title: BET Bromodomain Inhibition Blocks the Function of a Critical AR-Independent Master Regulator Network in Lethal Prostate Cancer

status: Public on Mar 20 2019

city: Portland

first: Joshi

last: Alumkal

state: OR

address: 3303 SW Bond Ave. CH14R

institute: Knight Cancer Institute

summary: BET bromodomain inhibitors are known to block prostate cancer cell survival through suppression of c-Myc and androgen receptor (AR) function. However, little is known about other transcriptional modulators whose function is blocked by these drugs and the anti-tumor activity of BET bromodomain inhibition in AR-independent castration-resistant prostate cancers (CRPC), whose frequency may be increasing. In this study we determined that BET bromodomain inhibition suppresses survival of a diverse set of CRPC cell models, including those that do not express the AR or in which c-Myc is not suppressed. To identify additional transcriptional regulators whose suppression contributes to the anti-tumor effects of BET bromodomain inhibition, we treated multiple CRPC cell lines with the BET bromodomain inhibitor JQ1, measured genome-wide gene expression changes, and then used the Master Regulator Inference Algorithm (MARINa). This approach identified transcriptional regulators whose function is blocked by JQ1 and whose suppression recapitulates the effects of BET bromodomain inhibition. High Expression of these Master Regulators in aggressive human CRPC demonstrates their clinical relevance.

overall_design: RNA-seq profiles of multiple prostate cancer cell lines to understand gene expression changes associated with JQ1 treatment; ChIP-seq profiles of BET bromodomain protein BRD4 binding in the PC3 prostate cancer cell line to understand changes in BRD4 chromatin occupancy associated with JQ1 treatment.

first: Daniel

last: Coleman

first: Lina

last: Gao

first: Carly

last: King

first: Jacob

last: Schwartzman

first: Joshua

last: Urrutia

first: Archana

last: Sehrawat

first: Junior

last: Tayou

first: Ariel

last: Balter

first: Julja

last: Burchard

first: Kami

middle: E

last: Chiotti

first: Laura

last: Heiser


title: Distinct cancer-promoting stromal gene expression depending on lung function

status: Public on Mar 05 2019

city: Stockholm

first: Ola

last: Larsson

department: Department of oncology-pathology

country: Sweden

institute: Karolinska Institutet

type: Expression profiling by high throughput sequencing

summary: Chronic obstructive pulmonary disease (COPD) is an independent risk factor for lung cancer, but the underlying molecular mechanisms are unknown. We hypothesized that lung stromal cells activate pathological gene expression programs supporting oncogenesis. To identify molecular mechanisms operating in the lung stroma that support development of lung cancer. Study subjects included patients with- or without- lung cancer across a spectrum of lung function. We conducted multi-omics analysis of non-malignant lung tissue to quantify the transcriptome, translatome and proteome. Cancer-associated gene expression changes predominantly manifested as alterations in the efficiency of mRNA translation modulating protein levels in the absence of corresponding changes in mRNA levels. The molecular mechanisms driving these cancer-associated translation programs differed based on lung function. In subjects with normal to mildly impaired lung-function, the mammalian target of rapamycin (mTOR) pathway served as an upstream driver; whereas in severe airflow obstruction, pathways downstream of pathological extracellular matrix (ECM) emerged. Consistent with a role during cancer initiation, both the mTOR and ECM gene expression programs paralleled activation of previously identified pro-cancer secretomes. Furthermore, in situ examination of lung tissue documented that stromal fibroblasts express cancer-associated proteins from the two pro-cancer secretomes including IL6 in mild or no airflow obstruction and BMP1 in severe airflow obstruction. Two distinct stromal gene expression programs promoting cancer initiation are activated in lung cancer patients depending on lung function. Our work has implications both for screening strategies and personalized approaches to cancer treatment.

overall_design: Polysome-profiling of non-cancerous lung stroma tissue samples from patients with or without lung cancer across a range of forced expiratory volume in one second (FEV1)

first: Chris

last: Wendt


title: Transcriptome analysis of mycorrhizal Sesbania cannabina reveals insight into the tolerance to salt stress

status: Public on Mar 06 2019

city: yantai

first: cheng-gang

last: ren

state: shandong

address: 17 Chunhui Road, Laishan District

country: China

institute: Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, China

summary: To better understand the molecular mechanisms of the response of arbuscular mycorrhizal S. cannabina to salt stress, the transcriptional profile in both mycorrhizal and non-mycorrhizal Sesbania cannabina subjected to 3 and 27 hours NaCl treatment respectively were performed using the Illumina HiSeq™ 2000 sequencing platform (Illumina Inc., San Diego, CA, USA). Bioinformatic analysis of transcriptome data was performed to allow identification and functional annotation of differentially expressed genes (DEGs). By comparing the different genes appeared in control and treatment groups, we can learn more about the species-specific responses employed by S. cannabina and find novel associated genes or strategies in mycorrhizal plant under salt stress.

overall_design: Leaf and root mRNA profiles of 30-day old mycorrhizal and non-mycorrhizal S. cannabina (control), 3h and 27h NaCl treatment were generated by deep sequencing, in duplicate, using Illumina HiSeq 2000.

first: Cheng-Gang

last: Ren

first: Cun-Cui

last: Kong


title: AMPK-dependent gene expression profiles in response to small molecule AMPK activators

status: Public on Mar 04 2019

city: Lausanne

first: Frederic

last: Raymond

address: Campus EPFL - Quartier de l'Innovation

department: Functional Genomics

country: Switzerland

institute: Nestle Institute of Health Sciences

summary: AMP-activated protein kinase (AMPK) is a major regulator of cellular energy homeostasis that coordinates metabolic pathways in order to balance nutrient supply with energy demand. AMPK elicits acute and diverse metabolic effects by directly phosphorylating various targets. AMPK activation also promotes metabolic reprogramming in longer term via effects on gene expression. The aim of this study is to elucidate molecular mechanism(s) by which AMPK activation modulates metabolic adaptation through its impact on gene regulation.

overall_design:
The mouse embryonic fibroblasts (MEFs) dataset comprises a) two genetic backgrounds (control and AMPK α1-/-/α2-/-), b) three treatments (vehicle, 991, AICAR), and c) four technical replicates per condition. One sample was excluded as outlier (control, 991-treated, technical replicate 1) for a total of 23 samples.
The primary hepatocytes expression profiling was generated using a) two genetic backgrounds (control and AMPK α1-/-/α2-/-), b) three treatments (vehicle, 991, AICAR), c) five technical replicates, and d) two biological replicates. One sample was excluded as outlier (AMPK α1-/-/α2-/- vehicle-stimulated, technical replicate 4, biological replicate 1) giving finally 59 samples.

first: Benoit

last: Viollet

first: Caterina

last: Collodet

first: Marc

last: Foretz

first: Sylviane

last: Metairon


title: SALL3 regulates propensity of human induced pluripotent stem cells to differentiate into distinct cell lineages [ChIP-Seq]

status: Public on Mar 12 2019

city: Setagaya

first: Takuya

last: Kuroda

state: Tokyo

address: 1-18-1 Kamiyoga

department: Division of cell-based therapeutic products

country: Japan

institute: National Institute of Health and Sciences

type: Genome binding/occupancy profiling by high throughput sequencing

summary: SALL3 binds to de novo DNA methyltransferase DNMT3B and influences the epigenetic profiles of hiPSCs

overall_design: To investigate the mechanisms by which SALL3 inhibits DNMT3B-mediated gene body methylation, we performed chromatin immunoprecipitation (ChIP)-seq analysis with anti-DNMT3B antibody using SALL3 KD cells.

first: Satoshi

last: Yasuda

first: Yoji

last: Sato


title: Gene expression profile of erythroblastic cells induced from congenital dyserythropoietic anemia (CDA) patient-derived induced pluripotent stem cells

city: Tokyo

first: Hiroshi

last: Kohara

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

department: Division of ALA Advanced Medical Research

institute: Institute of Medical Science, the University of Tokyo

summary: Analysis of erythroblastic cells differentiated from induced pluripotent stem cells (iPSCs) generated from peripheral blood T lymphocytes of CDA type IV patient. Type IV congenital dyserythropoietic anemia (CDA) is due to a monoallelic mutation at the second zinc finger of KLF1 (c.973G>A). Results provide insight into molecular mechanisms underlying CDA pathogenesis.

overall_design: We compared the global gene expression profiles between CD235a-expressing erythroblastic cells induced from CDA patient-derived iPSCs and healthy donor control.

first: Kenzaburo

last: Tani


title: The miRNA profiles of plasma extracellular vesicles (pEV) in melanoma patients and supernatant EV (sEV) of related cell cultures

city: Erlangen

first: Martin

last: Eberhardt

address: Hartmannstr. 14

department: Dermatology

country: Germany

institute: University Hospital Erlangen

summary: The dataset contains miRNA pEV profiles measured on Agilent Microarrays from three groups of melanoma patients (before or at resection, and after resection categorized into high-risk and low-risk groups) and healthy controls. These groups were compared to find differentially abundant miRNAs in the pEV of melanoma patients. In addition, two comparisons of short-term profile changes around the resection date are included, as well as six cell line sEV that play a role for the accompanying publication.

overall_design:
The four groups (14 healthy controls and 14 tumor, 15 high-risk, 11 low-risk patients) were subjected to differential expression analysis. The additional pEV samples served illustrational purposes as outgroup comparisons, and the six cell line samples were employed in an attempt to elucidate the putative source tissue of the pEV.
--------------------------------------
There are two subsets: the first one consists of the above mentioned patient samples and was used for the differential expression analysis in melanoma context, which is why there are only 54 columns in the normalized matrix. The remainder of the samples were used in very specific comparative analyses with the groups from the first subset. These two approaches have completely different scopes and subgroup-dependent normalizations were performed as necessary.

first: Nina

last: Koliha

first: Jochen

last: Dindorf

first: Stefan

last: Wild

first: Andreas

middle: S

last: Baur


title: Transfer RNA Genes Affect Chromosome Architecture and Function

city: Bethesda

first: Josefina

last: Ocampo

state: MD

address: 6 Center Drive

department: NICHD

country: USA

institute: NIH

summary: In this study we investigated the role of tDNAs in genomic organization and nuclear function by editing a chromosome so that it lacks any tDNAs.

overall_design: Mnase-seq of wildtype and tRNA-deleted S. cerevisiae strains.

first: David

middle: J

last: Clark


title: Single cell chromatin immunocleavage sequencing (scChIC-Seq) to profile histone modification

status: Public on Mar 28 2019

first: Keji

last: Zhao

address: Building 10 Room 7B06A

department: National Heart, Lung, and Blood Institute

institute: national Institute of Health

summary: We report a single-cell chromatin immunocleavage sequencing (scChIC-seq) methodology for analyzing histone modifications, which involves targeting of the micrococcal nuclease (MNase) by tethering it to an antibody and selective PCR amplification of cleaved target sites. We show that the protocol reliably detects the H3K4me3 and H3K27me3 target sites in single human white blood cells (WBC), resulting data for successful identification of unique blood cell types based on clustering analysis.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: The technique, scChIC-seq, was applied to profile H3K4me3 and H3K27me3 using small number of cells and  single cells. By comparing with the Bulk ChIP-seq signal, scChIC-seq was shown to have high specificity. scChIC-seq was applied to profile H3K4me3 using single human white blood cells. The highly co-methylated and highly variable peaks were shown to be related to underlying cellular populations.

