title: Hyperglycemia promotes an aggressive phenotype in breast cancer cells

status: Public on Aug 24 2019

city: Estado de Mexico

first: Rubi

last: Viedma

state: Estado de Mexico

address: Av. de los Barrios 1, Los Reyes Ixtacala,  Tlalnepantla,

department: bioquimica

country: Mexico

institute: unam

summary: Diabetes and breast cancer are common diseases with a major impact on the health sector in Mexico and worldwide. Epidemiological and experimental works support the link between type 2 diabetes and breast cancer; these data support that insulin resistance, hyperglycemia, hyperinsulinemia, and elevated levels of IGF-1 in patients with type II diabetes mellitus promote growth and invasiveness of tumor cells. The aim of the present work was to determine, by microarray, the mechanisms of action and signaling of a hyperglycemic microenvironment in the cell line (MDA-MB-231) and its effect to treatment with cisplatin (CCP). MDA-MB-231 breast cancer cells were cultured in DMEM medium, supplemented with 10% fetal bovine serum and antibiotics at 5% CO2, at 37 ˚C. We proceeded to extract total RNA for the analysis of microarrays under LG (low glucose) and HG (high glucose) conditions; for the cDNA synthesis, it was labeled with dUTP-Cy3 or dUTP-Cy5 fluorophores, using a CyScribe Firs-Strand cDNA kit. The analysis was carried out through the KEGG pathways program; some bioenergetic metabolism processes (glycolysis, biosynthesis of purines and pyrimidines, and metabolism of glycerol phospholipids) were found altered, which fulfill the feedback function to the cellular microenvironment, activating some signaling processes, such as the Hippo route, PI3K-Akt, Jak-STAT, MAPK, Ras, Wnt/β-catenin, apoptosis, and favoring an aggressive phenotype and drug resistance in a hyperglycemic microenvironment. The microarray analysis was validated by qRT-PCr of the tetraspanin and Frizzled genes.

overall_design: The cells were cultured in BG and HG media; 10 μg of total RNA were obtained and used for cDNA synthesis and labeling with a Super Script II kit Invitrogen, using the dUTP-Cy3 incorporation array for BG (control) and dUTP-Cy5 for HG. Incorporation efficiency was analyzed measuring absorbance at 555 nm for Cy3 and 655 nm for Cy5. Similar quantities of fluorophores labeled cDNA were hybridized on the oligonucleotides collection 50-mer Human10K from MWG Biotech Oligo Bio Sets (Germany). Images of the microarrays were acquired and quantified in a Scan Array 4000 using the Quant Array software from Packard BioChips (USA). A first analysis of the images and the data was performed using the Array-Pro Analyzer software from Media Cybernetics (USA).  Microarray data analysis was performed using the free software program genArise, allowing background correction, normalization, intensity filter, replicate analysis, and selection of differentially expressed genes; this program was developed in the Computing Unit of the Cellular Physiology Institute of the UNAM.

first: Luis

last: Arturo Baiza Gutman

first: Araceli

last: Rubí Vietma Rodriguez


title: TFPa/HADHA is required for fatty acid beta-oxidation and cardiolipin re-modeling in human cardiomyocytes

status: Public on Aug 25 2019

city: Seattle

first: Hannele

last: Ruohola-Baker

state: WA

address: 850 Republican Street

country: USA

institute: Institute for Stem Cell and Regenerative Medicine

type: Expression profiling by high throughput sequencing

summary: Mitochondrial trifunctional protein deficiency, due to mutations in hydratase subunit A (HADHA), results in sudden infant death syndrome with no cure.  To reveal the disease etiology, we generated stem cell-derived cardiomyocytes from HADHA-deficient hiPSCs and accelerated their maturation via an engineered microRNA maturation cocktail that upregulated the epigenetic regulator, HOPX.  Here we report, matured HADHA mutant cardiomyocytes treated with an endogenous mixture of fatty acids manifest the disease phenotype: defective calcium dynamics and repolarization kinetics which results in a pro-arrhythmic state.  Single cell RNA-seq reveals a cardiomyocyte developmental intermediate, based on metabolic gene expression.  This intermediate gives rise to mature-like cardiomyocytes in control cells but, mutant cells transition to a pathological state with reduced fatty acid beta-oxidation, reduced mitochondrial proton gradient, disrupted cristae structure and defective cardiolipin remodeling.  This study reveals that  HADHA (tri-functional protein alpha), a monolysocardiolipin acyltransferase-like enzyme, is required for fatty acid beta-oxidation and cardiolipin remodeling, essential for functional mitochondria in human cardiomyocytes.

overall_design: Bulk RNA-seq of individual microRNA OE and KO,HOPX OE, MiMac and empty vector control. Single cell RNA-seq of cardiomyocytes with different combinations of microRNA OE/KO and MiMAC. Single cell RNA-seq of wild type or HADHA mutant MiMac cardiomyocytes treated with SS-31

first: Yuliang

last: Wang


title: Characterization of ANGPTL4 function in macrophages and adipocytes using Angptl4-knockout and Angptl4-hypomorphic mice

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

summary: ANGPTL4 regulates plasma lipids, making it an attractive target for correcting dyslipidemia. However, ANGPTL4 inactivation in mice fed a high fat diet causes chylous ascites, an acute-phase response, and mesenteric lymphadenopathy. Here, we studied the role of ANGPTL4 in lipid uptake in macrophages and in the above-mentioned pathologies using Angptl4-hypomorphic and Angptl4-/- mice. Angptl4 expression in peritoneal and bone marrow-derived macrophages was highly induced by lipids. Recombinant ANGPTL4 decreased lipid uptake in macrophages, whereas deficiency of ANGPTL4 increased lipid uptake, upregulated lipid-induced genes, and increased respiration. ANGPTL4 deficiency did not alter LPL protein levels in macrophages. Angptl4-hypomorphic mice with partial expression of a truncated N-terminal ANGPTL4 exhibited reduced fasting plasma triglyceride, cholesterol, and non-esterified fatty acid levels, strongly resembling Angptl4-/- mice. However, during high fat feeding, Angptl4-hypomorphic mice showed markedly delayed and attenuated elevation in plasma serum amyloid A and much milder chylous ascites than Angptl4-/- mice, despite similar abundance of lipid-laden giant cells in mesenteric lymph nodes. In conclusion, ANGPTL4 deficiency increases lipid uptake and respiration in macrophages without affecting LPL protein levels. Compared with the absence of ANGPTL4, low levels of N-terminal ANGPTL4 mitigate the development of chylous ascites and an acute-phase response in mice.

overall_design: Peritoneal macrophages were obtained from Angptl4-/- mice and incubated with intralipid in the presence or absence of recombinant ANGPTL4, or PBS.

first: Antwi-Boasiako

last: Oteng

first: Philip

middle: M

last: Ruppert

first: Lily

last: Boutens

first: Wieneke

last: Dijk

first: Xanthe

middle: A

last: van Dierendonck

first: Gunilla

last: Olivecrona

first: Rinke

last: Stienstra

first: Sander

last: Kersten


title: Transcriptomic analysis of E11.5 AGM VE cadherin populations

city: Paris

first: Franck

last: Letourneur

address: 22 rue mechain

country: France

institute: INSERM

summary: We sorted endothelial (EC), hematopoietic (HC) and  hematopoietic stem/progenitor (HSPC) cell populations from AGM of E11.5 C57Bl6 embryos, established and compared their transcriptome to highlight specific regulators of hematopoietic emergence.

overall_design: CD144+CD45- endothelial cells (EC - n=3), CD144-CD45+ hematopoietic cells (HC - n=3) and CD144+CD45+ hematopoietic stem/progenitor cells (HSPC - n=3) sorted from E11.5 AGM were analyzed

first: Michèle

last: SOUYRI

first: Laurence

last: PETIT


title: Transcriptomic analysis of HSC-enriched population from adult C57Bl6 bone marrow

summary: HSC-enriched LSK CD150+CD48- and Lin+ hematopoietic populations were sorted from C57Bl6 adult bone marrow. Their transcriptome was established, and pair-wise comparison performed to establish molecular signatures specific of adult HSCs that could be compared to molecular signatures from AGM, fetal liver or placenta HSCs.

overall_design: Sorted adult BM lin+ HCs (n=4), BM CD150+CD48- LSK HSCs (n=4) were analyzed


title: Microarray upon Sp110 knockdown in HepG2.2.15 cells

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

summary:
Hepatitis B virus (HBV), belonging to Hepadnaviridae family, remains undetected in early infection and is known to be the cause of several hepatic diseases leading to cirrhosis and hepatocellular carcinoma. We have found that PML-Nuclear Body Speckled 110kDa (Sp110), is hyper-expressed upon HBV infection and intriguingly, Sp110 knock-down significantly reduced viral DNA-load in the culture supernatant of HepG2.2.15 (a HBV expressing cell-line). To understand the molecular basis underlying the viral elimination upon Sp110 silencing in HepG2.2.15 cells, we performed microarray to find the differential transcriptomics in Control siRNA treated vs. Sp110 siRNA treated cells.
To understand the molecular basis underlying the viral elimination upon Sp110 silencing in HepG2.2.15 cells, we performed microarray to find the differential transcriptomics in Control siRNA treated vs. Sp110 siRNA treated cells.

overall_design: Gene expression profile was compared between HepG2.2.15 Control siRNA treated vs. Sp110 siRNA treated cells

first: Isha

last: Sengupta

first: Dipanwita

last: Das

first: Shivaram

middle: P

last: Singh

first: Runu

last: Chakravarty

first: Chandrima


title: Rbfox1 up-regulation impairs BDNF-dependent hippocampal LTP by dysregulating TrkB isoform expression levels.

city: Bethesda

first: Skyler

middle: Alexander

last: Kuhn

state: Maryland

address: 41 CENTER DR, BG 41 RM B620

department: National Cancer Institute

institute: National Institutes of Health

summary: Brain Derived Neurotrophic Factor (BDNF) is a potent modulator of brain synaptic plasticity. Signaling defects caused by dysregulation of its NTrk2 (TrkB) kinase (TrkB.FL) and truncated receptors (TrkB.T1) have been linked to the pathophysiology of several neurological and neurodegenerative disorders. We found that upregulation of Rbfox1, an RNA binding protein associated with intellectual disability, epilepsy and autism, increases selectively hippocampal TrkB.T1 isoform expression. Physiologically, increased Rbfox1 impairs BDNF-dependent LTP which can be rescued by genetically restoring TrkB.T1 levels. RNA-seq analysis of hippocampi with upregulation of Rbfox1 in conjunction with the specific increase of TrkB.T1 isoform expression also shows that the genes affected by Rbfox1 gain of function are surprisingly different from those influenced by Rbfox1 deletion.  These findings not only identify TrkB as a major target of Rbfox1 pathophysiology but also suggest that gain or loss of function of Rbfox1 regulate different genetic landscapes.

overall_design: Hippocampi of 3 control mice (N-cre) and 3 Rbfox1 overexpressing mice (N-cre;Fox1) were used for RNA-seq isoform-expression analysis.

first: Francesco

last: Tomassoni-Ardori

first: Vishal

last: Koparde

first: Lino

last: Tessarollo


title: A combined epigenome- and transcriptome-wide association study of the oral masticatory mucosa assigns CYP1B1 a central role for epithelial health in smokers

city: Berlin

first: Gesa

middle: Marijke

last: Richter

address: Assmannshauser Str. 4-6

country: Germany

institute: Charité - University Medicine Berlin

summary: Healthy ex vivo biopsies from masticatory mucosa from 17 current and 21 never smokers were analysed using whole transcriptome RNA sequencing (16 mio reads/sample), showing significantly increased expression of CYP1B1 in smokers compared to non-smokers (p = 2.2 × 10−14), together with 13 significantly upregulated transcripts. Six transcripts were significantly downregulated.

