father or acquired through personal experience, sticklebacks produced the same set of predator-adapted phenotypes. Moreover, there were nonadditive effects of personal and paternal experience: animals that received cues from both sources resembled animals that received cues from a single source. A similar pattern was detected at the molecular level: there was a core set of genes that were differentially expressed in the brains of offspring regardless of whether risk was experienced by their father, themselves or both. These results provide strong support for cue integration theory because they show that cues provided by parents and personal experience are comparable at both the phenotypic and molecular level, and draw attention to the importance of nonadditive responses to multiple cues.

overall_design: The effects of personal and paternal experience with risk on offspring phenotypes were compared in a 2x2 factorial design. Fathers either were (N = 5) or were not (N = 5) exposed to predation risk while they were caring for their offspring (paternal experience: unexposed versus exposed). Within each family, siblings either were or were not personally exposed to predation risk as juveniles (personal experience: unexposed versus exposed).

first: Laura

last: Stein

first: Syed

last: Bukhari

last: M Bell


title: Combinitorial Approaches to Viral Attenuation

status: Public on Jun 07 2018

city: Austin

first: Claus

last: Wilke

state: Texas

address: 2500 Speedway, A4800

department: Integrative Biology

institute: University of Texas at Austin

summary: Attenuated viruses have numerous applications, in particular in the context of live viral vaccines. However, purposefully designing attenuated viruses remains challenging, in particular if the attenuation is meant to be resistant to rapid evolutionary recovery. Here we develop and analyze a new attenuation method, promoter ablation, using an established viral model, bacteriophage T7.  Ablating promoters of the two most highly expressed T7 proteins (scaffold and capsid) led to major reductions in transcript abundance of the affected genes, with the effect of the double knockout approximately additive of the effects of single knockouts.  Fitness reduction was moderate and also approximately additive; fitness recovery on extended adaptation was partial and did not restore the promoters.  The fitness effect of promoter knockouts combined with a previously tested codon deoptimization of the capsid gene was less than additive, as anticipated from their competing mechanisms of action.  In one design, the engineering created an unintended consequence that led to further attenuation, the effect of which was studied and understood in hindsight.  Overall, the mechanisms and effects of genome engineering on attenuation behaved in a predictable manner.  Therefore, this work suggests that the rational design of viral attenuation methods is becoming feasible.

overall_design: Examination of promoter knockouts, stop codon deletion, and codon-deoptimization on viral gene expression.

first: Matthew

middle: L

last: Paff

first: Benjamin

last: Jack

first: Bartram

last: Smith

first: James

last: Bull

middle: O


title: Maternal care boosted by paternal imprinting in mammals

status: Public on Jun 06 2018

city: Cardiff

first: Rosalind

last: John

address: Museum Avenue

department: Biosciences

country: United Kingdom

institute: Cardiff University

summary:
Previous work has suggested that the imprinted gene Phlda2 regulates the signalling function of the placenta by modulating the size of the endocrine compartment. This study investigated the affect that Phlda2 mutant placenta has upon the brains of the wildtype dams carrying different placenta and consequently offspring.
Affymetrix Mouse Microarray analysis of maternal hippocampus and hypothalamus was used to demonstrate gene expression changes in the maternal brains of wildtype dams carrying mutant placenta at E16.5.

overall_design: Hippocampus and Hypothalamus of WT dams carrying E16.5 Phlda2+/+(129) (non-transgenic; 1X), Phlda2-/+(129) (maternal KO; 0X) and Phlda2+/+BACx1(129) (single copy Phlda2 transgene; 2X) placenta(N=4 of each genotype, two independent litters) were used to extract RNA and hybridize to Affymetrix microarrays.

first: H

middle: D

last: Creeth

first: S

last: Tunster


title: miRNA and colorectal cancer:  associations with tumor phenotype and survival

