title: The global wheat gene expressional responses to fusaoctaxin A

first: Weihua

last: Tang

address: 300 Fenglin Rd

institute: Shanghai Inst. Plant Phys. & Eco.

summary:
Purpose: To assess global changes of wheat coleoptiles gene expression in response to fusaoctaxin A which is a linear, C-terminally-reduced and D-amino acid residue-rich octapeptide, as the product of the two non-ribosomal peptide synthetases encoded by Fusarium graminearum fg3_54 cluster.
Methods: For RNA seq of wheat coleoptiles, three biological replicates of mock-inoculated coleoptiles, wild-type PH-1 inoculated coleoptiles (3 dpi), ∆fg3_54 inoculated coleoptiles (3 dpi), after 3 hours fusaoctaxin A-treated coleoptiles, after 3 hours control (0.5% Tween-20) treated coleoptiles, after 24 hours fusaoctaxin A-treated coleoptiles and after 24 hours control (0.5% Tween-20) treated coleoptiles were sequenced.
Results: For each sample, 33-95 M RNA-seq clean reads were obtained mapped to the Triticum aestivum Chinesespring genome sequence.Our results of RNA sequencing indicated fusaoctaxin does not induce PR gene expression, but suppress plant immunity and chloroplastc activity.
Conclusions: Fusaoctaxin A represents an unprecedented virulence factor which can manipulate chloroplast and suppress host immunity.

overall_design: Three biological replicates of mock-inoculated coleoptiles, wild-type PH-1 inoculated coleoptiles (3 dpi), ∆fg3_54 inoculated coleoptiles (3 dpi), after 3 hours fusaoctaxin A-treated coleoptiles, after 3 hours control (0.5% Tween-20) treated coleoptiles, after 24 hours fusaoctaxin A-treated coleoptiles and after 24 hours control (0.5% Tween-20) treated coleoptiles were sequenced using Illumina NovaSeq 6000 Sequencing System.

first: Wan-Qiu

last: Wang

first: Dong

last: Zhang

first: Wei-Hua


title: Transcriptomes of E16 neocortical tissue knockout from Nfia, Nfib and Nfix knockout mice

status: Public on Jan 10 2019

city: St Lucia

first: Jens

last: Bunt

state: QLD

address: QBI Building 79

department: Queensland Brain Institute

country: Australia

institute: University of Queensland

type: Expression profiling by high throughput sequencing

summary: Here, we generated transcriptomes of microdissected neocortex of Nfix knockout and wildtype littermate embryos at embryonic day 16.


title: LincK promotes proliferation and epithelial-to-mesenchymal transition and contributes to tumorigenesis and growth in breast cancer II

status: Public on Jan 09 2019

city: San Diego

first: Yajing

last: Hao

state: CA

address: George Palade Laboratories 9500 Gilman Drive, Room 217

department: Dept. of Cellular and Molecular Medicine

country: USA

institute: University of California, San Diego

summary: We previously reported that transwell co-culture with hAD-MSCs cells can induce an EMT progress in MCF7 cells. To identify EMT-relevant lncRNAs, we conducted transcriptome microarray analysis of MCF7 cells at Day 0, 2, 4, 6, 8 and 10 after coculture.

overall_design: Time course microarray experiments, MCF-7 cells cultured alone (0 day) and co-cultured with hAD-MSCs for indicated times (2, 4, 6, 8 and 10days).Total RNA was extracted with Trizol and hybridized to custom lncRNA microarray

first: Jing

last: Li

first: Wenzhe

last: Mao

first: Xiaowei

last: Xue

first: Zhao

last: Sun

first: Jianjun

last: Luo

first: Runsheng

last: Chen

first: Chunhua

last: Zhao


title: RNA-seq of diabetic or non-diabetic murine bone marrow derived macrophages (BMDM)

status: Public on Jan 08 2019

city: Oxford

first: Laurienne

last: Edgar

address: L6 West Wing, John Radcliffe Hospital, Headley Way

department: Cardiovascular Medicine, Radcliffe Department of Medicine

country: United Kingdom

institute: University of Oxford

summary: The aim of this study was to interrogate whether BMDM basal or pro-inflammatory stimulated gene expression is altered by diabetes and persists despite in vitro glucose normalisation. Unstimulated BMDM from diabetic mice differentially express 632 genes (324 increased and 308 downregulated) compared to unstimulated control BMDM; this increases to 1,348 genes (802 increased and 546 decreased) upon stimulation (FDR<0.05, FC>1.5).

overall_design: 6 diabetic mice samples and 6 non-diabetic control mice samples were used. Each sample was split in half, one half submitted as a baseline, unstimulated control and the other was stimulated with LPS + IFNy.

first: Thomas

last: Krausgruber

first: Madeleine

middle: E

last: Lemieux

first: Robin

middle: P

last: Choudhury


title: High Phosphate Diet Induces Exercise Intolerance and Impairs Fatty Acid Metabolism in Mice

city: Dallas

first: Wanpen

last: Vongpatanasin

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

summary: Inorganic phosphate (Pi) is used extensively as a preservative and a flavor enhancer in the Western diet. Physical inactivity, a common feature of Western societies, increases cardiovascular morbidity and mortality. We explore the relationship between dietary Pi excess and impaired exercise tolerance and physical inactivity. Analysis of the Dallas Heart Study shows association of higher serum Pi with reduced time spent in moderate to vigorous physical activity and increased sedentary time in humans. To test for causality, we investigated the impact of chronic exposure of high dietary Pi on exercise capacity in mice. Consumption of a high Pi diet for 3 months does not change the body weight but reduces maximal oxygen uptake, treadmill duration, and spontaneous locomotor activity, which is accompanied by substantial reduction in fat oxidation and fatty acid (FA) levels and downregulation of genes involved in FA synthesis, release, and oxidation, including Fabp4, Hsl, Fasn, and Ppar in muscle. Similar results are recapitulated in in vitro by incubating C2C12 myotubes with high Pi media. In conclusion, our findings indicate that dietary phosphotoxicity reduces skeletal muscle FA metabolism and impairs exercise capacity independent of obesity, and may represent a novel and modifiable risk factor for cardiovascular disease.

overall_design: To understand the mechanistic basis of high intake of dietary phosphate we profiled the transcriptomes (using RNA-seq), of gastrocnemius muscle tissue treated with high phosphate diet for 12 weeks compared to normal phosphate diet.

first: Kedryn

middle: K

last: Baskin


title: High-throughput RNA-sequencing-based transcriptomic profiles of embryonic lens development for cataract gene discovery

city: Newark

first: Deepti

last: Anand

state: Delaware

address: 351 Wolf Hall, University of Delaware

department: Biological Sciences

institute: University of Delaware

summary: We applied previously established in silico whole-embryo body (WB)-subtraction-based  approach to identify “lens-enriched” genes. These new RNA-seq datasets on embryonic stages E10.5, E12.5, E14.5 and E16.5 confirmed high expression of established cataract-linked genes and identified several new potential regulators in the lens. Finally, we present lens stage-specific UCSC Genome Brower annotation-tracks; these are publicly accessible through iSyTE (https://research.bioinformatics.udel.edu/iSyTE/) and enable a user-friendly visualization of lens gene expression/enrichment to help prioritize genes from high-throughput data from cataract cases.

overall_design: RNA-sequencing datasets of microdissected embyonic eye lens samples from stages embryonic day E10.5, E12.5, E14.5 and E16.5 were generated. To estimate lens enriched genes we generated control “whole-embryo body (WB)” datasets. The lens enriched genes were used for enrichment level based clustering to identify gene clusters exhibiting distinct lens enrichment patterns across E10.5 to E16.5 developmental window. This new lens RNA-seq data and its accessibility through iSyTE 2.0 serves as a new integrative resource for prioritization of lens defects and/or cataract-linked candidate genes identified by other high-throughput analyses such as exome-seq and GWAS.

first: D

first: A

last: Kakrana

first: S

middle: A

last: Lachke


title: EndoC-βH1 multiomic profiling defines gene regulatory programs intrinsic to human β cell identity and function

city: Farmington

first: Michael

last: Stitzel

state: CT

address: 10 Discovery Drive

institute: The Jackson Laboratory

type: Genome binding/occupancy profiling by high throughput sequencing

type: Non-coding RNA profiling by high throughput sequencing

summary: EndoC-βH1 is emerging as a critical human β cell model to study the genetic and environmental etiologies of β cell (dys)function and diabetes. Comprehensive knowledge of its molecular landscape is lacking, yet required, for effective use of this model. Here, we report chromosomal (spectral karyotyping), genetic (genotyping), epigenomic (ChIP-seq and ATAC-seq), chromatin interaction (Hi-C and Pol2 ChIA-PET), and transcriptomic (RNA-seq and miRNA-seq) maps of EndoC-βH1. Analyses of these maps define known (e.g., PDX1 and ISL1) and putative (e.g., PCSK1 and mir-375) β cell-specific transcriptional cis-regulatory networks and identify allelic effects on cis-regulatory element use. Importantly, comparison with maps generated in primary human islets and/or β cells indicates preservation of chromatin looping but also highlights chromosomal aberrations and fetal genomic signatures in EndoC-βH1. Together, these maps, and a web application we created for their exploration, provide important tools for the design of experiments to probe and manipulate the genetic programs governing β cell identity and (dys)function in diabetes.

overall_design: Hi-C, RNA Pol2 ChIA-PET, ChIP-seq, ATAC-seq, RNA-seq, and miRNA-seq of EndoC-βH1 human pancreatic beta cell line. Hi-C of human pancreatic islet.

first: Nathan

last: Lawlor

first: Eladio

middle: J

last: Márquez

first: Peter

last: Orchard

first: Narisu

last: Narisu

first: Muhammad

middle: S

last: Shamim

first: Asa

last: Thibodeau

first: Arushi

last: Varshney

first: Romy

last: Kursawe

middle: R

last: Erdos

first: Matt

last: Kanke

first: Huiya

last: Gu

first: Evgenia

last: Pak

first: Amalia

last: Dutra

first: Sheikh

last: Russell

first: Xingwang

first: Emaly

last: Piecuch

first: Oscar

last: Chines

first: Christian

last: Fuchbserger

first: Praveen

last: Sethupathy

first: Aviva

last: Presser-Aiden

first: Yijun

last: Ruan

first: Erez

last: Lieberman-Aiden

first: Francis

last: Collins

first: Duygu

last: Ucar

first: Stephen

middle: C

last: Parker

middle: L


title: LncRNAs and open chromatin regions constitute midbrain dopaminergic neuron- specific molecular signatures

city: Paris

first: Philippe

last: Ravassard

address: 47, boulevard de l'Hôpital

country: France

institute: Brain & Spine Institute

summary:
Midbrain dopaminergic (DA) neurons are involved in diverse neurological functions, including control of movements, emotions or reward. In return, their dysfunctions cause severe clinical manifestations in humans, such as the appearance of motor and cognitive symptoms in Parkinson’s Disease. The physiology and pathophysiology of these neurons are widely studied, mostly with respect to molecular mechanisms implicating protein-coding genes. In contrast, the contribution of non-coding elements of the genome to DA neurons function is poorly investigated.
In this study, we isolated DA neurons from E14.5 ventral mesencephalons, and used RNA-seq and ATAC-seq to establish and describe the repertoires of long non-coding RNAs (lncRNAs) and putative DNA regulatory regions, such as enhancers, specific to this neuronal population. We identified 990 novel lncRNAs out of 1,363 expressed in DA neurons, and most of them were not found in hindbrain serotonergic (5-HT) neurons, indicating a high degree of cell-specificity. This feature was also observed regarding open chromatin regions, as 39% of the ATAC-seq peaks from the DA repertoire were not detected in the 5-HT neurons.
Our work provides for the first time DA-specific catalogues of non-coding elements of the genome that will undoubtedly participate in deepening our knowledge regarding DA neuronal development and dysfunctions.

