title: Comparison of young and aged mouse CD8 TN, TVM and TMEM cells directly ex vivo and after polyclonal stimulation

status: Public on Jun 19 2018

city: Clayton

first: Kylie

last: Quinn

state: VIC

address: 19 Innovation Walk

country: Australia

institute: Monash University

summary: The overall study (Quinn et al. Cell Reports, 2018) aimed to understand why CD8 virtual memory T (TVM) cells become markedly less proliferative in response to TCR-driven signals with increasing age, whereas CD8 true naive (TN) cells maintain their proliferative capacity. Age-associated decreases in primary CD8+ T cell responses occur, in part, due to direct effects on naïve CD8++ T cells to reduce intrinsic functionality, but the precise nature of this defect remains undefined. Ageing also causes accumulation of antigen-naïve but semi-differentiated “virtual memory” (TVM) cells but their contribution to age-related functional decline is unclear. Here, we show that TVM cells are poorly proliferative in aged mice and humans, despite being highly proliferative in young individuals, while conventional naïve T cells (TN cells) retain proliferative capacity in both aged mice and humans. Adoptive transfer experiments in mice illustrated that naïve CD8 T cells can acquire a proliferative defect imposed by the aged environment but age-related proliferative dysfunction could not be rescued by a young environment. Molecular analyses demonstrate that aged TVM cells exhibit a profile consistent with senescence, marking the first description of senescence in an antigenically naïve T cell population.

overall_design: In the RNA-Seq analysis uploaded here, we have sorted TN cells (CD44lo), TVM cells (CD49dlo CD44hi) and CD8 conventional memory T (TMEM) (CD49dhi CD44hi) cells from naive young mice (3 months old) or aged mice (18 months old). To sort enough cells of each type, we pooled 4 mice, so each replicate represents a pooled sample of 4 mice. Each replicate was split in half, with half the sample frozen in TRIzol immediately for our directly ex vivo or "unstim" sample and the other half of the sample stimulated with plate-bound anti-CD3 (10ug/mL), anti-CD8a (10ug/mL) and antiCD11a (5 ug/mL) and soluble recombinant human IL-2 (10U/mL) for 5 hours, before being frozen in TRIzol as our stimulated or "stim" samples. We therefore collected 2 replicates for each cell subsets (designated "1" and "2") and the "unstim" and "stim" samples are matched. Altogether, we had 24 samples (young (Y) and aged (A); replicate 1 and replicate 2, with cells pooled from 4 mice in each replicate; TN, TVM and TMEM cells; unstim and stim match across each replicate). Due to lane capacity limits for sequencing, we processed these samples for RNA and sequencing in two batches (Batch 1- Y1_Tn_Unstim, Y1_Tvm_Unstim, Y1_Tmem_Unstim, Y1_Tn_Stim, Y1_Tvm_Stim, Y1_Tmem_Stim, A1_Tn_Stim, A1_Tvm_Stim, A1_Tmem_Stim, A2_Tn_Stim, A2_Tvm_Stim, A2_Tmem_Stim. Batch 2- Y2_Tn_Unstim, Y2_Tvm_Unstim, Y2_Tmem_Unstim, Y2_Tn_Stim, Y2_Tvm_Stim, Y2_Tmem_Stim, A1_Tn_Unstim, A1_Tvm_Unstim, A1_Tmem_Unstim, A2_Tn_Unstim, A2_Tvm_Unstim, A2_Tmem_Unstim). Of note, in Batch 2 we ran a duplicate of Y1_Tn_Unstim (Y1_Tn_Unstim_norm) to test for any batch effect, but none was observed. Extracted RNA was treated with recombinant DNAse I (Roche) according to the manufacturer’s instructions, purified using the RNeasy MinElute Cleanup columns (Qiagen) and analysed for RNA quality using the RNA 6000 Nano kit (Agilent) on an Agilent 2100 Bioanalyzer. Samples were prepared with the Illumina TruSeq RNA v2 sample preparation protocol (cDNA synthesis, adapter ligation, PCR amplification) (Illumina) and run using 100 bp paired end sequencing on an Illumina Hi-Seq. Adapters were trimmed with Trim Galore and trimmed reads were aligned to mm10 genome with TopHat2 version 2.1.1 (Kim et al., 2013) keeping the strand information. Only concordantly aligned read pairs were retained, duplicate fragments were removed using MarkDuplicates from Picard tools and read pairs with mapping quality less than 5 were discarded. To generate a counts matrix, retained read pairs were assigned to genes using featureCounts function (Liao et al., 2014) from Bioconductor Rsubread package taking into account strand information.