first: Wai Lim

last: Ku

first: Kosuke

last: Nakamura

first: Weiwu

last: Gao

first: Kairong

last: Cui

first: Gangqing

last: Hu

first: Qingsong

last: Tang

first: Bing

last: Ni


title: A Low-Cost Multiplex Biomarker Assay Stratifies Colorectal Cancer Patient Samples into Clinically-Relevant Subtypes: Elements Chemistry

city: Sutton

first: Anguraj

last: Sadanandam

state: Surrey

address: 15 Cotswold Road

department: Molecular Pathology

country: United Kingdom

institute: Institute of Cancer Research (ICR), London

summary:
Objective: In order to personalize standard therapies based on molecular profiles, we previously classified colorectal cancers (CRCs) into five distinct subtypes (CRCAssigner) and later into four consensus molecular subtypes (CMS) with different prognoses and treatment responses. For clinical application, here we developed an inexpensive multiplex biomarker-based assay.Objective: In order to personalise standard therapies based on molecular profiles, we previously classified colorectal cancers (CRCs) into five distinct subtypes (CRCAssigner) and later into four consensus molecular subtypes (CMS) with different prognoses and treatment responses. For clinical application, here we developed a low-cost multiplex biomarker assay.
Design: Three cohorts of untreated fresh frozen CRC samples (n = 57) predominantly from primary tumours and profiled by microarray/RNA-Seq were analysed. A reduced 38-gene panel (CRCAssigner-38) was selected from the published 786-gene CRCAssigner signature (CRCAssigner-786) using an in-house gene selection approach. A customised NanoString Technologies nCounter platform-based assay (NanoCRCAssigner) was developed for comparison with different classifiers (CMS subtypes), platforms (microarrays and RNA-Seq), and gene sets (CRCAssigner-38 and CRCAssigner-786). An additional cohort of fresh-frozen paraffin embedded (FFPE) samples (n = 24) was subtyped using NanoCRCAssigner as a proof-of-concept.
Results: NanoCRCAssigner classified fresh frozen samples (n = 48; except those showing a mixture of subtypes) into all five CRCAssigner subtypes with overall high concordance across platforms (>87%) and with CMS subtypes (81%) irrespective of variable tumour cellularity. The association of subtypes with their known molecular (microsatellite-instable and stemness), mutational (KRAS/BRAF), and clinical characteristics (including overall survival) further demonstrated assay validity. To reduce costs, we switched from the standard protocol to a low-cost protocol with a high Pearson correlation co-efficient (0.9) between protocols. Technical replicates were highly correlated (0.98). FFPE samples were also successfully classified and showed high reproducibility (0.96).

overall_design: RNA from untreated CRC patients from 4 cohorts (n = 81; 57 fresh frozen and 24 FFPE) were profiled using elements chemistry on a custom nCounter panel. Technical replicates are included to demonstrate reproducibility of elements chemistry (n = 10).

first: Chanthirika

last: Ragulan

first: Katherine

last: Eason

first: Elisa

last: Fontana


title: A Low-cost Multiplex Biomarker Assay Stratifies Colorectal Cancer Patient Samples into Clinically-relevant Subtypes: Singapore Cohort RNA-seq

summary:
Objective: In order to personalise standard therapies based on molecular profiles, we previously classified colorectal cancers (CRCs) into five distinct subtypes (CRCAssigner) and later into four consensus molecular subtypes (CMS) with different prognoses and treatment responses. For clinical application, here we developed a low-cost multiplex biomarker assay.

Design: Three cohorts of primary (except one liver metastases) untreated and fresh frozen CRC samples (n=57) profiled by microarray and RNA-Seq were analyzed. A reduced 38-gene panel (CRCAssigner-38) was selected from the 786-gene CRCAssigner signature (CRCAssigner-786) using an in-house class prediction approach. A customised NanoString Technologies’ nCounter platform-based assay (NanoCRCAssigner) was developed for comparison with different classifiers (CMS subtypes), platforms (microarrays and RNA-Seq), and gene sets (CRCAssigner-38 and CRCAssigner-786).

Results: NanoCRCAssigner classified samples (n=48; except those showing a mixture of subtypes) into all five CRCAssigner subtypes with overall high concordance across platforms (>87%) and with CMS subtypes (81%) irrespective of variable tumour cellularity. The association of subtypes with their known molecular (microsatellite-instable and stemness), mutational (KRAS/BRAF), and clinical characteristics (including overall survival) further demonstrated assay validity. To reduce costs, we switched from standard protocol to a low-cost protocol with a high Pearson correlation co-efficient (0.9) between protocols. Technical replicates were highly correlated (0.98).

overall_design: Gene expression of primary CRC samples from the Singapore cohort was profiled using Illumina HiSeq and TPM values calculated for subsequent subtyping.

first: Yatish

last: Patil

first: Pawan

last: Poudel

first: Koo

last: Si-Lin

first: Tan

last: Wah Siew

first: Iain

last: Beehaut Tan


title: A Low-cost Multiplex Biomarker Assay Stratifies Colorectal Cancer Patient Samples into Clinically-relevant Subtypes

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

overall_design: Refer to individual Series


title: Sox2 is required for functional chromatin connectivity in brain-derived neural stem cells.

status: Public on Mar 07 2019

city: Milano

first: Federico

last: Zambelli

address: Via Giovanni Celoria 26

department: Department of Biosciences

country: Italy

institute: University of Milan


title: A Low-Cost Multiplex Biomarker Assay Stratifies Colorectal Cancer Patient Samples into Clinically-Relevant Subtypes: Standard Chemistry

summary:
Objective: In order to personalize standard therapies based on molecular profiles, we previously classified colorectal cancers (CRCs) into five distinct subtypes (CRCAssigner) and later into four consensus molecular subtypes (CMS) with different prognoses and treatment responses. For clinical application, here we developed an inexpensive multiplex biomarker-based assay.
Design: Three cohorts of untreated fresh frozen CRC samples (n = 57) predominantly from primary tumours and profiled by microarray/RNA-Seq were analysed. A reduced 38-gene panel (CRCAssigner-38) was selected from the published 786-gene CRCAssigner signature (CRCAssigner-786) using an in-house gene selection approach. A customised NanoString Technologies nCounter platform-based assay (NanoCRCAssigner) was developed for comparison with different classifiers (CMS subtypes), platforms (microarrays and RNA-Seq), and gene sets (CRCAssigner-38 and CRCAssigner-786). An additional cohort of fresh-frozen paraffin embedded (FFPE) samples (n = 24) was subtyped using NanoCRCAssigner as a proof-of-concept.
Results: NanoCRCAssigner classified fresh frozen samples (n = 48; except those showing a mixture of subtypes) into all five CRCAssigner subtypes with overall high concordance across platforms (>87%) and with CMS subtypes (81%) irrespective of variable tumour cellularity. The association of subtypes with their known molecular (microsatellite-instable and stemness), mutational (KRAS/BRAF), and clinical characteristics (including overall survival) further demonstrated assay validity. To reduce costs, we switched from the standard protocol to a low-cost protocol with a high Pearson correlation co-efficient (0.9) between protocols. Technical replicates were highly correlated (0.98). FFPE samples were also successfully classified and showed high reproducibility (0.96).

overall_design: 10 RNA samples purchased from OriGene (Rockville, MD, USA), 12 samples previously described in Del Rio et al. (PMID:17327601) and 24 FFPE samples from the RETRO-C study were profiled on a custom nCounter panel using standard chemistry. Samples were histopathologically validated colorectal adenocarcinoma from primary tumours or local/distant recurrence and were treatment naïve.


title: A Low-cost Multiplex Biomarker Assay Stratifies Colorectal Cancer Patient Samples into Clinically-relevant Subtypes: OriGene Cohort Microarray Data

overall_design: 17 RNA samples were purchased from OriGene (Rockville, MD, USA) and profiled on Affymetrix GeneChip Human Transcriptome Array 2.0. Samples were histopathologically validated colorectal adenocarcinoma from primary tumours and were treatment naïve.


title: Defining transcription factor networks that govers SCC growth [ChIP_seq_mm10]

status: Public on Mar 01 2019

city: New York

first: Markus

last: Schober

state: NY

address: 550 First Ave, Smilow 407

institute: New York University School of Medicine

summary: ChIP-seq analyses were perform to define the distribution of Pitx1, Sox2, Trp63 and Klf4 through the genome and define their interactions in SCC.

overall_design: ChIP-seq sequencing was done on TPC issolated from tumors or cultures cells in un differentiated or differentiated conditions. ChIPs for shPitx1 experimentes were performed 48 hours after Pitx1 depletion in replicates

first: Sastre-Perona

last: Ana

first: Schober

last: Markus


title: Defining transcription factor networks that govers SCC growth [ChIP_seq_hg19]

summary: ChIP-seq analyses were perform to define the distribution of PITX1, SOX2 and TP63  through the genome and define their interactions in SCC

overall_design: ChIP-seq sequencing was done on (HN)-SCC cultures cells.


title: Defining transcription factor networks that govers SCC growth


title: Defining transcription factor networks that govers SCC growth [ATAC-seq]

summary: Chromatin accessibility was deffine in TPCs from SCC in order to defines Pitx1, Sox2, Trp63 and Klf4 occupancy.

overall_design: ATAC-seq analysis was perform in freshly issolated TPCs in order to determine chromatin accessibility


title: Genome-wide microRNA screening in Nile tilapia reveals pervasive transcription of isomiRs, sex-biased arm switching and increasing complexity of expression throughout development

city: Botucatu

first: Danillo

last: Pinhal

state: SP

address: R. Prof. Dr. Antonio C. W. Zanin s/n

department: Genetics

country: Brazil

institute: Sao Paulo State University

type: Non-coding RNA profiling by high throughput sequencing

summary:
The elucidation of microRNA function and evolution depends on the identification and characterization of miRNA repertoire of strategic organisms, as the fast evolving cichlid fishes. Using RNA-seq and comparative genomics we carried out an in-depth report of miRNAs in Nile tilapia (Oreochromis niloticus). Our results enlarge vertebrate
miRNAs collection and reveal a notable differential expression of miRNAs arms and isoforms influenced by sex and developmental life stage, providing a better picture of the evolutionary and spatiotemporal dynamics of miRNAs.

overall_design: Discovery and evolutionary analysis of microRNAs

first: Luiz

middle: A

last: Bovolenta


title: Mucosal gene expression profiling in ileum of patients with Crohn's disease

city: Leuven

first: Sare

last: Verstockt

address: O&N4 Herestraat 49 box 610

country: Belgium

institute: KU Leuven

summary: In this study, we investigated gene expression profiles in ileal mucosa from CD patients in different settings (post-operative CD (Rutgeerts score i0); post-operative recurrent CD (i1), post-operative recurrent CD (≥i2b), newly diagnosed CD and late stage CD)) and controls.

overall_design:
Ileal mucosal biopsies were obtained during endoscopy from 65 CD (3 i0 CD, 6 post-operative recurrent (POR) i1 CD, 24 POR (≥i2b), 18 new and 14 late) patients and 12 normal controls.
Total RNA was isolated from ileal mucosal biopsies, labelled and hybridized to Affymetrix Genechip Human Gene 1.0ST Arrays.

first: Jan

last: Van der Goten

first: Leentje

last: Van Lommel

first: Frans

last: Schuit

first: Gert

last: Van Assche

first: Paul

last: Rutgeerts

first: Marc

last: Ferrante

first: Séverine

last: Vermeire

first: Ingrid

last: Arijs


title: Mucosal miRNA expression profiling in ileum of patients with Crohn's disease

summary: In this study, we investigated miRNA expression profiles in ileal mucosa from CD patients in different settings (post-operative recurrent (POR) CD, newly diagnosed CD and late stage CD)) and controls.