overall_design: comparison of Lnc-RNA expression and genome structure by ATAC-seq in 2 cell types.

first: Judith

last: Gendron

first: Claire

last: Colace-Sauty

first: Nicolas

last: Beaume

first: Hugue

last: Cartonnet

first: Justine

last: Guegan

first: Damien

last: Ulveling

first: Corinne

last: Pardanaud-Glavieux

first: Ivan

last: Moszer

first: Hélène

last: Cheval


title: Abnormalities in Behaviour, Histology and Prefrontal Cortical Gene Expression Profiles Relevant to Schizophrenia in Embryonic Day 17 MAM-Exposed C57BL/6 Mice

city: Beijing

first: Chunyue

last: Huo

address: You an men wai Xi tou tiao Road 10

country: China

institute: Capital Medical University

summary: Gestational and perinatal disruption of neural development increases the risk of developing schizophrenia (SCZ) later in life. Embryonic day 17 (E17) methylazoxymethanol (MAM) treatment leads to histological, physiological and behavioural abnormalities in post-puberty rats resembling those described in SCZ patients. However, the validity of E17 MAM-exposed mice as a SCZ model has not been explored. Here we treated E17 C57BL/6 mouse dams with various dosages of MAM. We found that this mouse strain was more vulnerable to MAM treatment than rats and there were gender difference in behavioural abnormalities, histological changes and prefrontal cortical gene expression profiles in MAM (7.5 mg/kg)-exposed mice. Both male and female MAM-exposed mice had deficits in prepulse inhibition but were normal in social interaction and novel object recognition tasks. Female MAM-exposed mice were hyperactive in spontaneous locomotion while male mice were normal. Consistently, only female MAM-exposed mice exhibited reduced brain weight, decreased size of prefrontal cortex (PFC) and enlarged lateral ventricles. Transcriptome analysis of the PFC revealed that there were more differentially expressed genes in female MAM-exposed mice than those in male mice. Moreover, expression of Pvalb, Arc and genes in their association networks were downregulated in the PFC of female MAM-exposed mice. These results show that E17 MAM-exposure in C57BL/6 mice leads to behavioural changes that mimic positive symptoms and sensorimotor gating deficits associated with SCZ. MAM-exposed female mice may be used to study gene expression changes, inhibitory neural circuit dysfunction and glutamatergic synaptic plasticity deficits related to SCZ.

overall_design: Prefrontal cortex mRNA profiles of E17 MAM-exposed mice were generated by deep sequencing, distinguishing gender, in triplicate, using Illumina X-10.

first: Haihong

last: Ye


title: High-throughput functional analysis of lncRNA core promoters elucidates rules governing tissue specificity

city: Boston

first: Martha

middle: L.

last: Bulyk

state: MA

address: 77 Avenue Louis Pasteur, Rm 468

department: Division of Genetics

institute: Brigham and Women's Hospital

summary: Bidirectional transcription initiates at both coding and non-coding genomic elements, including mRNA and long non-coding RNA (lncRNA) promoters and enhancer RNAs (eRNAs). However, each class has different tissue-specific expression profiles with lncRNAs and eRNAs being the most tissue-specific. How these complex differences in expression profiles and tissue-specificities are encoded in a single DNA sequence, however, remains an open question. Here, we address this question using multiple computational and experimental approaches, including massively parallel reporter assays (MPRA). As most transcription factors (TFs) are enriched near the transcription start sites (TSSs) of both promoters and enhancers, we focus our analyses on these core promoter regions. We find that divergent lncRNA and mRNA core promoters have higher capacities to drive transcription than non-divergent lncRNA and mRNA core promoters, respectively. Conversely, lincRNAs and eRNAs are more tissue-specific than divergent genes. This higher tissue-specificity is strongly associated with having less complex TF motif profiles at the core promoter. We confirm these findings using single-nucleotide deletions in MPRA and we identify specific TFs regulating a set of disease-related lncRNAs. Finally, we assess the effects of genetic variation at core promoters and find that 22% of common single nucleotide polymorphisms show significant regulatory effects. Collectively, our findings characterize the important role of core promoter sequences in determining expression levels across both coding and non-coding gene classes and highlight an unexpected role of TF motif architecture in explaining the more restricted expression patterns of lncRNAs and eRNAs.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: We designed two MPRAs: (1) a pool of 120,000 oligos corresponding to ~2,000 unique core promoter regions (POOL1) and (2) a pool of 119,082 oligos corresponding to single-nucleotide deletions across ~30 core promoter regions (POOL2). For POOL1, we performed the MPRA both with a minimal promoter (pMPRA1) and without a minimal promoter (pNoCMVMPRA1) to determine whether this had any effect on the assay results. We analyzed POOL1 in HeLa (4 replicates with and without minimal promoter), HepG2 (12 replicates with a minimal promoter, 4 replicates without), and K562 (4 replicates with and without minimal promoter). We analyzed POOL2 in HepG2 (8 replicates) and K562 (4 replicates). For each experimental set-up, we provide the raw fastqs of the input DNA library and the output RNA barcodes. We also include processed data in the form of DNA and RNA barcode counts.

first: Marta

last: Melé

first: Kaia

last: Mattioli

first: Chiara

last: Gerhardinger

first: Philipp

middle: G

last: Maass

first: John

last: Rinn


title: LSD1 inhibition by tranylcypromine derivatives interferes with GFI1-mediated repression of PU.1 target genes and induces differentiation in AML

city: Frankfurt am Main

first: Michael

last: Rieger

address: Theodor-Stern-Kai 7

country: Germany

institute: Universitätsklinikum Frankfurt/DKFZ

summary:
Lsd1KO and ATRA treatment in Hoxa9/Meis1- and MN1-transformed myeloid progenitor cells
LSD1 has emerged as a promising epigenetic target in the treatment of acute myeloid leukemia (AML). Inhibition of LSD1 has been shown to induce differentiation and facilitate the responsiveness of AML cells to all-trans retinoic acid. We used two murine AML models based on retroviral overexpression of Hoxa9/Meis1 (H9M) or MN1 to study the effect of Lsd1 knockout in AML. The conditional knockout of Lsd1 resulted in differentiation with both granulocytic and monocytic features in H9M-induced AML cells and enhanced their responsiveness towards ATRA treatment, which was not seen in MN1-driven AML. It also extended the survival of mice with H9M-driven AML. To identify molecular changes associated with the loss of Lsd1, we performed whole transcriptome analysis by RNA sequencing of H9M and MN1 Lsd1 fl/fl (Ctrl) and Lsd1cKO cells with or without ATRA treatment. The experiment was done in triplicates. The conditional knockout led to a broad increase in the expression of multiple genes regulated by the important myeloid transcription factors GFI1 and PU.1. These include the transcription factors GFI1B and IRF8, which may be relevant for the observed differentiation response.

overall_design: Examination of the effect of LSD1 knockout and ATRA treatment in two murine AML models

first: Tobias

last: Berg

first: Khalil

last: Abou-El-Ardat


title: Chemotherapeutic agent doxorubicin alters uterine gene expression in response to estrogen in ovariectomized CD-1 adult mice

status: Public on Jan 07 2019

city: Athens

first: Christian

last: Andersen

state: Georgia

address: 501 D.W. Brooks Dr., Physiology and Pharmacology

department: Physiology and Pharmacology

institute: University of Georgia

summary: Chemotherapy can potentially impair fertility in premenopausal cancer patients. Female fertility preservation has been mainly focused on the ovarian aspects and benefited greatly from assisted reproductive technologies, such as in vitro fertilization (IVF). The rate-limiting step for the success of IVF is embryo implantation in the uterus. Doxorubicin (DOX) is a widely used chemotherapeutic agent with ovarian toxicity. It remains unknown if the uterus is a direct target of DOX. To circumvent the indirect uterine effect from ovarian toxicity of DOX and to investigate potential long-term impact of DOX on the uterus, young adult ovariectomized CD-1 mice were given an intraperitoneal injection once with PBS or DOX (10 mg/kg, a human relevant chemotherapeutic dose), and 30 days later, each set of mice was randomly assigned into three groups and subcutaneously injected with oil, 17β-estradiol (E2, for 6 hours), and progesterone (P4, for 54 hours), respectively. Uterine transcriptomic profiles were determined using RNA-seq. Principal component analysis of the uterine transcriptomes revealed four clusters from the six treatment groups: PBS-oil & DOX-oil, PBS-P4 & DOX-P4, PBS-E2, and DOX-E2, indicating that DOX treatment did not affect the overall uterine transcriptomic profiles in the oil and P4-treated mice but altered uterine responses to E2 treatment. These data demonstrate that DOX can directly target the uterus and has a long-term impact on uterine responses to E2.

overall_design: Examination of the uterine transcriptome upon DOX or vehicle treatment

first: Mingjun

last: Liu

first: Zidao

last: Wang

first: Xiaoqin

first: Shuo

last: Xiao


title: Two distinct ontogenies confer heterogeneity to mouse brain microglia

city: Salt Lake City

first: Chris

last: Stubben

state: Utah

address: 2000 Cir of Hope Dr

department: University of Utah

institute: Huntsman Cancer Institute

summary: Hoxb8 mutant mice show compulsive behavior similar to trichotillomania, a human obsessive-compulsive-spectrum disorder. The only Hoxb8 lineage-labeled cells in the brains of mice are microglia, suggesting that defective Hoxb8 microglia caused the disorder. What is the source of the Hoxb8 microglia? It has been posited that all microglia progenitors arise at embryonic day (E) 7.5 during yolk sac hematopoiesis, and colonize the brain at E9.5. In contrast, we show the presence of two microglia subpopulations: canonical, non-Hoxb8 microglia and Hoxb8 microglia. Unlike non- Hoxb8 microglia, Hoxb8 microglia progenitors appear to be generated during the second wave of yolk sac hematopoiesis, then detected in the aorto-gonad-mesonephros (AGM) and fetal liver, where they are greatly expanded, prior to infiltrating the E12.5 brain. Further, we demonstrate that Hoxb8 hematopoietic progenitor cells taken from fetal liver are competent to give rise to microglia in vivo. Although the two microglial subpopulations are very similar molecularly, and in their response to brain injury and participation in synaptic pruning, they show distinct brain distributions which might contribute to pathological specificity. Non-Hoxb8 microglia significantly outnumber Hoxb8 microglia, but they cannot compensate for the loss of Hoxb8 function in Hoxb8 microglia, suggesting further crucial differences between the two subpopulations.

overall_design: Green (non-Hoxb8, control) and yellow (Hoxb8, experimental) microglia data sets

first: Mario

last: Capecchi

first: Shrutokirti

last: De


title: Gene expression in Dmxl2 knockout and wild type gonads at birth in mice

city: Jouy-en-Josas

first: Jouneau

last: Luc

address: Domaine de Vilvert

institute: INRA

summary: Testicular and ovarian gene expression changes with loss of DMXL2

overall_design: Total RNA was extracted from P0 WT or DMXL2 tm1a/tm1a (KO) mouse gonads (FVBN), There were 3 biological repeats by conditions.

first: Maëva

last: Elzaiat

first: Clara

last: Gobé

first: Luc

last: Jouneau

first: Wassila

last: Carpentier

first: Maëlle

last: Pannetier


title: RNA sequencing of mouse epidermis and papillomas treated with 20% camphor white oil or acetone vehicle

city: New York

first: Ellen

last: Lumpkin

state: NY

address: 1150 St. Nicholas Avenue, room 302

department: Physiology and Cellular Biophysics

institute: Columbia University

summary: Camphor white oil (CWO) application was found to induce regression of papillomas in a mouse chemical carcinogenesis model. In healthy epidermis, CWO induced increased proliferation of basal keratinocytes. RNA-sequencing was performed on epidermal cells 24 hours after CWO or vehicle application (N=3 mice/treatment), and on 4 pooled papillomas harvested after 6 weeks of treatment (N=3 mice/treatment). Sequencing identified transcripts that may alter skin physiology and induce tumor regression.

