title: Highly sensitive MLH1 methylation analysis in blood allows the identification of low-level epigenetic mosaicism

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: Constitutional MLH1 epimutations are a rare cause of Lynch syndrome. Low methylation levels (≤10%) have been occasionally described. The aim of this study was the identification of patients with low levels of epigenetic mosaicism in MLH1 gene.  Eighteen patients with MLH1 hypermethylated tumors and undetectable methylation in blood as assessed by Methylation-Specific Multiplex Ligation-Dependent Probe Amplification were included (MS-MLPA). Highly sensitive MS-Melting Curve Analysis (MS-MCA) at MLH1 promoter was used to screen for epigenetic mosaicism. Constitutional methylation was confirmed by other methods. Mutational analysis of hereditary cancer genes including MLH1 was performed.  MS-MCA analysis identified one case (5.6%) with low levels of methylation (1-2%) in blood DNA. The patient had developed 3 gastrointestinal tumors at ages 22, 24 and 25, sharing MLH1 promoter hypermethylation and loss of heterozygosity associated with c.655A allele. The presence of low MLH1 methylation levels was confirmed by clonal bisulfite sequencing, evidencing the association with c.-93G allele (in phase with c.655G). The extension of the hypermethylated region overlaps with the reported in constitutional MLH1 epimutation carriers. No rare germline variants were identified.  The use of highly sensitive techniques such as MS-MCA has demonstrated to be useful for the detection of low MLH1 methylation levels in blood.

overall_design: Case 29 was positive for germline MLH1 methylation. In order to confirm the presence of epimutation at the patient, her methylation values were compared against values reported for constitututional MLH1 epimutation carriers by Dámaso et al., 2019 (GEO Series=GSE107353).

last: Dámaso

first: Julia

last: Canet-Hermida

first: Gardenia

last: Vargas-Parra

first: Àngela

last: Velasco

first: Esther

last: Darder

first: Jesús

last: del Valle

first: Anna

last: Fernández

first: Fátima

last: Marin

first: Àngel

last: Izquierdo

first: Gemma

last: Mateu

first: Carmen

last: Escrivano

first: Virgínia

last: Piñol

first: Hugo-Ikuo

last: Uchima

first: José

last: Soto

first: Megan

last: Hitchins

first: Conxi

last: Lázaro

first: Bernat

last: Queralt

first: Joan

last: Brunet

first: Marta

last: Pineda

first: Gabriel

last: Capellá


title: Gene expression profiles of Jam2+ and Jam2- hematopoietic stem cells

status: Public on May 22 2019

city: Lund

first: Shamit

last: Soneji

address: Solvegatan 19

country: Sweden

institute: BMC

summary: Hematopoietic stem cells (HSCs: CD150+ CD48- c-kit+ Sca-I+ Lineage- cells) with or without cell surface expression of Jam2 were freshly sorted from C57BL/6 SJL mice. Total RNA was isolated from both, Jam2+ and Jam2- HSCs, using RNeasy Micro Kit (Qiagen) in accordance with the manufacturer's protocol. After the quality/quantity determination, RNA was subjected to expression analyses using Affymetrix GeneChip® Array / Mouse Gene 2.0 ST type.

overall_design: The cells were isolated from 5 male wildtype C57BL/6 SJL mice.

first: V

last: Radulovic

first: M

last: van der Garde

last: Sigurdsson

first: S

last: Lang

first: K

last: Miharada


title: Phenotypic cooperation of a KCNQ2 exon 7 partial duplication and compound copy number variations in genes associated to a severe epileptic and neurodevelopmental delay

city: Salamanca

first: Juan Luis

last: Garcia

state: Salamanca

address: Campus Miguel de Unamuno

country: Spain

institute: Centro de Investigación del Cáncer IBMCC-CIC

summary: A 6-year-old boy, second son of healthy parents affected with epileptic encephalopathy of neonatal onset. Pregnancy with gestational diabetes controlled with diet. Delivery was uneventful. Since 48 hours of life, he presented episodes of cyanosis, generalized hypertonia, and tonic asymmetric postures followed by apnea. Video-EEG at 5 days of life showed bilateral and asynchronous spike-and-wave. Seizures were refractory to phenobarbital but were controlled with phenytoin. Since 3 months of age, he presented with startle episodes without EEG correlate related to the wake and sleep transition together with dystonic postures. One month later, epileptic spasms without hypsarrhythmia were observed. No response to levetiracetam and valproic acid but stopped after lacosamide (LCS) treatment was initiated (11 months of age). Metabolic tests (including CSF studies), karyotype, and brain MRI were normal. Epileptic encephalopathy gene panel was negative including hyperekplexia related genes. Progressive increase of TSH was treated with oral L-t4. At 20 months he presented recurrence of spasms that were controlled with LCS dose adjustment. V-EEG: abnormal background activity and paroxysmal multifocal discharges that showed activation and generalization during sleep. After several years of good seizure control, LCS was discontinued. He suffered from decompensation of seizures with febrile viral infection and at 5 years of age he presented startle episodes associated to auditory stimulus without EEG correlate, but during sleep, he presented epileptic spasms with EEG correlate. Treatment with vigabatrine was initiated with a clinical and EEG improvement. At physical exam he presents severe axial hypotonia without head control. Hypertonia of 4 limbs with dystonic movements of upper limbs. No hand use and is not able to sit or crawl. No development of expressive language.GMFCS: V. No development of expressive language. Last v-EEG monitoring showed bilateral polyspike discharges and clinical spasms in polygraph recording without any clear EEG correlate. Whole exome sequencing was performed and partial exon 7 duplication, heterozygous variant, in KCNQ2 was found. aCGH study detected several CNV in genes associated to neural functions (losses: LRRC55, PCDH9, NALCN, RYR3, ELAVL2, CDH13, ATP1A2, SLC17A5, ANO3. Gains : PCDH19, TENM1, EFNA5).

overall_design: A high-density CytoScan® HD Array (Thermo Fisher Scientific, In), which includes 2.67 million markers for copy number (CN) analysis, 750,000 SNP probes and 1.9 million non-polymorphic probes for comprehensive whole-genome coverage was used. Following hybridization, the laser scanner (GeneChip® 3000 Scanner) was used for scanning the arrays, and the images were extracted and analyzed using Affymetrix Gene Chip Command Console software (version 4.0) and Chromosome analysis software (ChAS v.1.2/na33.2) (Fisher Scientific, Inc.), and interpreted with the aid of the UCSC genome browser.

first: P

middle: A

last: Lazo

first: J

middle: L

last: García-Hernández

last: Gómez-Puertas

first: I

last: Marcos-Alcalde

first: C

last: Arjona

first: A

last: Villarroel

first: R

last: González-Sarmiento

last: Fons


title: Deregulated MicroRNA and mRNA Expression Profiles in the Peripheral Blood of Patients with Marfan Syndrome

city: Homburg Saar

first: Masood

last: Abu-Halima

address: Kirrberger St 60

department: Human Genetics

country: Germany

institute: Univeristy of Saarland

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

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

overall_design: Refer to individual Series


title: Deregulated MicroRNA and mRNA Expression Profiles in the Peripheral Blood of Patients with Marfan Syndrome (microRNA)

summary: We performed integrated miRNA and mRNA expression profiling in blood samples of Marfan patients in order to investigate deregulated miRNA and mRNA networks in these patients which could serve as potential diagnostic and prognostic tools for MFS therapy.

overall_design: RNA was purified using the PAXgene Blood RNA Kit

middle: G

last: Meese


title: Next Generation Sequencing Facilitates Comparative Transcriptomes Analysis for Saccharomyces cerevisiae lines generated by SCRaMbLE

city: Tianjin

first: Bin

last: Jia

state: Tianjin

address: No 92, Weijin Road

department: School of chemical engineering and technology

country: China

institute: Tianjin University

type: Expression profiling by high throughput sequencing

summary:
Purpose: According to comparative transcriptomes data, the differentially expressed genes within these selected scrambled yeast strains can be digged out and further analyzed, seeking potential targets that were tuned drastically and might improve β-carotene production when modified.
Methods: mRNA profiles of two Saccharomyces cerevisiae strains H0, S3 (each named as yJBH000 and yJBH012 in related manuscript) were generated in triplicate using illumina. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) and index codes were added to each sample. The library preparations were sequenced on an Illumina Hiseq 4000 platform. 150 bp paired-end reads were generated as raw data. The read counts for each gene in the genome were summarized as processed data.
Results: The yJBH012 had an obviously different pattern of global transcription as compared with the control yJBH000. The upregulation of 589 genes and down regulation of 236 genes were observed in this analysis.

overall_design: The transcirptomes of different  Saccharomyces cerevisiae strains were sequenced by Illumina, giving both unchanged genes and differentially expressed genes that would affect β-carotene production.

first: Yingjin

last: Yuan


title: Deregulated MicroRNA and mRNA Expression Profiles in the Peripheral Blood of Patients with Marfan Syndrome (mRNA)


title: Connexin 43 controls the immunoregulatory phenotype of astrocytes

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

country: France

institute: IBENS

summary: BAC array purification of hippocampus astroglial ribosome-bound transcriptome  in astrocytes from Aldh1l1:Rpl10a eGFP/ Cx43 KO and Aldh1l1:Rpl10a eGFP/ Cx43FL mice

overall_design: Hippocampal astroglial ribosome-bound transcriptome  in astrocytes from Aldh1l1:Rpl10a eGFP/ Cx43 KO and Aldh1l1:Rpl10a eGFP/ Cx43FL mice

first: Anne-Cecile

last: Boulay

first: Alice

last: Gilbert

first: Vanessa

last: Moreira

first: Corinne

last: Blugeon

first: Sandrine

last: Perrin

first: Juliette

last: Pouch

first: Stéphane

first: Bertrand

last: Ducos

first: Martine

last: Cohen-Salmon


title: Receptor-like cytoplasmic kinase CDG1 negatively regulates Arabidopsis pattern-triggered immunity and is co-opted by the Pseudomonas syringae effector AvrRpm1

city: Guangzhou

first: Yang

middle: Qiu

last: Jiao

state: Guangdong

address: No.132, East Outer Ring Road

department: Academy of Life Science

institute: Sun Yat-Sen University

summary: In this study, we conducted protoplast-based gain-of-function assay to screen 23 members of the RLCK VII family for those whose overexpression can affect flg22-induced MAPK activation. We identified CDG1, a previously characterized positive regulator in brassinosteroid (BR) signaling (Kim et al., 2011), as a new negative regulator of flg22-triggered MAPK activation. We further found that CDG1 could constitutively associate with FLS2 and CERK1, and its transgenic overexpression could significantly reduce the abundances of these two essential PRRs, leading to impaired immune responses to both flg22 and chitin as well as increased susceptibility to bacterial and fungal pathogens. Surprisingly, the CDG1-mediated degradation of FLS2 and CERK1 is independent of E3 ubiquitin ligases PUB12/PUB13, but requires the kinase activity of MEKK1, a MAPKKK positively regulating plant innate immunity (Asai et al., 2002). Moreover, we demonstrated that RIN4 and the P. syringae effector AvrRpm1 could also interact with CDG1, and obtained evidence that CDG1 may be one of the RLCK VII members responsible for the AvrRpm1-induced RIN4 phosphorylation. Our data thus reveal multifaceted moonlight function of CDG1 in Arabidopsis innate immunity in addition to its originally characterized role in BR signaling.