overall_design:
Ileal mucosal biopsies were obtained during endoscopy from 35 CD (20 POR (Rutgeerts score ≥i2b), 8 new and 7 late) patients and 8 normal controls.
Total RNA, including small RNA, was isolated from ileal mucosal biopsies, labelled and hybridized to Affymetrix Genechip miRNA 2.0 Arrays.


title: Mucosal miRNA and gene expression profiling in ileum of patients with Crohn's disease

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

platform_organism:
Homo sapiens
synthetic construct


title: Gene expression data from MGH-U3, RT112 and UM-UC-5 following TYRO3 knock-down

status: Public on Feb 27 2019

city: paris

first: Elodie

last: chapeaublanc

address: 26 rue d'ulm

department: UMR 144

country: France

institute: Institut Curie

summary: To better understand the molecular mechanisms underlying TYRO3 oncogenic activity in bladder carcinomas, we made use of  MGH-U3, RT112 and UM-UC-5 cell lines, which were derived from a human bladder tumor and endogenously expressed the Tyro3 protein, the growth and transformation of these cell lines being dependent on Tyro3. We carried out a gene expression analysis using Affymetrix DNA arrays in this cell line treated or not withTYRO3 siRNAs.

overall_design: MGH-U3, RT112 and UM-UC-5 cells were transfected or not  with siRNA TYRO3. mRNA was extracted after 40h and gene expression analysis was assessed using the HG-U133 Plus 2.0 array (Affymetrix) array

first: Florent

last: Dufour

first: Linda

last: Silina

first: Hélène

last: Neyret-Kahn

first: Aura

last: Moreno-Vega

first: Clémentine

last: Krucker

first: Narjesse

last: Karboul

first: Marion

last: Dorland-Galliot

first: Pascale

last: Maillé

last: Chapeaublanc

first: Yves

last: Allory

first: Nicolas

last: Stransky

last: Haegel

first: Thierry

last: Menguy

first: Vanessa

last: Dunong

first: François

last: Radvanyi

first: Isabelle

last: Bernard-Pierrot


title: Assessment and site-specific manipulation of DNA (hydroxy-)methylation during mouse corticogenesis

status: Public on Feb 25 2019

city: Dresden

first: Federico

last: Calegari

address: Fetscherstr. 105

department: Center for Molecular and Cellular Bioengineering (CMCB)

institute: TU Dresden

type: Methylation profiling by high throughput sequencing

summary:
Purpose: In this study we investigated the molecular role of cytosine modification in the developing cortex of mice. To this aim we isolated thee linage related cell populations of the developing cortex and mapped both, 5mC as well as 5hmC on a genome-wide scale. Furthermore we established a system to site-specifcally demethylate DNA by using a dCas9-Tet1 fusion protein.
Methods: Neuronal stem cells (Btg2-/Tubb3-), neurogenic progenitors (Btg2+/Tubb3-) and neurons (Tubb3+) were isolated from E14.5 Btg2-RFP/Tubb3-GFP double heterozygous mouse embryos (Aprea et al. 2013) and were used for a comparative immunoprecipitation of 5mC and 5hmC (Tan et al. 2013).
Results: We were able to identify several genomic regions that change dynamically (hydroxy-)methylation patterns in specific cell type. Specifically for regions losing 5mC and gaining 5hmC we found a consistent enrichment in neurogenesis related GOterms, genomic features, transcription factor binding motifs and different histone marks. Furthermore we found that loss in 5mC and gain in 5hmC correlate with each other and lead to the upregulation of nearby genes. Site-specific demethylation of the identified differentially (hydroxy-)methylated regions in vivo, led to a premature upregulation of the nearby genes which resulted in an altered development of the brain.

overall_design: Genome-wide maps of 5-methylcytosine as well as 5-hydroxymethylcytosine in three lineage-related cell populations of the developing cortex of mice (E14.5).

first: Florian

last: Noack

first: Abhijeet

last: Pataskar

first: Martin

last: Schneider

first: Frank

last: Buchholz

first: Vijay

middle: K

last: Tiwari


title: Effects of Dpy30 loss on gene expression in mouse fetal liver HSCs

city: Birmingham

first: Hao

last: Jiang

state: AL

address: 1825 University Blvd

department: Biochemistry and Molecular Genetics

institute: University of Alabama at Birmingham

summary: Profound distinctions exist between fetal liver (FL) and adult bone marrow (BM) hematopoietic stem cells (HSCs) in many aspects. Previously we showed that efficient H3K4 methylation plays an essential role in the differentiation and long-term maintenance of adult hematopoietic stem cell. However, its role in fetal hematopoiesis is unknown. Here, we show that loss of Dpy30, a core subunit of Set1/Mll complexes that responsible for efficient global H3K4 methylation, in FL results in embryonic anemia as well as the accumulation of HSCs that are defective in multiple lineage reconstitution as shown in mixed chimera assays. Global gene expression analyses identified 21 genes co-downregulated by Dpy30 loss in FL and BM HSCs, among which we further demonstrate that Igdcc4 and Ntpcr are important for efficient colony formation capacity of both FL and BM HSCs in vitro. This study suggests that Dpy30 and certain Dpy30 targets are fundamentally important in regulating HSCs regardless of developmental stages, and that the identified common target genes may provide new insight into the molecular regulation of hematopoiesis.

overall_design: Purified HSCs from E14.5 embryos of control and Dpy30 KO genotypes (3 litters containing both genotypes in each litter) were used to isolate total RNAs for standard RNA-seq.

first: Zhenhua

last: Yang

first: Alireza

last: Khodadadi-Jamayran


title: Adenosine DeAminase-1 (ADA-1) improves Follicular helper T cell function and vaccine response [1]

city: Cleveland

first: Peter

last: Wilkinson

state: Ohio

address: 2103 Cornell Road

department: Pathology / Systems Biology & Bioinformatics

institute: Case Western Reserve University

summary: Follicular helper T cells (Tfh) is indispensable for T-cell dependent antibody responses. Understanding the underlying mechanisms of their differentiation and function is critical for vaccine development. Using unique gene array analysis, we identified adenosine deaminase-1 (ADA-1), as a novel key molecule that drives Tfh helper program in proliferating germinal centers Tfh and circulatory Tfh cells following their interactions with B cells. ADA-1 expression and enzymatic activity is significantly higher in Tfh cells when compared to non-Tfh cells. Exogenous ADA-1 enhances the ability of less efficient cTfh and pro-follicular Tfh cells to provide B cell help, while pharmacological inhibition of ADA-1 activity impeded Tfh function and blunted antibody response. Importantly, in vivo use of recombinant ADA-1 as an adjuvant in a DNA-based HIV vaccine enhanced Tfh differentiation and improved the quantity and the quality of HIV-specific antibody response. Thus, ADA-1 represents a good target for the design of new vaccine strategy.

overall_design: 28 samples across 6 donors consisting of 10 Tfh and 18 non-Tfh cell types.

first: V

last: Tardif

first: E

last: Gary

first: R

last: Cubas

first: M

last: Chakhtoura

first: T

last: Metcalf

last: Herro

last: Kutzler

last: Haddad

first: P

first: L

last: Pan

last: Cameron


title: Clinical Performance of a Stool RNA Assay for Early Detection of Precancerous Adenomas and Colorectal Cancer

city: Saint Louis

first: Erica

middle: Kay

last: Barnell

state: MO

address: 4444 Forest Park

department: McDonnell Genome Institute

institute: Washington University School of Medicine

summary:
Background and Aims: RNA biomarkers derived from sloughed enterocytes would provide an ideal, non-invasive method for early detection of colorectal cancer (CRC) and precancerous adenomas. To realize this goal, a highly reliable method to isolate preserved human RNA from stool samples is needed. Here we develop a protocol to identify RNA biomarkers associated with CRC to assess the use of these biomarkers for noninvasive screening of disease.
Methods: Stool samples were collected from 454 patients prior to a colonoscopy. A nucleic acid extraction protocol was developed to isolate human RNA from 330 stool samples and transcript abundances were estimated by microarray analysis. This 330-patient cohort was split into a training set of 265 individuals to develop a machine learning model and a testing set of 65 individuals to determine the model’s ability to detect colorectal neoplasms.
Results: Analysis of the transcriptome from 265 individuals identified 200 transcript clusters as differentially expressed (p<0.03). These transcripts were used to build a Support Vector Machine (SVM) based model to classify 65 individuals within the testing set. This SVM algorithm attained a 95% sensitivity for precancerous adenomas and a 65% sensitivity for CRC (stage I-IV). The machine learning algorithm attained a specificity of 59% for healthy individuals and an overall accuracy of 72.3%.
Conclusions: We developed an RNA-based neoplasm detection model that is sensitive for CRC and precancerous adenomas. The model allows for non-invasive assessment of tumors and could potentially be used to provide clinical guidance for individuals within the screening population for colorectal cancer.

overall_design:
Total RNA was isolated from 338 stool samples and the transcriptome was assessed using the Affymetrix Human Transcriptome Array 2.0. Differentially expressed genes were identified using the transcript fold change between healthy and diseased individuals. These transcriptomes were used to build a machine learning algorithm to classify individuals as diseased or not diseased.
Reference samples are 'normal,' cases are 'adenomas' or 'cancer'.

first: Yiming

last: Kang

first: Andrew

middle: R

first: Katie

middle: M

last: Campbell

first: Elizabeth

last: Wurtzler

first: Malachi

last: Griffith

first: Mark

last: Manary

first: Obi

middle: L


title: Adenosine DeAminase-1 (ADA-1) improves Follicular helper T cell function and vaccine response

last: Wilkinson


title: Adenosine DeAminase-1 (ADA-1) improves Follicular helper T cell function and vaccine response [2]

overall_design: There are 22 samples across 5 donor Tfh samples, and 4 pooled donor non-Tfh samples.

last: Tardif

first: MA


title: NFIA is a gliogenic switch enabling rapid derivation of functional human astrocytes from pluripotent stem cells

first: Lorenz

last: Studer

department: Developmental Biology

institute: Memorial Sloan Kettering Cancer Center

summary: The development of the central nervous system (CNS) depends on the orchestrated generation of neurons and glia from neural stem cells (NSCs). Although NSCs generate both cell types, they are produced sequentially as neurons are born first and glia later. In humans, this timing is extremely protracted and the underlying mechanisms remain unknown. Deriving glial cells such as astrocytes from human pluripotent stem cells requires 3-6 months of differentiation, greatly impeding their use in human disease modeling and regenerative medicine. Here, we report that expression of the transcription factor nuclear factor IA (NFIA) is sufficient to trigger glial competency in highly neurogenic NSCs and enables the derivation of human astrocytes within 10-12 days.  NFIA-induced astrocytes are functional and shown to promote synaptogenesis, protect neurons and generate calcium transients. The mechanism of NFIA-induced glial competency involves rapid but reversible chromatin remodeling, demethylation of the GFAP promoter and a striking effect on the cell cycle. NFIA titration and pharmacological studies indicate that acquisition of a glial-compatible G1 length is critical for achieving glial competency. Our results offer mechanistic insights into human glial competency and enable the routine use of astrocytes for studying human development and disease.

overall_design: The timecourse consists of 4 timpoints.  Day 0 (d0) represents neurogenic LTNSCs, day 3 (d3) represents overexpression of NFIA with doxycycline and cells were harvested in bulk, day 6 (d6) represents cells sorted for CD44 while NFIA is overexpressed, day 9 (d9) represents CD44+ sorted cells replated in culture without the addition of doxycyline to downregulate NFIA and day 12 (d12) represents the same cultures in d9, but with 3 additional days of no doxycycline treatment.  Each timepoint has a minimum of 3 biological replicates.  Rosette cells (H9 d0) and neurons (Dapt) were profiled as controls where rosettes were one sample and neurons were performed in duplicate.