overall_design: Examination of 2 tissue types treated with camphor white oil or vehicle.

first: Yalda

last: Moayedi

first: Sophie

last: Greenberg


title: Runx/Cbfβ complexes protect ILC2s from exhaustion during allergic airway inflammation

city: Akita City

first: Takashi

last: Ebihara

address: 1-1-1 Hondo

department: Department of Medical Biology

country: Japan

institute: Akita University Graduate School of Medicine

summary: Group 2 innate lymphoid cells (ILC2s) have tissue-resident competence and contribute to the pathogenesis of allergic diseases. Therefore, there should be mechanisms to maintain the capacity of ILC2s to produce TH2 cytokines under chronic inflammatory conditions. Here, we report that Runx proteins are essential to prevent exaggerated activation of ILC2, in part by antagonizing GATA-3 function at steady state. However, during allergic inflammation, the absence of Runx in ILC2s impaired their ability to proliferate and produce effector TH2 cytokines and chemokines, but instead induced expression of T cell exhaustion markers including IL-10 and TIGIT. These exhausted ILC2s were unabale to induce type 2 immune responses against repeated allergen inhalation. Thus, Runx proteins protect ILC2s from exhaustion during continuous allergic inflammation.

overall_design: RNA-seq data of lung ILC2s from Cbfb +/f PLZF-Cre mice and Cbfb f/f PLZF-Cre mice (biological triplicates). RNA-seq data of cultured lung ILC2s from Cbfb +/f PLZF-Cre mice and Cbfb f/f PLZF-Cre mice (biological triplicates). ChIP-seq data of ILC2s cultured with IL-2/IL-7 or IL-2/IL-7/IL-33 for bindings of CBFb, Runx1, Runx3, GATA-3, and H3K27 acetylation (technical duplicates).

first: Ebihara

last: Takashi


title: Transcriptional profile of lung adenocarcinoma (ADC) and squamous cell carcinoma (SCC) tumors from KRasG12D; Fbw7f/f mice

city: London

first: Richard

middle: James

last: Mitter

state: LONDON

address: 1 Midland Road

department: Bioinformatics & Biostatistics

institute: The Francis Crick Institute

summary: We performed lung ADC and SCC transcriptome profiling from KRasG12D; Fbw7f/f murine lung tumors by RNA-seq and compared them with a consensus lung SCC signature using data from two different SCC models (Lkb1f/f; Ptenf/f, Cancer Cell 2014 and LSL-Sox2; Ptenf/f; Cdkn2abf/f, Cancer Cell 2016) that has been validated in human lung SCC

overall_design: Transcriptome profiles of lung adenocarcinoma and squamous cell carcinoma were generated by deep sequencing, in triplicate (primary tumors) or duplicate (primary cells).

first: E

last: Ruiz

first: A

last: Behrens


title: Comprehensive catalog of dendritically localized mRNA isoforms from sub-cellular sequencing of single mouse neurons

city: Philadelphia

first: Junhyong

last: Kim

state: PA

address: 433 S University Avenue

department: Biology

institute: University of Pennsylvania

summary: To compare the RNAs present in dendrites and somas of individual neurons, we manually separated the dendrites and soma of primary mouse hippocampal neurons using a micropipette and performed RNA-sequencing on each subcellular fraction such that we obtained the subcellular transcriptomes of the same cell.

overall_design: 16 individual neurons were collected and dissected (yielding a total of 32 soma and dendrite samples) from multiple cultures across multiple days. ERCC spike-in control RNA was added to each sample.

first: Sarah

last: Middleton

first: James

last: Eberwine


title: Aberrant enhancer reprogramming drives hepatic carcinogenesis through global transcriptional reprogramming [RNA-seq]

status: Public on Jan 06 2019

city: Hong Kong

first: Alfred Sze-Lok

last: Cheng

address: Rm 405A, Lo Kwee-Seong Integrated Biomedical Sciences Building, Area 39, CUHK

department: School of Biomedical Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

summary: Hepatocellular carcinomas (HCC) exhibit distinct promoter hypermethylation patterns, but the epigenetic regulation and function of transcriptional enhancers remain unclear. Here, our affinity- and bisulfite-based whole-genome sequencing analyses reveal global enhancer hypomethylation in human HCCs. Integrative epigenomic characterization further pinpoints a recurrent hypomethylated enhancer of CCAAT/enhancer-binding protein-beta (C/EBPβ) which correlates with C/EBPβ over-expression and poorer prognosis of patients. Demethylation of C/EBPβ enhancer reactivates a self-reinforcing enhancer-target loop via direct transcriptional up-regulation of enhancer RNA. Conversely, deletion of this enhancer via CRISPR/Cas9 reduces C/EBPβ expression and its genome-wide co-occupancy with BRD4 at H3K27ac-marked enhancers and super-enhancers, leading to drastic suppression of driver oncogenes and abrogation of HCC tumorigenicity. Hepatitis B X protein transgenic mouse model of HCC recapitulates this paradigm, as C/ebpβ enhancer hypomethylation associates with oncogenic activation in early tumorigenesis. These results support a causal link between aberrant enhancer hypomethylation and C/EBPβ over-expression, thereby driving hepatocarcinogenesis through global transcriptional reprogramming.

overall_design: Examination of RNA profiles in WT and C/EBPB enh- HepG2 cells

first: Lei

last: Xiong

first: Feng

last: Wu

first: Ka

middle: W

last: Cheung

first: Myth

middle: T

last: Mok

first: Alfred


title: Identification of altered developmental pathways in human juvenile HD iPSC with 71Q and 109Q using transcriptome profiling

status: Public on Jan 05 2019

city: Poznan

first: Maciej

last: Figiel

address: Noskowskiego 12/14

department: Department of Molecular Neurobiology

country: Poland

institute: Institute of Bioorganic Chemistry Polish Academy of Sciences

summary:
Purpose: In Huntington disease (HD) subtle symptoms in patients may occur years or even decades prior to diagnosis. HD changes at a molecular level may begin as early as in cells that are non-lineage committed such as stem cells or HD patients induced pluripotent stem cells (iPSCs) offering opportunity to enhance the understanding of the HD pathogenesis. In addition, juvenile HD non-linage committed cells were previously not directly investigated in detail by RNA-seq.
Methods: Strand-specific RNA-seq of the whole transcriptome was performed using 3 clonal lines from each of 2 HD patients  (6 HD iPSC lines) with 71 or 109 CAG repeats in exon 1 of the HTT gene, and 2 healthy individuals, with 17/18 (2 clonal iPSC lines) and 21 CAG repeats (one iPSC line), to comprehensively identify mRNAs related to HD. A DESeq2 pipeline for transcripts of HD was developed to identify significantly dysregulated mRNAs. During the RNA-seq data analysis, we compared 6 HD iPSC lines vs control lines and also compared separately each set of 3 HD lines from one patient vs 3 control lines. As a result of such an approach, we generated statistical values for three comparison groups, HD vs WT, HD71Q vs WT and HD109Q vs WT
Methods: 9 pM-indexed libraries were sequenced with the use of Illumina HiSeq2000, rapid run with paired-end 75 bp reads. On average, 65 mln reads were collected per library
Results: We identified 107 (6 HD lines), 198 (3 HD71Q lines) and 217 (3 HD109Q lines) significantly dysregulated mRNAs in each comparison group.
Conclusion: The analyses showed that many of dysregulated transcripts in HD109Q iPSC lines are involved in DNA damage response and apoptosis, such as CCND1, CDKN1A, TP53, BAX, TNFRSF10B, TNFRSF10C, TNFRSF10D, DDB2, PLCB1, PRKCQ, HSH2D, ZMAT3, PLK2, and RPS27L. Most of them were identified as downregulated and their proteins are direct interactors with TP53. HTT probably alters the level of several TP53 interactors influencing apoptosis.This may lead to accumulation of an excessive number of progenitor cells and potential disruption of cell differentiation and production of mature neurons. In addition, HTT effects on cell polarization also demonstrated in the analysis may result in a generation of incorrect progenitors.

overall_design: Total RNA from 9 samples were isolated for RNA-seq analysis, including 3 from control iPSC lines, 3 from clonal iPSC lines with 71 CAG repeats and 3 from clonal iPSC lines with 109 CAG repeats.

first: Marek

last: Figlerowicz


title: A transient developmental hematopoietic stem cell that gives rise to innate-like B- and T-cells

status: Public on Jan 04 2019

city: Santa Cruz

first: Camilla

last: Forsberg

state: California

address: 1156 High Street

department: Biomolecular engineering

institute: University of California, Santa Cruz

summary: We sequenced mRNA from distinct fetal liver HSC populations identified in the mouse in order to determine novel molecular regulators of their unique functional properties.

overall_design: mRNA levels were examined in bulk Tom or GFP+ CD150+ Lin-cKit+Sca1+ cells  isolated from the fetal liver of FlkSwitch embryos at E14.5

last: Beaudin

first: J

last: Perez-Cunningham


title: Study evaluating striatal and hippocampal tissues between Helios full knockout and wild type mice

city: Barcelona

first: Albert

last: Giralt

state: Barcelona

address: C/ Casanova 143

country: Spain

institute: Universitat de Barcelona

summary: Striatal and hippocampal tissues were dissected out from wild type and helios knockout mice to perform comparisions by pairs of genotypes. First the comparision between wild type and helios knockout mice using striatal tissues and the second comparision was made between wild type and helios knockout hippocampal tissues

overall_design: 20 samples

last: Giralt Torroella

first: Josep

middle: M

last: Canals Coll


title: Aberrant enhancer reprogramming drives hepatic carcinogenesis through global transcriptional reprogramming [ChIP-seq]

overall_design: Examination of C/EBPB, BRD4 and H3K27ac binding in WT and C/EBPB enh- HepG2 cells


title: Specific induction of GPR15 expression in heterogeneous blood lymphocytes by smoking

first: Jörg

last: Hackermüller

address: Permoserstr. 15

institute: Helmholtz Centre for Environmental Research - UFZ

summary: Although a mucosal and cutaneous chemokine ligand for G protein –linked receptor GPR15 was recently identified, the physiological role of GPR15 remains yet elusive. In blood, in has been shown that smoking is, to date, the only specific condition leading to an increase in GPR15+ T cells. We therefore used transcriptome sequencing to describe GPR15-expressing blood T cells in more detail.

overall_design: Strand specific transcriptome sequencing rRNA depleted long RNA in two cell types

first: Mario

last: Bauer


title: Transcriptomic Responses to Lumacaftor/Ivacaftor Therapy in Cystic Fibrosis

status: Public on Jan 03 2019

city: Columbus

first: Benjamin

middle: T.

last: Kopp

state: Ohio

address: 700 Children’s Drive

department: Section of Pediatric Pulmonology

institute: Nationwide Children’s Hospital

summary: Cystic fibrosis (CF) remains a life-shortening disease without a definitive cure. Novel therapeutics targeting the causative defect in the cystic fibrosis transmembrane conductance regulator (CFTR) gene are now in clinical use.  Lumacaftor/ivacaftor is a CFTR modulator approved for patients homozygous for the CFTR mutation p.Phe508del, but there are wide variations in treatment responses preventing prediction of patient responses. We aimed to determine changes in gene expression related to treatment initiation and response. Whole-blood transcriptomics was performed using RNA-Seq in 20 patients with CF pre- and 6 months post-lumacaftor/ivacaftor (drug) initiation and 20 non-CF healthy controls.  Correlation with clinical variables was performed by stratification via clinical responses.  We identified 491 genes that were differentially expressed in CF patients (pre-drug) compared with non-CF controls. In addition, 36 genes were differentially expressed when comparing pre-drug to post-drug profiles within CF patients. Transcriptomics revealed novel pathways in CF patients at baseline compared to non-CF, and in clinical responders to lumacaftor/ivacaftor. Overall changes in gene expression post-lumacaftor/ivacaftor were modest compared to pre-drug CF profiles.

