title: Gene expression profiles in organoids derived from biliary tract carcinomas [MAA-17164_3]

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

summary: In the present study, we established organoids using cancer and non-cancer tissues obtained from patients with biliary tract carcinomas and investigated compehensive gene expression profiles.

overall_design: Organoids derived from biliary tract carcinomas and organoids derived from non-cancer tissues were established and total RNAs were extracted to acquire gene expression profiles.

first: Yoshimasa

last: Saito


title: microRNA expression profiles in organoids derived from biliary tract carcinomas [MAA-17164_2]

status: Public on Mar 15 2019

country: Japan

summary: In the present study, we established organoids using cancer and non-cancer tissues obtained from patients with biliary tract carcinomas and investigated compehensive microRNA expression profiles.

overall_design: Organoids derived from biliary tract carcinomas and organoids derived from non-cancer tissues were established and total RNAs were extracted to acquire microRNA expression profiles.


title: Recruitment of BRCA1 limits MYCN-driven accumulation of stalled RNA Polymerase in neuroblastoma

status: Public on Mar 21 2019

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

country: Germany

institute: University of Wuerzburg

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Deregulation of the MYCN gene drives the development of neuronal and neuroendocrine tumors and is often associated with a particularly poor prognosis. Here we show that activation of MYCN in human neuroblastoma cells induces promoter escape of RNAPII. If pause release of RNAPII fails, MYCN recruits the BRCA1 protein to promoter-proximal regions. Recruitment of BRCA1 prevents MYCN-dependent accumulation of stalled RNAPII and enhances transcriptional activation by MYCN. Mechanistically, BRCA1 stabilizes mRNA de-capping complexes and enables MYCN to suppress R-loop formation in promoter-proximal regions. Recruitment of BRCA1 is mediated by the ubiquitin-specific protease, USP11, which binds specifically to MYCN that is de-phosphorylated at Thr58. Thr58 phosphorylation promotes proteasomal turnover of MYCN, hence BRCA1 stabilizes chromatin association of MYCN. Since BRCA1 is highly expressed in neuronal progenitor cells during early development and since MYC is less efficient than MYCN in recruiting BRCA1, our findings argue that a cell lineage-specific stress response enables MYCN-driven tumors to cope with deregulated RNAPII function.

overall_design: ChIP-seq for RNAPII, BRCA1, NMYC and DCP1A and corresponding changes in gene expression were measured by mRNA-seq in SH-EP cells harbouring a NMYC-ER chimeric protein that can be activated by 4-hydroxytamoxifen (4-OHT). To identify genes that are critical for growh of these cells we performed an shRNA screen using a pGIPZ-based shRNA library. Nascent RNA was measured with GRO-seq in the same cell line.

first: Steffi

last: Herold

first: Jacqueline

last: Kalb

first: Gabriele

last: Buechel

first: Carsten

last: Ade

first: Apoorva

last: Baluapuri

first: Jiajia

last: Xu

first: Jan

last: Koster

first: Daniel

last: Solvie

first: Anne

last: Carstensen

first: Christina

last: Klotz

first: Sabrina

last: Rodewald

last: Schuelein-Voelk

first: Matthias

last: Dobbelstein

first: Elmar

last: Wolf

last: Molenaar

first: Rogier

last: Versteeg

first: Susanne

last: Walz


title: RNA-Seq of head tissue from Drosophila melanogaster Wild Type and Adar5G1 mutant

city: Stanford

first: Jin Billy

last: Li

state: California

address: 300 Pasteur Drive. Alway M303

department: Genetics

country: USA

institute: Stanford University

summary: We profiled gene expression in flies with and without A-to-I RNA editing (AdarEA mutant Drosophila melanogaster with a Canton-S background).

overall_design: mRNA profiles of heads of 3 day old male Adar5G1 mutant and wild type (w1118) flies

first: Patricia

last: Deng

first: Dionna

last: Jacobson

first: Anzer

last: Khan

first: Nagraj

last: Sambrani

first: Galit

last: Shohat-Ophir

first: Mary

middle: A

last: O'Connell

first: Liam

middle: P

last: Keegan

first: Jin

middle: B


title: Identifying urinary RNA from prospective urine as non-invasive biomarkers for kidney transplant patients

status: Public on Mar 16 2019

city: Ann Arbor

first: Markus

last: Bitzer

state: MI

address: 1500 E Medical Center Dr SPC 5361

institute: University of Michigan

type: Non-coding RNA profiling by high throughput sequencing

summary: To identify urinary RNA from prospective urine as non-invasive biomarkers for kidney transplant patients

overall_design: Urine samples from patients with nephrotic syndrome due to different types of glomerular diseases and stages of kidney disease.

first: Thomas

last: Tuschl

first: Jian

last: Shi

first: Klaas

last: Max


title: Expression data from the heart of sham and CKD mice

city: Chongqing

first: Yinghui

last: Huang

address: Shapingba

country: China

institute: Army medical university

summary:
High incidence of heart failure (HF) is a typical characteristic of chronic kidney disease (CKD). However, the pathogenesis of CKD-associated HF remains elusive. Here, we investigated the changes in myocardial energy metabolism in CKD mice and explored the underlying mechanisms.
To examine genome wide transcriptional changes in the heart of CKD mice, we performed microarray analysis using the Affymetrix Clariom S mouse.

overall_design: To obtain the differentially expressed genes of the heart between sham and CKD mice. Mice were inflicted with 2/3 electrocoagulation of the right renal cortex and received left total nephrectomy 2 weeks later to construct CKD model. Mice underwent laparotomy without kidney operation served as sham group. Total RNA was extracted from the heart and reversely transcripted. Then, cDNA was hybridized using the Affymetrix Clariom S Mouse microarrays in duplicate.

first: Jinghong

last: Zhao


title: Identifying urinary RNA from biopsy associated urine as non-invasive biomarkers for kidney transplant patients

summary: To identify urinary RNA from biopsy associated urine as non-invasive biomarkers for kidney transplant patients


title: microRNA and geneexpression profiles in organoids derived from biliary tract carcinomas

first: Satoshi

last: Kondo

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

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

overall_design: Refer to individual Series


title: Effect of knockdown of S100A4 on gene expression in A549 cells

city: Lexington

first: Min

last: Chen

state: KY

address: 741 South Limestone

department: Toxicology and Cancer Biology

institute: University of Kentucky

summary: S100A4 is a tumor metastasis-promoting protein and drives lung cancer cell invasion and its elevation level is associated with lymphovascular invasion and the decreased overall survival among lung cancer patients. However, how it alters cancer cell metabolism and how metabolic changes affect the invasive and metastatc capacity are unknown.

overall_design: We used microarray to identify the critical molecules downstream of S100A4 signaling that alters mitochondrial metabolism and promotes lung cancer cell invasion and metastasis.

first: Kathleen

middle: L

last: O'Connor


title: microRNA expression profiles in organoids derived from biliary tract carcinomas [MAA-17164_1]

first: Yoshimasa

last: Saito


title: Optimization of Ribosome Profiling Using Brain Tissue from Fragile X Mice

city: Worcester

first: Botao

last: Liu

state: Massachusetts

address: 373 Plantation Street

department: Program in Molecular Medicine

institute: University of Massachusetts Medical School

summary: Dysregulated protein synthesis is a major underlying cause of many neurodevelopmental diseases such as Fragile X Syndrome. A very robust technique is required to capture subtle but biologically significant differences in neurological disorders. Ribosome profiling, which is based on deep sequencing of mRNA fragments protected from ribonuclease digestion by ribosomes, is a powerful tool to study translational control. However, it has been mainly applied to rapidly dividing cells where translation is robust and where large amounts of starting material are readily available. The application of ribosome profiling to low-input brain tissue where translation is modest and where gene expression changes between genotypes are expected to be small has not been carefully evaluated. Using hippocampal tissue from wide type and fragile X mental retardation 1 (Fmr1) knockout mice, we show that variable RNase digestion can lead to significant sample batch effects. We also establish GC content and ribosome footprint length as quality control metrics for ribonuclease digestion. We performed ribonuclease titration experiments for low-input samples to identify optimal conditions for this critical step that is often improperly conducted. Our data reveal that optimal RNase digestion is essential to ensure high quality and reproducibility of ribosome profiling especially for low-input brain tissue.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Ribosome profiling libraries of wild type mouse hippocampus were generated with different concentrations of ribonucleases and sequenced with Illumina Nextseq500. 5 experimental and 51 QC samples.

first: Gemma

last: Molinaro

first: Huan

last: Shu

first: Emily

middle: E

last: Stackpole

first: Kimberly

middle: M

last: Huber

first: Joel

middle: D

last: Richter


title: Microarray expression profile of long non-coding RNAs and mRNAs associated with Extrahepatic Cholangiocarcinoma genesis and progression

city: Harbin

first: Fu Min

last: Zhang

state: Heilongjiang Province

address: Xuefu road no. 246 in nangang district

department: Department of Hepatopancreatobiliary Surgery

institute: Second Affiliated Hospital of Harbin Medical University

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

summary: The molecular mechanism of ECC in the genesis and progression is still unclear. Long non-coding RNAs (lncRNAs) have been shown to play critical regulatory roles in cancer biology. In order to understand lncRNAs expression patterns and their potential functional in ECC, we performed a transcriptome analysis of lncRNA and mRNA expression in ECC and paired adjacent noncancerous tissues using Agilent Human lncRNA +mRNA array V4.0 (4 × 180 K).

overall_design: Three pairs of ECC tissues and adjacent noncancerous tissues(frozen in liquid nitrogen) were used for microarray.The differential expression of lncRNAs and mRNAs will be detected in T vs.N tissues.Three biology replicates per array. We anticipate that these findings will lay the foundation for future experimental studies of candidate lncRNAs and identify their functional roles further in ECC.

first: Fumin

first: Yunfu

last: Cui


title: DNMT1 in Six2 progenitor cells is essential for transposable element silencing and kidney development

city: Bukgu

first: Jihwan

last: Park

state: Gwangju

address: 123 Cheomdangwagi-ro

country: South Korea

institute: GWANGJU INSTITUTE OF SCIENCE /TECHNOLOGY

type: Methylation profiling by high throughput sequencing

summary: Cytosine methylation (5mC) plays a key role in maintaining progenitor cell self-renewal and differentiation. Here, we analyzed the role of 5mC in kidney development by genome-wide methylation and expression profiling and by systematic genetic targeting of DNA methyltransferases (Dnmt) and Tet eleven hydroxylases (Tet). In mice, nephrons differentiate from Six2+ progenitor cells, therefore we created animals with genetic deletion of Dnmt 1, 3a, 3b, Tet1, or Tet2 in the Six2+ population (Six2Cre/Dnmt1flox/flox, Six2Cre/Dnmt3aflox/flox, Six2Cre/Dnmt3bflox/flox, Six2Cre/Tet2flox/flox or Tet1-/-). Genome-wide methylation analysis indicated marked loss of methylation of transposable elements in Dnmt1 knock-out mice. RNA sequencing detected dedifferention of progenitor cells andtranscription of  endogenous retroviral genes transcripts.

