title: A Phage-Like Chromosomal Island Impacts Global Transcription Patterns and Virulence in Streptococcus anginosus

city: Oklahoma City

first: William

middle: Michael

last: McShan

state: OK

address: 1110 N. Stonewall Ave.

department: Pharmaceutical Sciences

institute: University of Oklahoma Health Sciences Center

summary: Streptococcus anginosus is an important cause of brain and liver abscesses, meningitis, appendicitis, female genital tract infection, neonatal sepsis, and bacteremia.  Recent studies show that S. anginosus is responsible for around 30% of streptococci associated purulent infections of internal organs. Genome sequencing of S. anginosus identified a phage-like chromosomal island (SanCI) integrated into the DNA mismatch repair operon.  In S. pyogenes, related chromosomal islands (SpyCI) integrated into the same operon confer a mutator phenotype as well as alter global gene regulation, including the increased expression of many virulence factors. We hypothesized that SanCI will also alter global transcription patterns and virulence in S. anginosus.  The SanCI from strain F0211 was introduced into a SanCI-free S. anginosus strain (J4211) by natural transformation.  To provide a selectable marker for transformation, gene strA, encoding a predicted transcriptional regulator, was replaced in F0211 with the gene conferring erythromycin resistance (ermB), which after transfer created strain OKSan3.  A functional copy of strA was then returned to this derivative of J4211, creating strain OKSan4.  RNA sequencing (RNA-seq) of strains J4211, OKSan4 and OKSan3 confirmed that the addition of the SanCI altered S. anginosus global transcription patterns with increased expression of virulence, stress response and competence factors in a growth phase dependent manner.  Virulence studies using Galleria mellonella as an acute infection model showed significantly increased inflammation and mortality in larvae challenged with strains OKSan4 and OKSan3 as compare to SanCI-free strain J4211.  qRT-PCR analysis supported these results, revealing that antimicrobial factors of G. mellonella were more highly expressed after infection with OKSan4 compare to J4211 infection.  Further, RNA-seq suggested that SanCI-encoded gene strA may encode one of the factors responsible for altered global transcriptional changes.  The result of this study along with our previous studies in S. pyogenes demonstrate that streptococcal chromosomal islands are a unique class of virulence factors that improve the fitness of their host cell by altering global transcription patterns and increasing virulence.

overall_design: Comparison of three strains differing by the presence of a phage-like chromosomal island or the phage-like chromosomal lacking gene strA at early log or late log growth at 37°C.


title: Assessment of the Performance of the TGx-DDI Biomarker to Detect DNA Damage-Inducing Agents Using Quantitative RT- PCR in TK6 Cells

status: Public on Dec 21 2018

city: Ottawa

first: Eunnara

last: Cho

state: Ontario

address: 251 Sir Frederick Banting Driveway

country: Canada

institute: Health Canada

summary: Gene expression biomarkers are now available for application in the identification of genotoxic hazards. The TGx-DDI transcriptomic biomarker can accurately distinguish DDI from non-DDI exposures based on changes in the expression of 64 biomarker genes. The bioamarker was originally derived from DNA microarray gene expression profiles of TK6 human lymphoblastoid cells post 4-hour exposure to 28 reference DDI and non-DDI agents [Li et al. 2015]. To broaden the applicability of TGx-DDI, the biomarker was tested using quantitative RT-PCR (qPCR), which is accessible to most molecular biology laboratories. To assess the classification capability of the biomarker using qPCR, a custom 96-well TaqMan qPCR array (TGx-DDI qPCR array) was constructed using the 64 biomarker genes. TK6 cells were exposed to each of the 28 reference agents and their vehicle controls for 4 hours and the expression level of the TGx-DDI genes were profiled using the TaqMan arrays. This study provides reference qPCR expression profiles of the TGx-DDI biomarker for DDI chemical classification using qPCR.

overall_design: TK6 human lymphoblastoid cells were exposed to 28 reference DDI and non-DDI agents (29 treatment samples in total; two concentrations of EtOH were included) and  vehicle controls (9 control samples) for 4 hours. Two biological replicates for each treatment were generated (76 samples in total). Following RNA extraction and cDNA synthesis, each sample was loaded on one TGx-DDI qPCR array for gene expression profiling. Each 96-well TaqMan qPCR array contained 64 TGx-DDI biomarker genes and housekeeping genes (HPRT and GUSB; the average Ct value of the two genes were used) for normalization. The treatment concentration of each compound was determined in the original TGx-DDI publication by Li et al. [2015]. Briefly, TK6 cells were exposed to increasing concentrations of each agent for 4 hours. Cell viability was measured using MTT assay after 20-hour recovery (at 24h) and the expression of three genes, ATF3, GADD45A, and CDKN1A, were measured at 4h. The selected concentration maximally induced the three indicator genes, while maintaining cell viability above 50% at 24h [Li et al., 2015].  Following normalization of each gene using the housekeeping genes, gene expression fold changes due to chemical exposure were determined by normalizing each chemical treatment to its vehicle control.   The current dataset contains 61 genes; Ct values for three of the 64 TGx-DDI genes were above 40 in majority of the samples and, thus, were excluded.

first: Julie

middle: K

last: Buick

first: Andrew

last: Williams

first: Renxiang

last: Chen

first: Heng-Hong

last: Li

first: J

middle: C

last: Corton

first: Albert

middle: J

last: Fornace Jr.

first: Jiri

last: Aubrecht

first: Carole

middle: L

last: Yauk


title: The Pseudomonas aeruginosa PilSR two-component system regulates both twitching and swimming motilities

city: Hamilton

first: Sara

middle: LN

last: Kilmury

state: ON

address: 1280 Main St. W Room 4H13

department: Biochemistry

institute: McMaster University

type: Expression profiling by high throughput sequencing

summary: We used NGS to find that the PilS-PilR two component system of P. aeruginosa controls the expression of many non-pilus related genes and has a role in regulating swimming motility

overall_design: RNA profiles of P. aeruginosa strains grown on LB 1.5% agar plates for 16h were generated using deep sequencing on the Illumina HiSeq

first: Lori

last: Burrows


title: Expression data from bone marrow of human subjects (6 primary myelofibrosis, 3 essential thrombocythemia and 8 controls)

status: Public on Dec 22 2018

city: New York

first: Genta

last: Ishikawa

state: NY

address: One Gustave L. Levy Place Box 1232

department: Pulmonary, Critical Care and Sleep Medicine

country: USA

institute: Icahn School of Medicine at Mount Sinai

summary:
Fibrosis is the hallmark of primary myelofibrosis, a disease characterized by increased TGF-β bioavailability in bone marrow and spleen from both patients and mouse models. The aim of this study was to verify the role of TGF-β signaling in comparison to essential thrombocythemia and non-diseased control by using human bone marrow.
We used RNA microarrays to investigate gene expression in bone marrow and identified distinct classes of up/down-regulated genes during this process.

overall_design: RNA was extracted and purified with RNeasy Mini Kit (#79104 QIAGEN GmbH, Germany). Its concentrations were measured with NanoDrop (Thermo Scientific, Wilmington, DE, USA) and samples were run on the Illumina microarray Human HT-12_v4 Bead Chip gene expression array by the Genomics Core Facility of the ISMMS (Icahn School of Medicine at Mount Sinai).

first: Lilian

last: Varricchio


title: Expression analysis of epidermal barrier functions associated genes in HaCaT cell treated by All-trans retinoic acid and Nicotinamide

city: Xi'an

first: Jing

state: Shaanxi

address: 157 Xi Wu Road

department: Dermatology

country: China

institute: Northwest Hospital, Xi'an Jiaotong University

summary: Investigation of  molecular mechanisms of impaired skin barrier by ATRA

overall_design: A three chip study using total RNA  recovered from three treated cells, which were incubated with or without ATRA and ATRA with NIC for 36h.

first: Songmei

last: Geng


title: Delignification abilities of the white-rot fungus Polyporus brumalis explained by its oxidative enzymatic arsenal

city: Marseille

first: Marie-Noëlle

last: Rosso

address: 163 avenue de Luminy

department: Biodiversity and Biotechnology of Fungi - BBF

country: France

institute: INRAE - Aix Marseille University

summary: The fungus Polyporus brumalis is a wood decay fungus previously evidenced as efficient lignin degrader with high potential for plant biomass pre-treatment before conversion into bio-energy. Here we used an RNASeq approach that highlighted the active transcription of an unparalleled number of lignin active peroxidases and H2O2 generating enzymes during growth on wheat straw. These enzymes, together with metabolic processes related to detoxification appear as key determinants of the fungal adaption to lignin degradation.

overall_design: To identify the enzymatic determinants responsible for the observed selective degradation of lignin, we compared the transcription profiles of P. brumalis after 10-day growth on 2% malt extract (control) with the transcription profiles after 6-days growth on 2% malt extract followed by 4, 10 and 15 days fermentation on wheat straw.

first: Shingo

last: Miyauchi

first: Anaïs

last: Rancon

first: Sana

last: Raouche

first: Isabelle

last: Herpoël-Gimbert


title: Identification and characterization of a core set of ROS wave-associated transcripts involved in the systemic acquired acclimation response of Arabidopsis to excess light [Timecourse]

city: Memphis

first: Soham

last: Sengupta

state: TN

address: 262 Danny Thomas Place

institute: St. Jude Children's Research Hospital

summary: Transcriptome profiling (RNA-seq) of local and systemic leaves of Arabidopsis Col and rbohD plants exposed to a local treatment of high light

overall_design: Local leaves of 4– to 5-week-old Col (WT) and rbohD plants were exposed to a light intensity of 2000 µmol m-2 sec-1 for periods of 0, 2, 4 and 8 min using a gooseneck light source (ACE I; Schott). Total RNA of local and systemic tissue were  used and single-end sequenced reads were obtained from the Illumina NExtSeq platform

middle: I

last: Zandalinas

first: David

last: Burks

first: Rajeev

last: Azad

first: Ron

last: Mittler


title: Expression analysis of epidermal barrier functions associated genes in HaCaT cell and mouse epidermis treated by All-trans retinoic acid and Nicotinamide

last: Li

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Identification and characterization of a core set of ROS wave-associated transcripts involved in the systemic acquired acclimation response of Arabidopsis to excess light [DPI]

summary: Transcriptome profiling (RNA-seq) of local and systemic leaves of Arabidopsis Col treated with 50 mM DPI and exposed to a local treatment of high light

overall_design: To inhibit the propagation of the ROS wave from the local to the systemic leaf, a drop of 0.3% agarose-containing water or 50 mM DPI, was placed at the midpoint between the local and systemic leaves of 4– to 5-week-old Col-0 plants. Local tissue was then subjected to light stress for 8 min and both local and systemic leaves were used for RNA-Seq.


title: Identification and characterization of a core set of ROS wave-associated transcripts involved in the systemic acquired acclimation response of Arabidopsis to excess light [H2O2]

summary: Transcriptome profiling (RNA-seq) of Col seedlings growing in liquid MS culture and exposed to 1 mM H2O2 treatment

overall_design: 5-day-old Col seedlings growing in 0.5 x MS were exposed to 1 mM H2O2 treatment for periods of 0, 2, 4 and 8 min. Total RNA of H2O2-treated and nontreated (H2O) seedlings were  used and single-end sequenced reads were obtained from the Illumina NExtSeq platform


title: Role of P38α in stress erythropoiesis

city: Indianapolis

first: ping

last: hu

address: 420 University Blvd

institute: IUPUI

summary: The P38α modulates proliferation, survival and  differentiation of different kinds of celll. Here, we demonstrate that loss of P38α accelerates recovery from anemia in mice by promoting survival of erythroblasts. To identify gene expression changes  in P38α+/- versus  P38α-/- erythroblasts, we sorted erythroblasts from P38α+/- and  P38α-/- mice during recovery from anemia and performed microarray analysis.

