title: Defining stationary phase transcriptomes of Campylobacter jejuni cell morphotypes II

city: Loughborough

first: Ian

middle: Frank

last: Connerton

state: Leicestershire

address: College Road, Sutton Bonington

department: School of Biosciences

institute: University of Nottingham

summary: Filamentation, the transition from rod to filamentous cell morphology, has been identified as a response to stressful conditions in many bacterial species. Campylobacter jejuni exhibits filamentation upon entry to stationary phase. This study examines the cell mophotype specific transciptomes (RNAseq) of C. jejuni.

overall_design: Cell morphotypes were rapidly seperated by filtration from stationary phase Campylobacter jejuni cultures before RNA extraction. Ribosomal RNAs were removed and directional RNAseq perfomed (Illumina HiSeq 2500) to examine cell morphotype-specific transcription at stationary phase compared to short spiral forms harvested from exponential phase growth.

first: Nacheervan

last: Ghaffar

first: Phillippa

middle: L

middle: F


title: Skeletal muscle of Eif6 heterozygous mice - soleus

status: Public on Jul 07 2018

city: Liverpool

first: Kim

last: Clarke

address: Crown Street

country: United Kingdom

institute: University of Liverpool

summary: Soleus muscle from Eif6 heterozygous mice and wild-type mice profiled using Agilent gene expression arrays

overall_design: Four mutant mice were compared to four wild-type mice in two separate age groups, younger 8-16 weeks and mature 16-20 weeks. Mutant mice were randomly paired with age-matched wild type mice and labelled cRNA from each pair was hybridized to Agilent arrays using a two-color approach. Only the 6-10 week age group was used in the publication (pmid:29117557)

first: K

first: F

last: Falciani


title: Defining stationary phase transcriptomes of Campylobacter jejuni cell morphotypes

type: Expression profiling by high throughput sequencing

middle: M


title: Skeletal muscle of Eif6 heterozygous mice

summary: Tibialis anterior and gastrocnemius muscle from Eif6 heterozygous mice and wild-type mice profiled using Agilent gene expression arrays

overall_design: Four mutant mice were compared to four wild-type mice, age 8-16 weeks. Mutant mice were randomly paired with age-matched wild type mice and labelled cRNA from each pair was hybridized to Agilent arrays using a two-color approach.


title: mRNA loading on polysomes in skeletal muscle of Eif6 heterozygous mice

summary: Gastrocnemius muscle from Eif6 heterozygous mice and wild-type mice was used in a polysome profiling experiment. Total RNA was extracted from the whole muscle and from monosome/polysome fractions and profiled using Agilent gene expression arrays.

overall_design: Three mutant mice were compared to three wild-type mice, age 8-16 weeks. Gastrocnemius muscle from each mouse was used to isolate total RNA from whole muscle, and mRNA from monosome and polysome fractions. Each RNA sample was profiled using whole genome Agilent gene expression arrays. Only the polysome samples and total RNA samples were used in the analysis (pmid: 29117557)


title: Light enhances growth in non-phototropic Actinobacteria (Aurantimicrobium sp. MWH-Mo1)

city: Newark

first: Shawn

middle: William

last: Polson

state: DE

department: Center for Bioinformatics and Computational Biology

country: USA

institute: University of Delaware

summary: Light is a source of energy and an environmental cue that is available in excess in most surface environments. In prokaryotic systems, conversion of light to energy by photoautotrophs and photoheterotrophs is well understood, but the conversion of light to information and the cellular response to that information has been characterized in only a few species. Our goal was to explore the response of freshwater Actinobacteria, which are ubiquitous in illuminated aquatic environments, to light. We found that Actinobacteria without functional photosystems grow faster in the light, likely because sugar transport and metabolism are upregulated in the light, while protein synthesis is upregulated in the dark. Based on the action spectrum of the growth effect, and comparisons of the genomes of three Actinobacteria with this growth rate phenotype, we propose that the photosensor in these strains is a putative CryB-type cryptochrome. The ability to sense light and upregulate carbohydrate transport during the day could allow these cells to coordinate their time of maximum organic carbon uptake with the time of maximum organic carbon release by primary producers.

overall_design: Two bacterial strains (Rhodoluna lacicola and Aurantimicrobium sp. strain MWH-Mo1) grown in constant light or constant darkness until late exponential phase; 4 replicates each

first: Jessica

last: Keffer

first: Priscilla

last: Hempel

middle: W

first: Julia

middle: A

last: Maresca


title: Light enhances growth in non-phototropic Actinobacteria (Rhodoluna lacicola strain Ta8)


title: Small RNA (sRNA) sequencing data from pre-meiotic and meiotic anthers of H. lilioasphodelus (Daylily)

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

type: Non-coding RNA profiling by high throughput sequencing

summary:
Purpose: To study pre-meiotic (21-nt) and meiotic (24-nt) phasiRNA pathways in non-grass monocots

Methods: Anthers were dissected using a 2 mm stage micrometer in a stereo microscope, and immediately frozen in liquid nitrogen until total RNA isolation was performed. Small RNA, mRNA libraries were generated using short-read (Illumina) and Single Molecule Real Time SMRT (PacBio) sequencing approaches. Stages were assigned based on the morphology of archesporial (AR) and tapetal cells of H. lilioasphodelus (Daylily) anthers.

overall_design: The H. lilioasphodelus plants were harvested from fields at University of Delaware. Buds corresponding to pre-meiotic and meiotic stages were used to generate mRNA, full-length and sRNA libraries. Data from mRNA-seq and SMRT-seq were used for de novo transcriptome assemblies, so as to compensate for the lack of Daylily genome.  These assemblies were then used along with sRNA data to identify phased-siRNA precursor transcripts and other protein factors that play a role in reproductive phasiRNA pathways. mRNA-seq assembly was performed using “Trinity RNA-Seq assembler”, full-length transcript assembly was prepared using “SMRT-tools” (v2.3) provided by Pacific Biosciences. Phased siRNA precursors were identified using “PHASIS suite” (https://github.com/atulkakrana/PHASIS/wiki), and transcripts sfor protein-coding genes were identified using “Trinotate” (https://trinotate.github.io/).

first: Atul

last: Kakrana

first: Sandra

last: Mathioni

first: Olga

last: Shevchenko

first: Bruce

last: Kingham

middle: C


title: Small RNA (sRNA) sequencing data from pre-meiotic and meiotic anthers of Asparagus

summary:
Purpose: To study pre-meiotic (21-nt) and meiotic (24-nt) phasiRNA pathways in non-grass monocots

Methods: Anthers were dissected using a 2 mm stage micrometer in a stereo microscope, and immediately frozen in liquid nitrogen until total RNA isolation was performed. Small RNA, mRNA libraries were generated using short-read (Illumina) and Single Molecule Real Time SMRT (PacBio) sequencing approaches. Stages were assigned based on the morphology of archesporial (AR) and tapetal cells of A. officinalis (Asparagus) anthers.

overall_design: Flowering Asparagus plants were harvested from T.S. Smith and Sons Farms (Bridgeville, Delaware). Buds corresponding to pre-meiotic and meiotic stages were used to generate mRNA, full-length and sRNA libraries. Data from mRNA-seq and SMRT-seq were used for de novo transcriptome assemblies.  These assemblies were then used along with sRNA data to identify phased-siRNA precursor transcripts and other protein factors that play a role in reproductive phasiRNA pathways. mRNA-seq assembly was performed using “Trinity RNA-Seq assembler”, full-length transcript assembly was prepared using “SMRT-tools” (v2.3) provided by Pacific Biosciences. Phased siRNA precursors were identified using “PHASIS suite” (https://github.com/atulkakrana/PHASIS/wiki), and transcripts sfor protein-coding genes were identified using “Trinotate” (https://trinotate.github.io/).


title: Salt-responsive miRNAs and target genes of Salix matsudana Koidz

status: Public on Jul 06 2018

city: Hangzhou

first: Xiaojiao

last: Han

state: Zhejiang

address: Daqiao Road 73#

department: The Research Institute of Subtropical of Forestry

country: China

institute: Chinese Academy of Forestry

summary: In order to screening the responsive miRNAs and target genes of willow under salt stress, the 30-day-old plants were exposed to the salt solution (100 mmol L-1 NaCl) for 0 h and 2 d. then RNA isolated from root and stem tissues for the same time point were mixed respectively in equal amounts for small RNA (sRNA) sequencing. sRNAs with 16–30 nt were separated from 1 µg total RNA by size fractionation. Subsequently, the selected sRNA fragments were ligated with specialized adaptors to the 5’ and 3’ ends (Illumina) using T4 RNA ligase. Then, the ligated RNAs were reverse transcribed and amplified for sequencing using Illumina Hiseq2500 (LC Sciences, Hangzhou, China). Salt stress-responsive miRNAs were identified by comparing the expression levels of miRNAs between the two libraries. Equal amounts of all 2 RNA samples were mixed together to construct one degradome library, and then sent to Hangzhou LC-Bio Co., Ltd (Hangzhou, China) for sequencing by Illumina Genome Analyzer GA-I (Illumina, San Diego, CA, USA).

overall_design: comparing the sequences between untreated and treated by salt stress

first: Renying

last: Zhuo

first: Yunxing

last: Zhang

first: Dong

last: Xu


title: RNASeq study of testis from migratory bird under four seasonal states

status: Public on Jul 05 2018

city: DELHI

first: AAKANSHA

last: SHARMA

state: DELHI

address: CHATTRA MARG

department: ZOOLOGY

country: India

institute: UNIVERSITY OF DELHI

summary: We report the mRNA found in testis tissue of a migratory bird. The aim of this study was to investigate how the mRNA makeup of tissue varies under different seasonal states.

overall_design: Study of total mRNA from testis under four different seasonal states, using Illumina sequencing.

first: Devraj

last: Singh

first: Aakansha

last: Sharma

first: Subhajit

last: Das


title: Dysregulated circRNAs in plasma from active tuberculosis patients

city: Weifang

first: zhengjun

last: Yi

state: Shandong

address: No.7166, Baotong Xi (Western) Street, Weicheng District, Department of Laboratory Medicine

department: Department of Laboratory Medicine

institute: Weifang Medical University

summary: Role of circRNAs in active tuberculosis (TB) remains unknown. The present study was aimed to determine plasma circRNA expression profile in active TB patients to identify potential biomarker by circRNA microarrays.

overall_design: A total of 32 newly diagnosed active TB patients with a mean age of 36.1±13.4 yr (male/female=17/15) (BC group) were consecutively recruited from Weifang No.2 People’s Hospital. The diagnosis of active TB was based on compatible clinical symptoms, and at least one sputum smear or sputum culture positive. At the same time, 29 age-and-gender matched healthy controls with a mean age of 35.2±12.9 yr (male/female=15/14) (CC group) were enrolled from the staff of Affiliated Hospital of Weifang Medical University and Weifang No.2 People’s Hospital. For the study, all the active TB patients had no history of radiotherapy or chemotherapy before blood collection, and patients were excluded if they had a prior history of TB, a close contact with active TB patient, or other diseases like other infectious disease, cancer or diabetes. Three plasma samples randomly selected from each group (male/female=2/1; BC group including BC1, BC2 and BC10; CC group including CC6, CC7 and CC8) were applied for microarray analysis and all of the samples were used for further qRT-PCR validation.