overall_design: RRBS for P0 Dnmt1 f/f, P0 Six2Cre Dnmt1 f/f and adult wild type mice. mRNA sequencing for P0 Dnmt1 f/f and Six2Cre Dnmt1 f/f

first: Szu-Yuan

last: Li

first: Kiwung

last: Chung

first: Rojesh

last: Shrestha

first: Matthew

last: Palmer

first: Suszták

last: Katalin


title: Towards Precision Medicine for Stress Disorders:   Diagnostic Biomarkers and Targeted Drugs ( Molecular Psychiatry, under review)

city: Indianapolis

first: Dr. Alexander

middle: B.

last: Niculescu

state: IN

address: 320 W. 15th Street

department: Psychiatry

institute: Indiana University Medical School

summary: The biological fingerprint of environmental adversity may be key to understanding health and disease, as it encompasses the damage induced as well as the compensatory reactions of the organism. Metabolic and hormonal changes may be an informative but incomplete window into the underlying biology. We endeavored to identify objective blood gene expression biomarkers for psychological stress, a subjective sensation with biological roots. To quantify the stress perception at a particular moment in time, we used a simple visual analogue scale for life stress in psychiatric patients, a high risk group. Then, using a stepwise discovery, prioritization, validation, and testing in independent cohorts design, we were successful in identifying gene expression biomarkers that were predictive of high stress states, and of future psychiatric hospitalizations related to stress, more so when personalized by gender and diagnosis.

overall_design:
First, we used a powerful longitudinal within-subject design in individuals with psychiatric disorders to discover blood gene expression changes between self-reported low stress and high stress states. Second, we prioritized the list of candidate biomarkers with a Convergent Functional Genomics approach, comprehensively integrating previous published human and animal model evidence in the field, and directly citing it. Third, we validated our top biomarkers from discovery and prioritization in an independent cohort of psychiatric subjects with high scores on a clinical stress rating scale. Fourth, we tested if the candidate biomarkers from the first three steps are able to predict high stress state, and future psychiatric hospitalizations with stress, in another independent cohort of psychiatric subjects. We tested the biomarkers in all subjects in the independent test cohort, as well as in a more personalized fashion by gender and psychiatric diagnosis, showing increased accuracy with the personalized approach.
A. Independent Discovery Cohort (n=36) (91 visits)
B. Independent Validation Cohort with Clinically Severe Stress(n=48) (75 visits)

first: Alexander

first: Helen

last: Le-Niculescu


title: Characterization and Correlation of Tissue-Specific Profiles of Transcriptome Activity

city: Toulouse

first: Yannick

last: Lippi

address: 180 chemin de tournefeuille

department: GeT-TRiX facility

country: France

institute: INRAE

summary: While kinome analysis has proven valuable in unravelling complex biology and identifying therapeutic targets and biomarkers, considerably less is known about the extent to which kinome data can contribute to a systems biology perspective through integration with data from other omic approaches. To investigate, kinome and transcriptome analyses were performed on four tissues of distinct biological function: liver, spleen, jejunum, and jejunal Peyer’s patches. The objective was to identify tissue-specif expression profiles and correlations between kinome and transcriptome data.

overall_design: Six 10 weeks old pigs were sacrificed after ad libitum standard feeding. 4 organs samples were collected (Spleen, Jejunum, Liver, Jejunal Peyer's Patches) from each of 6 pigs, for a total of 24 samples.

first: Philippe

last: Pinton

first: Pascal

last: Gourbeyre

first: Isabelle

last: Oswald

first: Scott

last: Napper


title: Notch receptor expression in Trypanosoma cruzi infected Human Umbilical Vein Endothelial Cells treated with benznidazole or aspirin as revealed by microarray analysis

status: Public on Mar 14 2019

city: Santiago

first: Christian

last: Castillo

state: Metropolitana

address: Independencia 1027

department: Faculty of medicine

country: Chile

institute: Universidad de Chile

summary: Chagas disease is a parasitic infection originally endemic to latinamerican countries but now spreaded worldwide that can  be transmitted congenitally.  Current specific therapy involves benznidazole, however, other therapies may modify gene expression that can change genetic expression profile, allowing cell programming to provide a more unfavorable environment for intracellular parasite development.  Herein, microarray analysis was performed to Human Umbilical Vein Endothelial Cells (HUVEC), treated with benznidazole and the anti-inflammatory drugs aspirin or simvastatin, and infected with T. cruzi, the causative agent of Chagas disease.

overall_design: Human umbilical vein endothelial cells incubated for 24 hrs with Benznidazole (Bz) 20 µM, simvastatin (Simv) 5 µM, Aspirin (Asa) 125 uM, or Bz 10µM/Simv 1. After that, cells were challenged with Tryoanosoma cruzi trypomastigotes in cell:parasite ratio of 1:10. Total RNA was extarcted and microaray analysis was performed against SurePrint G3 Human GE 8x60K chips. Cells without parasites or pharmacological treatment were used as uninfected control.

first: Campos-Estrada

last: Carolina

first: Gonzalez-Herrera

last: Fabiola

first: Greif

last: Gonzalo

first: Guzmán-Rivera

last: Daniela

first: Carrillo

last: Ileana

first: Liempi

last: Ana

first: Robello

last: Carlos

first: Kemmerling

last: Ulrike

first: Castillo

last: Christian

first: Maya

last: Juan Diego


title: Gene expression profiling in brain of sleep-deprived and fear conditioned zebrafish groups

city: Incheon

first: Yunkyoung

last: Lee

address: Inha-ro 100

institute: Inha University

summary:
Sleep is an evolutionarily conserved physiological process implicated in the consolidation of learning and memory. In our study, sleep deprivation-induced cognitive deficits in zebrafish are mediated through reduction in glucose metabolism to the hexosamine biosynthetic pathway.
Therefore, we perform the microarray to confirm glucose metabolic pathway- and nerve system-related genes expression using mRNA from brains of control, sleep-deprived and fear-conditioned zebrafish groups.

overall_design: Naïve fish were maintained under a 14:10 light-dark cycle (light off at 22:00, light on at 8:00). For generating the SD model, zebrafish were exposed to extended light (24:0) for 3 days. We performed inhibitory avoidance learning for fear conditioning.

first: Inn-Oc

last: Han


title: Stabilization of the Max homodimer with a small molecule attenuates Myc-driven transcription

city: Houston

first: Charles

middle: Yang

last: Lin

state: TX

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

summary: The transcription factor Max is a basic helix-loop-helix leucine zipper (bHLHLZ) protein that forms homodimers or interacts with other bHLHLZ proteins, including Myc and Mxd proteins. Among this dynamic network of interactions, the Myc/Max heterodimer has crucial roles in regulating normal cellular processes, but its transcriptional activity is deregulated in a majority of human cancers. Despite this significance, the arsenal of high-quality chemical probes to interrogate these proteins remains limited. We utilized small molecule microarrays (SMMs) to identify compounds that bind Max in a mechanistically unbiased manner. We discovered the asymmetric polycyclic lactam, KI-MS2-008, which stabilizes the Max homodimer while reducing Myc protein and Myc-regulated transcript levels. KI-MS2-008 also decreases viable cancer cell growth in a Myc-dependent manner and suppresses tumor growth in vivo. This approach demonstrates the feasibility of modulating Max with small molecules and supports altering Max dimerization as an alternative approach to targeting Myc.

overall_design: ChIP-seq in P493-6 cells treated with KI-MS2-008

middle: Y

first: Nicholas

last: Struntz

first: Andrew

last: Chen

first: Angela

middle: N

last: Koehler


title: Glial cells maintain synapses by inhibiting an activity-dependent retrograde protease signal

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

summary:
We utilized genetic methods to examine how Schwann cells prevent degeneration of motor neurons (MNs) in the spinal cord.
Blocking peripheral, neuromuscular activity completely rescued MNs and neuromuscular junctions (NMJs) in erbB3 mutant mice lacking Schwann cells, which normally exhibit profound neurodegeneration.
We searched for the molecular basis of this effect by examining the transcriptomes (all of the expressed genes) in the muscle of control mice with Schwann cells and erbB3 mutant mice without them.
We found evidence that a negative signal expressed by muscle was regulated by neural activity and normally blocked by factors produced in Schwann cells.  When we eliminated this activity-induced negative signal (thrombin) from muscle, MNs and NMJs were protected in erbB3 mutants, similar to the effects of eliminating activity.  Together, these results suggest that Schwann cells prevent neurodegeneration by inhibiting the effect of activity-induced, muscle-derived negative factors, rather than by providing trophic positive factors.

overall_design: 2 biological replicates of erbB3 WT, 2 biological replicates of erbB3 KO, and 2 biological replicates of Wnt1-Cre, Ribotag.

first: Thomas

middle: W

last: Gould

first: Bertha

last: Dominguez

first: Fred

last: de Winter

first: Patrick

last: Liu

first: Balaji

last: Sundararaman

last: Stark

first: Anthony

last: Vu

first: Jay

last: Degen

first: Weichun

last: Line

first: Kuo-Fen


title: Whole blood RNAseq following live attenuated influenza vaccine in Gambian children

city: Fajara

first: Karim

last: MANE

address: Atlantic Boulevard

department: Statistics and Bioinformatics

country: Gambia

institute: MRCG @ LSHTM

summary: The goal of this study was to identify differentially expressed genes between pre-vaccination and day 2 post-vaccination with LAIV in children aged 2 - 4 years old who seroconvert to LAIV. Seroconversion was defined as a 4-fold rise in haemagglutination inhibition titre between baseline and day 21 following vaccination.

overall_design: Open label cohort study

first: Thushan

last: de Silva

last: Mane


title: A critical regulator of Bcl2 revealed by systematic transcript discovery of lncRNAs associated with T-cell differentiation

city: Marseille

first: Yasmina

last: Kermezli

address: Luminy

institute: AIX Marseille university

summary:
Normal T-cell differentiation requires a complex regulatory network which supports a series of maturation steps, including lineage commitment, T-cell receptor (TCR) gene rearrangement, and thymic positive and negative selection. However, the underlying molecular mechanisms are difficult to assess due to limited T-cell models.
Here we explore the use of the pro-T-cell line P5424 to study early T-cell differentiation. Stimulation of P5424 cells by the calcium ionophore ionomycin together with PMA resulted in gene regulation of T-cell differentiation and activation markers, partially mimicking the CD4-CD8- double negative (DN) to double positive (DP) transition and some aspects of subsequent T-cell maturation and activation.
Global analysis of gene expression, along with kinetic experiments, revealed a significant association between the dynamic expression of coding genes and neighbor lncRNAs including many newly-discovered transcripts, thus suggesting potential co-regulation. CRISPR/Cas9-mediated genetic deletion of Robnr, an inducible lncRNA located downstream of the antiapoptotic gene Bcl2, demonstrated a critical role of the Robnr locus in the induction of Bcl2. Thus, the pro-T-cell line P5424 is a powerful model system to characterize regulatory networks involved in early T-cell differentiation and maturation.

overall_design: RNA-Seq and ChIp-Seq of P5424 cell lines before and after PMA-Ionomycin stimulation.

first: Wiam

last: Saadi

first: Lan

last: Dao

first: Evelyne

last: Mathieu

first: David

last: Santiago-Algarra

first: Magali

last: Torres

first: Mohamed

last: Belhocine

first: Lydie

last: Pradel

first: Beatrice

last: Loriod

first: Mourad

last: Aribi

first: Denis

last: Puthier

first: Salvatore

last: Spicuglia


title: Glucocorticoids Promote Breast Cancer Metastasis

city: Basel

last: Bentires-Alj

address: Hebelstrasse 20

department: DBM

country: Switzerland

institute: University Hospital Basel

summary: Next Generation Sequencing was applied to investigate the heterogeneity between tumors and distant metastases in different models of Breast Cancer cell lines and primary-derived xenografts. Global transcriptional profiling of the primary tumor and matched distant metastases (lung, liver, spleen) as well as circulating tumor cells (CTCs) allowed to identify glucocorticoid signalling as a mediator of metastasis.