first: Jason

last: Tchieu


title: Expression data from macrophages from control and BRD4 conditional KO mice

status: Public on Feb 21 2019

first: Anup

last: Dey

address: 9000 Rockville Pike

department: DDB

institute: NIH/NICHD


title: Genome-Scale Transcriptional Regulatory Network Models of Psychiatric and Neurodegenerative Disorders

status: Public on Feb 19 2019

city: Seattle

first: Jocelynn

middle: Renee

last: Pearl

state: Washington

address: 401 Terry Ave N

institute: Institute for Systems Biology

summary:
Transcriptional regulatory changes in the developing and adult brain are prominent features of brain diseases, but the involvement of specific transcription factors (TFs) remains poorly understood. We integrated brain-specific DNase footprinting and TF-gene co-expression to reconstruct a transcriptional regulatory network (TRN) model for the human brain. We identified key regulator TFs whose predicted target genes were enriched for differentially expressed genes in the prefrontal cortex of individuals with psychiatric and neurodegenerative diseases. Many of these TFs were further implicated in the same diseases through disruption of their binding sites by disease-associated SNPs and associations of TF loci with disease risk. Using primary human neural stem cells, we validated network predictions that link the TF POU3F2 to schizophrenia and bipolar disorder via both cis- and trans-acting mechanisms. Our models of brain-specific TF binding sites and target genes provide a resource for network analysis of brain diseases.
GPL 17077 Agilent-039494 SurePrint G3 Human GE v2 8x60K Microarray 039381

overall_design: A transcription factor related to psychiatric disease, POU3F2, is overexpressed in primary human neural stem cells.  RNA expression at 3 and 10 days post-puromycin selection is analyzed using microarrays as compared to cells transduced with a control vector that does not contain the POU3F2 cassette.

first: Seth

last: Ament


title: Expression data from activated peritoneal macrophages from control and BRD4 conditional KO mice

summary:
Macrophages are cells belongs to innate immune system, which  response to pathogen by the production of inflammatory proteins those that are effective in both combating pathogen and wound healing. Using small molecule inhibitors it has been shown that many of the inflammatory response genes were under control of BET proteins.
We used LysM-Cre to conditionally delete floxed BRD4 in resident peritoneal macrophages and monitored the effect on inflammatory gene expression

overall_design: Peritoneal macrophages were treated with either Interferon gamma and IL-4 alone or with LPS and  pre treatment of interferon gamma ex-vivo. In some experiment, animals were treated with IL-4 in vivo.  RNA  was extracted and biotin labeled cDNA was hybridized on Affym3trix microarray.   Untreated samples were used as control. To compare differential gene expression samples were prepared from wild type and BRD4  deleted macrophages.  Biological duplicates were used for each treatment condition

first: Keiko

last: Ozato


title: Analysis of differential gene expression and alternative splicing is significantly influenced by choice of mapping genome

status: Public on Feb 16 2019

city: Raleigh

first: Jigar

last: Desai

state: NC

address: 128 Polk Hall

department: Biochemistry

institute: NCSU

summary:
Purpose:  To demonstrate that gene expression and splicing analysis varies considerably depending on the mapping reference genome.
Methods: We mapped and analyzed submitted RNA reads using different tools and reference genomes to evaluate the influence of genome on DEG and alternative splicing tools.
Results: We observed that these differences in transcriptome analysis are, in part, due to the presence of single nucleotide polymorphisms between the sequenced individual and each respective reference genome, as well as annotation differences between the reference genomes that exist even between syntenic orthologs.
Conclusion: We conclude that even between two closely related genomes of similar quality, using the reference genome that is most closely related to the species being sampled significantly improves transcriptome.

overall_design: Overall design: Using AM and PM timepoints, we anazyled DEG and alternative splicing to determine the affect of reference genome on analysis tools.

first: Erin

last: Slabaugh

first: Ryan

middle: C

last: Sartor

first: Lovely

middle: F

last: Lawas

first: S

last: Jagadish

first: Colleen

last: Doherty


title: Gene expression profiling of nasal swabs samples from children with asthma or wheezing exacerbations.

status: Public on Feb 17 2019

city: Subiaco

first: Anthony

last: Bosco

state: WA

address: 100 Roberts Road

country: Australia

institute: Telethon Kids Institute

summary:
Nasal swab specimens were collected from children who presented to the emergency department with an acute exacerbation of asthma or wheeze. Samples were also collected from control subjects.
Convalescent/quiescent samples were collected from children who were followed-up at least 6 weeks after an acute exacerbation of asthma or wheeze. Gene expression was profiled on microarrays.

overall_design: The study was based on case/control comparisons between children with acute asthma/wheeze, versus convalescent samples or controls.

first: Siew-Kim

last: Khoo

first: Kimberley

last: Franks

first: Rose

last: Maciewicz

first: Peter

middle: N

last: Le Souëf

first: Ingrid

last: Laing


title: Expression data from activated bone marrow derived macrophages from control and BRD4 conditional KO mice

summary:
Macrophages are cells belongs to innate immune system, which response to pathogen by the production of inflammatory proteins those that are effective in both combating pathogen and wound healing. Using small molecule inhibitors it has been shown that many of the inflammatory response genes were under control of BET proteins.
We used LysM-Cre to conditionally delete floxed BRD4 in bone marrow derived macrophages and monitored it's effect on inflammatory gene expression

overall_design: Bone marrow derived macrophages were treated with either LPS, Interferon gamma and IL-4 alone or with LPS with a pre treatment of interferon gamma for RNA extraction and hybridization on Affymetrix microarray. Samples from untreated cells were used as control. To compare differential gene expression samples were prepared from wild type and BRD4 deleted macrophages. Biological duplicates were used for each treatment condition


title: Expression patterns in chronic thromboembolic pulmonary hypertension

status: Public on Feb 18 2019

city: Nashville

first: James

last: West

state: TN

address: 4200 E 9TH Ave, Box B133

department: Medicine

institute: Vanderbilt University

summary: We sequenced RNA from pulmonary arteries from CTEPH, IPAH or healthy, failed donors

overall_design: Expression pattern in human pulmonary arteries during CTEPH or IPAH, using healthy failed donors as control


title: Allele-specific expression profiling of imprinted genes in mouse isogenic pluripotent tissues and cell lines

city: Nijmegen

first: Hendrik

last: Marks

address: Geert Grooteplein 26/28

department: Molecular Biology

country: Netherlands

institute: Radboud University Nijmegen, RIMLS

summary: Genomic imprinting, resulting in parent-of-origin specific gene expression, plays a critical role in mammalian development. Here, we perform allele-specific RNA-Seq on isogenic B6D2F1 mice to assay imprinted genes in tissues from early embryonic stages and in pluripotent cell lines. For the cell lines, we include embryonic stem cells (ESCs) and epiblast stem cells (EpiSCs) derived from fertilized embryos or from embryos obtained after nuclear transfer (NT), as well as B6D2F1 ESCs and EpiSCs derived after parthenogenetic activation (PGA). Notably, the PGA-derived cell lines contain a mosaic genotype due to genomic recombination occurring in the parental B6D2F1 oocyte during meiosis. As the homozygous genomic regions of the PGA-derived cells are not compatible with allele-specific RNA-Seq, we developed an RNA-Seq based genotyping strategy that allows identification of the informative heterozygous regions. Global imprinting analysis shows that ESC lines largely lose imprints as compared to their corresponding embryonic tissues. Fertilized EpiSC and EpiSC-NT lines generally maintain imprinted gene expression. However, two EpiSC-NT lines show aberrant silencing of Rian and Meg3, two critically imprinted genes in mouse iPSCs. EpiSC-PGA lines display loss of imprinting, with known paternally-expressed genes being silenced and known maternally-expressed genes consistently showing doubled expression. Interestingly, most female EpiSC lines show monoallelic expression of Xist and full skewing of X inactivation, suggesting a (near) clonal origin. Together, our analysis provides a comprehensive overview of imprinted gene expression in pluripotency and provides a benchmark to allow identification of cell lines that faithfully maintain imprinted gene expression and therefore retain full developmental potential.

overall_design: We include RNA-Seq on conventional B6D2F1 ESCs derived from fertilized embryos, three ESC lines derived from nuclear transfer embryos generated using B6D2F1 mouse embryonic fibroblast (MEF) donor nuclei (ESC-NT1) or B6D2F1 cumulus donor nuclei (ESC-NT2 and ESC-NT3), as well as three ESC lines derived from PGA embryos generated using B6D2F1 oocytes (ESC-PGA). Also included is RNA-Seq of three fertilized B6D2F1 EpiSC lines, three EpiSC lines derived from nuclear transfer embryos generated using a B6D2F1 cumulus donor nuclei (EpiSC-NT) and two EpiSC-PGA lines. For fertilized ESCs, ESC-NTs and ESC-PGAs we include 1 replica each of H3K4me3 and H3K27me3 ChIP-Seq epigenetic profiling.

first: René

last: Dirks

first: Guido

last: van Mierlo

first: Hindrik

middle: H

last: Kerstens

first: Julien

last: Maruotti

first: Andreia

last: Bernardo

first: Julianna

last: Kobolák

first: István

last: Bock

first: Roger

last: Pedersen

first: András

last: Dinnyés

first: Martijn

last: Huynen

middle: G

last: Stunnenberg

first: Alice

last: Jouneau


title: Transcriptomic profiling of RV144 trial participants before and after vaccination with ALVAC-HIV and AIDSVAX B/E.[rv144pilot]

status: Public on Feb 15 2019

city: Chicago

first: Slim

last: Fourati

state: Illinois

address: 300 E Superior St

institute: Northwestern University

summary: The RV144 clinical trial evaluated the efficacy of a vaccine regimen that included ALVAC-HIV prime and AIDSVAX boost in preventing HIV-1 acquisition. The vaccine reduced the risk of HIV-1 acquisition by 31.2%; however the mechanisms that led to the protection induced by this vaccine remain poorly understood. Our objectives were to identify transcriptional correlates and mechanisms that could explain the reduced acquisition conferred by the vaccine. We assessed the transcriptomic profile of HIV Env stimulated peripheral blood mononuclear cells collected from 223 participants two weeks after vaccination and from 40 placebo recipients.

overall_design: Forty (40) participants of the RV144 clinical trial were primed twice with ALVAC-HIV (at week 0 and week 4) and boosted twice with AIDSVAX B/E in alum adjuvant (at week 12 and week 24). An additional ten (10) participants of the RV144 clinical trial received placebo at the same immunization timepoints (at week 0, week 4, week 12 and week 24). Blood samples were taken pre-vaccination and 2 weeks after the last immunization boost (week 26). All the participants remained HIV-1 negative at last follow-up (up to 3 years after vaccination). Peripheral blood mononuclear cells from those 50 participants was stimulated in vitro for 15 hours with Env peptides or with the vehicle (DMSO). RNA was then extracted and hybridized to Illumina beadchips.

first: Rafick-Pierre

last: Sékaly


title: Transcriptomic profiling of RV144 trial participants after vaccination with ALVAC-HIV and AIDSVAX B/E. [rv144]

overall_design: One hundred and eighty-three (183) participants of the RV144 clinical trial were primed twice with ALVAC-HIV (at week 0 and week 4) and boosted twice with AIDSVAX B/E in alum adjuvant (at week 12 and week 24). An additional thirty (30) participants of the RV144 clinical trial received placebo at the same immunization timepoints (at week 0, week 4, week 12 and week 24). Blood samples were taken 2 weeks after the last immunization boost (week 26). Forty-eight (48) participants acquired HIV-1 during the follow-up and 165 participants remained HIV-1 negative at last follow-up (up to 3 years after vaccination). Peripheral blood mononuclear cells from those 213 participants was stimulated in vitro for 15 hours with Env peptides or with the vehicle (DMSO). RNA was then extracted and hybridized to Illumina beadchips.