first: Zhengjun

first: Yurong

last: Fu

first: Kunshan

last: gao

first: Ruifang

last: Li


title: Characterization of the accessible genome in the human malaria parasite Plasmodium falciparum

city: Granada

first: Jose

middle: Luis

last: Ruiz Rodriguez

state: Granada

address: Avda. del Conocimiento 17. P. T. Ciencias de la Salud

country: Spain

institute: IPBLN-CSIC

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
Background: Human malaria is a major cause of disease and poverty in developing countries being P. falciparum the most deadly of malaria parasites. To successfully develop and adapt within hosts, P. falciparum undergoes drastic switches in chromatin structure and gene expression, but the identity and function of regulatory elements driving these events remain poorly understood. In this work, we performed genome-wide profiling of chromatin accessibility in two culture-adapted subclones and four developmental stages during the intraerythrocytic development by the Assay for Transposase-Accessible Chromatin by sequencing (ATAC-seq).
Results: ATAC Tn5 hypersensitivity sites (THSSs) localize preferentially at known Transcriptional Start Sites (TSSs). Chromatin accessibility by ATAC-seq is predictive of active transcription and of the levels of histone marks H3K9ac and H3K4me3 in a quantitative manner. Our assay allows us to characterize novel regulatory regions including TSS and enhancers-like elements. We show that the dynamics in the accessible chromatin profile matches temporal differences in gene expression during development, and that gene activation occurs concomitantly to DNA binding events. Motif analysis of stage-specific ATAC-seq footprints predicts the in vivo binding sites and function of a number of ApiAP2 transcription factors. Finally, the mutually exclusive expression and epigenetic switch of several clonally variant genes associates with a differential enrichment of ATAC-seq signal at their promoters.
Conclusion: Overall, this study allows us to characterize at a genome-wide level cis-regulatory regions likely to play an essential function in the developmental transitions and in clonally variant gene expression in P. falciparum.

overall_design: Genome-wide profiling of chromatin accessibility (ATAC-seq) in two P. falciparum culture-adapted subclones and four developmental stages during the intraerythrocytic development.

last: Ruiz

first: Juan

middle: J

last: Tena

first: Cristina

last: Bancells

first: Alfred

last: Cortés

first: José

last: Gómez-Skarmeta

first: Elena

last: Gomez-Diaz


title: Analysis of Wild Type and Leptin-overexpressing Pig PBMC Transcriptomes

city: changsha

first: junchen

last: chen

address: 87 Xiangya Road, Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan, P. R. China.

department: 1Department of Dermatology, Xiangya Hospital, Central South University

summary:
Purpose: To find the difference between leptin-overexpressing and wt pig.
Methods: Peripheral blood mononuclear cells (PBMCs) mRNA profiles of 6-month-old wild-type (WT) and leptin-overexpressing pig were generated by deep sequencing. Sequencing libraries were constructed according to the protocol for the Illumina TruSeq Sample preparation kit. Sequencing was performed on the Illumina X Ten sequencer. Library construction and sequencing were performed at the Genergy Biotech Co., Ltd. (Shanghai).
Results: RNA-seq was performed to detect the transcriptomic changes in PBMCs in the transgenic leptin pigs. With 2-folds change and p<0.05 threshold, we found that 84 transcripts were upregulated, and 124 transcripts were downregulated in the transgenic leptin pigs.
Conclusions: The leptin-overexpressing pigs exhibited remarkable resemblance to human SLE in multiple aspects of the disease.

overall_design: PBMC mRNA profiles of 6-month-old wild type (WT) and leptin-overexpressing pig were generated by deep sequencing.

first: Xiang

last: Chen

first: Hongjiang

last: Wei


title: Development and characterization of a clinically relevant model of breast cancer brain metastasis

status: Public on Jul 03 2018

city: Heidelberg

first: Richard

middle: P

last: Redvers

state: Victoria

address: 45 Studley Road

department: Translational Breast Cancer Program

country: Australia

institute: ONJCRI

summary: Breast cancer brain metastasis remains largely incurable. While several mouse models have been developed to investigate the genes and mechanisms regulating breast cancer brain metastasis, these models often lack clinical relevance since they require the use of immune-compromised mice and/or are poorly metastatic to brain from the mammary gland. We describe the development and characterization of an aggressive brain metastatic variant of the 4T1 syngeneic model (4T1Br4) that spontaneously metastasises to lung, bone and brain but is selectively more metastatic to the brain from the mammary gland than parental 4T1 tumors. The 4T1Br4 model will provide a clinically relevant tool to evaluate novel therapies against brain metastasis.

overall_design: Tumor cells were FACS isolated from biological replicate primary tumors, including 3 x 'BrMet' brain-metastatic tumors, 11 x 'HighMet' highly metastatic tumors and 3 x 'NonMet' non-metastatic tumors for gene level expression profiling on Affymetrix GeneChip Mouse Exon 1.0 ST Arrays

first: Robin

last: Anderson

first: Normand

last: Pouliot


title: Next Generation Sequencing Facilitates Quantitative Analysis of ltmA mutant and wild-type strains Transcriptomes in Mycobacterium smegmatis

status: Public on Jul 02 2018

city: Wuhan

first: Weihui

address: 1 str Sizisan

institute: Huazhong Agricultural University

summary: Compare the gene expression difference between ltmA knockout strains and wild-type strains by RNA sequencing in Mycobacterium smegmatis. The goal of this study is that detection LtmA acts as a transcriptional factor and regulates the target genes expression.

overall_design: Two samples in triplicate are analyzed. The control sample is the wild-type strains in Mycobacterium smegmatis.

first: Zhengguo

last: He


title: Expression data from human ovarian cancer cell line

status: Public on Jul 04 2018

city: Xuzhou

first: ning

last: sheng

state: Jiangsu

address: Shanghai road

institute: JSNU

summary:
LASS2 was used to identified as a novel suppressor in cancer development and progression. We explored roles of LASS2 in ovarian cancer invasion and metastasis. Lenti-LASS2 and Lenti-vector cells were constructed in 3AO cells through a lentiviral vector system.
We preformed global gene expression analysis between Lenti-LASS2 and Lenti-vector cells in accordance with standard Aglient protocols to explore differentially expressed genes and signaling pathways involved by LASS2 overexpression.

overall_design: RNA was isolated from Lenti-vector and Lenti-LASS2 cells and hybridized on Agilent microarrays. The two groups were as follows: Lenti-LASS2 cells and Lenti-vector cells.

first: Ning

last: Sheng

first: Shaohua

last: Fan


title: Microarray expression data from iSOD2 adapted livers

city: La Jolla

first: Gerald

last: Shadel

state: CA

address: 10010 N Torrey Pines Road MCBL-C

department: Biomedical Sciences

institute: Salk Institute for Biological Sciences

summary:
Transient mitochondrial stress can promote beneficial physiological responses and longevity, termed "mitohormesis." To interrogate mitohormetic pathways in mammals, we generated mice in which mitochondrial superoxide dismutase 2 (SOD2) can be knocked-down in an inducible and reversible manner (iSOD2-KD). Depleting SOD2 only during embryonic development did not cause post-natal lethality, allowing us to probe adaptive responses to mitochondrial oxidant stress in adult mice. Liver from adapted mice had increased mitochondrial biogenesis and antioxidant gene expression and fewer reactive oxygen species. Gene expression analysis implicated non- canonical activation of the Nrf2 antioxidant and PPAR-PGC-1 mitochondrial signaling pathways in this response. Transient SOD2 knock-down in embryonic fibroblasts from iSOD2-KD mice also resulted in adaptive mitochondrial changes, enhanced antioxidant capacity, and resistance to a subsequent oxidant challenge. We propose that mitohormesis in response to mitochondrial oxidative stress in mice involves sustained basal activation of mitochondrial and antioxidant signaling pathways to establish a heightened antioxidant state.
We used microarrays to determine differentially expressed genes in mouse liver after transient SOD2 knock-down during mouse embryogenesis.

overall_design: SOD2 was knocked down during days 0-12.5e in utero. At four weeks of age, animals were sacrificed and microarray analysis was conducted on mouse liver. Three iSOD2 adapted liver samples from shRNA 1 and three samples from shRNA 2 were analyzed. Four total rtTA only littermate controls were analyzed, including 3 from the shRNA 2 cohort and 1 from the shRNA 1 cohort. Approximately 1 mg of RNA was sent to the Yale Center for Genome Analysis for microarray analysis on Affymetrix Mouse 2.0st array plates.

first: Carly

middle: S

last: Cox


title: De novo transcriptome assembly and characterization of medicinal plant Lithospermum officinale to discover putative genes involved in specialized metabolites biosynthesis

status: Public on Jul 01 2018

city: Chiba

first: Mami

last: Yamazaki

address: Inohana 1-8-1, Chuo-ku

department: Graduate School of Pharmaceutical Sciences

country: Japan

institute: Chiba University

summary: In this study, we have performed Illumina based RNA sequencing to characterize the transcriptome and expression profiles of genes expressed in 3 tissues of L. officinale. RNA sequencing and de novo transcriptome assembly of L. officinale  resulted in a total of 77,047 unigenes with N50 value as 1524 bps. KEGG pathway and GO enrichment analysis using highly expressed unigenes across three tissues showed active secondary metabolic processes specifically enriched to the root of L. officinale. Expression of identified candidate unigenes for specialized metabolites biosynthesis were consistent with previous reports on accumulation of metabolites across different tissues of L. officinale.

overall_design: Examination of 3 tissues of Lithospermum offcinale using Illumina Hi Seq 2000 platform, paired-end, average sequence length as 101bps

first: Kazuki

last: Saito

first: Hideyuki

last: Suzuki

first: Michimi

last: Nakamura

first: Megha

last: Rai

first: Yohei

last: Shimizu

first: Taiki

last: Nakaya

first: Amit


title: Analysis of human macrophage splice variants

status: Public on Jun 30 2018

city: Chicago

first: Michael

last: Carrithers

state: IL

address: 912 S Wood

department: Neurology

institute: University of Illinois

summary:
gene expression and alternative splicing analysis in human macrophages versus dorsal root ganglia and heart
the focus was on alternatively spliced channel proteins in macrophages versus those expressed in excitable tissues

overall_design: HTA 2.0 (Affymetrix) analysis of alternatively spliced genes in human macrophages


title: Early metazoan cell type diversity and the evolution of multicellular gene regulation

city: Barcelona

first: Arnau

last: Sebe-Pedros

address: Dr. Aiguader 88

department: Systems Biology

institute: Centre for Genomic Regulation

summary: We performed single-cell transcriptome analysis (using MARS-seq) in the sponge Amphimedon queenslandica (adult and larval stages), in the ctenophore Mnemiopsis leidyi (adult stage), and in the placozoan Trichoplax adhaerens (adult stage). Additionally we performed bulk iChIP experiments (2 replicates of each experiment) using antibodies against H3K4me3 and H3K4me2 in adult Mnemiopsis leidyi and adult Trichoplax adhaerens.

sample_organism:
Trichoplax adhaerens
Mnemiopsis leidyi
Amphimedon queenslandica

overall_design: Multiple animals (20-25) were dissociated and pooled before sorting single-cells for scRNAseq. 200,000 cells were used in bulk iChIP experiments.