overall_design: mRNA profiles of ex vivo masticatory mucosa from 17 current smokers and 21 never smokers

first: Arne

middle: S

last: Schaefer


title: Physiological and transcriptional response of Candida parapsilosis to exogenous tyrosol

status: Public on Aug 23 2019

city: Debrecen

first: Agnes

last: Jakab

address: Nagyerdei krt 98.

country: Hungary

institute: University of Debrecen

summary: Tyrosol plays a key role in fungal morphogenesis and biofilm development. Also, it has a remarkable antifungal effect at supraphysiological concentrations. However, the background of the antifungal effect remains unknown, especially in the case of non-albicans Candida species such as Candida parapsilosis We examined the effect of tyrosol on the growth, adhesion, redox homeostasis, virulence, as well as on fluconazole susceptibility. To gain further insights into the physiological consequences of tyrosol treatment we also determined the caused genome-wide gene expression changes using RNA-Seq. Fifteen mM tyrosol caused significant growth inhibition within two hours of the addition of tyrosol, while the adhesion of yeast cells was not affected. Tyrosol increased the production of reactive oxygen species remarkably as revealed by the dichlorofluorescein-test, and it was associated with elevated superoxide dismutase, glutathione peroxidase, and catalase activities. The interaction between fluconazole and tyrosol was antagonistic. Tyrosol exposure resulted in 261 and 181 differentially expressed genes with at least a 1.5-fold increase or decrease in expression, respectively, were selected for further study. Genes involved in ribosome biogenesis showed down-regulation, while genes related to oxidative stress response, and ethanol fermentation were up-regulated. In addition, tyrosol treatment up-regulated the expression of efflux pump genes including MDR1 and CDR1 and down-regulated the FAD2 and FAD3 virulence genes involved in desaturated fatty acid formation. Our data demonstrate that exogenous tyrosol significantly affects the physiology and gene expression of C. parapsilosis, which could contribute to the development of treatments targeting quorum-sensing in the future.

overall_design: Examination of untreated control and 15 mM tyrosol-treated Candida parapsilosis cultures in three replicates.

first: Renátó

last: Kovács

first: Ágnes


title: Truncating variant in MYOF gene is associated with limb-girdle type muscular dystrophy and cardiomyopathy

city: Saint Petersburg

first: Anna

last: Kostareva

address: Ulitsa Akkuratova, 2

country: Russia

institute: Almazov National Medical Research Centre

summary: Even though genetic studies of individuals with neuromuscular diseases have uncovered the molecular background of many cardiac disorders such as cardiomyopathies and inherited arrhythmic syndromes, the genetic cause of a proportion of cardiomyopathies associated with neuromuscular phenotype still remains unknown.  Here, we present a clinical case with a combination of cardiomyopathy and limb-girdle type muscular dystrophy where whole exome sequencing identified myoferlin (MYOF) - a member of the Ferlin protein family and close homolog of DYSF - as the most likely candidate gene. The disease-causative role of the identified variant c.[2576delG; 2575G>C], p.G859fs is supported by functional studies in vitro using primary patient's satellite cells, including both RNA sequencing and morphological studies, as well as recapitulating of muscle phenotype in vivo in zebrafish experiments. We provide the first evidence supporting a role of MYOF in human muscle disease.

overall_design: A muscle biopsy taken from patient’s M. deltoideus was used for morphological examination and SMSC isolation. Control cells were obtained from the hip muscles of healthy donors. The cells were placed in proliferation media (DMEM supplemented with 10% FCS) on cell culture dishes and cultured until 80% confluence. Patient and donor cells were differentiated towards myotubes using low serum condition.

first: Artyom

last: Kiselev

first: Alexey

last: Sergushichev

first: Alexander

last: Predeus


title: A BAT-enriched RNA binding protein, Ybx2, regulates cold-induced brown fat activation by stabilizing Pgc1α mRNA

city: Singapore

first: Lei

last: Sun

address: 8 College Road

country: Singapore

institute: Duke-NUS

summary: To study the role of Ybx2 in brown fat activity, we performed the RNA-seq data for wildtype and Ybx2 knockout brown fat under room temperature and upon cold exposure as well as for wildtype and Ybx2 knockout brown adipocytes culture from stromal vascular fraction cells. To determine the targets of Ybx2, we performed RNA immunopercipitatoin followed by RNA-seq

overall_design: mRNA profiling of brown fat from wild type and Ybx2 knockout mice, of brown adipocyte culture (day 5) from WT and KO mice, of RNA immunopercipitation samples in brown fat

last: SUN

first: Yen

middle: C

last: Lim


title: miRNA profiling from different histological subtypes of colorectal carcinoma

city: Murcia

first: Angel

last: Esteban-Gil

state: Murcia

address: Campus de Ciencias de la Salud Carretera Buenavista s/n

department: Biomedical Informatics and Bioinformatics Platform

country: Spain

institute: Institute for Biomedical Research of Murcia (IMIB)

summary: Colorectal cancer (CRC) is the third leading cause of cancer mortality worldwide. Different pathological pathways and molecular drivers have been described and some of the associated markers are used to select effective anti-neoplastic therapy. This dataset is part of ColPortal, a platform that integrates transcriptomic, microtranscriptomic, methylomic and microbiota data of patients with colorectal cancer. ColPortal also includes information of histological features and digital histological slides from the study cases.

overall_design: In this study, we used miRNA expression arrays (Affymetrix GeneChip miRNA 3.0 arrays (Affymetrix, Inc., Santa Clara, CA, USA) containing 5,607 probe sets for human pre-miRNA, miRNAs, small nuclear RNA, and small Cajal body-specific RNA) to investigate differences between different histological subtypes of colorectal carcinomas (i.e.  conventional carcinoma (CC), serrated adenocarcinoma (SAC) and colorectal carcinoma having histological and molecular features of microsatelite instability (hmMSI-H))

first: Fernando

last: Pérez-Sanz

first: José

last: García-Solano

first: Begoña

last: Alburquerque-González

first: María

last: Parreño-González

last: del Carmen Legaz-García

first: Edith

last: Rodriguez-Braun

first: Paola

last: Pimentel

first: Ondrej

last: Slaby

first: Pablo

last: Conesa-Zamora


title: Transcriptome analysis of a nematode resistant and susceptible upland cotton line

status: Public on Aug 22 2019

city: Salinas

first: Pawan

last: Kumar

state: CA

address: 1636 E Alisal Street

institute: USDA-ARS

summary: We applied the comparative transcriptomic approach to compare expression profiles of genes between RKN susceptible and resistance genotypes at an early stage of RKN development that coincides with the establishment of a feeding site and at the late stage of RKN development that coincides with RKN egg production. Sequencing of cDNA libraries produced over 315 million reads of which 240 million reads (76%) were mapped on to the Gossypium hirsutum genome.

overall_design: Replicated set of cDNA libraries were constructed from M120 and C201 plants at 12, 30 DAI and untreated plants. All libraries were constructed using the NEBNext Ultra RNA library Prep Kit for Illumina (New England BioLabs Inc.) following the manufacturers protocol.  The NEBNext Multiplex Oligos for Illumina (Index Primers Set 2, New England BioLabs Inc.) containing adaptors and primers were used to label libraries facilitating pooling.

first: Peng

last: Chee


title: Identification of AIA-related genes

city: Beijing

first: Yanqiong

last: Zhang

address: No 16, Nanxiaojie, Dongzhimennei

country: China

institute: Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences

summary: To obtain AIA-related genes [the significant differentially expressed genes (DEGs) of AIA model group vs. Normal control group], the microarray analysis was carried out.

overall_design: 6 rat samples were randomly divided into two groups (3 per group): (1) Normal control group; (2) AIA model control group.

first: Weijie

last: Li

first: Xia

last: Mao


title: Transcriptomic responses to oil, a pathogen, or both in spleen and liver tissues from juvenile red drum (Sciaenops ocellatus)

city: Ocean Springs

first: Maria

middle: L

last: Rodgers

state: Mississippi

address: 103 McIlwain Drive

department: Coastal Sciences

institute: University of Southern Mississippi

summary: The objective of this study was to determine how transcriptomic responses in the spleen and liver are altered in juvenile Sciaenops ocellatus exposed to oil, a known fish pathogen (Vibrio anguillarum), or both.

overall_design: S. ocellatus juveniles were exposed to oil, a pathogen (Vibrio anguillarum) or both.  Oil exposure was for 5 days and pathogen exposure was for 1 hour, 24 hours before takedown.  Oil solutions used in exposures were derived from high energy water accommodated fractions (HEWAF) prepared using Macondo well oil from the Deepwater Horizon oil spill following established procedures.  At the end of the experiments, livers and spleen were taken from organisms, RNA was extracted and sequenced.

first: Robert

middle: J

last: Griffitt


title: CSF1R inhibitor-mediated microglial depletion prevents reductions in striatal volume, extracellular matrix alterations, and perineuronal net loss in a mouse model of Huntington’s disease

city: Irvine

first: Kim

last: Green

address: 3208 Biological Sciences 3

department: Neurobiology and Behavior

institute: University of California, Irvine

summary: This dataset allows for the exploration of gene expression of microdissected striatum from 11 week old wild-type and the R6/2 mouse model of Huntington's disease, in the presence or absence of microglia.  Microglia were depleted via dietary administration of the CSF1R inhibitor PLX3397 from 6 to 11 weeks of age.

overall_design: R6/2 and Wild-type mice treated with vehicle or PLX3397 (275 ppm in chow), to deplete all microglia, from 7 to 11 weeks of age. Brains microdissected into striatum. 3 mice/group


title: Epigenetic reprogramming of immune cells in women with PCOS impact genes controlling reproductive function [RNAseq]

city: Copenhagen

first: Lars

middle: Roed

last: Ingerslev

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

summary: Transcriptomic and genome-wide DNA methylation was performed on T helper cells using RNA-sequencing and Reduced Representation Bisulfite Sequencing, respectively. Specific genome-wide DNA methylation analysis of T helper cells from women with PCOS identified 5,581 differentially methylated CpG sites. Interestingly, functional gene ontology enrichment analysis showed that genes located at the proximity of differentially methylated CpG sites belong to pathways related to reproductive function and immune cell function. However, these genes were not altered at the transcriptomic level. Our results show that PCOS is associated with global and gene-specific DNA methylation remodelling in a cell-type specific manner.

overall_design: We performed  genome-wide DNA methylation analysis of t Helper cells   in women with and without PCOS.

first: Danielle

last: Hiam

first: David

last: Simar

first: Rhianna

last: Laker

first: Ali

last: Altıntaş

first: Romain

last: Barres

first: Nigel

last: Stepto


title: Epigenetic reprogramming of immune cells in women with PCOS impact genes controlling reproductive function [RRBS]

type: Methylation profiling by high throughput sequencing


title: Gene expression profiling in lung and breast cancer cells treated by Bloom-specific siRNAs

city: Spokane

first: Bin

last: Shan

state: Washington

address: 412 E Spokane Falls Blvd

department: Biomedical Sciences

institute: Washington State University

summary: A549 and MDA-MB-231 cells were transfected with the Bloom-specific siRNA. Total RNA was extracted using Trizol at 48 hours after transfection. RNA-SEQ was carried out to profile the gene expression in both culture conditions.

overall_design: The goal of this experiment was to profie the genes that are regulated by Bloom (BLM RecQ like helicase) in cancer cells. Gene expression was probed globally using RNA-SEQ.

first: Simon

last: Alsager


title: RNA-seq of KP and KPI tumor cells isolated from KP and KPI lung adenocarcinoma tumors

city: Jacksonville

first: Alan

last: Fields

address: 4500 San Pablo Road

institute: Mayo Clinic Jacksonville

summary: RNA-seq analysis of KP and KPI lung adenocarcinoma cells. Analysis revealed activation of Wnt signaling in KPI tumor cells.