overall_design: Three pairs of P38α+/- and P38α-/- mice were subjected  to phenylhydrazine (PHZ) treatment to induce hemolytic anemia. During the recovery, bone marrow erythroblasts were sorted from those mice. RNA from those cells were processed, amplified, labeled and hybridized to Agilent whole Mouse Genome Oligo Microarrays.

first: H

last: Ping

first: R

last: Kapur


title: Comparative transcriptome analysis of two cotton speices by RNA-seq

first: Peng

last: He

address: No. 620, West Chang'an Avenue, Chang'an District,

institute: Shaanxi Normal University

summary: We obtained a total of 8.4 GB  and 10.8 GB transcript sequence data from ‘Xuzhou142’ and ‘fl’ cultivars, respectively, which correspond to 43,532,778 and 55,844,768 reads. After quality assessment, the clean sequences where 43,036,504 and 55,325,412, respectively. Comparison of the RNA-seq data with genomic sequences revealed that 692 RNA editing sites were identified in mitochondrial genes, all of which were C-to-U conversions except for 13 U-to-C changes. we conducted a comparative transcriptome analysis of mitochondrial protein coding genes and investigated differences in RNA editing between the mitochondrial transcripts of G. hirsutum var. Xuzhou142 (WT) fiber and its near isogenic line, fuzzless-lintless mutant (fl) ovule. No significant difference was observed in the distribution of RNA editing sites in the non-coding regions between fiber and ovule cells. However, the editing efficiency of complex I, complex V, Ribosomal protein, and matR protein coding genes exhibited significant differences between fiber and ovule. Our results showed RNA editing events are abundant in the mitochondrial genome of cotton and some editing sites may closely associated with fiber elongation.

overall_design: Identify RNA editing sites in two cotton speices.

first: Jianing

last: Yu


title: Expression analysis of epidermal barrier functions associated genes in mouse epidermis treated by All-trans retinoic acid and Nicotinamide

summary: Investigation of  molecular mechanisms of impaired skin barrier by ATRA  in mouse epidermis

overall_design: A four chip study using total RNA  recovered from four mouse skin, which were treated with oil/water cream, topical 0.1% ATRA cream, topical 0.1% ATRA cream with NIC cream and NIC cream for 5 days.

last: Geng


title: Identification and characterization of a core set of ROS wave-associated transcripts involved in the systemic acquired acclimation response of Arabidopsis to excess light


title: Transcriptional profiling of Zygosaccharomyces bailii early response to acetic acid or copper stresses mediated by ZbHaa1

city: Lisbon

first: Isabel

last: Sá-Correia

address: Avenida Rovisco Pais, 1

department: Department of Bioengineering

country: Portugal

institute: Instituto Superior Técnico

summary: The non-conventional yeast species Zygosaccharomyces bailii is remarkably tolerant to acetic acid, a highly important microbial inhibitory compound in Food Industry and Biotechnology. ZbHaa1 is the functional homologue of S. cerevisiae Haa1 and a bifunctional transcription factor able to modulate Z. bailii adaptive response to both acetic acid and copper stresses. RNA-Seq was used to investigate genomic transcription changes in Z. bailii during early response to sublethal concentrations of acetic acid (140 mM, pH 4.0) or copper (0.08 mM), and uncover the regulatory network activated by these stresses under ZbHaa1 control.

overall_design: mRNA profiling of Z. bailii IST302 parental strain (Wt) and derived deletion mutant Zbhaa1∆ (Mut) unstressed cells or exposed to either acetic acid (AA) or copper (Cu) stresses. A total of 18 samples were analysed (3 replicates per condition)

first: Miguel

last: Antunes

first: Margarida

last: Palma


title: Human bone marrow-derived myeloid dendritic cells show an immature transcriptional and functional profile compared to their peripheral blood counterparts and separate from Slan+ non-classical monocytes

city: Lund

first: Kristina

last: Lundberg

address: Medicon Village building 406, Scheelevägen 8

department: Immunotechnology

country: Sweden

institute: Lund University

summary: The human bone marrow (BM) gives rise to all distinct blood cell lineages, including CD1c+ and CD141+ myeloid dendritic cells (DC) and monocytes. These cell subsets are also present in peripheral blood (PB) and lymphoid tissues. However, the difference between the BM and PB compartment in terms of differentiation state and immunological role of DC is not yet known. The BM may represent both a site for development as well as a possible effector site and so far, little is known in this light with respect to different DC subsets. Using genome-wide transcriptional profiling we found clear differences between the BM and PB compartment and a location-dependent clustering for CD1c+ and CD141+ was demonstrated. DC subsets from BM clustered together and separate from the corresponding subsets from PB, which similarly formed a cluster. In BM, a common proliferating and immature differentiating state was observed for the two DC subsets, whereas DC from the PB showed a more immune-activated mature profile. In contrast, BM-derived slan+ non-classical monocytes were closely related to their PB counterparts and not to DC subsets, implying a homogenous prolife irrespective of anatomical localization. Additional functional tests confirmed these transcriptional findings. DC-like functions were prominently exhibited by PB DC. They surpassed BM DC in maturation capacity, cytokine production and induction of CD4+ and CD8+ T cell proliferation. This first study on myeloid DC in healthy human BM offers new information on steady-state DC biology and could potentially serve as a starting point for further research on these immune cells in healthy conditions as well as in diseases.

overall_design: Genome-wide transcriptional analysis of slan+ cells, CD1c+ and CD141+ DC subsets in human peripheral blood and bone marrow.

first: Nathalie

last: van Leeuwen-Kerkhoff

first: Theresia

middle: M

last: Westers

first: Shahram

last: Kordasti

first: Hetty

last: Bontkes

first: Malin

last: Lindstedt

first: Tanja

middle: D

last: de Gruijl

first: Arjan

middle: A

last: van de Loosdrecht


title: In vitro transcription studies used in a proof of concept whole transcriptome model predition study - HepaRG cells (3 of 4)

city: Research Triangle Park

first: Michael

middle: B.

last: Black

state: North Carolina

address: 100 Capitola Dr., Suite 106

institute: Scitovation, LLC.

summary: HepaRG cells were exposed in triplicate to three agrichemicals for 24hrs at 8 concentrations and a DMSO vehicle control (0.001, 0.003, 0.01, 0.03, 0.1, 0.3, 1, 3, and 10 μM plus DMSO vehicle controls).  While a common set of DMSO controls was used, these CEL files were RMA normalized independently with each of the chemical treated groups.  Gene expression was measured on an Affymetrix GeneTitan system.  The compounds used were fenbuconazole (a.k.a FENB, CAS # 114369-43-6) a triazole fungicide, imazalil (a.k.a. IMAZ, CAS # 35554-44-0), an azole pesticide, and 2,4-dichlorophenoxyacetic acid (a.k.a. 2,4-D or 2-4-D in file names, CAS # 94-75-7), a chlorophenoxy herbicide.

overall_design: 24hr in vitro exposures in triplicate at 9 concentrations - 0.001, 0.003, 0.01, 0.03, 0.1, 0.3, 1, 3, and 10 μM plus DMSO vehicle controls

middle: B

first: Saad

last: Haider


title: In vitro transcription studies used in a proof of concept whole transcriptome model predition study - HepG2 cells (4 of 4)

summary: HpeG2 cells were exposed in triplicate to three agrichemicals for 24hrs at 8 concentrations and a DMSO vehicle control (0.001, 0.003, 0.01, 0.03, 0.1, 0.3, 1, 3, and 10 μM plus DMSO vehicle controls).  While a common set of DMSO controls was used, these CEL files were RMA normalized independently with each of the chemical treated groups.  Gene expression was measured on an Affymetrix GeneTitan system.  The compounds used were fenbuconazole (a.k.a FENB, CAS # 114369-43-6) a triazole fungicide, imazalil (a.k.a. IMAZ, CAS # 35554-44-0), an azole pesticide, and 2,4-dichlorophenoxyacetic acid (a.k.a. 2,4-D or 2-4-D in file names, CAS # 94-75-7), a chlorophenoxy herbicide.


title: In vitro transcription studies used in a proof of concept whole transcriptome model predition study


title: In vitro transcription studies used in a proof of concept whole transcriptome model predition study - MCF7 cells  (2 of 4)

summary: MCF7 cells were exposed in triplicate to three agrichemicals for 24hrs at 8 concentrations and a DMSO vehicle control (0.001, 0.003, 0.01, 0.03, 0.1, 0.3, 1, 3, and 10 μM plus DMSO vehicle controls).  While a common set of DMSO controls was used, these CEL files were RMA normalized independently with each of the chemical treated groups.  Gene expression was measured on an Affymetrix GeneTitan system.  The compounds used were fenbuconazole (a.k.a FENB, CAS # 114369-43-6) a triazole fungicide, imazalil (a.k.a. IMAZ, CAS # 35554-44-0), an azole pesticide, and 2,4-dichlorophenoxyacetic acid (a.k.a. 2,4-D or 2-4-D in file names, CAS # 94-75-7), a chlorophenoxy herbicide.


title: In vitro transcription studies used in a proof of concept whole transcriptome model predition study - A673 cells (1 of 4)

summary:
A673 cells were exposed in triplicate to three agrichemicals for 24hrs at 8 concentrations and a DMSO vehicle control (0.001, 0.003, 0.01, 0.03, 0.1, 0.3, 1, 3, and 10 μM plus DMSO vehicle controls).  While a common set of DMSO controls was used, these CEL files were RMA normalized independently with each of the chemical treated groups.  Gene expression was measured on an Affymetrix GeneTitan system.  The compounds used were fenbuconazole (a.k.a FENB, CAS # 114369-43-6) a triazole fungicide, imazalil (a.k.a. IMAZ, CAS # 35554-44-0), an azole pesticide, and 2,4-dichlorophenoxyacetic acid (a.k.a. 2,4-D or 2-4-D in file names, CAS # 94-75-7), a chlorophenoxy herbicide.
CEL files with _Rep2 in their file name indicate arrays that were re-scanned due to technical issues with the initial instrument scan of the GeneTitan peg array.


title: Hypothalamic transcriptome profiles of pigs divergent in feed efficiency

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

department: Genome Biology

country: Germany

institute: FBN Dummerstorf

summary: in vivo microarray study of transcriptional changes of the hypothalamus obtained from pigs divergent in feed efficiency.

overall_design: Six pigs per experimental group were collected for expression profiling.

first: Henry

last: Reyer

last: Oster


title: Transcriptome profiles of pigs divergent in feed efficiency


title: Ileal transcriptome profiles of pigs divergent in feed efficiency

summary: in vivo microarray study of transcriptional changes of ileal scratchings (mucosa) obtained from pigs divergent in feed efficiency.