first: Amos

last: Tanay


title: ArrayCGH on a cohort of pediatric T-ALL cases characterized by TCRAD-MYC translocation

city: Gent

first: Gloria

last: Milani

address: Pintelaan 185

country: Belgium

institute: Gent University

type: Genome variation profiling by genome tiling array

summary:
ArrayCGH was performed on a cohort of 25 specimens collected from children with newly diagnosed T-ALL characterized by TCRAD-MYC translocation
ArrayCGH analyses were perfomed to study genomic aberrations occurring in the rare subgroup of TCRAD-MYC rearranged T-ALL

overall_design: 25 DNA samples from pediatric T-ALL patients at diagnosis were analyzed on the Agilent SurePrint G3 Human CGH microarrays (G4449A, design ID: 022060). For every sample, the gender-matched control was labeled in parallel and hybridized together

first: Pieter

last: Van Vlierberghe


title: Genome location dictates the transcriptional response to sub-inhibitory concentrations of PolC-inhibitors in Clostridium difficile

city: Leiden

first: Ilse

middle: Michelle

last: Boekhoud

state: Zuid-Holland

address: Albinusdreef 2

department: Medical Microbiology

country: Netherlands

institute: Leiden University Medical Centre

summary: Clostridium difficile is a potentially lethal gut pathogen that causes nosocomial and community acquired infections. Limited treatment options and reports of reduced susceptibility to current treatment emphasize the necessity for novel antimicrobials. The DNA-polymerase of gram-positive organisms is an attractive target for the development of antimicrobials.  ACX362E (N2-(3,4-Dichlorobenzyl)-7-(2-[1-morpholinyl]ethyl)guanine; MorE-DCBG) is a DNA polymerase inhibitor in pre-clinical development as a novel therapeutic against C. difficile infection. This synthetic purine shows preferential activity against C. difficile Pol IIIC over those of other organisms in vitro and is effective in an animal model of C. difficile infection. In this study we have determined its efficacy against a large collection of clinical isolates. At concentrations below the minimal inhibitory concentration, the presumed slowing (or stalling) of replication forks due to ACX362E  leads to a growth defect. We have determined the transcriptional response of C. difficile to replication inhibition and observed an overrepresentation of up-regulated genes near the origin of replication in the presence of PolC-inhibitors, but not when cells were subjected to sub-inhibitory concentrations of other antibiotics. This phenomenon can be explained by a gene dosage shift, as we observed a concomitant increase in the ratio between origin-proximal versus terminus-proximal gene copy number upon exposure to PolC-inhibitors. Moreover, we show that certain genes differentially regulated under PolC-inhibition are controlled by the origin-proximal general stress response regulator sigma factor B.  Together, these data suggest that genome location both directly and indirectly determines the transcriptional response to replication inhibition in C. difficile

overall_design: Transcriptional changes resulting from treatment with polC inhibitors ACX362E or HPUra were analysed with RNA-seq. Per sample, three biological replicates were included in the RNA-seq experiment. In case of insufficient reads, the sample was re-run on another flow cell to reach satisfactory quantities (≥ 20 M).

first: E

last: van Eijk

first: I

first: W

middle: K

last: Smits


title: Development of gene expression signatures for lenalidomide treatement on megakaryocyte

city: Fukuoka

first: Taro

last: Tochigi

address: Maidashi

institute: Kyushu university

summary: To clarify the machinery how lenalidomide inhibit proplatelet formation of megakaryocytes, we performed transcriptome analysis of megakaryocytes derived from human hematopoietic stem/progenitor cells in the liquid culture system with or without lenalidomide. Differentially expressed genes were comprehensively evaluated by gene set enrichment analysis. Untreated megakaryocytes showed the estradiol-responded gene expression signatures, whereas the lenalidomide-treated megakaryocytes did not. Furthermore, we performed a rescue strategy with exogenous estradiol, confirming that lenalidomide-induced inhibition of proplatelet formation should be due to the deficiency of endogenous estradiol action in megakaryocytes.

overall_design: Lenalidomide treatment-induced difference in gene expression profile of human megakaryocytes were evaluated. Megakaryocytes were generated from hematopoietic stem/progenitor cells of 4 individual healthy volunteers in the presence or absence of 10 µM lenalidomide.

first: Yoshikane

last: Kikushige

first: Toshihiro

last: Miyamoto

first: Kiwamu

last: Hatakeyama

first: Teppei

last: Sakoda

first: Koji

last: Kato

first: Katsuto

last: Takenaka

first: Takahiro

last: Maeda

first: Takumi

last: Ito

first: Hiroshi

last: Handa

first: Koichi

last: Akashi


title: Commensal microbes drive the generation of large numbers of bone marrow plasma cells

city: Philadelphia

first: Joel

last: Wilmore

state: PA

address: 3620 Hamilton Walk

institute: University of Pennsylvania

summary: The mechanisms whereby enteric pathogens and microbes induce systemic antibody responses remain obscure. In contrast to accepted models, we show that commensal microbes have a dramatic impact on the bone marrow (BM) plasma cell pool. Unlike standard vendor mice, in mice reared in our colony the majority of long-lived BM plasma cells secreted IgA antibodies. Exposing vendor mice to a unique microflora or Helicobacter sp. led to the generation of IgA-secreting BM cells, while also inducing increases in serum IgA antibodies enriched for binding to several commensal bacterial taxa. Moreover, BM IgA-secreting plasma cells exhibited a common clonal ancestry with intestinal IgA+ plasma cells, and both populations possessed unique gene expression signatures compared to other long-lived BM plasma cells. We conclude that commensal microbes overtly influence the BM plasma cell pool, and suggest that select commensal microbes can facilitate the induction of systemic humoral immunity.

overall_design: Cells were sorted from B6.BlimpGFP reporter mice isolated from the bone marrow, lamina propria, or the spleen of naïve mice housed under SPF conditions. Plasma cells from the bone marrow were sorted based on viability, Dump-(CD4, CD8, F4/80, Ter119), IgD-, CD138+, Blimp+, and then either IgA+, IgM+, or IgA-IgM-. Plasma cells from the gut were sorted based on a surface phenotype of Dump-, IgD-, B220-, Blimp+, and IgA+. The cells were sorted two times to ensure greater purity. Replicate numbers for the plasma cell samples indicate the cells came from the same mouse. The follicular B cells were sorted from different mice from the spleen and had a phenotype of CD19+, B220+, CD23+, CD21-, and IgD+.

middle: R

first: Brian

middle: T

last: Gaudette

first: David

last: Allman


title: P. aeruginosa PAO1 wildtype versus PA1226 mutant

city: Honolulu

first: Tung

last: Hoang

state: HI

address: 1800 East-West Road

department: Microbiology

institute: University of Hawaii at Manoa

summary: In this study, we present a novel transcriptional regulator, PA1226, which modulates biofilm formation and virulence in P. aeruginosa. Mutation in this regulator abolished the ability of P. aeruginosa to produce biofilm in vitro, without any effect on the planktonic growth. This regulator is essential to the in vivo fitness and pathogenesis in both Drosophila melanogaster and BALB/c mouse lung infection models. Transcriptome analysis revealed that PA1226 regulates many essential virulence genes/pathways, including alginate, pili, and LPS biosynthesis.

overall_design: PAO1 wildtype versus PA1226 mutant both grown in LB media. cDNA samples were hybridized onto P. aeruginosa 70mer duplicate array (GEO accession number GPL10633).

first: Yun

last: Heacock-Kang


title: Chemotherapy modulates intestinal immune gene expression in piglets including surfactant protein-D and DMBT1

city: odense

first: mads

last: thomassen

address: soender boulevard 29

country: Denmark

institute: odense university hospital

summary: Cytotoxic therapy leads to marked changes in intestinal structure, function, immunity and microbiota. Information about chemotherapy-induced intestinal gene expression may provide insights into the mechanisms underlying gut toxicity, and help to identify biomarkers and targets for intervention. We investigated jejunal tissue from piglets subjected to two different, clinically-relevant chemotherapy regimens, 1) busulfan plus cyclophosphamide (BUCY) and 2) doxorubicin (DOX). Gene expression analysis identified 1328 and 594 differentially expressed genes in the BUCY and DOX pigs, compared with their respective controls. Similar changes in expression patterns across BUCY and DOX piglets were found for 137 genes (95 genes repressed and 42 induced).  Selected genes of potential biological significance were confirmed by real-time polymerase chain reaction. Key innate defense molecules, including surfactant protein-D (SP-D), deleted in malignant brain tumors 1 (DMBT-1) and peptidoglycan recognition protein 2 (PGLYRP2) were among the up-regulated genes for both chemotherapy treatments. Based on the results from the two different treatments, we conclude that chemotherapy induces reduced intestinal adaptive immunity while innate immune functions involved in surveillance, protection and homeostasis of mucosal surfaces are up-regulated. The results may be of value to understand monitor and prevent chemotherapy-induced intestinal mucositis by dietary or medical interventions.

overall_design: Twenty-two three day-old crossbred SPF piglets (Large White × Danish Landrace) were used for the experiments. All pigs were delivered to our research facilities after having suckled their mother from birth. The pigs were housed in individual cages and kept in an environmentally controlled room (12/12 light/dark rhythm, ~30 °C).  The studies were carried out in accordance with the recommendations in the Guide for the Care and Use of Laboratory Animals of the National Institutes of Health. The protocol was approved by the National Committee on Animal Experimentation (approval number: 2010/561-1760). The manuscript was prepared in accordance to the ARRIVE guidelines for reporting animal research (32).   The tissues used for the analyses originated from two separate studies on chemotherapy-induced GI toxicity in piglets. One experiment was based on treatment with a combination of busulfan and cyclophosphamide (BUCY) (26) while another experiment was based on a single dose of the topoisomerase II inhibitor, doxorubicin (DOX) (33). For all details regarding the clinical condition of the piglets and organ and physiological responses to chemotherapy, we refer the reader to these publications (26, 33). Prior to cytotoxic treatment pigs were anesthetized and fitted with orogastric tubes (6F Portex, Kent, UK) and a catheter (Tygon OD 0.070 ID 0.040 Saint-Gobain Performance Plastics, France) inserted in the external jugular vein for blood sampling and administration of drugs and fluids. Surgery was performed under zoletil mix anesthesia (i.m. tiletamine, 0.28 mg/kg; zolazepam, 0.28 mg/kg; xylazine, 0.56 mg/kg; ketamine, 0.56 mg/kg; butorphanol, 0.11 mg/kg). All animals were anesthetized and euthanized by an intracardial injection of sodium pentobarbital (200 mg/kg). Chemotherapeutic drugs were administered intravenously (i.v.) via the jugular vein catheter.

first: Mads

last: Thomassen


title: Sequencing quantitative analysis of altered expression and Prognostic impact of LncRNAs RVT1 knockdown in glioblastoma cell lines U87

city: nanjing

first: chen

last: wanghao

state: jiangsu

address: Ding Jiaqiao 87th

department: School of Medicine

institute: southeast university

summary: Glioblastoma multiforme (GBM) is the most malignant and lethal primary brain cancer. Despite advances in surgical resection followed by radiation and chemotherapy, the prognosis for patients with GBM remains dismal. LncRNAs regulate tumorigenesis and cancer metastasis by silencing tumor suppressors or activating oncogenes via different mechanisms, including epigenetic modification, alternative splicing, RNA decay, and post-translational modification.

overall_design: We performed an Aglient high-throughput microarray analysis of sh-NC and sh-RVT1 U87 cells. In total, many genes were differentially expressed after the knockdown of RVT1.

first: Wanghao

last: Chen

first: Fan

last: Lin

first: Lukui


title: Hepatic transcriptome of wildtype and Cugbp1 knockout mouse neonates.