title: Transcriptional Analysis of Foxp3+ Regulatory T Cells in Experimental Acute Lung Injury Resolution

status: Public on Feb 12 2019

city: Chapel Hill

first: Jason

middle: Robert

last: Mock

state: North Carolina

address: 125 Mason Farm Rd, Marsico Hall 7229G

department: Internal Medicine

institute: University of North Carolina

summary:
These studies profiled the expression of mRNA in lung and spleen regulatory T cells in Foxp3EGFP mice during lipopolysaccharide-induced lung injury.
Baseline, uninjured Lung Treg and Resolving Lung Tregs and Resolving Splenic Tregs were sorted (7 days after intratracheal instillation of LPS for Resolving conditions) and mRNAs differentially expressed (DE) between Control Lung Tregs, Resolving Lung Tregs and Resolving Splenic Tregs samples were identified using microarrays.

overall_design: Baseline, uninjured Lung Treg and Resolving Lung Tregs and Resolving Splenic Tregs were sorted for mRNA analysis. mRNA expression was profiled using Mouse Gene 2.1 ST arrays (Affymetrix, Santa Clara, CA) which cover over 28,000 RefSeq transcripts.

first: Hong

last: Dang

first: Claire

last: Doerschuk


title: Gene expression profiling of CAR-T cells pre-and post-adoptive transfer

status: Public on Feb 11 2019

city: Tampa

first: Daniel

last: Abate-Daga

state: Florida

address: 12902 Magnolia Dr.

department: Immunology

institute: H. Lee Moffitt Cancer Center and Research Institute

summary: Chimeric Antigen Receptors (CARs) are synthetic immune receptors introduced in cancer patients' autologous T Cells for cellular immunotherapy. The purpose of this study is to characterize the changes in gene expression induced by the presence of a CAR in human primary T cells (comparison A or B versus C); and the changes that take place for each group after transfer into a xenograft model of pancreatic cancer (comparison Post versus Pre).

overall_design: Primary human CD8 T cells were stimulated ex vivo and transduced to express either of 2 variants of an anti-PSCA CAR, or GFP as a control. Three independent cultures were maintained as biological replicates for each group. Two weeks later, they were injected into immunodeficient mice bearing HPAC-derived pancreatic tumors. Spleen-resident human CD8 T cells were isolated 30 days later, and the gene expression profiles of each group was analyzed using microarrays.

first: Sean

last: Yoder


title: BCR-ABL-mediated recruitment of STAT5 revealed by ChIPseq

city: Kyoto

first: Hideyo

last: Hirai

state: Kyoto

address: 54 Kawahara-cho, Sakyo-ku

institute: Kyoto University Hospital

summary: Even in the era of ABL tyrosine kinase inhibitors, eradication of chronic myeloid leukemia (CML) stem cells still remains to be a prerequisite for the complete cure of the disease. Interferon-α (IFNα), which has been used long for the treatment for CML-chronic phase, are now being re-evaluated. However, the molecular mechanism involved in the action of IFNα on CML stem cells have not been elucidated yet. In this study we have found that IFNα upregulates CCAAT/Enhancer Binding Protein β (C/EBPβ), a transcription factor required for demand-driven granulopoiesis, through activation of STAT1 and STAT5 in BCR-ABL-expressing cells. Activated STAT1 and STAT5 were recruited to the newly identified 3’ distal enhancer region of Cebpb, which contains tandemly aligned interferon-g activated sequences (GAS). Genome editing-mediated repression or deletion of the GAS elements significantly abrogated the IFNα-dependent upregulation of C/EBPβ. IFNα induces differentiation and exhaustion of CML stem cells both in vitro and in vivo in a C/EBPβ-dependent manner. In addition, IFNα upregulates C/EBPβ and induces exhaustion of CD34+ CML stem cells obtained from CML patients. Collectively, these data clearly show that C/EBPβ is a critical factor in IFNα signaling that induces differentiation and exhaustion of CML stem cells.

overall_design: Examination of STAT5 binding in 3 conditions in a cell line

first: Asumi

last: Yokota

first: Ryuichi

last: Sato

first: Hiroko

last: Adachi

first: Fumiko

first: Yoshihiro

last: Hayashi

first: Atsushi

first: Naoka

last: Kamio

first: Yasuo

last: Miura

first: Masakazu

last: Nakano

last: Tenen

first: Shinya

last: Kimura

first: Kei

last: Tashiro

first: Taira

last: Maekawa


title: Genome-wide mRNA expression and methylation patterns of neural genes in response to prenatal hormones

city: Athens

first: Kristen

middle: Jean

last: Navara

state: GA

address: 203 Poultry Science Building

department: Poultry Science

institute: The University of Georgia

summary: We explored the molecular mechanisms that mediate changes in neural gene expression (i.e., hypothalamus and nucleus taenia of the amygdala) and aggression in male and female zebra finches (Taeniopygia guttata) exposed to prenatal testosterone. We used egg injections of testosterone or the vehicle to mimic maternal hormones, which are transferred to offspring during prenatal development. Many researchers have postulated that prenatal maternal hormones can generate adaptive phenotypic plasticity; however, no study has determined the mechanism facilitating these long-term changes. Thus, we analyzed neural tissues from behaviorally relevant brain regions for changes in gene expression via RNA-Seq and methylation via Methyl-Seq resulting from the prenatal hormone treatment.

overall_design: RNA- and Methyl-Seq profiles of two brain regions of zebra finches exposed to prenatal testosterone or a control.

first: Alexandra

middle: B

last: Bentz

first: Chad

last: Niederhuth

first: Laura

last: Carruth


title: Phase Separation of Ligand-Activated Enhancers Licenses Cooperative Chromosomal Enhancer Assembly [ATAC-seq]

status: Public on Feb 10 2019

city: San Diego

first: Qi

last: Ma

address: 9500 Gilman Dr,

institute: UCSD

summary: Detailed analysis of estrogen mediated enhancer landscape and chromosomal architectural changes specifically in human chromosome 21.

overall_design: ATAC-seq experiments are designed to elucidate chromatin openness in human breast cancer cells (MCF7 WT and mutant) under basal or estrogen treated conditions.

first: Sreejith

last: Nair


title: Transcriptomic profiling of RV144 trial participants

first: Slim

last: Fourati

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

overall_design: Refer to individual Series


title: Phase Separation of Ligand-Activated Enhancers Licenses Cooperative Chromosomal Enhancer Assembly [4C-seq]

overall_design: Circularized Chromosome Conformation Capture designed to study the estrogen depended interaction of TFF1 enhancer to other first-tier enhancers


title: The CDK7 Inhibitor THZ1 Alters RNA Polymerase Dynamics at the 5’ and 3’ Ends of Genes

first: Scott

last: Hiebert

address: Vanderbilt University, 2220 pierce Avenue, 512 PRB

summary: The t(8;21) is one of the most frequent chromosomal translocations associated with acute myeloid leukemia (AML). We found that t(8;21) AML were extremely sensitive to THZ1, which triggered apoptosis after only 4 hr. We used precision nuclear run-on transcription sequencing (PROseq) to define the global effects of THZ1 and other CDK inhibitors on RNA polymerase II dynamics. Inhibition of CDK7 using THZ1 caused wide-spread loss of promoter-proximal paused RNA polymerase. This loss of 5’ pausing was associated with accumulation of polymerases in the body of  a large number of genes. However, there were modest effects on genes regulated by “super-enhancers”. At the 3’ ends of genes, treatment with THZ1 suppressed RNA polymerase “read through” at the end of the last exon, which resembled a phenotype associated with a mutant RNA polymerase with slower elongation rates. Consistent with this hypothesis, polyA site-sequencing (PolyA-seq) did not detect differences in polyA sites after THZ1 treatment.  PROseq analysis after short treatments with THZ1 suggested that these 3’ effects were due to altered CDK7 activity at the 5’ end of long genes, and were likely to be due to slower rates of elongation.

overall_design: Kasumi-1 cells were treated with DMSO, 400nM flavopiridol (FVP), 25nM dinaciclib (Dina), 5uM PHA-767491 (PHA), 400nM THZ1 and 5uM palbociclib (Palbo) for 1hr and PROseq and RNAseq were performed to study changes in transcription and gene expression. Kasumi-1 cells were treated with 400nM THZ1 for 0, 15, 30,60 and 120 minutes and PROseq was performed. RNAseq was performed for 0 and 2hr THZ1 treated samples. Two biological replicates were included for each time point.

first: Shilpa

last: Sampathi

first: Pankaj

last: Acharya

middle: W


title: miRNA expression alterations in liraglutide treated rats arota

city: Beijing

first: Qian

last: Zhang

address: No. 1 Shuaifuyuan, Dongcheng District

institute: Peking Union Medical College Hospital

summary: liraglutide may distrub miRNA expression in diabetic rats arota

overall_design: miRNA array in liraglutide-treated rat arota

first: Xinhua

last: Xiao

first: Jia

last: Zheng

first: Ming

last: Li

first: Miao

last: Yu

first: Fan

last: Ping

first: Cuijuan

last: Qi

first: Tong

last: Wang

first: Xiaojing

first: Liyuan

last: Zhou


title: An actionable pathway connecting NFATc2 to FOXM1 and EZH2 controls the MITFlo/invasive melanoma phenotype

status: Public on Feb 06 2019

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

institute: IRCSS Istituto Nazionale Tumori

summary: Dissection of melanoma heterogeneity through gene expression profiling has led to the identification of two major phenotypes, conventionally defined as “MITF high / proliferative” and “AXL high / invasive”. Tumors or single melanoma cells characterized by a predominant AXL-related gene program show enhanced expression of sets of genes involved in motility, invasion and regulation of epithelial-mesenchymal transition (EMT), while these genes are downregulated in tumors or cells with a predominant MITF-related gene program. The activation of the AXLhi/MITFlo invasive gene program in melanoma is characterized by aberrant expression of transcription factors (TFs) involved in the embryonic EMT process. Additional master genes involved in promoting melanoma growth and invasive state have been identified within the family of epigenetic regulators. Two of these genes, RNF2 and EZH2, components of the polycomb repressive complexes 1 and 2, act by epigenetically silencing tumor suppressors that in turn regulate the invasive and EMT-like phenotype of melanoma cells. Additional master genes involved in promoting melanoma growth and invasive state have been identified within the family of epigenetic regulators. Two of these genes, RNF2 and EZH2, components of the polycomb repressive complexes 1 and 2, act by epigenetically silencing tumor suppressors that in turn regulate the invasive and EMT-like phenotype of melanoma cells. Here we provide evidence for a new actionable pathway that controls melanoma EMT-like/invasive phenotype. We show that in MITFlo melanomas, the TF NFATc2 controls the EMT-like transcriptional program, the invasive ability of neoplastic cells, as well as in-vitro and in-vivo growth, through a pathway that functionally links c-myc to FOXM1 and EZH2. Targeting of NFATc2, FOXM1 or EZH2 inhibited melanoma migratory and invasive activity. Moreover, pharmacological co-targeting of NFATc2 and EZH2 promoted apoptosis of BRAF-mutant melanomas with intrinsic resistance to BRAF inhibition.