overall_design: We noted that the growth defects of CDG1 OE plants were largely suppressed in the mekk1/pMEKK1::MEKK1K361M-FLAG/CDG1 OE (hereafter referred to as MEKK1K361M/CDG1 OE) plants. We want to know which genes transcriptional level variation leads the growth defects  of CDG1 OE .So we prepared the samples for RNAseq. We use 4 samples, WT is control. There are not repetitions.

first: Q

last: Yang

first: J

last: Guo

first: H

last: Zeng

first: L

last: Xiu

first: Jian-Feng

last: Li


title: Total RNA expression profiling in mesenteric arteries of mice infused or not with angiotensin II for 7 and 14 days

city: Montreal

first: Pierre

last: Paradis

state: QC

address: 3755 ch. de la Côte-Sainte-Catherine

country: Canada

institute: Lady Davis Institute for medical research, Jewish General Hospital, McGill University

summary: We used next-generation sequencing (NGS) to profile total RNA in small arteries of mice infused or not with angiotensin (Ang) II for 7 and 14 days. The goal was to identify differentially expressed genes that are associated with Ang II-induced vascular injury and hypertension.

overall_design: Ten to 12-week-old male C57BL/6J WT (Harlan laboratories, Indianapolis, IN) mice were infused SC with Ang II (1000 ng/kg/min) with ALZET osmotic mini pumps (model 1002, Durect Corporation) for 7 or 14 days. Control mice underwent sham surgery. At the end of the treatments, total RNA was extracted from mesenteric arteries for RNA profiling using NGS by Illumina HiSeq 2500.

first: K

last: Huo

first: Chantal

last: Richer

first: Olga

last: Berillo

first: Nada

last: Mahjoub

first: Julio

middle: C

last: Fraulob-Aquino

first: Tlili

last: Barhoumi

first: Sofiane

last: Ouerd

first: Suellen

last: Coelho

first: Daniel

last: Sinnett

first: Ernesto

last: Schiffrin


title: Chromodomain Helicase DNA-binding 4 (CHD4) is required for B cell identity and lineage progression

city: Denver

first: James

middle: R

last: Hagman

state: Colorado

address: 1400 Jackson St

department: Biomedical Research

country: USA

institute: National Jewish Health

summary: B cell specification and identity are controlled by transcription factors and cytokine receptors that drive the expression of stage-specific transcriptomes during lineage progression. A key feature of these mechanisms is the repression of inappropriate transcription. Here, we utilized RNA-seq to demonstrate that chromodomain helicase DNA-binding protein 4 (CHD4), an ATPase/helicase subunit of Mi-2/NuRD chromatin remodeling complexes, is essential for B cell identity. In mice that lack CHD4 selectively in the B lineage, defects include developmental arrest at the early pro-B cell stage. While many pro-B-specific genes are expressed in the mutant cells, transcripts that are normally restricted to other tissues including pancreas and bone are expressed out of context. Moreover, CHD4-deficient pro-B cells do not proliferate in response to IL-7, exhibit greatly decreased utilization of distal VH segments and accumulate DNA damage. Together, our data confirm the importance of CHD4 and NuRD complexes for the generation of functional B cells.

overall_design: RNA-seq transcriptome analysis of three independent RNA samples each from wild type or Chd4 conditional knockout pro-B cells sorted as B220+CD43+CD24+BP1-IgM- bone marrow cells. Following analysis of RNA-seq, the mutant cell population was found to have increased enrichment of plasmacytoid dendritic cells. The data was not used in the publication, 'Arends, T, C Dege, A Bortnick, et al. CHD4 is essential for transcriptional repression and lineage progression in B lymphopoiesis. PNAS USA [Epub ahead of print]. (PMID: 31085655)'.

first: C

last: Dege

first: T

last: Arends

first: A

last: Bortnick

last: Jia

first: D

last: Straign

last: Harmacek

last: Walton

first: S

middle: M

last: Leach

last: Danhorn

middle: J

last: Feeney

last: Murre

first: B

last: O'Connor


title: miRNA expression profiling in mesenteric arteries of mice infused or not with angiotensin II for 7 and 14 days

first: Pierre

last: Paradis

type: Non-coding RNA profiling by high throughput sequencing

summary: We use next-generation sequencing (NGS) to profile miRNA in small arteries of mice infused with angiotensin (Ang) II for 7 and 14 days. The goal is to identify differentially expressed miRNAs that are associated with Ang II-induced vascular injury and hypertension.

overall_design: Ten to 12-week-old male C57BL/6J WT (Harlan laboratories, Indianapolis, IN) mice were infused SC with Ang II (1000 ng/kg/min) with ALZET osmotic mini pumps (model 1002, Durect Corporation) for 7 or 14 days. Control mice underwent sham surgery. At the end of the treatments, total RNA was extracted from mesenteric arteries for miRNA profiling using NGS by Illumina HiSeq 2500.

first: K

last: Huo

last: Richer

last: Berillo

last: Mahjoub

last: Fraulob-Aquino

last: Barhoumi

last: Ouerd


title: Molecular expression in endometrial biopsies of non-viable ectopic and intrauterine pregnancies.

status: Public on May 21 2019

city: Joint Base Lewis-McChord

first: Zachary

middle: Tyler

last: Colburn

state: WA

address: 9040A Jackson Ave

department: Department of Clinical Investigation

institute: Madigan Army Medical Center

summary: Ectopic pregnancy is the leading cause of morbidity and mortality among women in the first trimester. A reliable diagnostic test for the detection of ectopic pregnancy in cases of non-viable pregnancy of unknown location (NV-PUL) is needed.  The objective of the current study is to prospectively validate our previous findings of a 12-cilia gene classifier for the identification of ectopic pregnancy. Molecular interrogation is performed to define differences in molecular expression profiles in ectopic and abnormal intrauterine pregnancies. These samples come from a prospective cohort study comparing transcriptome profiles from women with ectopic pregnancy (ECT) or non-viable intrauterine pregnancy (NV-IUP). Samples were analyzed with the Affymetrix Human Gene 2.0 ST Array.

overall_design: 13 endometrial biopsies taken from women with non-viable intrauterine (n=1) and ectopic (n=12) pregnancies

first: Jessica

last: Lentscher

middle: T

first: Nicole

last: Ortogero

first: Laurel

last: Gillette

first: Richard

middle: O

last: Burney

first: Gregory

last: Chow


title: Development of a general defined media for Pichia pastoris

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

summary: Pichia pastoris is widely used as a host for recombinant protein production. More than 500 proteins have been expressed in the organism at a variety of cultivation scales, from small shake flasks to large bioreactors. Large-scale fermentation strategies typically employ chemically-defined growth media because of its greater batch-to-batch consistency and in many cases, lower cost compared to complex media. For biopharmaceuticals, defined growth media may also simplify downstream purification and regulatory documentation. Standard formulations of defined media for Pichia are minimal ones that lack the metabolic intermediates provided by complex components such as peptone and yeast extract. As a result, growth rates and per-cell productivities are significantly lower than in complex media. We have designed an improved defined media for Pichia pastoris, rich defined medium (RDM), by systematically evaluating nutrients of increasing complexity and identifying those that are most critical for growth. We have also demonstrated the use of RDM for expression of three heterologous proteins, at titers comparable to or higher than in standard complex medium. Rich defined medium has the potential to improve productivity of Pichia pastoris fermentations and accelerate process development for new molecules.

overall_design:
There are 12 samples, representing 3 conditions and 4 replicates for each condition. The 3 conditions are different media formulations
---------------------
mcbart_FPKM.xlsx.gz: normalized abundance measurements
mcbart_rawcounts.xlsx.gz: raw counts
WT.v1.fa.gz: fasta format genome assembly
phaffii_WT.c2.gtf.gz: gtf format gene annotation file
mcbart_GeneIDtoSymbol.xlsx.gz: excel file linking gene IDs in gtf file to informative symbols

first: M

last: Bartlett

first: Angel

last: Kuo

first: Kerry

last: R Love

first: J

last: Love


title: Expression profiling in mesenteric arteries of mice infused or not with angiotensin II for 7 and 14 days

last: Paradis


title: Differences in gene expression between WT and IRF2 KO cells

city: South San Francisco

first: Rohit

last: Reja

state: CA

address: 1 DNA Way

institute: Genentech

summary:
Gasdermin-D (GSDMD) is cleaved by caspase-1/4/11 in response to canonical and non-canonical inflammasome activation. Upon cleavage,
GSDMD oligomerizes and forms membrane pores, resulting in IL-1Î² secretion, pyroptotic cell death and inflammatory pathologies including periodic
fever syndromes and septic shock â a plague on modern medicine. The transcriptional machinery that drives the expression of GSDMD is unknown.
Here we show that IRF2, a member of the interferon-regulatory factor (IRF) family, is essential for the transcriptional activation of GSDMD.
A forward genetic screen with ethyl-N-nitrosourea (ENU)-mutagenized mice unequivocally linked IRF2 to inflammasome signaling. Indeed,
GSDMD transcript levels were highly attenuated in Irf2â/â macrophages upon Irf2 deficiency in macrophages, endothelial cells, and multiple organs,
corresponding to attenuated IL-1Î² secretion and inhibited pyroptosis. Mechanistically, IRF2 binds a previously uncharacterized site within the GSDMD
promoter to directly drive GSDMD transcription for execution of pyroptosis in response to canonical and non-canonical inflammasome activation.
Our data illuminate a prominent transcriptional mechanism for the expression of GSDMD, a key mediator of inflammatory pathologies.

overall_design:
RNA was extracted from HOXB-8 cells for the following genotypes
- Irf2 wild type (Parental) and Irf2 knock out(IRF2 KO).


title: Histone mark modifications in murine ovary after gestational exposure to chlordecone

city: Rennes

first: Fatima

last: SMAGULOVA

address: 9 av. Prof. Léon Bernard

institute: Irset - U1085

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We hypothesized that gestational exposure to chlordecone can lead to alteration of murine ovary's epigenetic landscape. To test our hypothesis, we exposed mice to chlordecone during embryonic development and we analyzed F1 female progeny epigenetic mark H3K4me3 in ovaries. We performed ChIP using anti-H3K4me3 commercial antibody (Merck Millipore, 07-473). DNA-protein complexes were immunoprecipitated, eluted and then DNA were purified.

overall_design: We exposed mice to chlordecone during embryonic development and we analyzed F1 female progeny epigenetic mark H3K4me3 in ovaries.