title: ENPP6 as a neural regulator of visceral adiposity

city: Edinburgh

first: Iain

last: Williamson

address: Crewe Road

department: Chromosomes and Gene Expression

country: United Kingdom

institute: IGMM MRC Human Genetics Unit

summary: Accumulation of visceral fat around internal organs, is a strong risk predictor for cardiometabolic disease. Although fat deposition at distinct anatomical sites is influenced by genetic factors their functional mechanism remains poorly understood. Here, we show ENPP6 as a neural determinant of selectively visceral adiposity. Through dual-energy X-ray absorptiometry (DXA) body composition analysis in 1,301 individuals from the isolated population of Orkney, we identified low-frequency variants at 4q35.1 associated with a reduction of DXA fat distribution (rs144607341/rs17583822, P = 2.7 x 10-10/ 2.0 x 10-9). A decrease in abdominal fat% and visceral fat mediate the altered fat distribution. We replicated these associations in 3,219 Icelanders for abdominal fat mass by computerized-tomography (P = 0.02/ 0.003). Rs17583822 and nearby SNPs mapped within the second intron of ENPP6 that is predicted as a site of transcriptional regulator. We observed close proximity of these variants and the promoter of ENPP6 by 3D-fluorescent in situ hybridization (3D-FISH) in human neurons but not in adipocytes, supporting a regulatory relationship in the brain. Moreover, enriched 5C interactions across the TAD containing ENPP6 and STOX2 in neurons, especially between a STOX2 intronic region and ENPP6 introns one and two, suggests that this region is more compact in cells where both genes are active and they both share cis regulatory elements. Enpp6 knockout mice exhibited reduced visceral fat, improved glucose tolerance, resistance to fatty liver, and maintenance of energy-dissipation of white fat depots when exposed to high fat diet. Our results reveal ENPP6 as a potential therapeutic target for selective accumulation of high-risk visceral obesity and diabetes.

overall_design: 5C oligonucleotides were designed around EcoRI restriction sites following an alternative scheme

first: Katarina

middle: E

last: Shraut

first: Wendy

last: Bickmore

first: Nicholas

last: Morton


title: Duodenal transcriptome profiles of pigs divergent in feed efficiency

summary: in vivo microarray study of transcriptional changes of duodenum scratchings (mucosa) obtained from pigs divergent in feed efficiency.


title: Jejunal transcriptome profiles of pigs divergent in feed efficiency

summary: in vivo microarray study of transcriptional changes of jejunal scratchings (mucosa) obtained from pigs divergent in feed efficiency.


title: High-throughput gene expression in soil invertebrate embryos – mechanisms of Cd toxicity in Enchytraeus crypticus

city: Aveiro

first: Susana

middle: Isabel Lopes

last: Gomes

address: Campus Universitário de Santiago, Departement of Biology, University of Aveiro

department: Biology

institute: CESAM & University of Aveiro

summary:
Gene expression can vary with the organisms' life stage. It is known that embryos can be more sensitive to toxicant exposure, as previously demonstrated for Enchytraeus crypticus (Oligochaeta) exposed to cadmium (Cd), known to cause embryotoxicity and hatching delay. It was shown that Ca enters embryos via the L-type Ca channels in the cocoon membrane, this being affected in Cd exposed embryos (Cd-Ca competition is well-known). In the present study, the embryotoxic mechanisms of Cd were studied via
high-throughput gene expression for E. crypticus. Cocoons (1e2 days old), instead of the adult organism, were exposed in Cd spiked LUFA 2.2 soil during 1 day. Results showed that Cd affected Ca homeostasis which is implicated in several other molecular processes. Several of the major modulators of Cd toxicity (e.g., impaired gene expression, cell cycle arrest, DNA and mitochondrial damage) were identified in the
embryos showing its relevancy as a model in ecotoxicogenomics. The draft Adverse Outcome Pathway was improved. Previously was hypothesized that gene regulation mechanisms were activated to synthesize more Ca channel proteins e this was confirmed here. Further, novel evidences were that, besides the extracellular competition, Cd competes intracellularly which causes a reduction in Ca efflux, and potentiates Cd embryotoxicity.

overall_design: Gene expression profile of Enchytraeus crypticus cocoons was analysed after 1 day of exposure to 5 and 16 mg Cadmium/kg soil, cadmium concentrations known to affect the embryonic development of E. crypticus. Three biological replicates per test treatment and control (un-spiked LUFA 2.2 soil) were used.

first: Micael

middle: F

last: Gonçalves

first: Rita

last: Bicho

first: Carlos

middle: P

last: Roca

first: Amadeu

last: Soares

first: Janeck

last: Scott-Fordsmand

first: Mónica

last: Amorim


title: B-box family proteins BBX18 and BBX23 control thermoresponsive hypocotyl growth in Arabidopsis

city: Shanghai

first: Lan

last: Ding

address: No.2005 in Songhu Road

department: School of Life Science

institute: Fudan University

summary: Plants coordinate their growth and developmental programs with various endogenous signals and environmental challenges such as seasonal and diurnal temperature fluctuations. The bHLH transcription factor PIF4 plays critical roles in thermoresponsive hypocotyl growth in Arabidopsis, and the evening complex component ELF3 negatively regulates PIF4's activity for downstream gene expression and hypocotyl elongation at elevated temperature. However, how warm temperature signal is transmitted to ELF3 is not known. Here, we report the identification of two B-Box protein BBX18/BBX23 as new regulators of thermomorphogenesis in Arabidopsis. Mutations of BBX18/BBX23 confer reduced thermoresponsive hypocotyl elongation. Overexpression of BBX18 enhances the sensitivity of hypocotyl growth to elevated temperature, which is dependent on the function of PIF4 and RING E3 ligase COP1, respectively. Both BBX18 and BBX23 interact with ELF3 or COP1, relegating the protein abundance of ELF3 at warm temperature. Further, the expression of multiple thermoresponsive genes is impaired in both the PIF4 single mutant and BBX18/BBX23 double mutant. In addition, both the transcription and protein levels of BBX18/BBX23 are up-regulated by elevated ambient temperature. Thus, our findings reveal the important roles of B-Box proteins in plant thermomorphogenesis, and build a new connection from warm temperature information to ELF3 and its downstream signaling components.

overall_design: Totally 18 samples with three genotypes and two treatments,both of which are in triplicates.

first: Jian-Xiang

last: Liu


title: Next Generation Sequencing Facilitates Quantitative Analysis of Mycobacterium smegmatis C2 155 Transcriptomes treated with rifampicin and glutamine

city: Chongqing

first: Xue

last: Huang

address: Tiansheng load, Beibei, Chongqing

summary: We report the application of single-molecule-based sequencing technology for high-throughput profiling of histone modifications in mycobacterium smegmatis C2 155. By obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of Mycobacterium smegmatis C2 155. We find that amino acids synthesis and degradation genes,  genes that are expressed.The ratio of gene expression based on transcriptome substantiate an enhanced TCA cycle. The upregulation of Lys1  was found to prompt this degradation of lysine. The transformation from glutamine to glutamate as well as arginine was mediated by glsA (MSMEG_3818) , of which glutamate engaged into the TCA cycle via α-ketoglutarate. The phenylalanine was degraded into fumarate via mhpB. The succinate formation from asparate degradation was mediated by methylcitrate dehydratase (MSMEG_6645), carboxyvinyl-carboxyphosphonate phosphorylmutase (MSMEG_2506)  and MSMEG_6855. and therefore reflect metabolism state of strains. Data from sample treated with rifampicin/glutamine reveals the upregulation of respiration.

overall_design: mRNA profiles of M.smegmatis exposed in rifampicin with or without glutamine were generated by deep sequencing, using Illumina Hiseq.

first: Jianping

last: Xie


title: Analysis of three kinds of tumors gene expression by RNA microarray

status: Public on Dec 20 2018

city: HangZhou City

first: Li

last: Xu

state: ZheJiang Province

address: BinWen Street  358#

institute: ZJTCMU

summary: In order to detect the difference of tumorigenicity induced by different cell lines in nude mice. We have employed whole genome microarray expression profiling as a discovery platform to identify the difference of genes expression. 10 week old 44 thymus-free nude mice were randomly divided into four groups, control group, A549 group, H1299 group and A549+H1299 group. 0.2ml saline suspension containing 5×10^6 cells were implanted subcutaneously in the flanks of each nude mouse in the control group. A549+H1299 group means 0.2ml saline suspension containing 2.5×10^6 A549 cells and 2.5×10^6 H1299 cells. After 30 days, Tumor tissue in each nude mouse Tumor tissue was taken out and detected with Agilent Human 4x44K Gene Expression Microarrays.

overall_design: Gene expression in tumor tissue from A549, H1299 and A549+H1299 group were used for gene expression. Three independent experiments were performed at each group.

first: Bin


title: Microarray expression profiling data for sorted prostate epithelial subpopulations based on LY6D

city: Boston

first: Zhe

last: Li

state: MA

address: 77 Avenue Louis Pasteur, Room 466

department: Medicine, Genetics Division

institute: Brigham and Women's Hospital

summary: In the normal prostate, most basal and some luminal cells are castration-resistant (CR). The identity of these CR cells and their relation to CR prostate cancer are unresolved. We compared single-cell expression profiles of prostate cells sorted from hormonally naïve (HN) and castrated mice. We found both basal and luminal-localized cells, particularly the latter, were molecularly heterogeneous. CR luminal cells and a subset of HN luminal cells exhibited a similar “intermediate” expression pattern, including high-level expression of multiple prostate stem/progenitor marker genes and androgen receptor gene. We validated LY6D as a marker linking CR luminal cells to luminal progenitors. LY6D+ prostate cells, including LY6D+ luminal cells, were enriched for organoid-forming potential regardless of the presence or absence of androgen. Krt8-based lineage-tracing revealed that LY6D+ CR luminal cells produced LY6D- normal luminal cells upon regeneration, but LY6D+ luminal cancer cells under PTEN-deficiency. Furthermore, prostate cancers originating from CR luminal cells (LY6D+) exhibited a more advanced phenotype than those from HN luminal cells (LY6D+ or LY6D-). Lastly, LY6D amplification/upregulation appear associated with advanced prostate cancer in patient samples. Together, our studies demonstrate LY6D as a novel progenitor marker predictive of lethal CR disease.

overall_design: Subpopulations of prostate epithelial cells based on Sca1, CD49f, LY6D and lineage markers (negative for CD45, CD31, Ter119) were sorted from wild-type hormone-naïve mice; total RNAs were prepared from each sorted sample and subjected to microarray expression profiling.

first: Hubert

last: Pakula


title: Approaches for Surveying Cosmic Radiation Damage in Large Populations of Arabidopsis thaliana Seeds- an Antarctic Example

city: Gainesville

first: Robert

middle: J.

last: Ferl

state: Florida

address: 1301 Fifield Hall PO Box 110690

department: Horticultural Sciences

institute: University of Florida

type: Genome variation profiling by high throughput sequencing

summary: The Cosmic Ray Exposure Sequencing Science (CRESS) payload system is a proof of concept experiment to assess the genomic impact of space radiation on seeds. CRESS was designed as a secondary payload for the December 2016 high-altitude, high-latitude, and long-duration balloon flight carrying the Boron And Carbon Cosmic Rays in the Upper Stratosphere (BACCUS) experimental hardware. Investigation of the biological effects of Galactic Cosmic Radiation (GCR), particularly those of ions with High-Z and Energy (HZE), is of interest due to the genomic damage this type of radiation inflicts. The biological effects of upper-stratospheric mixed radiation above Antarctica (ANT) were sampled using Arabidopsis thaliana seeds and were compared to those resulting from a controlled simulation of GCR at Brookhaven National Laboratory (BNL) and to laboratory control seed. The payload developed for Antarctica exposure was broadly designed to 1U CubeSat specifications (10cmx10cmx10cm, ≤1.33kg), maintained 1 atm internal pressure, and carried an internal cargo of four seed trays (about 580,000 seeds) and twelve CR-39 Solid-State Nuclear Track Detectors (SSNTDs). The irradiated seeds were recovered, sterilized and grown on Petri plates for phenotypic screening. BNL and ANT M0 seeds showed significantly reduced germination rates and elevated somatic mutation rates when compared to non-irradiated controls, with the BNL mutation rate also being significantly higher than that of ANT. Genomic DNA from mutants of interest was evaluated with whole-genome sequencing using PacBio SMRT technology. Sequence data revealed the presence of an array of genome structural variants in the genomes of M0 and M1 mutant plants.