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

summary: We characterize the hepatic transcriptome of wildtype and Cugpb1 knockout mice at day 3 of life using the Agilent Whole Mouse Genome Oligo Microarray, focusing on the role of Cugbp1 in the differentiation of hepatic stem cells into hepatocytes.

overall_design: Transcriptomic profiles were obtained for wildtype and Cugbp1 mice in triplicate using the Agilent Whole Mouse Genome Oligo Microarray.

first: Nikolai

last: Timchenko


title: microRNA expression profiling of Drosophila melanogaster peripheral sensory neurons.

city: Washington,DC

first: Nino

last: Gustavo

state: Washington,DC,

address: Sheikh Zayed Campus,111 Michigan Avenue,

department: Center for Precision Medicine and Genomics Research

institute: Childrens National Hospital

summary: While microRNAs (miRNAs) have recently emerged as critical post-transcriptional modulators of gene expression in neuronal development, very little is known regarding the roles of miRNA-mediated regulation in the specification of cell-type specific dendritic complexity. The dendritic arborization (da) sensory neurons of the Drosophila PNS offer an excellent model system for elucidating the molecular mechanisms governing class specific dendrite morphogenesis and for exploring miRNA-mediated control of this process. To facilitate functional analyses of miRNA regulation in da neurons, we have conducted whole-genome miRNA expression profiling as well as mRNA expression profiling of three distinct classes of da neurons, thereby generating a comprehensive molecular gene expression signature within these individual subclasses of da neurons. To further validate the role of these expressed miRNAs in directing dendritic architecture, we conducted a genome-wide UAS-miRNA phenotypic screen using live-image confocal microscopy followed by semi-automated neurometric quantification, to directly assess the effect of over/mis-expression of individual and clustered miRNAs on neurons of varying dendritic complexity. Through this approach, we have identified numerous miRNAs with previously unknown functions in dendritic development. Gain-of-function and loss-of-function analyses revealed an endogenous role miR-2b and miR-13b (members of the K-box family) and miR-12/283/304 in dendritic patterning in da neuron subclasses. Moreover, using an integrative bioinformatic analysis approach involving inverse correlation between miRNA and mRNA expression profiling data in combination with existing target prediction algorithms, we have identified putative target of these miRNAs in regulating da neuron dendritic development. Validation of these predicted miRNA-target relationships via phenotypic analyses as well as QPCR, revealed the regulatory effect of these molecules in restricting dendritic branching in da neurons.

overall_design: miRNA expression profiling of Class I, Class III and Class IV da neurons, isolated via magnetic bead sorting method (using protocols as described in Iyer et al., 2009), was performed at the third instar larval stage of development. 40-50 age-matched third instar larvae expressing mCD8::GFP under the control of the GAL80ppk.1.9; GAL4221 (CI), GAL80ppk.1.9, GAL4ppk,(CIII) or GAL4ppk.1.9 (CIV)  drivers was used for isolating class specific miRNAs. The microarray was performed in a two color platform using the Hy3 as the test (Class I/Class III/ Class IV miRNAs) and total RNA extracted from the whole larval body as the Control (Hy5). The microarray analysis was performed in triplicates.

first: Srividya

last: Chandramouli Iyer

first: Surajit

last: Bhattacharya

first: Daniel

middle: N

last: Cox


title: Superiority of spatially fractionated over broad beam synchrotron radiotherapy

city: LA TRONCHE

first: Michèle

last: EL ATIFI

address: Chemin fortuné ferrini

country: France

institute: INSERM

summary: Transcriptomic response of tumoral and normal brain tissue, treated with the MRT irradiation or  the BB irradiation, after 6 h, 48 h, 8 days, 15 days, using Affymetrix GeneChip® Rat 230_ 2.

overall_design: The orthotopic tumor-bearing rats were either treated with the MRT or BB radiation (MRT-treated tumors or BB-treated tumors), either untreated (Untreated Tumors). In the same way, the hemispheres without tumor received or not, irradiation treatment (MRT-Contralateral, BB-Contralateral or Untreated Contralateral).  At different times after treatment, 6 hours, 48 hours, 8 days and 15 days, the tumors and their contralateral regions were resected and analysed for their transcriptomic response.

first: Audrey

last: Bouchet

first: Elke

last: Bräuer-Krisch

first: Yolanda

last: Prezado

last: El Atifi

first: Léonid

last: Rogalev

first: Céline

last: Le Clec’h

first: Jean

last: Laissue

first: Laurent

last: Pelletier

first: Géraldine

last: Le Duc


title: Analysis of Claudin 18 deficiency in lung epithelial type 2 cells.

city: Los Angeles

first: Nyam-Osor

last: Chimge

address: 2250 Alcazar street

department: IGM

institute: USC

summary:
Constitutive knockdown of Cldn18 in mice showed lung enlargement and increased proliferation of alveolar epithelial type II (AT2) cells.
Lung AT2 cells were isolated from wild-type and knockout mice and subjected to microarray analysis. Results provide insight into the role of Cldn18 in controlling organ size and stem progenitor cells.

overall_design: Cldn18-/- mice were obtained by crossing Cldn18 floxed mice with CMV-Cre mice.  Deletion of exons 2 and 3 of Cldn18 by Cre/loxP recombination resulted in truncation of both lung- (Cldn18.1) and stomach-specific (Cldn18.2) isoforms in Cldn18-/- mice.


title: Expression data from Arabidopsis wild-type, DUF761-1 knock-out mutant and DUF761-1 overexpression strains

city: Guiyang

first: Xiaozhen

last: Huang

state: Guizhou

address: South campus of Guizhou University, Huaxi, Guiyang

institute: Guizhou University

summary:
Expression data from two weeks old Arabidopsis wild-type (Nössen:NO) and at4g16790 (here renamed DUF761-1) knock-out mutant RATM11-0975-1_H (here named duf761-1); Expression data from two weeks old Arabidopsis wild-type (Columbia-0) and transgenic plant overexpressing DUF761-1 (at4g16790) plants(here named OE6)
Microarray assays can facilitate elucidation of cellular processes and gene network functions in the processes of plant growth and development. To gain further insight into the potential molecular role of the at4g16790 gene (here named DUF761-1), we performed Affymetrix whole-genome microarray analysis (http://www.affymetrix.com/) on Nössen and duf761-1plants, and on Columbia-0 and OE6 plants, to compare their genome-wide expression profiles under 22 °C.
The differently expressed genes revealed by transcriptional profiling  indicate that DUF761-1 may involve in  plant cell wall biology and defense response of Arabidopsis.

overall_design: Total RNAs were extracted using the Plant RNA Prep Kit (Qiagen, Hilden, Germany) from 2-week-old seedlings of the wild-type (NO) and duf761-1, and from the Col-0 and OE6, grown on 1/2 MS medium containing 2% sucrose at 22˚C under a 16-h light/8-h dark photoperiod at 100 μmol m–2 s–1. 6μg of total RNA was used to synthesize biotin-labeled cDNA, which was then hybridized with the ATH1 oligonucleotide chips as instructed by the manufacturer (Affymetrix).


status: Public on Jun 29 2018

city: Leipzig

first: Kristin

last: Reiche

address: Perlickstr. 1

department: Diagnostics

country: Germany

institute: Fraunhofer Institute for Cell Therapy and Immunology

summary: Expression and differential expression analysis of milk samples from healthy and diseased diary cows. Diseases were grouped by their occurrence in the mammary gland or extra-mammary. Furthermore, the diseases were classified by their severity. All cows were examined thoroughly by the dairy herd manager, trained staff, or a veterinarian. Expression and differential expression was assessed by using the Affymetrix Bovine Genome Array (GPL2112). Control animals (2-4 years old, 1st to 3th lactation, one animal 4th and one 8th lactation) showed no clinical signs of disease and had no abnormalities in the udder or milk. Their somatic cell count (SCC) was less than 100,000 cells/ml milk. Most of the control samples were taken during early lactation (10-100 days post-partum, dpp). Diseased cows were in their 1st to 8th lactation within 10-220 dpp.

overall_design: We analyzed 6 biological replicates each from milk samples from healthy diary cows, diary cows with mastitis and diary cows with endometritis.

first: K.

last: Zoldan

first: J.

last: Schneider

first: T.

last: Moellner

first: C.

last: Fueldner

last: Knauer

first: M.

last: Fuerll

first: A.

last: Starke

last: Specht

last: Hackermueller

first: S.

last: Kalkhof

last: von Bergen

first: U.

last: Bergfeld

first: R.

last: Fischer

last: Pache

last: Lehmann


title: VqmR sRNA target identification

status: Public on Jun 25 2018

city: Jena

first: Kathrin

last: Fröhlich

state: Thuringia

address: Winzerlaer Straße 2

department: Fakultät für Biowissenschaften, Bacterial RNA Biology

institute: Friedrich-Schiller-Universität Jena

summary: In this study, we determined the target spectrum of the VqmR sRNA via vqmR pulse-expression followed by RNA-sequencing.

overall_design: mRNA profiles of V. cholerae dvqmR strains carrying pBAD-ctr (empty vector control) or pBAD-vqmR (inducible sRNA expression vector). The bacteria were grown to exponential phase, expression of vqmR was induced by addition of L-arabinose, and RNA-samples were taken 15 minutes after induction. Three independent biological replicates for each condition are provided.

first: Roman

last: Herzog

first: Nikolai

last: Peschek

first: Kilian

last: Schumacher

first: Kai

last: Papenfort


title: Mesenchymal stem cells  gene expression on liver after ischemia-reperfusion injury.

city: Hong Kong

first: Kwong Wai

last: CHOY

address: Hong Kong

department: O and G

country: Hong Kong

institute: CUHK

summary: Analysis of topically applied adipose tissue deirved mesenchymal stem cells (ATSC) on the surface of liver with ischemia-reperfusion injury (IRI). Histology showed that topically applied ATSC on IRI liver surface gave a faster healing process and regeneration rate. Resutls provides insight of the expression pattern between ATSC topically applied on IRI and non-IRI liver  with reference of basal expression of the ATSC in in-vitro culture

overall_design: Totally 8 samples were analyzed. 3 samples from ATSC on IRI liver; 4 samples from ATSC on non-IRI liver; 1 sample from ATSC in in-vitro cutlure. Agilent Whole Rat Genome Microarray was used according to manufacturer protocol.

first: P

last: Lam


title: Effect of arsenate and arsenite on Lysinibacillus sp. B2A1 transcriptome

city: Tainan

first: Jiin-Shuh

last: Jean

address: 1st University Road

department: Department of Earth Science

country: Taiwan

institute: National Cheng Kung University

summary: RNA-seq based indentification of arsenic responsive genes which might provide resistance and are involved

overall_design: We used RNA-seq to understand the Lysinibacillus sp. B2A1 transcriptome differences under the 3h exposure of 50mM As(V) and 5mM As(III); No arsenic exposure was used as control.

first: Jagat

last: Rathod


title: Overexpression of miR-155 alters the hierarchy of gene master regulators in the adenocarcinomic human alveolar basal epithelial cell line A549

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

summary: Several reports indicated that miR155 is upregulated in many cancer forms, including lung adenocarcinoma. Studies perfomed in Calin's lab (e.g. Van Roosbroeck et al., Clin Cancer Res, doi: 10.1158/1078-0432.CCR-16-1025) demonstrated that miR-155 induces resistance to multiple chemotherapeutic agents. We hypothesize that the induced resistance is related to the rearrangement of cellular gene hierarchy. In previous papers (Iacobas & Iacobas, Cancer & Oncol Res DOI:10.13189/cor.2017.050301; Iacobas et al., Oncotarget doi: 10.18632/oncotarget.23417) we proved that cancer nodules and surrounding normal tissue are governed by different gene master regulators (GMRs) and that expression manipulation of a cancer GMR can selectively destroy cancer cells with minimal effects on the normal ones. GMR is defined as a coding or non-coding transcript whose strictly controled abundance by the cell homeostatic mechanisms regulates most major cell functional pathways. Here, we determined how the gene hierarchy in the standard adenocarcinomic human alveolar basal epithelial cell line A549 is altered by overexpressing miR155.