status: Public on Jun 09 2018

city: Salt Lake City

first: Jennifer

last: Herrick

state: UT

address: 295 Chipeta Way

department: Internal Medicine

institute: University of Utah

summary:
MicroRNAs (miRNA) are a class of small regulatory RNAs that mediate post-transcriptional silencing of specific target mRNAs.  Data suggest the importance of miRNAs to cancer development and possibly to survival.  Our overall hypothesis is that miRNA expression is unique to tumor molecular phenotype; that miRNA expression levels at time of diagnosis predicts survival; and that miRNA expression is associated with inflammation-related genetic and lifestyle factors key to colorectal cancer (CRC). This study takes a two pronged approach to addressing our hypotheses.  While we propose to validate previously identified miRNAs that have been identified as associated with CRC (either by differential expression or from assessment of mutations), we will add to the field through discovery of new and important associations that may be unique to specific molecular phenotypes, to polyp to cancer progression, and  to survival.  We have analyzed the expression of 2006 human miRNAs using data derived from tumor and paired normal tissue at time of diagnosis from:  1975 people with incident colon cancer or rectal cancer and 290 polyps from colon and rectal cases (included in this study) who reported a prior polyp.  MiRNA was obtained from dissected paraffin-embedded tissue and assessed using an Agilent microarray platform.  We intend to extend our validation of previously identified mutated miRNAs and differentially expressed miRNAs to determine if these alterations are associated with specific tumor molecular phenotype (TP53, KRAS2, CIMP+, and for colon tumors MSI+), inflammation-related factors, clinical factors and survival.  We will identify associations with miRNAs that are related to specific molecular phenotypes, with drivers in the carcinogenic process, and with clinical features and survival.  These miRNAs will be validated using targeted Agilent Platform. Associations will be tested based on differential expression for both individual and groups of miRNAs using recent extensions of several statistical methods including ANOVA, logistic regression, and Cox proportional hazards models.  Our sample size allows for both a training and validation component, and provides sufficient statistical power to meet the study goals.  MiRNAs that are differentially expressed in polyps and in subsequent tumors will provide new insights into targets for screening and treatment as well as provide support that miRNAs function as the “driver” in the carcinogenic process.  Testing of mutated miRNAs identified from sequencing in conjunction with tumor phenotype, clinical, and survival data will further validate the importance of these miRNAs, and provide insight as to which CRC molecular pathway the miRNAs function.  Our rich dataset of lifestyle, genetic, clinical and prognosis, and tumor molecular phenotype on 1975 CRC and paired normal tissue allows us to examine factors that are associated with miRNA expression and mutation in a large sample of population-based cases in the most cost-efficient manner possible. The miRNAs identified in these analyses will elucidate pathways important in the etiology of CRC and will provide insight into potential targets for screening and treatment.
MiRNAs are small, non-protein-coding RNA molecules that regulate gene expression either by post-transcriptionally suppressing mRNA translation or by mRNA degradation.  We examine differentially expressed miRNAs in colorectal carcinomas, adenomas, and normal colonic mucosa. Data come from population-based studies of colorectal cancer conducted in Utah and the Kaiser Permanente Medical Care Program.  A total of 1893 carcinoma/normal paired samples and 290 adenoma tissue samples were run on the Agilent Human miRNA Microarray V19.0 which contained 2006 miRNAs.  We tested for significant differences in miRNA expression between paired carcinoma/adenoma/normal colonic tissue samples.  Fewer than 600 miRNAs were expressed in >80% of people for colonic tissue; of these 86.5% were statistically differentially expressed between carcinoma and normal colonic mucosa using a False Discovery Rate of 0.05.  Roughly half of these differentially expressed miRNAs showed a progression in levels of expression from normal to adenoma to carcinoma tissue.  Other miRNAs appeared to be altered at the normal to adenoma stage, while others were only altered at the adenoma to carcinoma stage or only at the normal to carcinoma stage.    Evaluation of the Agilent platform showed a high degree of repeatability (r=0.98) and reasonable agreement with the NanoString platform.  Our data suggest that miRNAs are highly dysregulated in colorectal tissue among individuals with colorectal cancer; the pattern of disruption varies by miRNA as tissue progresses from normal to adenoma to carcinoma.

overall_design:
Population-based ascertainment of all diagnosed cases of colorectal cancer from Utah and Northern California Kaiser.

Please note that the 'characteristics: AJCC_stage' values for each sample have been updated on July 5th, 2018.

first: M

last: Slattery


title: MACROD2 Haploinsufficiency Impairs Catalytic Activity of PARP1 and Promotes Chromosome Instability and Growth of Intestinal Tumors

status: Public on Jun 05 2018

city: Parkville

first: Oliver

last: Sieber

state: VIC

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Insitute of Medical Reseach

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

summary: ADP-ribosylation is an important post-translational protein modification that regulates diverse biological processes, controlled by dedicated transferases and hydrolases. Here we show that frequent deletions (~30%) of the MACROD2 mono-ADP-ribosylhydrolase locus in human colorectal cancer (CRC) cause impaired PARP1 transferase activity in a gene dosage-dependent manner. MACROD2 haploinsufficiency alters DNA repair and sensitivity to DNA damage, and results in chromosome instability. Heterozygous and homozygous depletion of Macrod2 enhances intestinal tumorigenesis in ApcMin/+ mice and the growth of human CRC xenografts. MACROD2 deletion in sporadic CRC is associated with the extent of chromosome instability, independent of clinical parameters and other known genetic drivers. We conclude that MACROD2 acts as a haploinsufficient tumor suppressor, with loss of function promoting chromosome instability thereby driving cancer evolution.

overall_design: 651 colorectal cancer primary tumors were analyzed for DNA copy number profiles using Illumina Human610-Quad v1.0 BeadChip.

last: Sakthianandeswaren

last: Parsons

first: D

last: Mouradov

first: R

middle: N

last: MacKinnon

first: B

last: Catimel

last: Liu

last: Palmieri

first: C

last: Love

last: Jorissen

last: Li

first: L

last: Whitehead

first: T

last: Putoczki

last: Preaudet

last: Tsui

last: Nowell

last: Ward

first: N

last: Hawkins

first: J

last: Desai

first: P

last: Gibbs

last: Ernst

first: I

last: Street

last: Buchert

first: O


title: A compendium of long non-coding RNAs transcriptional fingerprint in multiple myeloma.

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

summary:
Multiple myeloma (MM) is a malignant proliferation of bone marrow plasma cells (PCs) characterized by highly heterogeneous genetic background and clinical course, and whose pathogenesis remains largely unknown. Long ncRNAs (lncRNAs) are a large class of non-protein-coding RNA, involved in many physiological cellular and genomic processes as well as in carcinogenesis, cancer metastasis and invasion. Although still in its infancy, the knowledge of the role of lncRNAs in MM is progressively expanding. Besides studies on selected candidates, lncRNAs expression at genome-wide transcriptome level is confined to microarray technologies, thus investigating a limited collection of transcripts.  Herein, we assessed the lncRNAs expression profiling by RNA-sequencing in a cohort of 30 MM patients, aimed at defining a comprehensive catalogue of lncRNAs specifically associated with the main MM molecular subgroups and genetic alterations. We identified 391 deregulated lncRNAs, 67% of which were also detectable and validated by whole-transcript microarrays. In addition, we identified a list of lncRNAs, with potential relevance in MM, co-expressed and in close proximity to genes that might undergo a cis-regulatory relationship.
Herein, we assessed the lncRNAs expression profiling by RNA-sequencing in a cohort of 30 MM patients, aimed at defining a comprehensive catalogue of lncRNAs specifically associated with the main MM molecular subgroups and genetic alterations. We identified 391 deregulated lncRNAs, 67% of which were also detectable and validated by whole-transcript microarrays. In addition, we identified a list of lncRNAs, with potential relevance in MM, co-expressed and in close proximity to genes that might undergo a cis-regulatory relationship.