overall_design: Arabidopsis thaliana seeds of the Columbia (Col-0) ecotype were placed into 24 x 24 bin seed trays (modified 1536-well plates) with bins which were then covered by polyolefin sealant film [USA Scientific] and flanked by CR-39 SSNTDs, for two non-concurrent exposures. In the BNL exposure, one seed tray with three CR-39 sheets on each side was placed in a modified T-25 flask for irradiation (H, 250 MeV, 10.62 Rad; He, 250 MeV, 3.165 Rad; O, 350 MeV, 1.08 Rad; Ti, 300 MeV, 0.735 Rad). The Antarctica exposure was 30 days in duration at an altitude of ~35 km. Four seed trays were arranged in a stack with three CR-39 plates at each end, and two sheets between each tray. After irradiation, seeds were returned to the University of Florida and stored at -20 °C until planting. Seeds were planted on Phytagel™-based nutrient media and grown for 14 days, at which time Petri plates were evaluated for germination and mutation rates. Mutants of interest were tracked, and preserved in liquid nitrogen if growth was deemed too impaired for the plant to mature. Whole genomic DNA was extracted from 10 mutants, which was used to prepare SMRT-Bell libraries (4 individual mutants, 1 pool of 6 mutants). The PacBio Sequel was used for Whole-Genome Sequencing of the samples, and the output sequences were processed to detect structural variants using the NGMLR and Sniffles softwares.

first: Brandon

last: Califar

first: Rachel

last: Tucker

first: Juliana

last: Cromie

first: Natasha

last: Sng

first: R

last: Schmitz

first: Jordan

last: Callaham

first: Bradley

last: Barbazuk

first: Anna-Lisa

last: Paul


title: Regulation of breast cancer-induced osteoclstogenesis by mH2A1.2 involving EZH2-mediated H3K27me3

city: Los Angeles

first: Vasu

last: Punj

state: CA

address: Biggy Street

institute: USC

summary: In breast cancer metastasis soluble factors secreted by breast cancer cells trigger a cascade of events that stimulate osteoclast differentiation in the bone microenvironment. macroH2A is a unique histone variant with a C-terminal nonhistone domain and play a crucial role in modulating chromatin organization and gene transcription. To study the effect of macroH2A1.2, an isoform of  macroH2A, on  breast cancer-derived osteoclastogenesis, we performed gene expression array  studies in wild type and mH2A1.2 knockout MDA-MB-468 cells .

overall_design: Total RNA was isolated from MDA-MB-468 cells in which mH2A1.2  gene  have been depleted along with the wild type cells to study the differenetial regulation of various genes in each case.

first: Jin-Man

last: Kim

first: Yonghwan

last: Shin

first: Sunyoung

last: Lee

first: MiYeong

first: Hong-In

first: Kyunghwan

first: Tobias

middle: S

last: Ulmer

first: Woojin

last: An


title: Soil salinity and mechanical obstruction differentially affects embryonic root architecture in native rice varieties of West Bengal

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

country: India

institute: Genotypic Technology

summary: Roots make the first contact with the soil environment and are the first responders of stress. These root behaviors are quantifiable and adaptive. The response of rice varieties in mechanical and salinity stress was measured in a novel experimental setup that mimics the soil environment. We analyzed the response of roots by means of SAC (Stress Adaptation Coefficient) in 28 rice varieties that include high-yield salt tolerant varieties as well as geographically isolated native rice varieties. cDNA microarray of IR64 root-tip shows about 6000 common transcripts to be differentially regulated among the two stresses and common pathways were identified. Overall, our study indicates that there is an important commonality in the molecular basis of salt and mechanical stress and presents an easy-to-perform early establishment stress screen for rice varieties.

overall_design: Transcriptional response of rice variety IR64 to mechanical and salinity stresses.

first: Sanghamitra

last: Adak

first: Sonali

last: Sengupta

first: Arindam

last: Roy

first: Abhishek

last: Mukherjee

first: Arun

last: Majumder

first: Bipin

last: Chand


title: Treatment of human hepatoma and primary human hepatocyte cultures (PHH) with fatty acids and/or fatty acids and TNFa

status: Public on Dec 19 2018

city: Hannover

first: Juergen

last: Borlak

state: Lower Saxony

address: Feodor-Lynen-Str. 35

department: Centre for Pharmacology and Toxicology

institute: Hannover Medical School

summary: Treatment of the human hepatoma cell lines HepG2, HUH7 and PHH with a mixture of fatty acids caused heaptic steatosis. The combined lipid and TNFa treatment mimics inflammation. Cells were harvested and processed for microarray analysis

overall_design: Three independent experiments were performed with the human hepatoma cell line HepG2, HUH7 and primary human hepatocytes (PHH)

first: Stephanie

last: Breher-Esch

first: Jürgen


title: Zeocin induced genomic instaiblity in yeast

city: Hangzhou

first: Daoqiong

last: Zheng

state: Zhejiang

address: 866 Yuhangtang Road

department: Institute of Microbiology

institute: College of Life Sciences, Zhejiang University

summary: Yeast Saccharomyces cerevisiae has been widely used as a model system for studying physiological and pharmacological action of small-molecular drugs. Here, a heterozygous diploid S. cerevisiae strain QSS4 was generated to determine whether drugs could induce chromosomal instability by determining the frequency of mitotic recombination. In combination of a custom SNP microarray, the patterns of chromosomal instability induced by drugs could also be explored at a whole genome level in QSS4. Using this system, we found Zeocin (a member of bleomycin family) treatment resulted in hundreds-fold higher rate of genomic alterations, including aneuploidy, loss of heterozygosity (LOH), and chromosomal rearrangement.

overall_design: QSS4 cells were first synchronized at G1 phase using α-factor. After treatment of Zeocin (4 μg/mL) for 1 h, QSS4 cells were plated on MAB6 plates that is more favorable to pigment accumulation for QSS4 than YPD plates. After incubation at 30°C for 3 days, it was calculated that white/red sectored colonies appeared at a rate of 1.2×10-2. Genomic DNA of the cells purified from the red and white sides of 13 independent QSS4-derived sectored colonies was separately extracted and analyzed by the SNP-specific microarrays.

first: Dao-Qiong

first: Thomas

last: Petes


title: Yarrow and marigold extracts and their effect in pancreatic cancer cells [CAL]

city: MADRID

first: ROBERTO

last: MARTIN-HERNANDEZ

address: CANTOBLANCO

department: BIOSTATISTICS AND BIOINFORMATICS UNIT

country: Spain

institute: IMDEA ALIMENTACION

summary: determine the molecular effect of yarrow and marigold supercritical extracts in gene expression of pancreatic cancer cells (MIA PaCa-2)

overall_design: we have analyzed two doses (30 and 70 µg/ml) of marigold (CAL).  After 48 hours of exposure, RNAs were collected. 3 independent experiments were performed for each dose, except for their control, 4 experiments,

first: Ana

last: Ramirez de Molina

first: Lamia

last: Mouhid

first: Marta

last: Gomez de Cedron


title: Expression data from TOLS2-treated root

city: Kobe

first: Hidehiro

last: Fukaki

state: Hyogo

address: 1-1 Rokkodai

department: Department of Biology

country: Japan

institute: Kobe University

summary: TOLS2 regulates lateral root initiation in Arabidopsis thaliana.

overall_design: This inculdes expression data from 3-hour treatment of TOLS2 on wild-type, rlk7-3, and puchi-2 5-day-old roots in comparison with non-treatment experiments. Three replicates for each condition and genotypes. Collect about 80 1-cm root tips for each sample.

first: Koichi

last: Toyokura


title: Kin recognition: neurogenomic response to sib mating avoidance in a parasitic wasp

city: Villeurbanne

first: aurore

last: gallot

address: 43, Bd du 11 Novembre 1918

institute: universite Lyon 1

summary: Sib mating increase homozygosity and can lead to inbreeding depression. Selective pressures have favored the evolution of kin recognition and sib avoidance in mate choice. Such avoidance behavior has been recorded in the parasitoid wasp Venturia canescens where the sex determining system (single-locus complementary sex determination, sl-csd) introduces an extra short-term cost to inbreeding; females preferentially mate with unrelated males. The genetics underlying mate choice of females and kin recognition remains largely unexplored. Here we analyzed the head transcriptomic changes after exposure to distinct stimulus: courtship by unrelated male or courtship by brother, while transcriptome of females alone was used as control. Our results demonstrate that male courtship provokes a major transcriptome reprogramming in females heads. The transcriptomic response is highly dependent on the compatibility of the courting male. We subdivided the socially responsive genes using an integrative gene network analysis, we highlighted genes regulated by courtship, whatever the relatedness of the courting male. We also showed that the regulation of some peculiar group of genes is very specific of compatible male courtship, while others are regulated only by incompatible male courtship. We suggest that those different transcriptomic responses lead to mating decision or sib mating avoidance behavior observed in this species.

overall_design: Venturia canescens females head transcriptome after 10 minutes : i) courtship by compatible male (unrelated); ii) courtship by incompatible male (brother); iii) isolated (control). X 3 biological replicates; X 2 technical replicates (18 RNAseq librairies)

first: Aurore

last: Gallot

first: Sandrine

last: Sauzet

first: Emmanuel

last: Desouhant


title: Peripheral T-cell lymphomas not otherwise specified correspond to distinct mature T-cell populations based on the global gene expression profile

city: Bologna

first: Fabio

last: Fuligni

address: Via Massarenti 9

department: Department of Experimental, Diagnostic, and Specialty Medicine Bologna University Medical School

country: Italy

institute: University of Bologna

summary: Genome-wide analysis of nodal peripheral T-cell lymphomas (PTCL/NOS, AITL and ALCL) was used to identify molecular signatures corresponding to different subgroups. We also aimed to define the counterparts of PTCLs/NOS based on their global gene expression profiles. We developed a new molecular classifier able to distinct PTCL/NOS heterogeneity due to the correspondence to different counterparts.

overall_design: 102 PTCL samples divided in 80 PTCL\NOS, 10 AITL, and 12 ALCL, and 15 normal controls derived from CD4-CD8 cells, were analyzed.

first: Pier

last: Piccaluga

first: Claudio

last: Agostinelli

last: Tripodo

first: Maura

last: Rossi

first: Clara

last: Bertuzzi

first: Simona

last: Righi

first: Maria

middle: R

last: Sapienza

last: Laginestra

first: Antonio

last: de Leo

first: Davide

last: Gibellini

first: Anna

last: Gazzola

first: Claudia

last: Mannu

first: Ottavio

last: Piccin

first: Sylvia

last: Hartmann

first: Martin

last: Hansmann

first: Javeed

last: Iqbal

first: John

last: Chan

first: Julie

last: Vose

first: Giorgio

last: Inghirami

first: Stefano

last: Pileri


title: Cellular response to Foot-and-mouth disease virus (FMDV) infection in the BHK-21 transcriptome

city: Wuhan

first: Jiadai

last: Li

state: Hubei

address: Luojiashan street  No.16

department: College of Life Science

institute: Wuhan University

summary: We used RNA-sequencing on the Illumina platform to analyze transcriptome profiles of BHK-21 acutely infected with FMDV. In total, we obtained more than 342.8 million raw sequencing reads. And approximately 336.5 million clean reads (98.14%) were acquired by filtering out the adapters and trimming ambiguous reads. We found that cellular response of BHK-21 is related to certain types of alterations in the host cell transcriptome profiles at 24 h post infection.