overall_design: Examination of active signaling in KPI tumor cells

first: Ning

last: Yin

first: E

last: Thompson

first: Xue

last: Wang


title: Epigenetic reprogramming of immune cells in women with PCOS impact genes controlling reproductive function

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

overall_design: Refer to individual Series


title: Cell-specific ablation of Hsp47 defines the collagen producing cells in the injured heart

city: Cincinnati

first: Vikram

last: Prasad

state: OH

address: 240, Albert Sabin Way

department: Molecular Cardiovascular Biology

institute: Cincinnati Children's Hospital Medical Center

summary: Overall goal: To elucidate fibroblast-specific role of Hsp47 in fibroblast activation, collagen production, and cardiac fibrosis and their differentiation to myofibroblasts. Purpose of analysis: To generate transcriptional profile of HSP47-deficient fibroblasts in the context of pathological cardiac remodeling associated with chronic pressure-overload.

overall_design: Experimental structure: Activated fibroblasts (labeled with eGFP+ reporter, induced upon activation of Postn-MCM) were FACS isolated from hearts after 4-weeks of pressure-overload following transaortic coarctation (TAC) surgery in mice, with and without fibroblast-specific (Postn-MCM-driven) Hsp47 deletion. RNA was isolated from these cells, total RNA amplified, and library generated according to established procedures. Transcriptional profile was generated using RNAseq (Illumina HiSeq2500) and differential gene expression analyses carried out using AltAnalyze.

first: Jeff

last: Molkentin

first: Hadi

last: Khalil


title: RNA sequencing of bone marrow WT and SLAMF9-/- pDCs

city: Rehovot

first: Gilgi

last: Friedlander

address: Hertzel st

country: Israel

institute: Weizmann Institute of Science

summary: SLAMF9 belongs to the conserved lymphocytic activation molecule family (SLAMF). Unlike other SLAMs, which have been extensively studied, the role of SLAMF9 in the immune system remained mostly unexplored. By generating CRISPR/CAS9 SLAMF9 knockout mice, we analyzed the role of this receptor in plasmacytoid dendritic cells (pDCs), which preferentially express the SLAMF9 transcript and protein. These cells display a unique capacity to produce type I interferon and bridge between innate and adaptive immune response. Analysis of pDCs in SLAMF9-/- mice revealed an increase of immature pDCs in the BM and enhanced accumulation of pDCs in the lymph nodes. In the periphery, SLAMF9 deficiency resulted in lower levels of the transcription factor SPIB, elevation of pDC survival, and attenuated IFNand TNFproduction. To define the role of SLAMF9 during inflammation, pDCs lacking SLAMF9 were followed during induced experimental autoimmune encephalomyelitis (EAE). SLAMF9-/- mice demonstrated attenuated disease and delayed onset, accompanied by a prominent increase of immature pDCs in the LN, with a reduced co-stimulatory potential and enhanced infiltration of pDCs into the central nervous system (CNS). These results suggest the crucial role of SLAMF9 in pDC differentiation, homeostasis and function in the steady state and during EAE.

overall_design: Comparing the transcriptom of pDCs derived from WT and SLAMF9-/- mice

first: Lital

last: Sever

first: Idit

last: Shachar


title: Mapping the targeting transcripts and binding sites of ALKBH5 by individual-nucleotide resolution UV crosslinking and immunoprecipitation-based sequencing (iCLIP-seq)

first: Yang

last: Liu

address: Dongdan Santiao 5

department: Immunology

institute: Peking Union Medical College&Chinese Academy of Medical Sciences

summary: To investigate whether the ALKBH5-mediated metabolic changes via demethylation of its target mRNA(s) is important in regulating viral response,  we mapped the targeting transcripts and binding sites of ALKBH5 in the virus infected cells and uninfected cells by using iCLIP-seq. Biological replicates of iCLIP-seq confirmed that OGDH is the direct targeting transcript of ALKBH5 and the binding capacity of ALKBH5 to OGDH mRNA was decreased upon viral infection. By combining the ALKBH5-iCLIP-seq results with m6A-seq data, we identified that there are overlapped ALKBH5-iCLIP peaks and m6A-seq peaks on OGDH mRNA. Furthermore,  other mRNAs, such as GOT2 mRNA, were also the ALKBH5’s targeting transcripts and m6A demethylation substrates. GOT2 is an important metabolic enzyme well known to be involved in host response to viral infection. These data demonstrated that ALKBH5-mediated metabolic rewiring via demethylation of target OGDH mRNA and other transcripts is important in regulating cellular viral replication.

overall_design: Mapping the targeting transcripts and binding sites of ALKBH5 in macrophages infected with or without VSV by iCLIP-seq, two biological replicates.


title: Next Generation Sequencing Analysis of the Transcriptomes of Wild Type and ALKBH5-/- Peritoneal Macrophages

summary: By performing RNA sequencing (RNA-seq) analysis on the peritoneal macrophages that derived from ALKBH5-/- mice and littermate mice infected with or without vesicular stomatitis virus (VSV), we want to investigate whether deficiency of ALKBH5 controls viral replication through a more general mechanism such as enhancing innate response, and if not, what's the critical downstream target(s) of ALKBH5. RNA-seq analysis showed that mRNA expression of innate genes remained unchanged or not increased in ALKBH5-deficient cells. While thourgh KEGG pathway enrichment analysis of the RNA-seq data, we found that metabolic pathways were the ones most significantly affected in ALKBH5-deficient macrophages upon VSV infection. These results demonstrated that deficiency of ALKBH5 controls viral replication by significantly changing the metabolism-related genes expression.

overall_design: Transcriptomes profiles of gene expression changes in wild type and ALKBH5-/- peritoneal macrophages infected with or without VSV, two biological replicates.


title: Analysis of mRNA expression changes caused by mdt-15(tm2182) mutation at 15oC and 25 oC

city: Daejeon

first: Seung-Jae

middle: V

last: Lee

address: 291 Daehak-ro

department: Biological Sciences

country: South Korea

institute: KAIST

summary: To determine the role of MDT-15 in mRNA expression changes at different temperatures, we sequenced mRNAs obtained from day 1 adult Caenorhabditis elegans. Bristol N2 (wild-type) and mdt-15(tm2182) mutant animals that cultured at 25oC or 15oC were used.

overall_design: Measurement of mRNA levels in Bristol N2 (wild-type) and mdt-15(tm2182) animals cultured at 25oC or 15oC by deep sequencing (Macrogen, South Korea) in triplicate

first: Dongyeop

first: Seon-Woo

last: An

first: Yoonji

last: Jung


title: MondoA Links Muscle Lipid Accumulation and Insulin Resistance Driven by Nutrient Overload

city: Philadelphia

first: Byungyong

last: Ahn

state: Pennsylvania

address: 3400 Civic Center Blvd Bldg 421

department: Penn Cardiovascular Institute

institute: University of Pennsylvania

type: Genome binding/occupancy profiling by high throughput sequencing


title: Environmental Factors Influence the Epigenetic Signature of Newborns from Mothers with Gestational Diabetes

first: Lars

last: Ingerslev

summary: Here we investigated the degree by which epigenetic signatures in children from mothers with obesity or gestational diabetes mellitus are influenced by environmental factors.   We profiled the DNA methylation signature of whole blood from lean, obese and gestational diabetes mellitus mothers and their respective newborns.  DNA methylation profiles of mothers showed high similarity across groups, while on the contrary, newborns from GDM mothers showed a marked distinct epigenetic profile compared to newborns of both lean and obese mothers. Analysis of variance in DNA methylation levels between newborns showed higher variance in the GDM group. Our work suggest that environmental factors, rather than direct transmission of epigenetic marks from the mother, are involved in establishing the epigenetic signature associated with GDM.

overall_design: We performed Reduced Representation Bisulfite Sequencing on 8 lean, 8 obese and 8 gestational diabetic mother-newborn pairs.

first: Emil

last: Andersen

first: Ali

last: Altıntaş

first: Ulrika

last: Andersson-Hall

first: Agneta

last: Holmäng

first: Romain

last: Barrès


title: Transcriptome profiling in primary human skeletal myotubes with MondoA knockdown

summary: It is well known that insulin resistance in the obese state is associated with accumulation of neutral lipid in extra-adipose tissues. This phenomenon is particularly well-documented in skeletal muscle. The mechanistic underpinnings of this linkage are not fully understood. To define new MondoA target gene and pathway in human myotubes, we performed whole genome RNA sequencing.

overall_design: RNA seq was performed with total RNA isolated from differentiated primary human skeletal myotubes. These cells were transfected with siRNA of control or MondoA. Three biologic replicates for each condition were included.

first: Shibiao

last: Wan

first: Kyong-Jae

last: Won

first: Daniel

last: Kelly


title: Expression profiles of miRNA derived from exosomes for ectoderm-biased substate of human pluripotent stem cells.

city: Tsukuba

first: Yuzuru

last: Ito

state: Ibaraki

address: Central 6, Higashi 1-1-1

department: Biotechnology Research Institute for Drug Discovery

country: Japan

institute: National Institute of Advanced Industrial Science and Technology (AIST)

summary: We established two different substates in human ES cell line, H9 cells, by changing the extracellular matrices. To examine a global miRNA expression comparison between the substate 1 and substate 2 cells, miRNA microarray was performed.

overall_design: Human ES cell line, H9 cells, was maintained on Vitronectin XF (STEMCELL Technologies) in TeSR-E8 (STEMCELL Technologies) with feeder free conditions. We changed the extracellular matrices from Vitronectin to Matrigel (BD Biosciences). The H9 cells cultured on Matrigel contained two different substates. Exosomes in the cell culture medium were precipitated by ExoQuick-TC (System Biosciences, EXOTC50A-1). The miRNAs of substate 1 and substate 2 were extracted from the exosomes by using miRNeasy Mini Kit (QIAGEN, 217004). miRNA microarray were performed by a SurePrint G3 miRNA Microarray Kit, 8 x 60K (Agilent, G4872A).

first: Shuuji

last: Mawaribuchi


title: Genomic profiling of MondoA and H3K27ac in primary human skeletal myotubes

summary: It is well known that insulin resistance in the obese state is associated with accumulation of neutral lipid in extra-adipose tissues. This phenomenon is particularly well-documented in skeletal muscle. The mechanistic underpinnings of this linkage are not fully understood. To define direct MondoA target genes, we performed MondoA ChiP sequencing in human myotubes.

overall_design: ChiP seq was performed in differentiated primary human skeletal myotubes. These cells were transfected with siRNA of control or MondoA. Two biological replicates for each condition were included.


title: Expression profiles of miRNA derived from cells  for ectoderm-biased substate of human pluripotent stem cells.

overall_design: Human ES cell line, H9 cells, was maintained on Vitronectin XF (STEMCELL Technologies) in TeSR-E8 (STEMCELL Technologies) with feeder free conditions. We changed the extracellular matrices from Vitronectin to Matrigel (BD Biosciences). The H9 cells cultured on Matrigel contained two different substates. The miRNAs were extracted from substate 1 and substate 2 cells by using miRNeasy Mini Kit (QIAGEN, 217004). miRNA microarray were performed by a SurePrint G3 miRNA Microarray Kit, 8 x 60K (Agilent, G4872A).


title: mRNA expression profiles for ectoderm-biased substate of human pluripotent stem cells.

summary: We established two different substates in human ES cell line, H9 cells, by changing the extracellular matrices. To examine a global gene expression comparison between the substate 1 and substate 2 cells, DNA microarray was performed.