overall_design: 20 control non-CF samples,  20 CF samples pre-drug,  20 samples from the same CF patients 6 months-post drug

last: Fitch

first: Lisa

last: Jaramillo

first: Chandra

last: Shrestha

first: Shuzhong

last: Zhang

first: Sabrina

last: Palacios

first: Fred

last: Woodley

first: Don

last: Hayes Jr

first: Octavio

last: Ramilo

first: Peter

last: White

first: Asuncion

last: Mejias


title: Next Generation Sequencing Facilitates Quantitative Analysis of Peritoneal Macrophage Transcriptomes

city: hangzhou

first: Wanwan

last: Huai

address: yuhangtang road

institute: zhejiang university

summary:
Purpose:The purpose of this study is to detect activated or silenced genes during KAT8-deficient peritoneal macrophages and the control cells. Gene expression differences between two samples could be found using transcriptome profiling (RNA-seq) analysis.
Methods:Mouse peritoenal macrophages were harvested from mice 3 days after thioglycollate (Merck) injection. Macrophages RNA profiles were generated by deep sequencing,using Illumina.
Results: We mapped about 10 million sequence reads per sample to the mouse genome, identified hundreds of genes with significant mRNA variation between KAT8-deficient macrophages and the control cells.

overall_design: Peritoneal macrophage mRNA profiles of KAT8fl/flLyz2-cre- and KAT8fl/flLyz2-cre+ mice were generated by deep sequencing.

first: Huai

last: Wanwan

first: Liu

last: Xingguang


title: Examining serotonergic neuron differentiation from human iPSCs

city: Freiburg im Breisgau

first: Galina

last: Erikson

address: Stübeweg 51

institute: Max Planck Institute of Immunobiology and Epigenetics

summary: The goals of this study were to study serotonergic neuron differentiation from patient derived iPSCs

overall_design: Human induced pluripotent stem cells (hiPSC) and hiPSC-derived serotonergic neurons, 3 replicates each

first: Krishna

last: Vadodaria

last: Gage


title: Viral infection enhances NK cell activation via Type I dependent pathways and can be utilized to enhance influenza-specific monoclonal antibody therapies

city: Melbourne

first: Hyon Xhi

last: Tan

state: Victoria

address: 792 Elizabeth St

department: Department of Microbiology and Immunology

institute: The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity

summary: NK cells are an essential component for the control of influenza infection, acting to both clear virus-infected cells and release antiviral cytokines. Engagement of the NK cell CD16-receptor by antibody-coated influenza-infected cells results in antibody-dependent cellular cytotoxicity (ADCC). Though NK cell-mediated ADCC is an important mechanism to control influenza, influenza infection itself may act to enhance the potency of NK cell ADCC. To understand if virus-infected cells increase NK cell activation, we co-cultured human PBMCs with influenza-infected human alveolar epithelial (A549) cells and evaluated the capacity of NK cells to mediate ADCC. Pre-incubation of PBMCs with influenza-infected target cells markedly enhanced the functionality of NK cells by ADCC antibodies in response to HA immune-complexes containing intravenous immunoglobulin (IVIG), allogenic target cells, with and without rituximab. Trans-well and supernatant transfer experiments showed that virus released into the supernatant is responsible for the enhanced functionality of NK cells, which is apparent at both the protein and RNA transcriptomic levels.  Furthermore, cytokine multiplex data, RNA sequencing and cytokine blocking/supplementation experiments showed Type I interferons released from PBMCs were the primary mechanism of the influenza-induced increased NK cell functionality and ADCC potency. Importantly, the influenza infection-mediated increase in NK cell mediated anti-influenza ADCC was mimicked by the type I interferon agonist Poly-IC. This suggests a potential mechanism for enhancing monoclonal antibody therapies for influenza. We conclude that influenza-infection induced secretion of type I interferons enhances the ADCC capacity of NK cells and this pathway may potentially be manipulated to improve anti-influenza therapies.

overall_design: Three separate donor PBMCs were incubated with either infected A549 cells or uninfected A549 cells for 12 hours. Target cell populations of lymphocytes gated on LIVE/DEAD negative populations or LIVE/DEAD negative CD3-CD56+ NK cells of interest were subsequently sorted from these PBMCs. Transcriptional profiling and differential gene expression was performed using RNA sequencing.

first: Sinthujan

last: Jegaskanda

first: Hyon-Xhi

first: Sheilajen

last: Alcantara

first: Kathleen

last: Wragg

first: Hillary

last: Vanderven

first: Matthew

last: Parsons

first: Amy

last: Chung

first: Jennifer

last: Juno

first: Stephen

last: Kent


title: A radical switch in clonality reveals the formation of a stem cell niche in the epiphyseal growth plate

city: Stockholm

first: Eva

last: Hedlund

address: Svante Arrhenius v. 16C

department: Department of Biochemistry and Biophysics

country: Sweden

institute: Stockholm University

overall_design: Cells from three zones of the growth plate were captured with LCM: resting zone (R), hypertophic zone (H) and proliferative zone (P). Six biological replicates were taken for each zone, each of the biological replicates were sequenced.

first: Phillip

last: Newton

first: Christoph

last: Schweingruber

first: Artem

middle: V

last: Artemov

first: Andrei

last: Chagin


title: Comprehensive molecular characterization of liver cancer and inheritance of the phenotypic traits during tumor recurrence [methylation - recurrence]

city: Bunkyo-ku

first: Kaoru

last: Mogushi

state: Tokyo

address: 1-5-45 Yushima

department: Department of Molecular Oncology

institute: Tokyo Medical and Dental University

summary: Hepatocellular carcinoma (HCC) is a heterogeneous disease with a variety of etiological factors, and ranks as the second leading cause of cancer-related mortality worldwide due to multifocal recurrence. Comprehensive molecular evaluation of HCC by multiplatform analysis defined three major subtypes: (1) mitogenic and stem cell-like tumors with chromosomal instability; (2) CTNNB1-mutated tumors displaying DNA hypermethylation; and (3) metabolic syndrome-associated tumors, which included an immunogenic subgroup characterized by macrophage infiltration and favorable prognosis. Although genomic and epigenomic analysis explicitly discriminated HCC with intrahepatic metastasis (IM) from multicentric HCC (MC), the phenotypic similarity between the primary and recurrent tumors was not linked to the IM/MC diagnosis, but rather the integrated classification. Thus, identification of these HCC subtypes provides insights into patient stratification and opportunities for therapeutic development.

overall_design: For the Recurrence study, genomic DNA were obtained from primary and recurrent tumors and adjacent liver tissues of 18 HCC patients (L031 to L048, L037 contained re-recurrence HCC), respectively.

first: Shu

last: Shimada

first: Yoshimitsu

last: Akiyama

first: Takaki

last: Furuyama

first: Shuichi

last: Watanabe

first: Kosuke

last: Ogawa

first: Hiroaki

last: Ono

first: Yusuke

last: Mitsunori

first: Daisuke

last: Ban

first: Atsushi

last: Kudo

first: Shigeki

last: Arii

first: Minoru

last: Tanabe

first: Shinji

last: Tanaka


title: Comprehensive molecular characterization of liver cancer and inheritance of the phenotypic traits during tumor recurrence [tissue]

overall_design: A total of 183 patients who underwent curative hepatic resection for HCC between 2006 and 2013 at Tokyo Medical and Dental University Hospital participated in integrative analysis of classification. Fifteen adjacent liver tissues obtained from patients with metastasis of colorectal cancer who had not received chemotherapy were used as control.


title: Comprehensive molecular characterization of liver cancer and inheritance of the phenotypic traits during tumor recurrence [methylation - classification]

overall_design: For the Classification study, genomic DNA were obtained from 29 pairs of HCC and adjacent liver controls (L001 to L030, L022 was excluded because of low tumor purity).


title: Aberrant enhancer reprogramming drives hepatic carcinogenesis through global transcriptional reprogramming

first: Alfred Sze-Lok

last: Cheng

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

overall_design: Refer to individual Series


title: The Jumonji-domain histone demethylase inhibitor JIB-04 deregulates oncogenic programs and increases DNA damage in Ewing Sarcoma, resulting in impaired cell proliferation and survival, and reduced tumor growth

city: Sheridan

first: Kenneth

last: Jones

state: Wyoming

address: 1309 Coffeen Avenue STE 10090

institute: Bioinformatic Solutions LLC

summary: The overall goal of this study was to characterize the activity and mechanism(s) of action of the pan-Jumonji domain histone demethylase small molecule inhibitor JIB-04 in the pediatric bone and soft tissue cancer Ewing Sarcoma.

overall_design: RNA-seq was used to define the effects of JIB-04 on the transcriptome of the patient-derived Ewing Sarcoma cell line A673.

first: Paul

last: Jedlicka

first: Janet

last: Parrish

first: Tyler

last: McCann

first: Marybeth

last: Secher

first: Lays

last: Sobral

first: Wenhua

last: Ren

first: AikChoon

last: Tan


title: Comprehensive molecular characterization of liver cancer and inheritance of the phenotypic traits during tumor recurrence

first: Kaoru

last: Mogushi

type:
Expression profiling by array
Methylation profiling by array


title: Comprehensive molecular characterization of liver cancer and inheritance of the phenotypic traits during tumor recurrence [cell line]

overall_design: To identify genes reppressed by DNA methylation, eight human HCC cell lines (Hep3B, HepG2, HLE, HLF, Huh1, Huh7, JHH2 and JHH4) were exposed and unexposed to 5 μM 5-azacitidine, a demethylating agent, for three days.

first: Shu

last: Shimada

first: Yoshimitsu

last: Akiyama

first: Takaki

last: Furuyama

first: Shuichi

last: Watanabe

first: Kosuke

last: Ogawa

first: Hiroaki

last: Ono


title: Spontaneous DIPG Modeling Reveals Novel H3.3 K27M-Mediated Oncogenic Mechanisms Acting Through Epigenetic Effects [ChIP-seq]

city: Memphis

first: Hongjian

last: Jin

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hospital

summary: A mouse knock-in model engineered for Cre recombinase-activated expression of the endogenous mouse H3f3a allele generating an epitope-tagged H3.3 equipped with or without a K27M mutation to investigate H3.3 K27M effects on brain cell and tumor growth, gene expression and epigenetics.

overall_design: RNA-seq and ChIP-seq for three histone marks in cells and tumors from a mouse knock in model of H3f3a K27M

first: Jon

middle: D

last: Larson

first: Kasper

last: Lawryn

first: Suzanne

last: Baker


title: Spontaneous DIPG Modeling Reveals Novel H3.3 K27M-Mediated Oncogenic Mechanisms Acting Through Epigenetic Effects


title: Genome-wide DNA methylation analysis in primary antiphospholipid syndrome neutrophils

status: Public on Jan 02 2019

city: Pittsburgh

first: Amr

last: Sawalha

address: 4401 Penn Avenue

institute: University of Pittsburgh

summary: Antiphospholipid syndrome (APS) is a systemic autoimmune disease characterized by thromboembolic events and pregnancy loss. We sought to characterize the DNA methylation profile of primary APS in comparison to healthy controls and individuals with SLE.