overall_design: RNA-Seq in 4 different Breast Cancer models to investigate glucorticoid signalling role in metastasis

first: Atul

last: Sethi


title: Transcriptomic analysis of agr-deficient Staphylococcus aureus

city: Tampa

first: Lindsey

last: Shaw

state: FL

address: 4202 E Fowler Avenue

department: CMMB

institute: University of South Florida

summary: S. aureus response to agr operon and a SAUSA300_1984 deletion.

overall_design: S. aureus RNA was extracted to compare global gene expression of three samples: SAUSA300 LAC MRSA wild type, agr operon null, SAUSA300_1984 null. Each sample was generated by pooling three independent biological replicate RNA preps.

first: Brooke

middle: R

last: Tomlinson


title: NRDE2 negatively regulates nuclear exosome functions I

city: Shanghai

first: Hong

last: Cheng

address: 320 YueYang Road

department: Shanghai Institute of Biochemistry and Cell Biology

institute: Shanghai Institutes for Biological Sciences

summary: To examine whether NRDE2 can impact the competition between hMTR4 and ALYREF, we performed stranded RNA-seq to detect total RNAs isolated from NRDE2 and control knockdown cells.

overall_design: rRNA-depleted RNAs isolated from control, NRDE2 knockdown HeLa cells were generated by deep sequencing, using Illumina HiSeq X Ten.

first: Xudong

last: Wu

first: Guifen


title: Unscheduled HDAC4 repressive activity in human fibroblasts triggers TP53-dependent senescence and favours cell transformation

city: udine

first: raffaella

last: picco

address: piazzale kolbe 4

department: department of medical and biological sciences

country: Italy

institute: university of Udine

summary: In this study we investigated changes in gene expression induced by HDAC4 and RAS in BJ/hTERT LT/ST cells, 48h after the seeding. The goal of the experiment is: a) to find a common signature of transformation between RAS and HDAC4 over-expressing cells; b) to find the peculiarities of the two oncogenic responses.

overall_design: Gene expression profiles of BJ/hTERT LT/ST HDAC4/TM and RAS cells are compared to the profiles of HYGRO cells. For each sample two replicates have been done. Cells were infected with the respective retrovirus (pWZL-HYGRO, HDAC4/TM AND HRAS G12V), selected and check for protein expression. 14 days after the infection, two independent cultures of each polyclonal population were harvested and seeded for RNA extraction. RNA was collected 48h after the seeding from 1*10^6 cells.

first: Harikrishnareddy

last: Paluvai

first: Eros

last: Di Giorgio

first: Claudio

last: Brancolini


title: NRDE2 negatively regulates nuclear exosome functions

summary: The exosome functions in the degradation of diverse RNA species, yet how it is negatively regulated remains largely unknown. Here, we show that NRDE2 forms a 1:1 complex with MTR4, a nuclear exosome cofactor critical for exosome recruitment, via a conserved MTR4-interacting domain (MID). Unexpectedly, NRDE2 mainly localizes in nuclear speckles, where it inhibits MTR4 recruitment and RNA degradation, and thereby ensures efficient mRNA nuclear export. Structural and biochemical data revealed that NRDE2 interacts with MTR4's key residues, locks MTR4 in a closed conformation, and inhibits MTR4 interaction with the exosome as well as proteins important for MTR4 recruitment, such as the cap-binding complex (CBC) and ZFC3H1. Functionally, MID deletion results in the loss of self-renewal of mouse embryonic stem cells. Together, our data pinpoint NRDE2 as a nuclear exosome negative regulator that ensures mRNA stability and nuclear export.

overall_design: Refer to individual Series


title: Environmentally-induced epigenetic conversion of a piRNA cluster

city: Paris

first: Antoine

last: Boivin

address: 9 Quai St Bernard

department: Institut Biologie Paris-Seine

institute: Sorbonne Universite

summary: Transposable element (TE) activity is repressed in animal gonads by PIWI-interacting RNAs (piRNAs) produced by piRNA clusters. Current models propose that piRNA clusters are functionally defined by the maternal inheritance of piRNAs produced during the previous generation. Taking advantage of an inactive cluster of P-element derived transgene insertions in Drosophila melanogaster, we show here that raising flies at high temperature (29°C) instead of 25°C results in stable conversion of this locus into an active piRNAs producing one reporting thus the first case of the establishment of an active piRNA cluster by environmental changes and without maternal inheritance of homologous piRNAs.

overall_design:
Small RNAs were prepared from ovaries of Drosophila females and high-throughput sequenced using Illumina Hi-seq 2500 by Fasteris. 9 samples were processed

All genotypes contain seven repeats of /P(lacW) /inserted in tandem on the second chromosome. This cluster, called BX2, can be in different epigenetic states, i.e. producing or not small RNAs called piRNAs.

BX2theta and BX2* genotype piRNAs but not BX2OFF.
P(TARGET) is a P(lacZ) transgene inserted in the second chromosome but at another place and used as a readout of the epigenetic state of BX2: if BX2 is ON, P(TARGET) is repressed, if BX2 is OFF, P(TARGET) is expressed.

first: Karine

last: Casier


title: NRDE2 negatively regulates nuclear exosome functions IV

summary: To examine whether NRDE2 can impact the competition between hMTR4 and ALYREF, we performed stranded RNA-seq to detect RNAs isolated from MTR4 IP in NRDE2 and control knockdown cells.

overall_design: RNAs isolated from MTR4 IP in control and NRDE2 knockdown HeLa cells were generated by deep sequencing, using Illumina HiSeq X Ten.


title: NRDE2 negatively regulates nuclear exosome functions II

summary: To examine whether NRDE2 can impact the competition between hMTR4 and ALYREF, we performed stranded RNA-seq to detect nuclear RNAs isolated from NRDE2 and control knockdown cells.

overall_design: rRNA-depleted nuclear RNAs isolated from control, NRDE2 knockdown HeLa cells were generated by deep sequencing, using Illumina HiSeq X Ten.


title: Next Generation RNA sequencing of 30 human liver tissues at different developmental stages (10 each of Fetal, Pediatric and Adult)

first: Yunlong

last: Liu

address: 410 west 10th street

institute: Indiana University

summary: miRNAs have emerged as key regulators of gene expression. Here we sequenced mRNA from 30 human liver samples to identify genetic polymorphisms in predicted miRNA binding regions that show allele-specific gene expression. These genetic variants will be functionally tested for miRNA-mediated regulation.

overall_design: Standard methods were used for RNA-sequencing library construction, EXBead preparation, and Next-Generation sequencing, based on the protocol provided for the Life Technologies SOLiD4 system. Briefly, 2μg of total RNA per sample of 30 human liver samples (fetal, pediatric, and adult; n=10) were used for library preparation. The rRNA was depleted using RiboMinus Eukaryote Kit for RNA-Seq.

first: Todd

middle: C

last: Skaar


title: NAD+ metabolism governs proinflammatory senescence secretome

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: Cellular senescence is a stable cell growth arrest that is implicated in tissue aging and cancer. Senescent cells are characterized by an upregulation of proinflammatory and immunosuppressive cytokines and chemokines, which is termed as senescence-associated secretory phenotype (SASP).  NAD+ metabolism plays a critical role in both tissue aging and cancer.  However, the role of NAD+ metabolism in regulating the SASP is not well understood.  Here we show that nicotinamide phosphoribosyltransferase (NAMPT), the rate-limiting enzyme of the NAD+ salvage pathway, governs the strengths of proinflammatory SASP during senescence.  In contrast to downregulation of NAMPT during replicative senescence, NAMPT is upregulated during oncogene-induced senescence.  NAMPT selectively regulates proinflammatory, but not immunosuppressive, SASP.  NAMPT is regulated by HMGA1 through a distal enhancer element during senescence.  HMGA1/NAMPT/NAD+ signaling axis promotes proinflammatory SASP through enhancing glycolysis and mitochondria respiration.  Mechanistically, HMGA1/NAMPT promotes proinflammatory SASP through NAD+-mediated suppression of AMPK kinase, which suppresses p53-mediated inhibition of p38MAPK to enhance NFb activity.  SASP regulation by NAD+ metabolism is independent of senescence-associated cell growth arrest.  An increase in NAD+ levels is sufficient to convert SASP from low to high levels during replicative senescence. Together, we conclude that NAD+ metabolism governs the strengths of proinflammatory SASP.  Given the tumor promoting effects of proinflammatory SASP, our results suggest that anti-ageing dietary NAD+ augmentation should be administered with precision.

overall_design: HMGA1 CHIP-seq done in RAS-induced senescent (RAS) and growing control vector cells (vector)

first: Rugang

last: Zhang

first: Timothy

last: Nacarelli


title: p63 regulated epithelial-to-mesenchymal transition state heterogeneity drives collective invasion.

status: Public on Mar 13 2019

city: Washington

first: Gray

middle: Waite

last: Pearson

state: DC

address: 3970 Reservoir Rd NW

department: Department of Oncology

institute: Georgetown University

summary: Analysis of P63-regulated genes at gene expression level. The hypothesis tested in the present study was that P63 regulates specific epithelial-to-mesenchymal transition states in breast cancer cells.

overall_design: Total RNA obtained from SUM159 trailblazer cells stably expressing ΔNP63α-V5 or control empty vectors in the presence or absence of doxycycline for 5 days.

first: Jill

last: Westcott

first: Molly

last: Huysman

first: Tuyen

middle: T

last: Dang

first: Noah

last: Sorelle

first: Rolf

last: Brekken


title: Small RNA-mediated genomic silencing promotes telomere stability in the absence of telomerase

city: Chapel Hill

first: Shawn

last: Ahmed

state: North Carolina

address: 216 Fordham Hall, 133 Medical Drive

institute: UNC Genetics Department

summary: Telomerase deficiency and progressive telomere erosion in human somatic cells results in senescence. Small RNAs that target telomeres have been observed in diverse organisms but their functions are not well characterized. We define an endogenous small RNA pathway in Caenorhabditis elegans that promotes heterochromatin formation at telomeres via Dicer, the perinuclear Argonaute protein WAGO-1 and the nuclear Argonaute protein HRDE-1. Loss of telomerase induces biogenesis of siRNAs that target the telomeric lncRNA TERRA, whereas loss of both telomerase and small RNA-mediated telomeric silencing induces TERRA expression, DNA damage, and an accelerated sterility phenotype. The latter phenotypes can be rescued by exogenous telomeric siRNAs or by loss of the DNA damage response protein EXO-1.  Thus, endogenous siRNAs interact with TERRA to promote heterochromatin formation in a manner that is critical for the stability of naturally eroding telomeres.  We propose that small RNA-mediated heterochromatin defects could contribute to proliferative aging by promoting genome stability.

overall_design: RNA-seq of small RNAs from wild-type, trt-1 and trt-1 dcr-1 mixed stage whole worms. Two replicates per genotype.