overall_design: One condition, 4 replicas

first: Sanda

first: Katrien

last: Van Roosbroeck

first: George

last: Calin


title: The APETALA2-like transcription factor SUPERNUMERARY BRACT controls rice seed shattering and seed size

city: Beijing

first: Ma

last: Xin

state: --- Select a state ---

address: 2 Yuanmingyuan West Road, Haidian District, Beijing, China, 2 Yuanmingyuan West Road, Haidian District, Beijing, China

institute: China Agricultural University

summary: The APETALA2-like transcription factor SUPERNUMERARY BRACT confers seed shattering by positively regulating qSH1 and SH5, while altering seed size by modulating longitudinal cell elongation in rice glumes.

overall_design: Total RNA was isolated from development panicles of the wild type YIL100 and the ssh1 mutant, in triplicate, using Illumina system Hiseq2500.

first: Lu

middle: B

last: Tan


title: Colorectal cancer initiation site

status: Public on Jun 18 2018

city: Singapore

first: Peh Yean

last: Cheah

address: 20 College Road

department: Colorectal Surgery

country: Singapore

institute: Singapore General Hospital

summary:
The role of stem cells in solid tumors remains controversial. In colorectal cancers (CRC), this is complicated by the conflicting ‘top-down’ or ‘bottom-up’ hypothesis of cancer initiation. We profiled the expressions of genes from the top (T) and bottom (B) fractions of the crypt in morphologically normal-appearing colonic mucosa (M) and contrasted this to that of matched mucosa adjacent to tumors (MT) in twenty three sporadic CRC patients. In thirteen patients, the genetic distance (M-MT) between the B fractions is smaller than the distance between the T fractions indicating that the expressions of significant genes diverge further in the top fractions (B<T). In the remaining ten patients, the reverse is observed (B>T).
Taking genetic divergence as an intermediate endpoint, the data indicates that it is equally likely that CRC initiates from ‘top-down’ via dedifferentiated colonocytes or ‘bottom-up’ via dysregulated intestinal stem cells. This has important ramification for subsequent therapeutic considerations.

overall_design: Total RNA from 23 sporadic CRC patients matched mucosa (M) and mucosa next to tumor (MT) top and bottom crypt fractions were profiled with Affymetrix GeneChip human gene 1.0 ST array. The genetic distance between M and MT  (M-MT) for 80 significantly differentially expressed genes were calculated for both top and bottom fractions. The genetic distance  (M-MT) for the top (T) fractions were compared to  the bottom (B) fractions for every patient to decide whether the divergence is greater in the bottom fraction (B >T) or top (B<T).

first: Cheah

last: Yean

first: Hong

last: Yi


title: Calcipotriol vs. calcitriol in hepatocellular gene expression

status: Public on Jun 14 2018

city: Frankfurt am Main

first: Christian

middle: M

last: Lange

address: Theodor-Stern-Kai 7

department: Department of Medicine 1

institute: Goethe University Hospital Frankfurt

summary: We aimed to explore the potential and mechanism of calcipotriol to regulate the hepatocellular transcriptome in comparison to calcitriol.

overall_design: Human hepatoma cell lines (Huh-7.5) were treated with calcitriol or calcipotriol followed by RNA isolation, cDNA generation and fragmentation, and hybridization to GeneChip Human Gene 1.0 ST arrays (Affymetrix).

first: Claudia

last: Döring

first: Maged

last: Saleh


title: Waterborne exposure of adult zebrafish to silver nanoparticles and ionic silver results in silver accumulation and effects at cellular and molecular levels

status: Public on Jun 12 2018

city: Leioa

first: José María

last: Lacave

state: Bizkaia

address: Sarriena s/n

department: Zoology and Animal Cell Biology

institute: University of the Basque Country

summary: Effects of silver nanoparticles (Ag NPs) on freshwater species have been reported in several studies, but there is not information on the potential long-term consequences of a previous exposure. In this work, we investigated the long-term effects of maltose-coated Ag NPs (20 nm) and of ionic silver (10 µg/L) after 21 days of exposure and at 6 months post-exposure (mpe) in adult zebrafish. Exposure resulted in significant silver accumulation in the whole body of fish exposed to ionic silver, but not in those exposed to Ag NPs. However, autometallography revealed metal accumulation in the liver and intestine of fish treated with the two silver forms and especially in the intestine of fish exposed to Ag NPs. X-ray microanalysis showed the presence of silver in gills, liver and intestine and of Ag NPs in gill and liver cells. Inflammation and hyperplasia were evident in the gills after both treatments and these histopathological conditions remained at 6 mpe. According to the hepatic transcriptome analysis, at 3 days ionic silver regulated a larger number of transcripts (410) than Ag NPs (129), while at 21 days Ag NPs provoked a stronger effect (799 vs 165 regulated sequences). Gene ontology terms such as “metabolic processes” and “response to stimulus” appeared enriched after all treatments, while “immune system” or “reproductive processes” were specifically enriched after the exposure to Ag NPs. This suggests that the toxicity of Ag NPs may not be solely related to the release of Ag ions, but also to the NP form. No evident effects were found on protein oxidation or on hepatocyte lysosomal membrane stability during exposure, but effects recorded on liver lysosomes and persistent damage on gill tissue at 6 mpe could indicate potential for long-term effects in exposed fish.

overall_design: 20 samples per group, 5 replicates (4 liver per replicate), 3 groups x 2 times, control, ionic silver and Ag NPs, 3 and 21 days of exposure

first: Jose

first: Unai

last: Vicario-Parés

first: Eider

last: Bilbao

first: Douglas

last: Gilliland

first: Francesco

last: Mura

first: Luciana

last: Dini

first: Miren

last: Cajaraville

first: Amaia

last: Orbea


title: DNA Methylation by Restriction Modification Systems Affects the Global Transcriptome Profile in Borrelia burgdorferi.

status: Public on Jun 05 2018

city: Grand Forks

first: Tim

last: Casselli

state: ND

address: UND School of Medicine & HS 1301 N Columbia Road Stop 9037

department: Basic Sciences

institute: University of North Dakota

type: Methylation profiling by high throughput sequencing

summary: Single Molecule Real Time (SMRT) sequencing was utilized to map the genome-wide DNA methylation pattern, and to identify consensus modified motifs in B. burgdorferi as well as isogenic methyltransferase mutants. Four conserved m6A modification motifs were identified, and were fully attributable to the presence of specific methyltransferases. Next, RNA-seq was compared between strains to determine the effects of altering global DNA methylation patterns on gene expression. Whole-genome transcriptome changes were observed in conjunction with the loss of methyltransferase enzymes, indicating that DNA methylation by restriction modification systems has effects on gene expression in B. burgdorferi.

overall_design: In vitro log-phase cultures of wild-type Borrelia burgdorferi isolate B31 (A3) and mutant strains lacking methyltransferases bbe02 (A3-NP1) or bbeo2 and bbq67 (5A18-NP1) were grown intriplicate. Genomic DNA was isolated and pooled for each strain for methylome analysis using PacBio SMRT sequencing. Transcriptomes were generated for each replicate by deep sequencing using Illumina miseq. Note: one replicate of A3-NP1 was discarded for transcriptome analysis.

first: Timothy

first: Adam

last: Scheidegger


title: Integrative analysis of copy number and gene expression data suggests novel pathogenic mechanisms in Primary Myelofibrosis

status: Public on May 21 2018

city: Modena

first: Rossella

last: Manfredini

address: Via Gottardi 100

department: Life Sciences

country: Italy

institute: Centre for Regenerative Medicine

summary:
Primary myelofibrosis (PMF) is a Myeloproliferative Neoplasm (MPN) characterized by megakaryocyte hyperplasia, progressive bone marrow fibrosis, extramedullary hematopoiesis and transformation to Acute Myeloid Leukemia (AML). Beginning in early 2005, a number of novel mutations involving JAK2, CALR, MPL, TET2, ASXL1, DNMT3a, CBL, IDH1 and IDH2 have been described in MPNs, depicting a really complex genomic landscape for MPNs. To shed light on the genomic lesions that can contribute to disease phenotype and/or development, we integrated gene expression and copy number signals and identified several genomic abnormalities leading to a concordant alteration in gene expression levels. In particular, copy number gain in the polyamine oxidase (PAOX) gene locus is accompanied by a coordinated transcriptional up-regulation in PMF patients. Inhibition of PAOX resulted in rapid cell death in PMF progenitor cells, but not in normal cells, suggesting that PAOX inhibition could represent a therapeutic strategy to selectively target PMF cells without affecting normal hematopoietic cells’ survival. Moreover, copy number loss in the chromatin modifier HMGXB4 gene correlates with a concomitant transcriptional down-regulation in PMF patients. Interestingly, silencing of HMGXB4 induces megakaryocyte differentiation, while inhibiting erythroid development, in human hematopoietic stem/progenitor cells. These results highlight a previously un-reported, yet potentially interesting role of HMGXB4 in the hematopoietic system suggesting that genomic and transcriptional imbalances of HMGXB4 could contribute to the aberrant expansion of the megakaryocytic lineage that characterize PMF patients.
In this study, the authors take advantage of the integrative analysis of gene expression and copy number data to identify the concordant gain/up-regulation of the polyamine oxidase PAOX and the loss/down-regulation of the chromatin modifier HMGXB4. This work sheds light on the influence of genomic abnormalities on gene expression regulation in PMF CD34+ cells and on their contribution to specific features of PMF, such as a hyperplastic megakaryopoiesis.

overall_design:
Gene expression profile [GEP; GSE41812, GSE53482] and Copy Number Analysis (CN) were performed on 31 PMF patients and 31 healthy donors (n=16 PB CD34+, n=15 BM CD34+) (1 replicate for each sample).

Please note that [1] the copy number status for the PMF samples have been determined using the HapMap database as a reference, so for this analysis, the nomal donor samples are not required. [2] the accession number for gene expression data for each sample is indicated in the description field.

first: Simona

last: Salati

first: Silvio

last: Bicciato

first: Roberta

last: Zini

first: Paola

last: Guglielmelli

first: Valentina

last: Pennucci

first: Tiziana

last: Fanelli

first: Costanza

last: Bogani

first: Sebastiano

last: Rontauroli

first: Ruggiero

last: Norfo

first: Samantha

last: Ruberti

first: Zelia

last: Prudente

first: Elisa

last: Bianchi

first: Gianni

last: Barosi

first: Mario

last: Cazzola

first: Alessandro

last: Rambaldi

first: Enrico

last: Tagliafico

last: Vannucchi


status: Public on May 03 2018

city: Boston

first: Fasih

middle: Mubtasim

last: Ahsan

state: MA

address: 185 Cambridge Street, CPZN 6500

department: Center for Genomic Medicine

institute: Massachusetts General Hospital

summary: Transcriptional profiling of PNPase KO liver hepatocytes (HepKO) generated from Albumin-Cre/wt (liver-specific) Pnpt1 fl/fl C57BL/6J mice. Samples comparing liver hepatocyte PNPase KO (HepKO) cells to litter-, age-, and sex-matched wildtype hepatocyte control cells. The goal of this experiment was to determine effects of PNPase loss on the total RNA transcriptome under physiologic in vivo conditions.

overall_design: Two conditions: PNPASE KO liver hepatocytes (HepKO) vs matched WT (control) hepatocytes. Biological replicates: Two biological replicates in each condition; one age-, litter-, and sex- matched male pair of HepKO and WT mice, and another age-, litter-, and sex- matched female pair of HepKO and WT mice. Comparison was performed in sex-matched fluor-reversed pairs.