overall_design: The human melanoma cell lines Ctrl_shRNA 1, Ctrl_shRNA 2, NFATc2_shRNA 1, NFATc2_ shRNA 2  were established in our laboratory after NFATc2 silencing with shRNA in melanoma cell line 21158, derived from a  a surgical specimens. Cells were routinely maintained in RPMI medium 1640 supplemented with 10% FBS and 2 mM glutamine. Cells were maintained at 37°C in a water-saturated atmosphere of 5% CO2 in air. 6x10^6 cells were seeded in 75 cm2 flasks. Each treatment or combination was performed in triplicate. The cells were collected and RNA extracted.

first: L

first: A

last: Anichini


title: Genome-wide regulatory adaptation shapes population-level genomic landscapes in Heliconius [ChIP-seq]

status: Public on Feb 05 2019

city: Ithaca

first: James

middle: Joseph

last: Lewis

address: 215 TOWER ROAD

department: Ecology & Evolutionary Biology

institute: Cornell University

summary: We test the hypothesis that intraspecific genomic divergence is linked to regulatory variation between Heliconius butterfly populations. We show that population-level divergence in chromatin accessibility and regulatory activity during wing development is abundant, and that differences in regulatory activity between populations are strongly associated with developmental stage. Genomic regions with high Fst are highly enriched for regulatory variants, and enrichment patterns vary significantly across development. Regulatory variants are associated with most differential gene expression between populations, and our data point to two roles for histone modifications in the evolution of gene expression.

sample_organism:
Heliconius himera
Heliconius erato petiverana
Heliconius erato lativitta

overall_design: Examination of 2 different histone modifications in wing tissue over 2 developmental stages.

first: Robert

middle: D

last: Reed

middle: J


title: Gene expression analysis of human fetal pancreatic niche cell lines: Wk17.5h and Wk20.1

status: Public on Feb 01 2019

city: Houston

first: Malgorzata

last: Borowiak

address: 1 Baylor Plaza

institute: Baylor College of Medicine

summary: We derived cell lines from the human pancreatic niche from different sites during different temporal stages of fetal development when beta cells are differentiating and maturing. This screen uncovered differences between the human pancreatic niche at fetal week 17.5 head of pancreas(Wk17.5h) and 20.1 doudeum (Wk 20.1) and control cell line human dermal fibroblast(HDF), illustrating a temporally changing, developmentally significant microenvironment.

overall_design: We characterized gene expression of human fetal-derived pancreatic mesenchymal and endothelial cell lines Wk 17.5h and Wk 20.1, with control cell line HDFs

first: Diane

last: Yang

first: Jolanta

last: Chmielowiec


title: Short-term low calorie diet remodels skeletal muscle lipid profile and metabolic gene expression in obese adults

city: Stockholm

first: Leonidas

middle: S

last: Lundell

state: Stockholm

address: Von Eulers Väg 4a

department: Physiology and Pharmacology

institute: Karolinska Institute

summary: OBJECTIVE Diet intervention in obese adults is the first strategy to induce weight loss and to improve insulin sensitivity. We hypothesized that improvements in insulin sensitivity after weight loss from a short-term dietary intervention tracks with alterations in expression of metabolic genes and abundance of specific lipid species. RESEARCH DESIGN AND METHODS Eight obese, insulin resistant, non-diabetic adults were recruited to participate in a three-week low calorie diet intervention study (1000 kcal/day). Fasting blood samples and vastus lateralis skeletal muscle biopsies were obtained before and after the dietary intervention. Clinical chemistry and measures of insulin sensitivity were determined. Unbiased microarray gene expression and targeted lipidomic analysis of skeletal muscle was performed. RESULTS Body weight was reduced, insulin sensitivity (HOMA-IR) was enhanced, and serum insulin concentration and blood lipid (triglyceride, cholesterol, LDL and HDL) levels were improved after dietary intervention. Gene set enrichment analysis of skeletal muscle revealed that oxidative phosphorylation and inflammatory processes were among the most enriched KEGG-pathways identified after dietary intervention. mRNA expression of PDK4 and MLYCD increased, while SCD decreased in skeletal muscle after dietary intervention. Dietary intervention altered the intramuscular lipid profile of skeletal muscle, with changes in content of phosphatidylcholine and triglyceride species among the pronounced. CONCLUSIONS Short-term diet intervention and weight loss in obese adults alters metabolic gene expression and reduces specific phosphatidylcholine and triglyceride species in skeletal muscle, concomitant with improvements in clinical outcomes and enhanced insulin sensitivity.

overall_design: Eight obese non-diabetic (two men and six women) participants were recruited to enroll in the study. Two of the participants were on hypertensive medication (calcium channel blocker, Amlodipin and ACE inhibitor, Enalapril), and one participant was on medication for hyperlipidemia (HMG-CoA reductase inhibitor, Simvastatin). Participants with a fasting plasma glucose of >7 mmol/L or with medication for type 2 diabetes were not enrolled in the study. The participants underwent a three-week (23±9 days) low calorie diet  consisting of 1000 kcal/day (40-50% carbohydrate, 30-40% protein and 20% fat as percentage of the total calories). All meals were replaced with nutritional formulas from various manufacturers (Modifast, Allévo or Nutrilett) and the participants could select the products to achieve the daily 1000 kcal. Informed written consent was obtained from the participants. The study was approved by the regional ethics committee of Stockholm and conducted according to the Declaration of Helsinki.

first: Carolina

last: Nylén

first: Julie

last: Massart

first: Juleen

last: Zierath

first: Erik

last: Näslund


title: Genome-wide regulatory adaptation shapes population-level genomic landscapes in Heliconius

platform_organism:
Heliconius himera
Heliconius erato petiverana
Heliconius erato lativitta


title: MiRNAs expression in peripheral blood monouclear cells from stable COPD and healthy adults

first: Tianyu

address: No.8 Xishiku Street

department: Respiratory and Critical Care

institute: Peking University First Hospital

summary:
To explore which miRNAs were altered in COPD, we performed a microRNA microarray analysis of peripheral blood mononuclear cells from stable COPD patients (n=6) and healthy controls (n=6). Sex, age, BMI and history of cigarette smoke were matched between different groups.
Blood samples were obtained from stable COPD patients(n=6) and healthy adults (n=6) from clinical trial (NCT02037828). The study was in compliance with the Declaration of Helsinki and was approved by Peking University Institutional Review Board Office.

overall_design: Tianyu, Zhou

first: Guangfa


title: BRCA1 haploinsufficient Mesenchyme Derived from human peripheral blood Induced Pluripotent Stem Cell

status: Public on Jan 31 2019

city: VILLEJUIF

first: christophe

last: desterke

address: 14-16 avenue Paul Vaillant Couturier

department: UFR medecine institute Andre Lwoff

institute: university Paris Sud11

summary:
BRCA1 molecule, known to be implicated in DNA repair and its alterations were associated to familial breast cancer prediposition.
Genome of the patients with familial breast cancer predispostion harbor some germinal alterations in BRCA1 locus. Cells from peripheral blood of human with haplodeficiency BRCA1 locus and also from comparative sample (BRCA1 unaffected) were collected to produce induced pluripotent stem cell by classical protocol (Yamanaka OKSM) and Sendai Stem cell reprogammation which was validated by expression assessment of pluripotent stem cell markers and induction of teratoma after xenotransplantation mice model. Induced pluripotent stem cell (IPSC) were differentiated in mesenchymal lineage in order to see influence of BRCA1 effects during developmental steps of the stroma: effectively microenvironment of breast tumor is infiltrate of mesenchymal stromal cell. Total RNA of the mesenchyme derived IPS from control and BRCA1 haploinsufficient were respectively collected to screen whole expression analysis by transcriptome microarray.

overall_design: total RNA from mesenchyme derived from peripheral blood IPSC was extracted in duplicate for wide type control sample and from BRCA1 haploinsufficient samples. Each individual sample were hybridized on Afymmetrix microarray Human Gene ST2.0

first: Frank

last: Griscelli

first: Christophe

last: Desterke

first: Annelise


title: Genome expression analysis of Lung Progenitors matured in the presence of constitutively active or pharmacologically inhibited Glycogen Synthase Kinase 3

status: Public on Jan 30 2019

city: New York

first: Hans-Willem

last: Snoeck

address: 650 W. 168th Street, BB816

institute: Columbia University Medical Center

summary: In 3D cultures of hPSC-derived lung progenitors withdrawal of the GSK3 inhibitor, CHIR99021, induces multilineage maturation, including of proximal cells, type I alveolar epithelial cells and morphologically mature type II cells.

overall_design: Lung Progenitors and D50 differentiated cells mRNA profiles were generated by deep sequencing, in triplicate, using Illumina HiSeq2500. D50 differentiated lung progenitor single-cell RNA profiles were generated using HiSeq4000 and 10x genomics' cellranger pipeline v2.0.0.

first: Ana

last: de Carvalho

first: Alexandros

last: Strikoudis


title: Phase Separation of Ligand-Activated Enhancers Licenses Cooperative Chromosomal Enhancer Assembly

first: Qi

last: Ma


title: SCD – Stem Cell Differentiation on board the International Space Station [microarray on total RNA]

first: Silvia

last: Bradamante

address: Via Golgi 19

institute: CNR-ISTM, Institute of Molecular Science and Technology

summary:
The bone loss observed in astronauts and animal models after spaceflight is attributable to alterations in the bone tissue formation that depends from the continuous remodeling through the activities of bone-resorbing osteoclasts of hematopoietic lineage and bone-forming osteoblasts of mesenchymal origin.
This disease is frequent in aged people, but develops much more rapidly in space. Our experiment, selected by ESA (European Space Agency), aimed to determine how human bone marrow mesenchymal stem cells (hBMSCs) react and differentiate in real microgravity, on board the International Space Station, in approx. 2 weeks time.

overall_design:
The SCD experiment consisted of 24 experimental hardware modules (EH) (12 flight modules and 12 ground modules), each of which had one experiment unit (EU) integrated into the KUBIC interface container single level (KIC-SL).
Each EU consisting of a brick containing 5 cylinders (for the medium and chemicals), a cell culture chamber (CC), and connecting channels. Five small valves were placed to separate the different fluids and the CC. Each cylinder had a piston to inject a new fluid into the CC; the waste medium was collected in the previously emptied cylinder and suitably preserved.
EH were trasferred on board the ISS by the Soyuz-TMA-16M (ISS 42S, launched on March 27, 2015); 27°C was the temperature recorded for the samples in the Soyouz vehicle before docking and installation in the KUBIK incubator on board the ISS
The experimental proifile consisted of: 1) installation in KUBIK (T0); 2) Start with the first medium exchange (T0+7h); 3) Second medium exchange (T0+7d); 4)Third medium exchange with PBS (T0+14d); 5) Stop by means of two subsequent exchanges with RNAlater
Here, the effect of microgravity on hBMSCs were investigated by means of microarray analysis of total RNA.