first: Nicole

last: La Gruta

first: Brendan

last: Russ

first: Jasmine

last: Li

first: Moshe

last: Olshanksy

first: Haroon

last: Naeem

first: Kirill

last: Tsyganov

last: Powell


title: DNA methylation profiling in nonfunctioning pituitary adenomas

status: Public on Jun 14 2018

city: Warsaw

first: Mateusz

last: Bujko

address: Roentgena 5

department: Molecular Oncology Department

country: Poland

institute: Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology

type: Methylation profiling by genome tiling array

summary: Nonfunctioning pituitary adenomas (NFPAs) are among the most frequent intracranial tumors but their molecular background, including changes in epigenetic regulation, remains poorly understood. We performed genome-wide DNA methylation profiling of 34 NFPAs and normal pituitary samples. Methylation status of the selected genomic regions and expression level of corresponding genes were assessed in a group of 75 patients. NFPAs exhibited distinct global methylation profile as compared to normal pituitary. Aberrant DNA methylation appears to contribute to deregulation of the cancer-related pathways as shown by preliminary functional analysis. Promoter hypermethylation and decreased expression level of SFN, STAT5A, DUSP1, PTPRE and FGFR2 was confirmed in the enlarged group of NFPAs. Difference in the methylation profiles between invasive and non-invasive NFPAs is very slight. Nevertheless, invasiveness-related aberrant epigenetic deregulation of the particular genes was found including upregulation of ITPKB and downregulation CNKSR1 in invasive tumors.

overall_design: Genome-wide DNA methylation profiling involved 31 gonadotroph NFPAs, two NFPAs that were positive for gonadotropins (FSH, LH, α-subunit), as well as TSH, and one sample classified as null-cell adenoma. Six samples of normal human pituitaries obtained from autopsies were used for DNA methylation profiling and treated as control samples.


title: miRNAs expression patterns during mouse retina development

status: Public on Jun 12 2018

city: Guangzhou

first: YISHEN

last: WANG

address: No.54 Xianlie South Road, Yuexiu District

country: China

institute: State Key Laboratory of Ophthalmology, Image Reading Center, Zhongshan Ophthalmic Center, Sun Yat-Sen University

summary: The goal of this study was to gain a detailed postnatal expression pattern of miRNAs involving time points and to identify miRNAs essential for retinal development in the mouse.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Total RNA was extracted from normal C57 mouse retina at nine different postnatal time points. These time points were: P0, P1, P3, P4, P7, P8, P10, P14, P21


title: The marked diversity of unique cortical enhancers enables the generation of neuron-specific tools by Enhancer-Driven Gene Expression (EDGE)

status: Public on Aug 19 2018

city: Farmington

first: Justin

last: Cotney

state: CT

address: 400 Farmington Avenue

department: Genetics and Genome Sciences

country: USA

institute: UConn Health

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Detection of enhancers in mouse cortical subregions

overall_design: Identifying active enhancers through H3K27ac and H3K4me2 ChIP-seq to distinguish differences in Enhancer-Driven Gene Expression (EDGE) among closely related mouse cortical subregions

first: Andrea

last: Wilderman


title: Expression data of 13 surgical samples of adenoid cystic carcinoma (ACC), 2 ACC xenografts, and 7 normal salivary gland tissues (NSGs)

status: Public on Jun 01 2018

city: Gothenburg

first: Mattias

last: Andersson

address: Medicinaregatan 1F

department: Sahlgrenska Cancer Center

country: Sweden

institute: University of Gothenburg

summary: This experiment investigates differences in global gene expression between ACC and NSG.

overall_design: A total of 22 samples are analyzed of which 7 are control samples.

