title: Expression data from human AML blasts and healthy CD34+ bone marrow cells

city: Barcelona

first: Maria

middle: Belen

last: Lopez-Millan

state: Barcelona

address: Carrer Casanova 143

institute: Josep Carreras Leukaemia Research Institute

summary: Treatment for acute myeloid leukemia (AML) remains suboptimal and many patients remain refractory or relapse upon standard chemotherapy based on nucleoside analogs plus anthracyclines. The crosstalk between AML cells and the bone marrow (BM) stroma is a major mechanism underlying therapy resistance in AML. Lenalidomide and pomalidomide, a new generation immunomodulatory drugs (IMiDs), possess pleiotropic anti-leukemic properties including potent immune-modulating effects and are commonly used in hematological malignances associated with intrinsic dysfunctional BM such as myelodysplastic syndromes and multiple myeloma. Whether IMiDs may improve the efficacy of current standard treatment in AML remains understudied. Here, we have exploited in vitro and in vivo preclinical AML models to analyze whether IMiDs potentiate the efficacy of AraC/Iradubicin (standard AML chemotherapy) by interfering with the BM stroma-mediated chemoresistance. We report that lenalidomide and pomalidomide have cytotoxic effects on neither AML cells nor BM-MSCs, but they increase the immunosuppressive/immunomodulatory properties of BM-MSCs. When combined with AraC and Idarubicin, IMiDs fail to circumvent BM stroma-mediated resistance of AML cells in vitro and in vivo but induce robust extramedullary mobilization of AML cells. When administered as a single agent, lenalidomide highly mobilizes AML cells, but not healthy CD34+ cells, to peripheral blood (PB) likely through specific downregulation of CXCR4 in AML blasts. Global gene expression profiling supports a migratory/mobilization gene signature in lenalidomide-treated AML blasts but not in CD34+ cells. Collectively, IMiDs mobilize AML blasts to PB through downregulation of CXCR4 but do not improve AraC/Idarubicin activity in a preclinical model of AML.

overall_design: AML blasts samples (n=3) and BM-CD34+ cells (n=2) were FACS purified (CD45+CD33+ and CD34+ purity >98%) and cultured with 10 µM lenalidomide for 48h before global gene expression profiling (GEP)

first: Belen

first: Pablo

last: Menendez


title: Somatic loss of WWOX is associated with TP53 perturbation in basal-like breast cancer

status: Public on May 17 2019

city: Jerusalem

first: Suhaib

middle: Khaled

last: Abdeen

address: Ein kerem

department: Immunology and cancer research

country: Israel

institute: Hebrew Univeristy

type: Expression profiling by high throughput sequencing

summary: Inactivation of WW domain-containing oxidoreductase (WWOX), the gene product of the common fragile site FRA16D, is a common event in breast cancer and is associated with worse prognosis of triple-negative breast cancer (TNBC) and basal-like breast cancer (BLBC). Despite recent progress, the role of WWOX in driving breast carcinogenesis remains unknown. Here we report that ablation of Wwox in mammary tumor-susceptible mice results in increased tumorigenesis, and that the resultant tumors resemble human BLBC. Interestingly, copy number loss of Trp53 and downregulation of its transcript levels were observed in the Wwox knockout tumors. Moreover, tumors isolated from Wwox and Trp53 mutant mice were indistinguishable histologically and transcriptionally. Finally, we find that deletion of TP53 and WWOX co-occurred and is associated with poor survival of breast cancer patients. Altogether, our data uncover an essential role for WWOX as a bona fide breast cancer tumor suppressor through the maintenance of p53 stability.

overall_design: mRNA profiling of mammary epithelial cells isolated from normal WT and normal Wwox KO vs Wwox KO tumors

middle: K

first: Rami

middle: I

last: Aqeilan


title: Individual Assignment of Adult Diffuse Gliomas into the EM/PM Molecular Subtypes Using a TaqMan Low-Density Array [Human Clariom D array]

status: Public on May 16 2019

city: Beijing

first: Fan

last: Xiaolong

address: No.19,Waida Jie,Xinjie Kou, Haiding District

country: China

institute: Beijing Normal University

summary: Diagnosis of glioma into the hierarchy of human brain development would greatly facilitate mechanistic studies and clinical services in combating glioma. By analysing the multi-dimension big data of glioma genome and clinical manifestations, we have recently developed an EM/PM classification scheme anchored in the brain development and glioma pathogenesis (Sun et al., PNAS 111:3538-3543, 2014). To translate the EM/PM classification into a clinical diagnostic tool, we here designed and validated a TaqMan low-density RT-PCR array (TLDA) and a support vector machine (SVM) based prediction model that enables individual diagnosis of gliomas into the EM/PM subtype with high accuracy and precision. Results of 153 individually diagnosed adult diffuse gliomas of WHO grades II-IV derived from Chinese or Swedish patients confirmed our previous data base investigations: EM and PM gliomas show distinct prognosis, occur at different ages, and harbor mutually exclusive patterns of genomic alterations detected by Sanger sequencing and shallow-coverage whole genome sequencing (WGS). Further, we show that shallow-coverage WGS enabled a systematic identification of clonal and subclonal copy number variations (CNV) in glioma genomes, and the extent and the pattern of CNV can serve as an objective marker of tumor progression in the PM gliomas harboring IDH mutations.

overall_design: A validation cohort that contains 31 glioma samples and 9 non-tumor brain tissues were analyzed by Human Clariom D array. Then, we assigned them into EM/PM subtypes according to the gene chip data, and compared the result with the EM/PM classification label derived from TLDA data.

first: Jiuyi

last: Li

first: Anna

last: Wenger

first: Yang

last: Xue

first: Zeng

last: Wang

first: Boglarka

middle: F

last: Rydenhag

first: Bertil

first: Chuanbao

last: Zhang

first: Asgeir

middle: S

last: Jakola

first: Tao

last: Jiang

first: Helena

last: Carén

first: Xiaolong

last: Fan


title: Arabidopsis heat stress-induced proteins are enriched in electrostatically charged amino acids and intrinsically disordered regions

city: Valencia

first: Francisco

last: Vera-Sirera

address: Ingeniero Fausto Elio, s/n

country: Spain

institute: IBMCP (UPV-CSIC)

summary: Comparison of the proteins of thermophilic, mesophilic and psychrophilic prokaryotes has revealed a number of features characteristic to proteins adapted to high temperatures, which increase their thermostability. These characteristics include an excess of disulfide bonds, salt bridges, hydrogen bonds, and hydrophobic interactions, and a depletion in intrinsically disordered regions. It is unclear, however, whether such differences can also be observed when comparing proteins that are adapted to temperatures that are more subtly different. When an organism is exposed to high temperatures, a subset of its proteins are overexpressed (heat-induced proteins), whereas others are repressed (heat-repressed proteins). Here, we determine the expression levels of all Arabidopsis thaliana  genes at 22 and 37°C, and compare the amino acid compositions and levels of intrinsic disorder of heat-induced and heat-repressed proteins. We show that heat-induced proteins are enriched in electrostatically charged amino acids and depleted in polar amino acids, mirroring thermopile proteins. However, in contrast with thermophile proteins, heat-repressed proteins are enriched in intrinsically disordered regions and depleted in hydrophobic amino acids. These results indicate that temperature adaptation at the level of amino acid composition and intrinsic disorder can be observed not only in proteins of thermophilic organisms, but also in eukaryotic heat-induced proteins; however, the underlying adaptation pathways are similar but not exactly the same.

overall_design: Col-0 seedlings were grown in MS plates under darkness conditions . There were keep at 22°C for 72 hours, at this moment plates were either kept at 22 ºC or transferred to 37º C, also one control sample with four replicates that we call time 0h was collected. Seedlings were harvested after 24 hours with four biological replicates. All samples were Cy3 labelled.

first: David

last: Alvarez-Ponce

first: Mario

middle: X

last: Ruiz-González

first: Felix

last: Feyertag

first: Miguel

last: Ángel Pérez-Amador

middle: A

last: Fares


title: RNA-seq analyses of human prostate cancer cells

city: Quebec City

first: Étienne

last: Audet-Walsh

state: Quebec

address: 2705 Boulevard Laurier, R-4714

country: Canada

institute: Centre de recherche du CHU de Québec - Université Laval

summary: To study the transcriptome of human prostate cancer cells, RNA-seq experiments were performed.

overall_design: RNA was harvested after 72h of steroid deprivation to study the basal transcriptome of LNCaP and 22rv1 cells, two human AR-positive prostate cancer cell lines,

first: Raghavendra

middle: T

last: Poluri


title: Massively parallel whole-organism lineage tracing using CRISPR/Cas9 induced genetic scars

city: Berlin

first: Bastiaan

last: Spanjaard

address: Robert-Rössle-Straße 10

country: Germany

institute: Max Delbrück Center

summary: A key goal of developmental biology is to understand how a single cell transforms into a full-grown organism consisting of many cells. Although impressive progress has been made in lineage tracing using imaging approaches, analysis of vertebrate lineage trees has mostly been limited to relatively small subsets of cells. Here we present scar-trace, a strategy for massively parallel whole-organism lineage tracing based on Cas9 induced genetic scars in the zebrafish.

overall_design:
Sequencing of CRISPR/Cas9 induced genetic scars was done by targeted PCR
A Cas9-based method for massive genomic marker-based lineage tracing in zebrafish.
Plase note that the 'Barcodes_zf1fin3.xlsx' annotates GSM2258256-GSM2258282 data.

first: Jan

middle: P

last: Junker

first: Josi

last: Peterson-Maduro

first: Anna

last: Alemany Arias

first: Bo

last: Hu

first: Maria

last: Florescu

first: Alexander

last: van Oudenaarden


title: Transcriptomic analysis of Boswellia sacra wounding stress responses during resin extraction

status: Public on May 15 2019

city: Nizwa

first: Abdul Latif

last: Khan

address: Barkatulmouz

country: Oman

institute: University of Nizwa

summary: Here we report the RNAseq data, related to wounding stress caused for resin production. We extracted RNA from the stem of B. sacra plant collected after 0 day and 30 min of wounding stress (two biological replicates) using the Pure Link Plant RNA reagent kit (Life Technologies, USA) with some modifications and in-house developed HMW RNA extraction method. The de novo assembled transcripts of B. sacra were annotated by performing a BLAST search with the software Blast2GO v.2.6.0 (Conesa et al., 2005). The BLASTx search was done with cut-off E-values of 1.0e−1 and 1.0e−3 against the non-redundant protein sequence database. The same software was used to obtain the gene ontology (GO) information for the assembled transcripts describing different biological processes, molecular function and cellular components.

overall_design: Examination of wounding and control stem.

first: Abdul

middle: L

first: Ahmed

last: Al-Harrasi


title: SCAF4 and SCAF8, Transcriptional Anti-Terminator Proteins (mRNA-Seq)

city: London

first: Richard

middle: James

last: Mitter

state: LONDON

address: 1 Midland Road

department: Bioinformatics & Biostatistics

country: United Kingdom

institute: The Francis Crick Institute

summary: Accurate regulation of RNA Polymerase II (RNAPII) transcriptional termination is a prerequisite for correct gene expression. Here we describe a role for SCAF4 and SCAF8 as anti-terminators, suppressing the use of early, alternative polyadenylation sites (PASs). The SCAF4/8 proteins bind the hyper-phosphorylated RNAPII C-terminal repeat domain (CTD) modified on both Ser2 and Ser5, and are detected at early, alternative PASs. Concomitant knockout of human SCAF4 and SCAF8 results in altered PAS selection, leading to expression of truncated mRNAs and proteins lacking functional domains, and is cell-lethal. While SCAF4 and SCAF8 thus work redundantly to suppress early termination, they also have independent, non-essential functions. SCAF8 is a positive RNAPII elongation factor, whereas SCAF4 is required for correct termination at canonical transcription termination sites in the presence of SCAF8. Together, SCAF4 and SCAF8 coordinate the transition between elongation and termination, directing PAS selection to ensure correct RNAPII transcriptional termination in human cells.