last: Smagulova

first: Louis

last: Legoff


title: Comprehensive analysis of circulating microRNAs in plasma of patients with pituitary adenomas

city: Budapest

first: Kinga

last: Nemeth

address: Szentkiralyi street 46

department: Department of Laboratory Medicine

country: Hungary

institute: Semmelweis University

summary: Background: Circulating miRNAs in pituitary adenoma would help patient care especially in non-functioning adenoma cases as minimally invasive biomarkers of tumor recurrence and progression.  Aim: Our aim was to investigate plasma miRNA profile in patients with pituitary adenoma.  Materials and Methods: 149 plasma and extracellular vesicle (preoperative, early- and late postoperative) samples were collected from 45 pituitary adenoma patients. Adenomas were characterized based on anterior pituitary hormones and transcription factors by immunostaining. MiRNA next generation sequencing was performed on 36 samples (discovery set). Individual TaqMan assay was used for validation on extended sample set. PA tissue miRNAs were evaluated by TaqMan array and literature data.  Results: Global downregulation of miRNA expression was observed in plasma samples of pituitary adenoma patients compared to normal samples. Expression of 29 miRNAs and isomiR variants were able to distinguish preoperative plasma samples and normal controls. MiRNAs with altered expression in both plasma and different adenoma tissues were identified. 3, 7 and 66 miRNAs expressed differentially between preoperative and postoperative plasma samples in growth hormone secreting, FSH/LH+ and hormone-immunonegative groups, respectively. MiR-143-3p was downregulated in late- but not in early postoperative plasma samples compared to preoperative ones exclusively in FSH/LH+ adenomas. Plasma level of miR-143-3p discriminated these samples with 81.8% sensitivity and 72.3% specificity (AUC=0.79; p=0.02).  Conclusions: Differentially expressed miRNAs in pituitary adenoma tissues have low abundance in plasma minimizing their role as biomarkers. Plasma miR-143-3p decreases in patients with FSH/LH+ adenoma indicated successful surgery, but its application for evaluating tumor recurrence needs further investigation.

overall_design: Altogether 38 plasma samples were analysed by high-throughput miRNA expression profiling. 36 samples were obtained from 18 pituitary adenoma patients before and after pituitary adenoma removal, and 2 samples were derived from healthy volunteers without any known disease.

first: Henriett

last: Butz


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

city: Beijing

first: Fan

last: Xiaolong

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

institute: Beijing Normal University

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

overall_design: Over 200 glioma samples were divided into training, validation and test cohort and were then tested by a custom Taqman Low Density Array which contains 44 classifiers and 4 reference genes. The result data were used to train and validate an individual EM/PM GEP subtype predictor using SVM algorithm for glioma.

first: Jiuyi

last: Li

first: Anna

last: Wenger

first: Yang

last: Xue

first: Zeng

last: Wang

first: Boglarka

middle: F

last: Rydenhag

first: Bertil

first: Chuanbao

last: Zhang

first: Asgeir

middle: S

last: Jakola

first: Tao

last: Jiang

first: Helena

last: Carén

first: Xiaolong

last: Fan


title: Unveiling the roles of metabolites and gene regulation in sexual maturation and spawning of blunt snout bream (Megalobrama amblycephala)

city: wuhan

first: lifang

last: liu

address: HZAU

institute: HZAU

summary: The endocrine changes and gene regulation patterns responding to sexual maturation and spawning have not been clarified in fish species. To identify the potential metabolites and genes regulating the ovarian development and spawning, we employed the approach integrating the metabolic and RNA-seq techniques to investigate the metabolites and candidate genes participating in the sexual maturation and spawning of female blunt snout bream Megalobrama amblycephala. This data descriptor provides metabolic and transcriptomic information for the blood tissue at different developmental stages of female M. amblycephala. With UPLC-MS/MS method, a total of 763 and 173 differential ions were detected from the pairwise comparisons of the four groups in positive and negative mode, respectively. Meanwhile, 191.65 Mb raw reads were generated using illumina Hiseq platform with 50 bp single-end strategy. We then analysed the differential metabolites and differentially expressed genes and their functions among the four groups. This data descriptor will contribute to understanding the dynamics of metabolites and gene regulation in ovarian development and spawning and reuse to support physiological and genetic researches in aquaculture.

overall_design: In this study, we integrated transcriptomic and metabolomics approaches to comprehensively detect the metabolites and gene expression profiling in blood tissue of M. amblycephala from four groups, i.e., 1-year-old immature females, 2-year-old immature females, 2-year-old mature females and the females after successful spawning, each have two replicates.

first: Ze-Xia

last: Gao

first: Shaokui

last: Yi

first: Lai-Fang

last: Zhou

first: Li-Fang

last: Liu

first: Bo-Wen

last: Zhao


title: A mutagenic screen identifies a TonB-dependent receptor required for the lanthanide metal switch in the Type I methanotroph “Methylotuvimicrobium buryatense” 5GB1C

city: Seattle

first: Mitchell

middle: William

last: Pesesky

address: 616 NE Northlake Place

institute: University of Washington

summary: Several of the metabolic enzymes in methanotrophic bacteria rely on metals for both their expression and their catalysis. The MxaFI methanol dehydrogenase enzyme complex uses calcium as a cofactor to oxidize methanol, while the alternative methanol dehydrogenase XoxF uses lanthanide metals such as lanthanum and cerium for the same function. Lanthanide metals, abundant in the earth’s crust and widely used in electronic devices, strongly repress the transcription of mxaF yet activate the transcription of xoxF. This phenomenon of mxaF repression and xoxF activation in the presence of lanthanides is called the “lanthanide switch.” To better understand components of the lanthanide switch in the Type I gammaproteobacterial methanotroph “Methylotuvimicrobium buryatense” 5GB1C, we designed a mutagenesis system and selected for mutants unable to repress the mxaF promoter in the presence of lanthanum. Whole genome resequencing for multiple lanthanide switch mutants identified several unique point mutations in a single gene encoding a TonB-dependent receptor, which we have named LanA. While the LanA TonB-dependent receptor is absolutely required for the lanthanide switch, it does not affect lanthanum uptake by the bacterium. Deletion of a separate lanthanide-repressible gene encoding a TonB protein had no effect on the lanthanide switch or on lanthanum uptake. The discovery of this novel component of the lanthanide regulatory system highlights the complexity of this circuit and suggests further components are likely involved.

overall_design: Wild-type and lanA mutants were each assesed in the presence and absence of lanthanum, with two biological replicates for each strain in each condition (total 8 samples).

first: Joseph

middle: D

last: Groom

first: Stephanie

last: Ford

middle: W

first: Mary

last: Lidstrom


title: Interrupted reprogramming into induced pluripotent stem cells does not rejuvenate human mesenchymal stromal cells

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

institute: RWTH Aachen University

summary: Replicative senescence hampers application of mesenchymal stromal cells (MSCs) because it limits culture expansion, impairs differentiation potential, and hinders reliable standardization of cell products. MSCs can be rejuvenated by reprogramming into induced pluripotent stem cells (iPSCs), which is associated with complete erasure of age- and senescence-associated DNA methylation (DNAm) patterns. However, this process is also associated with erasure of cell-type and tissue-specific epigenetic characteristics that are not recapitulated upon re-differentiation towards MSCs. In this study, we therefore followed the hypothesis that overexpression of pluripotency factors under culture conditions that do not allow full reprogramming might reset senescence-associated changes without entering a pluripotent state. MSCs were transfected with episomal plasmids and either successfully reprogrammed into iPSCs or cultured in different media with continuous passaging every week. Overexpression of pluripotency factors without reprogramming did neither prolong culture expansion nor ameliorate molecular and epigenetic hallmarks of senescence. Notably, transfection resulted in immortalization of one cell preparation with gain of large parts of the long arm of chromosome 1. Taken together, premature termination of reprogramming does not result in rejuvenation of MSCs and harbours the risk of transformation. This approach is therefore not suitable to rejuvenate cells for cellular therapy.

overall_design: The Affymetrix CytoScan® HD Array was applied on DNA extracted from transfected human MSCs of donor 2 at passage 4 and 12 because cells displayed altered morphology and immunophenotype at late passage. Consequently, we performed copy number variation (CNV) analysis to look for possible contaminations with other cell lines or chromosomal aberrations at late passage.

first: Carolin

last: Goebel

first: Roman

last: Goetzke

first: Thomas

last: Eggermann


title: CRISPR-Cas9 screening of KSHV-transformed cells identifies XPO1 as a vulnerable target of cancer cells by inducing p62 SQSTM1-mediated p53 activation in PML bodies

city: Xuzhou

first: Hui

state: Jiangsu

address: #1 Daxue Road

institute: China University of Mining and Technology

summary: Mislocalization of oncogenes and tumor suppressors resulting from aberrant nuclear export promotes uncontrolled cell proliferation and growth transformation of cancer cells. We performed a genome-wide CRISPR-Cas9 screening in matched primary and KSHV-transformed cells, and identified genes that were pro-growth and growth-suppressive of both types of cells, of which exportin XPO1 was a critical factor for the survival of transformed cells. Using XPO1 inhibitor KPT-8602 and by siRNA-mediated knockdown, we confirmed the essential role of XPO1 in cell proliferation and growth transformation of KSHV-transformed cells, as well as cell lines of other types of cancer including gastric cancer and liver cancer. XPO1 inhibition induced cell cycle arrest and p53 activation, which depended on the formation of PML nuclear bodies. Furthermore, XPO1 induced relocalization of autophagy adaptor protein p62 (SQSTM1), recruiting p53 for activation in PML nuclear bodies. Our findings highlight a novel mechanism of p53 activation and identify XPO1 as a vulnerable target of cancer cells.

overall_design: To identify key genes responsible for KSHV-related survival, a CRISPR pooled libraries containing sgRNAs that specifically target all known cellular genes were transduced into Cas9-expressing KSHV-transformed primary rat mesenchymal embryonic stem cells (KMM) and control primary rat mesenchymal stem cells (MM). Genomic DNA from surviving MM and KMM cells at day 1, 4, 11 and 21 post-transduction were collected and sequenced, and the results were analyzed for the gain or loss of sgRNAs.

first: Marion

last: Gruffaz

first: Hongfeng

last: Yuan

first: Sangsu

last: Bae

first: Jin-Soo

last: Kim

first: Chun

last: Lu

first: Yufei

last: Huang

first: Shou-Jiang


title: RNA-seq-based transcriptome profiling of hawk tea extract (HTE)-fed hypercholesterolemic rat livers

first: Juan

last: Feng

address: No.30, Shuangqing Road, Haidian District

department: School of Medicine

institute: Tsinghua University

summary: The  high-fat diet (HFD)-feeding significantly stimulated hypercholesterolemia in male SD rats. Simultaneous feeding of hawk tea extracts (HTE) reversed the hypercholesterolemia in rats by lowering the serum total cholesterol and low-density lipoprotein cholesterol levels. To understand the molecular mechanism underlying the cholesterol-lowering effects of HTE, we performed the RNA-seq analysis. Consequently, the change in mRNA levels of genes invovled in metabolism of lipid and lipoprotein, primary bile acid synthesis, and ABC transporters itriggered by HFD-feeding were reversed by the co-administration of HTE (200 mg/kg/day for 11 weeks).

overall_design: Liver mRNA profiles of rats fed on ND, HFD, HFD+HTE were generated by RNA sequencing in triplicate per group.

first: Ruijun

last: Wang

first: Lan

last: Xie


title: Natural genetic variation reveals key features of epigenetic and transcriptional memory in virus-specific CD8 T cells

city: Shanghai

first: Yi

last: Zhong

address: 227 South Chongqing Rd.