first: S

last: Frenk


title: Zebrafish BBB transcriptome

city: Gosselies

first: Raoul

last: Germano

address: 12, rue des Profs. Jeener et Brachet

department: Institute of Molecular Biology and Medicine

country: Belgium

institute: Free University of Brussels

summary: To unravel novel genes and pathways involved in barriergenesis a transcriptomic dataset of 3 dpf and adult brain vasculature was generated by isolating the brain endothelium exploiting the selective uptake of the cation DAPI by the central nervous system vasculature.

overall_design: two condition experiments:  3dpf DAPI positive vascular cells versus peripherial vasculature, adult brain versus liver vasculature, 3dpf wild type vasculature versus peripheral tissue, and 3dpf gpr124 mutant versus wild type vasculature. biological replicates: 2. In brief: After DAPI exposure, Tg(kdrl:GFP) embryos were enzymatically and mechanically digested to generate a single cell suspension, followed by fluorescent activated cell sorting (FACS). RNA was processed and hybridized to Agilent zebrafish (V3) 4x44K to perform dual-color Microarray gene expression analysis (MOgene).

middle: F


title: The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis

city: Nijmegen

first: Leonie

last: Kamminga

address: Geert Grooteplein 28

department: Molecular Biology

country: Netherlands

institute: Radboud University

summary: Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP-sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA-sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages (1, 2, 3 dpf)

overall_design: RNAseq of 3dpf Danio rerio whole embyos, wild types and rnf2 mutants (8 and 7 replicates, respectively); ChIPseq for rnf2 in 3dpf Danio rerio wild type (2 replicates) and rnf2 mutant (1 sample) embryos (all 3 with Drosophila spike in);  ChIPseq for H327me3 in 3dpf Danio rerio wild type (2 replicates) and rnf2 mutant (2 replicates) embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type (2 replicates) and rnf2 mutant (1 sample) embryos (all 3 with Drosophila spike in); RNAseq of 1, 2 and 3 dpf Danio rerio dissected hearts, wild types (9, 13 and 10 replicates, respectively) and rnf2 mutants (8, 9 and 9 replicates, respectively)

first: Naomi

last: Chrispijn

first: Dei

last: Elurbe

first: Marco

last: Aben

first: Dennis

last: de Bakker

first: Jeroen

last: Bakkers


title: Dependence on Myb expression is attenuated in myeloid leukemia with N-terminal   CEBPA mutations

city: Freiburg

first: Pierre

middle: Daniel

last: Cauchy

state: Baden-Württemberg

address: Breisacher Str. 115

department: Zentrum für Translationale Zellforschung

institute: University Medical Center Freiburg

summary: Mutations altering the normal function of C/EBPα are frequent in acute myeloid leukaemia with normal karyotype. MYB, a cooperating partner of C/EBPα, is likewise heavily implicated in AML. Here we investigate how the relative requirement for the transcription factor MYB in AML relates to the particular combinations of wild type and mutated alleles of CEBPA. Through knockdown of Myb in murine cell lines modelling the spectrum of CEBPA mutations we show that the consequences of reduced Myb depend on the mutational status of Cebpa. Importantly, Myb knockdown fails to override the block in myeloid differentiation in cells with biallelic N-terminal C/EBPα mutations, demonstrating for the first time that the dependency on Myb observed in AML is much lower in leukaemia with this combination of mutations. By comparing genome-wide analyses of gene expression following Myb knockdown and ChIP-seq data for the binding of C/EBPα isoforms, we provide evidence for a functional cooperation between C/EBPα and Myb in the maintenance of the leukaemia state. This co-dependency breaks down when both alleles of CEBPA harbour N-terminal mutations, as a subset of C/EBPα-regulated genes only bind the short p30 C/EBPα isoform and, unlike other C/EBPα regulated genes, do so without a requirement for Myb.

overall_design: Gene expression analysis of FMH9, KL and LL cells with and without Myb knockdown

first: Giacomo

last: Volpe

first: David

last: Walton

first: Carl

last: Ward

first: Daniel

last: Blakemore

first: Rachael

last: Bayley

first: Mary

last: Clarke

first: Luisa

last: Schmidt

first: Claus

last: Nerlov

first: Paloma

last: García

first: Stéphanie

last: Dumon

first: Florian

last: Grebien

first: Jon

last: Frampton


title: RNA-seq analysis of hPSC-derived brain pericyte-like cells, hPSC-derived neural crest stem cells, and primary human brain pericytes

first: Benjamin

last: Gastfriend

address: 9500 Gilman Dr

institute: University of California, San Diego

summary: hPSCs were differentiated to brain pericyte-like cells through a neural crest stem cell intermediate and compared to primary human brain pericytes

overall_design: 13 total samples were analyzed. Of these, 5 are hPSC-derived brain pericyte-like cells at D25 of the differentiation procedure (three biological replicates from the H9 cell line and one biological replicate each from the IMR90C4 and CS03n2 cell lines). Also included are H9 hPSCs, H9 hPSC-derived neural crest stem cells (NCSCs) at D15 of the differentiation procedure, H9 hPSC-derived NCSCs maintained to D55, and H9 hPSC-derived brain pericyte-like cells at D19, D22, and D45 of the differentiation procedure. For comparison, two samples of primary human brain pericytes are also included.

first: Matthew

last: Stebbins

first: Sean

middle: P

last: Palecek

first: Eric

middle: V

last: Shusta


title: Transcriptional profiling of human microglia reveals grey-white matter heterogeneity and multiple sclerosis-associated changes

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

summary: Microglia are brain-resident, myelin-phagocytosing cells, yet their role in lesion initiation in grey and white matter regions in multiple sclerosis (MS) is unclear. We isolated primary microglia from both, occipital cortex and corpus callosum, of 10 MS and 11 control donors and studied their transcriptional profile by RNA sequencing, thereby identifying regional and MS-associated changes. Identification of pathways underlying regional differences showed a relatively increased type I interferon response in cortical grey matter microglia, while white matter microglia more highly expressed NF-κB pathway genes. In  normal-appearing white matter MS tissue, lipid metabolism genes were increased, suggesting processing of myelin by microglia already in areas seemingly devoid of MS pathology. Normal-appearing grey matter MS microglia showed increased activation of glycolysis and metal ion homeostasis, possibly reflecting microglia reacting to iron depositions. Notably, expression of genes associated with microglia homeostasis were hardly changed, suggesting that subtle regional changes in MS-associated microglia do not yet affect their resting state.

overall_design: In total 31 human microglia samples were analyzed from 10 MS donors, including 5 grey matter and 10 white matter samples, and from 11 control donors, including 5 grey matter and 11 white matter samples. From each sample total RNA was extracted.

first: Marlijn

last: van der Poel

first: Thomas

last: Ulas

first: Mark

last: Mizee

first: Cheng-Chih

last: Hsiao

first: Suzanne

last: Miedema

first: Karianne

middle: G

last: Schuurman

first: Boy

last: Helder

first: Sander

last: Tas

middle: L

first: Jörg

last: Hamann

first: Inge

last: Huitinga


title: Transcriptome analysis of Mycobacterium tuberculosis mutant strain devoid of exopolyphosphatases.

city: Faridabad

first: Ramandeep

last: Singh

state: Haryana

address: NCR-BSC

department: Vaccine and Infectious Disease Research Centre

country: India

institute: Translational Health Science and Technology Institute

summary: We report the effects of simultaneous deletion of ppx1 and ppx2 on transcription profiles of M. tuberculosis

overall_design: RNA was isolated from mid-log phase culture of parental and double mutant strain. Experiments were repeated twice for each strain. Controal samples were S1 and S13 (S1_R1 & S1_R2; S13_R1 & S13_R2). RNA isolated from mutant strains were S2 and S3 (S2_R1& S2_R2; S3_R1 & S3_R2)

first: Prabhakar

last: Tiwari

first: Saurabh

last: Chugh


title: An EZH2-FBP1 Feedback Circuitry Promotes Tumorigenesis in Gluconeogenic Tissues

status: Public on Mar 12 2019

city: Guangzhou

first: Bo

last: Li

address: 74 Zhongshan 2nd Rd.

institute: Sun Yat-sen University

summary: We report that enhancer of zeste homologue 2 (EZH2) represses the expression of a rate-limiting gluconeogenic enzyme fructose-1, 6 -bisphosphatase 1 (FBP1) to promote tumorigenesis. More intriguingly, FBP1 inhibits EZH2 methyltransferase activity by binding EZH2 at targeted loci and dissembles the polycomb complex, which constitutes a negative feedback loop for EZH2-initiated signalings. We performed ChIP-Seq assays using the EZH2 and H3K27me3 antibody in HCC cells with vector control, FBP1 wild-type (WT) or FBP1 S169A re-expression. FBP1 WT severely reduced EZH2 and H3K27me3 signals. Conversely, FBP1 S169A exhibits much less effects on global or target-specific H3K27me3. In addition, ChIP-Seq assays with the FBP1 uncover a significant overlap between EZH2 and FBP1 binding sites, confirming that FBP1 inhibits EZH2 though physical interactions in the vicinity of chromosomes. Collectively, these studies reveal an unexpected crosstalk between metabolic and epigenetic events, and identify a new mechanistic circuitry highlighting EZH2 inhibitors as liver and kidney cancer therapeutics.

overall_design: We performed ChIP-Seq assays using the EZH2 and H3K27me3 antibody in HCC Hep3B cells with vector control, FBP1 wild-type (WT) or FBP1 S169A re-expression.

first: Xinggui

last: Wu

first: Kun

last: Liao

first: Shuye

last: Deng


title: Single cell RNA-seq identifies a unique microglia subtype associated with retinal degeneration

city: Durham

first: Daniel

last: Saban

state: NC

address: 2351 Erwin Rd, Duke Eye Center

institute: Duke University

summary: In many forms of retinal degenerative diseases in human, microglia relocate to and accumulate in the subretinal space. However, the roles of microglia in retinal degeneration are poorly understood. By leveraging single cell RNA-seq, we identified a distinct microglia subtype in the subretinal space. These microglia underwent transcriptional reprogramming characterized by reduced expression of homeostatic checkpoint genes and upregulation of injury-responsive genes. Importantly, this transition is associated with protection of the retinal pigment epithelium from damage caused by disease. Therefore, our data demonstrated microglial heterogeneity in retinal degeneration and may provide important implications for developing new strategies to prevent loss of vision.

overall_design: Transcriptional profiling of Cx3cr1+ single cells from the mouse model of light-induced retinal degeneration with matched control, generated from single cell RNA-sequencing of over 10,000 cells.

first: Chen

last: Yu


title: Recovery of the synaptic transmission genomic fabrics in the hypothalamic paraventricular nucleus of a rat model of autism treated with PMX53

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

summary: We profiled the whole transcriptomes of male and female rat hypothalamic paraventricular nuclei to determine the remodeling of the genomic fabrics responsible for the glutamatergic, GABAergic, dopaminergic, cholinergic and serotonergic transmission in epilepsy and recovery following treatment with PMX53. The rats were prenatally exposed (G15) to betamethasone followed by repeated adiministration of N-Methyl-D-Aspartic acid (NMDA) on postnatal days 12, 13 and 15 which triggered infantile spasms and autistic behavior. Pups were treated with PMX53 (a potent C5ar1 antagonist) on days 13, 14 and 15 prior to NMDA administration to determine what effects the treatment had on transcriptome recovery. Our Genomic Fabric Paradigm (GFP) is proposed as a transformative research approach to enhance the understanding of the brain transcriptomic alterations in epileptic rats and recovery following various treatments. The genomic fabric of a particular synapse is the structured transcriptome associated with the most interconnected and stably expressed gene network responsible for that type of neurotransmission. GFP refines the description of functional pathways by selecting the most prominent genes and determining their networking.  Moreover, it quantifies the remodeling of functional pathways and their interplay in disease and recovery in response to a treatment. We found that priming with betamethasone had substantial consequences on the topology of the genomic fabrics of all kind of synaptic transmission, that NMDA-induced spasms strongly exacerbated the remodeling of these fabrics and that PMX53 treatment recovered partially the the normal synaptic transcriptomes.