overall_design: Illumina methylation array of genomic DNA from neutrophils extracted from whole blood  from 10 antiphospholipid syndrome (APS) patients and 12 healthy controls (CON). Initially, 12 participants with primary APS were recruited from the University of Michigan rheumatology clinics. All met the Sydney APS Classification Criteria. From this group, 10 were successfully run on the DNA methylation array, and as such the final primary APS cohort was comprised of these 10 individuals. A total of 12 controls were matched to the original 12 primary APS participants by age (± 5 years), sex, and ethnicity. All participants in both groups were of European-American ethnicity.

middle: H

first: Patrick

last: Coit


title: RNAseq of CD8+ and CD8- MAIT cells in human peripheral blood

first: Marcus

last: Buggert

address: C2:94; Karolinska Universitetssjukhuset Huddinge

department: Microbiology

institute: Karolinska Institutet

summary: Mucosa-associated invariant T (MAIT) cells are unconventional innate-like T cells that recognize microbial riboflavin metabolites presented by the MHC class I-like protein MR1. Human MAIT cells predominantly express the CD8α co-receptor (CD8+), with a smaller subset lacking both CD4 and CD8 (DN). However, it is unclear if these two MAIT cell sub-populations distinguished by CD8α represent functionally distinct subsets. To address this, we investigated the phenotypic, transcriptional, and functional differences between CD8+ and DN MAIT cells using human samples from peripheral blood, mucosal tissues, and fetal tissues.

overall_design: We FACS sorted CD8+ and CD8- MAIT cells from human peripheral blood and performed bulk RNAseq on these cells

first: Joana

last: Dias

first: Son

last: Nguyen


title: RNA-seq in scraped colon epithelium after deletion of Synbindin in mice in colitis-associated cancer model

city: Shanghai

first: Luoyan

last: Ai

state: Shanghai

address: 145 Middle Shandong Road

department: Division of Gastroenterology and Hepatology

institute: Shanghai Jiao Tong University

summary: We previously identified Synbindin promoted gastric and colon cancer development by activating ERK on the Golgi in vitro. Advanced in vivo evidence is required.In this study, we genetically manipulated Synbindin expression in the intestinal epithelium using loss-of-function mouse models and subject them to AOM/DSS induced colitis-associated cancer model. At the end of the model, mice were sacrificed and colon tumors and adjacent colon epithelium were scraped and used for RNA-seq.

overall_design: Colon mRNA profiles of Synbindinflox and SynbindinΔIEC mice were generated by deep sequencing, in triplicate,using illumina Hiseq.


title: Spontaneous DIPG Modeling Reveals Novel H3.3 K27M-Mediated Oncogenic Mechanisms Acting Through Epigenetic Effects [RNA-seq]

overall_design: RNA-seq and ChIP-seq for three histone marks in cells and tumors from a mouse knock-in model of H3f3a K27M.


title: Dual-center, dual-platform microRNA profiling identifies plasma biomarkers of adult temporal lobe epilepsy [Marburg miRNA-seq]

city: Dublin

first: Catherine

last: Mooney

address: Belfield

department: School of Computer Science

country: Ireland

institute: University College Dublin

summary: There are no blood-based molecular biomarkers of temporal lobe epilepsy (TLE) to support clinical diagnosis. MicroRNAs are short noncoding RNAs with strong biomarker potential due to their cell-specific expression, mechanistic links to brain excitability, and stable and reliable detection in biofluids. Altered expression of circulating microRNAs has been reported in human epilepsy, but most studies collected samples from one clinical site, relied on a single platform for profiling or conducted minimal validation. We collected plasma samples from video-electroencephalogram-monitored adult TLE patients at epilepsy specialist centers in two different countries, performed genome-wide PCR-based and RNA sequencing during the discovery phase and validated in a large cohort of samples (>300 samples) that included patients with psychogenic non-epileptic seizures. After profiling, validation of the discovery cohort and validation in the larger patient groups we identified miR-27a-3p, miR-328-3p and miR-654-3p with strong TLE biomarker potential. Plasma levels of these microRNAs were regulated in the same direction in plasma from epileptic mice, and furthermore were not different to healthy controls in patients with psychogenic non-epileptic seizures. The biomarker potential was extended by determining microRNA copy number in plasma and we demonstrate rapid detection of these microRNAs using an electrochemical RNA microfluidic disk as a prototype point-of-care device. Investigation of the molecular transport mechanism in plasma determined analysis of all three microRNAs within the exosome-enriched provided highest diagnostic accuracy while levels of Argonaute-bound miR-328-3p selectively increased in patient samples collected after seizures. In situ hybridization revealed the presence of miR-27a-3p and miR-328-3p within neurons in human brain and bioinformatics analysis predicted targets linked to growth factor signaling and apoptosis. Taken together, this study extends evidence for the biomarker potential of circulating microRNAs for epilepsy diagnosis and mechanistic links to underlying pathomechanisms.

overall_design: microRNA expression in the plasma of 16 patients with epilepsy, before and after seizure, and 16 controls was pooled and measured by microRNA sequencing.

first: Rana

last: Raoof

first: Sebastian

last: Bauer

first: Hany

middle: E

last: Naggar

first: Niamh

last: Connolly

first: Gary

middle: P

last: Brennan

first: Elizabeth

last: Brindley

first: Thomas

last: Hill

first: Hazel

last: McArdle

first: Elaine

last: Spain

first: Robert

last: Forster

first: Jochen

last: Prehn

first: Hajo

last: Hamer

first: Norman

last: Delanty

first: Felix

last: Rosenow

first: David

last: Henshall


title: Dual-center, dual-platform microRNA profiling identifies plasma biomarkers of adult temporal lobe epilepsy [Beaumont miRNA-seq]

middle: J


title: SMARCA4 loss is synthetic lethal with CDK4/6 via restriction CCND1 chromatin accessibility in lung cancer

city: Montreal

first: William

middle: Abraham

last: Pastor

state: QC

address: 3655 Promenade Sir William Osler

department: Biochemistry

institute: McGill University

summary: Tumor suppressor SMARCA4 (BRG1), a key SWI/SNF chromatin remodelling gene, is frequently inactivated in cancers which is not directly druggable. We recently uncovered that SMARCA4 loss in an ovarian cancer subtype causes cyclin D1 deficiency leading to susceptibility to CDK4/6 inhibition. Here, we show that this vulnerability is conserved in non-small cell lung cancer (NSCLC), where SMARCA4 loss also results in reduced cyclin D1 expression and selective sensitivity to CDK4/6 inhibitors. In addition, SMARCA2, another SWI/SNF subunit lost in a subset of NSCLCs, also regulates cyclin D1 and drug response when SMARCA4 is absent. Mechanistically, SMARCA2/4 loss reduces cyclin D1 expression by a combination of restricting CCND1 chromatin accessibility and suppressing c-jun, a transcription activator of CCND1. Furthermore, SMARCA4 loss is synthetic lethal with CDK4/6 inhibition both in vitro and in vivo, suggesting that FDA-approved CDK4/6 inhibitors could be effective to treat this significant subgroup of NSCLCs.

overall_design: This dataset includes 3-ATAC-seq and 11 ChIP-seq samples

first: Sidong

last: Huang

middle: A


title: Transcriptional dynamics of microRNAs and their targets during Drosophila neurogenesis

city: Berlin

first: Peter

last: Menzel

address: Robert-Rössle-Str. 10

institute: Max-Delbrück-Center for Molecular Medicine

summary: During Drosophila melanogaster embryogenesis, a tight regulation of gene expression in time and space is required for the orderly emergence of the various specific cell types. While the general importance of microRNAs in modulating and regulating eukaryotic gene expression has already been well-established, their role in early neurogenesis remains to be addressed. In this survey, we investigate the transcriptional dynamics of microRNAs and their target transcripts during the neurogenesis of Drosophila melanogaster. To this end, we use the recently developed DIV-MARIS protocol, a method for enriching specific cell types from the Drosophila embryo in an in vivo setting, to sequence the tissue-specific transcriptomes. We generate dedicated small and total RNA-seq libraries for neuroblasts, neurons and glia cells at an early (6–8 h after egg laying) and late (18–22 h after egg laying) developmental stage. This strategy allows us to directly compare the transcriptomes of these cell types and investigate the potential functional roles of individual microRNAs with unprecedented spatiotemporal resolution, which is beyond the capabilities of existing in-situ hybridization studies. In total, we identify 74 microRNAs that are significantly differentially expressed between the three cell types and the two developmental stages.

overall_design: In total, 20 smallRNA-seq libraries are made from the marker-positive and marker-negative FACS fractions using the markers repo and elav at 6-8h and 18-22 as well as prospero at 6-8h; all in biological duplicates.

first: Alexandra

last: McCorkindale

first: Stefan

middle: R

last: Stefanov

last: Zinzen

first: Irmtraud

last: Meyer


title: Expansion of Islet-Resident Macrophages Leads to Inflammation Affecting Beta Cell Proliferation and Function in Obesity

city: La Jolla

first: Jason

middle: Samuel

last: Seidman

state: CA

address: 9500 Gilman Drive, Mail code 0651

department: Cellular and Molecular Medicine

institute: University of California San Diego

summary: Inflammation is a key component of the pathogenesis of obesity-associated type 2 diabetes (T2D). However, the nature of T2D-associated islet inflammation and its impacts on T2D-associated beta cell abnormalities remain poorly defined. Using both diet-induced and genetically modified T2D animal models, we explore immune components of islet inflammation and define their roles in regulating beta cell function and proliferation. Our studies show that T2D-associated islet inflammation is uniquely dominated by macrophages, without the involvement of adaptive immune cells. We identify two islet macrophage populations, characterized by their distinct phenotypes, anatomical distributions and functional properties. Obesity induces a local expansion of intra-islet macrophages, independent of the replenishment from circulating monocytes. In contrast, the abundance of peri-islet macrophages is negligibly affected by obesity. Functionally, intra-islet macrophages impair beta cell function in a cell-cell contact dependent manner. In contrast, both intra- and peri-islet macrophage populations are able to promote beta cell proliferation. Together, these data provide a definitive view of the genesis of T2D-associated islet inflammation and define specific roles of islet macrophages in regulating beta cell function and proliferation.

overall_design: RNA-Seq of F480 Hi and CD11c Hi Islet macrophages in nomal chow diet and high fat diet fed mice

first: Jerrold

last: Olefsky

first: Wenxian

last: Fu


title: Premature polyadenylation-mediated loss of stathmin-2 is a hallmark of TDP-43-dependent neurodegeneration

status: Public on Jan 01 2019

first: Don

last: Cleveland

address: 9500 Gilman Drive

institute: Ludwig Institute for Cancer Research

summary: Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are associated with loss of nuclear TDP-43. Here we identify that TDP-43 regulates expression of the neuronal growth-associated factor stathmin-2. Lowered TDP-43 levels, which reduce its binding to sites within the first intron of stathmin-2 pre-mRNA, uncover a cryptic polyadenylation site whose utilization produces a truncated, non-functional mRNA. Reduced stathmin-2 expression is found in neurons trans-differentiated from patient fibroblasts expressing an ALS-causing TDP-43 mutation, in motor cortex and spinal motor neurons from sporadic ALS patients and familial ALS patients with expansion in C9orf72, and in induced pluripotent stem cell (iPSC)-derived motor neurons depleted of TDP-43. Remarkably, while reduction in TDP-43 is shown to inhibit axonal regeneration of iPSC-derived motor neurons, rescue of stathmin-2 expression restores axonal regenerative capacity. Thus, premature polyadenylation-mediated reduction in stathmin-2 is a hallmark of ALS/FTD that functionally links reduced nuclear TDP-43 function to enhanced neuronal vulnerability.

overall_design: Analysis of gene expression changes linked to TDP-43 loss by siRNA (n=3 biological replicates each conditon) or linked to mutant TDP-43 expression by genome editing in SH-SY5Y cells (n=2 biological replicates each condition).