overall_design: To study the function of SCAF4 and SCAF8 in human cells, we used CRISPR-Cas9 nickase technology to generate single and double knockouts (KOs) in HEK293 Flp-In TREX cells, which also contained a single copy of a doxycycline (Dox)-inducible SCAF4 or SCAF8 rescue construct, with the encoded GFP-tagged protein expressed at near-normal levels. All cell lines were maintained in the presence of Dox to ensure expression of the CRISPR-resistant rescue gene during and after KO cell line generation. Expression of the rescue protein reaches undetectable levels after 5 days growth in Dox-free media, resulting in effective single of double KOs. Due to the manner in which these cell lines were generated, a total of 12 cell types (6 different cell lines grown with or without Dox) were often analysed together. For example, SCAF4 SCAF8 double KOs were generated either by first knocking out SCAF4 and then SCAF8, or vice versa, and these different cell lines were in turn also derived from cell lines containing either a Dox-inducible SCAF4- or a SCAF8 rescue gene, giving rise to a total of 4 genotypically identical SCAF4 SCAF8 dKO cell lines. Moreover, a SCAF4 SCAF8 double KO that expresses a rescue gene (i.e. grown in the presence of doxycycline) is effectively a single KO; for example, a SCAF4 SCAF8 double KO expressing the SCAF4 rescue gene is genotypically and phenotypically a single SCAF8 KO cell line. For PAR-CLIP experiments, HEK293 Flp-In TREX cells stably expressing FLAG-tagged SCAF4 or SCAF8 were used for FLAG immunoprecipitations from RNA-protein crosslinked extracts.

first: Lea

middle: H

last: Gregersen

first: Alejandro

last: Ugalde

first: Takayuki

last: Nojima

first: Jesper

middle: Q

last: Svejstrup


title: Large, Diverse Population Cohorts of hiPSCs and Derived Hepatocyte-like Cells Reveal Functional Genetic Variation at Blood Lipid-Associated Loci

city: Philadelphia

first: Daniel

middle: J

last: Rader

state: PA

address: 3400 Civic Center Blvd

department: ITMAT

country: USA

institute: University of Pennsylvania

summary: Musunuru, Brown, Rader, and colleagues of the NHLBI NextGen consortium use multi-ethnic population cohorts of iPSCs and differentiated hepatocyte-like cells, in combination with mouse models, to discover and validate functional DNA variants and genes at blood lipid- associated loci previously identified by genome-wide association studies.

overall_design:
Peripheral blood mononuclear cells (PBMCs) isolated 91 individuals (43% African Americans and 55% European Americans; 60% women and 40% men) were used to generate iPSCs. PBMCs were differentiated into HLCs which were morphologically similar to primary hepatocytes. RNA-seq data was generated from iPSCs (n=89), HLCs (n=86), primary hepatocytes (n=4) and whole liver in GTEx cohort (n=96).
The majority of data for this study is deposited in at dbGaP for controlled access:
https://www.ncbi.nlm.nih.gov/gap/?term=phs001341

first: Evanthia

middle: E

last: Pashos

first: YoSon

last: Park

first: Xiao

last: Wang

first: Avanthi

last: Raghavan

first: Wenli

last: Yang

first: Deepti

last: Abbey

first: Derek

last: Peters

first: Juan

last: Arbelaez

first: Mayda

last: Hernandez

first: Nicolas

last: Kuperwasser

first: Wenjun

last: Li

first: Zhaorui

last: Lian

first: Ying

last: Liu

first: Wenjian

last: Lv

first: Stacey

last: Lytle-Gabbin

first: Dawn

last: Marchadier

first: Peter

last: Rogov

first: Jianting

last: Shi

first: Katherine

last: Slovik

first: Ioannis

middle: M

last: Stylianou

first: Li

first: Ruilan

last: Yan

first: Xiaolan

last: Zhang

first: Sekar

last: Kathiresan

first: Stephen

last: Duncan

first: Tarjei

last: Mikkelsen

first: Edward

last: Morrisey

first: Christopher

middle: D

last: Brown

first: Kiran

last: Musunuru


title: The long non-coding RNA Morrbid regulates CD8 T cells in response to viral infection

first: Jonathan

last: Kotzin

address: 421 Curie Boulevard, Biomedical Research Building II/III, Room 312

institute: UPenn

summary: The transcriptional programs that regulate CD8 T cell differentiation and function in the context of viral infections or tumor immune surveillance have been extensively studied; yet, how long non-coding RNAs (lncRNAs) and the loci that transcribe them contribute to the regulation of CD8 T cells during viral infections remains largely unexplored. Here, we report that transcription of the lncRNA Morrbid is specifically induced by T cell receptor (TCR) and type I IFN stimulation during the early stages of acute and chronic lymphocytic choriomeningitis virus (LCMV) infection. In response to type I IFN, the Morrbid RNA and its locus control CD8 T cell expansion, survival, and effector function by regulating the expression of the pro-apoptotic factor, Bcl2l11, and by modulating the strength of the PI3K-AKT signaling pathway. Thus, our results demonstrate that inflammatory cue-responsive lncRNA loci represent fundamental mechanisms by which CD8 T cells are regulated in response to pathogens and potentially cancer.

overall_design: Total RNA profiles of stimulated sorted naïve (CD62Lhi CD44lo) wild type and Morrbid-/- CD8 T cells

first: Fany

last: Iseka

first: Jorge

last: Henao-Mejia


title: Changes in m6A RNA methylation contribute to heart failure progression by modulating translation

city: Göttingen

first: Gaurav

last: Jain

state: Lower Saxony

address: Von-Siebold-Str. 3a, Office no: 2.212

institute: The German Center for Neurodegenerative Diseases (German: Deutsches Zentrum für Neurodegenerative Erkrankungen DZNE)

summary: We analysed m6A RNA methylation via next generation sequencing (NGS). We found that approximately one quarter of the transcripts in the healthy mouse and human heart exhibit m6A RNA-methylation. There was a mild positive correlation of m6A RNA-methylation at the 5’UTR and coding region with transcript level while m6A RNA-methylation at the 3’UTR showed a mild negative correlation. When we analyzed heart failure in mice and humans we observed that changes in m6A RNA-methylation exceed changes in gene-expression. In mouse and human heart failure transcripts with altered m6A RNA-methylation were mainly linked to metabolic and regulatory pathways while changes in transcript level mainly represented changes in structural plasticity. Mechanistically we could link m6A RNA-methylation to altered RNA translation and protein production. Furthermore, mice with a cardiomyocyte restricted knockout of the demethylase Fto show an impaired function compared to control mice.  Thus, we describe for the first time m6A RNA methylation at the genome-wide level in the human heart and in addition use mouse models to provide evidence that changes in m6A RNA-methylation play an important role in heart failure development by affecting regulatory pathways distinct from those genes with altered expression levels regulate. Our data suggest that modulation of epitranscriptomic processes such as m6A-methylation might be an interesting target for therapeutic interventions.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We analyzed m6A RNA methylation via next generation sequencing (NGS) in mouse models for heart hypertrophy and heart failure along with human failed heart samples. Moreover, we show that methylation levels in heart failure is positively associated with polysome occupancy and thus with translation

first: Tea

last: Berulava

first: Eric

last: Buchholz

first: Vakhtang

last: Ellerdashvilli

first: Tonatiuh

last: Pena

first: Andre

last: Fischer

first: Karl

last: Toischer


title: PI3K-Yap activity drives cortical gyrification and hydrocephalus in mice

city: Seattle

first: Kimberly

last: Aldinger

state: WA

address: 1900 Nineth Ave

institute: Seattle Children's Research Institute

summary: Mammalian brain evolved through several transitions between gyrencephaly and lissencephaly. Mechanisms generating gyrified or smooth brain are incompletely understood. Here we demonstrate that a short embryonic pulse of activating mutations in Pik3ca, the catalytic subunit of PI3K enzyme is sufficient to cause mouse cortical gyrification. We demonstrate that this gyrification phenotype is initiated by subtle focal regulation of apical cell adhesion and proliferation via PI3K-dependent localization of Yap protein. Treatment with verteporfin (Drug)  a nuclear Yap inhibitor, attenuated over-proliferation and adhesion abnormalities, and subsequently gyrification. The purpose of this study was to compare the control and mutant mouse transcriptome, and their respective effect upon verteprofin treatment.

overall_design: Mouse RNA profiles from postnatal day (P)0 hGFAP-cre;Pik3ca H1047R mutant and control hippocampal CA1 region, in presence or absence of a drug Verteporfin

first: Achira

last: Roy

first: Kathleen

last: Millen


title: Chromatin restriction by the nucleosome remodeler Mi-2β and functional interplay with lineage-specific transcription regulators controls B cell differentiation

city: Charlestown

first: Katia

last: Georgopoulos

state: MA

address: 1st and 13th St

department: CBRC

institute: Harvard Medical School

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Coordinated induction but also repression of genes is key to normal differentiation.   Although the role of lineage-specific transcription regulators has been extensively studied, their functional integration with chromatin remodelers, one of the key enzymatic machineries that control chromatin accessibility, remains ill-defined. Here we investigate the role of Mi-2b, a SNF-2-like nucleosome remodeler and key component of the Nucleosome Remodeling Deacetylase (NuRD) complex in early B cells. Inactivation of Mi-2b arrested differentiation at the large pre-B cell stage and caused de-repression of cell adhesion and cell migration signaling factors by increasing chromatin access at poised enhancers and chromosome architectural elements. Mi-2b also supported IL-7R signaling, survival and proliferation by repressing negative effectors of this pathway. Importantly, over-expression of Bcl2, a mitochondrial pro-survival factor and target of IL-7R signaling, partly rescued the differentiation block caused by Mi-2b loss. Mi-2b stably associated with chromatin sites that harbor binding motifs for IKAROS and EBF1 and physically associated with these transcription factors both on and off chromatin.  Notably, Mi-2b shared loss-of-function cellular and molecular phenotypes with IKAROS and EBF1 albeit in a distinct fashion. Thus the nucleosome remodeler Mi-2b promotes pre-B cell differentiation by providing repression capabilities to distinct lineage-specific transcription factor-based regulatory networks.

overall_design: 13 mRNA-seq, 12 ATAC-seq, 2 ChIP_seq samples

first: Toshimi

last: Yoshida


title: SREBP1 drives Keratin 80-dependent cytoskeletal changes and invasive behavior in endocrine resistant ERα breast cancer

city: Vienna

first: Iros

last: Barozzi

address: Borschkegasse 8a

country: Austria

institute: Medical University Vienna

summary: Approximately 30% of women diagnosed with ERα breast cancer relapse with metastatic disease following adjuvant treatment with endocrine therapies. The connection between acquisition of drug resistance and invasive potential is poorly understood. In this study, we demonstrate that the type II keratin topological associating domain (TAD) undergoes epigenetic reprogramming in cells that develop resistance to aromatase inhibitors (AI), leading to keratin 80 (KRT80) upregulation. In agreement, an increased number of KRT80-positive cells are observed at relapse in vivo while KRT80 expression associates with poor outcome using several clinical endpoints. KRT80 expression is driven by de novo enhancer activation by sterol regulatory element-binding protein 1 (SREBP1). KRT80 upregulation directly promotes cytoskeletal rearrangements at the leading edge, increased focal adhesion maturation and cellular stiffening, which collectively promote cancer cell invasion. Shear-wave elasticity imaging of tumors from prospectively recruited patients shows that KRT80 levels correlate with stiffer tumors in vivo. Collectively, our data uncover an unpredicted and potentially targetable direct link between epigenetic and cytoskeletal reprogramming promoting cell invasion in response to chronic AI treatment.