institute: SJTU

summary: Stable changes in chromatin states and gene expression in cells of the immune system form the basis for their memory of infections and other challenges. We used naturally occurring cis-regulatory variation in wild-derived inbred mouse strains to explore the mechanisms underlying long-lasting vs. transient gene regulation in antigen-specific CD8 T cells responding to acute viral infection. Our observations provide novel insights into the mechanisms driving stable and reversible transcriptional and epigenetic memory in virus-specific CD8 T cells. These findings suggest a general mechanism for the formation of epigenetic memory in CD8 T cells and other immune and non-immune cells.

overall_design: The project studied the chromatin accessibility and gene transcription of CD8+ T cell in response to viral infection. 70 samples were analysed in total, including 22 ATAC-Seq, 29 RNA-Seq, 18 ChIP-Seq and 1 single cell RNA-Seq samples.

first: Joris

last: van der Veeken

first: Roshan

last: Sharma

first: Linas

last: Mazutis

first: Phuong

last: Duo

first: Dana

last: Pe’er

first: Christina

last: Leslie

first: Alexander

last: Rudensky


title: UM171 expands distinct types of myeloid and lymphoid progenitors from human pluripotent stem cells.

city: Madison

first: Oleg

last: Moskvin

state: WI

address: 1220 Capitol Court

institute: University of Wisconsin-Madison

summary: Overall, our studies revealed that UM171 differentially enriches specific populations of hematopoietic progenitors, in HSC expansion and lymphoid culture conditions, and that it is a potent small molecule agonist for expansion of granulocytic progenitors and lymphoid progenitors from hPSCs.

overall_design: hPSC derived hematopoietic progenitors generated from H1 hESCs on day 9 of differerntiation (Uenishi et all, Stem cell Reports, 2014) expanded for 16 hrs or 5 days with UM171 were subject to gene expression profiling . DMSO treated hPSC derived hematopoietic progenitors were used as the vehicle control.

first: Igor

last: Slukvin

first: Walatta

last: Mesquitta

first: Scott

last: Swanson

first: Matthew

last: Wandsnider


title: Analysis of miRNA-seq in the liver of common carp (Cyprinus carpio L.) in response to different environmental temperatures

city: Haikou

first: JunLong

last: Sun

state: Hainan

address: No.58 Renmin Avenue, Haikou City, Hainan Province

institute: Hainan University

summary: We found a total of 110 known miRNAs were identified by aligning the sequencing data with the known C. carpio miRNAs listed in miRBase 20.0. From 29 known miRNAs that were differentially expressed in low- and high-temperature groups, as compared with in control group, we selected 10 (let-7a, miR-135c, miR-184, miR-203a-3p, miR-210-3p, miR-27d, miR-301a, miR-92b-3p, miR-187 and miR-10d-5p) for validation by quantitative real-time PCR. Bioinformatics tools were used to predict the potential target genes of differentially expressed miRNAs. Gene Ontology and KEGG enrichment analysis indicated that the miRNAs may play important roles in metabolism and processing information about the environment, thus enabling common carp to adapt to their immediate environment. Specifically, we considered the insulin-signaling pathway and glycerophospholipid metabolism pathways. The results show that the gpam gene was negatively regulated by miR-301a and miR-27d, and miR-210 was negatively regulated by the prkaa1 gene in the insulin-signaling pathway. In glycerophospholipid metabolism pathways, the psid and agpat3 genes were negatively regulated by miR-302b-5p and miR-9-5p, respectively; the cdipt and gpam genes were negatively regulated by miR-27d; and the pgs1 gene was negatively regulated by miR-92b-3p and miR-155. These findings suggest that significant changes occur in the energy metabolism and metabolic processes associated with components of the cell membrane of carp at different environmental temperatures. The new data provide a foundation for further studies of the role of miRNAs in environmental adaptation in fish and may help to identify novel targets for additional study, with applications for reducing environmental stress in farmed fish.

overall_design: We used small RNA sequencing to detect miRNA transcriptomes of liver from common carp with low temperature group (LTG) and high temperature group (HTG) compared them with control libraries (CG) (3 vs. 3).

first: Junlong

first: Song

last: Yang


title: Individual Assignment of Adult Diffuse Gliomas into the EM/PM Molecular Subtypes

first: Fan

last: Xiaolong

type:
Expression profiling by array
Expression profiling by RT-PCR

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

overall_design: Refer to individual Series


title: NCOA5 knockout suppresses epithelial-to-mesenchymal transition (EMT) impairing cell proliferation and migration in Hepatocellular Carcinoma cells

first: Jingcai

last: He

address: 13 Shi Liu Gang Avenue

institute: TCM-Integrated Cancer Center of Southern Medical University

summary: Nuclear receptor coactivator 5 (NCOA5) is an AF2-independent coactivator that contains both transcriptional activation and repression domains. Previous studies have shown that NCOA5 plays an important role in the development of a variety of malignancies. However, the underlying mechanisms remain unclear. In our study, we successfully generated the NCOA5 knockout liver cancer cell lines by CRISPR/Cas9 -mediated genome editing and found that NCOA5 knockout inhibited the proliferation and migration of hepatocellular carcinoma (HCC) cells significantly, meanwhile led to a marked decrease in tumor microsphere formation. Furthermore, mechanistic analyses indicated that NCOA5 knockout can inhibit the EMT process. In this study, knocking out NCOA5 in hepatoma cells LM3 with CRISPR/Cas9 provides an important cellular model for studying role of NCOA5 in HCC. In conclusion , Oour study provides new insights and evidence that NOCA5 was significantly correlated with the progression of HCC and was particularly involved in EMT.

overall_design: Hepatocellular Carcinoma cells  mRNA profiles of wide type(WT) and NCOA5 knockout LM3 cells were generated by deep sequencing, using Illumina HiSeq.

first: Rongcheng

last: Luo


title: Gene expression profiling of primary HER2-positive breast cancers before and after brief exposure to single agent neoadjuvant trastuzumab

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

summary: Tumor incisional biopsies were obtained at baseline and after brief-exposure to single-agent trastuzumab from patients enrolled on the TRastuzumab-UPfront-in-HER2-positive-locally-advanced- BC (TRUP) window-of-opportunity trial. Gene expression profiling was conducted on these tumor biopsies to identify transcriptional features at baseline and changes upon brief-exposure to trastuzumab associated with response to short term trastuzumab and the complete pre-operative therapy

overall_design: Gene expression profiling was performed using RNA from frozen core biopsies from 17 patients with primary HER2-positive (HER2+) tumors before and after brief-exposure treatment with single agent neoadjuvant trastuzumab.

first: Tiziana

last: Triulzi


title: Analysis of gene expression in colorectal cancer RKO cells with UHRF1 depletion and HDAC inhibition

city: Sapporo

first: Hiromu

last: Suzuki

state: Hokkaido

address: S1, W17, Chuo-ku

department: Department of Molecular Biology

country: Japan

institute: Sapporo Medical University

summary: UHRF1 is a major regulator of epigenetic mechanism and is overexpressed in various human malignancies. In this study, we examined the involvement of UHRF1 in aberrant DNA methylation in colorectal cancer (CRC). In CRC cells, transient UHRF1 knockdown rapidly induced DNA demethylation across entire genomic regions, including CpG islands, gene bodies and repetitive elements. Nonetheless, UHRF1 depletion only minimally reversed CpG island hypermethylation-associated gene silencing. However, the combination of UHRF1 depletion and histone deacetylase (HDAC) inhibition synergistically reactivated the silenced genes and strongly suppressed CRC cell proliferation. Our results suggest that (i) maintenance of DNA methylation in CRC cells is highly dependent on UHRF1; (ii) UHRF1 depletion rapidly induces DNA demethylation, though it is insufficient to fully reactivate the silenced genes; and (iii) dual targeting of UHRF1 and HDAC may be an effective new therapeutic strategy.

overall_design: RKO cells were transfected with a control siRNA (Thermo Fisher Scientific) or siRNAs targeting UHRF1 (Thermo Fisher Scientific) using using Lipofectamine RNAiMAX (Thermo Fisher Scientific) and incubated for 72 h. Cells were then treated with mock (ethanol) or 300 nM Trichostatin A (TSA) for additional 24 h. RKO cells were also treated with AZA.


title: NUP155 insufficiency recalibrates a pluripotent transcriptome with network remodeling of a cardiogenic signaling module  of a pluripotent network

city: Sioux Falls

first: Randolph

last: Faustino

state: SD

address: 2301 East 60th Street North

department: Genetics and Genomics

institute: Sanford Research

summary:
Background: Atrial fibrillation is a cardiac disease driven by numerous idiopathic etiologies. NUP155 is a nuclear pore complex protein that has been identified as a clinical driver of atrial fibrillation, yet the precise mechanism is unknown. The present study employs a systems biology algorithm to identify effects of NUP155 disruption on cardiogenicity in a model of stem cell-derived differentiation.
Methods: Embryonic stem (ES) cell lines (n=5) with truncated NUP155 (Nup155+/-) were cultured in parallel with wild type (WT) ES cells (n=5), and then harvested for RNAseq. Samples were run on an Illumina HiSeq 2000. Reads were analyzed using Strand NGS, Cytoscape, DAVID and Ingenuity Pathways Analysis to deconvolute the NUP155-disrupted transcriptome. Network topological analysis identified key features that controlled framework architecture and functional enrichment.
Results: In NUP155 truncated ES cells, significant expression changes were detected in 326 genes compared to WT. These genes segregated into clusters that enriched for specific gene ontologies. Major network drivers included TP53, a regulator of genome integrity. Deconvolution of the collective framework into discrete sub-networks identified a module with the highest score that enriched for Cardiovascular System Development, and revealed NTRK1/TRKA and SRSF2/SC35 as critical hubs within this cardiogenic module.
Conclusions: The strategy of pluripotent transcriptome deconvolution used here identified a novel association of NUP155 with potential drivers of arrhythmogenic AF. Here, NUP155 regulates cardioplasticity of a sub-network embedded within a larger framework of genome integrity, and exemplifies how transcriptome cardiogenicity in an embryonic stem cell genome is recalibrated by nucleoporin dysfunction.

overall_design: Embryonic stem (ES) cell lines (n=5) with truncated NUP155 were cultured in parallel with wild type (WT) ES cells (n=5), harvested for RNAseq and run on an Illumina HiSeq 2000.

first: Claudia

last: Preston


title: Analysis of gene expression in colorectal cancer DLD1 cells with UHRF1 depletion and HDAC inhibition

overall_design: DLD1 cells were transfected with a control siRNA (Thermo Fisher Scientific) or siRNAs targeting UHRF1 (Thermo Fisher Scientific) using using Lipofectamine RNAiMAX (Thermo Fisher Scientific) and incubated for 48 h. Cells were then treated with mock (ethanol) or 300 nM Trichostatin A (TSA) for additional 24 h.


title: Analysis of DNA methylation in colorectal cancer RKO cells with UHRF1 depletion and HDAC inhibition

type: Methylation profiling by genome tiling array

overall_design: RKO cells were transfected with a control siRNA (Thermo Fisher Scientific) or siRNAs targeting UHRF1 (Thermo Fisher Scientific) using using Lipofectamine RNAiMAX (Thermo Fisher Scientific) and incubated for 72 h. Cells were then treated with mock (ethanol) or 300 nM Trichostatin A (TSA) for additional 24 h.


title: Infection with Chlamydia trachomatis reprograms human cells through inhibition of protein synthesis