overall_design: One tissue (P = hypothalamic paraventricular nucleus) x one prenatal exposures (B = betamethasone) x one condition for the betamethasone exposed rats (Y with infantile spasms) x one postnatal treatment (P = PMX53) x two sexes (M, F) . Biological replicates:  4 PBYPM, 4 PBYPF.

middle: A

first: Tamar

last: Chachua

first: Sanda

first: Melissa

last: Benson

first: Karin

last: Borges

first: Jana

last: Velíšková

first: Libor

last: Velíšek


title: Expression data from limbic area of mouse brain

city: Tsukuba

first: Kazunori

last: Sasaki

address: AIST Tsukuba Central 5-2

institute: AIST

summary:
Microarray results revealed that EEA treatment induced variations in several genes associated with pro-inflammatory and dopaminergic, cholinergic, glutamatergic, and serotonergic synapses.
DNA microarray analysis was conducted on isolated RNAs extracted from the limbic area of EEA-treated brains

overall_design: Briefly, purified aRNA was fragmented using the GeneAtlas 3´ IVT Express Kit and hybridized for 16 h at 45°C using the GeneChip MG-430 PM microarray (Affymetrix Inc., Santa Clara, CA, USA). The chip was washed and stained in the Gene Atlas Fluidics Station 400 (Affymetrix Inc., Santa Clara, CA, USA), and the resulting image was scanned using the GeneAtlas Imaging Station (Affymetrix Inc., Santa Clara, CA, USA). Data analysis was performed using the expression console and Visualization and Integrated Discovery (DAVID) v6.8 (National Institute of Allergy and Infectious Diseases (NIAID). Compared with the control (vehicle-treated group), fold-changes in the expression of the imipramine- or EEA-treated groups were calculated and converted to linear data.


title: Remodeling of synaptic transmission genomic fabrics in the hypothalamic paraventricular nucleus of a rat model of autism

summary: We profiled the whole transcriptomes of male and female rat hypothalamic paraventricular nuclei to determine the remodeling of the genomic fabrics responsible for the glutamatergic, GABAergic, dopaminergic, cholinergic and serotonergic transmission in autism. The rats were prenatally exposed (G15) to betamethasone followed by repeated adiministration of N-Methyl-D-Aspartic acid on postnatal days 12, 13 and 15 which triggered the infantile spasms and autism spectrum disease behavior. Pups were treated with saline on days 13, 14 and 15 prior to NMDA administration. Our Genomic Fabric Paradigm (GFP) is proposed as a transformative research approach to enhance the understanding of the brain transcriptomic alterations in autistic rats . The genomic fabric of a particular synapse is the structured transcriptome associated with the most interconnected and stably expressed gene network responsible for that type of neurotransmission. GFP refines the description of functional pathways by selecting the most prominent genes and determining their networking.  Moreover, it quantifies the remodeling of functional pathways and their interplay in disease and recovery in response to a treatment. We found that priming with betamethasone had substantial consequences on the topology of the genomic fabrics of all kind of synaptic transmission and that NMDA-induced spasms strongly exacerbated the remodeling of these fabrics.

overall_design: One tissue (P = hypothalamic paraventricular nucleus) x one prenatal exposures (B = betamethasone) x one condition (with (Y autistic behavior) x one postnatal treatment (S = saline) x two sexes (M, F). Biological replicates: 4 PBYSM, 4 PBYSF.


title: Transcriptome analyses of trophoblast upon ALKBH5 knockdown

city: shanghai

first: ql

last: zheng

address: xiangyin

institute: immunity

summary: ALKBH5 play important role in regulation of trophoblast invasion, we examined the downstream genes of ALKBH5 via transcriptome sequencing

overall_design: Transcriptome analyses of mRNAs from trophoblast cells upon ALKBH5 knockdown

first: Qingliang

last: Zheng


title: Single-Cell Transcriptomes Reveal Molecular Specializations of Neuronal Cell Types in the Developing Cerebellum

first: Peng

last: Jian

address: 320 Yue Yang Road

department: Institute of Neuroscience

institute: University of Chinese Academy of Sciences

summary: We analyzed transcriptome profiles of 21,119 single cells of the postnatal mouse cerebellum and identified 8 main cell clusters (Granule precursors, Granule cells, Astrocytes, Interneurons, Oligodendrocytes, Microglia, Purkinje cells, Endothelial cells).

overall_design: Examination mouse cerebellum of 2 postnatal 8 days and 1 postnatal 0 day

first: Jian

last: Peng

first: Zhen-Ge

last: Luo


title: Genomic Reorganization of Lamin-Associated Domains in Cardiac Myocytes is Associated with Differential Gene Expression and DNA Methylation in Human Dilated Cardiomyopathy

city: Houston

first: AJ

last: Marian

state: Texas

address: 3742 Arnold St

department: Institute of Molecular Medicine

institute: The University of Texas Health Science Center Houston

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

overall_design: Refer to individual Series


title: Real-time quantitative PCR analysis of human exosomes

city: MURCIA

first: Raul

last: Teruel-Montoya

address: Ronda Garay s/n

department: Hematology and Medical Oncology Deparment

country: Spain

institute: Centro Regional de Hemodonación, Morales Meseguer University Hospital, IMIB-Arrixaca

summary: Paroxysmal Nocturnal Hemoglobinuria (PNH) is a clonal disease of blood cells caused by the lack of glycosyl phosphatidyl inositol anchored proteins bound to the cell membrane. In consequence, erythrocytes lead to intravascular hemolysis upon complement activation, which promotes high risk of thrombosis, intravascular hemolytic anemia, and bone marrow failure in patients. The mechanisms of thrombosis in PNH are still poorly understood. Treatment with eculizumab reduces intravascular hemolysis and thrombotic risk, but not in all cases. Exosomes are extracellular vesicles released by cells and whose secretion is closely related to the inflammatory status. They participate in cell communication by activating signaling pathways and transferring genetic material and proteins to host cells. In consequence, exosomes may serve as surrogate biomarkers for the prognosis and/or diagnosis of a disease. Isolation of exosomes was carried out from healthy controls and from three groups of PNH patients, i.e. i) with no eculizumab treatment; ii) under treatment with eculizumab that have not suffered thrombosis; and iii) under treatment with eculizumab but that have suffered thrombosis. The miRNAome and proteome was analyzed using plasma focus miRNAs PCR panel and LC-MS analysis, respectively. We found differential expression of miRNAs miR-148b-3p, miR-423-3p, miR29b-3p, miR15b-5p, let-7e-5p, miR126-3p, miR-125b-5p and miR-376c-3p as well as hemoglobin, haptoglobin, protein S and C4-binding protein in healthy controls vs PNH patients. Our results warrant further research and provide new information on the content of exosomes that could play a role in the hypercoagulable state in this disease.

overall_design: qPCR gene expression profiling. Circulating exosomes RNA from three donors and nine Paroxysmal Nocturnal Hemoglobinuria patients were used.

first: Irene

last: Martinez-Martinez


title: Dlk1-Mediated Temporal regulation of Notch Signaling is Required for Differentiation of Alveolar Type II to Type I Cells during Lung Repair

city: Chicago

first: Issam

last: Awad

state: IL

address: 5841 S. Maryland Avenue

department: Department of Neurology

institute: The University of Chicago

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived retinal transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis
Methods: Lung epithelia cells were collected after 10 days of treatment by pseudomonas aeruginosa (PA), RNA-Seq and qRT-PCR were applied to analyze the high-throughput data
Results: In general, the mutant type II-like cells expressed higher levels of type I cell markers and lower levels of type II cell markers

overall_design: Total RNA profiles of mutant(SpC-CreER/Dlk1flox/ROSA-Tomato) and wild-type(SpC-CreER/ROSA-Tomato) mice were generated by deep sequencing, in triplicate, using Illumina HiSeq4000.

first: Yuru

last: Liu

first: Wei

last: Zhang

first: Asrar

last: Malik


title: Genomic Reorganization of Lamin-Associated Domains in Cardiac Myocytes is Associated with Differential Gene Expression and DNA Methylation in Human Dilated Cardiomyopathy [ChIP-Seq]

summary: Mutations in the LMNA gene causes set of disorders collectively referred to as laminopathies that  include dilated cardiomyopathy. Lamin A/C proteins a components of nuclear lamina forms distinct nuclear domains called lamina associated domains (LADs). The roles of LADs in DCM is not known.  To identify LADs and characterize their associations with CpG methylation and gene expression in human cardiac myocytes isolated from patients with DCM and controls we performed   Chromatin immunoprecipitation-sequencing (ChIP-Seq), reduced representative bisulfite sequencing (RRBS), and RNA-sequencing (RNA-Seq) in 5 control and 5 DCM hearts with defined pathogenic variants in the LMNA gene. LADs are redistributed in DCM, are associated with CpG methylation and suppressed transcription, contributing to the pathogenesis of DCM in laminopathies.

overall_design: integrated analysis  of  ChIP-seq for LMNA from Cardiac myocytes and RNA-seq and RRBS  from  5 control and 5 DCM human heart sample

first: Sirisha

middle: M

last: Cheedipudi

first: Scot

last: Matkovich

first: Cristian

last: Coarfa

first: Xin

last: Hu

first: Priyatansh

last: Gurha

first: Ali


title: Genomic Reorganization of Lamin-Associated Domains in Cardiac Myocytes is Associated with Differential Gene Expression and DNA Methylation in Human Dilated Cardiomyopathy [RNA-Seq]

first: Matthew

last: Robertson


title: Functional heterogeneity of mouse prostate stromal cells revealed by single cell RNA-seq

first: Chad

last: Creighton

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary: We perform a single cell RNA-seq analysis to investigate the phenotypic and functional heterogeneity of the adult mouse prostate stromal cells. Our analysis identifies three major cell populations representing the smooth muscle cells and two types of fibroblast cells enriched by CD90 and CD34, respectively. The CD90+ stromal cells are in direct contact with the epithelial cells and express plentiful growth factors and genes associated with cell motility, developmental process, and androgen biosynthesis. This suggests that they may regulate epithelial cell survival and growth. The CD34+ stromal cells highly express genes associated with the extracellular matrix and cytokine-mediated signaling pathways, indicating a role in tissue repair and immune responses. The CD34+ stromal cells significantly suppress the luminal differentiation of the basal cells in the organoid culture assay. Our study identifies novel surface markers enabling physical separation of stromal cell subpopulations and generate gene expression profiles that imply their cellular functions.

overall_design: Prostate stromal cells were FACS-isolated from 8-10 week old C57Bl/6 mice based on their surface antigen expression profile (Lin-CD24-CD49f-). We employed the iCell8 single cell system from Wafergen BioSystems for single cell capture to achieve an intermediate in-depth expression profiling of single prostate stromal cells.  In-chip RT-PCR amplification and single cell RNA-seq library construction were performed following the iCELL8 single cell polyA transcriptome amplification hands-on workflow checklist and preparation guide.