overall_design: Total RNA profiling of MCF7 breast adenocarcinoma cell line and MCF7 overexpressing KRT80. Experiments were carried out in four replicates in both cell lines.

first: Y

last: Perone

first: A

last: Farrugia

last: Rodríguez Meira

first: B

last: Győrffy

first: C

last: Ion

first: D

last: Patten

last: Uggetti

last: Chronopoulos

first: M

last: Faronato

last: Shousha

first: Davies

last: Claire

first: J

last: Steel

first: N

last: Patel

last: del Rio Hernandez

first: R

middle: C

last: Coombes

first: G

last: Pruneri

last: Lim

first: F

last: Calvo

last: Magnani


title: Identify genes involved in ER stress in wheat using RNA sequencing

city: zhengzhou

first: Xing

last: Yu

state: Henan

address: 95 Wenhua Road

institute: Henan Agricultural University

summary: We used dithiothreitol (DTT) and tauroursodeoxycholic acid (TUDCA) to induce or suppress ER stress in wheat cells, respectively, with the aim to reveal the molecular background of ER stress responses using RNA sequencing. Transcriptomic analysis revealed that 8204 genes were differentially expressed in three treatment groups. Among these genes, 158 photosynthesis-related genes, 42 antioxidant enzyme genes, 318 plant hormone-related genes and 457 transcription factors (TFs) might play vital roles in regulating wheat response to ER stress.

overall_design: Experiments were established with three treatments: control (C), DTT (D), and DTT+TUDCA (T). Three independent biological replicates were performed, and a total of nine leaf samples were performed by RNA sequencing.

first: Zeyu

last: Xin


title: Transcriptome analysis of normal-appearing white matter reveals cortisol- and disease-associated gene expression profiles in multiple sclerosis

city: Amsterdam

first: Inge

last: Huitinga

address: Meibergdreef 47

department: Neuroimmunology

country: Netherlands

institute: Netherlands Institute for Neuroscience

summary: Inter-individual differences in cortisol production by the hypothalamus–pituitary–adrenal (HPA) axis are thought to contribute to clinical and pathological heterogeneity of multiple sclerosis (MS). At the same time, accumulating evidence indicates that MS pathogenesis may originate in the normal-appearing white matter (NAWM). Therefore, we performed a genome-wide transcriptional analysis of post-mortem NAWM of 9 control subjects and 18 MS patients to investigate to what extent gene expression reflects disease heterogeneity and HPA-axis activity. Activity of the HPA axis was determined by cortisol levels in cerebrospinal fluid and by numbers of corticotropin-releasing neurons in the hypothalamus, while duration of MS and time to EDSS6 served as indicator of disease severity. Applying weighted gene co-expression network analysis led to the identification of a range of gene modules with highly similar co-expression patterns that strongly correlated with various indicators of HPA-axis activity and/or severity of MS. Interestingly, molecular profiles associated with relatively mild MS and high HPA-axis activity were characterized by increased expression of genes that actively regulate inflammation and by molecules involved in myelination, anti-oxidative mechanism, and neuroprotection. Additionally, group-wise comparisons of gene expression in white matter from control subjects and NAWM from (subpopulations of) MS patients uncovered disease-associated gene expression as well as strongly up- or downregulated genes in patients with relatively benign MS and/or high HPA-axis activity, with many differentially expressed genes being previously undescribed in the context of MS. Overall, the data suggest that HPA-axis activity strongly impacts on molecular mechanisms in NAWM of MS patients, but partly also independently of disease severity.

overall_design: Microarray gene expression analysis was performed on subcortical normal-appearing white matter from 18 MS donors and white matter (WM) of 9 control donors. A reference sample of pooled brain RNA was co-hybridised with each sample.

first: Jeroen

last: Melief

first: Marie

last: Orre

first: Koen

last: Bossers

first: Corbert

middle: G

last: van Eden

first: Karianne

last: Schuurman

first: Matthew

middle: R

last: Mason

first: Joost

last: Verhaagen

first: Jörg

last: Hamann


title: p53 promotes cancer cell adaptation to glutamine deprivation by upregulating Slc7a3 to increase arginine uptake

city: Duarte

first: Haiqing

last: Li

state: CA

address: 1500 East Duarte Road

department: Department of Computational & Quantitative Medicine

institute: Beckman Research Institute of City of Hope, Center for Informatics

summary: Cancer cells heavily depend on the amino acid, glutamine, to meet the demands associated with growth and proliferation. Due to its rapid consumption, cancer cells frequently undergo glutamine starvation in vivo. We and others have shown that p53 is a critical regulator in metabolic stress resistance. To better understand the molecular mechanisms by which p53 activation promotes cancer cell adaptation to glutamine deprivation, we identified p53-dependent genes that are induced upon glutamine deprivation using RNA-seq analysis. We show that Slc7a3, an arginine transporter, is significantly induced by p53. We show the concomitant rise in intracellular arginine levels following glutamine deprivation is dependent on p53. The influx of arginine has minimal effect on known metabolic pathways upon glutamine deprivation. Instead, we found arginine serves as an effector for mTORC1 activation to promote in vitro and in vivo cell growth in response to glutamine starvation. Therefore, we identify a novel p53-inducible gene that contributes to the metabolic stress response.

overall_design: mRNA profiles of p53-expressing and non-expressing MEF cell lines cultured in the presence or absence of glutamine

first: Xazmin

last: Lowman

first: Eric

last: Hanse

first: Ying

last: Yang

first: Mari

middle: B

last: Ishak-Gabra

first: Thai

last: Tran

first: Mei

last: Kong


title: Enhanced early-life nutrition upregulates cholesterol biosynthetic gene expression and Sertoli cell maturation in testes of pre-pubertal Holstein bulls

city: Calgary

first: Chinju Therese

last: Johnson

state: Alberta

department: Production Animal Health

institute: University of Calgary

summary: Pre-pubertal Holstein bull calves fed a higher plane of nutrition had larger testes, earlier puberty, higher serum LH, testosterone and greater sperm production potential than those fed a restricted diet. In addition, pre-pubertal calves fed a high-nutrition diet had higher IGF-I and more proliferating and differentiating Sertoli cells much earlier in life, compared to those fed normal or low-nutrition diets. The objective was to determine changes in mRNA expression of genes in the testes of bulls fed either a high or low pre-pubertal diet.  Holstein bull calves maintained on either a high (20% crude protein (CP) and 71.6% Total Digestible Nutrients (TDN)) or low (12% CP and 64.4% TDN) diet from 2 wk of age, were castrated at 8, 16, 24 and 32 wk and testicular mRNA extracted and sequenced. Differential expression of genes mainly occurred at 16 and 24 wk, with minor changes detected at 32 wk. At 16 wks, functional analysis of DE mRNA with DAVID revealed the common biological processes enriched to be "cholesterol" and "fatty acid biosynthesis" with majority of the genes including HMGCR, HMGCS1, HSD17 being upregulated in high-diet bulls (P<0.05). Major pathways enriched at 16 wks were "cholesterol biosynthesis", "steroid metabolism" and "activation of gene expression by Sterol regulatory element-binding protein (SREBP)" (P<0.05). Mature Sertoli cell marker Connexin 43, was upregulated at 16 wk, whereas an immature Sertoli cell marker, AMH was downregulated at 24 wk, in the high-diet group. Network analysis using IPA, revealed an indirect interaction between insulin family receptor and most upregulated cholesterol biosynthesis genes, implying regulation of testicular function. Thus, enhanced pre-pubertal nutrition in Holstein bulls enhanced testicular cholesterol/steroid biosynthesis and Sertoli cell maturation to promote early reproductive development.

overall_design: Holstein bull calves (n=28) maintained on either a high or low diet from 2 wk of age, were castrated at 8, 16, 24 and 32 wk and testicular mRNA extracted and sequenced.

first: Chinju

first: Jacob

last: Thundathil


title: Regulation of cardiac transcription by thyroid hormone and Med13

city: Iowa City

first: Chad

last: Grueter

state: Iowa

address: PBDB RM 4332

department: Internal Medicine

institute: University of Iowa

summary: Purpose: The objective of this study was to determine cardiac transcriptional pathways regulated in response to 1.) hypothyroidism and re-establishment of a euthyroid state and 2.) Med13-dependent cardiac transcriptional pathways regulated in response to hypothyroidism and re-establishment of a euthyroid state

overall_design: Methods: WT and Med13 cardiac-specific knockout mice (Med13cKO) were put on a normal chow or PTU diet at 8 weeks of age for a duration of 4 weeks.  A third group was put on a PTU diet for 4 weeks followed by 3 daily injections of T3.

first: Rachel

last: Minerath


title: Transcriptional cofactors display core promoter class-specificity in human

first: Vanja

last: Haberle

address: Campus-Vienna-Biocenter 1

institute: The Research Institute of Molecular Pathology (IMP)

summary: Transcriptional cofactors communicate regulatory cues from enhancers to promoters and are central effectors of transcription activation and gene expression, which is a hallmark of all multicellular organisms. However, the extent to which different cofactors display intrinsic specificity for distinct promoters is unclear. Testing intrinsic COF – core promoter (CP) compatibilities requires the systematic assessment of transcriptional activation for many CPs in the presence or absence of a given COF in an otherwise constant standardized reporter system. We therefore combined a plasmid-based high-throughput reporter assay, Self-Transcribing Active Core Promoter-sequencing (STAP-seq), with the specific recruitment of individual COFs to create a high-throughput activator bypass-like assay. Using this assay, we tested whether 5 different individually tethered human COFs (MED15, BRD4, EP300, MLL3 and EMSY) activate transcription from a selection of 12,000 candidate sequences encompassing different types of gene core promoters, enhancers and control sequences. In addition, we used the strong transcriptional activator P65 as a positive control and GFP as a negative control. We found that different COFs preferentially activate different CPs. For instance, MED15 prefers TATA-box containing CPs, while MLL3 preferentially activates CpG island promoters. The observed compatibilities between cofactors and promoters can explain how different enhancers specifically activate distinct sets of genes or alternative promoters within the same gene, and may underlie distinct transcriptional programs in human cells.

overall_design: STAP-seq upon recruitment of individual transcriptional cofactor in HCT116 cells with 5 different cofactors and 2 controls, each in biological triplicate.

first: Cosmas

last: Arnold

first: Michaela

last: Pagani

first: Martina

last: Rath

first: Katharina

last: Schernhuber

first: Alexander

last: Stark


title: Gene expression data from remote ischemic postconditioning in rat model of ischemia reperfusion injury

city: Shenzhen

first: Zanxin

last: Wang

state: Guangdong

address: #12 Langshan Road, Nanshan District

institute: Shenzhen Sun Yat-sen Cardiovascular Hospital

summary:
Restoration of blood flow is the definitive therapy to salvage myocardium following ischemic injury. However, sudden restoration of blood flow to the ischemic myocardium causes ischemia reperfusion injury (IRI).
Here, the cardioprotective effect of remote ischemic postconditioning (RPostC) was investigated, based on our in vitro rat model of myocardial IRI. Three groups, including Sham, IRI, and IRI+ RPostC, were utilized for the analysis of Affymetrix Rat Gene 2.0 ST chip.