first: Damariz

last: Rivero

first: Livia

last: Barenghi

first: Michele

last: Balsamo

first: Simone

last: Minardi

first: Francesco

last: Vitali

first: Duccio

last: Cavalieri


title: MicroRNA-122 supports robust innate immunity in hepatocytes by targeting the RTKs/STAT3 signaling pathway

status: Public on Feb 02 2019

city: Guangzhou

first: Hui

last: Xu

address: 135#, Xingangxi Road

department: School of Life Sciences

institute: Sun Yat-Sen University

summary:
MicroRNA-122 (miR-122) is the most abundant microRNA in hepatocytes and a central player in liver biology and disease. Herein, we report a previously unknown role for miR-122 in hepatocyte intrinsic innate immunity. Restoring miR-122 levels in hepatoma cells markedly enhanced the activation of interferons (IFNs) in response to a variety of viral nucleic acids or simulations, especially of hepatitis C virus RNA and poly (I:C). Mechanistically, miR-122 down-regulated the phosphorylation (Tyr705) of STAT3 and thereby removed the negative regulation of STAT3 on IFN-signaling. While STAT3 represses IFN expression by inhibiting interferon regulatory factor 1 (IRF1); miR-122 targets MERTK, FGFR1 and IGF1R, three receptor tyrosine kinases (RTKs) that directly promote STAT3 phosphorylation. This work identifies a miR-122–RTKs/STAT3–IRF1–IFNs regulatory circuitry, which may play a pivotal role in regulating hepatocyte innate immunity. These findings renewed our knowledge about miR-122’s function and have important implications for treating hepatitis viruses.
We used microarrays to analyze which genes were down-regulated by miR-122.

overall_design: In order to accurately obtain the gene pools down-regulated by miR-122, we employed both transient and stable miR-122 over-expression in HepG2 cells. Transient over-expression was performed by transfection of miR-122 mimics. For stable over-expression of miR-122, we generated a miR-122-Tet-On HepG2 cell line in which the miR-122 is under the control of an inducible promoter. Adding doxycycline to the culture medium induced high level of miR-122 expression. RNAs were sent to microarray analysis with GeneChip® Human Genome U133 Plus 2.0 Arrays.

first: Shi-Jun

first: Liang-Hu

last: Qu


title: Tyrosine kinase c-Abl couples RNA polymerase II transcription to an RNA-dependent DNA damage response

status: Public on Feb 04 2019

city: Oxford

first: Monika

last: Gullerova

address: South Parks Road

department: Sir William Dunn School of Pathology

institute: University of Oxford

summary: Various modes of DNA repair counteract genotoxic DNA double-strand breaks (DSBs) to maintain genome stability. Recent findings suggest that the human DNA damage response (DDR) utilises damage-induced small RNA for efficient repair of DSBs. However, production and processing of RNA is poorly understood. Here we show that localised induction of DSBs triggers phosphorylation of RNA polymerase II (RNAPII) on carboxy-terminal domain (CTD) residue tyrosine-1 in an Mre11-Rad50-Nbs1 (MRN) complex-dependent manner. CTD Tyr1-phosphorylated RNAPII synthetises, strand-specific, damage-responsive transcripts (DARTs). DART synthesis occurs via formation of transient RNA-DNA hybrid (R-loop) intermediates. Impaired R-loop formation attenuates DART synthesis, impairs recruitment of repair factors and delays the DDR. Collectively, we provide mechanistic insight in RNA-dependent DSB repair.

overall_design: Nascent RNA was isolated from WT U2OS cells and AsiSI-ER U2OS cells using immunopurification of mammalian nascent elongating transcripts (mNET-IP) as described in Nojima 2016. For ChIP-seq: Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with Tyrosine 1-p antibody.

first: Kaspar

last: Burger

first: Margarita

last: Schlackow

first: Mat

last: Davis


title: HNF4a Mediated Formation of Hepatic Progentiors [array expression data set]

status: Public on Jan 28 2019

city: Charleston

first: Stephen

middle: A

last: Duncan

state: SC

address: 173 Ashley Avenue, BSB 6th Floor, Room 657A

department: Regenerative Medicine and Cell Biology

institute: Medical University South Carolina

summary:
HNF4a has been shown to be a central regulator of hepatocyte differentiation and function in adult mice.  It was recently shown the HNF4a regulates the onset of hepatic gene expression during liver differentiation in vitro and is critical for the specification of liver towards a hepatic fate
We examined the global gene expression of the differentiaiton of iPS cells into specified hepatic cells on consecutive days of liver differentiation (Mallanna et al 2013) to determine the onset of hepatic gene expression and the role HNF4a plays during hepatic specification.

overall_design: Performed gene array analyses on consecutive days of the differentiation of iPS cells into specified hepatic cells, days 3 - 8,  in biological duplicate.

first: Ann

last: De La Forest


title: HNF4a Mediated Formation of Hepatic Progenitors


title: The zinc-finger protein CLAMP promotes gypsy chromatin insulator function in Drosophila

city: Bethesda

first: Cameron

last: Palmer

state: MD

address: 50 South Drive

department: National Institute of Diabetes and Digestive and Kidney Diseases

institute: National Institutes of Health


title: miR-140 mutation and skeletal dysplasia

status: Public on Jan 29 2019

city: Nagoya

first: Hiroshi

middle: I.

last: Suzuki

address: 65 Tsurumai-cho, Showa-ku

department: DIvision of Molecular Oncology, Graduate School of Medicine

institute: Nagoya University


title: Combined chemosensitivity and chromatin profiling prioritizes drug combinations in CLL

status: Public on Jan 26 2019

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

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

summary: The Bruton tyrosine kinase (BTK) inhibitor ibrutinib has substantially improved therapeutic options for chronic lymphocytic leukemia (CLL). Although ibrutinib is not curative, it has a profound effect on CLL cells and may create new pharmacologically exploitable vulnerabilities. To identify such vulnerabilities, we developed a systematic approach that combines epigenome profiling (charting the gene-regulatory basis of cell state) with single-cell chemosensitivity profiling (quantifying cell-type-specific drug response) and bioinformatic data integration. By applying our method to a cohort of matched patient samples collected before and during ibrutinib therapy, we identified characteristic ibrutinib-induced changes that provide a starting point for the rational design of ibrutinib combination therapies. Specifically, we observed and validated preferential sensitivity to proteasome, PLK1, and mTOR inhibitors during ibrutinib treatment. More generally, our study establishes a broadly applicable method for investigating treatment-specific vulnerabilities by integrating the complementary perspectives of epigenetic cell states and phenotypic drug responses in primary patient samples.

overall_design: 38 ATAC-seq samples from primary peripheral blood mononucleated cells (PBMC) from chronic lymphocytic leukemia patient with high leukemic cell count were produced.

first: Christian

last: Schmidl

first: Gregory

middle: I

last: Vladimer

first: André

last: Rendeiro

first: Susanne

last: Schnabl

first: Tea

last: Pemovska

first: Thomas

last: Krausgruber

first: Mohammad

last: Araghi

first: Nikolaus

last: Krall

first: Berend

last: Snijder

first: Rainer

last: Hubman

first: Anna

last: Ringler

first: Dita

last: Demirtas

first: Oscar

last: Lopez de la Fuente

first: Martin

last: Hilgarth

first: Cathrin

last: Skrabs

first: Edit

last: Porpaczy

first: Michaela

last: Gruber

first: Gregor

last: Hörmann

first: Stefan

last: Kubicek

first: Philipp

last: Staber

first: Medhat

last: Shehata

first: Ulrich

last: Jäger

first: Giulio

last: Superti-Furga


title: DNA hypermethylation encroachment at CpG island borders in cancer is predisposed by H3K4 monomethylation [WGBS_Mm]

status: Public on Jan 23 2019

city: Sydney

first: Ksenia

last: Skvortsova

state: NSW

address: 384 Victoria St, Darlinghurst

department: Genomics and Epigenetics

institute: Garvan Institute

summary: The crosstalk between H3K4 monomethylation and DNA methylation has been receiving little attention to date. We investigated a mouse model harboring a loss-of-function mutation of lysine methyltransferase 2D (KMT2D), which catalyzes the monomethylation of lysine 4 on histone H3. We performed H3K4me1 ChIP-seq in spleen B cells with the wild type (WT) KMT2D as well as heterozygous (HET) and homozygous (HOM) chr15: 98,835,228 A>T KMT2D mutation. Alongside, using WGBS, we performed genome-wide DNA methylation profiling in spleen B cells with the WT KMT2D as well as HET and HOM chr15: 98,835,228 A>T  KMT2D mutation.

overall_design: Genome-wide analysis of DNA methylation using WGBS in B cells and blood from mice with the wild type KMT2D, heterozygous Ile5482Asn KMT2D mutation and homozygous Ile5482Asn KMT2D mutation.

first: Etienne

last: Masle-Farquhar

first: Phuc-Loi

last: Luu

first: Susan

last: Clark

first: Clare

last: Stirzaker


title: DNA hypermethylation encroachment at CpG island borders in cancer is predisposed by H3K4 monomethylation [WGBS_Hs]

summary: DNA methylation plays a key role in demarcation of regulatory regions, including promoter-associated CpG islands. While CpG islands are typically maintained in an unmethylated state in normal cells, a proportion of CpG islands are subject to hypermethylation in cancer cells. It still remains elusive how the exquisite demarcation of the bimodal methylation state is established and maintained at the CpG island flanks and conversely what triggers the erosion of CpG island DNA methylation in tumorigenesis. Here, we applied whole-genome bisulphite sequencing to study the comprehensive methylation patterns of prostate normal and cancer tissues. Alongside we performed TET-assisted bisulphite sequencing to study genome-wide DNA hydroxymethylation patterns of normal prostate and prostate cancer tissues.

overall_design: Clinical prostate samples were identified from the Garvan Institute/St Vincent's Prostate Cancer biobank with human ethics approval (SVH File Number 12/231). Formalin-fixed, paraffin-embedded radical prostatectomy blocks were retrieved and H&E sections reviewed by a specialist prostate cancer pathologist. Five 2 mm core biopsies were taken from 1) each of the dominant nodules in areas of >90% cancer cell density, and 2) adjacent benign prostate tissue. DNA was extracted using the AllPrep DNA/RNA kit (Qiagen, USA).

first: Timothy

last: Peters


title: DNA hypermethylation encroachment at CpG island borders in cancer is predisposed by H3K4 monomethylation [ChIP-Seq]

overall_design: Genome-wide analysis of H3K4me1 histone mark in mouse B cells with the wild type KMT2D, heterozygous Ile5482Asn KMT2D mutation and homozygous Ile5482Asn KMT2D mutation.

first: Cathryn

middle: M

last: Gould

first: Christopher

last: Goodnow


title: DNA hypermethylation encroachment at CpG island borders in cancer is predisposed by H3K4 mono-methylation patterns.