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

institute: University of Lübeck

summary: The obligate intracellular bacterium Chlamydia trachomatis replicates in a cytosolic vacuole in human epithelial cells. Infection of human cells with C. trachomatis causes substantial changes to many host cell signalling pathways but the molecular basis of such influence is not well understood. Studies of gene transcription of the infected cell have shown altered transcription of many host cell genes, indicating a transcriptional response of the host cell to the infection. We here describe that infection of human cells with C. trachomatis as well as infection of murine cells with C. muridarum profoundly inhibits protein synthesis of the infected host cell. This inhibition was accompanied by changes to the ribosomal profile of the infected cell indicative of a block of translation initiation, most likely as part of a stress response. The chlamydial protease CPAF also reduced protein synthesis in uninfected cells although CPAF-deficient C. trachomatis showed no defect in this respect. Analysis of polysomal mRNA as a proxy of actively transcribed mRNA identified a number of biological processes differentially affected by chlamydial infection. Mapping of differentially regulated genes onto a protein interaction network identified nodes of up- and down-regulated networks during chlamydial infection. Proteomic analysis of protein synthesis further suggested translational regulation of host cell functions by chlamydial infection. These results demonstrate reprogramming of the host cell during chlamydial infection through the alteration of protein synthesis.

overall_design: HeLa cells were infected with C. trachomatis L2 for 33h or left untreated and polysomal as well as total RNA was isolated.

first: Melanie

last: Boerries

first: Michaela

last: Ohmer

first: Tina

last: Tzivelekidis

first: Georg

last: Häcker


title: Analysis of DNA methylation in colorectal cancer DLD1 cells with UHRF1 depletion and HDAC inhibition


title: TAp73 functions through posttranscriptional codes in brain multiciliogenesis

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

summary: Although being essential to respiratory and reproductive tracts multiciliogenesis, TAp73 is dispensable for multiciliogenesis in the ventricles. TAp73 KO is accompanied by dramatic changes in ciliogenic microRNAs miR34bc and miR449 family members, suggestin TAp73 functions partially thorugh posttranscriptional nodes in brain ciliogenesis.

overall_design: Total RNA from WT and TAp73 KO lateral ventricles/CP were isolated by phenol/chloroform method.

first: Merit

last: Wildung

first: Tilman

middle: U

last: Esser

first: Katie

middle: B

last: Grausam

first: Cornelia

last: Wiedwald

first: Li

last: Li

first: Jessica

last: Zylla

first: Ann-Kathrin

last: Guenther

first: Magdalena

last: Wienken

first: Evrim

last: Ercetin

first: Felix

last: Bremmer

first: Orr

last: Shomroni

first: Stefan

last: Andreas

first: Haotian

last: Zhao

first: Muriel

last: Lizé


title: UHRF1 depletion and HDAC inhibition synergistically reactivate epigenetically silenced genes in colorectal cancer cells

first: Hiromu

last: Suzuki


title: Changes in transcript abundance in the shoot apex highlight chloroplast development

city: Rehovot

first: Gilgi

last: Friedlander

address: Hertzel st

country: Israel

institute: Weizmann Institute of Science

summary: In dicots, proplastids present in the central region of L2 layer of SAM that lack chlorophyll-binding proteins and thylakoid membranes, give rise to all green tissues of plants. These cells after a few cell divisions, reach to the periphery of the SAM, near the interface with the primordial leaves and acquire thylakoid membranes during this transition. We obtained [(i) proplastid containing, CZ, (ii) partially developed thylakoids containing, PZ and (iii) highly developed thylakoids containing, LP samples along this gradient with Laser microdissection, based on Chlorophyll fluorescence identification of cells. We performed RNA-seq with RNA obtained from these tissues, by using CEL sequencing (Cell Expression by Linear amplification and Sequencing) protocol. Similarly obtained RNA was also used for performing HT-qPCR on 190 genes from an initial list of 704 DEGs. Genes that passed the filters from the combined list were  denoted as DEGs .

overall_design: CEL sequencing was performed on three different samples in triplicate with Illumina HiSeq 2500.

first: Vijay

last: Dalal

first: Shlomi

last: Dagan

first: Ralph

last: Bock

first: Dana

last: Charuvi

first: Ziv

last: Reich

first: Zach

last: Adam


title: Nudt12 is an mRNA DeNADding Enzyme

status: Public on May 20 2019

city: Piscataway

first: Ronald

middle: P.

last: Hart

state: NJ

address: 604 Allison Rd Rm B430

department: Cell Biology & Neuroscience

institute: Rutgers University

summary: The 5´-end 7-methylguanosine cap structure has long been known as a signature feature of eukaryotic cellular and viral mRNAs that confers mRNA stability and efficient translation.  Recent findings in diverse organisms have demonstrated that RNAs can additionally possess a non-canonical cap structure consisting of a nicotinamide adenosine dinucleotide (NAD+) at their 5´ end in place of m7G.  It has been shown that 5´ end-NAD+ cap promotes rapid decay of the RNA at least in part by the DXO family of proteins in mammalian cells.  This observation led to the hypothesis that mammalian cells harbor additional deNADding enzymes that may function in distinct pathways.  Here we report Nudt12 efficiently removes NAD+ caps and functions as alternate cellular deNADding enzyme that targets NAD+-capped RNAs distinct from DXO.  Importantly, with the use of an NAD-Cap Detection (NAD-CapD) approach that utilizes enzymatic properties to release intact NAD+/NADH from the 5´ end of NAD-capped cellular RNAs and a colorimetric NAD Quantitation to detect released NAD+/NADH, we can follow total cellular NAD+ cap levels.  Removal of Nudt12 or DXO deNADding enzymes from cells significantly increased levels of NAD+-capped cellular RNAs.  Moreover, fungal Rai1 and Dxo1, previously demonstrated to possess deNADding activity in vitro, can also function as deNADding enzymes in yeast cells.  Double disruption of Rai1 and Dxo1 in yeast cells lead to accumulation of NAD+-capped RNAs, indicating that both enzymes function to clear NAD+ from the 5´ end of RNAs.  Finally, our findings established that alterations in cellular NAD+ levels impact NAD+-capped RNA levels implying NAD+ capping is a modulated process that may be linked to the metabolic state of the cell.

overall_design: Three replicates each of HEK293T-Nudt12-KO (N12-KO) cell RNA were prepared and enriched by NAD-Capture for sequencing library preparation and seqeuencing.  Results were compared with previously-published samples of HEK293T-WT and HEK293T-DXO-KO prepared by identical methods.

first: Ewa

last: Grudzien-Nogalska

first: Xinfu

last: Jiao

first: Megerditch

last: Kiledjian

middle: P


title: Single cell RNA-seq analysis of hair cell regeneration in the mammalian vestibular system and its potentiation by Atoh1

city: HOUSTON

first: Yichi

last: Niu

state: TX

address: ONE BAYLOR PALAZA

department: Molecular & human genetics

institute: Baylor college of medicine

summary: We used single cell RNA-seq to probe the transcriptional responses of utricle supporting cells to damage and Atoh1 transduction.

overall_design: mRNA profiles of 4-6 weeks old mice utricle supporting cell cultured for 10 days and supporting cells with overexpression of Atoh1 cultured for 10 days were generated by deep sequencing, using Illumina Nextseq 500.

first: Andrew

middle: K

last: Groves


title: Inducible histone K-to-M mutations are dynamic tools to probe the physiological role of site-specific histone methylation in vitro and in vivo [ATAC]

city: Boulder

first: Justin

last: Brumbaugh

state: CO

address: 347 UCB

department: Molecular, Cellular, and Developmental Biology

institute: University of Colorado Boulder

summary: Here, we developed mouse models expressing inducible lysine to methionine mutants of histone H3, which function as dominant negative inhibitors of methylation at their respective sites. Upon induction of H3K9M or H3K36M, we observed potent differentiation defects in stem cells and regenerative tissues. This work covers RNA-seq and ATAC-seq in this model system.

overall_design: ATAC-seq in blood stem and progenitor cells as well as embryoid bodies.

first: Fei

last: Ji


title: Inducible histone K-to-M mutations are dynamic tools to probe the physiological role of site-specific histone methylation in vitro and in vivo [RNA]

overall_design: RNA-seq in blood stem and progenitor cells, intestine, and testes.


title: Inducible histone K-to-M mutations are dynamic tools to probe the physiological role of site-specific histone methylation in vitro and in vivo


title: Differential expression of keratinocyte-derived extracellular vesicle miRNAs discriminate exosomes from apoptotic bodies and microvesicles

city: Brisbane

first: Dominic

last: Guanzon

state: Queensland

address: Building 71/918 RBWH Herston

department: UQCCR

country: Australia

institute: University of Queensland

summary: Extracellular vesicles (EVs) are mammalian cell-derived nano-scale structures enclosed by a lipid bilayer that were previously considered to be cell debris with little biological value. However, EVs are now recognized to possess biological function, acting as a packaging, transport and delivery mechanism by which functional molecules (i.e. miRNAs) can be transferred to target cells over some distance. To examine the miRNA from keratinocyte-derived EVs, we isolated three distinct populations of EVs from both HaCaT and primary human keratinocytes (PKCs) and characterized their biophysical, biochemical and functional features by using microscopy, immunoblotting, nanoparticle tracking, and next generation sequencing. We identified 1048; 906; and, 704 miRNAs, respectively, in apoptotic bodies (APs), microvesicles (MVs) and exosomes (EXs) released from HaCaT, and 608; 506; and, 622 miRNAs in APs, MVs and EXs released from PKCs. In which, there were 623 and 437 identified miRNAs common to three HaCaT-derived EVs and PKC-derived EVs, respectively. In addition, we found hundreds of exosomal miRNAs that were previously un-reported and that differences in the abundance levels of the identified EV miRNAs could discriminate between the three EV populations. These data contribute to EV-identified miRNA database, especially keratinocyte-derived EV miRNA content.

overall_design: miRNAs were profiled in extracellular vesicles (exosomes, microvesicles and apoptotic bodies) derived from primary keratinocytes.

first: Uyen

last: Than

first: Tony

last: Parker


title: Gene Expression Analysis of Dual-κ B cells in Lupus

city: Aurora

first: Roberta

last: Pelanda

address: 12800 East 19th Avenue

department: Immunology&Microbiology

institute: University of Colorado Anschutz Medical Campus

summary: Autoreactive B cells expressing two different immunoglobulin light chains are present in elevated numbers in a subset of systemic lupus erythematosus patients and in MRL and MRL/lpr mouse models of lupus. Using RNAseq and genetic pathway analyses together with in vitro studies we demonstrate a role for TLR and IFN signaling in MRL/lpr dual-κ B cell expansion and/or activation. Dual-κ cells also showed increased expression of co-receptors used for T cell cognate interaction as well as enrichment of pathways involved in their signaling. Overall, our studies identify molecular pathways involved in the enrichment of dual-reactive effector B cells and reveal potential targets for their selective ablation in autoimmunity.

overall_design: Examination of sorted single and dual-κ B cells from either the marginal zone or the follicles in the spleen of MRL/lpr lupus-prone mice.