first: Ze'ev

last: Melamed

first: Ouyang

last: Zhengyu

first: Clotilde

last: Lagier-Tourenne


title: Whole genome resequencing of liver in mice model

city: Beijing

first: LI

middle: Yong

last: Ning

address: 7 Panjiayuan Nanli

institute: China National Center for Food Safety Risk Assessment

summary: Four groups of C57 mice were gavaged with CMC, ethanol, DEHP and ethanol+DEHP for 28 continuous days. At the end of the experiment, livers were harvested to carry out Whole genome resequencing, we found that metabolism related genes were significantly changed in the DEHP and ethanol+DEHP groups compared with control groups, but there was no  significant change between them.

overall_design: Liver mRNA profiles of mice models were generated by sequencing, using Illumina Hiseq.

first: Hui

last: Yang

first: Yongning

last: Li


title: MicroRNA (miR)-211 loss promotes metabolic vulnerability and BRAF inhibitor sensitivity in melanoma

city: ORLANDO

first: Anupama

last: Sahoo

state: Florida

address: 6400 SANGER ROAD

institute: SBPMRI

summary: We report that miR-211 loss-of-function in the pigmented melanoma cell line SKMEL-28  slowed growth and invasion in vitro, inhibited phosphoinositol-3-kinase (PI3K) signaling,  rendered these melanoma cells metabolically vulnerable by attenuating mitochondrial respiration and tricarboxylic acid (TCA) cycling and inhibited melanoma growth in vivo.

overall_design: mRNA profiles of SKMEL28 (WT) and SK-P8-2(miR-211 deletion) cells and xenografts in SCID  mice were generated by deep sequencing using Illumina HiSeq 2500.

first: Ranjan

last: Perera


title: Transcriptomic and epigenetic analyses of mouse organoids expressing BrafV600E mutation [Exome-seq]

city: BALTIMORE

first: hari

last: easwaran

state: MD

address: 1650 Orleans Street, CRB1, Room 530

department: Oncology

institute: Johns Hopkins University

type: Genome variation profiling by high throughput sequencing

summary: Abnormal promoter DNA hypermethylation arises early during tumorigenesis and yet its role in cancer initiation has remained underexplored. An important scenario for examining this is, BRAFV600E-mutant colon adenocarcinomas (COAD) which most often arise in the proximal colon and harbor extensive, abnormal gene promoter CpG-island methylation or the methylator phenotype (CIMP). How CIMP and BRAF-mutations specifically interact for COAD initiation has remained unclear. Using mouse colon-derived organoids, we show promoter hypermethylation spontaneously arises in wild type cells mimicking “aging like” phenotype. The silenced genes sufficiently activate the Wnt pathway, causing a stem–like state and profound differentiation block. This phenotype renders long-term cultured organoids to be rapidly susceptible to transformation by BRAFV600E with features of typical right-sided COAD. Our studies tightly link epigenetic abnormalities, suggested to arise with aging, to intestinal cell fate changes and define an “epi-driver” role for multiple abnormally silenced genes that predispose to BRAFV600E-driven colon tumorigenesis.

overall_design: Cre-activable BrafV600E and wild type proximal colon organoids were derived from mice carrying heterozygous Cre-activable BrafV600E (termed Braf+/LSL). Lentiviral delivery of Cre with the lentiviral backbone alone serving as control (EV), is used to subsequently activate BrafV600E in the organoids. Expression and methylation analyses were done in organoids 5m after induction of oncogene, and in organoids selected to grow in medium without stem-cell niche factors (Base medium). Two biological replicates of BrafEV organoids are grown for over 12-14 months which were labeled as BRAF1_EV_12m and BRAF3_EV_14m.

first: Hari

last: Easwaran


title: Dual-center, dual-platform microRNA profiling identifies plasma biomarkers of adult temporal lobe epilepsy

first: Catherine

last: Mooney


title: Gonadal supporting cells acquire sex-specific regulatory elements during mammalian sex determination

city: Chicago

first: Christopher

last: Futtner

state: Il

address: 303 E. Superior St, Lurie 7-220

department: Endocrinology

institute: Northwestern University

summary:
Purpose: In this study we employed unbiased, genome-wide techniques to identify regulatory elements during murine sex determination.
Methods: We performed ATAC-seq on 60K FACS-purified XX and XY gonadal cells before and after sex determination to map nucleosome depleted regions (NDRs) indicative of regulatory elements. To determine whether these are active enhancers, we performed ChIP-seq for H3K27ac, a histone modification that marks active enhancers in both sexes and time points. Transient transgenics was performed on select enhancers to determine whether they are functional in gonads during the sex determination stage.
Results: We have produced a genome wide map of potential regulatory elements and active enhancers during the process of murine sex determination. Furthermore, we validated the power of our dataset by identifying a novel enhancer downstream of Bmp2, a female-specific gene.
Conclusions: This work supplies a powerful resource for identifying chromatin regulatory elements active during mammalian sex determination.

overall_design: ATAC-seq was performed in duplicate on FACS-sorted XX and XY gonadal supporting cells from E10.5 and E13.5 mouse embryonic gonads. ChIP-seq for H3K27ac was performed in duplicate on FACS-sorted  XX and XY gonadal supporting cells from E10.5 and E13.5 mouse embryonic gonads. Each replicate contained pooled cells from multiple embryos.

first: S

last: Garcia-Moreno


title: SMARTer single cell total RNA sequencing [SK-N-BE-2C]

city: Ghent

first: Celine

last: Everaert

address: De Pintelaan 185

country: Belgium

institute: University Ghent

summary: single cell polyA+ and total RNA-seq data was generated for NGP, SK-N-BE-2C and SHSY5Y-MYCN-TR cells

overall_design: This submission consists of SK-N-BE-2C cell line data.

first: Karen

last: Verboom

first: Nathalie

last: Bolduc

first: Ken

last: Livak

first: Nurten

last: Yigit

first: Dries

last: Rombaut

first: Jasper

last: Anckaert

first: Morten

last: Venø

first: Jørgen

last: Kjems

first: Frank

last: Speleman

first: Pieter

last: Mestdagh

first: Jo

last: Vandesompele


title: Molecular Pathology of adverse local tissue reaction caused by metal-on-metal implants

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

summary:
RNA-sequencing analysis of periacetabular synovial tissue collected from patients undergoing a revision total hip arthroplasty (rTHA) after failure of a Cobalt Chromium implant. Comparisons were made to periacetabular synovial tissue collected from patients undergoing primary THAs (pTHA).
Results: Analysis of tissue biopsies by RNA-sequencing revealed that MoM patient samples exhibit significantly increased expression of immune response genes but decreased expression of genes related to extracellular matrix (ECM) remodeling.

overall_design: RNA was extracted from 3 pTHA and 3 rTHA samples and used for RNA-sequencing. Comparative analysis was performed using RPKM values obtained after processing of sequencing data.

first: Matthew

last: Abdel

first: Andre

last: van Wijnen


title: SMARTer single cell total RNA sequencing [NGP]

overall_design: This submission consists of NGP cell line data.


title: CNS cell-type specific gene profiling of aging P301S tau transgenic mice

city: Sydney

first: Lars

last: Ittner

state: NSW

address: Research Dirve

institute: Macquarie University

summary: RNA sequencing of cortex from  young (3mo) and old (10mo) P301S tau transgenic mice

overall_design: 3 biological replicas per age and genotype (transgenic and non-transgenic)

first: Yazi

last: Ke


title: SMARTer single cell total RNA sequencing [SHSY5Y-MYCN-TR]

first: Celine

last: Everaert

overall_design: This submission consists of SHSY5Y-MYCN-TR cell line data.


title: ChIPseq on H3K27ac, H3K27me3 and H2AK119Ub on TXY cell line

city: Paris

first: Aurélie

last: Bousard

address: 26, rue d'Ulm

institute: Institut Curie

summary: During development, changes in gene transcription are accompanied by changes in chromatin modification but the order and causality of events often remain unclear. Here we address this question using X-chromosome inactivation (XCI), which entails chromosome-wide gene silencing and heterochromatin formation. We initiate XCI in female, mouse embryonic stem cells by inducing Xist expression and monitor subsequent changes in transcription and chromatin modification by allele-specific TTseq and ChIPseq respectively. An unprecedented temporal resolution has enabled us to define early alterations in chromatin that are induced upon Xist RNA coating. Xist-induced repression begins with histone deacetylation, which involves the histone deacetylase HDAC3 and occurs before efficient loss of H3K4me3 and H3K4me1 modifications. Polycomb-associated repressive histone marks accumulate rapidly, starting with PRC1-associated H2AK119Ub and followed by PRC2-associated H3K27me3. However, polycomb accumulates initially at large premarked domains, some of which correspond to Xist entry sites, and then spreads into genes. We also show that spreading can only ensue when transcriptional silencing has occurred. These results establish a detailed epigenomic time course for XCI and reveal a hierarchy of events with chromatin playing an important role in transcriptional silencing of the X chromosome.

overall_design: Native ChIPseq on H3K27me3 and H2AK119Ub on TXY:Xist and TXY:XistdeltaA  cell line, after 2 days of differentiation, with or without DOX, in replicates.

first: Jan

last: Żylicz

first: Kristina

last: Žumer

first: Eusra

last: Mohammad

first: Simão

last: Teixeira da Rocha

first: Björn

last: Schwalb

first: Laurène

last: Syx

first: Patrick

last: Cramer

first: Edith

last: Heard


title: Mammalian Nucleolar Protein DCAF13 Confers Developmental Competence on Growing Oocytes

city: Hangzhou

first: Li

last: Shen

state: Zhejiang Province

address: 866 Yuhangtang Road

institute: Life Sciences Institute, Zhejiang University

summary: During mammalian oocyte growth, chromatin configuration transition from the nonsurrounded nucleolus (NSN) to surrounded nucleolus (SN) type plays a key role in the regulation of gene expression and in acquisition of meiotic and developmental competence by the oocyte. Nonetheless, the mechanism underlying chromatin configuration maturation in oocytes is poorly understood. Here we show that nucleolar protein DCAF13 is an important component of the ribosomal RNA (rRNA)-processing complex and is essential for oocyte NSN–SN transition in mice. A conditional knockout of Dcaf13 in oocytes led to the arrest of oocyte development in the NSN configuration, follicular atresia, premature ovarian failure, and female sterility. The DCAF13 deficiency resulted in pre-rRNA accumulation in oocytes, whereas the total mRNA level was not altered. Further exploration showed that DCAF13 participated in the 18S rRNA processing in growing oocytes. The lack of 18S rRNA because of DCAF13 deletion caused a ribosome assembly disorder and then reduced global protein synthesis. DCAF13 interacted with a protein of the core box C/D ribonucleoprotein, fibrillarin, i.e., a factor of early pre-rRNA processing. When fibrillarin was knocked down in oocytes from primary follicles, the follicle development was inhibited as well, indicating that an rRNA processing defect in the oocyte indeed stunts chromatin configuration transition and follicle development. Taken together, these results elucidated the in vivo function of novel nucleolar protein DCAF13 in maintaining mammalian oogenesis.

overall_design: RNA-seq comparing mouse growing and fully grown stage oocyte in DCAF13-deletion and WT sample; 10 oocytes per sample

first: Jue

last: Zhang

first: Yinli

first: Longwen

last: Zhao

first: Jingxin

last: Guo

first: Jiali

last: Yu

first: Shuyan

last: Ji

first: Lanrui

last: Cao

first: Songying

first: Xianghong

last: Ou

first: Hengyu

last: Fan


title: Analysis of the IFNgamma induced pathways  in murine macrophages

city: Boston

first: Alexander

last: Gimelbrant

state: Massachusetts

address: 450 Brookline Avenue

institute: Dana-Farber Cancer Institute and Harvard Medical School

summary: Macrophages derived from the CH3 mice were treated with the increasing concentrations of the IFNgamma followed by the RNA-Seq analysis.