overall_design: BHK-21 was infected with FMDV at 10^(-3) TCID50/cell. The mock infected BHK-21 cells served as a negetive control. Three independent replicates were conducted in each sample. Cellular response was analyzed by RNA-sequencing.


title: Profiles of antibiotic resistance genes (ARGs) and virulence genes (VGs) and their temporal interactions in OD and MBR

city: Beijing

first: Bing

last: Zhang

state: Beijing

address: Rm 437, School of Environment, Tsinghua University

department: School of Environment

institute: Tsinghua University

summary: Antibiotic resistance genes (ARGs) and virulence genes (VGs) associated with bacterial pathogens are of great concern in WWTPs, while current knowledge of their profiles and co-occurrence patterns in different time intervals is barely sufficient. Moreover, the impacts of treatment process on ARG/VGs diversity also remain clear. To this end, this study was launched to address the differences of the ARG/VGs diversity between an oxidation ditch (OD) and an membrane bioreactor (MBR) and the co-occurrence patterns in different time intervals using a functional gene array-GeoChip.

platform_organism: Bacteria Archaea Eukaryota Viruses

overall_design: Two full-scale wastewater treatment systems applying the processes of oxidation ditch (OD) and membrane bioreactor (MBR) were investigated. They treated identical wastewater at the same scale and ran parallelly.  A total of 48 samples were collected, 24 out of which were taken in the short term and the remaining 24 samples were taken in the long term. In each time interval, 12 mixed-liquor suspended sludge (MLSS) samples were collected daily or weekly on 12 consecutive days/weeks from each system and the extracted DNA were analyzed by functiional gene-based GeoChip.

first: Xianghua

last: Wen


title: Gene expression analysis of Arabidopsis root in LBD16-GR overexpression line

first: Hidehiro

last: Fukaki

address: Rokko-dai 1-1

summary: Lateral roots (LRs) are formed post-embryonically and contribute to root architecture formation in vascular plants. LATERAL ORGAN BOUNDARIES-DOMAIN 16 (LBD16) is a key transcription factor to initiate LR formation. LBD16 functions downstream of AUXIN RESPONSE FACTOR 7 (ARF7) and ARF19, and overexpression of LBD16 partially restores LR formation in the absence of ARF7 and ARF19. To identify downstream targets of LBD16, we engineered a transgenic line with inducible LBD16 activity by overexpressing a fusion protein of LBD16 and rat glucocorticoid receptor (GR) in arf7 arf19 mutant. Here we identified primary response genes of LBD16 from transcriptome analysis of 35Spro:LBD16:GR arf7 arf19 line.

overall_design: Overexpression line of LBD16-Glucocorticoid Receptor (GR) driven by CaMV35S promoter in arf7 arf19 mutant was used for LBD16 induction. We collected roots from 5-day-old seedlings of 35S:LBD16:GR arf7 arf19 line 4 hours after treatment with/without dexamethazone (DEX) and cycloheximide (CHX). Three independent sets of mRNA samples for each treatment were used for this analysis

first: Tatsuaki

last: Goh

first: Takeo

last: Uehara

first: Yoko

last: Okushima


title: Azacitidine Modulates the Mesenchymal Stromal Cell Compartment in Myelodysplastic Syndromes

city: Planegg-Martinsried

first: Sonja

last: Grath

state: Bavaria

address: Grosshaderner Str. 2

department: Department Biology II

institute: Ludwig-Maximilians University Munich

summary: Mesenchymal stromal cells (MSC) are crucial components of the bone marrow (BM) microenvironment essential for regulating self-renewal, survival and differentiation of hematopoietic stem/progenitor cells (HSPC) in the stem cell niche. MSC are functionally and phenotypically altered in myelodysplastic syndromes (MDS), contributing to disease progression. MDS MSC do not harbor recurrent genetic alterations but have been shown to exhibit an altered methylome compared to MSC from healthy controls. We examined growth, differentiation and HSPC-supporting capacity of ex vivo expanded MSC from MDS patients in comparison to age-matched healthy controls after direct treatment in vitro with the hypomethylating agent azacitidine (AZA). We show that AZA exerts a direct effect on MSC by modulating their differentiation potential. Osteogenesis was significantly boosted in healthy MSC while adipogenesis was inhibited in both healthy and MDS MSC. In co-culture experiments, both AZA treated MDS MSC and healthy MSC exhibited enhanced support of non-clonal HSPC which was associated with increased cell cycle induction. Conversely, clonal MDS HSPC were inhibited by contact with AZA treated MSC. RNA-sequencing analyses of stromal cells revealed changes in pathways essential for HSPC support as well as in immune regulatory pathways. In sum, our data demonstrate that AZA treatment of stromal cells leads to upregulation of HSPC-supportive genes and cell cycle induction in co-cultured healthy HSPC, resulting in a proliferative advantage over clonal HSPC. Thus, restoration of functional hematopoiesis by AZA may be driven by activated stromal support factors in MSC providing cell cycle cues to healthy HSPC.

overall_design: RNA sequencing was performed on a mesenchymal stromal cell line (EL08-1D2), either untreated or treated with Azacitidine [(-)AZA vs. (+)AZA].

first: Catharina

last: Wenk

first: Katharina

last: Götze


title: Transcriptome-wide analysis of gene expression using detached first-pair rosette leaves before culture (time 0) and 1 day after culture (DAC) from 9-day-old, 12-day-old and 15-day-old Col-0 seedlings

first: Lin

last: XU

address: 300 Fenglin Road

department: Chinese Academy of Sciences

institute: Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences

summary: To analyze the molecular mechanism behind the relationship between Arabidopsis leaf maturation and de novo root regeneration, we carried out an RNA-seq analysis using detached first-pair rosette leaves before culturing (time 0) and 1 d after culturing (DAC) from 9-, 12- and 15-d-old Col-0 seedlings. We first analyzed gene expression levels in the leaves before detachment (at time 0) from the three developmental states. Changes in gene expression could be grouped into six clusters. Many genes were upregulated or downregulated during leaf maturation. Next, we analyzed gene expression levels in the leaf explants from 9- and 15-d-old seedlings at 1 DAC compared with gene expression levels at time 0. By comparing up- or downregulated genes (1 DAC vs time 0) between leaves from 9- and 15-d-old seedlings, we found that many of the genes were particularly up- or downregulated only in immature leaves or only in mature leaves after 1 d of culturing.

overall_design: RNA-Seq data for 9-, 12- and 15-d-old Col-0 seedlings grown under 24-h constant light conditions. Detached leaf explants were cultured on B5 medium without sucrose at 22°C under 24-h light conditions. Biological duplicates were performed for each developmental stage and treatment analyzed.

first: Jing

last: Pan

first: Fei

last: Zhao

first: Guifang

last: Xu


title: The transcriptome of human endometrial mesenchymal stem cells under TGFβR inhibition reveals improved potential for cell-based therapies

city: Clayton

first: Shanti

last: Gurung

state: Vic

address: 27-31 Wright Street

country: Australia

institute: Hudson Institute of Medical Research

summary: Mesenchymal stem/stromal cells (MSCs) are multipotent cells with favorable properties for cell therapy and regenerative medicine. Human endometrium harbors a small population of perivascular, clonogenic MSCs (eMSCs) identified by the SUSD2 marker. As for other MSCs, eMSCs require extensive in vitro expansion to generate clinically relevant numbers of cells, resulting in spontaneous differentiation, replicative senescence, and cell death, decreasing therapeutic potency. We previously demonstrated that A83-01, a TGF-b receptor inhibitor maintained eMSCs clonogenicity, promoted proliferation, prevented apoptosis and maintained MSC function in vitro. Here we compare the transcriptome of passaged eMSCs from six women cultured with and without A83-01 for 7 days. We identified 1206 differentially expressed genes using a false discovery rate cut-off at 0.01 and fold change >2. Significant enrichment of genes involved in inflammatory responses, angiogenesis, cell migration and proliferation, and reduced smooth muscle proliferation, collagen fibril and extracellular matrix organization genes were revealed. TGF-b, Wnt and Akt signaling pathways were decreased. Anti-fibrotic and anti-apoptotic genes were induced, and fibroblast proliferation and myofibroblast related genes were down-regulated. We validated the enhanced potency of A83-01-treated eMSCs and found increased MSC potency genes (TWIST1, TWIST2, JAG1, LIFR, and SLIT2) and no pluripotency gene expression. Increased angiogenic capacity was functionally demonstrated in vitro, and our angiogenic and cytokine protein arrays further confirmed the angiogenic, antifibrotic and immunomodulatory phenotype of A83-01-treated eMSCs. Overall, we showed that eMSCs culture expanded with A83-01 have improved potential for cell-therapies and regenerative medicine applications.

overall_design: This data is RNA-seq of passaged 6 endometrial mesenchymal stem cells treated with DMSO control or 1mM A83-01. Each group has cells from six independent female donors (paired untreated/U and A83-01 treated/T1).

first: Sarah

last: Williams

first: James

last: Deane

first: Jerome

last: Werkmeister

first: Caroline

last: Gargett


title: Yarrow and marigold extracts and their effect in pancreatic cancer cells [MIL]

first: ROBERTO

last: MARTIN-HERNANDEZ

overall_design: we have analyzed two doses (30 and 70 µg/ml) of Yarrow (MIL).  After 48 hours of exposure, RNAs were collected. 3 independent experiments were performed for each dose, except for their control, 4 experiments,

first: Ana

last: Ramirez de Molina

first: Lamia

last: Mouhid

first: Marta

last: Gomez de Cedron


title: Altered social behavior in mice carrying a cortical Foxp2 deletion

status: Public on Dec 18 2018

city: Martinsried

first: Christoph

last: Ziegenhain

address: Großhaderner Str. 2

summary: Genetic disruptions of the forkhead box transcription factor FOXP2 in humans cause an autosomal-dominant speech and language disorder. While FOXP2 expression pattern are highly conserved, its role in specific brain areas for mammalian social behaviors remains largely unknown. Here we studied mice carrying a homozygous cortical Foxp2 deletion. The postnatal development and gross morphological architecture of mutant mice was indistinguishable from wildtype (WT) littermates. Unbiased behavioral profiling of adult mice revealed abnormalities in approach behavior towards conspecifics as well as in the reciprocal responses of WT interaction partners. Furthermore mutant mice showed alterations in acoustical parameters of ultrasonic vocalizations (USV), which also differed in function of the social context. Cell type-specific gene expression profiling of cortical pyramidal neurons revealed aberrant regulation of genes involved in social behavior. In particular Foxp2 mutants showed the downregulation of Mint2 (Apba2), a gene involved in approach behavior in mice and autism spectrum disorder in humans. Taken together these data demonstrate that cortical Foxp2 is required for normal social behaviors in mice.