first: Yiqun

first: Li

last: Xin


title: Depletion of limiting rDNA structural complexes triggers chromosomal instability and replicative aging of Saccharomyces cerevisiae

city: New York

first: Ryan

middle: D

last: Fine

state: NY

address: 435 E 30th Street

department: Center for Human Genetics and Genomics

institute: NYU Langone

summary: Sir2 is a highly conserved NAD+-dependent histone deacetylase that functions in heterochromatin formation and promotes replicative lifespan (RLS) in the budding yeast, Saccharomyces cerevisiae. Within the yeast rDNA locus, Sir2 is required for efficient cohesin recruitment and maintaining stability of the tandem array. In addition to the previously reported depletion of Sir2 in replicatively aged cells, we discovered that subunits of the Sir2 containing complexes, SIR and RENT, were depleted. Several other rDNA structural protein complexes also exhibited age-related depletion, most notably the cohesin complex. We hypothesized that mitotic chromosome instability (CIN) due to cohesin depletion could be a driver of replicative aging. ChIP assays of the residual cohesin (Mcd1-13xMyc) in moderately aged cells showed strong depletion from the rDNA and initial redistribution to the point centromeres, which was then lost in older cells. Despite the shift in cohesin distribution, sister chromatid cohesion was partially attenuated in aged cells and the frequency of chromosome loss was increased. This age-induced CIN was exacerbated in strains lacking Sir2 and its paralog, Hst1, but suppressed in strains that stabilize the rDNA array due to deletion of FOB1 or through caloric restriction (CR). Furthermore, ectopic expression of MCD1 from a doxycycline-inducible promoter was sufficient to suppress rDNA instability in aged cells and to extend RLS. Taken together we conclude that age-induced depletion of cohesin and multiple other nucleolar chromatin factors destabilize the rDNA locus, which then results in general CIN and aneuploidy that shortens RLS.

overall_design: 2 WT HiC samples with 2 sequencing runs each.

first: Nazif

last: Maqani

first: Mingguang

last: Li

first: Elizabeth

last: Franck

first: Jeffrey

middle: S

last: Smith


title: Gene expression profiling of Smad2/3 cKO mice

summary: Uterine double conditional inactivation of Smad2 and Smad3 in mice results in endometrial dysregulation, infertility, and uterine cancer. Smad2/3 cKO mice demonstrate abnormal expression of genes involved in inflammation, cell-cycle checkpoint, migration, steroid biosynthesis, and SMAD1/5-driven genes. We performed RNA-sequencing to identify the gene expression differences between the uterine epithelium of control and Smad2/3 cKO. To control for estrous cycle variations, the uterine epithelium was collected from mice at 0.5 dpc. Global gene expression profiles of Smad2/3 cKO versus control mice was analyzed. Our RNA sequencing analysis was performed at 6 weeks of life and already showed significant differences in migratory (Agr2,Slit2) and inflammatory (Ccl20, Crispld2) markers between Smad2/3 cKO and control mice.

overall_design: Two group comparison: uterine epithelium of control and Smad2/3 cKO mice. We generated a conditional knockout of Smad2/3 in the uterus and demonstrated that Smad2/3 plays a critical role in the endometrium, with disruption resulting in pubertal-onset uterine hyperplasia and ultimately fatal uterine cancer.

first: Maya

last: Kriseman

first: Martin

last: Matzuk


title: Fate-mapping within human iPSC-derived kidney organoids reveals conserved mammalian nephron progenitor lineage relationships.

city: Parkville

first: Andrew

last: Lonsdale

state: VIC

address: 50 Flemington Rd

country: Australia

institute: Murdoch Children's Research Institute

summary: Early human kidney development is poorly documented due to tissue inaccessibility and a lack of genetic tractability. Here we combine reprogramming, CRISPR/Cas9 gene-editing and organoid technologies to study the nephron lineage in a human context. We confirm the presence of a SIX2+ population in early kidney organoids with a transcriptional profile akin to human fetal nephron progenitors. Using lineage-tracing analyses, we show that SIX2-expressing cells contribute to nephron formation but not to the putative collecting duct epithelium. Labeling of SIX2+ cells at various time-points during organoid differentiation revealed a markedly reduced capacity for these cells to contribute to nephron formation over time. This suggests human kidney organoids lack a true nephron progenitor niche, as the developing kidney does in vivo, capable of both self-renewal and ongoing nephrogeneis. Nonetheless, human iPSC-derived kidney tissue maintains previously identified lineage relationships, which supports the utility of in vitro organoid models for interrogating the molecular and cellular basis of early human development.

overall_design: Single cell RNA-seq generated on a 10x Chromium genomics platform from iPSC-derived human kidney organoids. Each sample represents 6 pooled organoids derived from a single well of a transwell plate, generated from individual iPSC-derived reporter lines and harvested at either Day 18 (D18) or Day 25 (D25) of the differentiation protocol. The aggregated data contains 5365 cells (1865 from D18 and 3500 from D25) that passed QC and contains populations representing stroma, early/late nephron segments (podocytes, progenitors and proximal tubule) and distal tubule/collecting duct, as well as small off-target populations with similarity to neurons and muscle.

first: Sara

middle: E

last: Howden

first: Jess

last: Vanslambrouck

first: Melissa

middle: H

last: Little

first: Sean

middle: B

last: Wilson


title: Generation of FOXO3 engineered human stem cells with enhanced efficacy and safety

city: Beijing

first: Ping

last: Lu

address: 5 Yiheyuan Road

institute: Peking University

summary: FOXO3 is an evolutionally conserved transcription factor that has been linked to longevity. Here we asked whether human stem cells could be functionally enhanced by engineering them to express an activated form of FOXO3. This was accomplished via HDAdV-mediated gene editing of human embryonic stem cells. These cells were then differentiated into a range of vascular cell types, as FOXO3 has been shown to play a protective role in the cardiovascular system. FOXO3-enhanced vascular cells exhibited delayed senescence and increased resistance to oxidative injuries, compared with wild type cells. When tested in a therapeutic context, FOXO3-enhanced human mesenchymal stem cells promoted vasculature regeneration in a mouse model of ischemic injury, and were resistant to tumorigenic transformation, both in vitro and in vivo. Mechanistically, constitutively active FOXO3 conferred cytoprotection by transcriptionally downregulating CSRP1. Taken together, our findings provide mechanistic insights into FOXO3-mediated vascular protection, and indicate that FOXO3 activation may provide a means for generating more effective and safe biomaterials for cell replacement therapies.

overall_design: In this study, we investigated the functions of FOXO3-enhanced human embryonic stem cells (hESCs), vascular endothelial cells (hVECs), vascular smooth muscle cell (hVSMCs), mesenchymal stem cells (hMSCs) and transformed mesenchymal stem cells (transMSCs) through multi-omics analysis.

first: Fuchou

last: Tang

first: Guanghui

last: Liu


title: Abnormalities in Prefrontal Cortical Gene Expression Profiles Relevant to Schizophrenia in MK801-Exposed C57BL/6 Mice.

first: Jialu

last: Zhao

address: You an men wai Xi tou tiao Road 10

institute: Capital Medical University

summary: MK-801, a non-competitive NMDA receptor (NMDAR) antagonist, disturbs NMDAR function in rodents and induces psychological and behavioral changes similar to schizophrenia(SCZ). However, the effects of MK-801 treatment on gene expression in prefrontal cortex (PFC) are largely unknown. We have established MK-801 animal models to explore the etiology and pathophysiology of schizophrenia. Transcriptome analysis of the prefrontal cortex reveals that the differentially expressed genes mainly aggregate in chemical synaptic transmission and immune system process. Gene association patterns which are involved in synaptic vesicle cycle and mitochondrial electron transport chain have also been altered. Together, these observations underscore that dysfunction in glutamatergic synaptic vesicle cycle and mitochondrial electron transport chain has an impact on the pathogenesis of SCZ.

overall_design: Prefrontal cortex mRNA profiles of three saline control mice and six MK801-exposed mice were generated by RNA-seq, using Illumina X-10.

first: Haihong

last: Ye


title: Suppression of glioblastoma by a drug cocktail inducing tumor cells toward a neuronal fate

first: Longfei

last: Gao

address: 650 West 168th Street

institute: Columbia University

summary: Glioblastoma (GBM), the most common and aggressive malignant tumor in adult brain, is a notoriously fatal tumor. For many years, surgical resection and postoperative radiotherapy had been used for the treatment of GBM, which resulted in a poor median survival of about 12 months. Currently, Temozolomide (TMZ) as a clinically meaningful chemotherapy drug has become the standard first-line treatment for GBM, but with an increase of the median survival for about only 2.5 months. In this study, encouraged by previous findings that human astrocytes could be converted into neuronal cells with small molecules and that human GBM cells could be induced into neuronal like cells by transcription factors, we intended to test whether GBM cells could be induced into neuronal like cells by a cocktail of approved drugs and whether this drug cocktail help to suppress GBM in patient derived xenograft (PDX). Here we screened and identified TMZ, Tranilast, and Fasudil, three approved clinical drugs (TTF), to induce GBM cells toward a neuronal fate. Both serum and serum-free cultured GBM cells exhibited neuronal morphology and expressed neuronal genes under TTF treatment. Malignant properties including uncontrolled proliferation and intensive invasion of GBM cells were also attenuated with TTF treatment. Most importantly, when administrated in PDX, TTF cocktail significantly suppressed GBM growth in vivo and prolonged the survival of tumor-bearing mice, as compared to TMZ alone. Our study indicated that using the approved drug cocktail to induce tumor cells toward a neuronal fate might be a clinically promising strategy for GBM treatment.

overall_design: In this data set, we include RNA-Seq data of human glioblastoma cells treated with a drug cocktail (TMZ, Tranilast, and Fasudil) for 0, 2, and 10 days, as well as human neurons

first: Hong

last: Zhang

first: Wei

last: Hua

first: Shunmei

last: Xin

first: Lin

last: Cheng

first: Wuqiang

last: Guan

first: Yongchun

last: Yu

first: Ying

last: Mao

first: Gang

last: Pei


title: Insights into the Biology of Hearing and Deafness Revealed by Single-Cell RNA Sequencing

city: Philadelphia

first: Paul

last: Ranum

address: 3501 Civic Center Blvd.

department: Center for Cellular and Molecular Therapy

institute: The Children's Hospital of Philadelphia

summary: The goal of this study was to isolate individual cochlear hair cells and supporting cells from wild type animals in order to characterize the transcriptome of functionally mature auditory hair cells in the mammalian cochlea.

overall_design: Single-cell RNA sequencing is a powerful tool by which to characterize the transcriptional profile of low-abundance cell types, however its application to the inner ear has been hampered by the bony labyrinth, tissue sparsity and difficulties in dissociating the ultra-rare cells of the membranous cochlea.  Herein, we present a method to isolate individual inner hair cells (IHCs), outer hair cells (OHCs) and Deiters’ cells (DCs) from the murine cochlea at any post-natal time point. We isolated of 132 single cells from OHC, IHC, and DC cell types at postnatal day 15 (p15) and performed RNA-Sequencing of these cells using smartseq2 and Illumina HiSeq. An additional 12 single OHCs from the same timepoint were isolated and sequenced using smartseq2 and the Nanopore MinION 1D reads.  We leverage single-cell RNA sequencing to analyze these three cell types and generate a multidimensional overview of their transcriptomes. The data provide new insights into OHC motility and the architecture of gene products implicated in hereditary hearing loss.  This refined view of transcription in the organ of Corti will enhance to our understanding of the biology of hearing and deafness.