overall_design: Total RNAs were extracted and purified from the heart tissues of three groups using TRIzol reagent (Life Technologies) and RNeasy mini kit (Qiagen). Next, we synthesized the cDNA using an Ambion WT Expression Kit (Affymetrix), and obtained the cRNA by using a GeneChip WT Terminal Labeling and Controls Kit (Affymetrix, Inc.). Affymetrix Human Transcriptome Array 2.0 was then utilized to hybridize the fragmented cRNA product. After washing and staining in the GeneChip Fluidics Station 450, Affymetrix® GeneChip Command Console (AGCC) and robust multichip analysis (RMA) algorithms were used to scan the arrays and analyze the data

first: Minxin

last: Wei


title: Genome wide DNA methylation analysis of isolated endometrial epithelial cells from obese women

city: Tokyo

first: Naofumi

last: Miwa

country: Japan

institute: Toho University

summary: Genomo wide DNA methylation analysis of isolated endometrial epithelial cells from obese women. The illumima Infinium MethylationEPIC was used to obtain DNA methylatoin profiles across approximately 850K CpGs in isolated cultured cells. Total eight samples (five controls and three obese cases) were included in the file.

overall_design: Bisulphite converted DNA from the eight samples were hybridized to the lllumina Infinium MethylationEPIC.

first: M

last: Nagashima

first: N


title: HOS15 interacts with a histone deacetylase to control gene expression and development

city: St Louis

first: Xuehua

last: Zhong

state: MO

address: One Brookings Drive

department: Biology

institute: Washington University in St. Louis

summary: This study identified HOS15, a protein with a WD40-repeat, as an interactor with the HDA9-PWR histone deacetalyse complex. HOS15 has an essential role in controlling HDA9-specific gene expression and development.

overall_design: Immunopreciptation and mass spectrometry of epitope-tagged expressed transgenes (HDA9, PWR, and HOS15) confirmed all interact with one another in vivo. Genetic analysis of mutant combinations suggest each member is indispensible for the complex's molecular and physiological functions.

first: Kevin

last: Mayer

first: Xiangsong

last: Chen

first: Dean

last: Sanders


title: Alterations in Gene Expression in Arabidopsis thaliana Expressing ISPS

city: East Lansing

first: Thomas

last: Sharkey

state: MI

address: 612 Wilson Rd, Rm 210 Plant Biology Building

department: Biochemistry and Molecular Biology

institute: Michigan State University

summary: Genetically engineering Arabidopsis thaliana to express Isoprene Synthase (ISPS) leads to changes in expression of genes assoiated with many growth regulator signaling pathways and signaling networks involved in abiotic and biotic stress responses.

overall_design: Arabidopsis thaliana transformed with a Eucalyptus globulus ISPS (line B2) and a line transformed with empty vector DNA (EV-B3), grown under unstressed growth conditions were subjected to RNA-Seq


title: Alterations in Gene Expression in Nicotiana tabacum Expressing ISPS

summary: Genetically engineering Nicotiana tabacum to express Isoprene Synthase (ISPS) leads to changes in expression of genes assoiated with many growth regulator signaling pathways and signaling networks involved in abiotic and biotic stress responses.

overall_design: Nicotiana tabacum transformed with a Populus alba ISPS (line NE) and the corresponding non-emitting azygous control (NE), grown under unstressed growth conditions were subjected to RNA-Seq


title: Alterations in Gene Expression in Arabidopsis thaliana and Nicotiana tabacum Expressing ISPS

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

sample_organism:
Arabidopsis thaliana
Nicotiana tabacum

platform_organism:
Arabidopsis thaliana
Nicotiana tabacum

overall_design: Refer to individual Series


title: Human macrophages exhibit high activity to clear intracellular biovar Microtus strain of Y. pestis

city: Beijing

first: Zongmin

last: Du

address: No. 20, Fengtai Dongdajie Street

institute: Beijing Institute of Microbiology and Epidemiology

summary: human peripheral lymphocytes were infected with the full virulent strain 141 or human avirulent Microtus strain 201, and their transcriptomes were determined and compared. The most impressive finding is that robust responses of lysosome, TLR signaling and FcR mediated phagocytosis pathways were provoked at 2 hpi in 201- but not in 141-infected lymphocytes, suggesting that human lymphocytes might be able to constrain infection caused by strain 201 but not 141.

overall_design: We used RNA-sequencing technology to analyze transcriptomic of human peripheral lymphocytes infected with the full virulent strain 141 or human avirulent Microtus strain 201, and these transcriptomes were  further compared and functionally validated.

first: Qingwen

last: Zhang

first: Tong

first: Youquan

last: Xin

first: Haihong

last: Zhao


title: Global RNA expression profiles between shNC and shcircβ-catenin in PLC/PRF/5 cells

city: Hong Kong

first: Weicheng

last: Liang

address: Area 39

country: Hong Kong

institute: The Chinese University of Hong Kong

summary: Circular RNAs are a class of non-coding RNA transcripts, which are ubiquitously expressed in eukaryotes. In the current study, we identified a novel circRNA derived from β-catenin gene locus, which was named “circβ-catenin”. In order to characterize the function of circβ-catenin in modulating Wnt pathway, we conducted RNA-seq to evaluate the effect of circβ-catenin on global RNA expression profiles.

overall_design: Examination of RNA expression profiles on shNC and shcircβ-catenin PLC/PRF/5 cells

first: Jinfang


title: RIP-seq of the Arabidopsis mRNA export mutant aly1 and associated controls.

city: St. Louis

first: R. Keith

last: Slotkin

state: Missouri

address: 975 North Warson Road

institute: Donald Danforth Plant Science Center

summary: RNA-directed DNA methylation (RdDM) is a set of mechanisms by which transcriptionally-repressive DNA methylation and histone modifications are targeted de novo to transposable element and transgene regions of the genome. We identified a mutant in which all forms of RdDM are deficient, leading to the transcriptional activation of some transposable elements and the complete inability to initiate transgene silencing. The mutated gene, ALY1, encodes an RNA-binding nuclear export protein belonging to a family of four ALY proteins in Arabidopsis. ALY proteins function together to export a large number of mRNAs from the nucleus for translation, but we found that ALY1 is unique in its ability to enable RdDM. We sequenced methylomes (via MethylC-seq) to identify the genome-wide loss of CHH methylation targeted by RdDM in aly1 mutants. We sequenced small RNAs and determined that ALY1 functions in RdDM downstream of small RNA production and export. We sequenced total, nuclear and cytoplasmic mRNAs to determine that ALY1 functions in the nuclear export directly or indirectly on 2,612 mRNAs. Additionally, we sequenced RNAs bound to the ALY1 protein using RNA-immunoprecipitation followed by high throughput sequencing.

overall_design: Examination of ALY1-bound RNA population in two replicates of wild-type Columbia and four replicates of the ALY1pro::ALY1-GFP transgene complementing the aly1-1 mutation, using a GFP antibody.

first: Sarah

last: Choudury

first: Saima

last: Shahid

first: R

middle: K


title: Transcriptome of the Arabidopsis mRNA export mutant aly1 and associated controls

overall_design: Examination of steady state poly(A)+ mRNA accumulation in total, nuclear and cytoplasmic fractions of wild-type Columbia and aly1-2 mutants.

first: Andrea

last: McCue


title: Methylome, transcriptome, RIP-seq and small RNA-seq of the Arabidopsis mRNA export mutant aly1 and associated controls

type: Methylation profiling by high throughput sequencing

type: Non-coding RNA profiling by high throughput sequencing


title: Small RNA-seq of the Arabidopsis mRNA export mutant aly1 and associated controls

overall_design: Examination of small RNA accumulation in three replicates of wild-type Columbia and four mutants.

first: Diego

last: Cuerda-Gil

first: Kaushik

last: Panda


title: IL1b signaling in human coronary artery endothelial cells

city: Zürich

first: TOM

last: SKARIA

address: Rämistr. 100

department: INTERNAL MEDICINE

country: Switzerland

institute: UNIVERSITY HOSPITAL ZURICH

summary:
IL1b signaling is critically involved in inflammatory diseases. However, the gene targets and mechanisms of IL1b mediated inflammatory processes in adult human vascular endothelium still remain unclear.
We show that IL1b  regulates genes coding for inflammatory cytokines, cell adhesion molecules and pathways through NFkB transcriptional activation. We further identify the genes regulated by IL1b that regulate endothelial barrier function and act as targets for known clinically relevant compunds.  These findings stimulate further research to identify novel signaling mechanisms  modulating endothelial barrier function in IL1b driven inflammatory pathologies.

overall_design: A two color competitive hybridization design was chosen.  Samples from respective treatments are labelled with Cy5  and hybridized against a Cy3 labelled non-treated reference sample from the same experiment.

first: Tom

last: Skaria

first: Gabriele

last: Schoedon


title: Methylome of the Arabidopsis mRNA export mutant aly1 and associated controls

overall_design: Examination of whole genome methylation in three replicates of wild-type Columbia and eleven mutants.


title: Comparative transcriptomic analyses provide insights into key genes involved in niche-associated functions of primary murine LEC and BEC in homeostasis

city: Charlottesville

first: Alexander

middle: Fritz

last: Koeppel

state: VA

address: 1640 Jefferson Park Avenue

department: School of Medicine

institute: University of Virginia

summary:
Purpose: The goal of this study is to compare the transcriptome profiles of freshly isolated primary murine endothelial populations, namely the lymph node-derived lymphatic endothelial cell (LN-LEC) and blood endothelial cell (LN-BEC), and the diaphragm-derived LEC (D-LEC) in homeostasis.
Methods: LN-LEC and LN-BEC total RNA samples were prepared by pooling inguinal, axillary, brachial, cervical, and mesenteric LNs from wild-type C57BL/6 (B6) mice (6-8 weeks of age, purchased from NCI), followed by mechanical and enzymatic digestion, CD45- cell lineage enrichment using MACS beads (deplete S protocol in AUTOMACS), and sorted by flow cytometry based on CD45, CD31, and podoplanin expressions using Influx (BD) into RNA Protect (Qiagen). D-LEC total RNA samples were prepared by mechanical and enzymatic digestion of tissues, followed directly by flow cytometry sorting as described above. Total RNA extraction was performed using RNAeasy mini kit (Qiagen) as per manufacturer’s instructions. The cDNA library preparation and sequencing were performed by the Genomic Services Laboratory at Hudson Alpha, USA. Briefly, purified total RNAs (RIN score of 7.0 or higher) were prepared for sequencing using the Ovation RNA-seq System V2 kit (Nugen) followed by RNA-sequencing of 100 paired-end reads using the Illumina HiSeq 2500 v4 platform. Raw RNA-sequencing read quality was assessed using FastQC and low quality regions were trimmed using Fastx-trimmer. Cleaned reads were aligned to the mouse reference genome (build mm9) using STAR and read counts on known mouse genes were calculated using featureCounts, part of the Subread package. Next, uniquely aligned reads were analyzed using the DEseq2 package in the R statistical computing environment to obtain normalized counts, estimate dispersion, and determine a negative binomial model for each gene. Differentially expressed genes (DEG) were determined using DESeq2 and the Benjamini-Hochberg False Discovery Rate procedure was used to re-estimate the adjusted p-values. Differentially expressed genes (DEGs) were subsequently identified as those with an FPKM of 1 or greater, p-adjusted < 0.05, and additionally 5X-DEG subsets were identified as those with fold-change of 5 or greater.
Results: Post-sort analyses of LN-LEC, LN-BEC, and D-LEC replicates showed 92.6-98.6% purity. RNAseq yielded 48-98 million reads per replicate, with an average length of 180 nucleotides, and an average of 85.7% uniquely mapped reads. These reads mapped a total of 23284 genes, of which 15331 were considered expressed based on an average FPKM of 1 or greater in at least one cell type. Of this number, 14718, 14893, and 14384 genes were considered expressed in LN-LEC, LN-BEC, and D-LEC, respectively. Principal component analysis revealed that the transcriptional profiles of sample replicates clustered tightly, and that those of LN-LEC, LN-BEC, and D-LEC differed from each other.
Conclusions: Our study provides insights into key genes involved in niche-associated functions of primary murine LEC and BEC in homeostasis. The RNA-seq data reported here may provide a conceptual framework for future comparative investigations of LN-LEC, LN-BEC, and D-LEC phenotypic expression profiles, heterogeneity, and niche-specific functions in homeostasis as well as disease.