overall_design: Wild-type mice and mice carrying a heterozygous Foxp2 deletion in the cortex were analyzed by RNA sequencing

first: Vera

last: Medvedeva


title: Dynamic Profiles of transcriptome in Oryza sativa leaf

first: Yuhua

last: Fu

address: No.1, Shizishan Street, 430070, Wuhan, China

department: College of Animal Science and Technology

institute: Huazhong Agricultural University

summary: To evaluate the roles of gene regulation in Oryza sativa leaf, dynamic profiles of transcriptome were investigated in Oryza sativa L. spp. indica with different treatments, the aerial tissues of one-month-old plants from four different areas (groups 1–4) were treated with 0, 40 mL of 25% azoxystrobin, 0.01 g of VdAL, or 40 mL of 25% azoxystrobin plus 0.01 g VdAL, respectively.

overall_design: Using high-throughput sequencing technology to reveal the characteristic of  transcriptome during Oryza sativa leaf development.

first: Junsheng

last: Qi


title: MicroRNAs regulate differential innate immune response to uropathogenic and commensal-like Escherichia coli infection in the surrogate insect model Galleria mellonella

city: Giessen

first: Daniel

last: Amsel

address: Aulweg 128

institute: Justus Liebig University

type: Non-coding RNA profiling by high throughput sequencing

summary: Identification and expression analysis of microRNAs in infected larvae of the insect model Galleria mellonella with uropathogenic (UPEC) and commensal E. coli strains that are known to cause symptomatic and asymptomatic bacteriuria (ABU) in humans, respectively.

overall_design: three smallRNA samples

first: Krishnendu

last: Mukherjee


title: PBMC expression signatures of controlled and uncontrolled hypertensives

city: São Paulo

first: Michelle Sabrina

last: Moreira Silva

state: SP

address: Av. Dr. Enéas de Carvalho Aguiar

country: Brazil

institute: Heart Institute - InCor

summary:
There is high variability in responses to drug therapy for hypertension. Gene expression may help enlighten molecular mechanisms of genome control underlying pathophysiology.
This study identifies and characterizes, in replicate samples, a gene expression signature that classifies individuals into controlled and uncontrolled hypertensives.

overall_design: 20 hypertensive patients (58±13 yrs) under a standardized antihypertensive medication were examined twice, five months apart with measures of 24-hour ambulatory blood pressure (BP) monitoring and genome-wide gene expression analysis of peripheral blood mononuclear cells (PBMCs).

first: Michelle

last: Silva

first: Alexandre

last: da Costa Pereira


title: Expression data from hearts (left ventricle apex) of rats with and without phenformin treatment

status: Public on Dec 17 2018

city: Wuppertal

first: Heidrun

middle: Christine

last: Ellinger-Ziegelbauer

address: Aprather Weg 18a

institute: Bayer Pharma AG

summary: In a subacute study, male Wistar rats were treated daily by gavage with 800 mg/kg metformin for 1, 3, or 14 consecutive days, followed by necropsy 24h after the last application. The biguanide phenformin was used as antidiabetic drug due to its antihyperglycaemic effect, but was withdrawn from the market in the 1970s for safety reasons. In recent years, biguanides received great interest in oncology research after an epidemiological study showed a link between the treatment with metformin, another biguanide with a better safety profile, and a reduced cancer risk in diabetic patients. Since mitochondrial metabolism has become a target for possible cancer therapeutic approaches, especially for tumors relying on oxidative metabolism, mitochondrial complex I inhibition is under discussion to be responsible for the anti-cancer effect of metformin. The known strong complex I inhibitor Rotenone has also shown anti-cancer activity, however is associated with toxic effects. Therefore, we compared metformin and phenformin, with rotenone, to elucidate potential mechanisms rendering biguanides apparently less toxic than rotenone. In this context, various blood and tissue parameters as well as histopathology were measured and/or evaluated.  Moreover, gene expression profiling was conducted in liver and heart due to the high metabolic activity and high energy demand. All investigations were based on an experimental design previously described for mechanistic investigations of the effects of rotenone. Our examinations regarding gene expression showed that 1630 transcripts were deregulated by rotenone, metformin and/or phenformin in liver, whereas 777 transcripts were deregulated in heart, indicating that the heart is less affected by these compounds. Overall, the mechanistic profile of phenformin appears to be similar to that of rotenone, yet at a quantitatively reduced level, whereas metformin displayed only transient similarities after one day of treatment. These differences are likely due to differential molecular properties of these compounds, especially concerning their effects on mitochondria: Metformin, in contrast to rotenone, requires a certain mitochondrial potential to allow accumulation in this organelle, thereby self-limiting its entry and thus ability to inhibit mitochondrial function, whereas rotenone and to some extent also phenformin can enter mitochondria freely. Thus, our more detailed molecular characterization of these compounds suggests that inhibition of mitochondrial functions can serve as target for an anti-cancer mode of action, yet should be self-limited or balanced to some extent to avoid exhaustion of all energy stores.

overall_design: Male RccHan Wistar rats at the age of 7-8 weeks were randomly assigned to the vehicle or treatment group (n=5). Then 0 or 3000 ppm phenformin (Sigma Aldrich, Steinheim, Germany) was administered in the diet for 3 or 14 consecutive days, followed by necropsy. Blood was collected for clinical chemistry and hematology and several organs were removed, weighted, aliquoted, fixed in formalin for histopathological examinations or flash frozen in liquid nitrogen and stored at −80 °C for RNA isolation.

first: Sabrina

last: Heinz


title: Expression data from livers of rats with and without metformin treatment

summary: In a subacute study, male Wistar rats were treated daily by gavage with 800 mg/kg metformin for 1, 3, or 14 consecutive days, followed by necropsy 24h after the last application. The biguanide metformin is a widely used antidiabetic drug, which has received great interest in oncology research in recent years after an epidemiological study showed a link between metformin treatment and a reduced cancer risk in diabetic patients. Since mitochondrial metabolism has become a target for possible cancer therapeutic approaches, especially for tumors relying on oxidative metabolism, mitochondrial complex I inhibition is under discussion to be responsible for the anti-cancer effect of metformin. The known strong complex I inhibitor Rotenone has also shown anti-cancer activity, however is associated with toxic effects. Therefore, we compared metformin and phenformin, another biguanide withdrawn from the marked as antidiabetic due to safety reasons, with rotenone, to elucidate potential mechanisms rendering biguanides apparently less toxic than rotenone. In this context, various blood and tissue parameters as well as histopathology were measured and/or evaluated.  Moreover, gene expression profiling was conducted in liver and heart due to the high metabolic activity and high energy demand. All investigations were based on an experimental design previously described for mechanistic investigations of the effects of rotenone. Our examinations regarding gene expression showed that 1630 transcripts were deregulated by rotenone, metformin and/or phenformin in liver, whereas 777 transcripts were deregulated in heart, indicating that the heart is less affected by these compounds. Overall, the mechanistic profile of phenformin appears to be similar to that of rotenone, yet at a quantitatively reduced level, whereas metformin displayed only transient similarities after one day of treatment. These differences are likely due to differential molecular properties of these compounds, especially concerning their effects on mitochondria: Metformin, in contrast to rotenone, requires a certain mitochondrial potential to allow accumulation in this organelle, thereby self-limiting its entry and thus ability to inhibit mitochondrial function, whereas rotenone and to some extent also phenformin can enter mitochondria freely. Thus, our more detailed molecular characterization of these compounds suggests that inhibition of mitochondrial functions can serve as target for an anti-cancer mode of action, yet should be self-limited or balanced to some extent to avoid exhaustion of all energy stores.

overall_design: Male RccHan Wistar rats at the age of 7-8 weeks were randomly assigned to the vehicle or treatment group (n=5). Then 0 or 800 mg/kg metformin (Sigma Aldrich, Steinheim, Germany) was administered by gavage for 1, 3 or 14 consecutive days, followed by necropsy. Blood was collected for lactate determination and several organs were removed, weighted, aliquoted, fixed in formalin for histopathological examinations or flash frozen in liquid nitrogen and stored at −80 °C for RNA isolation.


title: Expression data from livers of rats with and without phenformin treatment


title: Changes in miRNA expression in circulating whole blood resutling from exposure to neurotoxic doses of D-amphetamine

city: Jefferson

first: John

middle: Francis

last: Bowyer

state: AR

address: 3900 NCTR Drive

department: Neurotoxicology

institute: National Center for Toxicological Research FDA

summary:
These experiments were designed to compare the miRNA expression in whole circulating blood in animals exposed to D-amphetamine to the expression under control condition.  This is the final set of RNA seq data to be generated by the experiments that have previously generated mRNA transcriptomes (GSE62368 and GSE64778).  The study objectives were to detect miRNA changes in blood resulting from a neurotoxic exposure to amphetamine that may result from organ and tissue damage or immune function changes
Amphetamine effects on gene expression are dependent on body temperature and indicate that many significant changes in genes related to the immune system occur, some likely in response to damage, even when animals remain normothermic during amphetamine exposure.  Also, hyperthermia alone produces many changes in immune related genes in blood

overall_design:
The study was conducted in adult male Sprague Dawly rats comprised of seven saline controls and seven amphetamine exposed rats. Four injections of amphetamine were sequentially given with 2 h between each injection. Dosing started at 7:30 to 8:30 a.m.  The AMPH group became very hyperthermic during dosing, which is necessary to produce both neurotoxicity ti  Animals were sacrificed 9 h after the first injection. Five ml of blood was obtained from cardiac puncture, separated into multiple aliquots and snap frozen on dry ice.  Total RNA from the blood was later isolated using the Triazole method.
Details of RNA extraction and processing in PLoS One. 2015 Jul 15;10(7):e0133315. doi: 10.1371/journal.pone.0133315. eCollection 2015

first: Luisa

last: Camacho

first: Camila

first: Nysia

last: George


title: A Novel Cereblon Modulator Targets eRF3 Family Proteins For Cereblon-dependent Destruction

city: San Diego

first: Antonia

last: Lopez-Girona

state: California - CA

address: 10300 Campus Point Dr

department: Molecular ＆ Medical Science

institute: Celgene Corporation

summary:
To discern why GSPT1 depletion induced growth inhibition, we utilized RNA microarray analysis to profile the transcriptional changes in cells treated with CC-885 or DMSO. To discern why CC-885 induced growth inhibition, we utilized RNA microarray analysis to profile the transcriptional changes in cells treated with CC-885 or DMSO
Several key markers of the ATF4 pathway including ATF3, CHOP (DDIT3), and ATF4 were significantly induced by CC-885 treatment.

overall_design: Human breast cancer cell line (T47D) were treated with CC-15885 or DMSO for 1,2,4, or 8hr in replicate. The RNA samples were assayed on Affymetrix microarrays.

first: Gang

last: Lu

first: Shuichan

last: Xu


title: Rat liver and heart treated with either metformin or phenformin

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

overall_design: Refer to individual Series


title: Expression data from hearts (left ventricle apex) of rats with and without metformin treatment

overall_design: Male RccHan Wistar rats at the age of 7-8 weeks were randomly assigned to the vehicle or treatment group (n=5). Then 0 or 800 mg/kg metformin (Sigma Aldrich, Steinheim, Germany) was administered by gavage for 1, 3 or 14 consecutive days, followed by necropsy. Blood was collected for for lactate determination and several organs were removed, weighted, aliquoted, fixed in formalin for histopathological examinations or flash frozen in liquid nitrogen and stored at −80 °C for RNA isolation.