overall_design: Human ES cell line, H9 cells, was maintained on Vitronectin XF (STEMCELL Technologies) in TeSR-E8 (STEMCELL Technologies) with feeder free conditions. We changed the extracellular matrices from Vitronectin to Matrigel (BD Biosciences). The H9 cells cultured on Matrigel contained two different substates. The total mRNAs were extracted from substate 1 and substate 2 cells by using ISOGEN (NIPPON GENE). DNA microarray were performed by a SurePrint G3 Human GE Microarray Kit, 8 x 60 K Ver. 3 (Agilent, G4851C).


title: Transcriptomic analysis of 13.5dpc embryonic ovaries exposed to the acetaminophen (APAP) and ibuprofen (IBU) combination in mice

city: Montpellier

first: Brigitte

last: Boizet Bonhoure

address: 141 rue de la Cardonille

department: Human Genetic Institute

institute: CNRS UMR9002

summary: Nonsteroidal anti-inflammatory drugs such as ibuprofen (IBU) and analgesic drugs, such as acetaminophen (APAP), are the most frequently medications taken by pregnant women, even in combination. They were shown to target fetal gonadal development acting as endocrine disruptors, that might favour genital malformations in new-born boys and reproductive disorders in adults, in an intergenerational manner. However, the consequences on postnatal ovarian development and female reproductive health after in utero exposure are still unknown. Here, we show that in utero exposure to therapeutic doses of the widely used APAP-IBU combination during the sensitive window of sex determination leads to an increased proliferation of female embryonic germ cells and a delayed entry into meiosis in 13.5dpc exposed ovaries. Consequently, the primordial follicle formation is enhanced in postnatal ovaries and is followed by a reduced follicular activation through the Akt/FoxO3 pathway and an increased follicular apoptosis. Subsequently, a reduced ovarian reserve in adult ovaries of exposed animals and in their offspring (F1) is observed. This leads to the subfertility of 6-month-old F1 animals that show an accelerated ovarian aging, a Premature Ovarian Insufficiency-like phenotype, with an abnormal persistence of corpora lutea due to the decreased apoptosis and an increased luteal Akt-mediated cell survival. Our data suggest that the use of APAP+IBU during this critical period of development that occurs during the first trimester of gestation (6 to 10 weeks), could lead in humans to adverse effects that could be passed to the offspring.

overall_design: mRNA profiles of 13.5 days post coitum wild type and APAP+IBU exposed ovaries were generated by deep sequencing, in triplicate

last: Boizet-Bonhoure


title: The differentially expressed circular RNAs in the hippocampus of Nrf2-knockout mice

city: Shijiazhuang

first: Lei

last: Wang

address: Hebei Medical University, No. 361, Zhongshan East Road, Chang'an District

institute: Heibei Medical University

summary: Non-coding circular RNAs (circRNAs) have displayed dysregulated expression in the hippocampus of Nrf2-knockout mice.

overall_design: To compare the profile differences in the hippocampus tissues between Nrf2 (+/+) and Nrf2 (-/-) mice.

first: Shaoguang

last: Sun


title: Engineered adoptive T cell therapy prolongs survival in a preclinical model of advanced stage ovarian cancer

city: Seattle

first: Kristin

middle: Gail

last: Anderson

address: 1100 Fairview Ave N

department: Clinical Research Division

institute: Fred Hutchinson Cancer Research Center

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: The EN1 transcription factor drives neural features and brain metastases in triple negative breats cancer (TNBC)

city: Boston

first: Kornelia

last: Polyak

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: To define transcriptional dependencies of TNBCs, we identified transcription factors highly and specifically expressed in primary TNBCs and tested their requirement for cell growth in a panel of breast cancer cell lines. We found that EN1 is overexpressed in TNBCs and its downregulation preferentially and significantly reduces cellular viability and tumorigenicity in TNBC cell lines. Based on RNA-seq and ChIPseq we found that EN1 regulates genes involved in angiogenesis, neurogenesis, and axon guidance in breast cancer cells. Higher expression of EN1 correlates with shorter overall survival among TNBC patients and with higher risk of developing brain metastases. Thus, EN1 is a prognostic marker and a therapeutic target in this particularly lethal subset of TNBCs.

overall_design: Bulk RNA-Seq: Gene expression analysis of SUM149 and SUM159 cell lines with TET-inducible shRNA against EN1 with the following variables: Two different shRNA labeled shEN1-1 and shEN1-2, doxycyclin (plus/treatment) and no doxycyclin (minus/control), 3 days and 5 days after doxycyclin treatment. All conditions were sequenced in biological duplicates (32 samples). For the MCF7 cellline samples, differential gene expression analysis was performed with inducible overexpression of EN1 with the following variables:  doxycyclin (plus/treatment) and no doxycyclin (minus/control). All conditions were sequenced in biological duplicates (4 samples). ChIP-Seq: ChIP-Seq for exogenously expressed V5-tagged EN1 in SUM149, SUM159 and MCF7. ChIP-Seq for histone H3 lysine 27 acetyl (H3K27ac) in SUM149 and SUM159. ChIP-Seq for the transcription factor FOXA1 in MCF7 cells of both LacZ condition and EN1-expressing condition. ChIP-Seq for the transcription factor Beta-catenin in MCF7 cells of both LacZ condition and EN1-expressing condition, and in SUM149 with and without EN1 knockdown. ChIP-Seq for TLE3 in MCF7 cells of both LacZ condition and EN1-expressing condition, and in SUM149 and SUM159 with and without EN1 knockdown.

first: Guillermo

last: Peluffo

first: Ashim

last: Subedee

first: Nicholas

middle: W

last: Harper

first: Natalie

last: Kingston

first: Bojana

last: Jovanovic

first: Felipe

last: Flores

first: Francisco

last: Beca

first: Anne

last: Trinh

first: Chandra

last: Chilamakuri

first: Eva

last: Papachristou

first: Ying

last: Su

first: Andriy

last: Marusyk

first: Clive

last: D'Santos

first: Andrew

last: Beck

first: Carlos

last: Caldas

first: Jason

last: Carroll


title: Engineered adoptive T cell therapy prolongs survival in a preclinical model of advanced stage ovarian cancer [Mouse]

first: Kristin

last: Anderson

summary: Purpose: Adoptive T cell therapy using high affinity T cell receptors (TCRs) to target tumor antigens has potential for improving outcomes in high-grade serous ovarian cancer (HGSOC) patients. Ovarian tumors develop a hostile, multicomponent tumor microenvironment containing suppressive cells, inhibitory ligands, and soluble factors that facilitate evasion of anti-tumor immune responses. Developing and validating an immunocompetent mouse model of metastatic ovarian cancer that shares antigenic and immunosuppressive qualities of human disease would facilitate establishing effective T cell therapies.   Experimental Design: We used deep transcriptome profiling and immunohistochemical analysis of human HGSOC tumors and disseminated mouse ID8VEGF tumors to compare immunologic features. We then evaluated the ability of CD8 T cells engineered to express a high-affinity TCR specific for mesothelin, an ovarian cancer antigen, to infiltrate advanced stage ID8VEGF murine ovarian tumors and control tumor growth. Human CD8 T cells engineered to target mesothelin were also evaluated for ability to kill HLA-A2+ HGSOC lines.  Results: Immunohistochemistry and gene expression profiling revealed striking similarities between tumors, including processing/presentation of similar candidate target antigens, suppressive immune cell infiltration, and expression of molecules that inhibit T cell function. Engineered T cells infiltrated mouse tumors but became progressively dysfunctional and failed to persist within tumors. Treatment with repeated doses of T cells maintained functional activity, significantly prolonging survival of mice harboring late-stage disease at treatment onset. Human CD8 T cells engineered to target mesothelin were tumoricidal for three HGSOC lines.   Conclusions: Treatment with engineered T cells may have clinical applicability in patients with advanced-stage HGSOC.

overall_design: Late-stage tumors isolated from 3 ID8-VEGF mice were analyzed.

middle: G

first: Valentin

last: Voillet

first: Raphael

last: Gottardo

first: Philip

middle: D

last: Greenberg


title: RNA-Seq of CD34+ Bone Marrow Progenitors from Healthy Donors

first: Nathan

last: Salomonis

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

summary: To evaluate the transcriptome and splicing repertoire of bulk CD34+ sorted bone marrow progenitors we performed RNA-Seq. These data highlight an AML prognostic splicing signature that is present in healthy donors at equivalent frequencies to that found in AML bone marrow.

overall_design: Bulk RNA-Seq of 12 biological replicates

first: Kasiani

last: Myers


title: Engineered adoptive T cell therapy prolongs survival in a preclinical model of advanced stage ovarian cancer [Human]

overall_design: Matched normal tissue, primary ovarian tumor, and metastatic tumor samples from untreated patients were analyzed.


title: miRNA expression profile of Idh1 wild-type and mutant glioma initiating cells

city: London

first: Sebastian

last: Brandner

state: State...

address: Queen square house, UCL Institute of Neurology

department: Institute of Neurology

country: United Kingdom

institute: University College London

type: Non-coding RNA profiling by high throughput sequencing

summary: Human astrocytomas and oligodendrogliomas are defined by mutations in the metabolic enzyme isocitrate dehydrogenase (IDH) 1 or 2. Mutant IDH1 causes the production and accumulation of the metabolite 2 hydroxyglutarate, which induces genome-wide hypermethylation, and is thought to be a driver mutation of these tumours. However, there are multiple contradictory effects of mutant IDH1 in cell lines and in vivo models, prompting us to study the effect of mutant IDH1 on cell differentiation, proliferation, and apoptosis. Here we established mouse glioma initiating cells (GIC) by inactivating the tumour suppressor genes Pten and p53 in the neural stem/progenitor cell population of the forebrain, and compared these GIC with triple mutant tumours expressing in addition the Idh1 R132H mutation. We found that Idh1 mutant cells proliferate less in vitro and mice with Idh1 mutant tumour survived significantly longer than their Idh1 wild type counterparts. By comparing the miRNA expression profiles of Idh wild-type and Idh mutant cells and tumours we identified miR-183-5p as a differentially expressed miRNA.

overall_design: The miRNA sequencing was performed on two Pten-/-/p53-/- (in short Pten/p53) glioma initiating cell lines, and two Idh1R132H/Pten/p53 glioma initiating cell lines.

first: Ningning

last: Li

first: Kastytis

last: Sidlauskas

last: Zhang


title: Gene expression profile of Idh1 wild-type and mutant glioma initiating cells

summary: Human astrocytomas and oligodendrogliomas are defined by mutations in the metabolic enzyme isocitrate dehydrogenase (IDH) 1 or 2. Mutant IDH1 causes the production and accumulation of the metabolite 2 hydroxyglutarate, which induces genome-wide hypermethylation, and is thought to be a driver mutation of these tumours. However, there are multiple contradictory effects of mutant IDH1 in cell lines and in vivo models, prompting us to study the effect of mutant IDH1 on cell differentiation, proliferation, and apoptosis. Here we established mouse glioma initiating cells (GIC) by inactivating the tumour suppressor genes Pten and p53 in the neural stem/progenitor cell population of the forebrain, and compared these GIC with triple mutant tumours expressing in addition the Idh1 R132H mutation. We found that Idh1 mutant cells proliferate less in vitro and mice with Idh1 mutant tumour survived significantly longer than their Idh1 wild type counterparts. By comparing the RNA expression profiles of Idh wild-type and Idh mutant cells and tumours we identified endoplasmic reticulum stress pathways were significantly associated with Idh1 mutation.

overall_design: The RNA sequencing was performed on two Pten-/-/p53-/- (in short Pten/p53) glioma initiating cell lines, and two Idh1R132H/Pten/p53 glioma initiating cell lines.