overall_design: Total RNA samples from highly purified plasma cells of 30 MM cases at onset and 4 normal controls (purchased from  Voden, Medical Instruments IT).

first: Domenica

last: Ronchetti

first: Alessandro

last: Pietrelli

first: Katia

last: Todoerti

first: Martina

last: Manzoni

first: Elisa

last: Taiana

first: Antonino

last: Neri


title: Early cell death induced by Clostridium difficile TcdB

status: Public on May 31 2018

city: Hannover

first: Ralf

last: Gerhard

state: Lower Saxony

address: Carl-Neuberg-Str. 1

department: Institute of Toxicology

institute: Hannover Medical School

summary: This study primarily shows the transcripts for all genes possibly involved in uptake of C. difficile TcdB. The long term effect of the second receptor binding domain (aa 1101-1873) of TcdB  (2 µg/ml) on Hep-2 cells was investigated after 72 hours of incubation.

overall_design: Hep-2 cells were kept in 75 cm culture flasks. The experiment comprises two untetaed controls and two samples treated with TcdB fragment for 78 hours.


title: Genome-wide profiling of histone lysine crotonylation reveals positive regulation of transcription in rice

status: Public on Jun 01 2018

city: Madison

first: Yufeng

last: Wu

state: WI

address: 1575 Linden Drive

institute: UW-Madison

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Histone lysine crotonylation (Kcr) is a newly discovered post-translational modification (PTM) existing in mammalian. To assess relevance in histone Kcr and genome, we performed on genomic localization analysis of histone Kcr by ChIP-seq analysis.

overall_design: To explore the in vivo function of histone Kcr in plants. We performed ChIP-seq analysis with the pan anti-Kcr antibody to determine the genomic distribution of histone Kcr in the rice seedling tissue consisting mainly of leaves with a small proportion of stem tissues. Two biological replicates of ChIP-seq libraries were constructed and then sequenced using the HiSeq 2500 platform with the paired-end method. To further validate the whole genome data of histone Kcr, we selected another antibody specific for H3K14cr, following by ChIP-seq analysis with two biological replicates.

first: Shuai

last: Liu

first: Chao

last: Xue

first: Yuan

last: Fang

first: Yong

last: Zhou

first: Chen

last: Chen

first: Guanqing

first: Minghong

last: Gu

first: Kai

last: Wang

first: Wenli

last: Zhang

first: Zhiyun

last: Gong


title: The influenza B virus hemagglutinin head domain is less tolerant to transposon mutagenesis than that of the influenza A virus

first: Peter

last: Palese

state: New York

address: 1 Gustave L. Levy Place, Box 1124

department: Department of Microbiology

institute: Icahn School of Medicine at Mount Sinai

summary: To determine if the influenza B virus HA is under constraints that limit its antigenic variation, we performed a transposon screen to compare the mutational tolerance of the currently circulating influenza A virus HAs (H1 and H3 subtypes) and influenza B virus HAs (B/Victoria87 and B/Yamagata88 antigenic lineages). A library of insertional mutants for each HA was generated and deep sequenced after passaging to determine where insertions were tolerated in replicating viruses.

sample_organism:
Influenza A virus
Influenza B virus

platform_organism:
Influenza A virus
Influenza B virus

overall_design: RNA-seq of influenza virus HA libraries

first: Benjamin

last: Fulton


title: Connexin 30 deficiency attenuates A2 astrocyte responses and induces severe neurodegeneration in a 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine hydrochloride Parkinson’s disease animal model

city: Fukuoka

first: Atsushi

last: Fujita

address: 3-1-1 Maidashi, Higashi-ku

department: Department of Neurology

institute: Graduate School of Medical Sciences, Kyushu University

summary: Cx30 deficiency induced acceleration of dopaminergic neuron death upon MPTP toxicity. Gene expressions in the striatum of wild type and Cx30 KO mice after MPTP treatment were different in the aspect of neuroprotective A2 response.

overall_design: We have resected striata from wild type and Cx30 deficient mice 1 day after MPTP treatment. Each group contained 2 mice. Collected striata were pooled for analysis.

first: Hiroo

last: Yamaguchi

first: Ryo

last: Yamasaki

first: Tiwen

last: Cui

first: Yuta

last: Matsuoka

first: Ken-ichi

last: Yamada

first: Jun-ichi

last: Kira


title: Epigenomics of Medicago truncatula

status: Public on May 22 2018

city: Athens

first: Robert

last: Schmitz

state: GA

address: B416 Davison Life Sciences

institute: University of Georgia

type: Methylation profiling by high throughput sequencing

type: Non-coding RNA profiling by high throughput sequencing

summary: Cytosine methylation is a base modification that is often used by genomes to store information that is stably inherited through mitotic cell divisions. Most cytosine DNA methylation is stable throughout different cell types or by exposure to different environmental conditions in plant genomes. Here, we profile the epigenomes of ~100 Medicago truncatula lines to explore the extent of natural epigenomic variation. We also use these data to determine the extent to which DNA methylation variants are linked to genetic variations.