first: Richard

middle: J

last: Smith


title: Whole transcriptome targeted gene quantification provides new insights on pulmonary sarcomatoid carcinomas

city: Pisa

first: Gabriella

last: Fontanini

state: Italy

address: Via Roma 57

department: Department of Surgical, Medical, Molecular Pathology and Critical Area

institute: University of Pisa

summary: Pulmonary sarcomatoid carcinomas (PSCs) are rare and aggressive histological types of non-small cell lung cancer (NSCLC) with a median overall survival of about 9-12 months. In detail, PSCs comprise five different histological subtypes: pleomorphic carcinoma (PLC), giant cell carcinoma (GCC), spindle cell carcinoma (SCC), carcinosarcoma (CS) and pulmonary blastoma (PB). Preoperative pathological diagnosis may fail to identify these tumors and therapeutic options are still limited. PSCs have been scarcely characterized from a molecular point of view because of their rarity, and to date no specific markers have been found for PSCs in comparison with other NSCLC types. In this study a highly sensitive amplicon based whole transcriptome quantification analysis was performed, using the Ion AmpliSeq Transcriptome Human Gene Expression Kit (Life Technologies) on a selected series of 14 PSCs (1 PB, 4 CS, 2 SCC, 2 GCC, 5 PLC) and 3 samples of normal lung parenchyma. PSCs expression data were then compared with transcriptome data of lung adenocarcinoma and squamous cell carcinoma available on The Cancer Genome Atlas database. Thirty-eight genes specifically deregulated in PSC samples were identified. Among these, IGJ and SLMAP were validated by immunohistochemistry on an independent cohort (30 PSCs, 31 lung adenocarcinoma and 31 squamous cell carcinoma cases). Furthermore, a pathway enrichment analysis, performed on differentially expressed genes, revealed that FOXO signalling and Fanconi Anemia pathways, playing a pivotal role in cancer development and progression, are enriched in PSC tumors. The description of peculiar molecular profiles besides increasing our knowledge on PSCs biology may suggest new diagnostic and therapeutic strategies.

overall_design: Whole transcriptome targeted gene quantification analysis was perfomed on a selected series of 14 pulmonary sarcomatoid carcinomas (1 pulmonary blastoma, 4 carcinosarcomas, 2 spindle cell carcinomas, 2 giant cell carcinomas, 5 pleomorphic carcinomas) and 3 samples of normal lung parenchyma, using the Ion AmpliSeq Transcriptome Human Gene Expression Kit ( Life Technologies).

first: Greta

last: Alì

first: Rossella

last: Bruno

first: Anello

last: Poma

first: Ornella

last: Affinito

first: Antonella

last: Monticelli

first: Paolo

last: Piaggi

first: Sara

last: Ricciardi

first: Marco

last: Lucchi

first: Franca

last: Melfi

first: Sergio

last: Cocozza


title: miRNA expression in BMSCs

status: Public on Mar 11 2019

first: Yunfei

last: Zheng

state: Beijing

address: 22 Zhongguancun Avenue South, Haidian District

department: Oral and Maxillofacial Surgery

institute: Peking University School and Hospital of Stomatology

summary: We performed microarray analysis to determine the expression profiles of miRNAs during osteoblast differentiation of BMSCs

overall_design: BMSCs were cultured in osteogenic medium for 7 days. We performed microarray analysis to identify miRNAs that were differentially expressed in osteogenically differentiated human BMSCs between day 0 (D0) and day 7 (D7).

last: zheng


title: circRNA expression in BMSCs

summary: We performed microarray analysis to determine the expression profiles of circRNAs during osteoblast differentiation of BMSCs

overall_design: BMSCs were cultured in osteogenic medium for 7 days. We performed microarray analysis to identify circRNAs that were differentially expressed in osteogenically differentiated human BMSCs between day 0 (D0) and day 7 (D7).


title: COX-2 mediates tumor-stromal Prolactin signaling to initiate tumorigenesis [ChIP-seq]

city: Boston

first: Ben

middle: S.

last: Wittner

state: MA

address: 149 13th Street

department: Center for Cancer Research

institute: Massachusetts General Hospital

summary: Tumor-stromal communication within the microenvironment contributes to initiation of metastasis and may present a therapeutic opportunity. Using serial single cell RNA-sequencing in an orthotopic mouse prostate cancer model, we find upregulation of Prolactin receptor as cancer cells that have disseminated to the lung expand into micrometastases. Secretion of the ligand Prolactin by adjacent lung stromal cells is induced by tumor cell production of the COX-2 synthetic product prostaglandin E-2 (PGE-2). PGE-2 treatment of fibroblasts activates the nuclear orphan receptor NR4A (Nur77), with Prolactin as a major transcriptional target for the NR4A-Retinoid X receptor (RXR) heterodimer. Ectopic expression of Prolactin receptor in mouse cancer cells enhances micrometastasis, while treatment with the COX-2 inhibitor Celecoxib abrogates Prolactin secretion by fibroblasts and reduces tumor initiation. Across multiple human cancers, COX-2, Prolactin, and Prolactin receptor show consistent differential expression in tumor and stromal compartments. Such paracrine crosstalk may thus contribute to the documented efficacy of COX-2 inhibitors in cancer suppression.

overall_design: We performed H3K27ac ChIP-seq on primary dermal fibroblasts treated for six hours with PGE-2 or untreated.

first: Yu

first: Valentine

last: Comaills

first: Risa

last: Burr

first: Gaylor

last: Boulay

first: David

last: Miyamoto

first: Erin

last: Emmons

first: Srinjoy

last: Sil

first: Michael

middle: W

last: Koulopoulos

first: Katherine

last: Broderick

first: Eric

last: Tai

first: Shruthi

last: Rengarajan

first: Anupriya

last: Kulkarni

first: Toshi

last: Shioda

first: Chin-Lee

last: Wu

first: Sridhar

last: Ramaswamy

last: Ting

first: Mehmet

last: Toner

first: Miguel

last: Rivera

first: Shyamala

last: Maheswaran

first: Daniel

last: Haber


title: Genome-wide identification of cancer-specific alternative splicing in circRNA

city: Wuhan

first: Chunjiang

last: He

state: Hubei

address: Donghu Road 185

institute: Wuhan University

summary: Circular RNA (circRNA) is a group of RNA family generated by RNA circularization, which was discovered ubiquitously across different cancers. However, the internal structure of circRNA is hard to be determined since of the alternative splicing happened in exons and introns of circRNA and the cancer-specific alternative splicing of circRNA is less to be identified. Here we proposed a custom tool CircSplice, which could identify internal alternative splicing of circRNA and compare the differential splicing between samples. By applying CircSplice in ccRCC, we identified cancer-specific alternative splicing (AS) events belong to circRNAs in ccRCC. We further confirmed the existence of alternative splicing events in circRNAs by RT-PCR. This study is the first exploration of cancer-specific alternative splicing in circRNAs, which helps researchers to better understand potential functions of splicing of circRNAs in cancers.

overall_design: Circular RNAs profiles of three pairs of Clear Cell Renal cell carcinoma tissues and adjacent normal tissues were generated by RNA deep-sequencing, using HiSeq2500, Illumina.

first: Xin

last: Dong


title: Transcriptomic profiling of a eIF2B mutant mouse with a chronic Integrated Stress Response

city: South San Francisco

first: Carmela

last: Sidrauski

state: California

address: 1170 Veterans Blvd

institute: Calico Life Sciences

summary:
Purpose: The integrated stress response (ISR) attenuates the rate of protein synthesis while inducing expression of stress proteins in cells. Various insults activate kinases that phosphorylate the GTPase eIF2 leading to inhibition of its exchange factor eIF2B. Vanishing White Matter (VWM) is a neurological disease caused by eIF2B mutations that, like phosphorylated eIF2, reduce its activity. We performed RNA-seq analysis of cerebellum collected from mice harboring a homozygous point mutation in eIF2B5 (HO R191H), a mutation that causes a severe form of VWM in humans and compared gene expression to wildtype age-matched littermates to identify transcriptomic differences at early, mid and late time points during disease progression. We also performed RNA-seq on cerebellum collected from animals treated with the eIF2B activator 2BAct for 1 month to determine to what extent small molecule treatment could normalize the VWM transcriptome.
Methods: Samples were collected at 2, 5, and 7 months of age. In addition, HO R191H and WT mice treated with and without with the eIF2B activator 2BAct for 1 month were profiled. RNA-seq libraries were prepared using purified RNA isolated from frozen tissue using the RNeasy Mini kit. RNA quality and concentration were assayed using a Fragment Analyzer instrument. RNA-seq libraries were prepared using the TruSeq Stranded Total RNA kit paired with the Ribo-Zero rRNA removal kit. Libraries were sequenced on an Illumina HiSeq 4000 instrument. For the experiment comparing different ages, N = 3 males/genotype/time point. For the 4-week 2BAct treatment experiment, N = 3 females/condition.
Conclusions: HO R191H mutant brains show an elevated gene expression signature of the Integrated Stress Reponse in mice as early as 2 months, preceding the appearance of overt pathology in these animals. The expression of the ISR-related genes does not significantly increases at 5 months and 7 months of age. One month of treatment with 2BAct completely prevented the expression of ISR-related in genes in 2 month old animals.

overall_design: RNA extracted from cerebella of male HO R191H and WT mice at 2, 5, and 7 months were sequenced in triplicate. RNA extracted from cerebella of 2 month female HO R191H and WT mice, treated with either 2BAct or vehicle for 1 month, were sequenced in triplicate.

first: Lauren

last: LeBon


title: Branching Gene Regulatory Network for Neurotransmitter versus Axonal Pathfinding

city: Linkoping

first: Johannes

last: Stratmann

state: Ostergotland

address: Linkoping University Campus HU

department: Insitute for clinical and experimental medicine

country: Sweden

institute: Linkoping Univeristy

summary: In previous studies we found that the two transcription factors collier (FB:knot, kn) [vertebrate Ebf1] and ladybird early (lbe) [vertebrate Lbx1/2], when co-misexpressed from elav-Gal4, generate ectopic Nplp1 neuropeptidergic cells in the entire ventral nerve cord during Dmel. embryonic development. We also found that the axon generated by the ectopic Nplp1 cells, seem to follow the same fascicle as the wild type Nplp1 neurons. Therefore we used RNA-seq on control and UAS‑col,lbe co-misexpression to find candidate factors important in axon pathfinding of the Nplp1 neurons. We also included single misexpression of UAS-col and UAS-lbe, together with co-misexpression of UAS-ap, eya, since we know that col and lbe activate those two factors during the cell fate specification of Nplp1 neurons.

overall_design: We generated single misexpression lines UAS-col-HA (ChrIII) and UAS-myc-lbe (ChrIII). Then we generated the double misexpression lines UAS-col, lbe (UAS-col-HA, UAS-myc-lbe) and UAS-ap, eya (UAS-Flag-ap; UAS-eya-HPC4). We misexpressed these constructs from elav-Gal4, a pan neuronal driver mostly active in postmitotic neurons, and compared the TPMs of the misexpression to the TPMs of the control (in our case elav-Gal4 heterozygous over a wildtype chromosome from the OregonR stock). We performed the same experiments at two different time points in embryonic development i.e. stage16 and at the late stage AFT (air filled trachea). Within each experiment, we have three biological replicates per genotype (control and misexpressions). In total, we have had 30 samples (3 samples over 5 groups per experiment, at two different time points).