title: Analysis of NK cells in liver cancer patients and normal donors

city: Hefei

first: Xiaohu

last: Zheng

state: Anhui

address: Huang Shan Road

department: School of Life Sciences

institute: University of Science and Technology of China

summary: Analysis of the gene expression profiles of NK cells from liver cancer patients and normal donors

overall_design: Find potential therapeutic targets on NK cells for liver cancer

first: Haiming

last: Wei


title: Application of the High-throughput TAB-Array for the Discovery of Novel 5-Hydroxymethylcytosine Biomarkers in Pancreatic Ductal Adenocarcinoma

city: Chicago

first: Wei

state: IL

address: 680 N Lake Shore Drive, Suite 1400

department: Preventive Medicine

institute: Northwestern University

summary: Genome wide DNA hydroxymethylation profiling of tumor and adjacent tissue samples in pancreatic cancer. The Illumina Infinium MethylationEPIC BeadChip was used to obtain DNA hydroxymethylation profiles across approximately 850,000 CpGs in paired tumor and tumor adjacent tissues in 17 adult patients with primary pancreatic adenocarcionoma .

overall_design: Bisulphite converted DNA from the 17 paired samples were hybridised to the Illumina Infinium MethylationEPIC BeadChip

first: W

first: J

last: Wang

first: B

last: Chiu

first: L

last: Hou

first: Z

first: C

last: Zeng


title: The transcriptomic profile of human microvascular endothelial cells after exposure to preeclamptic or normotensive third trimester trophoblast debris

city: AUCKLAND

first: Larry

last: Chamley

address: 85 Park Road

department: Obstetrics and Gynaecology

country: New Zealand

institute: The University of Auckland

summary:
The human placenta is covered by a single multinucleated fetal cell, the syncytiotrophoblast, which is bathed in maternal blood. During all pregnancies, membrane enclosed extracellular vesicles derived from the syncytiotrophoblast are extruded into the maternal blood.The large size of these extracellular vesicles (diameter larger than 10 µm) is referred to as trophoblast debris in this study. We have shown in the past that trophoblast debris from first trimester can contribute to maternal cardiovascular physiological  adaptations. This study aimed to characterise the transcriptional changes that occur in human vascular endothelial cells following exposure to preeclmaptic and normotensive trophoblast debris.
Primeview human gene expression arrays were used to probe transcriptomic changes in human microvascular endothelial cells after exposure to preeclmaptic or normotensive trophoblast debris for 21 hours

overall_design: Trophoblast debris were isolated by four individual preeclmaptic and three gestational controlled normotensive human placentae. HMEC-1 cells were co-cultured with trophoblast debris (60ug/ml total debris protein contents) for 21 hours before RNA extraction. Untreated HMEC-1 cells were used as negative controls. In total, 10 samples were analyzed.

first: Lawrence

first: Jia


title: Transcriptomic profile reveals the global remodeling of blastocyst for implantation

city: Xiamen

first: Shuangbo

last: Kong

state: Fujian

address: Xiangan south Rd

institute: Xiamen University

summary: Implantation of the blastocyst into the uterus is a developmental milestone in mammalian embryonic development, which is the gateway for further development of fetus. At this time, remodeling of the blastocyst to an implantation competent status, which is known as blastocyst activation, is indispensable for embryo implantation.This RNA sequence data is from the Dormant, Reactivating and Reactivated blastocyst.

overall_design: Examination of blastocysts with different implantation competency

first: Bo

last: He

first: Haibin


title: Nascent Polypeptide Domain Topology and Elongation Rate Direct the Cotranslational Hierarchy of Hsp70 and TRiC/CCT

city: Stanford

first: Kevin

middle: C.

last: Stein

state: California

address: Clark Center E200, 318 Campus Drive

department: Biology

institute: Stanford University

summary: Folding newly synthesized proteins relies on the ribosome intricately coordinating mRNA translation with a network of ribosome-associated machinery. The principles that drive the coordination of this diverse machinery remain poorly understood. Here, we use selective ribosome profiling to determine how the essential chaperonin TRiC/CCT and the Hsp70 Ssb are recruited to ribosome-nascent chain complexes to mediate cotranslational protein folding. Whereas substrate localization and nascent chain sequence are the major determinants of cotranslational recruitment of Ssb, we found that temporal and structural elements drive TRiC engagement. For both chaperones, however, local slowdowns in translation enhance chaperone enrichment. This work helps define the principles that dictate the coordinated activity of ribosome-associated factors to perform their critical role in maintaining a properly folded nascent proteome.

overall_design: Replicate ribosome profiling libraries were prepared of immunoprecipitated TRiC/CCT- and Ssb-bound ribosome nascent chain complexes compared to the total ribosome pool, using wild-type yeast and yeast harboring the atp2-P353A,P355A mutations. Additional ribosome profiling libraries were prepared to monitor translation kinetics in yeast not treated with cycloheximide.

first: Allison

last: Kriel

first: Judith

last: Frydman


title: Genome-wide RNA-seq from GALNT14-depleted and GALNT14 overexpressing MDA-MB-231 LM2 and Par cells

city: DaeJeon

first: Mi Young

last: Kim

address: Biological science

summary:
Purpose: To identify downstream signaling pathways that mediate functions of GALNT14
Methods: RNAs isolated from MDA231-LM2 cells expressing shCntr or shGALNT14 and MDA231-Par cells expressing pBabe-Hygro control vector or GALNT14 expression vector were analyzed by using an Illumina HiSeq 2500
Conclusions: Our study represents the first transcriptome profile of GALNT14-depleted MDA231-LM2 and GALNT14-overexpressing Par cells.

overall_design: mRNAs prepared from GALNT14 knockdown or GALNT14 over-expressing MDA-MB-231 cells were analyzed in duplicaters by Illumina HiSeq 2500. RNA-Seq reads were aligned to the human reference genome (NCBI 37, hg19) using the spliced read aligner TopHat version 1.4.0.

first: Ki-Hoon

last: Song

first: Tulip

last: Nandu

first: Shrikanth

last: Gadad


title: Immuno-PET identifies the myeloid compartment as a key contributor to the outcome of the anti-tumor response under PD-1 blockade [scRNA-seq]

status: Public on Aug 21 2019

first: Mohammad

last: Rashidian

address: 1  Blackfan Circle, Karp Research Lab building

institute: Boston Children's Hospital

summary: Immunotherapy using checkpoint-blocking antibodies against PD-1 has produced impressive results in a wide range of cancers. However, the response remains heterogeneous among patients. We used noninvasive immuno-positron emission tomography (PET), using 89Zr-labeled PEGylated single-domain antibody fragments (nanobodies or VHHs), to explore the dynamics and distribution of intratumoral CD8+ T cells and CD11b+ myeloid cells in response to anti-PD-1 treatment in the MC38 colorectal mouse adenocarcinoma model. Responding and nonresponding tumors showed consistent differences in the distribution of CD8+ and CD11b+ cells. Anti-PD-1 treatment mobilized CD8+ T cells from the tumor periphery to a more central location. Only those tumors fully infiltrated by CD8+ T cells went on to complete resolution. All tumors contained CD11b+ myeloid cells from the outset of treatment, with later recruitment of additional CD11b+ cells. As tumors grew, the distribution of intratumoral CD11b+ cells became more heterogeneous. Shrinkage of tumors in responders correlated with an increase in the CD11b+ population in the center of the tumors. The changes in distribution of CD8+ and CD11b+ cells, as assessed by PET, served as biomarkers to gauge the efficacy of anti-PD-1 treatment. Single-cell RNA sequencing of RNA from intratumoral CD45+ cells showed that CD11b+ cells in responders and nonresponders were markedly different. The responders exhibited a dominant population of macrophages with an M1-like signature, while the CD45+ population in the nonresponders displayed an M2-like transcriptional signature. Thus, by using immuno-PET and single-cell RNA sequencing, we show that anti-PD-1 treatment not only affects interactions of CD8+ T cells with the tumor but also impacts the intratumoral myeloid compartment.

overall_design: Animals were inoculated with 50,000 MC38-GFP+ cells, subcutaneous, below the right shoulder, and were treated with a sub-optimal dose of anti-PD-1 antibody (100 ug per mouse, on days 12, 15, 18 and 22). Tumors were excised and cancer cells and CD45+ immune cells were sorted, and submitted separately for bulk RNAseq analysis (tumor cells), and single cell RNAseq analysis (immune cells). For a detailed procedure, please see the manuscript (PMID: 31375632).

first: M

middle: I

last: Barrasa

first: Hidde

last: Ploegh


title: Immuno-PET identifies the myeloid compartment as a key contributor to the outcome of the anti-tumor response under PD-1 blockade

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

overall_design: Refer to individual Series


title: Gene Expression data from SH3GL2 overexpressing SUM-159 cells

city: Tyler

first: Santanu

last: Dasgupta

state: Texas

department: Cellular and Molecular Biology

institute: UT Health Science Center at Tyler

summary:
SH3GL2 acts as a tumor suppressor. Our aim was to idenfy SH3GL2 regulatory pathways.
We stably introduced SH3GL2 in SUM159 cells, exhibiting reduced cancer growth and pulmonary metastasis

overall_design: We employed Affymatrix cDNA microarray analysis to identify potential oncoproteins associated with SH3GL2 function


title: Zfp189 Mediates Stress Resilience Through a CREB-Regulated Transcriptional Network in Prefrontal Cortex

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

summary: Stress resilience involves numerous brain-wide transcriptional changes. Determining the organization and orchestration of these transcriptional events may reveal novel antidepressant targets, but this remains unexplored. Here, we characterize the resilient transcriptome with co-expression analysis and identify a single transcriptionally-active uniquely-resilient gene network. Zfp189, a previously unstudied zinc finger protein, is the top network key driver and its overexpression in prefrontal cortical (PFC) neurons preferentially activates this network, alters neuronal activity and promotes behavioral resilience. CREB, which binds Zfp189, is the top upstream regulator of this network. To probe CREB-Zfp189 interactions as a network regulatory mechanism, we employ CRISPR-mediated locus-specific transcriptional reprogramming to direct CREB selectively to the Zfp189 promoter. This single molecular interaction in PFC neurons recapitulates the pro-resilient Zfp189-dependent downstream effects on gene network activity, electrophysiology and behavior. These findings reveal an essential role for Zfp189 and a CREB-Zfp189 regulatory axis in mediating a central transcriptional network of resilience.

overall_design: Nuclease-dead, RNA-guided, DNA-binding protein Cas9 was fused to a constitutively active, phosphomimetic mutant form of CREB S133D (dCas9-CREB S133D ) and sgRNAs to target near the consensus CRE motif were designed in the promoter region of Zfp189. Herpes simplex virus (HSV) vectors, which target neurons selectively, were used to overexpress Zfp189 plus GFP or GFP alone in PFC neurons and mice were exposed to an accelerated social defeat paradigm.

first: Zachary

last: Lorsch

first: Peter

last: Hamilton

first: Li

last: Shen

first: Rosemary

last: Bagot

first: Eric

last: Nestler


title: Expression data from mouse embryo salivary glands treated by TGF-beta 1

city: ChengDu

first: Liu

last: Zhikai

address: People South street

institute: SiChuan University

summary:
Branching morphogenesis is a basic way of the kinds of complex organs’ development including lungs, kidneys, thyroid glands and salivary glands.1 Submandibular gland (SMG) development is a classic model to reveal the mechanism of branching morphogenesis and it also provides novel approaches to tissue engineering for salivary glands regenerating or for creating artificial salivary glands.And for murine salivary glands’ development, two main components are formed, epithelial and mesenchyme. The elongation and branch of epithelial make up the main process of its development which supported by mesenchymal secretion.This processes are controlled by many factors like growth factors, hormones and miRNAs etc.567 All these factors play different roles in the branching morphogenesis of mouse salivary glands. Transforming growth factor β1 (TGF-β1) is a pivotal factor of them and it has a huge impact on SMG development through its action on the mesenchyme.
We used microarrays to detail the global programme of gene expression during the branching morphogenesis and identified distinct classes of up/down-regulated genes during this process.