overall_design: Examination of the response of the macrophages  to IFNgamma treatment

first: Igor

last: Kramnik

first: Sujoy

last: Chatterjee

first: Bidisha

last: Bhattacharya

first: Anwesha

last: Nag

first: Kyomi

last: Igarashi

first: Marina

last: Kasaikina

first: Denis

last: Lafontaine


title: Trancriptomic and epigenetic analyses of mouse organoids expressing BrafV600E mutation [MBD-seq]

first: hari

last: easwaran

type: Methylation profiling by high throughput sequencing

overall_design:
Cre-activable BrafV600E and wild type proximal colon organoids were derived from mice carrying heterozygous Cre-activable BrafV600E (termed Braf+/LSL). Lentiviral delivery of Cre with the lentiviral backbone alone serving as control (EV), is used to subsequently activate BrafV600E in the organoids. Expression and methylation analyses were done in organoids 5m after induction of oncogene, and in organoids selected to grow in medium without stem-cell niche factors (Base medium).
This Series represents the methylation analysis.

first: Hari

last: Easwaran


title: The SUMO Pathway as a Therapeutic Option in Pancreatic Cancer

first: Matthias

last: Wirth

address: Hindenburgdamm 30

institute: Charité Berlin

summary: Pancreatic ductal adenocarcinoma (PDAC) still carries a dismal prognosis with overall five-year survival of 8%. Conventional combination chemotherapies are a clear advance in the treatment of PDAC, however subtypes of the disease exist, which exhibit extensive resistance to such therapies. Genomic MYC amplifications represent a distinct subset of PDAC with an aggressive tumor biology. It is clear that hyperactivation of MYC generates dependencies, which can be exploited therapeutically. To find MYC-associated dependency we analyzed human PDAC expression dataset. We observed that MYC is connected to the sumoylation machinery in PDAC. Components of the SUMO pathway mark a PDAC subtype with worse prognosis and we provide evidence that PDACs with a MYChigh/SUMOhigh phenotype respond to a novel SUMO inhibitor, offering the opportunity to develop novel stratified PDAC therapies

overall_design: IMIM-PC1 cells stably expressing the MYC-ER fusion protein were treated with 500nM 4-OHT for an interval of 24h.

last: Biederstädt

first: Ulrich

last: Keller

first: Günter

last: Schneider


title: N6-Methyladenosine Modification of Hepatitis B Virus RNA Differentially Regulates The Viral Life Cycle

city: Zurich

first: A

last: McIntyre

address: Winterthurerstrasse 190

department: Molecular Life Sciences

country: Switzerland

institute: University of Zurich

summary: N6-methyladenosine (m6A) RNA methylation is the most abundant epitranscriptomic modification of eukaryotic messenger RNAs (mRNAs). Previous reports have found m6A on both cellular and viral transcripts and defined its role in regulating numerous biological processes, including viral infection. Here, we show that m6A and its associated machinery regulate the life cycle of hepatitis B virus (HBV). HBV is a DNA virus that completes its life cycle via an RNA intermediate, termed pregenomic RNA (pgRNA). Silencing of enzymes that catalyze the addition of m6A to RNA resulted in increased HBV protein expression, but overall reduced reverse transcription of the pgRNA. We mapped the m6A site in the HBV RNA and found that a conserved m6A consensus motif situated within epsilon (stem loop structure is the site for m6A modification. The epsilon stem loop is located in the 3’ terminus of all HBV mRNAs and both termini (5’ and 3’) of the pgRNA. Mutational analysis of the identified m6A site in the 5’ epsilon stem loop of pgRNA revealed that m6A at this site is required for efficient reverse transcription of pgRNA, while m6A of the 3’ epsilon stem loop results in destabilization of all HBV transcripts, suggesting that m6A has dual regulatory functions in pgRNA. Overall, this study reveals how m6A regulates HBV gene expression and reverse transcription, leading to a new level of understanding of the HBV life cycle. .

overall_design: Study of m6A in HBV RNA using three MeRIP-seq replicates for HepG2 cells.

first: Hasan

last: Imam

first: Mohsin

last: Khan

first: Nandan

middle: S

last: Gokhale

first: Alexa

middle: B

first: Jae

middle: Y

last: Jang

first: Seong-Jun

last: Kim

first: Christopher

last: Mason

first: Stacy

last: Horner

first: Aleem

last: Siddiqui


title: A Human Embryonic Stem Cell Reporter Line for Studying Cardiomyocyte Biology

city: New York

first: Shuibing

last: Chen

state: NY

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

summary: Human embryonic stem cells (hESCs) can be used to generate scalable numbers of cardiomyocytes for studying cardiac biology, disease modeling, drug screens, and potentially for regenerative therapies. Directed differentiation protocols for cardiomyocytes using hESCs are well established, but methods to isolate highly pure population of cardiomyocytes are limited. Reporter cell lines can be valuable for purification and visualization of cells for such applications. We used CRISPR/Cas9 in hESCs to place an mCherry reporter gene into the MYH6 locus, facilitating a simple method to purify cardiomyocytes. MYH6:mCherry positive cells express atrial and ventricular markers and display a range of cardiomyocyte action potential morphologies. At 20 days of differentiation, MYH6:mCherry+ cells show features characteristic of human cardiomyocytes and can be used successfully to monitor drug-induced cardiotoxicity and oleic acid-induced cardiomyocyte arrhythmia. The MYH6:mCherry hESC reporter line should serve as a useful tool for disease modeling and drug development relevant to cardiomyocyte biology.

overall_design: Total RNA was isolated using the Qiagen RNeasy mini kit according to manufacturer’s instructions. The quality of RNA samples was examined by Agilent bioanalyzer (Agilent). cDNA libraries were generated using TruSeq RNA Sample Preparation kits (Illumina). Each library was sequenced using single-end reads in HiSeq4000 (Illumina). Gene expression levels were analyzed with TopHat and Cufflinks by the Weill Cornell Genomic Core facility.

first: Todd

last: Evans

first: Su-Yi

last: Tsai


title: Sex Differences in the Late First Trimester Human Placenta Transcriptome

city: Charlottesville

first: Stephen

last: Turner

state: VA

address: 1670 Discovery Drive

institute: Signature Science, LLC

summary: This study is the first characterization of the first trimester placenta transcriptome, highlighting similarities and differences among the sexes in ongoing human pregnancies resulting in live births. Sexual dimorphism may contribute to pregnancy outcomes, including fetal growth and birth weight, which was seen in our cohort, with males significantly heavier than females at birth. This transcriptome provides a basis for development of early diagnostic tests of placental function that can indicate overall pregnancy heath, fetal-maternal health, and long term adult health.

overall_design: Examination of gene expression in Males vs. Females.

first: Tania

middle: L

last: Gonzalez

first: Tianyanxin

last: Sun

first: Alexander

middle: F

last: Koeppel

first: Bora

last: Lee

first: Erica

middle: T

last: Wang

first: Charles

last: Farber

last: Rich

first: Lauren

middle: W

last: Sundheimer

first: Rae

last: Buttle

first: Yii-Der

middle: I

first: Jerome

last: Rotter

first: John

last: Williams III

first: Mark

middle: O

last: Goodarzi

first: Margareta

last: Pisarska


title: Knockdown of Tis7 in mouse erythroblasts

city: Amsterdam

first: Kat

last: Moore

address: Plesmanlaan 125

country: Netherlands

institute: Sanquin Research

summary: DNA-binding factor Tis7 (Ifrd1) shows increased ribosome recruitment during eIF2 phosphorylation during proteotoxic stress in erythroblasts. Here, we examine the effect of Tis7 knockdown on RNA expression at different time points after tunicamycin exposure.

overall_design: Samples treated with control scrambled (Sc) shRNA or anti-Tis7 shRNA were exposed to tunicamycin and harvested at time points 0, 4, and 8 hr.

first: Nahuel

last: Paolini

first: Benoit

last: Nicolet

first: Eline

last: Pronk

first: Nurcan

last: Yagci

first: Ilja

last: Vietor

first: Marieke

last: von Lindern


title: Differential Gene Expression in Erlotinib-Treated Fibroblasts

city: Baltimore

first: Theresa

middle: K

last: Hodges

address: 801 W. Baltimore Street

department: Institute for Genome Sciences

institute: University of Maryland Baltimore

summary: Analysis of human, adult, dermal fibroblasts following treatment with 100nM or 1 uM of erlotinib, a tryrosine kinase inhibitor (TKI) that targets the epidermal growth factor receptor (EGFR) inhibiting EGFR activation and signaling. Erlotinib is widely used to effectively treat patients with advanced non-small cell lung cancer but treatment with erlotinib and other EGFR TKIs are associated with a painful skin rash. Results identified significantly differentially expressed genes in fibroblasts treated with erlotinib providing insight into how the drug alters the transcriptome in ways that may contribute to the TKI-related rash.

overall_design: Fibroblasts from a human cell line were treated for three days with either erlotinib (100nM or 1uM), 1uM of DMSO, or no treatment. The cells were harvested on the fourth day for total RNA extraction and hybridization on Affymetrix Human GeneChip 133 Plus 2.0 microarrays.

first: K

middle: E

last: Wickersham

first: T

first: M

last: Edelman

first: Y

last: Song

first: A

last: Shuldiner

first: C

middle: M

last: Fraser

first: S

last: G. Dorsey


title: PIMT/NcoA6IP deletion in the mouse heart causes delayed cardiomyopathy attributable to perturbation in energy metabolism

first: Matthew

middle: J.

last: Schipma

state: IL

address: 750 N. Lake Shore Drive

department: Biochemistry and Molecular Genetics

summary: Global gene expression analysis reveals that PIMT regulates many genes involved in energy metabolism, calcium signaling, and oxidative phosphorylation in myocardium.

overall_design: RNA samples were prepared from hearts of 5 control PIMT floxed mice (PIMTfl/fl) and 5 Cre-loxP-mediated cardiomyocyte-specific deletion of PIMT (csPIMT-/-) mice. RNA were pooled and subjected to RNA-seq analysis.

first: Yuzhi

last: Jia

first: Ning

last: Liu

first: Navin

last: Viswakarma

middle: J

first: Ruya

last: Sun

first: Bayar

last: Thimmapaya

first: Janardan

last: Reddy


title: Trancriptomic and epigenetic analyses of mouse organoids expressing BrafV600E mutation

first: hari

last: easwaran

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

overall_design: Refer to individual Series


title: A novel global cDNA amplification technology directly from an RNA template via reverse transcription

city: Wako

first: Itoshi

last: NIKAIDO

state: Saitama

address: 2-1 Hirosawa

department: Center for Biosystems Dynamics Research

institute: RIKEN

summary: We developed a method, Reverse Transcription with Random Displacement Amplification (RT-RamDA), to reverse transcribe and amplify cDNA directly from RNA templates using strand displacement and RNA-dependent DNA polymerase activity. This method resulted in a cDNA yield approximately 100-fold higher than conventional RT with high sensitivity, enabling gene expression profiling of low-expression genes with a small amount of RNA, such as that obtained at the single-cell level.

overall_design: 12 samples purified total RNA samples diluted to 10 pg were sequenced by using RT-RamDA and DNA SMART ChIP-Seq Kit. RT-RamDA was performed using different conditions of reverse transcription primer, oligo (dT), N6, not-so-random (NSR) primers which developed to reduce the synthesis of cDNAs derived from ribosomal RNAs with random priming (33), N6/oligo (dT) and NSR/oligo (dT). Moreover, 3 rRNA-depleted samples derived from 200 ng of total RNA were sequenced by using KAPA RNA HyperPrep Kit with RiboErase (Kapa Biosystems).