overall_design: mRNA profiles of 4 LN-LEC, 3 LN-BEC, and 3 D-LEC samples from wild-type C57BL/6 (B6) mice (6-8 weeks of age) were generated by RNA-sequencing using the Illumina HiSeq 2500 v4 platform.

first: Stella

last: Berendam

middle: F

first: Nicole

last: McKenna

first: Sherin

last: Rouhani

first: Stephen

last: Turner

first: Victor

last: Engelhard


title: Structural variation targets neurodevelopmental genes and identifies SHANK2 as a tumor suppressor in neuroblastoma

city: New York

first: Gonzalo

last: Lopez

state: NY

address: 1399 Park avenue

department: Genetics and Genomic Sciences

institute: Mount Sinai School of Medicine

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

summary: Neuroblastoma, like many childhood cancers, exhibits a relative paucity of somatic single nucleotide variants (SNVs). Here, we assess the contribution of structural variation (SV) in neuroblastoma using a combination of whole genome sequencing (WGS; n=135) and single nucleotide polymorphism (SNP) genotyping (n=914) of matched tumor-normal pairs. Our study design provided means for orthogonal validation of SVs as well as validation across genomic platforms. SV frequency, type, and localization varied significantly among high-risk tumors, with MYCN non-amplified tumors harboring an increased SV burden overall (P=1.12x10-5). Genes disrupted by SV breakpoints were enriched in neuronal lineages and autism spectrum disorder. The postsynaptic adapter protein-coding gene SHANK2, located on chromosome 11q13, was disrupted by SVs in 14% and 10% of MYCN non-amplified high-risk tumors based on WGS and SNP array cohorts, respectively. Forced expression of SHANK2 in neuroblastoma cell models resulted in significant growth inhibition (P=2.62x10-2 to 3.4x10-5) and accelerated neuronal differentiation following treatment with all-trans retinoic acid (P=3.08x10-13 to 2.38x10-30). These data further define the complex landscape of structural variation in neuroblastoma and suggest that events leading to deregulation of neurodevelopmental processes, such as inactivation of SHANK2, are key mediators of tumorigenesis.

overall_design: 1747 Samples

first: Jo

last: Rokita


title: Immunotherapeutic effects of intratumoral nanoplexed Poly I:C

city: Pamplona

first: Maria

middle: Angela

last: Aznar

address: Pio XII num 55

institute: Center for applied medical research (CIMA)


title: Transcriptional single cell analysis of human umbilical cord derived mesenchymal stem cells

city: shanghai

first: Yufang

last: Shi

state: Shanghai

address: 320 Yueyang Road

institute: Chinese Academy of Science

summary: Mesenchymal stem cells (MSCs) are a population of multipotent cells with an attractive ability to promote tissue repair by regulating regeneration and inflammation. Ironically, the immune regulatory capacity of MSCs, regardless of their tissue origin, is endowed by inflammatory cytokines (e.g., IFNg plus TNFa). Effective application of MSCs relies on the production of relatively homogeneous MSCs. However, the cellular heterogeneity, and the differentiation trajectories of in vitro expanded MSCs remains unclear. We profiled the transcriptomes of 361 single MSCs derived from two umbilical cords (UC-MSCs). The MSCs are from different passages and culture conditions with or without inflammatory cytokine stimulation. Weighted gene correlation network analysis for the expression of their highly variable genes revealed that UC-MSCs surprisingly possess only limited heterogeneity. Cell cycle based principal component analysis showed that the limited heterogeneity identified in these UC-MSCs was strongly associated with their entrance into the G2/M phase. This was further proven by the observation that one featured gene CD168 was expressed in a cell-cycle dependent manner. When CD168high UC-MSCs were sorted and cultured in vitro, they repopulated into a new community that is similar to the original status. Our results demonstrated that in vitro expanded UC-MSCs is a well-organized population with limited heterogeneity dominated by cell cycle status. Thus, our studies argues that standardization of MSCs for disease treatment is possible.

overall_design: MSCs isolation from the umbilical cord, in vitro expansion, pretreatment approach, single cell capture, and RNA sequencing. Cells isolated from two different donors are sequenced in three passages with or without cytokine stimulation.Donor1, passage5, naive, 52cells; Donor2, passage5, naive, 50cells; Donor2, passage2, naive, 50cells; Donor2, passage0, naive, 50cells; Donor1, passage5, stimulation, 59cells; Donor2, passage5, stimulation, 50cells; Donor2, passage2, stimulation, 50cells;

first: Yin

last: Huang

first: Qing

last: Li

first: Kunshan

last: Zhang

first: Mingyuan

last: Hu

first: Yu

last: Wang

first: Kai

last: Qi

first: Liming

last: Du

first: Liangyu

last: Lin

first: Siguang

first: Ying


title: Immunotherapeutic effects of intratumoral nanoplexed Poly I:C (B16OVA tumors)

summary:
Poly I:C is a powerful immune adjuvant as a result of its agonist activities on TLR-3, MDA5 and RIG-I. Intratumoral administration is conceivably safer than systemic delivery and allows concentrate proinflammatory adjuvanticity in the tumor microenvironment and tumor-draining lymphoid tissue. BO-112 is a nanoplexed formulation of Poly I:C complexed with polyethylenimine that causes tumor cell apoptosis showing immunogenic cell death features and that upon intratumoral release results in more prominent tumor infiltration by T lymphocytes. Intratumoral treatment of subcutaneous tumors derived from MC38, 4T1 and B16F10 with BO-112 leads to remarkable local disease control mediated by CD8+ T lymphocytes, as concluded from selective depletion experiments. Some degree of control of non-injected tumor lesions upon BO-112 intratumoral treatment was found in mice bearing bilateral B16OVA melanomas, that was enhanced when co-treated with systemic anti-CD137 and anti-PD-L1 immunomodulatory mAbs. More abundant CD8+ T lymphocytes were found in tumor-draining lymph nodes and in the tumor microenvironment following intratumoral treatment with BO-112. Enhanced numbers of tumor-specific CTLs recognizing melanosomal antigens and ovalbumin were readily detected among them. Genome-wide transcriptome analyses of injected tumor lesions were consistent with a marked upregulation of the type-I interferon pathway. Intratumorally delivered BO-112 is being tested in cancer patients (NCT02828098) and our results in mice suggest prominent anti-tumor local control through its proimmune effects.
Intratumoral administration of BO-112, a nanoplexed form of PolyI:C, triggers an efficacious antitumor response in different tumor models as a consequence of proimmflamatory activity and its direct effects in tumor cells. BO-112 local administration induces direct tumor cell death by apoptosis, showing signs of immunogenic cell death, and a strong release of IFNα/β and other proinflammatory mediators. As a result, a tumor-specific CD8+ immune response is mounted or augmented to the point of controlling tumor progression both in the locally injected lesion and to some extent on distantly implanted tumor nodules

overall_design: B16OVA tumors intratumorally injected with BO-112 (n=5) is compared to the vehicle-injected B16OVA tumors (n=5)

middle: A

first: Ignacio

last: Melero

first: Lourdes

last: Planelles

first: Marisol

last: Quintero


title: Immunotherapeutic effects of intratumoral nanoplexed Poly I:C (B16-OVA cell line)

summary:
Poly I:C is a powerful immune adjuvant as a result of its agonist activities on TLR-3, MDA5 and RIG-I. Intratumoral administration is conceivably safer than systemic delivery and allows concentrate proinflammatory adjuvanticity in the tumor microenvironment and tumor-draining lymphoid tissue. BO-112 is a nanoplexed formulation of Poly I:C complexed with polyethylenimine that causes tumor cell apoptosis showing immunogenic cell death features and that upon intratumoral release results in more prominent tumor infiltration by T lymphocytes. Intratumoral treatment of subcutaneous tumors derived from MC38, 4T1 and B16F10 with BO-112 leads to remarkable local disease control mediated by CD8+ T lymphocytes, as concluded from selective depletion experiments. Some degree of control of non-injected tumor lesions upon BO-112 intratumoral treatment was found in mice bearing bilateral B16OVA melanomas, that was enhanced when co-treated with systemic anti-CD137 and anti-PD-L1 immunomodulatory mAbs. More abundant CD8+ T lymphocytes were found in tumor-draining lymph nodes and in the tumor microenvironment following intratumoral treatment with BO-112. Enhanced numbers of tumor-specific CTLs recognizing melanosomal antigens and ovalbumin were readily detected among them. Genome-wide transcriptome analyses of injected tumor lesions were consistent with a marked upregulation of the type-I interferon pathway. Intratumorally delivered BO-112 is being tested in cancer patients (NCT02828098) and our results in mice suggest prominent anti-tumor local control through its proimmune effects.
To compare the in-vitro and in vivo transcriptional profile induced by BO-112, B16-OVA cell lines were incubated with BO-112 for 24h. BO-112 induces a specific transcriptional profile in B16-OVA cell cultures. Key immunoregulatory genes were found to be differentially expressed between BO-112 and Vehicle-incubated B16-OVA cells.

overall_design: B16-OVA cells were incubated either with BO-112 at 0.5 µg/mL (n=3) or identical volumes of vehicle (5%glucose, n=3) for 24h


title: Hypoxia Inducible Factor 1 Confers Androgen Independence in Prostate Cancer

city: Cambridge

first: Chandra

last: Chilamakuri

address: Robinson Way

institute: Cancer Research UK Cambridge Institute


title: Regulation of nitrogen and carbon metabolism in Aspergillus nidulans.

city: Warsaw

first: Agnieszka

last: Dzikowska

address: Pawinskiego 5A

country: Poland

institute: University of Warsaw

summary: In Aspergillus nidulans, nitrogen and carbon metabolism are under the control of wide-domain regulatory systems, including nitrogen metabolite repression, carbon catabolite repression. Transcriptomic analysis of the wild type strain grown under different combinations of carbon and nitrogen regimes was performed, to identify differentially regulated genes. Carbon metabolism predominates as the most important regulatory signal but for many genes, both carbon and nitrogen metabolisms coordinate regulation.

overall_design: Global transcriptional analysis in the wild type strain (biA1) grown  under four different nitrogen and carbon regimes. RNA was isolated from three biological replicates grown under the same conditions and combined in one sample for RNA-seq.