overall_design: mouse embryos were selected at stage(T13) of early development for RNA extraction and hybridization on Affymetrix microarrays. We sought to treated them with nothing or TGF-β1 to see what would happen to them.

first: ZhiKai

last: Liu

first: ChunJie

last: Li

first: XiangHe

last: Qiao


title: Transcriptome profiling reveals functional variation in Plasmodium falciparum parasites from controlled human malaria infection studies

city: Singapore

first: Regina

last: Hoo

address: 60, Nanyang Drive

department: School of Biological Science

institute: Nanyang Technological University

summary: The objective of this study is to characterize the overall transcriptome of P. falciparum NF54 derived from a controlled-human malaria infection (CHMI) study. Healthy, immunologically naïve human volunteers were infected intradermally or intravenously with different dosages of Plasmodium falciparum sporozoites (Sanaria® PfSPZ Challenge). Parasites were isolated from these volunteers and subjected to a range of in vitro culture generation prior to RNA collection.

sample_organism:
Plasmodium falciparum NF54
Plasmodium falciparum 3D7

overall_design: P. falciparum parasites strain NF54 obtained from the dose escalation CHMI of Sanaria® PfSPZ Challenge (TÜCHMI-001-NCT01624961) derived from a single P. falciparum NF54 (PfNF54) working cell bank were subjected to RNA isolation and microarray hybridization. In brief, on the day of positivity in patients enrolled in the trial, 0.25 ml of patient blood was used to establish 10 ml in vitro cultures. As soon as the parasitemia reached 3-4%, the culture were expanded into a 20 ml culture. RNA was harvested as soon as an individual 20 ml parasite culture reached a parasitemia of 3-5%, and then every 2-3 generations thereafter. 20 ml parasite cultures were synchronized twice per day with 5% (v/v) sorbitol in water to obtain ring-stage parasites. A total of 55 RNA samples were collected, including 3 pre-mosquito parental culture at synchronized ring stage. RNA were extracted and synthesis and amplification of cDNA was carried out as previously described in Bozdech, Z., S. Mok & A. P. Gupta, (2013). cDNA generated was used for microarray hybridizations against a common RNA reference pool of P. falciparum 3D7 strain.

first: R

first: L

last: Zhu

first: E

last: Bruske

first: S

last: Dimonte

first: Z

last: Bozdech

last: Frank

first: P

middle: R

last: Preiser


title: Phf6-null hematopoietic stem cells have enhanced self-renewal capacity and oncogenic potentials

city: Taipei

first: Yueh-Chwen

last: Hsu

address: No.7, Chung Shan S. Rd.

country: Taiwan

institute: National Taiwan University Hospital

summary: Plant homeodomain finger gene 6 (PHF6) encodes a 365-amino-acid protein containing two plant homology domain fingers. Germline mutations of human PHF6 cause Börjeson–Forssman–Lehmann syndrome, a congenital neurodevelopmental disorder. Loss-of-function mutations of PHF6 are detected in patients with acute leukemia, mainly of T cell lineage and in a small proportion of myeloid lineage. The functions of PHF6 in physiological hematopoiesis and leukemogenesis remain incompletely defined. To address this question, we generated a conditional Phf6 knockout mouse model and investigated the impact of Phf6 loss on the hematopoietic system. We found that Phf6 knockout mice at 8-week age had reduced numbers of CD4+ and CD8+ T cells in the peripheral blood compared to the wild-type littermates. There were decreased granulocyte-monocytic progenitors but increased Lin-c-Kit+Sca-1+ (LSK) cells in the marrow of young Phf6 knockout mice. Functional studies including competitive repopulation unit and serial transplantation assays revealed an enhanced reconstitution and self-renewal capacity in Phf6 knockout hematopoietic stem cells (HSCs). Aged Phf6 knockout mice had myelodysplasia-like presentations including decreased platelet counts, megakaryocyte dysplasia, and enlarged spleen related to extramedullary hematopoiesis. Moreover, we found that Phf6 loss lowered the threshold of NOTCH1-induced leukemic transformation at least partially through increased leukemia-initiating cells. Transcriptome analysis on the restrictive rare HSC subpopulations revealed upregulated cell cycling and oncogenic functions, with alteration of expression of key genes in those pathways. In summary, our studies demonstrate the in vivo crucial roles of Phf6 in physiological and malignant hematopoiesis.

overall_design: We sorted 100 to 200 cells of LT-HSC, MPP2, and MPP3 from the 4 pairs of Phf6 wild-type and knockout mice, followed by RNA extraction, cDNA synthesis  and NGS.

first: Chia-Lang


title: Custom selection of reference genes for transcriptomic analysis

city: Trois-Rivières

first: KarenCristine

last: GonçalvesdosSantos

state: QC

address: 3351 boulevard des Forges

department: Chemistry, biochemistry and physics

country: Canada

institute: Université du Québec à Trois-Rivières

summary: We developed a R-based script to select internal control genes based solely on read counts and gene sizes. We used this method to pick custom reference genes for the differential expression analysis of three transcriptome sets from transgenic Arabidopsis plants expressing heterologous fungal effector proteins tagged with GFP (using GFP alone as the control). The custom reference genes showed lower covariance and fold change as well as a broader range of expression levels than commonly used reference genes. When analyzed with NormFinder, both typical and custom reference genes were considered suitable internal controls, but the custom selected genes were more stable. geNorm produced a similar result in which most custom selected genes ranked higher (i.e. were more stable) than commonly used reference genes.

overall_design: Transgenic Arabidopsis thaliana Columbia-0 plants expressing GFP alone (Control) or fused to a candidate secreted effector protein of the fungus Melampsora larici-populina (Mlp37347 or Mlp124499) were used for the transcriptome analysis.   RNA was extracted from pooled aerial tissue of 2-week-old soil-grown plants, doing four replicates per genotype. Libraries were generated  using the TruSeq Stranded mRNA Library Prep kit (Illumina) and 100 ng of total RNA. The libraries were sequenced with Illumina HiSeq 4000 Sequencer paired-end reads of 100nt. Trimmomatic (LEADING:4 TRAILING:4 SLIDINGWINDOW:4:20 MINLEN:20) and then the surviving paired reads were aligned to the TAIR10 assembly of the genome of A. thaliana with TopHat v2.0.14 in Galaxy (default options, with average mate inner distance varying for each replicate and standard deviation of distance between pairs of 50 base pairs). Further analyses were done using R software v.3.2.5. Genomic ranges of Arabidopsis transcripts were obtained from Ensembl plants with GenomicFeatures and overlaps of sequencing reads with the transcripts were counted using GenomicAlignments, using options for paired-end reads and union mode.

first: Karen

last: Goncalves dos Santos

first: Isabel

last: Desgagné-Pénix

first: Hugo

last: Germain


title: The miRNA Profile and Bioinformatic Analysis for Diagnosis in Patients with Stage IIIA Colon Cancer

city: SANLIURFA

first: Cigdem

last: GUNGORMEZ

address: HUBTAM

country: Turkey

institute: Harran University

summary: The aim of this study is to analyze microRNA expression profile, and through bioinformatic analyses determine the cellular processes of potential target genes and understand their molecular mechanism in stage IIIA colon cancer patients. The microRNA expression profiles of both normal and tumor tissues of seven patients were analyzed using the Affymetrix microarray system.

overall_design: miRNA profiling was performed using 7 normal and 7 human tumor tissues of colon cancer stage IIIA.

last: Gungormez

first: Emine

last: Teker

first: Sema

last: Atmanoglu

first: Ersin

last: Borazan


title: Tissue-specific transcriptomes reveal gene expression trajectories in two maturing skin epithelial layers in zebrafish embryos

city: Los Angeles

first: Shawn

middle: J.

last: Cokus

address: UCLA, 3000 Terasaki Life Sciences Building, 610 Charles Young Drive East

country: USA

institute: UCLA

summary: We purified (FACS) and profiled (RNA-Seq) zebrafish embryo skin cells vs. nonskin cells at three early developmental stages. At two of the stages, we further purified and profiled two distinct epithelial layers of the skin: the periderm and basal cells. Our comprehensive expression analysis provides the first reported transcriptomes of these two cell types, reveals gene expression dynamics in space and time, and identifies common and distinct features of epithelial maturation in the two layers. Given the conserved nature of skin development, we believe our study to be of interest to those studying skin in other vertebrates.

overall_design: At each of 20 SS, 52 hpf, and 72 hpf, we used krt4:dsRed transgenic zebrafish embryos and FACS to prepare and run two RNA-Seq conditions: all skin vs. nonskin1, with two replicates for each condition. At each of 52 hpf and 72 hpf, we used krt4:dsRed;krt5:GFP transenic zebrafish embryos and FACS to prepare and run three RNA-Seq conditions: periderm vs. basal cells vs. nonskin2, with two replicates for each condition, except 52 hpf nonskin2 has only one replicate.

first: Fang

last: Wang

first: Alvaro

last: Sagasti


title: Dicer-dependent small RNAs production from antisense long non-coding RNAs in N. castellii

city: Paris

first: Maxime

last: Wery

address: 26 rue d'Ulm

country: France

institute: Institut Curie

summary: Antisense (as)lncRNAs are extensively degraded by the nuclear exosome and the cytoplasmic exoribonuclease Xrn1 in the budding yeast Saccharomyces cerevisiae, lacking RNA interference (RNAi). Whether the ribonuclease III Dicer affects aslncRNAs in close RNAi-capable relatives remains unknown. Using genome-wide RNA profiling, here we show that aslncRNAs are primarily targeted by the exosome and Xrn1 in the RNAi-capable budding yeast Naumovozyma castellii, Dicer only affecting Xrn1-sensitive lncRNAs (XUTs) levels in Xrn1-deficient cells. The dcr1 and xrn1 mutants display synergic growth defects, indicating that Dicer becomes critical in the absence of Xrn1. Small RNA sequencing showed that Dicer processes aslncRNAs into small RNAs, with a preference for asXUTs. Consistently, Dicer localizes into the cytoplasm. Finally, we observed an expansion of the exosome-sensitive antisense transcriptome in N. castellii compared to S. cerevisiae, suggesting that the presence of cytoplasmic RNAi has reinforced the nuclear RNA surveillance machinery to temper aslncRNAs expression. Our data provide fundamental insights into aslncRNAs metabolism and open perspectives into the possible evolutionary contribution of RNAi in shaping the aslncRNAs transcriptome.

overall_design: Small RNA-Seq analysis in wild-type (WT), dcr1, xrn1 and xrn1 dcr1 mutant strains of N. castellii.

first: Ugo

last: Szachnowski

first: Sara

last: Andus

first: Dominika

last: Foretek

first: Antonin

last: Morillon


title: Immuno-PET identifies the myeloid compartment as a key contributor to the outcome of the anti-tumor response under PD-1 blockade [bulk RNA-seq]

city: Boston

first: Mohammad

last: Rashidian

first: M

last: Barrasa

first: Hidde

last: Ploegh


title: Endogenous RNAi pathway evolutionarily shapes the destiny of the antisense lncRNA transcriptome


title: mouse lung single cell RNA-seq

city: los angeles

first: Changfu

last: Yao

state: Ca

address: 8700 Beverly Blvd. AHSP Room A9401

department: Lung and Regenerative Medicine Institutes

institute: cedars-sinai medical center

summary: Single cell RNA-seq profiling adult mouse lung cells reveal the cell heterogeneity and mechanism during lung fibrosis process.

overall_design: Single cell RNA-seq using 10x chromium system on 4 different experiment groups (WTD0, Sdc1D0, WTBleoD21, Sdc1BleoD21), we have pooled cells from three different animal together for each group, and mixed immune cells (DAPI-, CD31-, Epcam-,CD45+), endothelial cells ( DAPI-, CD45-, Epcam-, CD31+), epithelial cells (DAPI-, CD31-, CD45-, Epcam+), stromal cells ( DAPI1-, CD31-, CD45-, Epcam-) in proportion to generate equal represent of each cell type.