overall_design: 97 MethylC-seq, 87 RNA-seq  and 89 smallRNA-seq for Medicago truancatula

first: Scott

last: Jackson

first: Marc

last: Libault


title: Transcriptional profiling of immune-related genes in Leishmania infantum-infected mice: identification of potential biomarkers of infection and progression of disease [BIOMARKERS]

city: La Laguna

first: Emma

last: Carmelo

state: SANTA CRUZ DE TENERIFE

address: C/ Astrofisico Francisco Sanchez s/n, Campus de Anchieta

department: University Institute of Tropical Diseases and Public Health

institute: University of La Laguna

summary: Leishmania spp. is a protozoan parasite that affects millions of people around the world. At present, there is no effective vaccine to prevent leishmaniases in humans. A major limitation in vaccine development is the lack of precise understanding of the particular immunological mechanisms that allow parasite survival in the host. The parasite-host cell interaction induces dramatic changes in transcriptome patterns in both organisms, therefore, a detailed analysis of gene expression in infected tissues will contribute to the evaluation of drug and vaccine candidates, the identification of potential biomarkers, and the understanding of the immunological pathways that lead to protection or progression of disease.   High-throughput real-time quantitative PCR is a highly sensitive, and specific technique that allows analysis of gene expression in multiple genes at the same time. Hence, it is an interesting approach that may bring light to this complex topic. In this large-scale analysis, forty-seven BALB/c mice were divided in two groups: control mice and mice infected with L. infantum promastigotes. After infection animals were sacrificed at different timepoints, RNA was purified from spleens and expression of 112 genes related with immune system was determined by high-throughput qPCR.  These extensive gene-expression analyses reveal a selective recruitment of lymphocytes to the spleen and an immunosuppressive response, which favors parasite persistence, in early stages of the infection. In later stages of infection, gene-expression patterns suggest an inflammatory process that should resolve infection. Nevertheless, a detailed analysis reveals that L. infantum infection induces a regulatory process that counteracts the Th1/M1 response.  This large pool of data was also used to identify a group of potential biomarkers of infection and parasitic burden in spleen, on the bases of two different statistical models, a logistic regression analysis and a linear regression analysis.  Given the results, it seems clear that gene expression signature analysis is a useful tool to identify the mechanisms involved in disease outcome and to establish a rational approach for the identification of potential biomarkers useful for monitoring disease progression, new therapies or vaccine development in Leishmaniases.

overall_design: 61 BALB/c  mice (14-15 weeks old) were randomly separated in two groups: (i) 30 control mice and (ii) 31 mice  that were infected with 10^6 stationary-phase L. infantum promastigotes via tail vein. Mice were euthanized by cervical dislocation and spleens were removed and immediately stored in RNAlater at -70ºC. After RNA extraction and reverse transcription, the expression of 112 genes related with immune system was determined by high-throughput qPCR using QuantStudio 12K Flex Real-Time PCR System.  This large pool of data was used to identify a group of potential biomarkers of infection and parasitic burden in spleen, on the bases of two different statistical models, a logistic regression analysis and a linear regression analysis. From the complete pool of 61 mice used in the logistic regression model, , 75% of them (47 mice), were randomly selected and used for its development and 25% of them (14 mice) were used for its evaluation (metadata template 1).  From the complete pool of 31 infected mice used in the  linear regression model, 75% of them (23 mice), were randomly selected and used for its development and 25% of them (8 mice) were used for its evaluation (metadata template 2).

first: Eduardo

last: Ontoria

first: Yasmina

last: Hernandez-Santana

first: Ana

last: Gonzalez-García

first: Manuel

last: López

first: Basilio

last: Valladares


title: Transcriptional profiling of immune-related genes in Leishmania infantum-infected mice: identification of potential biomarkers of infection and progression of disease

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

overall_design: Refer to individual Series


title: Transcriptional profiling of immune-related genes in Leishmania infantum-infected mice: identification of potential biomarkers of infection and progression of disease [MODEL]

summary: Leishmania spp. is a protozoan parasite that affects millions of people around the world. At present, there is no effective vaccine to prevent leishmaniases in humans. A major limitation in vaccine development is the lack of precise understanding of the particular immunological mechanisms that allow parasite survival in the host. The parasite-host cell interaction induces dramatic changes in transcriptome patterns in both organisms, therefore, a detailed analysis of gene expression in infected tissues will contribute to the evaluation of drug and vaccine candidates, the identification of potential biomarkers, and the understanding of the immunological pathways that lead to protection or progression of disease.   High-throughput real-time quantitative PCR is a highly sensitive, and specific technique that allows analysis of gene expression in multiple genes at the same time. Hence, it is an interesting approach that may bring light to this complex topic. In this large-scale analysis, forty-seven BALB/c mice were divided in two groups: control mice and mice infected with L. infantum promastigotes. After infection animals were sacrificed at different timepoints, RNA was purified from spleens and expression of 112 genes related with immune system was determined by high-throughput qPCR.  These extensive gene-expression analyses reveal a selective recruitment of lymphocytes to the spleen and an immunosuppressive response, which favors parasite persistence, in early stages of the infection. In later stages of infection, gene-expression patterns suggest an inflammatory process that should resolve infection. Nevertheless, a detailed analysis reveals that L. infantum infection induces a regulatory process that counteracts the Th1/M1 response.    Given the results, it seems clear that gene expression signature analysis is a useful tool to identify the mechanisms involved in disease outcome and to establish a rational approach for the identification of potential biomarkers useful for monitoring disease progression, new therapies or vaccine development in Leishmaniases.

overall_design: 47 BALB/c  mice (14-15 weeks old) were randomly separated in two groups: (i) 23 control mice and (ii) 24 mice  that were infected with 10^6 stationary-phase L. infantum promastigotes via tail vein. Mice were euthanized by cervical dislocation and spleens were removed and immediately stored in RNAlater at -70ºC. After RNA extraction and reverse transcription, the expression of 112 genes related with immune system was determined by high-throughput qPCR using QuantStudio 12K Flex Real-Time PCR System.


title: Transcriptomic analysis of Wt Mtb H37Rv and WhiB4 Complemented strains on treatment with 0.25 mM Cumene hydroperoxide (CHP) for 2 h at 37°C.