first: Allison

last: Sang

first: Thomas

last: Danhorn

first: Brian

last: O'Connor

first: Sonia

last: Leach

first: Raul

last: Torres


title: An RpaA-dependent sigma factor cascade sets the timing of circadian transcriptional rhythms in Synechococcus elongatus

city: Cambridge

first: Kathleen

middle: Elizabeth

last: Fleming

address: 52 Oxford Street, NW Labs

department: Molecular and Cellular Biology

institute: Harvard University

summary: The circadian clock of the cyanobacterium Synechococcus elongatus PCC 7942 drives oscillations in global mRNA abundances with 24 hour periodicity under constant light conditions. The transcription factor RpaA, a circadian clock-regulated transcription factor, controls the timing of circadian gene expression, but the mechanisms underlying this control are not well understood. Here we show that four RpaA-dependent sigma factors – RpoD2, RpoD6, RpoD5, and SigF2 – are sequentially activated downstream of active RpaA and are required for proper expression of circadian mRNAs. We find that RpoD6, RpoD5, and SigF2 exhibit circadian oscillations with different timing relative to each other at the level of mRNA expression and protein abundance. By measuring global gene expression in strains modified to individually lack rpoD2, rpoD6, rpoD5, and sigF2 we identify how expression of circadian mRNAs – including sigma factor mRNAs – is altered in the absence of each sigma factor. Broadly, our findings suggest that a single transcription factor, RpaA, is sufficient to generate complex circadian expression patterns in part by regulating an interdependent sigma factor cascade.

sample_organism: Synechococcus elongatus PCC 7942 = FACHB-805

overall_design: Mapping of RNA polymerase locked at initiation sites over circadian time was determined by time-series ChIP-seq: immunoprecipitation of RNA polymerase bound to DNA in cells treated with rifampicin to lock RNA polymerase at initiation sites genome-wide.Transcriptome profiling by RNA-seq was performed over time in wild-type cells and in sigF2∆ cells in constant light conditions. Transcriptome profiling by RNA-seq was performed over time in OX-D53E cells (kaiBC∆, rpaA∆, Ptrc::rpaA(D53E), hereafter OX-D53E strain), in OX-D53E rpoD2∆ cells, in OX-D53E rpoD6∆ cells, and in OX-D53E rpoD5∆ cells grown in light following induction of active RpaA(D53E) by addition of IPTG after T=0h (dawn following two-consecutive 12h light-12h dark entrainment cycles).

middle: E

first: Erin

last: O'Shea


title: Single cell ATAC-seq identifies broad changes in neuronal abundance and gene regulation in Down Syndrome

city: Ithaca

first: Roman

last: Spektor

state: New York

address: 618 Tower Rd, Vet Research Tower, Room T2 007

institute: Cornell University

summary: To characterize cellular and molecular changes associated with Down Syndrome, we performed single-cell combinatorial indexing assay for transposase accessible chromatin using sequencing (sci-ATAC-seq) on cortices of adult Ts65Dn mice and control littermates.  Analyses of 13,766 cells revealed 26 classes of cells in the cortices of both genotypes.  The most abundant cells, a class of excitatory neurons, was reduced by (~17 %) in Ts65Dn mice; three of the four most common classes of interneurons were increased, with a total increase of ~50 % of all interneurons. Ts65Dn mice display changes in accessibility at motifs of transcription factors encoded within the triplicated locus, and those that are determinants of neuronal lineage.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: sci-ATAC-seq on 2n and Ts65dn cortex

first: Paul

last: Soloway


title: small RNAs in Metarhizium robertsii wild type and Δdcl2

city: Hefei

first: Yulong

last: Wang

address: 130 West Changjiang Road

institute: Anhui Agricultural University

summary: Small RNAs profiling by high throughput sequencing in the WT and Δdcl2 mutant.

overall_design: Dicers are RNase III ribonucleases that generate the small RNA duplexes from double-stranded RNA (dsRNA) precursors. Despite their importance, the potential roles of Dicers in entomopathogenic fungus are still unknown. Based on the clear phenotype in the Δdcl2 mutant, we applied high-throughput sequencing technology to identify sRNAs that are differentially expressed in the WT and Δdcl2 and found that 4 known milRNAs and 8 novel milRNAs were Mrdcl2-dependent in M. robertsii. Taking together, Dicer and the sRNAs it produces, play very important roles in growth and development in M. robertsii by regulating gene expression.

first: Hui-min

last: Meng

first: Bo

last: Huang


title: Characterization of Transcriptional Complexity during Longissimus Muscle Development in Bovines Using High-throughput Sequencing

status: Public on May 19 2019

city: Yangling

first: Hua

last: He

state: Shaanxi

address: Xinong Road NO.22

department: College of Animal Science and Technology

institute: Northwest A&F University

summary: RNA sequencing of beef cattle was performed using the Illumina High-Seq2000 platform. A total of 25,605,140 and 26,214,800 reads were sequenced for embryonic and adult pooled samples, respectively. We detected the expression levels of 16,174 genes, and 6,800 genes exhibited differential expression between the two pooled samples with a false discovery rate ≤ 0.001.

overall_design: two pooled samples were analyzed

first: Yongzhen

first: Xiaolin

last: Liu


title: FAIRE-seq and Bisulfite-seq of Arabidopsis wild type and msh1 memory line

status: Public on May 18 2019

city: University Park

first: Hardik

last: Kundariya

state: PA

address: 361 N. Frear

institute: The Pennsylvania State University

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: The effects of chemokines CCL2/7 on MDA-MB-231-FOXC1 cells

city: Los Angeles

first: Xiaojiang

last: Cui

address: 3884 Fredonia  Dr#F

department: Surgery Dept

institute: Cedars Sinai Medical Center

summary: Our preliminary studies performed in vitro show that MDA-MB-231-FOXC1 cell, which were used to mimic the lung-colonizing triple-negative breast cancer cells, was an indispensable component for the induction of migration and tube formation of lung endothelial cells. Moreover, our results further show that mouse lung fibroblast-derived chemokines CCL2/7 act on MDA-MB-231-FOXC1 cells, which mediates the migration and tube formation of lung endothelial cells in vitro. To understand the signaling pathways activated by CCL2/7 in MDA-MB-231-FOXC1 cells, we performed RNA-Seq assay.

overall_design: MDA-MB-231-FOXC1 cells were treated with recombinant mouse Ccl2 (10 nM)/7 (50 nM) for 6 hours.

first: Bingchen

last: Han

last: Deng


title: Impact of Orthosiphon stamineus aqueous leave extract on global gene expression of uropathogenic Escherichia coli

city: Muenster

first: Ulrich

last: Dobrindt

state: NRW

address: Mendelstrasse 7

department: Institute of Hygiene

institute: University of Münster

summary: Specific recognition and bacterial adhesion to host cells by uropathogenic E. coli (UPEC) are the first steps towards infection of epithelial tissue of the human urogenital system. Therefore, targeting of UPEC virulence factors, relevant for adhesion, is a promising approach for prevention of recurrent urinary tract infections (UTI). A fully characterized plant-derived aqueous extract from the leaves of Orthosiphon stamineus (OWE), a plant traditionally used in clinical practice in Europe and Asia for UTI, has been shown to exert strong antiadhesive effects under in vitro and in vivo conditions. For improved understanding of the underlying mechanisms transcriptome analysis of OWE-treated UPEC strain UTI89 by Illumina sequencing and cross-validation of these data by qPCR indicated significant down-regulation of bacterial adhesins (curli, type 1-, F1C- and P fimbriae) and of the chaperone-mediated protein folding/unfolding and pilus assembly process; in contrast flagellar and motility-related genes  were upregulated. We conclude that OWE transforms the sessile lifestyle of bacteria into a motile one and therefore disables bacterial attachment to the host cell. Additionally, the extract inhibited gene expression of multiple iron acquisition systems (Ent, Fep, Feo, Fhu, Chu, Sit, Ybt) concomitant with an upregulated expression of the ferric uptake regulator (Fur) repressor. The present study explains the antiadhesive and antiinfective effect of the plant extract by pinpointing specific biochemical and molecular targets.

overall_design: Examination of the transcriptome of uropathogenic E. coli after 2 h incubation time with OWE in pooled human urine (one replicate) in comparison to 2 h incubation in pooled human urine (one replicate).

first: Shabnam

last: Beydokhti

first: Christoph

last: Stork

first: Andreas

last: Hensel


title: RNA-seq of manually sorted transgenically labeled sNPFr-Gal4 and TRH-Gal4 drosphila neurons

city: Boston

first: Benjamin

last: Okaty

state: MA

address: 77 Avenue Louis Pasteur

institute: Harvard Medical School

summary: RNA-seq was used to molecularly characterize two drosophila neuron subtypes with demonstrated roles in the modulation of aggression

overall_design: Small pools (15-60 cells) and single cells were manually sorted from protease digested, acutely dissociated (TRH-Gal4) or pinned (sNPFR-Gal4) fly brains, cDNA was synthesized and amplified using SMART-Seq v4 kit (Takara), and RNA-seq libraries were prepared using Nextera XT kit (Illumina)

first: Olga

last: Alekseyenko


title: RNA-Seq transcriptome analysis on Pdx1 + Ngn3 co-transfected rat bmMSCs

city: Shenyang

first: hongtu

last: li

state: Liaoning

address: No.10, Puhe street, Huanggu District

institute: Liaoning Province Research Institute of Family Planning

summary: We report the application of RNA-Seq technology for transcriptome analysis on Pdx1 + Ngn3 co-transfected bmMSCs. Bioinformatics analyses indicated that clean reads of the two libraries accounted for 97.24% and 97.97% of the total reads, which indicated high quality of the raw datasets. Total 2325 differentially expressed genes (DEGs) were identified in reprogrammed bmMSCs compared to the negative control, including 1476 genes up-regulated and 849 genes down-regulated. The RNA-Seq analysis globally validated in the reprogrammed cells the expression of a large number of genes involved in pancreas development, endocrine specification and islet differentiation. To the best of our knowledge, this is the first application of RNA-Seq analysis on reprogrammed MSCs towards pancreatic cells.

overall_design: RNA was extracted from the untransfected bmMSCs (as the negative control, NC) and the reprogrammed bmMSCs 10 days after transfection with Pdx1 + Ngn3.

first: Hongtu

last: Li

first: Xining

last: Pang


title: Beneficial effect of an adenosine A2AR antagonist in the APPswe/PS1dE9 mouse model of Alzheimer’s Disease

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

institute: Lille University

overall_design: Heterozyguous males APPswe/PS1dE9 (APP/PS1) mice were treated either with water or MSX-3 (0.3g/L), a water soluble prodrug of the potent and highly selective A2AR antagonist from 4 to 9-10 months of age through drinking water

first: David

last: Blum


title: Autism-associated deletions of the lncRNA PTCHD1-AS result in synaptic dysfunction in human neurons

city: Toronto

first: James

last: Ellis

state: Ontario

address: 686 Bay Street

department: Developmental and Stem Cell Biology

institute: Hospital for Sick Children

summary: The long non-coding (lnc) RNA PTCHD1-AS is frequently disrupted in males with autism spectrum disorder (ASD), but its role in neuron function is unknown. We generated induced pluripotent stem (iPS) cells from two ASD subjects with PTCHD1 locus microdeletions, and produced neurons that exhibited reduced miniature excitatory post-synaptic current (mEPSC) frequency and NMDA receptor hypofunction. Mutation of the lncRNA PTCHD1-AS had no impact on expression of the divergently transcribed neighboring PTCHD1 gene in cis, but 14 genes were differentially expressed. Alternative splicing patterns of the nuclear lncRNA were affected by exon 3 loss, and its importance was reinforced by discovery of a novel ASD-associated exon 3 deletion. Finally, genome editing of exon 3 in iPS cells recapitulated diminished mEPSC frequency in neurons. Our findings directly implicate PTCHD1-AS in excitatory synapse function, and reveal the first association of lncRNA deletion with neuronal under-connectivity in ASD.