first: Tanyalak

last: Parimon

first: Peter

last: Chen

first: Barry

last: Stripp


title: Methylation of a gestational choriocarcinoma

city: L'Hospitalet de Llobregat, Barcelona

first: Jose Ramon

last: Hernandez

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

department: Cancer Epigenetics and Biology Program (PEBC)

institute: Institut d'Investigació Biomèdica de Bellvitge (IDIBELL)

summary: Gestational choriocarcinoma arises from the cells of conception and is usually characterized as a fast growing, invasive and aggressive malignancy. The overall incidence is approximately 1 case per 50,000 pregnancies and aside from increasing maternal age does not appear to have any other risk factors. In contrast to most malignancies, gestational choriocarcinoma is frequently treated on a clinical diagnosis without a biopsy and therefore tumor samples of sufficient quantity to permit detailed genetic analysis are exceptionally rare. As a result, no previous whole genome sequencing or methylation studies have been reported for this rare diagnosis.   With the aim of investigating the potential contribution of epigenetic changes to the pathogenesis of this rare malignancy, we have performed a methylation analysis from routine processed FFPE material in a case of intra-placental choriocarcinoma.

overall_design: Bisulphite converted DNA from a gestational choriocarcinoma and its placenta samples were hybridized to the Illumina Infinium HumanMethylationEPIC BeadChip.

first: Jose

first: David

last: Monk


title: Epigenetic regulation of unique genes and repetitive elements by KRAB zinc finger protein ZFP57 in embryonic stem cells

city: Cambridge

first: Hui

last: Shi

address: Downing Street

department: Department of Physiology, Development and Neuroscience

institute: University of Cambridge

summary: KRAB-zinc finger proteins (KZFPs) represent one of the largest families of DNA binding proteins in vertebrate genomes and appear to have evolved to silence transposable elements (TEs) including endogenous retroviruses through sequence-specific targeting of repressive chromatin states. However, one member, ZFP57, is required to maintain the post-fertilization DNA methylation memory of parental-origin at genomic imprints. We have conducted RNA-seq and ChIP-seq analyses in normal and ZFP57 mutant ES cells to characterize the targets of ZFP57 in more detail. Over 80% of ZFP57 targets are TEs. However, mutants indicate that ZFP57 is not essential for their repression in ES cells. The remaining targets lie within unique imprinted and non-imprinted sequences. Though loss of ZFP57 influences imprinted genes as expected, the majority of unique gene targets lose H3K9me3 with little effect on DNA methylation and with very few exhibiting alterations in expression. Furthermore, comparison with DNA methyltransferase-deleted ES cells (TKO) identifies remarkably similar losses of H3K9me3 and changes in expression, defining regions where H3K9me3 is secondary to DNA methylation. We determine that ZFP57 is the principal methylation-sensitive KZFP recruiting KAP1 and H3K9me3 in ES cells. Finally, like imprints, other unique targets of ZFP57 are enriched for germline-derived DNA methylation including oocyte-specific methylation that is resistant to post-fertilisation epigenetic reprogramming. Our analyses suggest the evolution of a DNA methylation sensitive KZFP, that may serve to reinforce the silenced state at TEs, but whose primary function is to maintain DNA methylation and repressive histone marks at imprinted regions.

overall_design: ChIP-seq using WT and ZFP57 KO ESCs for ZFP57, KAP1 and H3K9me3. RNA-seq using the same WT and KO ESCs. Additional ChIP-seq for H3K9me3 using hybrid ES cells with maternal zygotic ZFP57 deletion. Sequencing was performed using Illumina HiSeq 2000 and HiSeq 4000 platforms. All data were mapped to mm10.

first: Ruslan

last: Strogantsev

first: Nozomi

last: Takahashi

first: Anastasiya

last: Kazachenka

first: Matthew

last: Lorincz

first: Myriam

last: Hemberger

first: Anne

last: Ferguson-Smith


title: Sex chromsomes affect gene expression of autoantigen specific CD4+ T cells.

first: Yuichiro

last: Itoh

address: 635 Charles E. Young Drive South

department: Neurology

summary: To determine the role of sex chromsomes in sex differences of autoimmune disease, we used high throughput RNA sequencing to analyze the transciptomes of autoantigen specific CD4+ T cells from XX and XY- mice using the “four core genotypes” mouse model.

overall_design: Female mice from the "four core genotypes" mouse model (XX and XY-) were gonadectomized at 4-6 weeks old and subsequently immunized with PLP 139-151 peptide emulsified in complete fraunds adjuvant, suppplemented with myobacterium tuberculosis H27Ra for 10 days. Auxillary, brachial, and inguinal draining lymph nodes were collected and processed into single cell suspensions. Cells were stiumulated with PLP 139-151 for 36 hours. Stimulated cells were sorted for CD4+ T cells using the EasySep Mouse CD4+ T cell isolation kit (STEMCELL), and RNA was isolated for analysis by high throughput RNA sequencing.

first: Lisa

last: Golden

first: Noriko

first: Rhonda

last: Voskuhl


title: RNA sequencing of 32D clone 3 cells transfected with CXCR2 (pEGFP-N1-CXCR2) or an empty vector(pEGFP-N1)

city: Changchun

first: Xianlu

last: Zeng

address: No. 5268, Renmin Avenue

institute: Northeast Normal University

summary: Purpose: CXCR2 was transfected into 32D clone 3 cells simulating the granulocyte and macrophage progenitor cells(GMPs) to confirm the role of CXCR2 in the differentiation of GMPs to macrophage and dendritic cell progenitor cells

overall_design: RNA of 32D clone 3 cells transfected with CXCR2 or an empty vector (both incubated with CXC1 and CXCL2 for 4 h) were generated by deep sequencing, using Illumina HiSeq 2500 instrument

first: Xiaoqing

last: Han


title: Genome-wide study of NF-YC11 regulatory network in rice

city: Wuhan

first: Yufei

last: Xiong

state: Hubei

address: No. 1, Shizishan Street, Hongshan District

institute: Huazhong Agricultural University

summary: Rice NF-YC11 is a transcription factor that plays a key regulatory role in storage substance accumulation during rice grain filling. To reveal the transcription regulatory network of NF-YC11 in rice, we performed genome-wide identification of NF-YC11 targets by immunoprecipitation sequencing (ChIP-seq) analyses  in the  NF-YC11-overexpression plants.

overall_design: Genome-wide identification binding sites of NF-YC11 in rice endosperm. Examination of 7 days after pollination (DAP) NF-YC11-FLAG rice endosperm with FLAG antibody and Input seres as control.

first: Jialing

last: Yao


title: Global gene expression analysis in Naive vs. ASC KO murine CD4 T cells post-activation

first: Bernett

last: Lee

address: 8A Biomedical Grove #03-06 Immunos

institute: Singapore Immunology Network

summary: Naïve CD62L+ CD44- CD25- CD4+ splenic mouse T cells from WT or ASC KO cells were left untreated or treated with Anti-CD3/28 antobodies for 12hr

overall_design: Naïve Splenic murine CD4+ T cells from WT or SC KO mice were stimulated with anti-CD3/CD28 antobodies and the differential gene expression of activated WT vs. KO cells were assessed via RNA-sequencing

first: Hanif

last: Khameneh

first: Keith

last: Leong

first: Andrea

last: Mencarelli

first: Maurizio

last: Vacca

first: Bezalel

last: Mambwe

first: Kurt

last: Neo

first: Alice

last: Tay

first: Francesca

last: Zolezzi

first: Michael

last: Poidinger

first: Alessandra

last: Mortellaro


title: Rpv3-1 Locus Mediated Resistance to Grapevine Downy Mildew is Associated with Specific Host Transcriptional Responses and the Accumulation of Stilbenes

city: Tuebingen

first: Stefan

last: Czemmel

address: Auf der Morgenstelle 10

department: University of Tuebingen

country: Germany

institute: Quantitative Biology Center (QBiC)

summary: European grapevine cultivars (Vitis vinifera spp.) are highly susceptible to the downy mildew pathogen Plasmopara viticola. Breeding of resistant V. vinifera cultivars is a promising strategy to reduce the impact of disease management. Most cultivars that have been bred for resistance to downy mildew, rely on resistance mediated by the Rpv3 (Resistance to P. viticola) locus. However, despite the extensive use of this locus, little is known about the mechanism of Rpv3-mediated resistance. In this study, Rpv3-mediated defense responses were studied in Rpv3+ and Rpv3ˉ grapevine cultivars following inoculation with two distinct P. viticola isolates avrRpv3+ and avrRpv3ˉ, with the latter being able to overcome Rpv3 resistance. Based on comparative microscopic, metabolomic and transcriptomic analyses, our results show that the Rpv3-mediated resistance is associated with a defense mechanism that triggers synthesis of fungi-toxic stilbenes and programmed cell death (PCD), resulting in reduced but not suppressed pathogen growth and development. Functional annotation of the encoded protein sequence of genes significantly upregulated during the Rpv3-mediated defense response revealed putative roles in pathogen recognition, signal transduction and defense responses.

overall_design: Gene expression profiles of a susceptible and a resitant grapevine cultivars in response to downy mildew infection at 6 hours post inoculation were generated by RNA-Seq, in duplicates.

first: Jochen

last: Bogs

first: Birgit

last: Eisenmann


title: Next Generation Sequencing Facilitates Quantitative Analysis of ZH11 and nf-yc11 mutant plants Transcriptomes

summary:
Purpose: Analysis of gene expression level.
Methods: Retinal mRNA profiles of 7 DAP endosperm of the wild-type (WT) and NF-YC11 knockout mutant were generated by deep sequencing, in triplicate, using Illumina 2000.

overall_design: Examination of mRNA levels in nf-yc11 mutants and WT.


title: A HIF-1α/Wnt signaling-dependent control of gene transcription regulates neuronal differentiation of glioblastoma stem cells

city: padova

first: silvia

last: bresolin

state: padova

address: via giustiniani 3

department: department of women's and children's health

country: Italy

institute: università di padova

summary:
HIF-1α plays a crucial role in sustaining glioblastoma (GBM) cell growth and the maintenance of their undifferentiated phenotype. However, HIF-1α has been suggested to interplay with Wnt signaling components, thus activating a neuronal differentiation process in both GBM and normal brain. Here, we show that a β-catenin/TCF1/HIF-1α complex directly controls the transcription of neuronal differentiation genes in hypoxia. Conversely, at higher oxygen levels, the increased expression of TCF4 exerts a transcriptional inhibitory function on the same genomic regions, thus counteracting differentiation. Moreover, we demonstrate the existence of a positive correlation between HIF-1α, TCF1 and neuronal phenotype in GBM tumors, accompanied by the over-expression of several Wnt signaling components, finally impacting on patient prognosis. In conclusion, we unveil a mechanism by which TCF1 and HIF-1α induce a reminiscent neuronal differentiation of hypoxic GBM cells, which is hampered, in normoxia, by high levels of TCF4, thus de facto sustaining cell aggressiveness.
In this study we unveil a tightly regulated mechanism by which HIF-1α controls the balance of Wnt signaling co-factors and how their molecular interplay regulates the peculiar transcriptional events responsible for the phenotypic shift of GBM stem cells toward a reminiscent neuronal differentiation, which might represent a future potential strategy to therapeutically weaken their aggressiveness.

overall_design: Gene expression was measured on Clariom S platform of cells derived from internal or periphery region of GBM tumors of 4 primary samples.