title: mRNA sequencing of field-grown Glycine max whole leaflets at four time points

status: Public on Dec 16 2018

city: Raleigh

first: Anna

last: Locke

state: NC

address: 4112 Williams Hall, 101 Derieux Place

institute: USDA-ARS

summary: The diurnal transcriptome of field-grown Glycine max was investigated in relation to diurnal physiological processes in the field and compared to diurnal transcription data from growth chamber studies

first: Donald

last: Ort


title: Interferon-gamma protects sympathetic neurons from apoptosis at the point of cytochrome c release

city: Chapel Hill

first: Mohanish

last: Deshmukh

address: 7109E Neuroscience Research Building, 105 Mason Farm Road

department: Cell Biology and Physiology

institute: University of North Carolina

summary: While immune responses during nervous system injury and disease are well studied, exactly how primary neurons respond to immune signals is still largely unknown.  We find that primary sympathetic neurons respond unexpectedly to interferon-gamma (IFN-γ), a cytokine released by immune cells in response to infection.  While IFN-γ induces apoptosis in many cell types, it has the opposite effect on sympathetic neurons by protecting them from apoptotic stimuli.  We found that IFN-γ addition enabled sympathetic neurons to become resistant to nerve growth factor (NGF) deprivation- or pan-kinase inhibition-induced apoptosis.  In investigating how interferon modulates the apoptotic pathway, we discovered that c-jun phosphorylation and Bim induction in response to NGF deprivation were unchanged with IFN-γ.  Downstream of the mitochondria, however, IFN-γ blocked cytochrome c release and caspase-3 activation in NGF-deprived neurons.  Microinjection of cytochrome c into XIAP-/- neurons revealed no difference in cell death with IFN-γ addition, demonstrating a role for IFN-γ at the point of mitochondria permeabilization.  Levels of Bax and Bcl-XL, molecules that help regulate mitochondrial permeabilization, were unchanged.  These results identify Bax activation as the likely point at which IFN-γ acts to inhibit neuronal apoptosis.

overall_design: reference x sample

first: Elizabeth

last: Knight


title: Expression data from mouse preadipocyte 3T3-L1 and slincRAD-shRNA-8 cells

status: Public on Dec 15 2018

first: fan

last: yi

address: Xue Yuan Road 38

department: Peking University

institute: State Key Laboratory of Natural and Biomimetic Drugs

summary: We used microarrays to detail the global programme of gene expression in 3T3-L1 preadipocytes and identified regulated genes upon knockdown of lncRNA slincRAD.

overall_design: Small hairpin RNAs (shRNA) targeting to lncRNA slincRAD was stably transfected to 3T3-L1 preadipocytes. 3T3-L1 wildtype and slincRAD-shRNA-8 cells induced on  day (-2), day (0), day (+2) and day (+4) of adipogenesis were harvested for RNA extraction and hybridization on Affymetrix microarrays.

first: Fan

last: Yi


title: mProx24 cell: control vs diabetic condition (microRNA)

city: Otsu

first: Shinji

last: Kume

state: Shiga

address: Seta Tsukinowa-cho

department: Medicine

institute: Shiga University of Medical Science

summary: Transcriptional profiling of mProx24 in control, high glucose, high FFAs, hypoxia, triple stimuli and triple stimuli + Rapamycin

overall_design: Six-condition experiment in mProx24 cell

first: Shogo

last: Kuwagata


title: mProx24 cell: control vs diabetic condition (mRNA)


title: mProx24 cell: control vs diabetic condition

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


title: Genome-wide lncRNAs identification and meta-analysis for cold-responsive genes at the booting stage in rice (Oryza sativa L)

city: Harbin

first: Yue

last: Leng

address: Xiangfang District Timber Street

institute: Northeast Agricultural University

summary: Long non-coding RNAs (lncRNAs) are essential regulators of a broad range of biological processes in plants. Spectacular progress in next-generation sequencing technologies has enabled genome-wide identification of lncRNAs in multiple plant species. In this study, genome-wide lncRNA sequencing technology was used to identify cold-responsive lncRNAs at the booting stage in rice by comparison of a tolerant variety, Kongyu131 (KY131), and a sensitive variety, Dongnong422 (DN422). GO and KEGG enrichment analysis were performed, focusing on the cis- and trans- target genes of differential lncRNAs. To identify cold-responsive genes, a meta-analysis was used to integrate cold-tolerant QTLs at the booting stage. In total, 13 cold-responsive target genes were obtained by KEGG enrichment analysis combined with meta-analysis, as confirmed by qRT-PCR. Finally, three of these genes were identified in response to cold stress. These results sought to provide new insight into cold-resistance research for rice.

overall_design: A total of 12 sample data from two treatment groups and two control groups

first: Detang

last: Zou


title: Expression analysis of low-temperature and warming treated Chiifu and Kenshin inbred lines to identify high-temperature adaptation-related gene in Brassica rapa.

status: Public on Dec 14 2018

city: Daejeon

first: Yoonkang

last: Hur

address: 99 Daehak-ro, Yuseong-gu

department: Biological Sciences

country: South Korea

institute: Chungnam National University

summary: Methionine sulfoxide reductases catalyze the reduction of MetSO back to the correct Met residue. Previously, the gene of Capsicum annuum methionine sulfoxide reductase B2 was isolated and CaMSRB2-overexpressing tomato shows enhanced growth, which may trigger increased resistance to the pathogens. To assess the role of this enzyme in rice, we generated transgenic lines under the control of the rice Rab21 (responsive to ABA protein 21) promoter with/without Bar marker gene. Several physiological tests such as MV and Fv/Fm, indicators of an oxidative stress-inducing agent and a potential maximal PSII quantum yield, respectively strongly suggested CaMSRB2 confers drought tolerance to rice. Using 3′-tiling microarray covering the whole rice genes, we carried out genome-wide expression analyses with CaMsrB2-transformed rice (Oryza sativa L. cv. ILMI).  Rice was grown in port for six weeks and treated with drought by water withholding for two days.

overall_design: A total of 6 chips were used for the microarray experiment.  RNA was extracted from plants just before and 2 days after the duration of water withdrawl for the control and the comparison, respectively. Experiments were performed with three or two biological replicates.


title: Identification of lncRNAs Differentially Expressed in Basal-like Breast Cancer

city: Chicago

first: Yoo-Jeong

last: Han

state: IL

address: 900E. 57th street

institute: University of Chicago

summary: To characterize lncRNA expression in breast tumors and identify lncRNAs specifically expressed in the basal-like subtype of breast tumors

overall_design: Isolation of total RNAs from OCT-embeded frozen breast tissues/tumors

first: Olufunmilayo

last: Olopade


title: Gene expression Analysis of wild type (WT) and Blnc1 adipose specific transgenic mice (Tg)  epididymal WAT (eWAT) Transcriptomes after 21 weeks high fat diet (HFD) feeding

city: Ann Arbor

first: xuyun

last: zhao

state: Michigan

address: 210 washtenaw ave

institute: Life Sciences Institute

summary: Long noncoding RNAs (lncRNAs) are emerging as powerful regulators of adipocyte differentiation and gene expression. However, their physiological role in adipose tissue biology and systemic energy metabolism has not been established. Here we show that adipose tissue expression of Blnc1, a conserved lncRNA regulator of thermogenic genes, is highly induced in obese mice. Fat-specific inactivation of Blnc1 impairs cold-induced thermogenesis and browning, exacerbates obesity-associated brown fat whitening, and worsens adipose tissue inflammation and fibrosis, leading to more severe insulin resistance and hepatic steatosis. On the contrary, transgenic expression of Blnc1 in adipose tissue elicits the opposite and beneficial metabolic effects, supporting a critical role of Blnc1 in driving adipose adaptation during obesity. Mechanistically, Blnc1 cell-autonomously attenuates proinflammatory cytokine signaling and promotes fuel storage in adipocytes through its protein partner Zbtb7b. This study illustrates a surprisingly pleiotropic and dominant role of lncRNA in driving adaptive adipose tissue remodeling and preserving metabolic health.

overall_design: eWAT mRNA profiles of WT and Blnc1 adipose specific Tg mice after 21 weeks HFD feeding were generated by microarray, in triplicate

first: Xuyun

last: Zhao

first: Jiandie

last: Lin


title: Transcriptional analysis of trigeminal ganglia in a CFA-induced rat orofacial pain model

city: Pecs

first: Zsuzsanna

last: Helyes

address: Szigeti u. 12

department: Pharmacology and Pharmacotherapy

country: Hungary

institute: University of Pecs Medical School

summary: Although several underlying pathophysiological processes have been explored, the origin and precise pathomechanism of migraine are still being debated. Inflammatory pathways have been suggested to play role in migraine, trigeminal nociceptor sensitisation, thereby causing hyperalgesia and allodynia. The aim of the present study was to investigate gene expression changes in trigeminal ganglia (TRG), central trigeminal nucleus caudalis (TNC) and peripheral blood mononuclear cells (PBMC) evoked by Complete Freund’s Adjuvant (CFA) induced peripheral inflammation. 512  differentially expressed genes were found between CFA-treated and contralateral TRG samples 7 days after CFA injection. The mRNA expression changes of G-protein coupled receptor 39 (Gpr39), kisspeptin-1 receptor (Kiss1r), kisspeptin (Kiss1) and Lkaaear1 were selected for validation. They were most upregulated on day 3 in TRGs of the CFA-treated side. CFA-induced significant orofacial mechanical allodynia in one day with a maximum on day 3. This correlated with patterns of neuronal (Fosb), glial (Iba1), and astrocyte (Gfap) activation markers in both TRG and TNC, and surprisingly in PBMCs. Similar transcriptional changes of Cgrp, the well-known key molecule in migraine pathophysiology, were also revealed. In TNCs, gene expression changes similar to TRGs were observed but Kiss1r transcripts were not significantly altered while Neurod2 was observed only in TNC. These results could indicate the involvement of Gpr39, Kiss1r and synaptic plasticity associated Lkaaear1, Neurod2 genes in the cascade of events resulting in the sensitization underlying migraine headache and the accompanying facial allodynia.

overall_design: Orofacial inflammation was induced by unilateral s.c. injection of 50 µl complete Freund's adjuvant (CFA; 1 mg/ml) into the whisker pad of male rats (n=8). After 7 days, trigeminal ganglia tissue were excised from both sides of each animal (control and treated side). 15 RNA samples were sent for microarray analysis.

first: Tibor

last: Rauch


title: Expression profiles of male and female Drosophila melanogaster with X-chromosomes that were subjected to male-limited evolution

city: Lund

first: Jessica

middle: K.

last: Abbott

address: Sölvegatan 37

department: Dept. of Biology

institute: Lund University

summary:
Due to its hemizygous mode of inheritance and role in sex determination, the X chromosome is expected to play an important role in the evolution of sexual dimorphism, and to be enriched for sexually antagonistic genetic variation. By forcing the X chromosome to only be expressed in males over many generations, we changed the selection pressures on the X to become similar to those experienced by the Y chromosome. This releases the X from any constraints arising from selection in females, and is predicted to lead to specialization for male fitness, including masculinization of phenotypes that normally experience sexually antagonistic selection. Indeed, we found evidence of this via upregulation of male-benefit sexually antagonistic genes, and downregulation of X-linked female benefit genes. Interestingly, we could detect evidence of microevolutionary changes consistent with previously documented patterns of macroevolutionary change, such as changes in expression consistent with previously established patterns of sexual dimorphism, an increase in the expression of metabolic genes related to mitonuclear conflict, and evidence that dosage compensation constitutes a constraint for male-benefit genes. These results confirm the importance of the X in the evolution of sexual dimorphism and as a source for sexually antagonistic genetic variation, and demonstrate that experimental evolution can be a fruitful method for testing theories of sex chromosome evolution.
Microarray data was used to detect differences in gene expression as result of experimental evolution.