last: Macios

first: Gareth

last: Weedal

first: Mark

middle: X

last: Caddick


title: Gene expression analysis of androgen treatment and stable HIF1a expression in LNCaP cell line

summary:
Androgen receptor (AR) and hypoxia inducible factor 1a (HIF1a) are transcription factors that promote prostate cancer progression. This study investigated the relationship between the AR and HIF1a signaling pathways.
Gene expression analysis identified transcriptional changes in response to androgen treatment and stable HIF1a expression.

overall_design: 42 samples analyzed

first: Maxine

last: Tran

first: Becky

last: Bibby

first: Ian

last: Mills

first: David

last: Neal


title: Transcriptional cofactors display core promoter class-specificity

city: Vienna

first: Vanja

last: Haberle

summary: Transcriptional cofactors communicate regulatory cues from enhancers to promoters and are central effectors of transcription activation and gene expression, which is a hallmark of all multicellular organisms. However, the extent to which different cofactors display intrinsic specificity for distinct promoters is unclear.  Testing intrinsic COF – CP preferences requires the systematic assessment of transcriptional activation for many CPs in the presence or absence of a given COF in an otherwise constant standardized reporter system. We therefore combined a plasmid-based high-throughput reporter assay, Self-Transcribing Active Core Promoter-sequencing (STAP-seq), with the specific recruitment of individual COFs to create a high-throughput activator bypass-like assay. Using this assay, we tested whether 23 different individually tethered Drosophila melanogaster COFs could activate transcription from any of 72,000 CP candidates in S2 cells. We selected COFs that represent different functional classes and enzymatic activities: histone-acetyl transferases (Nejire - the fly ortholog of CBP/P300, Mof, Gcn5 - ortholog of pCAF, Atac2, Tip60, Br140), three components of the COMPASS-like histone H3K4 methyltransferase complexes (Lpt, Trr and Trx), nucleosome remodeling ATP-ase (Brm), two Chromo or Chromo-shadow domain (Chro and Mof) and three Bromodomain (Brd8, Brd9 and fs(1)h - ortholog of Brd4) -containing COFs, three subunits of the Mediator Complex (MED15, MED24 and MED25), three subunits of the TFIID general transcription factor (Taf4, Tbp and Trf2) and three less well-characterized COFs (EMSY, Gfzf and Pzg). We used the strong transcriptional activator P65 as a positive and GFP as a negative control. In addition, we tested 6 COFs and the 2 controls in two other Drosophila cell lines: ovarian somatic cells (OSC) and Kc167 cells.  We uncovered five classes of core promoters, distinguished by their differential response to specific cofactors and by the presence of known sequence elements, such as the TATA-box, Down-stream Promoter Element, or TCT motif. Moreover, the five promoter types show distinct chromatin properties at endogenous loci. The observed compatibilities between cofactors and promoters can explain how different enhancers specifically activate distinct sets of genes, alternative promoters within the same genes, or even distinct transcription starting sites within the same promoters. Thus, cofactor–promoter compatibilities may underlie distinct transcriptional programs.

overall_design: STAP-seq upon recruitment of individual transcriptional cofactor in S2 cells with 23 different cofactors and 2 controls, each in biological triplicate.

first: Cosmas

last: Arnold

first: Michaela

last: Pagani

first: Martina

last: Rath

first: Katharina

last: Schernhuber

first: Alexander

last: Stark


title: Gene Expression of murine mammary stem-like cells, HC11: Control vs miRNA206 mimic treatment

city: Solna

first: Cecilia

last: Williams

address: Tomtebodav 23

department: Protein Science

country: Sweden

institute: KTH Royal Institute of Technology

summary: MicroRNAs are likely to play pivotal roles in both stem cells and cancer, and are further promising candidates for future therapeutic purposes. To understand the role of miR206 in mammary cell differentiation,  we profiled the transcription of  mamary stem-like cells,  comparing control HC11 cells (unspecific miRNA mimic treated)  with HC11 cells transfected with miRNA-206 mimic.

overall_design: Comparison of NC mimic-treated vs.miR-206 mimic treated HC11 cells. Mouse Operon’s long oligonucleotide- spotted arrays  were used (Microarray Inc.,Huntsville, Alabama). Microarray analysis was based on hybridization between the transcript and its corresponding probes. 2-color comparative microarray  assays were carried out that each sample (Control and miRNA206 treatment) was labeled with either Cy3 or Cy5 dye. Errors introduced by differential labeling were adjusted using dye-swap replicates.

first: Aydogdu

last: Eylem

first: Williams

last: Cecilia


title: Comparative Transcriptome Analysis of lncRNAs and mRNAs associated with different coat colours in Pashmina fiber

city: Gandarbal

first: Basharat

middle: Ahmad

last: Bhat

state: Kashmir

address: Shuhama

department: Animal Biotechnology

country: India

institute: Sher-e-Kashmir University of Agricultural Sciences and Technology

summary: Introduction: Identification of genes (mRNA + lncNRA) that regualte coat colouring and pigmentation in pashmina goat.

overall_design: 6 pashmina goats of the same age (26 months) and sex (doves) from each colour group viz grey, white and black were selected for sampling from the SKUAST-Kashmir goat farm located in the northern Himalayas (Satakna, Ladakh) at an altitude of 12000 feet above sea level.

first: Nazir

last: ganai


title: The histone demethylase KDM3A regulates the transcriptional program of the androgen receptor in prostate cancer cells

city: Merced

first: Fabian

middle: Volker

last: Filipp

state: California

address: 5200 North Lake Road

department: Systems Biology and Cancer Metabolism, Program for Quantitative Systems Biology

institute: University of California Merced

summary: The lysine demethylase 3A (KDM3A, JMJD1A or JHDM2A) controls transcriptional networks in a variety of biological processes such as spermatogenesis, metabolism, stem cell activity and tumor progression. We matched transcriptomic and ChIP-Seq profiles to decipher a genome-wide regulatory network of epigenetic control by KDM3A in prostate cancer cells. ChIP-Seq experiments monitoring histone 3 lysine 9 (H3K9) methylation marks show global histone demethylation effects of KDM3A. Combined assessment of histone demethylation events and gene expression changes presented major transcriptional activation suggesting that distinct oncogenic regulators may synergize with the epigenetic patterns by KDM3A. Pathway enrichment analysis of cells with KDM3A knockdown prioritized androgen signaling indicating that KDM3A plays a key role in regulating androgen receptor activity. Matched ChIP-Seq and knockdown experiments of KDM3A in combination with ChIP-Seq of the androgen receptor resulted in a gain of H3K9 methylation marks around androgen receptor binding sites of selected transcriptional targets in androgen signaling including positive regulation of KRT19, NKX3-1, KLK3, NDRG1, MAF, CREB3L4, MYC, INPP4B, PTK2B, MAPK1, MAP2K1, IGF1, E2F1, HSP90AA1, HIF1A, and ACSL3. The cancer systems biology analysis of KDM3A-dependent genes identifies an epigenetic and transcriptional network in androgen response, hypoxia, glycolysis, and lipid metabolism. Genome-wide ChIP-Seq data highlights specific gene targets and the ability of KDM3A to control oncogenic pathways in prostate cancer cells.

overall_design: Examination of binding of epigenomic modifer and histone modifications

first: Stephen

last: Wilson

first: Lingling

last: Fan

first: Natasha

last: Sahgal

first: Jianfei

last: Qi

middle: V


title: RNA polymerase II-Independent Recruitment of SPT6L at Transcription Start Sites in Arabidopsis

city: Guangzhou

first: Chen

last: Chen

address: 723 Xinke Rd.

institute: South China Botanical Garden, Chinese Academy of Science

summary: SPT6 is a conserved elongation factor that is associated with phosphorylated RNA polymerase II (RNAPII) during transcription. Recent transcriptome analysis in yeast mutants revealed its potential role in the control of transcription initiation at genic promoters. However, the mechanism by which this is achieved and how this is linked to elongation remains to be elucidated. Here, we present the genome-wide occupancy of Arabidopsis SPT6-like (SPT6L) and demonstrate its conserved role in facilitating RNAPII occupancy across transcribed genes. We also further demonstrate that SPT6L enrichment is unexpectedly shifted, from gene body to transcription start site (TSS), when its association with RNAPII is disrupted. Protein domains, required for proper function and enrichment of SPT6L on chromatin, are subsequently identified. Finally, our results suggest that recruitment of SPT6L at TSS is indispensable for its spreading along the gene body during transcription. These findings provide new insights into the mechanisms underlying SPT6L recruitment in transcription and shed light on the coordination between transcription initiation and elongation.

overall_design: Examination of RNA Polymerase II genome-wide binding in 10 days WT, spt6l, and spt6lSPT6LΔSH2-GFP seedlings. After introducing ProSPT6L:SPT6L-GFP into spt6l seedlings, the genome-wide occupancy of SPT6L was examined. And then, a serial domain deletion of SPT6L was conducted and introduced into spt6l background. Finally, the genome-wide occupancy of SPT6LΔHtH, SPT6LΔYqgF, SPT6LΔSH2, SPT6LΔHtHΔSH2, and SPT6LΔYqgFΔSH2 were performed.

first: Yuhai

last: Cui


title: RNA-seq analysis of gene expression in the liver of control and Mst1/2 deficient mice

city: Boston

first: Wantae

last: Kim

state: Massachusetts

address: 188 Longwood Ave.

institute: Harvard School of Dental Medicine

summary: RNA-sequencing results with livers obtained from  control and Mst1/2 deficient mice

overall_design: To examine changes in gene expression by loss of Mst1 and Mst2 in liver, we performted multiplex RNA-sequencing.

first: Yingzi

last: Yang


title: RNA-sequencing of adipocyte and stromal vascular cells (SVCs) of epididymal and inguinal adipose tissue from high-fat diet (HFD)-fed mice

status: Public on May 14 2019

city: Seoul

first: Jae Bum

address: Bldg 105-Rm. 333, Seoul National University, San 56-1, Sillim Dong, Kwanak-Gu

department: School of Biological Sciences

country: South Korea

institute: Seoul National University

summary: We report the transcriptomes of adipocytes and SVCs derived from HFD-fed obese mouse epididymal adipose tissue (EAT) or inguinal adipose tissues (IAT). By the comparisons of transcriptome of adipocyte and SVC from EAT and IAT, we find that the gene clusters of gamma-aminobutyric acid (GABA) signaling among the three-hundred fourteen pathways annotated in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database was differentially regulated in SVCs from IAT compared to SVCs from EAT. Q-RT-PCR analyses confirmed the reliability and high degree of sensitivity of gene the RNA-sequencing results. Further, when the SVC from IAT with the SVC from EAT were compared, six pathways were included in the Pareto optimal set, excluding pathways below 1.0 and –log10(0.05) for the x and y-axis, respectively. Selected pathways and their differentially expressed genes were visualized as a bipartite graph using Cytoscape software to reveal that differentially regulated GABA signaling pathways could be associated with immune cell adhesions.

overall_design: Examination of 12 samples derived from EAT and IAT

first: Injae

last: Hwang

first: Kyuri

last: Jo

first: Sun

first: Jae


city: Padua

first: Karina

last: Fincati

address: V.le G. Colombo, 3

department: Department of Biology, University of Padua

country: Italy

institute: CNR-Institute for Biomedical Technologies

summary: Microarray analysis on human neuroblastoma cells exposed to iron, B-amyloid or the B-amyloid iron complex. Alzheimer's disease is associated with an abnormal accumulation of certain metal ions.

overall_design: Analysis used a neuronal cell lines, the SH-SY5Y, exposed to either AB,  the AB-Fe complex or Fe alone. The SH-SY5Y without treatment were used that a control. For the exposure to AB, six replicates were performed (three dye swap and three non-dye swap), while for exposure to AB-Fe and Fe  two replicates each were made (one dye swap and one non-dye swap).