overall_design: Neural precursor cells from iPSC lines of two probands (Prb1 and Prb2) and two controls (Ctl1 and Ctl2) were differentiated into neurons. At three weeks of differentiation, neurons were purified using magnetic activated cell sorting and seeded onto plates. Following a one-week recovery, RNA was harvested. The experiment was repeated in duplicate. We compared transcriptomes of Ctl vs. PRB1 and Ctl vs. PRB2 separately.

first: Peter

middle: J

last: Ross

first: Wen-bo

last: Zhang

first: Kirill

last: Zaslavsky

first: Eric

last: Deneault

first: Rebecca

last: Mok

first: Lia

last: D'Abate

first: Deivid

last: Carvalho-Rodrigues

first: Wei

last: Wei

first: Alina

last: Piekna

last: Pasceri

first: Stephen

last: Scherer

first: Michael

last: Salter


title: Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) sequencing of msh1 memory line

first: Hardik

last: Kundariya

summary: Col-0 wild type and msh1 memory line were grown, crosslinked and chromatin isolated  as described in (Omidbakhshfard et al., 2014). Briefly, plants were germinated in MS media at 24°C, 12 hr light and 12 hr dark cycle for 14 days and crosslinked with formaldehyde. DNA was sonicated to get a size range of 250-800bp. Samples were divided equally into two lots and one was used directly for FAIRE experiments while the other lot was decrossed-linked and compared with the crosslinked samples to confirm he FAIRE treatment. FAIRE analysis was carried out on crosslinked sampes of wild ype and msh1 memory line.

overall_design: Two Col-0 wild type crosslinked and three msh1 memory crosslinked plants were sequenced. Pool of three decrossed plants for each Col-0 wild type and msh1 memory line were sequnced to confirm the FAIRE treatment.

first: Xiaodong

last: Yang

first: Sally

last: Mackenzie


title: The effects of chemokines CXCL1/2/8 on mouse lung fibroblasts

status: Public on May 17 2019

first: Xiaojiang

last: Cui

state: CA

summary: Our preliminary data show that the primary triple-negative breast tumor-derived chemokines CXCL1/2/8 promote migration and tube formation of mouse lung endothelial cells, which is mediated by lung fibroblasts. To explore the molecular events underlying this mediator function of lung fibroblasts, we treated freshly-isolated lung fibroblasts with chemokines CXCL1/2/8 and performed RNA-Seq assay.

overall_design: Freshly-isolated mouse lung fibroblasts were treated with recombinant human CXCL1 (8 nM)/2 (2 nM)/8 (20 nM) proteins for 3 hours.

first: Bingchen

last: Han

last: Deng


title: Blocking expression of inhibitory receptor NKG2A overcomes tumor resistance to NK cells

city: Singapore

first: Dario

last: Campana

address: 14 medical drive, MD6 #09-02

department: Pediatrics

country: Singapore

institute: National University of Singapore

summary: A key mechanism of tumor resistance to immune cells is mediated by expression of peptide-loaded HLA-E in tumor cells, which suppresses natural killer (NK) cell activity via ligation of the NK inhibitory receptor CD94/NKG2A. To bypass HLA-E inhibition, we developed a way to generate highly functional NK cells lacking NKG2A. Constructs containing a single-chain variable fragment derived from an anti-NKG2A antibody were linked to endoplasmic reticulum-retention domains. After retroviral transduction in human peripheral blood NK cells, these NKG2A Protein Expression Blockers (PEBLs) abrogated NKG2A expression. The resulting NKG2Anull NK cells had higher cytotoxicity against HLA-E-expressing tumor cells.

overall_design: We examined the expression of NK cell receptor in NKG2A-prified NK cells after transduction with PEBL or green fluorescent protein by using RNA-seq.

first: See

middle: V

last: Seow

first: Zhen

middle: H

last: Li


title: Genome-wide assessment of H4K20me1 chromatin profile in D458 shNull and shSETD8 medulloblastoma cells

first: Rajeev

last: Vibhakar

department: Pediatrics/Hematology/Oncology

summary: The goal of this study was to examine the H4K20me1 profile in medulloblastoma cells with wild type SETD8 or depleted SETD8.

overall_design: to determine how the H4K20me1 landscape changed in response to SETD8 depletion.

first: Bethany

last: Veo

first: Etienne

last: Danis


title: RNA-Sequencing of ST2+ Treg cells in response to IL-33 stimulation

city: Pittsburgh

first: Uma

last: Chandran

address: 5150 Center Ave

department: BioMedical Informatics

institute: University of Pittsburgh

summary: The effects of IL-33 on ST2+ Treg cells were not studied thouroughly.  We FACS-sorted in vitro expanded ST2+ Treg cells from C57BL/6 Foxp3-IRES-mRFP (B6 FIR) mice. We next used RNA-seq techonology to define how recombinant IL-33 (rIL-33) may impact mouse Treg by to assessing the transcriptome of IL-33-stimulated ST2+ Treg cells compared to that of untreated ST2+ Treg cells. Our data revealed that ST2+ Treg stimulated with rIL-33 for 6 hours exhibited increased expression of Il10 and Il13 compared to unstimulated ST2+ Treg cells.

overall_design: Examine of transcriptome of rIL-33-treated or untreated ST2+ Treg cells.

first: Heth

middle: R

last: Turnquist

first: Anish

last: Chakka


title: Enhancement of direct reprogramming from fibroblasts to epithelial lineages by OVOL2-induced mesenchymal-to-epithelial transition [ATAC-seq]

city: Yokohama

first: Kazuhide

last: Watanabe

state: Kanagawa

address: 1-7-22 Suehiro-cho Tsurumi-ku

department: Center for Integrative Medical Sciences

institute: Riken

summary: Mesenchymal-to-epithelial transition (MET) is an important step in cell reprogramming from fibroblast, a most frequently used cell type for this purpose, to various epithelial cell types. However, how MET can be induced in fibroblast has not been fully studied. In this study, we sought for transcription factors (TFs) that can efficiently induce MET in dermal fibroblasts and identified OVOL2 as a potent inducer of key epithelial genes. In addition, OVOL2 cooperatively enhanced MET induced by HNF1A, TP63 and KLF4, known reprogramming TFs to epithelial lineages. In TP63/KLF4-induced fibroblast-keratinocyte cell reprogramming, OVOL2 greatly facilitated activation of epithelial genes as well as keratinocyte-specific genes. This enhancement of epithelial gene expression program was accompanied by enhanced changes in chromatin accessibility across the genome. Mechanistically, motif enrichment analysis revealed that target loci of KLF4 and TP63 become accessible upon reprogramming while OVOL2 target loci become inaccessible, indicating that KLF4 and TP63 positively regulate their targets while OVOL2 primarily induces closed chromatin state at its target loci.  Thus, OVOL2 and tissue-specific reprogramming factors cooperatively facilitate cell reprogramming of fibroblast into epithelial lineages through distinct mechanisms.

overall_design: Primary fibroblasts are infected with doxycycline (DOX)-inducible Control vector (MCS), TK (TP63+KLF4), TK+ OVOL2 (Group5), or OVOL2 (Group6). After selection with Puromycin, DOX treatment (500ng/mL) was started at day0 for 5 days (until day5). At day2, medium was changed to KGM medium. RNA samples were collected at day7.


title: Transcriptome analysis of mdx hearts and skeletal muscles treated with cardiac progenitor cells and their exosomes

city: Los angeles

first: Xiangming

last: Ding

address: 650 Charles E Young Dr S, Los Angeles, CA 90095

institute: UCLA

summary: Aged mdx mice were treated with 2.5x105 cardiosphere-derived cells (CDCs) or 2.0x109 exosomes intravenously. Hearts and skeletal muscles were harvested 3 weeks post-treatment and prepared for RNA sequencing.

overall_design: Comparison of transcriptomic changes in mdx hearts and skeletal muscles by cardiac progenitor cell and exosome treatments

first: Russell

middle: G

last: Rogers

first: Eduardo

last: Marban


title: Enhancement of direct reprogramming from fibroblasts to epithelial lineages by OVOL2-induced mesenchymal-to-epithelial transition


title: Transcriptome sequencing analysis of  Mesenchymal Stem Cells derived from the Human Placenta and Umbilical Cord

city: Guangzhou

first: Yi

last: Xiao

address: No. 253, Industrial Avenue, Haizhu District

institute: Southern Medical University

summary: Based on transcriptome sequencing analysis, umbilical cord mesenchymal stem cells and placental mesenchymal stem cells share a total of 10529 common genes (called hpcCS consensus genes), which are umbilical cord-placental-consistent DEGs. The UC-MSC-specific region (referred to as the UC-specific gene) has most of the DEG (383 genes). The AM-MSC specific region (referred to as the AM specific gene) has 311 DEGs. The CM-MSC specific region (referred to as the CM specific gene) has 182 DEGs. The CV-MSC specific region (referred to as a CV-specific gene) has 169 DEGs. These results suggest that hMSCs from the umbilical cord and placenta have similar gene expression patterns, but have their own specific genes. The specific genes are not only involved in cell cycle, cell division, cell death, cell growth and development, transcriptional regulation, DNA repair, DNA. Replication plays an important role in chromosomal stability and is also involved in the movement of cellular or subcellular components, cellular communication and cell projection tissue, cytokine secretion and hormonal metabolism. The results of transcriptome sequencing analysis explain to some extent the differences in the biological characteristics of MSCs from different sources at the gene level.

overall_design: We compared the transcriptional profiles of four different placenta-drived MSCs using RNA-sequencing (RNA-seq)

first: Chen

last: Feng


title: A dormant T cell population with autoimmune potential exhibits low self-reactivity and infiltrates islets in type I diabetes

city: Houston

first: Maria

last: Bettini

address: 1102 Bates St

institute: Baylor College of Medicine

summary: T cells have been established as the key drivers of autoimmune diabetes. However, it is unknown whether all T cells that infiltrate the pancreas are equally pathogenic, and how the level of reactivity for self-antigen modulates differentiation and pathogenic potential of effector T cells.  Moreover, the contribution of bystander, non-antigen reactive T cells in islet autoimmunity has not been resolved. Using multi-color flow cytometry in combination with Nur77-GFP reporter of TCR signaling we identified a “dormant” population of CD4+ T cells that infiltrate the islets of pre-diabetic NOD mice and constitute a significant proportion of all islet infiltrating T cells (~47%). We analyzed TCR repertoire, transcriptional profile, effector function, and autoimmune potential of this subpopulation. This T cell population, characterized by low level expression of CD5 and a unique TCR repertoire, exhibited central memory phenotype with reduced activation and effector function; however, induced rapid diabetes upon transfer. Overall, our study suggests that the strength of reactivity for tissue antigen dictates the level of T cell activation and differentiation; however, cells with low level of TCR signaling and reactivity for islet antigen infiltrating the pancreas of NOD mice are pathogenic and are capable of inducing beta cell destruction.