first: Michael

last: Teitell


title: A time-course profiling of the effects of maslinic acid on mRNA expression of chemically induced Raji cells.

status: Public on May 02 2018

city: Bandar Sungai Long

first: Wai

middle: Meng

last: Lau

state: Selangor

address: Lot PT 21144

department: Faculty of Medicine and Health Sciences

country: Malaysia

institute: Universiti Tunku Abdul Rahman

summary:
Maslinic acid is a novel phytochemical reported to exert prominent anti-cancer effects and it was hypothesized that this compound induces cellular apoptosis through the activation of the mitochondrial apoptotic pathway (Martin et al, 2007) — thereby resulting in significant inhibition of cell proliferation in a dose-dependent manner (Reyes-Zurita et al, 2009). Prior studies on maslinic acid in its function as a time-dependent inhibitor in both tumorigenesis and inflammation events by targeting multiple signaling pathways; particularly the NF-ĸB, MAPK (Li et al, 2010; Yap, et al, 2011) and JNK (Reyes-Zurita et al, 2011) pathways were mostly based on proteomic analyses (Li et al, 2010; Yap et. al., 2011). However, these results may not depict an accurate scenario of the signaling networks involved due to protein degradation, alternate splicing and extensive post-translational processing. Hence, this study aimed to construct a temporal-based global gene expression profile of the effects of maslinic acid by using the microarray technology.
The aim of this project is to construct the complete global mRNA profile of the effects of maslinic acid in inhibiting early-antigen formation in Raji cells.

overall_design: Phorbol ester and sodium butyrate induced Raji cells were first treated with maslinic acid and the cells were harvested at the 0th, 4th, 8th, 12th, 24th, 48th hour. Total RNA was extracted and its mRNA was subsequently isolated for hybridization on Affymetrix microarray. The experiment was done in triplicates per sample.

first: Yang

last: Lim


title: Long non-coding RNA Expression Profiling in Breast Cancer (Ma-T) and in normal breast tissue (Ma-N)

status: Public on May 01 2018

city: Heidelberg

first: Sven

last: Diederichs

address: Im Neuenheimer Feld 280

department: RNA Biology & Cancer

institute: German Cancer Research Center (DKFZ)

summary:
The expression of long non-coding RNAs - lncRNAs - was profiled in the ER/PR-positive invasive ductal carcinoma of the breast (Ma-T) and in normal breast tissues using the Invitrogen NCode Human lncRNA Array Platform.
published in: Maria Polycarpou-Schwarz et al., Oncogene 2018

overall_design: 44 tumor samples, 13 normal samples, data provided as log2 signal intensities quantile normalized with a minimum signal intensity (threshold 1.0)

first: Maria

last: Polycarpou-Schwarz

first: Joachim

last: Rom

first: Sebastian

last: Aulmann

first: Hans-Peter

last: Sinn


title: Differential expression of IBD susceptibility and IL23R associated pathway genes during ongoing anti-TNF therapy (anti-TNF non-responder vs anti-TNF responder)

city: Erlangen

first: Heike

last: Schmitt

address: Ulmenweg 18

department: First Department of Medicine

institute: University of Erlangen-Nuremberg

summary: IL23R signaling dependent genes are significantly upregulated in Crohn’s disease non-responders compared to responders during ongoing anti-TNF therapy

overall_design: For microarray experiments gene expression profiles of isolated LPMCs from three responders and  three non-responders to anti-TNF therapy in CD patients were analyzed

first: Ulrike

last: Billmeier

first: Walburga

last: Dieterich

first: Timo

last: Rath

first: Sophia

last: Sonnewald

first: Stephen

last: Reid

first: Simon

last: Hirschmann

first: Kai

last: Hildner

first: Maximilian

last: Waldner

first: Jonas

last: Mudter

first: Arndt

last: Hartmann

first: Robert

last: Grützmann

first: Clemens

last: Neufert

first: Tino

last: Münster

first: Markus

middle: F

last: Neurath

first: Raja

last: Atreya


title: Hsa-miR99b/let-7e/miR125a cluster regulates pathogen recognition receptor-stimulated suppressive APCs

status: Public on May 15 2018

first: Mariel

last: Eberle

address: Im Neuenheimer Feld 324

department: Department of Hygiene and Microbiology

institute: University Hospital Heidelberg

summary: Antigen presenting cells (APCs) regulate the balance of our immune response towards microbes. Whereas immunogenic APCs boost inflammation and activate lymphocytes, the highly plastic cells can switch into a tolerogenic/suppressive phenotype that dampens and resolves the response. Thereby the initially mediated inflammation seems to prime the switch of APCs while the strength of activation determines the grade of the suppressive phenotype. Recently we showed that pathogen recognition receptor-mediated pro-inflammatory cytokines reprogram differentiating human blood monocytes in vitro towards an immunosuppressive phenotype through prolonged activation of signal transducer and activator of transcription (STAT) 3. The TLR7/8 ligand R848 (Resiquimod) triggers the high release of cytokines from GMCSF/IL-4-treated monocytes. These cytokines subsequently upregulate T cell factors, such as Programmed death-ligand 1 (PD-L1) and Indolamin-2,3-Dioxygenase (IDO) suppressive through cytokine receptor-mediated STAT3 activation. Here we reveal an essential role for the micro-RNA (miR) hsa-miR99b/let-7e/miR125a cluster in stabilizing the suppresive phenotype of R848-stimulated APCs on different levels. On the one hand the miR cluster boosts R848-stimulated cytokine production through regulation of MAPkinase inhibitor Tribbles homolog 2 (TRIB2), thereby enhancing cytokine-stimulated activation of STAT3. One the other hand, the STAT3 inhibitor suppressor of cytokine signaling-1 (SOCS-1) is targeted by the miR cluster, stabilizing the STAT3-induced expression of immunosuppressive factors PD-L1 and IDO. Finally hsa-miR-125a/let7e/99b cluster regulates generation of the suppressive tryptophan (Trp) metabolite kynurenine by targeting the tryptophanyl -tRNA synthetase WARS, the direct competitor of IDO in terms of availability of Trp. In summary, our results reveal the hsa-miR99b/let-7e/miR125a cluster as an important player in the concerted combination of mechanisms that stabilizes STAT3 activity and thus regulate R848-stimulated suppressive APCs.

overall_design: Monocytes were isolated out of PBMCs from fresh blood or buffy coat. The cells were treated with R848 during the period of differentiation into dendritic cells. After 72 h, the cells were harvested and the immune status was analyzed in terms of miRNA expression profile. R848-treated antigen presenting cells (APCs) were compared to unstimulated, immature dendritic cells (iDCs). Experimental setup was performed with three independent donors.

first: Dagmar

last: Hildebrand

middle: E

first: Sabine

last: Wölfe

first: Franziska

last: Egler

first: Delal

last: Sahin

first: Aline

last: Sähr

first: Konrad

middle: A

last: Bode

first: Klaus

last: Heeg


title: LncRNA and mRNA expression of cisplatin-resistant versus parental SCC9 cells

city: Guangzhou

first: Bodu

last: Liu

state: State...

address: School of Life Sciences, Sun Yat-sen U East Camp, High. Edu. Meg. Cntr.

institute: Sun Yat-sen University

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

summary: Increasing evidence has shown that chemoresistance is related to the process of epithelial-mesenchymal transition (EMT) and increased invasiveness by tongue squamous cell carcinoma (TSCC) cells. Long noncoding RNAs (lncRNAs) play pivotal roles in tumour metastasis and progression. However, the roles and mechanisms of lncRNAs in cisplatin resistance induced EMT and metastasis are not well understood. In this study, a Chemotherapy Induced Long non-coding RNA 1 (CILA1) was discovered by using microarrays and was functionally identified as a regulator of chemo-sensitivity in TSCC cells.Upregulation of CILA1 promotes EMT, invasiveness and chemoresistance in TSCC cells, whereas the inhibition of CILA1 expression induces MET and chemosensitivity and inhibis the invasiveness of cisplatin-resistant cells both in vitro and in vivo. We also found that CILA1 exerts its functions via the activation of the Wnt/ β-catenin signalling pathway.High CILA1 expression levels and low levesl of phosphorylated β-catenin were closely associated with cisplatin-resistance and advanced disease stage, and were predictors of poor prognosis in TSCC patients. These findings provided a new biomarker for Increasing evidence has shown that chemoresistance is related to the process of epithelial-mesenchymal transition (EMT) and increased invasiveness by tongue squamous cell carcinoma (TSCC) cells. Long noncoding RNAs (lncRNAs) play pivotal roles in tumour metastasis and progression. However, the roles and mechanisms of lncRNAs in cisplatin resistance induced EMT and metastasis are not well understood. In this study, a Chemotherapy Induced Long non-coding RNA 1 (CILA1) was discovered by using microarrays and was functionally identified as a regulator of chemo-sensitivity in TSCC cells.Upregulation of CILA1 promotes EMT, invasiveness and chemoresistance in TSCC cells, whereas the inhibition of CILA1 expression induces MET and chemosensitivity and inhibis the invasiveness of cisplatin-resistant cells both in vitro and in vivo. We also found that CILA1 exerts its functions via the activation of the Wnt/ β-catenin signalling pathway.High CILA1 expression levels and low levesl of phosphorylated β-catenin were closely associated with cisplatin-resistance and advanced disease stage, and were predictors of poor prognosis in TSCC patients. These findings provided a new biomarker for the chemosensitivity of TSCC tumours and a therapeutic target for TSCC treatment.

overall_design: SCC9 cells were treated with gradually increased concentration of cisplatin to accquire cisplatin-resistance. RNA from three biological replicates of both cisplatin-resistant and parental SCC9 cells were collected for microarray analysis.

first: Zhaoyu

last: Lin

first: Lijuan

last: Sun

first: Shule

last: Xie

first: Shanyi

last: Zhang

first: Song

last: Fan

first: Qunxing

last: Li

first: Weixiong

last: Chen

first: Guokai

last: Pan

first: Weiwei

last: Wang

first: Bin

last: Weng

first: Zhang

first: Jinsong


title: The CRISPR/Cas system in Neisseria meningitidis affects bacterial adhesion to human nasopharyngeal epithelial cells

city: Irvine

first: Lei

state: CA

address: University of California, Irvine

institute: University of California, Irvine

summary: Neisseria meningitidis, a commensal β-proteobacterium of the human nasopharynx, constitutes a worldwide leading cause of sepsis and epidemic meningitis. The molecular basis for their "accidental" pathogenicity is still not fully understood. Here, we show that knock-out strains lacking the Cas9 protein are impaired in the adhesion to human nasopharyngeal cells which constitutes a central step in the pathogenesis of invasive meningococcal disease. Transcriptome sequencing data suggest that meningococcal Cas9 does not affect the expression of classical surface adhesins but rather exerts its effect on cell adhesion in an indirect manner. Consequently, we speculate that the meningococcal type II-C CRISPR/Cas system exerts novel functions beyond its established role in defence against foreign DNA.

overall_design: 8 SAMPLES WITHOUT REPLICATES

first: Nadja

last: Heidrich

first: Antony

last: Hagmann

first: Saskia

last: Bauriedl

first: Jörg

last: Vogel

first: Christoph

last: Schoen


title: Transcriptomics analysis of guinea pig heart, fetus to adult progression

city: Cambridge

first: Aurora

last: Gomez-Duran

state: Cambridge

address: Welcome Trust/MRC Building

department: Department of Clinical Neurosciences

country: United Kingdom

institute: Cambridge University

summary: We report the outcomes of next-generation sequencing (RNA-Seq) of guinea pig (Cavia porcellus) heart tissue and compare relative transcript abundances between fetus and adult.