middle: K

first: Göran

last: Stenman


title: Extracellular RNA profiles with human age

status: Public on Jun 04 2018

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

type: Expression profiling by high throughput sequencing

summary: Circulating extracellular RNAs (exRNAs) are potential biomarkers of disease. We thus hypothesized that age-related changes in exRNAs can identify age-related processes. We profiled both large and small RNAs in human serum to investigate changes associated with normal aging. exRNA was sequenced in 13 young (30-32 yrs.) and 10 old (80-85 yrs.) African American women to identify all RNA transcripts present in serum. We identified age-related differences in several RNA biotypes, including mitochondrial transfer RNAs, mitochondrial ribosomal RNA, and unprocessed pseudogenes. Age-related differences in unique RNA transcripts were further validated in an expanded cohort. Pathway analysis revealed that EIF2 signaling, oxidative phosphorylation, and mitochondrial dysfunction were among the top pathways shared between young and old. Protein interaction networks revealed distinct clusters of functionally-related protein-coding genes in both age-groups. These data provide timely and relevant insight into the exRNA repertoire in serum and its change with aging.

overall_design: Profiling of extracellular RNA (exRNA) from human serum in 13 young (30.9 ± 0.60 yrs) and 10 old (81.8 ± 1.87 yrs) individuals.

first: Douglas

middle: F

last: Dluzen

last: Noren Hooten

first: William

middle: H

last: Wood III

first: Yongqing

last: Zhang

first: Kevin

middle: G

last: Becker

first: Alan

middle: B

last: Zonderman

first: Toshiko

last: Tanaka

first: Luigi

last: Ferrucci

first: Michele

last: Evans


title: Global hypomethylation mediated changes regulate constitutive PD-L1 expression in melanoma [RRBS]

status: Public on May 24 2018

city: Dunedin

first: Aniruddha

last: Chatterjee

state: Otago

address: 270 Great king Street

department: Pathology

country: New Zealand

institute: University of Otago

type: Methylation profiling by high throughput sequencing

summary: PD-L1 is a ligand for the inhibitory PD1 receptor on T cells and its expression in some cancers inhibits anti-cancer immune response. In melanoma, PD-L1 expression is induced in response to immune stimuli but in a proportion of melanomas it is constitutively expressed. Factors that drive constitutive expression of PD-L1 are unknown. Here we performed genome-scale methylation analysis of six cell lines that constitutively express PD-L1 (PD-L1 positive, referred to as PD-L1CON) and six cell lines that only express PD-L1 after treatment with IFN- (PD-L1 negative, referred to as PD-L1IND)

overall_design: Here we generated single-nucleotide resoultion DNA methylation map of a total of 12 cell lines using Reduced Representation Bisulfite Sequencing (RRBS). We have two groups, each with 6 cell lines each (inducible group and constitutive group)

first: Peter

middle: A

last: Stockwell

first: Antonio

last: Ahn

first: Euan

middle: J

last: Rodger

first: Matthew

last: Parry

first: Jyoti

last: Motwani

last: Hersey

first: Michael

middle: R

last: Eccles


title: Global hypomethylation mediated changes regulate constitutive PD-L1 expression in melanoma [RNA-Seq]

summary: PD-L1 is a ligand for the inhibitory PD1 receptor on T cells and its expression in some cancers inhibits anti-cancer immune response. In melanoma, PD-L1 expression is induced in response to immune stimuli but in a proportion of melanomas it is constitutively expressed. Factors that drive constitutive expression of PD-L1 are unknown. Here we performed RNA-Seq analysis of six cell lines that constitutively express PD-L1 (PD-L1 positive, referred to as PD-L1CON) and six cell lines that only express PD-L1 after treatment with IFN- (PD-L1 negative, referred to as PD-L1IND)

overall_design: Here we generated gene expression profile of 12 cell lines using RNA-Sequening. We have two group each consisting of 6 cell lines (inducible and constitutive)

first: Micheal


title: ETS1 acts as a tumor suppressor in breast cancer by inhibiting growth-related factors

status: Public on May 10 2018

city: Pohang

first: Gi-Cheon

middle: careful

last: Kim

state: Hyoja-dong Namgu

address: POSTECH, postech biotech center Rm 430, Hyoja-dong Namgu, pohang

country: South Korea

institute: IBS

summary: To characterize the effect of Core regulatory element (CRE) deletion in breast cancer cell line (MDA-MB-231 cells), we performed gene expression RNA-seq analysis for WT and KO (Core Regulatory Element deleted) MDA-MB-231 cells after 0h, 6h and 24h of P/I treatment.