overall_design: 2 Islet Teff Hi samples, 2 Islet Teff low samples. Compared also to samples submitted in GEO GSE102231 and GSE106467

first: Yuelin

last: Kong

first: Marissa

middle: A

last: Scavuzzo

first: Malgorzata

last: Borowiak

first: Maran

last: Sprouse

first: Matthew

middle: L


title: Gene expression activation in CLL mediated by MSCs contact

city: Cambridge

first: Ingo

last: Ringshausen

address: Cambridge biomedical campus

country: United Kingdom

institute: University of Cambridge

summary: Survival of primary CLL cells is mediated by mesenchimal stromal cells in vitro. The goal of this study is to compare the gene expression profile of primary CLL cells in monoculture to that one following cell-cell contact with MSCs

overall_design: Primary CLL cells isolated from 6 different patients were cultured for 4h in normal growing medium or for 48h in coculture with EL08-1d1 cells

first: Ludger

last: Klein-Hitpass

first: Maurizio

last: Mangolini


title: Chromatin accessibility of ex vivo derived Be-g2 cells

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

summary: Naive B cells cultured in the presence of IL-2 and IFN-g (Be-g2) leads to a distinct programming outcome.  To determine the epigenetic programming changes during Be-g2 differentiation ATAC-seq was performed on Be-0, Be-IL2, Be-IFNg, and Be-g2 cells.  These data define the chromatin accessibility landscape of Be-g2 cells and the changes that occur during thier differentiation.

overall_design: Be-0, Be-IFNg, Be-IL2, Be-IFNg, and Be-g2 cells were analyzed by ATAC-seq.

first: C

first: F

last: Lund


title: Genome-wide maps of histone modifications in endometrial cancer cell lines

city: Brisbane

first: Tracy

last: O'Mara

state: QLD

address: 300 Herston Road

institute: QIMR Berghofer Medical Research Institute

summary: DNA regulatory elements are reported to be enriched for variants identified by genome-wide association studies to be significantly assocaited with risk of complext traits. Here, we have performed genome-wide mapping of histone modifications in two endometrial cancer cell lines and performed interestions of these sites with genetic risk variants identified by genome-wide association study of endometrial cancer. Histone modifications indicative of enhancers (H3K4Me1 and H3K27Ac) and promoters (H3K27Ac and H3K4Me3) were identified by ChIP-seq in Ishikawa and JHUEM-14 cells, pre- and post-stimulation by estrogen. Overall, 73% of endometrial cancer genetic risk variants overlapped at least histone modification site. This overlap was significantly greater than the overlap observed for these histone marks with genetic risk variants related to, for example, endometriosis (51%; Fisher’s Exact p = 8.7x10-8) or schizophrenia (40%; Fisher’s Exact p < 2.2x10-16). These findings indicate the relevance of the selected cell and tissue types for informing endometrial cancer biology. Overlaps between genetic risk variants and histone modification sites increased significantly after stimulation with estrogen (50% versus 38% for unstimulated features; Fisher’s Exact p = 5.6x10-3), emphasizing the importance of estrogen in endometrial cancer aetiology.

overall_design: ChIP-seq of 3 different histone modifications in 2 endometrial cancer cell lines, before and after estrogen stimulation

first: Dylan

middle: M

last: Glubb

first: Amanda

last: Spurdle


title: Characterization and therapeautic application of mesenchymal stem cells with neuromesodermal origin from human pluripotent stem cells

first: Weiqiang

last: Li

address: Zhongshan Road 2

institute: Sun Yat-sen university

summary: Here, human pluripotent stem cells (including hiPSC and hESC) were induced to differentiate to mesenchymal stem cells (MSC) through the intermediate stage of neuromesoderm (NMP). We sequenced mRNA samples at different stages during NMP-MSC differentiation of human pluripotent stem cells to generate the gene expression profiles of these cells.

overall_design: 12 samples, including undifferentiated hPSC (hiPSC, H1, and H9), hPSC-NMP-derived paraxial mesoderm (hPSC-NMP-PM; including hiPSC-NMP-PM, H1-NMP-PM, and H9-NMP-PM), hPSC-NMP-MSC (Passage 5; including hiPSC-NMP-MSC, H1-NMP-MSC, H9-NMP-MSC1, and H9-NMP-MSC2), BMSC1 (Passage 5), and BMSC2 (Passage 5), were analyzed.

first: Zhichen

last: Zhai

first: Dairui

first: Huiyan

last: Wang

first: Andy

last: Xiang


title: Effects of aging and chronic cigarette exposure on ocular circulatory microRNAs in the Rhesus macaque

city: Davis

first: Zeljka

last: Smit-McBride

address: One Shields Ave, Tupper Hall #2403

department: Ophthalmology & Vision Science

institute: University of California, Davis Eye Center

summary: Purpose: The purpose of this study was to identify cigarette smoke (CS) induced changes in circulatory microRNA (miRNA) in the plasma and ocular fluids of the Rhesus macaque and compare them to normal age-related changes, with the ultimate goal to develop an animal model of early dry age-related macular degeneration (AMD). AMD is a blinding disease having both genetic and environmental components, with cigarette smoke exposure (CS) as the leading environmental risk factor.   Methods: All Rhesus macaques were housed at the California National Primate Research Center (CNPRC) at UC Davis. We used 6 animals of the same gender per group: Group 1 (young, 2-4 years old), Group 2 (old, 20-25 years old), Group 3 (middle aged, 9-12 years old) and Group 4 (9-12 years old, exposed to smoke for 1 month). Group 4 macaques were clinically assessed prior to and following CS exposure. Ocular fluids and plasma samples were collected, miRNA isolated, and expression data obtained from Affymetrix miRNA GeneTitan Array Plates 4.0, followed by bioinformatics analysis on Affymetrix Expression Console (EC) and Transcriptome Analysis Software (TAS), and using ANOVA.   Results: Statistically significant changes were seen in miRNA populations in ocular fluids and plasma. In the plasma samples, 45 miRNAs were strongly upregulated (Fold Change >+/-1.5, p<0.05) upon CS exposure, while in aging monkeys different miRNAs in plasma were affected, and downregulated. In the vitreous, 3 miRNAs were downregulated in animals exposed to CS, intriguing enough two of them (miR-6794 and miR-6790) were the same ones downregulated with age. Retinal imaging using OCT did not show any significant changes in retinal thickness.  Cotinine assays showed that animals received on average dose of 50-60 ng/ml cotinine, a marker for significant CS exposure.  Conclusions: One month of CS exposure of Rhesus macaques resulted in significant changes of expression of circulatory miRNAs. We identified several CS related miRNA changes that are plasma or ocular fluid-specific. Healthy aging changes of miRNAs populations were different from the CS exposure induced changes in plasma, while the ones in vitreous were similar. This data will be utilized to develop an animal model of early dry AMD, using a monkey model exposed to CS.

overall_design: The miRNA samples (10-20 nanograms) were labeled as probes using FlashTag kit. The Affymetrix microRNA microarrays were run at the Genomics Shared Resource (GSR), UC Davis Health System in Sacramento, while 2 X GeneTitan Plates 4.0, each with 24 samples, for a total of 48 samples, were run at The UCSF Institute for Human Genetics (IHG). Comparative analysis of human and primate samples was done on 3 vitreous and 3 plasma samples from each species, for a total of 12 samples run on Affymetrix 3.0 GeneChips.


title: Enhancement of direct reprogramming from fibroblasts to epithelial lineages by OVOL2-induced mesenchymal-to-epithelial transition [CAGE]

first: Kazuhide

last: Watanabe


title: Pancreatic cancer cell CFPAC-1: shBACH1 vs. shControl

first: Xudong

last: Huang

address: 651 Dongfeng East Road

institute: Sun Yat-sen University Cancer Center

summary: Gene expression profiling of pancreatic cancer cell CFPAC-1 when BACH1 knockdown. BACH1 is a transcription repressor and its regulation networks is poorly understood in pancreatic ductal adenocarcinoma. We used the total RNA from shControl and shBACH1 CFPAC-1 cells to analyze the differentially expressed genes which were regulated by BACH1, and further explored the biological processes that BACH1 may involved.

overall_design: Two-condition experiment, shBACH1 vs. shControl CFPAC1 cells. Biological replicates: 1 shBACH1 cell, 1 shControl cell.

first: Dongxin

last: Lin


title: Guanidineacetic acid regulate myogenic differentiation through miR-133a-5 and miR-1a-3p co-mediated PI3K-Akt-mTOR signaling pathway

city: chengdu

first: wang

middle: yu

last: jie

address: 211 Huimin Road, Wenjiang District, Chengdu

institute: Sichuan Agricultural University

summary: Through small RNA sequencing, we finded that a total of 8 miRNAs, including miR-133a-3p and miR-1a-3p cluster, showed differential expression after guanidineacetic acid supplement. To further study the function of miR-133a-3p and miR-1a-3p in guanidineacetic acid induce myotube hypertrophy, we transfected miR-133a-3p and miR-1a-3p mimics, that also induce myotube hypertrophy. Through bioinformatics and dual-luciferase reporter system, the target gene of miR-133a-3p and miR-1a-3p were respectively determined. Meanwhile, miR-133a-3p and miR-1a-3p modulate PI3K-Akt-mTOR signaling pathway by restraining target gene expression.

overall_design: We used small RNA sequencing to detect miRNA transcriptomes of myotubes after  20 mM guanidineacetic acid treatment (GAA) or nagtive control(NC)  (2 vs. 2).

first: Yujie

first: Jideng

last: Ma


title: Transcriptome analysis in shNull and shSETD8 medulloblastoma cells

city: Aurora

first: Rajeev

last: Vibhakar

institute: University of Colorado Anschutz Medical Campus

summary: The goal of this study was to determine the effect on gene transcription profiles in medulloblastoma cells that were depeleted of the epigenomic modifier SETD8 vs control.

overall_design: RNA-seq was performed using the illumina HiSEQ 4000 HT for 1x50 sequencing.  High quality base calls at 95% ≥ Q30 were obtained with 53M-69M single reads.  Statistical analysis of count data was performed with DESeq2 R package.

first: Bethany

last: Veo

first: Katrina

last: Diener


title: Be1 and Be2 B cells are transcriptionally distinct

first: Chris

last: Scharer

summary: B cells cultured in the presence of Th1 CD4 T cells (Be1) or Th2 CD4 T cells (Be2) lead to distinct phenotypic outcomes.  To determine when the phenotypic differences emerged, IgD positive and IgD negative Be1 and Be2 cells were isolated from cultures derived from 3 independent donors and RNA-seq performed.  These data define the transcriptional differences of Be1 and Be2 cells ad distinct differentiation stages and show that Be1 B cells contain a pre-ASC signature that is absent from Be2 B cells.

overall_design: Be1 and Be2 cells that were IgD positive and IgD negative from three different donors were analyzed by RNAseq.

first: C

middle: D

first: F

last: Lund