first: Tetsutaro

last: Hayashi

last: Nikaido


title: An atlas of genetic influences on osteoporosis in humans and mice

status: Public on Dec 31 2018

first: John

middle: A

last: Morris

state: New York

address: 101 Avenue of the Americas, 4th Floor

institute: New York Genome Center

summary: In our study, we leveraged RNA-seq data from four different human osteoblast cell lines and ATAC-seq data from one human osteoblast cell line to identify target genes for plausibly causal SNPs influencing bone density. We also re-called ENCODE generated osteoblast DNase hypersensitive sites, and have uploaded them here for sharing.

overall_design: RNA-seq in four human osteoblast cell lines and ATAC-seq in one human osteoblast cell line. DHS re-called from ENCODE primary osteoblast data. Dnase-seq data obtained from ENCODE under accessions ENCLB776DWN and ENCLB906BCL

first: Brent

last: Richards


title: microRNA-252 and FoxO regulate inflammaging through dual inhibition on Dawdle/Acticin of TGF-β pathway in Drosophila

city: Shanghai

first: Xiaofen

last: Wu

address: 345 Lingling Rd

department: Shanghai Institute of Organic Chemistry

institute: Chinese Academy of Sciences

summary:
Innate immunity is a highly reactive response aiming at clearing pathogens. Abnormal induction of innate immune genes can lead to deleterious consequences to the host. However, little is known about the intrinsic signaling pathway that prohibits constitutive activation of innate immunity. Here using fruit flies, we profile the microRNA targetomes in young and aged animals. We demonstrate FoxO, and miR-252 inhibit spontaneous induction of innate immunity by repressing Daw.
We further determine the signaling cascade by which Daw causes the reduction of Atg8a-mediated selective autophagy on kenny protein, which in turn activates Relish protein and consequential upregulation of innate immune genes. Finally, while aging leads to a decline in FOXO signaling activity concomitant with a progressive induction of innate immune genes, transgenic increase of FoxO, miR-252, and Atg8a in wild-type Drosophila promotes longevity and mitigates the expression of age-onset innate immune genes. Together, we propose that FoxO and miR-252 define a pro-survival mechanism by inhibiting constitutive innate immunity.

overall_design: Find new miRNA-mRNA aging regulator by performing 3d- and 30d-old adult fly RipSeq, explore their mechanism by comparing transcriptome differences between WT and mutant flies, analyze their changes with age using RNA-sequencing data performed at 3d, 15d, 30d and 45d age of WT flies.


title: Inhibition of the integrin alpha-V beta-3 reverts the paradoxical effect of levothyroxine replacement during bexarotene therapy in cutaneous T-cell lymphoma

first: Maria

middle: Victoria

last: Revuelta

address: 1300 York Avenue

department: Medicine

institute: Weill Cornell Medicine

summary: Bexarotene is a specific RXR agonist that has been used for the treatment of cutaneous T-cell lymphoma (CTCL). The mechanism of action is pleiotropic but impacts directly on CTCL cell proliferation, chemotaxis and apoptosis, and indirectly on lymphoma immunity. Bexarotene causes hypothyroidism in more than 90% of patients thus requiring the concomitant administration of levothyroxine. Hereon we investigated the consequence of levothyroxine administration to the antineoplastic effect of bexarotene in CTCL. We found that bexarotene induces transcriptional and biological changes in CTCL cells related to decreased cell proliferation and chemotaxis, as well as increased proliferation and interferon response. Although lack of levothyroxine supplementation during bexarotene treatment increased apoptosis and decreased cell proliferation of CTCL cells in vitro and in vivo, it also decreased the lymphoma immunity. Since levothyroxine activates both the ubiquitous TRA nuclear receptor and the more restricted integrin V3 membrane receptor that is overexpressed in CTCL cells, we investigated their role in bexarotene treatment. We demonstrated that genetic and pharmacologic inhibition of the integrin V3 receptors resulted in improved bexarotene-induced effects on apoptosis, cell proliferation and chemotaxis while maintaining the lymphoma immunity. Our results provide a mechanistic rationale for evaluating the addition of the integrin V3 inhibitor cilengitide to CTCL therapeutic regimens that are based on bexarotene and levothyroxine supplementation.

overall_design: RNA was isolated from HuT 78 cells transfected with siRNA for integrins (si-ITGAV/B3); TRA (si-TR) or non-target sequences (si-CT) followed by treatment with bexarotene in the presence of physiological concentrations of TH, for 6 hours using TRI-REAGENT

first: Florencia

last: Cayrol

first: Mercedes

last: Debernardi

middle: V

first: Alejandra

last: Paulazo

first: Jude

last: Phillip

first: Nahuel

last: Zamponi

first: Helena

last: Sterle

middle: C

last: Díaz Flaqué

first: Cynthia

last: Magro

first: Jia

last: Ruan

first: Leandro

last: Cerchietti

first: Graciela

last: Cremaschi


title: Antiviral and anti-inflammatory properties of novel anti-HIV candidate ABX464 promotes specifics RNA splicing while preserving cellular RNA integrity.

city: Montpellier

first: Laurent

last: MANCHON

address: 1919 Route de Mende

institute: CNRS

summary:
Purpose: To ensure that ABX464 acted specifically on HIV splicing and did not significantly or globally affect the splicing events of human genes, we used an assembly approach of HIV (YU2 strain) putative transcripts and human long non-coding sequences from paired-reads (2x75bp) captured on a NimbleGen SeqCap® EZ Developer Library (Roche/NimbleGen).
Methods: Cells were infected with 80 ng of p24/106 cells of the YU-2 strain for 4 to 6 hours and then rinsed with PBS before medium renewal, followed by high-throughput RNAseq from custom SeqCap EZ capture libraries. Each raw dataset of the samples contained between 5 and 30 million paired-end reads (75 bp), with an average of approximately 12 million raw reads per sample.
Results: The raw reads were then cleaned and assembled per library to generate contigs, giving an average of 930 contigs per sample for further analyses.
Conclusions: Our results show that high-throughput analyses coupled with bioinformatics-specific tools offers a comprehensive and more accurate view of mRNA splicing within a cell.

overall_design: We used buffy coats from HIV-negative individuals were obtained from the local blood donation center, then human peripheral blood mononuclear cells (PBMCs) were isolated by Ficoll (Histopaque, Sigma) gradient centrifugation. Cells were infected with 80 ng of p24/106 cells of the YU-2 strain for 4 to 6 hours and then rinsed with PBS before medium renewal.

last: Manchon

first: Jamal

last: Tazi


title: Genome-wide DNA methylation profiling of primary colorectal laterally spreading tumors identifies disease-specific epi-mutations on common pathways

first: Liangliang

last: Zhu

address: NO. 168, Changhai Road, Yangpu

institute: Changhai Hospital of Shanghai

type: Methylation profiling by genome tiling array

summary: Colorectal laterally spreading tumors (LSTs) are rare comparing to adenomas but are becoming more prevalent. Unlike many neoplasms in colons, LST grows to extremely large size, usually greater than 10mm in diameter while rarely invades deeply. Also, there is a low tendency for LSTs to become cancerous. The epigenetic landscape of LST has not been defined. In this study, we used a genome-wide methylation profiling technology, i.e. the Illumina Human Methylation 450K array, to query the main epigenetic difference between LST and para-cancerous samples. Our results suggest that LST displays significant decrease in DNA methylation, especially in some intergenic regions (IGR). By integration of public data for adenomas and colorectal cancers, we defined the commonality and specific epigenetic signatures for these three types of neoplasms in colon, in particular LST and adenomas which represent precancerous conditions. These three diseases shared little specific DNA methylation abnormalities. However, our pathway-level analysis revealed that certain pathways were common targets of epimutation. More interestingly, different diseases seem to employ distinct epigenetic insult to disturb these pathways. Between LST and adenoma, we found eight pathways were commonly targeted but the epi-mutation patterns were opposite between the two diseases. Comparison between precancerous conditions and invasive states revealed the key pathways governing the progression to malignancy, including CAMs and PI3K-Akt pathways.

overall_design: In this study, we used a genome-wide methylation profiling technology, i.e. the Illumina Human Methylation 450K array, to query the main epigenetic difference between LST and para-cancerous samples. The tissue samples were collected by endoscopic biopsy from lesions of LST patients (10 cases) and from matched normal samples (LST-P) as part of an IRB approved study (Changhai Hospital, affiliated with Second Military Medical University). Histologic grading and typing were reviewed by experienced pathologists.

first: Feihu

last: Yan

first: Zhen

last: Wang

first: Chengling

last: Bian

first: Ting

first: Enda

last: Yu

first: Jing

last: Li


title: Early onset preeclampsia (EOPE) in a model for early stage human placental trophoblast

city: Columbia

first: Toshihiko

last: Ezashi

state: MO

address: 240a CS Bond Life Sciences Center

department: Animal Sciences

institute: University of Missouri-Columbia

summary: Early onset preeclampsia (EOPE) affects about 0.4% of pregnancies and is characterized by impaired trophoblast (TB) invasion, resulting in a poorly perfused placenta. Here we have used an in vitro model for mimicking early trophoblast development to determine how early placental development differs between normal pregnancies and those affected by EOPE. Induced pluripotent stem cells (iPSC) were generated from umbilical cords of infants born to mothers who had EOPE and from controls. These iPSC were converted to TB, by exposing them to BMP4 and inhibitors of ACTIVIN A and FGF2 signaling (BAP treatment), under 5 % and 20 % O2, hypothesizing that 20% O2 would act as a stressor. Two embryonic stem cell lines (ESC; H1 and H9), 8 control (CTL) iPSC and 14 EOPE iPSC were tested to assess how well the differentiated TB cells invaded through a Matrigel-coated membrane.

overall_design: To identify gene expression changes that might be driving the invasion defect in EOPE-TB at 20% O2, RNA was collected from CTL-TB (n = 10) and EOPE-TB (n = 14) cultured in both O2 conditions for sequencing.

first: Megan

last: Sheridan

first: Ying

last: Yang

first: R

last: Roberts


title: H3K14me3 Genomic Distributions and its regulation by KDM4 family demethylases

first: Fei

last: Lan

address: 130 Dong An Road

institute: Fudan university

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Jagged1/Notch2 controls kidney fibrosis via Tfam-mediated metabolic reprogramming

city: Bukgu

first: Jihwan

last: Park

state: Gwangju

address: 123 Cheomdangwagi-ro

country: South Korea

institute: GWANGJU INSTITUTE OF SCIENCE /TECHNOLOGY

summary: While Notch signaling has been proposed to play a key role in fibrosis, the direct molecular pathways targeted by Notch signaling and the precise ligand and receptor pair that are responsible for kidney disease remain poorly defined. In this study, we found that JAG1 and NOTCH2 showed the strongest correlation with the degree of interstitial fibrosis in a genome wide expression analysis of a large cohort of human kidney samples. Transcript analysis of mouse kidney disease models, including folic-acid-induced nephropathy, unilateral ureteral obstruction, or APOL1-associated kidney disease, indicated that Jag1 and Notch2 levels were higher in all analyzed kidney fibrosis models. Mice with tubule-specific deletion of Jag1 or Notch2 (Kspcre/Jag1flox/flox and Kspcre/Notch2flox/flox) had no kidney-specific alterations at baseline, but showed protection from folic acid induced kidney fibrosis. Tubule-specific genetic deletion of Notch1 and global knock-out of Notch3 had no effect on fibrosis. In vitro chromatin immunoprecipitation experiments and genome-wide expression studies identified the mitochondrial transcription factor A (Tfam) as a direct Notch target. Re-expression of Tfam in tubule cells prevented Notch-induced metabolic and profibrotic reprogramming. Kidney tubule specific deletion of Tfam resulted in fibrosis. In summary, Jag1/Notch2 plays a key role in kidney fibrosis development by regulating Tfam expression and metabolic reprogramming.

overall_design: Tubule epithelial cells from TGFbeta treated wild type mice

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