overall_design: Total RNA was extracted from WT and KO (CRE deleted) MDA-MB-231 cells of mock and PMA/Ionomycin treated group.

first: Ho-keun

last: Kwon

first: Choong-gu

last: Lee

first: Ravi

last: Verma

first: Taemook

first: Keunsoo

last: Kang

first: Young

first: Jong

last: Nam

first: Sin-Hyeog

last: Im


title: Transforming the Spleen into a Functioning Liver In Vivo

status: Public on May 31 2018

city: Nanjing

first: Wang

last: Lintao

address: 163 Xianlin Avenue

department: School of Life Sciences

institute: Nanjing University

summary: We demonstrate a different strategy that successfully transformed an existing, functionally dispensable organ to regenerate another, functionally vital one in the body. Specifically, we injected STH into the mouse spleen to remodel its tissue structure, and implanted in there human or rat liver cell lines. The remodeled spleen developed an immunosuppressive, yet highly vascularized microenvironment, in which the trans-species cells proliferated fast and developed the functions of the human liver through 8 weeks, without exerting adverse responses.

overall_design: The Gene Expression profiling of normal spleens (Normal) vs the translocated spleens (Post-surgery), Normal as control;  the translocated spleens treated with PBS vs the translocated spleens treated with STH, PBS as control; the PBS-treated spleens implanted with HepG2 (PBS+HepG2) vs the STH-treated spleens implanted with HepG2 (STH+HepG2)，PBS+HepG2 as control; splenic macrophages treated with PBS (PBS (macrophage)) vs macrophages treated with STH (STH(macrophage)), PBS (macrophage) as control.  Five cell/spleen samples were pooled according to individual groups.

first: Junfeng

last: Zhang

first: Lei

last: Dong


title: A single-cell transcriptome atlas of the ageing Drosophila brain

status: Public on Jun 13 2018

city: LEUVEN

first: Stein

last: Aerts

address: Herestraat 49, bus 602

department: Center for Brain & Disease Research

country: Belgium

institute: KULeuven/VIB

summary: The diversity of cell types and regulatory states in the brain, and how these change during ageing, remains largely unknown. We present a single-cell transcriptome atlas of the entire adult Drosophila melanogaster brain sampled across its lifespan. Cell clustering identified 87 initial cell clusters that are further subclustered and validated by targeted cell-sorting. Our data shows high granularity and identifies a wide range of cell types. Gene network analyses using SCENIC revealed regulatory heterogeneity linked to energy consumption. During ageing, RNA content declines exponentially without affecting neuronal identity in old brains. This single-cell brain atlas covers nearly all cells in the normal brain and provides the tools to study cellular diversity alongside other Drosophila and mammalian single-cell datasets in our unique single-cell analysis platform. These results allow comprehensive exploration of all transcriptional states of an entire ageing brain.

overall_design: scRNA-seq (10x Genomics CHROMIUM Single Cell 3’ Solution V2 Chemistry and Drop-seq) of adult brains from Drosophila melanogaster at various ages; SMART-seq2 on FAC-sorted R23E10-Gal4 positive neurons of adult brains from Drosophila melanogaster; Adapted SMART-seq2 on FAC-sorted R23E10-Gal4 positive neurons of adult brains from Drosophila melanogaster; CEL-seq2 on FAC-sorted R23E10-Gal4 positive neurons of adult brains from Drosophila melanogaster; Bulk RNA-seq of adult brains from Drosophila melanogaster; ATAC-seq of young (0 days) and old (50 days) adult brains from Drosophila melanogaster