status: Public on May 05 2018

city: New York

first: SAURABH

last: MISHRA

address: 1300 York Ave, Box 62, New York

department: Microbiology and Immunology

institute: Weill Cornell Medicine

summary: WhiB4 regulates expression of anti-oxidant genes and survival of Mtb in resposne to oxidaitve stress. Thus, we did microarray upon exposure to 0.25 mM CHP for Wt Mtb and MtbΔwhiB4 strain complemented with whiB4 gene to study the restoration of gene expression to wild type levels.

overall_design: Wt Mtb H37Rv and WhiB4 Complemented strains were grown till early log phase and exposed to 0.25 mM CHP for 2 hours at 37 degree at 150rpm. Three independent experiments were done for each of the strain, respectively.

first: Kushi

last: Anand

first: Saurabh

last: Mishra

first: Amit

last: Singh


title: SWI/SNF subunit CHR2 remodels pri-miRNAs via microprocessor component SE to inhibit miRNA production DMS-MaPseq)

status: Public on May 18 2018

city: college station

first: Xiuren

last: Zhang

address: 2123 tamu

department: biochemistry & biophysics

institute: texas a&m university

summary: Here we present dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq) prepared from leaves of adult plants in Arabidopsis. Chromatin remodeling factor 2 (CHR2) positively regulates transcription of MIR loci whereas repressing microRNA (miRNA) accumulation in vivo. CHR2 can directly bind to and unwind primary miRNAs (pri-miRNAs) and inhibit their processing; and this inhibition entails its remodeling activity in vitro and in vivo.

overall_design: Use DMS-MaPseq to probe in vivo RNA structure.

first: Zhiye

last: Wang

first: Zeyang

last: Ma

first: Claudia

last: Castillo-González

first: Di

last: Sun

first: Yanjun

last: Li

first: Bin

last: Yu

first: Pingwei


title: The KNOXI gene SHOOT MERISTEMLESS regulates floral fate in Arabidopsis

status: Public on May 04 2018

city: Tel Aviv

first: Eilon

last: Shani

address: Ramat Aviv

country: Israel

institute: TAU

summary: Plants have evolved a unique and conserved developmental program that enables the conversion of leaves into floral organs. Elegant genetic and molecular work has identified key regulators of floral meristem identity. However, further understanding of flower meristem specification has been hampered by redundancy and by pleiotropic effects. The KNOXI gene STM transcription factor is a well-characterized regulator of shoot apical meristem maintenance. stm loss-of-function mutants arrest shortly after germination, and therefore the knowledge on later roles of STM, including flower development, is limited. Here, we uncover a role for STM in the specification of flower meristem identity. Silencing STM in the AP1 expression domain in the ap1-4 mutant background resulted in a complete leafy-like flower phenotype and an intermediate stm-2 allele enhanced the floral meristem identity phenotype of ap1-4. Transcriptional profiling of STM perturbation suggested that STM activity affects multiple meristem identity and flower transition genes, among them the F-Box gene UFO. In agreement, stm-2 enhanced the ufo-2 floral meristem fate phenotype, and ectopic UFO expression rescued the leafy flowers in genetic backgrounds with compromised AP1 and STM activities. This work suggests a molecular mechanism that underlies the activity of STM in the specification of flower meristem identity.

first: Ohad

last: Roth


title: Transcriptomic analysis of the Pseudomonas sp. AP3_22 exposed to the sodium dodecyl sulfate

status: Public on May 01 2018

city: Warsaw

first: Ewa

last: Furmanczyk

address: Pawinskiego 5a

department: Institute of Biochemistry and Biophysics

country: Poland

institute: Polish Academy of Sciences

summary: Here we presented the detailed transcriptomic analysis for Pseudomonas sp. AP3_22, an effective sodium dodecyl sulfate degrader isolated from the soil sample from wastewater treatment plant, cultured in the presence of SDS to get the first insight in the global bacterial response toward Sthis anionic detergent. Our results suggest showed that although SDS could be used as a carbon source, in the first place it acts influence on  integrity of the cell envelopes and causes global stress response together combined with cell wall modification and repair induction. These results suggest that the modulation of the membrane content composition is first adaptation step in a typical response to detergent exposure. As the second response to the sodium dodecyl sulfate the AP3_22 strain metabolism was shifted from the lipid biosynthesis to the lipid catabolism and the SDS degradation started.

overall_design: AP3_22 strain was precultured overnight in LB medium. Then washed with minimal medium and diluted in the fresh 0.1 LB medium with or without (the control sample) SDS (5 g/L) to the initial OD600=0.4 and cultured in 30°C with 140 rpm agitation. The samples for RNA isolation were collected at following time points: at the beginning (0 minutes) and after: 30 minutes; 60 minutes; and 150 minutes of the experiment. The experiment was made in triplicate (three biological replicates for control and three biological replicates for the sample).

first: Leszek

last: Lipinski

first: Andrzej

last: Dziembowski

first: Adam

last: Sobczak


title: ZINC-FINGER interactions mediate transcriptional regulation of hypocotyl growth in Arabidopsis

status: Public on May 17 2018

city: Glasgow

first: Eirini

last: Kaiserli

address: University Avenue

department: Institute of Molecular, Cell & Systems Biology

institute: University of Glasgow

summary: Integration of environmental signals and interactions among photoreceptors and transcriptional regulators is key in shaping plant development. TANDEM ZINC-FINGER PLUS3 (TZP) is an integrator of light and photoperiodic signaling that promotes flowering in Arabidopsis thaliana. Here we elucidate the molecular role of TZP as a positive regulator of hypocotyl elongation. We identify an interacting partner for TZP, the transcription factor ZINC-FINGER HOMEODOMAIN 10 (ZFHD10), and characterize its function in coregulating the expression of blue-light dependent transcriptional regulators and growth-promoting genes. By employing a genome-wide approach, we reveal that ZFHD10 and TZP coassociate with promoter targets enriched in light-regulated elements. Furthermore, using a targeted approach, we show that ZFHD10 recruits TZP to the promoters of key coregulated genes. Our findings not only unveil the mechanism of TZP action in promoting hypocotyl elongation at the transcriptional level but also assign a function to an uncharacterized member of the ZFHD transcription factor family in promoting plant growth.