first: Silvia

last: Bresolin

first: Luca

last: Persano


title: Identify the binding sites of mTERF5 in chloroplast of Arabidopsis thaliana through cpChIP-seq (additional experiments)

city: Beijing

first: Zhang

last: Yi

state: Beijing

address: No.20 Nanxincun, Xiangshan

department: Key Laboratory of Photobiology

institute: Institute of Botany, CAS

summary: We performed chloroplast ChIP-seq (cpChIP-seq) to identify the possible DNA-binding sites of mTERF5 in Arabidopsis thaliana. To this end, we generated transgenic Arabidopsis plants expressing mTERF5 carrying an HA tag under the control of the CaMV 35S promoter. Then, We used the polyclonal antibody (abcam, ab9110, lot GR304617-8 ) against HA tag which conjugated to ChIP-Grade protein A/G agarose (Thermo scientific, 26161, lot QJ223903) to perform cpChIP assay. The obtained chromatin immunoprecipitated DNA of chloroplasts were used to build DNA libaries for  high-throughput sequencing. Finally, we showed that three potenssial DNA regions across the chloroplast genome compared to the control group were enriched by mTERF5.

overall_design: Deep sequencing was used for examination of mTERF5 associated DNA regions in chloroplast of  Arabisopsis thaliana. Two biological replicates were performed, and the "Input sample" was used as a reference sample. Rabbit IgG (abmart, B30011, lot 294670) was used as negetive antibody control for IP.

first: Yi

last: Zhang

first: Congming

last: Lu


title: Electronic cigarettes

city: Philadelphia

first: Blanca

middle: E

last: Himes

state: PA

address: 423 Guardian Dr

department: Department of Biostatistics, Epidemiology and Informatics

institute: University of Pennsylvania

summary:
Electronic cigarettes (e-cigarettes) have gained their popularity as a substitute for cigarettes or cigars. Despite the widespread use of flavoring chemicals in e-cigarettes, the health impacts of the flavoring compounds, in particular their effects on critical cellular function in the lung, remain largely unknown. The goal of this study was to identify transcriptomic changes and impacted biological pathways in primary human bronchial epithelial cells (HBECs) exposed to flavoring chemicals (diacetyl or 2,3-pentanedione) and to flavored e-cigarette smoke.
An airway-liquid interface culturing method was used to differentiate primary human bronchial epithelial cells (HBECs) into mature epithelial cells, which were then treated with 25 ppm diacetyl, 100 ppm 2,3 pentanedione, or e-cigarette smoke solution containing 2 ppm diacetyl. Poly(A)-selected RNA-Seq libraries were prepared with the PrepX RNA-Seq for Illumina Library kit. An Illumina HiSeq 2500 instrument was used to generate 50 base pair single-end reads. STAR was used to align sequencing reads to the hg38 reference genome, and HTSeq was used to quantify transcript levels. DESeq2 was used to perform differential expression analysis.

overall_design: Transcriptome profiles obtained via RNA-Seq for normal human bronchial epithelium cells (3-donor pool) treated in duplicate with 25 ppm diacetyl, 100 ppm 2,3 pentanedione, e-cigarette smoke solution containing 2 ppm diacetylor, or vehicle control for 24 hours were obtained to measure the effects of exposure to e-cigarette smoke and its flavoring chemicals.

first: Quan

first: Joseph

last: Allen

first: Hae-Ryung

last: Park


title: Transcriptional profile of injured hearts treated with the cholinesterase inhibitor pyridostigmine (PYR) at Day 5

city: Indianapolis

first: Scot

last: Matkovich

state: IN

address: Lilly Corporate Center

institute: Eli Lilly and Company

summary: It has been shown that acetylcholine has anti-inflammatory properties. The aim of this study is to investigate the role of acetylcholine in cardiac inflammation. We used the diphtheria toxin (DT)-cardiomyocyte ablation model (DTR model) (Lavine et al., 2014 - PNAS) to induce cardiac injury (DT, 2 days, 2.5µg/kg, IP). Beginning one week prior to DT injury, mice were treated with vehicle (PBS, phosphate buffered saline) or the cholinesterase inhibitor pyridostigmine (PYR, 3mg/kg, SQ). Hearts were harvested at Day 5 post-DT-injury. Here, we provide the transcriptional profile of wild-type/PBS, wild-type/PYR, DTR/PBS and DTR/PYR hearts.

overall_design: mRNA sequencing profiles were generated from 6 each of wild-type/PBS, wild type/PYR, DTR/PBS  and DTR/PYR hearts  on Illumina HiSeq 3000 instruments.

first: Cibele

last: Rocha-Resende

first: Douglas

last: Mann


title: Expression profiles of dark or red-light treated  WT and phytochrome mutants

city: Shanghai

first: weiwei

last: Qi

address: No 99 Shangda Road

institute: Shanghai  University

summary: The mRNA expression profiles of the wild type, phyB and phyAB mutants were analyzed with darkness or 1 hour red light treatment.  Results provide insight into the role of red-light and phytochromes in gene expression.

overall_design: Col, phyB and phyAB seedlings were treated with either darkness or 1h red light and two samples for each genotype that represent two replicates in each case.

first: Hong-quan

last: Yang


title: ENAP1 is involoved in the EIN3- mediated ethylene response

city: Austin

first: Hong

last: Qiao

state: TEXAS

address: 2506 speedway, NMS5.324

department: Department of Molecular Biosciences

institute: The University of Texas at Austin

summary: We report that ethylene reduce the ENAP1 binding. We perform Chip-sequencing of ENAP1 using chromatins isolated from 3-day old etiolated ein3eil1 seedlings treated with ethylene or air gas. Results show that ethylene reduce ENAP1 binding in TSS region of EIN3 targeted genes that are regulated at the transcriptional level by ethylene.

overall_design: Examination of 1 different protein binding in 1 Arabidopsis lines which under 2 different treatment.

first: Likai

last: Wang

first: Fan


title: Genome-wide study reveals dual function of histone binding protein ENAP1 in ethylene signaling in ein3eil1 mutant plants

summary: Purpose: Next-generation sequencing (NGS) has been used to study the gene expression in different samples under air and ethylene treatment. The goal of this study is to uncover how ENAP1 and H3K23Ac dynamically coordinate with EIN3 to regulate gene expression in response to ethylene.

overall_design: Whole seedling mRNA profiles of 3-day old ein3eil1 and ENAP1ox/ein3eil1 (in COL background) were generated by sequencing, in 2 replications, using Illumina HiSeq 2000


title: Total RNA-Seq in wild-type (WT), dcr1, xrn1 and xrn1 dcr1 strains of N. castellii

first: Maxime

last: Wery

summary: Antisense (as)lncRNAs are extensively degraded by the nuclear exosome and the cytoplasmic exoribonuclease Xrn1 in the budding yeast Saccharomyces cerevisiae, lacking RNA interference (RNAi). Whether the ribonuclease III Dicer affects aslncRNAs in close RNAi-capable relatives remains unknown. Using genome-wide RNA profiling, here we show that aslncRNAs are primarily targeted by the exosome and Xrn1 in the RNAi-capable budding yeast Naumovozyma castellii, Dicer only affecting Xrn1-sensitive lncRNAs (XUTs) levels in Xrn1-deficient cells. The dcr1 and xrn1 mutants display synergic growth defects, indicating that Dicer becomes critical in absence of Xrn1. Small RNA sequencing showed that Dicer processes aslncRNAs into small RNAs, with a preference for asXUTs. Consistently, Dicer localizes into the cytoplasm. Finally, we observed an expansion of the exosome-sensitive antisense transcriptome in N. castellii compared to S. cerevisiae, suggesting that the presence of cytoplasmic RNAi has reinforced the nuclear RNA surveillance machinery to temper aslncRNAs expression. Our data provide fundamental insights into aslncRNAs metabolism and open perspectives into the possible evolutionary contribution of RNAi in shaping the aslncRNAs transcriptome.

overall_design: Strand-specific total RNA-Seq analysis in wild-type (WT), dcr1, xrn1 and xrn1 dcr1 mutant strains of N. castellii

first: Ugo

last: Szachnowski

first: Sara

last: Andus

first: Dominika

last: Foretek

first: Antonin

last: Morillon


title: miRNA-27b-3p and miRNA-1228-3p correlate with the progression of Kidney Fibrosis in Diabetic Nephropathy

city: Bari

first: Paola

last: Pontrelli

address: Piazza G.Cesare 11

department: Dept. of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J)

institute: University of Bari

summary:
Diabetic Nephropathy (DN) is a chronic complication of diabetes and the primary cause of end stage renal disease. DN can be differentially diagnosed only through histological investigation. Therefore, there is need for molecular biomarkers, such as miRNAs, to discriminate among different histological lesions in diabetics. Aim of this study was to identify a pattern of differentially expressed miRNAs in kidney biopsies of DN patients and to assess their potential as differential diagnostic biomarkers.
Using microarray, we assayed miRNA expression in kidney tissue from 8 DN patients, 6 diabetic patients with membranous nephropathy and 4 patients with normal histology. Nine miRNAs were differentially expressed among the three groups of patients, thus underlying their potential role as markers of specific histological damage. In silico we identified 2 miRNAs (i.e., miR-27b-3p and  miR-1228-3p) showing an interaction with UBE2v1, an ubiquitin-conjugating E2 enzyme variant that mediates the formation of lysine 63-linked ubiquitin chains, a mechanism we showed as involved in DN kidney fibrosis. Both miRNAs were confirmed to be down-regulated in DN biopsies, using qPCR and in situ hybridization, and in urines of DN patients. Interestingly, the urinary levels of both miRNAs were also able to discriminate among different degrees of renal fibrosis. Finally, we showed that the combined urinary expression of both miRNAs was also able to discriminate DN patients from other glomerulonephritides, both in the presence and absence of T2D. We identified two regulatory miRNAs potentially useful as diagnostic biomarkers of tubular-interstitial fibrosis in diabetic patients with DN.

overall_design: A total of 16 RNA samples were employed in this study: 6 samples were taken from patients with type 2 diabetes (T2D) and biopsy-proven diabetic nephropathy (DN); 6 samples were taken from patients with T2D and biopsy-proven membranous nephropathy (T2D-MN); and 4 samples were from normal kidney (CTRL) patients who underwent kidney biopsy.

first: Francesca

last: Conserva

first: Mariagrazia

last: Barozzino

first: Francesco

last: Pesce

first: Chiara

last: Divella

first: Annarita

last: Oranger

first: Massimo

last: Papale

first: Simona

last: Simone

first: Luigi

last: Laviola

last: Giorgino

first: Anna

last: Gallone

first: Loreto

last: Gesualdo


title: Damage-associated molecular patterns induce macrophage polarization toward an M1 pro-inflammatory phenotype

first: Scot

last: Matkovich

summary: Dying cells release Damage-Associated Molecular Patterns (DAMPs) that can initiate and perpetuate sterile inflammatory responses. However, the effect of DAMPs on macrophages biology remains unclear. We therefore studied the effect of DAMPs on primary peritoneal macrophages (PPM) in vitro. We first performed unbiased transcriptomic profiling with RNA-seq of PPMs cultured for up to 72 hours in the presence and absence of: 1) liposaccharide (LPS), which is known to provoke an “M1” phenotype, 2) IL-4, which is known to provoke an “M2” phenotype, or 3) cytosolic extracts (CEs) from necrotic H9C2 cells to mimic the release of cardiomyocyte DAMPs. We found that the transcriptional profile of PPMs stimulated with CEs resembled the transcriptional profile of PPMs stimulated with LPS.

overall_design: All primary peritoneal macrophages were derived from the same initial isolate (pooled from multiple mice). Three to four replicates of each timepoint and condition were used for RNA extraction, RNAseq library preparation with Diagenode CATS procedures, and single-end 50 bp Illumina sequencing.

first: Wenlong

last: Jiang

first: Douglas

last: Mann