first: K

last: Davie

first: J

last: Janssens

first: D

last: Koldere

first: S


title: The role of PKC-beta in B cell activation

status: Public on Jun 05 2018

city: London

first: Carlson

last: Tsui

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

summary: PKCb-null (Prkcb-/-) mice are severely immunodeficient. Here we show that mice whose B cells lack PKCb fail to develop germinal centers and plasma cells, which in concert undermine affinity maturation and antibody production in response to immunization. Moreover, Prkcb-/- B cells fail to differentiate into plasma cells in response to viral infection. At a cellular level, we show that activated Prkcb-/- B cells exhibit defective antigen polarization and mTORC1 signaling. While the loss of antigen polarization impairs antigen presentation and restricts the potential of Prkcb-/- B cells to develop into GC B cells, altered mTORC1 signaling affects gene expression, metabolic reprogramming and mitochondrial remodeling which together overwhelmingly oppose commitment to plasma cell differentiation. Mechanistically, we show that PKCb-mediated metabolic reprogramming is required for sustained heme biosynthesis that is essential for effector fate decision in B cells. Taken together, our study reveals mechanistic insights into the function of PKCb as a key regulator of B-cell polarity and metabolic reprogramming that instructs B-cell fate.

overall_design: 10 samples (2x conditions; WT 3x biological replicate; KO 2x biological replicate)

first: Nuria

last: Martinez-Martin

first: Mauro

last: Gaya

first: Paula

last: Maldonado

first: Miriam

last: Llorian

first: Michelle

last: Legrave

first: Merja

last: Rossi

first: James

last: MacRae

first: Angus

last: Cameron

first: Peter

last: Parker

first: Michael

last: Leitges

first: Andreas

last: Bruckbauer

first: Facundo

last: batista


title: Basic Helix Loop Helix Enhancer 40 Null Mice Have Impaired Synaptic Plasticity, Enhanced Neuronal Excitability, and Decreased Expression of Insulin Degrading Enzyme

status: Public on May 03 2018

first: Supriyo

last: De

summary: Basic helix loop helix enhancer 40 (Bhlhe40) is a transcription factor expressed in rodent hippocampus, however, its role in neuronal function is not well understood.  Here, we used Bhlhe40 null mice on a congenic C57Bl6/J background (Bhlhe40 KO) to investigate the impact of Bhlhe40 on neuronal excitability and synaptic plasticity.  A whole genome expression array predicted that Bhlhe40 KO mice have up-regulated insulin-related pathways and down-regulated neuronal signaling-related pathways in the hippocampus.  We validated that insulin degrading enzyme mRNA (Ide) and IDE protein are significantly downregulated in Bhlhe40 KO hippocampi.  No significant difference was observed in hippocampal insulin levels.  In hippocampal slices, we found CA1 neurons have increased miniature excitatory post-synaptic current (mEPSC) amplitude and decreased inhibitory post-synaptic current (IPSC) amplitude, indicating hyper-excitability in CA1 neurons in Bhlhe40 KO mice.  At CA1 synapses, we found a reduction in long term potentiation (LTP) and long term depression (LTD), indicating an impairment in hippocampal synaptic plasticity in Bhlhe40 KO hippocampal slices.  Bhlhe40 KO mice displayed no difference in seizure response to the convulsant kainic acid (KA) relative to controls.  We found that while Bhlhe40 KO mice have decreased exploratory behavior they do not display alterations in spatial learning and memory.  Together this suggests that Bhlhe40 plays a role in modulating neuronal excitability and synaptic plasticity ex vivo, however, Bhlhe40 alone does not play a significant role in seizure susceptibility and learning and memory in vivo.  In addition, based on the reduction in IDE protein levels in these mice, there may be dysregulation of other known IDE substrates, namely insulin growth factor (Igf)-1, Igf-2, and Amyloid beta (Aβ).

overall_design: Hippocampus, cortex, and cerebellum was examined from naïve 3-5 month old WT (n=4/tissue) and Bhlhe40 KO (n=4/tissue) mice.

first: Kelly

last: Hamilton

first: Yue

last: Wang

first: Sophia

middle: M

last: Raefsky

first: Sean

last: Berkowitz

first: Ryan

last: Spangler

first: Caitlin

last: Suire

first: Simonetta

last: Camandola

first: Mark

middle: P

last: Mattson

first: Robert

last: Lipsky


title: Response of nor and nos contributes to Staphylococcus aureus virulence and metabolism.