overall_design: We performed whole-genome chromatin immunoprecipitation (ChIP-seq) analysis on 7-day-old Arabidopsis thaliana Columbia wild-type (Col-0), OX TZP and OX ZFHD10 seedlings exposed to continuous low blue-light (LBL).

first: G

last: Perrella

first: A

last: Nastase

first: P

last: Herzyk

first: E


title: Novel Protective Role of Nicotinamide Phosphoribosyltransferase in Acetaminophen-induced Acute Liver Injury in Mice

status: Public on Apr 03 2018

city: Kansas City

first: Shui

last: Ye

state: MO

address: 2411 Holmes Street

department: Departmetn of Biomedical and Health Informatics

institute: University of Missouri Kansas City School of Medicine

summary: Acetaminophen overdose is the most common cause of acute liver injury (ALI) or acute liver failure in the USA. Its pathogenetic mechanisms are incompletely understood. Additional studies are warranted to identify new genetic risk factors for more mechanistic insights and new therapeutic target discoveries. The objective of this study was to explore the role and mechanisms of nicotinamide phosphoribosyltransferase (NAMPT) in acetaminophen-induced ALI. C57BL/6 Nampt gene wild type (Nampt+/+)-, heterozygous knockout (Nampt+/-)-, and overexpression (NamptOE)-mice were treated with overdose of acetaminophen, followed by histological, biochemical, and transcriptomic evaluation of liver injury. The mechanism of Nampt in acetaminophen -induced hepatocytic toxicity was also explored in cultured primary hepatocytes. Three lines of evidence have convergently demonstrated that acetaminophen overdose triggers the most severe oxidative stress and necrosis, and the highest expression of key necrosis driving genes in Nampt+/- mice, while the effects in NamptOE mice were least severe relative to  Nampt+/+ mice. These findings support that NAMPT protects against acetaminophen induced ALI.

overall_design: Paired-end sequencing of 17 mouse liver RNA 24h after APAP or saline injection.

first: Li

last: Zhang

first: Marianne

last: Nsumu

first: Peixin

last: Huang

first: Daniel

middle: P

last: Heruth

first: Sean

last: Riordan

first: Katherine

last: Shortt

first: NiNi

first: Dmitry

last: Grigoryev

first: Ding-You

first: Craig

last: Friesen

first: Leon

last: Haandel

first: J

last: Leeder

first: Judy

last: Olson


title: Erroneous ribosomal RNAs promote the generation of antisense ribosomal siRNA

status: Public on May 02 2018

city: Hefei

first: Shouhong

last: Guang

state: Anhui

address: 443 HuangShan Road

department: School of Life Sciences

institute: University of Science & Technology of China

summary: Ribosome biogenesis is a multi-step process, during which mistakes could take place at any step of pre-rRNA processing, modification, and assembly of ribosomes. Misprocessed rRNAs are usually detected and degraded by surveillance machineries. Recently, we identified a class of antisense ribosomal siRNAs (risiRNAs) that downregulate pre-rRNAs through the nuclear RNAi pathway. To further understand the biological roles of risiRNA, we conducted both forward and reverse genetic screenings to search for more susi mutants. We isolated a number of genes that are broadly conserved from yeast to humans and are involved in pre-rRNA modification and processing. Among them, SUSI-2(ceRRP8) is homologous to human RRP8 and engages in m1A methylation of 26S rRNA. C27F2.4(ceBUD23) is a m7G methyltransferase of 18S rRNA. E02H1.1(ceDIMT1L) is a predicted m6(2)Am6(2)A methyltransferase of 18S rRNA . Mutation of these genes led to modification deficiency of rRNAs and elicited accumulation of risiRNAs, which further triggered the cytoplasm to nuclear and nucleolar translocation of an Argonaute protein NRDE-3. The processing deficiency of rRNAs resulted in the accumulation of risiRNAs as well. We isolated SUSI-3(RIOK-1) which is similar to human RIOK1 that cleaves 20S to 18S rRNA. We further utilized RNAi and CRISPR/Cas9 technologies to perform candidate-based reverse genetic screening and identified additional pre-rRNA processing factors that suppressed risiRNA production. Therefore, we concluded that erroneous rRNAs can trigger risiRNA generation and subsequently turn on the nuclear RNAi-mediated gene silencing pathway to inhibit pre-rRNA expression, which may provide a quality control mechanism to maintain the homeostasis of rRNAs.

overall_design: In this study, we compared total small RNAs from (1) control animals; (2) susi-2(ust49) mutant; (3) susi-3(ust51) mutant. And we also compared the NRDE-3 associated small RNAs in (4) control animals; (5) susi-2(ust49) mutant; and (6) susi-3(ust51) mutant.