overall_design: 24 samples were analyzed. Two treatments with three replicate populations in each treatment, two sexes in each replicate population, two technical replicates for each group (2 treatments x 3 populations x 2 sexes x 2 technical replicates = 24 samples in total).

middle: K

first: Adam

last: Chippindale

first: Edward

middle: H

last: Morrow


title: Compare the knock-down effects of SLC2A11-MIF and two parent genes in Hela cell line

city: Charlottesville

first: Fujun

last: Qin

state: VA

address: 345 Crispell Dr.

department: Pathology

institute: University of Virginia

summary:
Total RNA were extracted from five knocking down treated Hela cells using siRNA targeting fusion gene SLCC2A11-MIF and parental genes
To investigate the function of fusion gene and parental gene, we designed siRNAs specifically knocking down the fusion RNA SLC2A11-MIF and parental gene SLC2A11 respectively. Totally we have five samples. One sample is control, two siRNAs target parental genes and other two siRNAs target fusion genes. After 48hrs siRNA treatment, the RNAs were extracted from cells, and followed by RNA microarray.

overall_design: one siRNA negative control, four siRNAs against SLC2A11, MIF, and SLCA211-MIF(two siRNAs)

first: Peng

last: Wu

first: Hui

last: Li


title: Pharmacogenomic Predictor of Sensitivity to Preoperative Chemotherapy With Paclitaxel and Fluorouracil, Doxorubicin, and Cyclophosphamide in Breast Cancer [MDA4]

city: Bruxelles

first: David

last: Venet

address: Avenue Franklin Roosevelt 50

department: BCTL

country: Belgium

institute: Université Libre de Bruxelles

type:
Expression profiling by array
Third-party reanalysis

summary:
Background: Numerous studies have focused on the PI3K/AKT/mTOR pathway in estrogen receptor positive (ER) breast cancer (BC), as a linear signal transduction pathway and reported its association with worse clinical outcomes. To gain better insight into the relative contribution of each of the signalling pathways which lie downstream to PI3K (namely AKT and mTOR) to BC outcomes, we have developed a novel in silico approach which assessed the activation of each of these signalling pathways separately.
Methods: By analysing gene expression and matched proteomic data in ER-positive patients from the TCGA repository, we developed gene signatures that reflect the level of expression of phosphorylated-Serine473-AKT (pAKT) and phosphorylated-Serine2448-mTOR (p-mTOR) separately, capturing their corresponding level of pathway activation. Using pooled analysis of gene-expression data from over 7,000 patients with ER-positive early BC, we then investigated the association between pathway activation and outcomes.
Results: Our analysis revealed that the pAKT pathway activation (as measured by the developed signature) was associated with luminal A BC while the p-mTOR pathway activation was more associated with luminal B BC (Kruskal-Wallis test p<10-10). pAKT pathway activation was significantly associated with better outcomes (multivariable HR, 0.79; 95% CI, 0.74 to 0.85; p=2.5x10-10) whereas p-mTOR pathway activation showed worse outcomes (multivariable HR, 1.1; 95% CI, 1.1 to 1.2; p=9.9x10-4). Similar associations between activation and outcomes were obtained when the analysis was performed in patients who were treated with hormonal therapy. Additionally, pAKT pathway activation predicted better outcomes irrespective of the BC molecular subtypes (luminal A multivariable HR, 0.85; 95% CI, 0.75 to 0.96; p=0.01; luminal B HR, 0.91; 95% CI, 0.83 to 0.99; p=0.033). pAKT pathway activation was associated with PIK3CA mutations (p=0.0001) while p-mTOR pathway activation was associated with p53 mutations (p=0.04). Finally, we show that pAKT pathway activation was associated with less response to Everolimus.
Conclusions: Our data show that pAKT and p-mTOR pathway activation have differing impact on prognosis and suggest that they are not linearly connected in luminal breast cancers. These findings add to our understanding of signalling through the PI3K pathway and could have important implications for the treatment of luminal BC.

overall_design:
Data are from Hess et al., JCO 2006 (PMID 16896004) and are no longer available on the public DB. Version published here is as formatted for Haibe-Kains et al., JNCI 2007 (PMID 22262870), reused in Sonnenblick et al., NPJ Breast, in press.

Data were downloaded from the MDACC DB by Haibe-Kains before 2007. One hundred thirty-three patients with stage I-III breast cancer were included.


title: Identification of a robust gene signature that predicts breast cancer outcome in independent data sets [UCSF]

overall_design:
Data are from Korkola et al., BMC Cancer 2007 (PMID 17428335) and are no longer available on the web site. Version published here is as formatted for Haibe-Kains et al., JNCI 2007 (PMID 22262870), reused in Sonnenblick et al., NPJ Breast, in press.

Data were downloaded from the authors web site by Haibe-Kains before 2007. Fresh frozen breast tumors were collected from patients treated at UCSF and California Pacific Medical Centers after institutional review board approval. Randomly selected frozen tumor blocks were trimmed to ensure that a minimum of 70% of the remaining cells present were tumor. A total of 140 invasive ductal tumors, 17 invasive lobular tumors, 4 DCIS, 1 inflammatory, and 8 normal breast samples from reduction mammoplasties were analyzed. There were 4 DCIS, 35 Stage I, 80 Stage II, 16 Stage III, 6 Stage IV tumors, and 21 with unknown stage. ER negative tumors comprised 29% of the samples, and 45% of the samples were node negative.


title: Dissecting the AKT/mTOR pathway in estrogen receptor positive breast cancers identifies phosphorylated AKT to be associated with luminal A, PIK3CA mutations and good prognosis in contrast to phosphorylated mTOR


title: The Neurospora crassa VE-1/VE-2/LAE-1 velvet complex controls development, secondary metabolism and light-dependent carotenoid biosynthesis

city: Prague 2

first: Tereza

last: Ormsby

address: Hlavova 2030

country: Czech Republic

institute: Charles University in Prague

summary: Neurospora crassa is a reference organism to study carotene biosynthesis and light regulation for decades. However, there is no evidence of its capacity to produce secondary metabolites, a characteristic of many filamentous fungi. In this work, we report the role of the fungal specific velvet regulator complex in development and secondary metabolism in N. crassa. Four velvet genes were found in the genome. Deletion of ve-1 or ve-2 affects asexual and sexual development, secondary metabolism and light-dependent carotene biosynthesis. Deletion of vos-1 did not show significant differences in comparison to wild type. Deletion of lae-1 resulted in reduced protoperithecia formation and affected secondary metabolism. VE-1, VE-2, LAE-1 and VOS-1 showed nucleo-cytoplasmic localization, which was independent of light input. Two distinct velvet complexes were found in vivo: a heterotrimeric VE-1/VE-2/LAE-1 and a heterodimeric VE-2/VOS-1 complex, respectively. The heterotrimer-complex positively regulated sexual development and repressed asexual spore formation. Moreover, it repressed siderophore coprogen production under iron starvation conditions. The VE-1/VE-2 heterodimer controlled the production of carotene pigments. VE-1 regulated the expression of more than 15% of the whole genome, which corresponded mainly to regulatory, developmental and redox proteins. We also studied intergenera functions of the velvet complex through complementation of A. nidulans veA, velB, laeA, vosA mutants with their Neurospora crassa orthologues ve-1, ve-2, lae-1 and vos-1, respectively. Expression of VE-1 and VE-2 in A. nidulans successfully substituted the developmental and secondary metabolite functions of VeA and VelB by forming two functional chimeric velvet complexes in vivo, VelB/VE-1/LaeA and VE-2/VeA/LaeA, respectively. The N. crassa lae-1 and vos-1 genes did not complement respective A. nidulans mutants and failed to form corresponding complexes. Reciprocally, expression of veA restored the phenotypes of the N. crassa ve-1 mutant. All N. crassa velvet proteins heterologously expressed in A. nidulans were predominantly localized to nuclear fraction independent of light signal. These data highlight the conservation of the complex formation potential in N. crassa and A. nidulans. However, they also underline the similarities and differences of the velvet roles across genera according to the different life styles, niches and ontogenetic processes.

overall_design: Neurospora crassa wild-type or ve-1 duplicate cultures were incubated under standard and iron-free conditions for 48 hours and analyzed with polyA RNAseq.

first: Özlem

last: Bayram

first: Anne

last: Dettmann

first: Betim

last: Karahoda

first: Nicola

last: Moloney

first: Jamie

last: McGowan

first: Sara

last: Cea-Sánchez

first: Alejandro

last: Miralles-Durán

first: Guilherme

middle: T

last: Brancini

last: Fitzpatrick

last: Cánovas

first: Luis

middle: M

last: Corrochano

first: Sean

last: Doyle

first: Eric

middle: U

last: Selker

first: Stephan

last: Seiler

first: Özgür


title: Gene expression predictors of breast cancer outcomes [KOO]

overall_design:
Data are from Huang et al., Lancet 2003 (PMID 12747878) and are no longer available on the web site. Version published here is as formatted for Haibe-Kains et al., JNCI 2007 (PMID 22262870), reused in Sonnenblick et al., NPJ Breast, in press.

Data were downloaded from the authors web site by Haibe-Kains before 2007. The samples were obtained at biopsy of primary tumour at the Koo Foundation Sun Yat-Sen Cancer Centre (KF-SYSCC), Taipei, collected and banked between 1991 and 2001. Samples were taken according to institutional review board guidelines.


title: The circadian clock components BMAL1 and REV-ERB? regulate flavivirus replication

status: Public on Dec 13 2018

city: Oxford

first: Xiaodong

last: Zhuang

state: Oxfordshire

address: Old Road Campus, Roosevelt Drive

institute: University of Oxford

summary: We investigated the effect of the REV-ERB agonists on human hepatocytes. Since SR9009 showed the highest anti-viral activity and has been extensively studied in vivo we performed a whole genome microarray on SR9009 (20 µM) treated Huh-7 cells

overall_design: Two-condition experiment, Ctrl. vs. SR9009 treatment. Biological replicates: 3 control replicates, 3 treatment replicates.

first: Jane

last: McKeating


title: Expression data from bone marrow of human subjects (3 essential thrombocythemia, 2 primary myelofibrosis, and 3 controls)

city: New York

first: Genta

last: Ishikawa

state: NY

address: One Gustave L. Levy Place Box 1232

department: Pulmonary, Critical Care and Sleep Medicine

country: USA

institute: Icahn School of Medicine at Mount Sinai

summary:
Fibrosis is the hallmark of primary myelofibrosis, a disease characterized by increased TGF-β bioavailability in bone marrow and spleen from both patients and mouse models. The aim of this study was to verify the role of TGF-β signaling in comparison to essential thrombocythemia and non-diseased control by using human bone marrow.
We used RNA microarrays to investigate gene expression in bone marrow and identified distinct classes of up/down-regulated genes during this process.

overall_design: RNA was extracted and purified with RNeasy Mini Kit (#79104 QIAGEN GmbH, Germany). Its concentrations were measured with NanoDrop (Thermo Scientific, Wilmington, DE, USA) and samples were run on the Illumina microarray Human HT-12_v4 Bead Chip gene expression array by the Genomics Core Facility of the ISMMS (Icahn School of Medicine at Mount Sinai).

first: Lilian

last: Varricchio