overall_design: mRNA profiles were generated for adult and foetal guinea pig hearts in four biological replicates using an Illumina HiSeq  platform.

first: Pawel

last: Palmowski

first: Rachael

last: Watson

first: Jannetta

last: Steyn

first: Magdalena

last: Karolczak-Bayatti

first: G

last: Europe-Finner

first: Achim

last: Treumann

first: Michael

last: Taggart


title: Co-transcriptional association of Hfq and Crc with the Pseudomonas aeruginosa PAO1 genome

first: Simon

middle: L

last: Dove

address: 300 Longwood Ave

department: Division of Infectious Diseases

country: USA

institute: Boston Children's Hospital and Harvard Medical School

summary: Hfq is an RNA chaperone and an important post-transcriptional regulator in bacteria. Using chromatin immunoprecipitation together with DNA sequencing (ChIP-Seq), we show that Hfq associates with hundreds of different regions of the Pseudomonas aeruginosa chromosome. These associations are abolished when transcription is inhibited, indicating they reflect Hfq binding to transcripts during their synthesis. Analogous ChIP-Seq analyses with the post-transcriptional regulator Crc reveal that it associates with many of the same nascent transcripts as Hfq, an activity we show is Hfq dependent. Our findings indicate that Hfq binds many transcripts co-transcriptionally in P. aeruginosa, often in concert with Crc, and uncover direct regulatory targets of these proteins. They also highlight a general approach for studying the interactions of RNA-binding proteins with nascent transcripts in bacteria. The binding of post-transcriptional regulators to nascent mRNAs may represent a prevalent means of controlling translation in bacteria where transcription and translation are coupled.

overall_design: Genome-wide locations of Hfq and Crc with and without rifampicin treatment

first: Tracy

last: Kambara

first: Kathryn

last: Ramsey


title: OncoScan analysis to investigate CNV in breast tumors developed by ATM mutation carriers

city: Paris

first: Elodie

last: Girard

address: 11-13 rue Pierre et Marie Curie

institute: Institut Curie

summary:
The ataxia telangiectasia-mutated (ATM) gene is a moderate-risk breast cancer susceptibility gene; germline loss-of-function variants are found in up to 3% of hereditary breast and ovarian cancer (HBOC) families who undergo genetic testing. So far, no clear molecular features of breast tumors occuring in ATM deleterious variant carriers have been described,
but identification of an ATM-associated tumors signature may help patients' management. To characterize hallmarks of ATM-associated tumors, absolute copy number variation and loss of heterozygosity profiles were obtained from the OncoScan SNP array.

overall_design: Copy number analysis of Affymetrix OncoScan HD arrays was performed on 23 formamid-fixed paraffin-embedded breast tumors. Tumors were developed by carriers of one or two mutated copies of ATM.

first: Anne-Laure

last: Renault

first: Tatiana

last: Popova

first: Philippe

last: La Rosa

first: Fabienne

last: Lesueur


title: A cytoplasmic Argonaute protein promotes the inheritance of RNAi

status: Public on Apr 28 2018

city: Hefei

first: Shouhong

last: Guang

state: Anhui

address: 443 HuangShan Road

department: School of Life Sciences

country: China

institute: University of Science & Technology of China

summary: RNAi-elicited gene silencing is heritable and can persist for multiple generations after its initial induction in C. elegans. However, the mechanism by which parental-acquired trait-specific information from RNAi is inherited by the progenies is not fully understood. Here, we identified a cytoplasmic Argonaute protein, WAGO-4, necessary for the inheritance of RNAi. WAGO-4 exhibits asymmetrical translocation to the germline during early embryogenesis, accumulates at the perinuclear foci in the germline, and is required for the inheritance of exogenous RNAi targeting both germline- and soma-expressed genes. WAGO-4 binds to 22G-RNA and its mRNA targets. Interestingly, WAGO-4-associated endogenous 22G-RNA targets the same cohort of germline genes as CSR-1 and similarly contains untemplated addition of uracil at the 3' ends. The poly(U) polymerase CDE-1 is required for the untemplated polyuridylation of WAGO-4-associated 22G-RNAs and inheritance of RNAi. Therefore, we conclude that the cytoplasmic Argonaute protein WAGO-4 also promotes the inheritance of RNAi in addition to the nuclear RNAi pathway.

overall_design: In this study, we compared WAGO-4 associated small RNAs from (1) wild type animals; (2) after lin-15b RNAi. And we also investigated the function of WAGO-4 in RNAi inheritance by comparing WAGO-4 associated small RNAs in (3) no RNAi treatment; (4) oma-1 dsRNA treated P0; (5) F1 animals from oma-1 dsRNA-treated P0; (6) F3 animals from oma-1 dsRNA-treated P0.


title: Direct reprogramming of mouse fibroblasts into functional skeletal muscle progenitors

first: Ori

last: Bar-Nur

address: 185 Cambridge st.

department: Center of Regenerative medicine

institute: Harvard University

summary: Skeletal muscle harbors quiescent stem cells termed satellite cells and proliferative progenitors termed myoblasts, which play pivotal roles during muscle regeneration. However, current technology does not allow permanent capture of these cell populations in vitro. Here, we show that ectopic expression of the myogenic transcription factor MyoD, combined with exposure to small molecules, reprograms mouse fibroblasts into expandable induced myogenic progenitor cells (iMPCs). iMPCs express key skeletal muscle stem and progenitor cell markers including Pax7 and Myf5 and give rise to Dystrophin-expressing myofibers upon transplantation, a subset of which maintain Pax7 expression in vivo and sustain serial regenerative responses. Similar to satellite cells, iMPCs originate from Pax7+ cells and require Pax7 itself for maintenance. Finally, we show that iMPCs can be established from muscle tissue following small molecule exposure alone. This study thus reports on a robust approach to derive expandable myogenic stem/progenitor-like cells from multiple differentiated cell types.

overall_design: 5 samples were analyzed in total: MEFs, MEFs+MyoD (day 14 of reprogramming), MEFs+MyoD+F/R (day 14 of reprogramming),  iMPC clone and C2C12 myoblasts.

first: Konrad

last: Hochedlinger


title: Regulatory inversion in NAC networks steers the timing of age-dependent cell death in plants [Nanostring]

status: Public on Apr 29 2018

city: Daejeon

first: Ji-Hwan

last: Park

address: 125 Gwahak-ro, Yuseong-gu

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology (KRIBB)

summary: Aging is a time-dependent biological phenomenon governed by complex networks of regulatory components and their transitions over lifetime. Yet, there have been limited efforts to pin down age-associated networks and map their dynamic characteristics onto aging phenotypes. Here, we built time-course genetic regulatory networks of NAM/ATAF/CUC (NAC) transcription factors during the course of leaf aging in Arabidopsis, using causal regulatory relationships among NACs identified from mutants of 49 aging-associated NACs. These temporal networks revealed a regulatory inversion from activating to repressive regulatory modes at a pre-senescent stage. The inversion was governed by three hub NACs, and their mutants conferred earlier aging with altered expression of reactive oxygen species and salicylic acid response genes. Overexpression of the hub NACs delayed the regulatory inversion, rendering delayed age-dependent cell death. We conclude that the regulatory inversion in NAC networks at a pre-senescent stage directs when age-dependent cell death should proceed in plants.

overall_design:
We measured mRNA expression of 49 NACs in wild type (col-0) and 49 knockout mutant lines of NACs (duplicate for each mutant) at 4 stages (14, 18, 22, and 26 days of leaf age)
434 samples consist of:
34 wild type samples (=10, 8, 8 and 8 replicates for the four time points, respectively)
16 samples of anac092 mutant, one of the ANAC gene (=4 replicates for each of four time points)
384 samples of 48 anac mutants including at3g12910 and ntl9 (=2 replicates for each of four time points).

first: Hyo-Jung

last: Kim

first: Jingil

first: Jung-Ju

first: Sung-Hyun

last: Hong

first: Jeongsik

first: Jinhee

first: Hye-Ryun

last: Woo

first: Pyung-Ok

last: Lim

first: Daehee

last: Hwang

first: Hong-Gil

last: Nam


title: Transcriptomic analysis and mutational status of IDH1 in paired primary-recurrent intrahepatic cholangiocarcinoma

city: Biella

first: Paola

last: Ostano

address: via Malta 3

institute: Fondazione Edo ed Elvo Tempia

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

overall_design: Refer to individual Series


title: Expression data from distinct populations of iMC from the small intestine of Ackr4(+/gfp) mice

status: Public on Apr 26 2018

city: Glasgow

first: Jonathan

last: Cavanagh

address: 120 University Place

department: Immunology

institute: University of Glasgow

summary:
Mesenchymal cells play key roles in modulating tissue homeostasis in various organs, including the intestine. Here we show that the murine intestinal mesenchymal cells are heterogenous, comprising at least three distinct populations.
In this dataset, we include the expression data obtained from sorted subsets of CD45-Ter119-EPCAM-GP38+CD31- murine intestinal mesenchymal cell (iMC) populations. The iMC populations were separated into: CD146+ cells, which expressed CD9 and CD29, but not Ackr4, SCA1, ICAM1 or PDGFRa; GFP+ fibroblasts, which expressed Ackr4, SCA1, ICAM1 and PDGFRa; and GFP- fibroblasts, which also expressed SCA1, ICAM1 and PDGFRa, but were negative for Ackr4 expression.

overall_design: 8 Total samples were analyzed using Affymetrix Mouse Transcriptome arrays. 6 samples were used to generate a pairwise comparison between GFP+ vs GFP- fibroblasts. Analysis was performed using GeneSpring. Genes with an FDR≤10% and a fold-change ≥2 were selected. We did not generate pairwise comparisons for CD146+ cells vs GFP+ or GFP- fibroblasts because only two arrays were performed for CD146+ cells and data from these arrays contained significant variability.

first: Carolyn

last: Thomson

first: Serge

last: ven de Pavert

first: Michelle

last: Stakenborg

first: Evelien

last: Labeeuw

first: Gianluca

last: Matteoli

first: Allan

last: Mowat

first: Robert

middle: J

last: Nibbs


title: Transcriptomic analysis and mutational status of IDH1 in paired primary-recurrent intrahepatic cholangiocarcinoma [Agilent]

summary: Purpose: Effective target therapies for intrahepatic cholangiocarcinoma have not been identified so far. One of the reasons may be the molecular and genomic alteration difference between paired primary (PR) and recurrent (REC) tumors. We aim to identify peculiar characteristics and to select potential targets specific for recurrent tumors.  Experimental design: Thirteen ICC pairs from Italian patients were collected and analyzed for gene expression profiling and mutational status of IDH1. For two pairs, deep mutational analysis by Next Generation Sequencing was also carried out. An independent cohort of patients was used for validation.  Results: Two class paired comparison yielded 315 differentially expressed genes between REC and PR tumors. Up-regulated genes in RECs are involved in RNA/DNA processing, cell cycle, epithelial to mesenchymal transition (EMT), resistance to apoptosis, and cytoskeleton remodeling. Down-regulated genes participate to epithelial cell differentiation, proteolysis, apoptotic, immune response, and inflammatory processes. A 24 gene signature is able to discriminate RECs from PRs, and 9 genes predict recurrence in an independent cohort; FANCG is statistically associated with survival in the chol-TCGA dataset. IDH1 was mutated in the RECs of three patients. In the independent cohort, 2 out of 5 patients displayed the IDH1 mutation only in RECs. Deep sequencing revealed TP53, ASXL1, PTEN and DICER1 novel mutations.   Conclusions: RECs displayed more aggressive phenotype; EMT, resistance to apoptosis, and cytoskeleton remodeling were key players and druggable pathways in REC. IDH1 is mutated in about 30% of patients, becoming a marker of progression and a target for therapy.