title: Differential expression and co-expression gene networks reveal candidate biomarkers of boar taint in non-castrated pigs (RNA-seq data set)

status: Public on Apr 18 2018

city: Kongens Lyngby

first: Haja

last: Kadarmideen

address: Richard Petersens Plads, Building 324

department: Department of Applied Mathematics and Computer Science

institute: Technical University of Denmark

summary: Boar taint (BT) is an offensive odour or taste observed in pork from a proportion of non-castrated male pigs. Surgical castration is effective in avoiding BT, but animal welfare issues have created an incentive for alternatives such as genomic selection. In order to find candidate biomarkers, gene expression profiles were analysed from tissues of non-castrated pigs grouped by their genetic merit of BT. Differential expression analysis revealed substantial changes with log-transformed fold changes of liver and testis from −3.39 to 2.96 and −7.51 to 3.53, respectively. Co-expression network analysis revealed one module with a correlation of −0.27 in liver and three modules with correlations of 0.31, −0.44 and −0.49 in testis. Differential expression and co-expression analysis revealed candidate biomarkers with varying biological functions: phase I (COQ3, COX6C, CYP2J2, CYP2B6, ACOX2) and phase II metabolism (GSTO1, GSR, FMO3) of skatole and androstenone in liver to steroidgenesis (HSD17B7, HSD17B8, CYP27A1), regulation of steroidgenesis (STARD10, CYB5R3) and GnRH signalling (MAPK3, MAP2K2, MAP3K2) in testis. Overrepresented pathways included “Ribosome”, “Protein export” and “Oxidative phosphorylation” in liver and “Steroid hormone biosynthesis” and “Gap junction” in testis. Future work should evaluate the biomarkers in large populations to ensure their usefulness in genomic selection programs.

overall_design: Total RNA was extracted from liver and testis of 48 Danish Landrace pigs with low- medium and high genetic merit of boar taint and sequenced by Illumina HiSeq 2500.

first: Markus

last: Drag

first: Ruta

last: Skinkyté-Juskiené

first: Duy

last: Do

first: Lisette

last: Kogelman


title: Transcriptome analysis by microarray of human placental chorionic villi explants infected with Trypanosoma cruzi

status: Public on Apr 17 2018

city: Santiago

first: Ulrike

last: Kemmerling

address: Independencia 1027

department: Faculty of Medicine

country: Chile

institute: Universidad de Chile

summary: Chagas’ disease, one of the major public health concerns in Latin America, is caused by the  haemophlagelated protozoan Trypanosoma cruzi (T. cruzi). In the past few years congenital  transmission of T. cruzi has become more important, and partly responsible for the “globalization of  Chagas’ disease”. The congenital transmission, although with low rates, represents the main route of  transmission in non-endemic countries and endemic countries without vectorial transmission, and  represents one third of the new cases each year.  Diverse pathogens, including T. cruzi, are able to cross the placental barrier and infect both the  placenta and fetus. However, the exact cellular and molecular mechanisms of host-pathogen  interaction between T. cruzi and the placenta has been scarcely studied.  The use of microarray analysis to determine expression profiles constitutes a powerful tool in order to  identify genes and pathways related to the host response to infections. Here, we analyzed the  transcriptomic response of human placental chorionic villi explants (HPCVE) challenged with T. cruzi  trypomastigotes at low (105) and high (106) concentrations for 2 and 24 hours

overall_design: Human Placental Chorionic Villi Explants (HPE) were obtained from term placentas (>38 weeks) with an informed consent from heatlhy women in elective cesarean delivery. In a Level II biosafety cabinet, 0,5 cm3 HPE were isolated from the center of the cotyledon, washed with sterile PBS in order to remove excess of blood and later  incubated with 105 or 106 parasites/ml (Y Strain Tripomastigotes, the infective form of the parasite) for 2 and 24 hrs.

first: Christian

last: Castillo

first: Ileana

last: Carrillo

first: Gabriela

last: Libisch

first: Natalia

last: Juiz

first: Alejandro

last: Schijman

first: Carlos

last: Robello


title: Angiogenic patterning by STEEL, an endothelial-enriched long noncoding RNA

status: Public on Mar 30 2018

city: Toronto

first: Philip

last: Marsden

address: 209 Victoria Street, Room 522

department: Medicine

institute: University of Toronto

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


title: Comparison of STEEL siRNA-treated and control siRNA-treated human endothelial cells

summary: To determine the role of STEEL in endothelial cell (EC) gene regulation, gene expression analysis was conducted on control and STEEL siRNA-treated human dermal microvascular endothelial cells (HMVECs) and human umbilical vein endothelial cells (HUVECs). A total of 225 protein-coding genes were downregulated and 80 were upregulated when both EC types were grouped for analysis. In HMVEC alone, 544 protein-coding genes were downregulated and 218 were upregulated. In HUVEC alone, 177 protein-coding genes were downregulated and 125 were upregulated. Prominently, STEEL siRNA depletion results in the downregulation of two notable protein-coding genes, eNOS and KLF2, which are modulated in ECs subjected to continuous laminar shear stress.

overall_design: HUVECs and HMVECs were treated with control siRNA or STEEL siRNA for 48 hours. Subsequently, these samples were subjected to gene expression analysis using a custom agilent microarray that recognizes 30215 protein-coding transcripts and 33045 lncRNAs.

first: H

last: Man


title: Genotoxicity of nitrosamines

status: Public on Feb 21 2018

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

summary: We profiled the gene expression in eight chicken embryo livers in the 11th day of incubation. The eggs were injected on postincubation days 9, 10 and 11 with 4mg activation-dependent DNA reactive diethylnitrosamine (DEN) or its structural non-carcinogenic comparator, N-nitrosodiethanolamine (NDELA)DEN in 0.15 ml/egg deionized water. We found that both compounds induced simmilar massive transcriptomic alterations in the xenobioatic metabolism pathways when comparing with reference data in eggs injected with the vehicle only (deionized water).

overall_design: Differently labelled biological replicas were co-hybridized with the same microarray. Expression of genes in similarly labeled samples of the two conditions were compared and the results averaged.

first: Tetyana

last: Kobets

first: Michael

last: Iatropoulos

first: Jiandong

last: Duan

first: Klaus

last: Brunnemann

first: Sanda

first: Esther

last: Vock

first: Ulrich

last: Deschl

first: Gary

last: Williams


title: microRNA-218 modulates gene expression in fibroblast-like synovial cells in rheumatoid arthritis

status: Public on Mar 26 2018

city: Nagasaki

first: Naoki

last: Iwamoto

state: Nagasaki

address: 1-7-1 Sakamoto

department: Immunology and Rheumatology

institute: Nagasaki University

summary:
Objective: Fibroblast-like synovial cells (FLS) have multilineage differentiation potential including osteoblasts. We aimed to investigate the role of microRNAs during the osteogenic differentiation of rheumatoid arthritis (RA)-FLS.