first: Helen

last: Ekman

first: Stefan

last: Thor


title: Structural Analysis of the Ash2L/Dpy-30 Complex Reveals a Heterogeneity in H3K4 Methylation

first: Ali

last: Shilatifard

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

summary: Dpy-30 is a regulatory subunit controlling the histone methyltransferase activity of the KMT2 enzymes in vivo. Paradoxically, in vitro methyltransferase assays revealed that Dpy-30 only modestly participates in the positive heterotypic allosteric regulation of these methyltransferases. Detailed genome-wide, molecular and structural studies reveal that an extensive network of interactions taking place at the interface between Dpy-30 and Ash2L are critical for the correct placement, genome-wide, of H3K4me2 and H3K4me3 but marginally contribute to the methyltransferase activity of KMT2 enzymes in vitro. Moreover, we show that H3K4me2 peaks persisting following the loss of Dpy-30 are found in regions of highly transcribed genes, highlighting an interplay between Complex of Proteins Associated with SET1 (COMPASS) kinetics and the cycling of RNA polymerase to control H3K4 methylation. Overall, our data suggest that Dpy-30 couples its modest positive heterotypic allosteric regulation of KMT2 methyltransferase activity with its ability to help the positioning of SET1/COMPASS to control epigenetic signaling.

overall_design: 17 experiments: (4 genotypes x 2 ChIP antibodies x 2 replicates), 1 input

first: Jean-Francois

last: Couture

first: Ashley

last: Woodfin

first: John

middle: F

last: Haddad


title: Glycerol biosynthesis pathways from starch endowing Dunaliella salina adaptations to osmotic and oxidative stresses caused by salinity

status: Public on Mar 10 2019

city: Chengdu

first: Guoyin

last: Huang

state: Sichuan

address: No.24 South Section 1, Yihuan Road

department: College of Life Sciences

institute: Sichuan University

summary: Dunaliella salina, a unicellular and eukaryotic alga, has been found as one of the most salt-tolerant eukaryote with a short growth period and wide practical applications. To elucidate the underlying molecular mechanism involved in the response to salinity and its different effects, RNA-seq was used for global transcriptome profiling of D. salina exposed to NaCl, Sorbiol and H2O2 stress. To maintain osmotic pressure homeostasis under suboptimal environment condition, starch breakdown catalyzed by both alpha-amylase (AMY) and glycogen phosphorylase (PYG) with consecutive expression patterns and low activity of PYG at the beginning of salt stress might be caused by a shortage of ATP because of impaired photosynthesis. Moreover, clustering analysis of differentially expressed genes (DEGs) indicated that starch and sucrose metabolism as well as glycerol metabolism reprogrammed under high salt stress only. For redox homeostasis, glycerol-3-phosphate shuttle performed by mitochondrial glycerol-3-phosphate dehydrogenases (GPDHs) participates the redox imbalance under abiotic stresses. c23777_g1 is a gene of D. salina involved in glycerol 3 phosphate (G3P) shuttle under various abiotic stresses while c25199_g1 is a gene of G3P shuttle induced only by osmotic stress.

overall_design: Total mRNA profiles of D. salina exposed to NaCl, Sorbiol and H2O2 stress were generated by deep sequencing, in triplicate, using Illumina NextSeq500.

first: Ziyi

last: Tang


title: Differential expression of miRNAs in acute myeloid leukemia quantified by NGS of whole blood samples

city: Syracuse

first: Frank

last: Middleton

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

summary: We collected peripheral blood samples from 10 adult patients with newly diagnosed acute myeloid leukemia (AML), prior to induction chemotherapy, and 9 controls. Levels of miRNAs were obtained stranded small RNA-sequencing. We compared AML and control groups to identify differential miRNAs. In a subset analysis, patients with NPM1 and FLT3 mutations showed the greatest number of differentially expressed miRNAs compared to controls.  Some of these miRs have been described previously in association with leukemia, but many are new.

overall_design: Small RNA sequencing of peripheral whole blood in adult human subjects with AML before chemotherapy compared with controls.


title: Genome-wide maps in MCF-7 cells with six2 or CYP4Z1 3'UTR or CYP4Z2P 3'UTR overexpression or not

city: Nanjing

first: Lufeng

last: Zheng

state: Jiangsu

address: Tongjia Xiang 24

department: School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention

institute: China Pharmaceutical University

summary: Analysis of MCF-7 cells following  six2 or CYP4Z1 3'UTR or CYP4Z2P 3'UTR overexpression. Overexpression of six2 or CYP4Z1 3'UTR or CYP4Z2P 3'UTR positively regulates the abundance of embryonic stem cell function. Results provide insight into the role of six2 mediated-regulation on the ceRNA network between CYP4Z1 and pseudogene CYP4Z2P in breast cancer stemness.

overall_design: mRNA profiles of MCF-7 cells with six2 or CYP4Z1 3'UTR or CYP4Z2P 3'UTR overexpression or not were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000.

first: Tao

last: Xi


title: Gene expression differences in omental mesothelial cells from lean and obese human donors

status: Public on Mar 08 2019

city: RTP

first: Benjamin

last: Buehrer

address: 3200 East Hwy 54, Suite 100

institute: ZenBio, Inc.

summary: Visceral adipose tissue inflammation correlates with metabolic dysfunction in obesity.  However, critical cell types that trigger and contribute to inflammation in this depot are not completely understood.  Mesothelial cells line the omental fat depot and are thought to contribute to several intraperitoneal inflammatory conditions. Whether adipose-associated mesothelial cell inflammation is a feature of pathologic obesity is unclear. This study was performed to delineate a contribution of omental adipose mesothelial cells to visceral adipose tissue dysfunction in pathologic obesity. We performed a cross-sectional case-control study from two separate cohorts of patients undergoing abdominal surgery with varying degrees of obesity and metabolic disease.  Whole-genome expression profiling was conducted on mesothelial cells isolated from lean and obese surgical patients to determine differences in relevant pathways related to obesity and metabolic disease.

overall_design: Total RNA was isolated from three replicate samples of pooled donor omental mesothelial cells from obese donors compared to lean donors.

first: R

last: Cheatham


title: DNA methylation profiling identifies candidate genes for the pathogenesis of Hepatosplenic T-cell lymphoma

city: Hannover

first: Anke

middle: Katharina

last: Bergmann

address: OE 6300, Carl-Neuberg-Str. 1

department: human genetics

institute: Medical School Hannover

type: Methylation profiling by genome tiling array

summary: Genome wide DNA methylation profiling of HSTL in comparison to benign T-cell subsets. The Illumina Infinium 450k Human DNA methylation Beadchip was used.

overall_design: Bisulphite converted DNA samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip. The Illumina Infinium 450k Human DNA methylation Beadchip was used.

middle: K


title: Genome-wide maps of chromatin state in MCF-7 cells with six2 overexpression or not

summary: By obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA in MCF-7 cells with six2 overexpression or not, we generated genome-wide chromatin-state maps of these two cells. We identified the detailed binding sites of six2 in MCF-7 cells.

overall_design: ChIP DNA profiles of MCF-7 cells with six2  overexpression or not were generated by deep sequencing, in triplicate, using Illumina HiSeq X Ten.


title: Comprehensive constitutional genetic and epigenetic characterization of Lynch-like individuals [Blood]

status: Public on Mar 09 2019

city: L'Hospitalet de Llobregat

first: Estela

last: Damaso

state: Barcelona

address: Av.Gran Via de l'Hospitalet, 199-203

department: Hereditary Cancer Program

institute: Catalan Institute of Oncology (ICO)

summary:
Background: In ~50% of Lynch syndrome (LS)-suspected patients (also called Lynch-like syndrome, LLS), the causal mechanism for cancer predisposition remains unknown. Our aim was to elucidate the constitutional basis of mismatch repair (MMR) deficiency in LLS patients throughout a comprehensive genetic and epigenetic analysis.
Methods: One hundred and fifteen LLS patients harboring MMR deficient tumors and no pathogenic germline MMR gene mutations were included in this study. Mutational analysis of 26 colorectal cancer associated genes was performed by using a customized multigene panel and massively parallel sequencing. Pathogenicity of MMR variants was assessed by mRNA analysis and multifactorial likelihood calculations. Genome-wide methylome analysis was perfomed by using the Infinium HumanMethylation450K BeadChip.
Results: The multigene panel analysis revealed the presence of two MMR gene truncating mutations not found in previous analysis. Of a total of 15 MMR variants of unknown significance identified, five - present in 6 unrelated individuals- were reclassified as pathogenic. In addition, 13 predicted deleterious variants in other CRC-predisposing genes (MSH3, MUTYH, POLD1, APC, EPCAM, BUB1, FAN1, EXO1 or PSM1) were found in 12 probands. Methylome analysis detected one constitutional MLH1 epimutation in an individual diagnosed with CRC at age 42, but no additional differentially methylated regions were identified in LLS compared to LS patients or healthy individuals.
Conclusions: In conclusion, the use of an ad-hoc designed gene panel combined with pathogenicity assessment of variants allows the identification of deleterious MMR mutations as well as new LLS candidate genes. Moreover, constitutional epimutations in non-LS-associated genes are not responsible for the MMR-deficient phenotype observed in LLS patients.

overall_design:
A total of 115 Caucasian Lynch-like syndrome patients harboring MMR deficient tumors MMR loss of expression and/or microsatellite instability (MSI) were analyzed by Infinium Human Methylation 450k Beadchip. From all included individuals, DNA from blood was collected. FFPE blocks of normal colorectal mucosa and colorectal cancer tissue were also included when available. The current subset includes only blood samples. FFPE samples can be found in the other associated dataset from Damaso et al.
Clinical data abbreviations:
clinical criteria (A=Amsterdam criteria; B+number=Revised Bethesda criteria; AP=Anatomopathological)
personal history of cancer (CRC=Colorectal Cancer; EC=Endometrial Cancer; OC=Ovarian Cancer; SBC=Small Bowell Cancer; BC=Breast Cancer; (x2)=synchronic)
microsatellite instability (MSI+=Microsatellite Instabillity; MSS=Microsatellite stable; NP=Not performed; NV=Not Valuable)
BRAF status (WT=wildtype; NP=Not performed)

last: Dámaso

first: Maribel

last: González-Acosta

first: Gardenia

last: Vargas-Parra

first: Matilde

last: Navarro

first: Judith

last: Balmaña

first: Teresa

last: Ramon y Cajal

first: Noemí

last: Tuset

first: Bryony

last: Thompson

first: Fátima

last: Marín

first: Anna

last: Fernández

first: Carolina

last: Gómez

first: Àngela

last: Velasco

first: Ares

last: Solanes

first: Sílvia

last: Iglesias

first: Gisela

last: Urgel

first: Consol

last: López

first: Jesús

last: del Valle

first: Olga

last: Campos

first: Maria

last: Santacana

first: Xavier

last: Matias-Guiu

first: Conxi

last: Lázaro

first: Laura

last: Valle

first: Joan

last: Brunet

first: Marta

last: Pineda

first: Gabriel

last: Capellá