overall_design: 10 primary intrahepatic cholangiocarcinomas, 3 recurrent intrahepatic cholangiocarcinomas and 7 paracenteses from advanced disease were analyzed

first: Caterina

last: Peraldo-Neia

first: Giuliana

last: Cavalloni

first: Ymera

last: Pignochino

first: Dario

last: Sangiolo

first: Loris

last: De Cecco

first: Edoardo

last: Marchesi

last: Ribero

first: Aldo

last: Scarpa

first: Agostino

last: De Rose

first: Antonio

last: Giuliani

first: Fulvio

last: Calise

first: Chiara

last: Raggi

first: Pietro

last: Invernizzi

first: Massimo

last: Aglietta

first: Giovanna

last: Chiorino

first: Francesco

last: Leone


title: Transcriptomic analysis and mutational status of IDH1 in paired primary-recurrent intrahepatic cholangiocarcinoma [Illumina]

first: Paola

last: Ostano

overall_design: Thirteen primary and recurrent ICC pairs from Italian patients were collected and analyzed for gene expression profiling


title: Gene expression profile of chronically activated CD4+ T cells from cancer patients

first: Olivier

last: Lantz

address: 26 rue d'Ulm

institute: Curie Institute

summary:
CD4+ T cells as mediators of antitumor responses are beginning to be appreciated. Our team demonstrated that chronically activated CD4+ T cells (chCD4+ T cells) were expanded in the blood of cancer patients and their expansion is correlated with tumor regression.
Here we characterized the gene expression profile of this population with therapeutic potential.

overall_design: Conventional CD4+ T cells (Tconv cells=CD3+CD4+CD127+CD25±) and chronically activated CD4+ T cells (chCD4 T cells=CD3+CD4+CD127-CD25-) were sorted from the blood of healthy donor or patients with metastatic uveal melanoma.

first: Isabelle

last: Péguillet


title: TosR-mediated regulation of adhesins and biofilm formation in uropathogenic Escherichia coli

status: Public on Apr 27 2018

city: Ann Arbor

first: Richard

middle: C

last: McEachin

state: United States

address: 2800 Plymouth Road

department: DCM&B

institute: University of Michigan

summary: Uropathogenic Escherichia coli utilize a variety of adherence factors that assist in colonization of the host urinary tract. TosA (type one secretion) is a non-fimbrial adhesin that is predominately expressed during murine urinary tract infection (UTI), binds to kidney epithelial cells, and promotes survival during invasive infections. The tosRCBDAEF operon encodes the secretory machinery necessary for TosA localization to the E. coli cell surface, as well as the transcriptional regulator TosR. TosR binds upstream of the tos operon and, in a concentration dependent manner, either induces or represses tosA expression. TosR is a member of the PapB family of fimbrial regulators that can participate in crosstalk between fimbrial operons. TosR also binds upstream of the pap operon and suppresses PapA production. However, the scope of TosR-mediated crosstalk is understudied and may be underestimated. To quantify the global effects of TosR-mediated regulation on the E. coli CFT073 genome, we induced expression of tosR, collected mRNA, and performed RNA-Seq. These findings show that production of TosR affected the expression of genes involved with adhesins, including P, F1C, and Auf; nitrate/nitrite transport; microcin secretion; and promoted biofilm formation.

overall_design: Examination of three biological replicates of CFT073 harboring pBAD or pBAD-tosR

first: Courtney

last: Luterbach

first: Valerie

last: Forsyth

first: Michael

middle: D

last: Engstrom

first: Harry

last: Mobley


title: Transcriptomic Analysis of Hepatic Cells in Multicellular Organotypic Liver Models

city: Blacksburg

first: T. M.

last: Murali

state: VA

address: 225 Stanger St.

department: Department of Computer Science

institute: Virginia Tech

summary: In this study, genome-wide gene expression profiles of primary hepatocytes and liver sinusoidal endothelial cells (LSECs) were measured at day 12 for each cell culture system using Affymetrix GeneChips and analyzed via Gene Set Enrichment Analysis (GSEA). The culture systems analyzed include the commonly used collagen sandwich and monolayers of hepatocytes, as well as 3-dimensional (3D) engineered liver models that contain hepatocytes and LSECs (3DHL) and hepatocytes, LSECs, and Kupffer cells (3DHLK). Our results highlight the up-regulation of several hepatocyte specific functions in hepatocytes and a novel interplay between Ppara signaling and bile acid biosynthesis in LSECs.

overall_design: We measured gene expression in hepatocytes, LSECs, and Kupffer cells from the 3DHL and 3DHLK models at day 12 to better understand LSEC function in in vitro liver cultures. For additional comparisons, we collected gene expression from hepatocytes in a collagen sandwich (CS) and hepatocyte monolayer (HM) as well as Kupffer cells at day 3 prior to their inclusion in the 3D liver model. We obtained Affymetrix microarray data for 23 samples, considering three cell-types and across four culture systems. Each cell-type culture system was performed in triplicate, except Kupffer cells at day 12 was performed in duplicate.

first: Allison

last: Tegge

first: T

first: Padmavathy

last: Rajagopalan


title: Gene expression profile of tumor antigen-specific CD4 T cells

summary:
Up to know CD4 T cell antitumor responses have been mostly studied in transplanted tumor models. However, although they are valuable tools, they are not suitable to study the long term interactions between tumors and the immune system
We used gene expression profiling to characterize the fate of naive tumor antigen-specific CD4 T cells in a genetically-induced lung adenocarcinoma expressing the MHC-II restricted DBY antigen as a model tumor antigen.

overall_design: Naïve DBY-specific Marilyn CD4 T (Marilyn) were transferred into mice bearing early or advanced tumors. Total tumor antigen-specific Marilyn CD4 T cells were purified from the tumor-draining lymph node 7 days after transfer.

first: Ruby

last: Alonso


title: Gene expression profiles of tumor-induced pTregs and anergic tumor-specific CD4+ T cells

summary: Up to now the role of tumor-specific pTregs and anergic cells during tumor development is not fully understood. Here we used a genetically-induced tumor expressing a MHC-II restricted DBY model antigen to characterize the tumor-induced pTregs and anergic cells that arise early during tumor development.

overall_design: Naïve DBY-specific Marilyn CD4 T cells were transferred into mice bearing DBY expressing tumors at different stages of tumor growth. Marilyn pTregs or anergic Marilyn cells were purified 7 days after transfer from the lymph node draining the tumor site.


title: A vitamin E- supplemented antioxidant diet interferes with the acute adaptation of the liver to physical exercise in mice

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

summary:
Objective: Physical exercise and vitamin E are considered effective treatments of nonalcoholic fatty liver and other metabolic diseases. However, vitamin E has also been shown to interfere with the adaptation to exercise training, in particular for the skeletal muscle. Here, we studied the hypothesis that vitamin E also interferes with the metabolic adaptation of the liver to acute exercise.
Methods: Male C57BL6/N mice were fed either control or vitamin E (α-tocopherol)- supplemented antioxidant diet during four weeks before being subjected to a non-exhaustive treadmill run. We assessed the acute transcriptional response of the liver as well as plasma corticosterone and free fatty acid (FFA) concentrations and monitored respiration in the exercising mice.
Results: Vitamin E counteracted exercise-induced hepatic inflammation and altered the metabolic adaptation of the liver on the level of gene transcription. Vitamin E interfered with the upregulation of key metabolic regulators and caused a paradoxical increase in transcripts involved in lipid and cholesterol synthesis, processes negatively regulated by FFA and usually suspended during physical exercise. Whole-body energy consumption as well as corticosterone levels and signalling were similar, arguing against acute differences in fatty acid oxidation or glucocorticoid action.
Conclusions: Our results show that vitamin E supplementation alters the inflammatory and transcriptional response of the liver to physical exercise. These effects of vitamin E could, on the long run, result in an impaired adaptation of the liver to physical exercise. Since exercise is clearly beneficial for general health and in reducing inflammation and dyslipidemia in nonalcoholic fatty liver disease, the interference of vitamin E with these processes may speak for a cautious use as dietary supplement.

overall_design: We performed gene expression microarray analysis on liver tissue derived from mice treated for four weeks with a vitamin E-enriched antioxidant diet prior to an acute non-exhaustive treadmill run and control mice.

first: Miriam

last: Hoene

first: Martin

last: Irmler

last: Hrabě de Angelis

first: Hans-Ulrich

last: Häring

first: Cora

last: Weigert


title: NUCLEAR FATE OF YEAST SNORNA IS DETERMINED BY COTRANSCRIPTIONAL RNT1 CLEAVAGE

status: Public on Apr 23 2018

city: Oxford

first: Nicholas

last: Proudfoot

address: South Parks Road

institute: Sir William Dunn School of Pathology,  University of Oxford

summary: We show that  in S. cerevisiae pre-snoRNA processing by the endonuclease Rnt1 occurs co-transcriptionally, removing the m7G cap to facilitate the formation of box C/D snoRNA. Failure to remove m7G cap from box C/D pre-snoRNA affects 3’ end processing, ribonucleoprotein complex formation and causes mislocalization to the cytoplasm. Consequently, Rnt1-dependent 5’ end processing of box C/D snoRNA is critical for snoRNA-dependent methylation of ribosomal RNA. Our results reveal that the 5’ end processing defines a distinct pathway for snoRNA maturation.

overall_design: Examination of snoRNA 5' and 3' end processing in S. Cerevisiae

first: Pawel

last: Grzechnik

first: Somdutta

last: Dhir


title: R-Ras2 is required for germinal center formation to aid B cells during energetically demanding processes

status: Public on Apr 25 2018

city: Madrid

first: Balbino

last: Alarcon

state: Madrid

address: Nicolas Cabrera 1

country: Spain

institute: Centro de Biologia Molecular Severo Ochoa

summary: Upon antigen recognition within peripheral lymphoid organs, B cells interact with T cells and other immune cells to transiently form morphological structures called germinal centers (GCs), which are required for B cells clonal expansion, immunoglobulin class switching, and affinity maturation. This process, known as the GC response, is an energetically demanding process that requires metabolic reprogramming of B cells. Here, we showed that the Ras-related guanosine triphosphate hydrolase (GTPase) R-Ras2 (also known as TC21) plays an essential, nonredundant, and B cell–intrinsic role in the GC response. Both the conversion of B cells into GC B cells and their expansion were impaired in mice lacking R-Ras2, but not in those lacking a highly-related R-Ras subfamily member or both the classic H-Ras and N-Ras GTPases. In the absence of R-Ras2, activated B cells did not increase oxidative phosphorylation or aerobic glycolysis. We showed that R-Ras2 was an effector of both the B cell receptor (BCR) and CD40 and that, in its absence, B cells exhibited impaired activation of the PI3K-Akt-mTORC1 pathway, reduced mitochondrial DNA replication, and decreased expression of genes involved in glucose metabolism. Because most human B cell lymphomas originate from GC B cells or B cells that have undergone the GC response, our data suggests that R-Ras2 may also regulate metabolism in B cell malignancies.

overall_design: We aimed to characterize differences in mRNA expression between germinal center B cells FACS sorted from wild type mice and germinal center B cells FACS sorted from RRas2-deficient mice. To generate germinal center B cells, all mice were immunized 7 days earlier by administration of sheep red blood cells by the intraperitoneal route.

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