first: Denise

last: Drago

first: Valentina

last: Gatta

first: Stefano

last: Sensi

first: Paolo

last: Zatta


title: ChIP-seq analysis of HIF and AR binding sites in LNCaP cell line

first: Chandra

last: Chilamakuri

summary:
Androgen receptor (AR) and hypoxia inducible factor 1a (HIF1a) are transcription factors that promote prostate cancer progression. This study investigated the relationship between the AR and HIF1a signaling pathways.
ChIP-seq analysis was performed on the LNCaP cell line to identify global HIF and AR binding sites within the genome, under hypoxia and normoxia and in the presence and absence of androgen treatment.

overall_design: 16 samples analyzed

first: Maxine

last: Tran

first: Becky

last: Bibby

first: Ian

last: Mills

first: David

last: Neal


title: Expression data of the cetuximab-resistant head and neck squamous cell lines and the parental cell lines.

city: Osaka

first: Kazuko

last: Sakai

address: 377-2, Osaka-sayama

department: Dept. of Genome Biology

institute: Kindai University Faculty of Medicine

summary:
The cetuximab resistant FaDuCR cell lines were established after continuous treatments with a 10 µg/mL final concentration of cetuximab. Those cells could freely proliferate in 10 µg/mL cetuximab containing medium, and were named FaDuCR.
We used microarrays to detail the gene expression in FaDuCR and FaDu-parental cells to screen for transcripts correlated with cetuximab resistance.

overall_design: Total RNA was purified using RNeasy Mini Kit (Qiagen), including a DNase digestion treatment. RNA concentrations were determined by NanoDrop 2000 (Thermo Scientific). RNA was labeled using the GeneChip® WT Terminal Labeling and Controls Kit combined with the Ambion® WT Expression Kit. Labeled cRNA was hybridized to GeneChip® Human Transcriptome Array 2.0 arrays (Affymetrix).

first: Kimio

last: Yonesaka

first: Kaoru

last: Tanaka

first: Mutsukazu

last: Kitano


title: Expression data from Jurkat cell line infected with pMIN-ERG+85 vector

city: Tel-Aviv

first: Michael

last: Milyavsky

state: Tel Aviv

address: Klatskin St 35

department: Pathology, Sackler School of Medicine

country: Israel

institute: Tel Aviv University

summary:
Jurkat cells infected with pMIN-ERG+85 express different tagBFP levels. Using flow cytometry sorting, highest and lowest tagBFP cells (10%) were sorted. High tagBFP cells are functionaly have more leukemia stem cell proprties in comparision to low tagBFP cells. Utilizing sorted cells to identifiy differential transcriptomics between two subpopulations
We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up/down-regulated genes that determine High tagBFP cells vs Low tagBFP

overall_design: Viral particles were generated by transient transfection of 293T cells using CMVDeltaR8.91 and pMD2G constructs as described elsewhere (Milyavsky et al. 2010). Jurkat leukemia cells were infected by addition of viral supernatant to obtain 10-30% infection rate. Jurkat cells were sorted using BD FACSAria™ Fusion sorter (BD Biosciences), RNA was extracted with the Trizol reagent (Invitrogen) and reverse transcribed with SuperScript III (Invitrogen),RNA from 100,000 or more sorted cells was used for microarray analysis by Human Gene Clariom S Assay (Thermo Fisher Scientific)

first: Muhammad

last: Yassin


title: RtcB RNAseq to map cyclic phosphate-bearing RNA fragments during poly I:C treatment

city: Princeton

first: Alexei

last: Korennykh

state: New Jersey

address: 216 Shultz Laboratory

department: Molecular Biology

institute: Princeton University

summary: RNase L is activated by 2-5A, which is synthesized specifically upon dsRNA sensing. Activated RNase L cleaves cellular RNAs, generating fragments that bear  2'-3' cylic phosphate and/or 5'-OH. Here we perform cyclic-phosphate capture and RNA-seq to map the precise sites at which cleavage is induced during dsRNA stress.

overall_design: A549 cells were treated +/- poly I:C for one hour and total RNA was extracted. Custom library prep was performed to capture and enrich fragments with a 2'-3' cyclic phosphate using RtcB enzyme, followed by RNA-seq.

first: Sneha

last: Rath

first: Eliza

last: Prangley


title: Quantifying differentially abundant RNA transcripts in mouse kidney tissue with chronic alcohol consumption

city: Louisville

last: Merchant

state: KY

address: 570 South Preston Street, Room 102S Donald Baxter Research Building

department: Medicine

institute: University of Louisville

summary: Chronic and binge ethanol consumption in humans and in animal models has been associated with the induction of injury (such as fibrosis and scarring) in the liver as well as the intestine, brain, lung and immune system. The effects of chronic ethanol consumption on the human kidney are protective as seen in large population studies are controversial with the preponderance of the data suggesting protection less so than injury. The most recent meta-analysis was by Konig et al (2015) who studied 5476 participants aged 28–75 years from the Prevention of Renal and Vascular End-Stage Disease (PREVEND) study to assess associations between alcohol consumption and risk of chronic kidney disease (CKD). They found in this population-based cohort, alcohol consumption was inversely associated with the risk of developing CKD. The protective effects of ethanol on the kidney present a unique model system to develop new hypothesis on protection against end organ damage by fibrosis.    The data on the effects of alcohol or alcohol consumption at the molecular level on renal parenchyma are sparse. In cell culture and animal models chronic ethanol exposure has been show to induce protein post-translational modification (acetylation), protein expression (upregulation of cytochrome P450 CYP2E1 and local platelet-activating factor receptor (PAFR) ligand formation) as well as neutrophil infiltration and activation. Since hepatocytes do not express PAFR, these data suggest that the response of the kidney to chronic alcohol consumption is distinct from that of the liver or lung. Therefore, we hypothesized that mechanisms of ethanol-induced renal injury or protection are regulated by a protein signaling networks (PSN) modulated acutely by the phosphoproteome and long term epigenetically by the acetylproteome. To address this hypothesis we have initiated a tiered proteomics study to determine the effects of chronic alcohol consumption on the murine kidney and with a secondary insult of acute exposure of lipopolysaccharide (LPS) on the renal proteome, phosphoproteome and the acetylproteome. Data have already been collected on the total proteome and the phosphoproteome using a multiplexing approach. Data will be collected early spring on the acetylproteome.

overall_design: Kidneys from mice exposed to a two-hit model of 6 week Lieber-DeCarli ethanol exposure with and without lipopolysaccharide (LPS) injection 4h prior to sacrifice were collected for RNA analysis. The study involved four conditions: pair fed control (PF), pair fed control with lipopolysaccharide injection 4hr prior to sacrifice (PF4hLPS), ethanol exposure (EtOH), and ethanol exposure with lipopolysaccharide injection 4hr prior to sacrifice (EtOH4hLPS).  The comparisons made included PF4hLPS vs. PF; EtOH4hLPS vs EtOH; EtOH4hLPS vs PF4hLPS; EtOH vs PF, and EtOH AND EtOH4hLPS vs PF AND PF4hLPS.

first: Christine

last: Dolin

first: Eric

last: Rouchka

first: Gavin

last: Arteel

middle: L


title: Genome-wide DNA methylation level analysis in plants overexpressing METS1

city: Valencia

first: Pablo

last: Vera

state: Valencia

address: Ingeniero Fausto Elío s/n

country: Spain

institute: Instituto de Biología Molecular y Celular de Plantas (IBMCP); Consejo Superior de Investigaciones Científicas (CSIC)

summary: We report here with this study the genome-wide DNA methylation level analysis at single-nucleotide resolution by Next Gen bisulfite-sequencing using the Methyl-MaxiSeq platform from Zymo Research Services (Irvine, CA) in plants overexpressing the gene 5-Methyltetrahydropteroyltriglutamate Homocysteine Methyltransferase1 (METS1) comparatively to Col-0 plants both basal conditions and following Pseudomonas syringae DC3000 infection.

overall_design: We analyzed whole-genome DNA methylation level in the three methylation contexts CG, CHG and CHH (Methyl-seq) in Col-0 and 35::METS1#1 plants, and both under basal and P.s. DC3000-inductive conditions, using three biological replicates for each condition. The results from this analysis were confirmed for the most relevant condition (bacteria inoculation) with 35::METS1#2 plants.

first: Beatriz

last: González


title: Tobacco-related alterations in airway gene expression are rapidly reversed within weeks following smoking cessation

first: Kahkeshan

last: Hijazi

state: MA

address: 715 Albany Street

institute: Boston University

summary: RNA was obtained longitudinally  from normal nasal epithelium of smokers who have quit smoking over 6 months period. Statistical analysis of gene expression data identified genes differentially expressed with short-term smoking cessation and categorized the kinetics of of these genes in different biological functions with different dynamics following smoking cessation.

overall_design: Affymetrix GeneST arrays were run on total RNA obtained nasal epithelial brushings of 8 active smokers enrolled in smoking-cessation programs.  Brushings were obtained at baseline and at 4, 8, 16, and 24-weeks after smoking-cessation (n=33). Replicates are excluded.

first: Avrum

last: Spira


title: RNA-seq analysis of cultured neural stem cells (NSC) isolated from the subventricular zone and transformed lines GSC1 and GSC2 derived from these cells

city: London

first: Sanjay

middle: Padmakar

last: Khadayate

address: Du Cane Road

institute: MRC London Institute of Medical Sciences

summary: Cultured NSC, GSC1 and GSC2 were sequenced to determine gene expression profiles and differentiation status of the GSC lines

overall_design: 3 independent cultures of each cell type were sequenced

first: Simona

last: Parrinello

first: Cristina

last: Ottone

first: Meanie

last: Clements


title: Comparative analysis of microRNA expression profiles of adult Schistosoma japonicum isolated from water buffalo and yellow cattle

city: Shanghai

first: Xingang

last: Yu

address: 518 Ziyue Road, Minhang District,

country: China

institute: Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science,

summary: To investigate microRNAs (miRNAs) involving in the regulation of the schistosome development and survival, we compared miRNA expression profiles of adult Schistosoma japonicum derived from yellow cattle and water buffalo using high-throughput sequencing with Illumina Hiseq Xten.

overall_design: The water buffalo and yellow cattle were each challenged percutaneously with 1000 cercariae of S. japonicum.The miRNA expression profiles of four S. japonicum samples derived from yellow cattle and four S. japonicum samples obtained from water buffalo were sequenced with Illumina Hiseq Xten.

first: Jiaojiao

last: Lin

first: Qi

last: Zhai

first: Zhiqiang

last: Fu

first: Yang

last: Hong


title: Clonal evolution patterns in acute myeloid leukemia with NPM1 mutation (Affymetrix SNP data set)

city: Ulm

first: Sibylle

last: Cocciardi

address: Albert-Einstein-Allee 23

department: Department of Internal Medicine III

country: Germany

institute: University Hospital Ulm

summary: Mutations in the nucleophosmin 1 (NPM1) gene are considered founder mutations in the pathogenesis of acute myeloid leukemia (AML). To further characterize the genetic composition of NPM1 mutated (NPM1mut) AML, we assess mutation status of five recurrently mutated oncogenes (FLT3, DNMT3A, IDH1, IDH2, NRAS) in 129 paired NPM1mut samples obtained at diagnosis and relapse. We find a substantial shift in the genetic pattern from diagnosis to relapse including NPM1mut loss (n=11). To gain further insight into these NPM1mut loss cases, we perform whole exome sequencing (WES) and RNA-Seq. At the time of relapse, NPM1mut loss patients (pts) feature distinct mutational patterns that shared almost no somatic mutation with the corresponding diagnosis sample and impact different signaling pathways including loss of characteristic NPM1mut associated gene expression patterns. In contrast, profiles of pts with persistent NPM1mut at relapse are reflected by a high overlap of mutations between diagnosis and relapse. Thus, our findings confirm that relapse often originates from persistent leukemic clones, though NPM1mut loss cases suggest a second “de novo” or treatment-associated AML (tAML) as alternative cause of “relapse" in a subgroup of cases.