Methods: MicroRNA(miRNA) array analysis was performed to investigate the differentially expressed miRNAs during the osteogenic differentiation. Expression of miR-218-5p (miR-218) during the osteogenic differentiation was determined by quantitative real-time PCR. Transfection with miR-218 precursor and inhibitor were used to confirm the targets of miR-218 and to analyse the ability of miR-218 to induce osteogenic differentiation.

Results: The miRNA array revealed that 12 miRNAs were up-regulated and 24 miRNAs were down-regulated after osteogenic differentiation. We observed that miR-218 rose in the early phase of osteogenic differentiation and then decreased. Micro array analysis revealed the mir-218 modulate the expression of ROBO1 in RA-FLS. The induction of miR-218 in RA-FLS decreased ROBO1 expression, and promoted osteogenic differentiation.

overall_design:
Number of sample:4 sample

Method: For a transient transfection approach with the aim to inhibit or enhance the miR-218 function, RA-FLSs were transfected with synthetic precursor miRNA (pre-miR), with inhibitors of miR-218 (anti-miR), or with scrambled controls (Pre-miR/Anti-miR Negative Control #1; Ambion/Applied Biosystems, Foster City, CA) at a final concentration of 100 nM with the use of Lipofectamine 2000 reagent (Invitrogen, Carlsbad, CA, USA). After transfection we extracted RNA using mirVana miRNA Isolation kit(Ambion/Applied Biosystems). We investigated the gene expression after transfection of pre/anti-miR-218 using microarray.


title: Next-generation sequencing of three memory OT-I cell subsets from mice infected with Listeria monocytogenes

status: Public on Mar 01 2018

city: Vienna

first: Dietmar

last: Herndler-Brandstetter

address: Borschkegasse 8a

department: Institute of Cancer Research

country: Austria

institute: Medical University of Vienna

summary:
Purpose: RNA-seq analysis of three memory OT-I cell subsets (from a Klrg1-Cre fate reporter mouse model) isolated from the spleen of C57BL/6 mice infected with Listeria monocytogenes. The hypothesis tested in the present study was that KLRG1+ effector CD8 T lymphocytes differentiate into KLRG1- memory CD8 T lymphocytes and provide long-lasting immunity against infectious diseases and malignancies.
Methods: Total RNA was obtained from FACS-purified OT-I cell subsets isolated from spleen 104 (experiment 1) and 110 days post infection (experiment 2) with ovalbumin-expressing Listeria monocytogenes (LM-OVA).
Results: Using RNA-seq technology, we performed genome-wide transcriptional profiling of three memory OT-I cells (KLRG1+ Reporter+, KLRG1- Reporter+ (exKLRG1) and KLRG1- Reporter-) and identified 36 genes differentially expressed (> 1.5-fold) between exKLRG1 and KLRG1- Reporter- memory OT-I cells, and 132 differentially expressed genes between exKLRG1 and KLRG1+ Reporter+ memory OT-I cells. We then confirmed the expression of 15 genes/molecules by qRT-PCR and/or flow cytometry.
Conclusions: Our study represents the first fate mapping analysis of KLRG1+ effector OT-I cells, demonstrates that KLRG1+ effector OT-I cells differentiate into all memory T cell lineages thereby promoting protective immunity. RNA-seq also identified CX3CR1 as a marker of circulating exKLRG1 early memory OT-I cells.

overall_design: Total RNA was obtained from FACS-purified OT-I cell subsets isolated from spleen 104-110 days post infection with ovalbumin-expressing Listeria monocytogenes (LM-OVA).

first: Harumichi

last: Ishigame


title: Gene expression in chicken embryo liver

summary: We have profiled the gene expression in eight chicken embryo livers in the 11th day of incubation. Four eggs (labelled as WAT1-4) were injected with 0.15 ml/egg deionized water in days 9, 10 an 11 post incubation while four eggs (labeled CTR1-4) were kept as environmental controls. We found that water injections had a very small effect, regulating less than 1% of the genes. Both WAT and CTR data sets were used as references in further experiments for eggs expossed to various water-soluble carcinogenic compounds.


title: Identification of the tumour transition states occurring during EMT [p63 overexpression RNA-seq]

status: Public on Feb 15 2018

city: Brussels

first: Cédric

last: Blanpain

address: Route de Lennik 808

country: Belgium

institute: ULB

summary: EMT in cancer has been associated with tumour stemness, metastasis and resistance to therapy. It has recently been proposed that, rather than being a binary process, EMT occurs through distinct intermediate states. However,direct in vivo evidence supporting this possibility is still lacking. By screening a large panel of cell surface markers, we identified the existence of multiple tumour subpopulations associated with different EMT stages from epithelial to completely mesenchymal states passing through intermediate hybrid states in skin and mammary primary tumours. Although all EMT subpopulations presented similar tumour propagating cell capacity, they displayed different  , invasiveness and metastatic potential. Their transcriptional and epigenetic landscapes defined by RNA-seq and ATAC-seq identified the underlying gene regulatory networks, transcription factors and signalling pathways that control these different EMT transition states. Finally, these tumour subpopulations are localized in different niches that differentially regulateEMT transition states.

overall_design: RNA sequencing on the different intermediate states of EMT after overexpression of p63

first: Ievgenia

last: Pastushenko

first: Audrey

last: Brisebarre

first: Panagiota

last: Sotiropoulou


title: Identification of the tumour transition states occurring during EMT [RNA-seq]

overall_design: RNA sequencing on the different intermediate states of EMT


title: Identification of the tumour transition states occurring during EMT

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