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

overall_design: Refer to individual Series


title: Expression data from whole blood in CD patients undergoing HSCT.

city: Barcelona

first: Azucena

last: Salas

address: Rosselló, 149-153

department: Gastroenterology

country: Spain

institute: IDIBAPS

summary: Treatment of severely refractory Crohn’s disease (CD) patients remains a clinical challenge. Recent studies show efficacy of autologous hematopoietic stem cell transplant (HSCT) in these severely compromised patients. HSCT is thought to eliminate auto-reactive cells; however the mechanisms are incompletely understood. We followed a group of patients (n=18) receiving autologous HSCT, with 50% of them achieving endoscopic drug-free remission. To elucidate the mechanism driving efficacy we compared the immunological changes induced by HSCT in responders and non-responders.

overall_design: Blood from CD patients undergoing HSCT was collected into PAXgene tubes and frozen at -20ºC (PAXgene Blood RNA Tube / PreAnalytiX (Qiagen, Spain)). Simple Endoscopic Score for Crohn's Disease (SES-CD) index was used at baseline and during follow-up to assess endoscopic activity.  Magnetic Resonance Indeex of Activity (MaRIA) was used at baseline and during forllow up in those patients in whom lesions could not be assessed by ileocolonoscopy; mucosal healing was defined as a segmental index < 7 in all ileocolonic segments. Response was defined as mucosal healing at 52 weeks after-HSCT. Blood RNA isolation was performed with the PAXgene Blood RNA Kit using an automated protocol of QIAcube (Qiagen, Spain). Purity and integrity of the total RNA is assessed through 2100 Bioanalyzer (Agilent, Germany) and then quantified by NanoDrop spectrophotometer (NanoDrop Technologies, USA). A total of 42 samples belonging to 14 patients were analized.

first: Ana

last: Corraliza


title: SCD – Stem Cell Differentiation on board the International Space Station: the problem of human bone loss

first: Silvia

last: Bradamante


title: Replication timing and epigenome remodelling are associated with the nature of chromosomal rearrangements in cancer

city: Darlinghurst

first: Qian

last: Du

address: 384 Victoria St

institute: Garvan Institute of Medical Research


title: Replication timing and epigenome remodelling are associated with the nature of chromosomal rearrangements in cancer [ChIP-seq]

summary: DNA replication timing is known to facilitate the establishment of the epigenome, however, the intimate connection between replication timing and changes to the genome and epigenome in cancer remain largely uncharacterised. Here, we perform Repli-Seq and integrated epigenome analyses and demonstrate that genomic regions that undergo long-range epigenetic deregulation in prostate cancer also show concordant differences in replication timing. A subset of altered replication timing domains are conserved across cancers from different tissue origins. Notably, late-replicating regions in cancer cells display a loss of DNA methylation, and a switch in heterochromatin features from H3K9me3-marked constitutive to H3K27me3-marked facultative heterochromatin. Finally, analysis of 214 prostate and 35 breast cancer genomes reveal that late-replicating regions are prone to cis and early-replication to trans chromosomal rearrangements. Together, our data suggests that the nature of chromosomal rearrangement in cancer is related to the spatial and temporal positioning and altered epigenetic states of early-replicating compared to late-replicating loci.

overall_design: ChIP-seq was conducted in 2 human prostate cell lines: normal prostate epithelial cells (PrEC) and prostate cancer cells (LNCaP)


title: TiO2-induced gene expression profiles in rat lung: a subacute inhalation study.

status: Public on Jan 17 2019

city: Vadoeuvre-lès-Nancy

first: Laëtitia

last: CHEZEAU

address: 1 rue du Morvan

institute: INRS

summary: In this work we study the pulmonary toxicological properties of titanium dioxide using conventional and molecular toxicological approaches. For this, we exposed Fischer 344 rats by nose-only inhalation 6 hours/day, 5 days/week for 4 weeks to a nanoaerosol of TiO2 (10 mg/m3). Lung samples have been collected up to 180 days after the end of exposure. Biochemical and cytological analyses of the broncho-alveolar lavage fluid (BALF) were performed. In addition, transcriptomic and proteomic approaches were realised in the lung and BALF respectively.

overall_design: 12 week old male F344 rats were exposed by nose-only inhalation 6 hours/day, 5 days/week for 4 weeks to an aerosol of TiO2 P25 nanoparticles (Evonik, 10 mg/m3). TiO2-induced gene expression profile in rat lung was performed immediately, 3, 28, 90 and 180 days post exposure (5 time points).Each time point is compsed of 5 control and 5 exposed rats. A total of 50 samples (microarrays) was used.

last: Chézeau

first: Ramia

last: Safar

first: Olivier

middle: R

last: Joubert

first: Frédéric

last: Cosnier

first: Bertrand

last: Rihn

first: Laurent

last: Gaté


title: Global phosphoproteome and transcriptome integration of Chlamydia trachomatis infection

status: Public on Jan 16 2019

city: Berlin

first: Thomas

middle: F

last: Meyer

address: Chariteplatz 1

institute: Max Planck Institute for Infection Biology

summary: Gene expression profiles of RNA extracted at 24 or 48h from End1 cells infected with Chlamydia trachomatis or uninfected controls. This experiment forms part of the analysis of phosphoproteome changes after C.trachomatis infection.

overall_design: End1 cells were cultured as described in the accompanying publication. 2 biological replicates of the uninfected and C.trachomatis infected cells were generated. Total RNA was extracted from samples at 24h or 48h post infection and hybridized on Agilent-8x60k Human custom arrays as dual-color hybridizations with dye-swap technical replicates.

first: Piotr

last: Zadora

first: Cindrilla

last: Chumduri

first: Rajendra

middle: K

last: Gurumurthy

first: Hilmar

last: Berger


title: Genome-wide map of binding sites for HNF4a during hepatic specification of iPS cells

first: Stephen

last: Duncan

summary: HNF4a has been shown to be critical for hepatocyte differentiation from iPS cells.

overall_design: Chip-seq was performed on chromatin isolated from iPS cells differentiated to the onset of hepatic specification (day 8).

first: Ann

last: De La Forest


title: Evolution of an X-linked miRNA family predominately expressed in mammalian male germ cells

status: Public on Jan 19 2019

city: Shanghai

first: Fengjuan

last: Zhang

state: Shanghai

address: 320 Yueyang Road

department: Institute of Biochemistry and Cell Biology

institute: Shanghai Institutes for Biological Sciences, CAS

summary: microRNAs (miRNAs) are important post-transcriptional regulators of gene expression. However, comprehensive expression profiles of miRNAs during spermatogenesis in mammals is lacking. In the present study, we sequenced small RNAs in highly purified spermatogonial stem cells (SSCs), spermatocytes in the pre-leptotene, leptotene, zygotene and pachytene stages, haploid round spermatids and spermatozoa. We found that a family of X-linked miRNAs, named spermiRs, is predominantly expressed in spermatogonia and early meiotic phases. Profiling of small RNAs in different mammalian tissues revealed a conserved high expression pattern of spermiRs in testes. spermiR appears to originate from THER1 in marsupial, a retrotransposon that is extinct in current mammals. It has expanded rapidly and has diversified into two clusters, spermiR-L and spermiR-R, by tandem duplication, which was partially mediated by flanking retrotransposable elements. Notably, despite the highly frequent lineage-specific duplication events, all spermiR family members are strictly located between two conserved protein coding genes, Slitrk2 and Fmr1. Intriguingly, spermiR-Ls and spermiR-Rs have evolved different expression preferences during spermatogenesis in different mammals. Moreover, the sequences of spermiRs and their precursors, including the seed regions, are highly divergent within and among mammals. However, their target genes are largely overlapping in male reproduction-related pathways. When miR-741, the most highly expressed spermiRs during mouse spermatogenesis, was knocked out in SSCs, another spermiR, miR-465, was dramatically up-regulated and became the most abundant one, indicating functional compensation between spermiR family members. All these observations indicate a strong co-evolution between spermiRs and their targets.

sample_organism:
Sus scrofa
Oryctolagus cuniculus
Mus musculus
Rattus norvegicus

overall_design: Small RNA profiling of purified male germ cells during mouse spermatogenesis, different stages of rabbit testis, adult pig and rat testis, and miR-741 knock-out SSCs by TALEN and CRISPR.

first: Ying

first: Ligang

last: Wu


title: SETDB2 links E2A-PBX1 to cell cycle dysregulation in acute leukemia through CDKN2C repression

city: Stanford

first: Stephen HK

last: WONG

state: California

address: G2035 SIM1 Bldg

department: Pathology

institute: Stanford University


title: TBX3 defines the functional identity of hypothalamic melanocortin neurons

status: Public on Jan 22 2019

city: Neuherberg

first: Carmelo

last: Quarta

address: Ingolstaedter Landstraße 1

institute: Helmholtz Center Munich

summary:
Purpose: Identify cellular pathways controlled by Tbx3
Methods: RNA sequencing of hypothalamic primary neurons from Tbx3 loxP/loxP mice infected with Ad-Cre or Ad-GFP viruses.
Results: Unbiased pathway analysis revealed that Tbx3 deletion in primary neurons significantly affected the expression of genes involved in several pathways responsible for controlling cellular proliferation, differentiation and determination of cellular fate.
Conclusions: Tbx3 in primary neurons might be implicated in the development and maintenance of neuronal identity.

overall_design: Examination of loss-of-function of Tbx3 in hypothalamic neurons

first: Alexandre

last: Fisette


title: Gene expression profiling of differentiated mouse motor neurons

status: Public on Jan 09 2019

city: Münster

first: Susanne

last: Höing

state: Select if applicable

address: Röntgenstraße 20

institute: Max Planck Institute for Molecular Biomedicine

summary: The original objectives of the study were to identify surface markers specifically expressed in motor neurons. We now use the data to profile the expression of Cdk family members in motor neurons.

overall_design: HB9-GFP mouse embryonic stem cells were differentiated into motor neurons. GFP-low and GFP-high cells were sorted. RNA was isolated and used for microarray analysis.


title: Generation of Stem Cell-Derived Kupffer Cells for Application in Human In Vitro Inflammatory Liver Model

status: Public on Jan 07 2019

city: Singapore

first: Farah

last: Tasnim

address: 31 Biopolis Way

country: Singapore

institute: Institute of Bioengineering and Nanotechnology

summary:
There is an evident, unmet need to develop a commercially available in vitro system that can model inflammatory states of the liver and predict immune-mediated hepatotoxicity of drugs and xenobiotics taken under inflamed conditions. Hepatocyte-Kupffer cell co-cultures can model inflammation-mediated hepatotoxicity; however, Kupffer cell (KC) source remains an important bottleneck for the development of such models. Primary human Kupffer cells (PHKCs) are costly, limited in availability and exhibit donor variability. An alternative cell source for KCs has not been reported. Important paradigm shift from the classical dogma of adult blood-circulating monocyte-derived macrophages to intrahepatic precursor/fetal monocyte-derived macrophages has shed new light into the origin of KCs in vivo. Based on these recent findings, we report here, a novel method to generate human KCs in vitro from stem cells (hPSC-KCs) via fetal monocytes. hPSC-KCs expressed macrophage markers, CD11, CD14, CD68, CD163 and CD32 at gene and protein level and exhibited functional properties such as phagocytosis and Interleukin-6 and Tumor Necrosis Factor-4alpha production upon activation. Importantly, molecular signature, liver-macrophage specific CLEC-4F expression and cytokines production levels of hPSC-KCs were similar to PHKCs but different from non-liver macrophages. We used an inflammatory liver co-culture model to demonstrate that activated hPSC-KCs, but not non-liver macrophages, were able to recapitulate effects of PHKCs when stimulated with paradigm hepatotoxicants. hPSC-KCs developed in this study offer a renewable human cell source for liver-specific macrophages which can be used to develop in vitro systems for modelling the inflammatory state of the liver.
Gene expression profiles of 9 samples were determined using Human Gene 2.0 ST Array. These 9 samples included three replicates each of PHKCs (primary human Kupffer cells), human pluripotent stem cell-dervied Kupffer cells (hPSC-KCs) and non-liver macrophages (NL-Mφ).

overall_design: Human pluripotent stem cells were differentiated into Kupffer cells (hPSC-KCs). To analyze the molecular signature of hPSC-KCs, microarray was performed on three independent replicates (hPSC-KCs_1, hPSC-KCs_2 and hPSC-KCs_3). Microarray was also used to obtain gene expression profiles of primary human Kupffer cells (PHKCs) and non-liver macrophages (NL-Mφ) for comparison with hPSC-KCs. The data was normalized together with and compared to previously published data on hPSC-IMR90, bone marrow-derived monocytes, blood monocyte derived macrophages, alveolar macrophages and microglia from Zimmerlin L, et al. (PMID: 27660325), Abbas AR, et al. (PMID: 15789058), Beyer M, et al. (PMID: 23029029), Worgall S, et al. (PMID: 16041053) and Rock R, et al. (PMID: 16163375).

first: Jiangwa

last: Xing

first: Shupei

last: Mo

first: Hanry

last: Yu