overall_design: Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from 72 cryopreserved diagnostic bone marrow or peripheral blood samples.

first: Lars

last: Bullinger

first: Konstanze

last: Döhner


title: Ophiocordyceps sinensis raw sequence reads

city: Beijing

first: CH

last: Dong

address: NO.3 Park 1, Beichen West Road, Chaoyang District

department: Institute of Microbiology

institute: Chinese Academy of Sciences

summary: Chinese cordyceps is of particular interest for its confined distribution, mysterious lifecycle, ecological importance and developmental biology. The large scale artificial cultivation of this fungus has been succeeded in China until recently but with low efficiency and high cost being ascribed to too much unsolved biological issues, such as gene expression during development and the sexuality reproduction. The success of artificial cultivation provides the convenient for sampling during the different development stages.

overall_design: Retinal mRNA profiles ofdifferent developmental stages of O. sinensis including hyphae (HY), sclerotium (ST), primordium (PR), young fruitbody (YF), developed fruitbody (FD) and mature fruit body (MF), were generated by deep sequencing, in triplicate, using Illumina Hiseq 2000.

first: C

middle: H

first: Xiao

last: Li


title: Clonal evolution patterns in acute myeloid leukemia with NPM1 mutation (RNA-seq data set)

overall_design: RNA-Seq was performed on paired (diagnosis and relapse) samples of NPM1mut loss and NPM1mut persistent patients using an Illumina HiSeq2000.


title: Clonal evolution patterns in acute myeloid leukemia with NPM1 mutation

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

overall_design: Refer to individual Series


title: Tumor suppressor SMARCB1 suppresses super-enhancers to govern hESC lineage determination

city: Durham

first: Lee

last: Langer

state: NC

address: 111 TW Alexander Dr

department: ESCBL

institute: NIEHS

summary: The SWI/SNF complex is a critical regulator of pluripotency in human embryonic stem cells (hESCs), and individual subunits have varied and specific roles during development and in diseases. The core subunit SMARCB1 is required for early embryonic survival, and mutations can give rise to atypical teratoid/rhabdoid tumors (AT/RTs) in the pediatric central nervous system. We report that in contrast to other studied systems, SMARCB1 KD relieves bivalent gene repression in hESCs and promotes chromatin accessibility at super-enhancers. Moreover, and consistent with its established role as a CNS tumor suppressor, we find that SMARCB1 is essential for neural induction but dispensable for mesodermal or endodermal differentiation. Mechanistically, we demonstrate that SMARCB1 KD cells are robustly resistant to hESC super-enhancer silencing in neural differentiation conditions. This genomic assessment of hESC chromatin regulation by SMARCB1 reveals a novel positive regulatory function at super-enhancers and a unique lineage-specific role in regulating hESC differentiation.

overall_design: Examination of effects of SMARCB1 KD on transcription and accessibility in hESCs and differentiating neural stem cells

first: James

middle: M

last: Ward

first: Trevor

last: Archer


title: RNAseq analysis of lacrimal glands isolated from wild type and Aire-/- mice at 5 weeks of age

city: San Francisco

first: Sarah

last: Knox

address: 513 Parnassus Ave

department: Cell Tissue Biology

institute: University of California San Francisco

summary: We used freshly isolated lacrimal glands isolated from wild type and Aire-/- mice on a Balbc background. Mice were 5 weeks of age, with an n=4 for wild type and n=3 for Aire-deficient.

overall_design: Lacrimal gland mRNA profiles of 5 week old wild type (WT) and Aire-/- mice were generated by deep sequencing, in triplicate (Aire-/-) or quadruplicate (wild type), using Illumina HiSeq4000.

first: S


title: Molecular mechanism impacted by circadian disruption underscores the importance of timed anti-cancer treatment

city: Philadelphia

first: Yool

last: Lee

state: PA

address: SCTR 10-165, 3400 Civic Center Blvd, Bldg 421

institute: Perelman School of Medicine at the University of Pennsylvania

summary: Circadian disruption has multiple pathological consequences, but the underlying mechanisms are largely unclear. To address such mechanisms, we subjected cultured cells to chronic circadian desynchrony (CCD), mimicking a chronic jet-lag paradigm, and assayed a range of cellular functions.  The results indicated a specific circadian clock-dependent increase in cell proliferation. Transcriptome analysis revealed upregulation of G1-S-phase transition genes (cMyc, CyclinD1/3, Cdt1), concomitant with increased phosphorylation of the Retinoblastoma protein (Rb) by Cyclin D kinase 4/6 (CDK4/6) and increased G1-S progression. Phospho-Rb (Ser807/811) was found to oscillate in a circadian fashion and exhibit phase-shifted rhythms in circadian desynchronized cells. A CDK4/6 inhibitor approved for cancer treatment reduced growth of cultured cells and mouse tumors in a time-of-day specific manner, but the time dependence was lost with CCD. Our study identifies a mechanism that underlies effects of circadian disruption on tumor growth and underscores the importance of treatment timed to endogenous circadian rhythms.

overall_design: RNA samples collected every 6 hours for 24 hours from dexamethasone-synchronized U2OS cells. Prio to collection, cells syncrhonized using either a control (treated every 24 hours) or jet lag (8-hour advance in treatment every 2 days) schedule. Three replicates were collected per treatment schedule per timepoint. Expression profiles generated from each RNA sample sequencing on a HiSeq 4000.

first: Nicholas

last: Lahens

first: Shirley

last: Zhang

first: Joseph

last: Bedont

first: Jeffrey

last: Field

first: Amita

last: Sehgal


title: Gene expression prfile of ARID1A knockout N87 cells

city: Fukushima

first: Mai

last: Ashizawa

institute: Fukushima medical universsity

summary: To identify ARID1A-regulated genes in stomach cancer, we performed microarray profiling of RNA isolated from N87 stomach cancer cells, in which ARID1A expression was knocked down by two different siRNAs against ARID1A.

overall_design: N87 cells (human stomach cancer cell line) were transfected with a final concentration of 5nM siRNA oligos for ARID1A(siARID1A #1, siARID1A #2) or negative control. Total RNA purified from each treatment was used for microarray analysis.

first: Motonobu

last: Saito

first: Katsuharu

first: Takahiro

last: Sato

first: Tomohiro

last: Kikuchi

first: Hirokazu

last: Okayama

first: Shotaro

last: Fujita

first: Wataru

last: Sakamoto

first: Tomoyuki

last: Momma

first: Shinji

last: Ohki

first: Koji

last: Kono


title: miRNA profiling of extracellular vesicles from Theileria annulata infected B cells (TBL20) and their uninfected control counterparts (BL20)

city: Glasgow

first: Victoria

last: Gillan

address: bearsden road

institute: University of Glasgow

summary: We report significant changes in six bovine miRNA in vesicles from Theileria annulata infected cells

overall_design: EV were purified from BL20 and TBL20 cells by ultracentrifugation and RNA from these samples was used to perform RNA-Seq and determine differential expression of host (bovine miRNA). 8 samples were analysed. Two groups n=4. BL20 is the control group, TBL20 is the test group.


title: CRISPR-based molecular recording of mouse embryogenesis

first: Michelle

last: Chan

state: CA

institute: UCSF

summary: Understanding the emergence of complex multicellular organisms from single totipotent cells, or ontogenesis, represents a foundational question in biology. The study of mammalian development is particularly challenging due to the difficulty of monitoring embryos in utero, the variability of progenitor field sizes, and the indeterminate relationship between the generation of uncommitted progenitors and their progression to subsequent stages. Here, we present a flexible, high information, multi-channel molecular recorder with a single cell (sc) readout and apply it as an evolving lineage tracer to define a mouse cell fate map from fertilization through gastrulation. By combining lineage information with scRNA-seq profiles, we recapitulate canonical developmental relationships between different tissue types and reveal an unexpected transcriptional convergence of endodermal cells from extra-embryonic and embryonic origins, illustrating how lineage information complements scRNA-seq to define cell types.  Finally, we apply our cell fate map to estimate the number of embryonic progenitor cells and the degree of asymmetric partitioning within the pluripotent epiblast during specification.  Our approach enables massively parallel, high-resolution recording of lineage and other information in mammalian systems to facilitate a quantitative framework for describing developmental processes.

overall_design:
scRNA-seq of 7 E8.5 embryos with one embryo sampled twice (technical replicates).  All embryos have undergone CRISPR-based lineage tracing.
Please note that to generate 16 libraries, the samples were prepared halfway thru the 10x protocol and the cDNA pool was split. Half the pool is used to generate the RNA-seq libraries and the other half is used to make amplicon libraries (*target site amplicon samples).

first: Zachary

middle: D

last: Smith

first: Stefanie

last: Grosswendt

first: Helene

last: Kretzmer

first: Thomas

last: Norman

first: Britt

last: Adamson

first: Marco

last: Jost

middle: J

last: Quinn

first: Dian

last: Yang

first: Alexander

last: Meissner

first: Jonathan

middle: S

last: Weissman


title: The transgenerational effects of mitochondrial supplementation

city: Clayton

first: Justin

middle: C

last: St. John

state: Vic

address: 27-31 Wright St

department: Centre for Genetic Diseases

country: Australia

institute: Hudson Institute of Medical Research

summary: To determine the outcomes of offspring produced from mitochondrial supplementation to mature oocytes at the time of fertilisation, we generated three generations of offspring. Primordial follicles of the third generation female mice (postnatal day 3) were collected, and RNA sequencing was performed. We compared the treated and control gene expression data to determine differentially expressed genes between the two groups. Our data suggest that mitochondrial supplementation has transgenerational effects on offspring.

overall_design: 1. mitochondrial supplementation at the time of fertilisation was performed 2. three generations of offspring were produced to determine the transgeneration effects of the technique. 3. Primordial follicles of the third generation day 3 postnatal offspring were collected and extracted to compare the transcripts of treated vs control primordial follicles.


title: RNA sequencing  in hepatocytes and DR-derived hepatocytes

city: Woluwé

first: Jérôme

last: Ambroise

address: Avenue Hippocrate 54

department: Institut de Recherche Expérimentale et Clinique

country: Belgium

institute: Université catholique de Louvain

summary: During chronic liver injury, the ductular reaction generates hepatocytes. The aim of the analysis is to compare the phenotype of the DR-derived hepatocytes with that of native hepaotcytes in the same injured liver and control healthy hepatocytes.

overall_design:
We compared 5 biological replicates of each of the 3 populations. Due to technical constraints 10 samples were processed in a first experiment (Experiment 1) and 9 samples were processed in a second experiment (experiment 2). Log fold-change obtained from both experiment were highly correlated (r ~ 0.95).

Several of the same samples were processed in both Experiment 1 and Experiment 2: CTL 5, RED 2, RED 3, RED 4. For these samples, independent libraries were made for each Experiment following methods outlined in the Extraction protocol on the sample pages.

first: Jerome