status: Public on May 08 2018

city: Rochester

first: Steven

middle: R.

last: Gill

state: NY

address: 601 Elmwood Avenue

department: Microbiology & Immunology

institute: University of Rochester

summary: CC30 S. aureus were subjected to NO stress and Anaerobic growth and produced different transcriptomes

overall_design: Bacterial RNASeq between WT and nor and nos mutations was evaluated

first: Lacey

last: Favazzo


title: Rhizophora mucronata Lam. de novo transcriptome - Gene expression estimation

status: Public on Mar 22 2018

city: Thalassery

first: Anu

last: Augustine

state: Kerala

address: Kannur University, Thalassery Campus, Palayad P O

department: Department of Biotechnology and Microbiology

country: India

institute: Kannur University

summary: Rhizophora mucronata Lam., a prevalent mangrove variety of Indo-Pacific region is reported to defy saline stress up to 40 ppt, but the genome or transcriptome behind this tolerance is yet to be investigated. As an initiative to create a reference sequence database, we have forged a set of 46,366,348 paired end RNA-Seq raw reads of Rhizophora mucronata Lam. leaf tissues from Illumina HiSeq 2500 platform (SRA study accession SRP093200 ; Bioproject accession PRJNA345155). All possible gene transcripts were then reconstructed from the RNA raw seq data and 93960 Trinity assembled, annotated transcripts that are being actively expressed at a given time is proposed (TSA accession GGEC00000000). To estimate gene transcript expression, we used Bowtie 2 programme and successfully aligned back up to 95.14% of the filtered reads to the assembled transcriptome. We allowed up to 1-mismatches in the seed region (length =31bp) and all multiple mapped position were reported. Of all filtered reads about 95.14% of reads from each sample were properly aligned back to the assembled transcriptome. Overall we found 52,153 unique transcripts which have expression >=1 FPKM.

overall_design: Leaves randomly collected from three individual plants were pooled into two replicates and used for total RNA isolation using LiCl cold extraction method. RNA pool with RIN value 7.2 was processed for mRNA purification using poly-T oligo-attached magnetic beads. Isolated mRNA was then fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments were used as the template for reverse transcriptase to synthesize first strand cDNA followed by second strand cDNA synthesis and sequencing on Illumina HiSeq 2500 platform. After the sequencing run, Illumina RNA-Seq data were processed to generate FASTQ files and de novo assembled using Trinity (SRA study accession SRP093200 ; Bioproject accession PRJNA345155; TSA accession GGEC00000000). To estimate gene transcript expression, we used Bowtie 2 programme and successfully aligned back up to 95.14% of the filtered reads to the assembled transcriptome. We allowed up to 1-mismatches in the seed region (length =31bp) and all multiple mapped position were reported. Of all filtered reads about 95.14% of reads from each sample were properly aligned back to the assembled transcriptome. Overall we found 52,153 unique transcripts which have expression >=1 FPKM.

first: S

last: Meera

first: Anusha

last: Sreeshan


title: Cancer Associated Fibroblasts are defined by a core set of epigenome changes that contribute to the tumor phenotype [HuGene-1_0-st]

status: Public on Mar 26 2018

city: Darlinghurst

first: Ruth

last: Pidsley

state: NSW

address: 384 Victoria Street

institute: Garvan Institute of Medical Research

summary: Cancer Associated Fibroblasts (CAFs) play an active role in tumourigenesis. It is unknown how the permanent phenotypic changes in CAFs are encoded at the molecular level. Here we use whole genome sequencing and microarray analysis to interrogate the epigenome, transcriptome and genome of patient-matched CAF and non-malignant prostate fibroblast (NPF) cells.

overall_design: WGBS, RNA-seq, and microarrays were used to study epigenetics, transcriptomics and genetics in human cancer associated fibroblasts (CAFs) and non-malignant prostate fibroblasts (NPFs)

first: R

first: L

last: Mitchell


title: Cancer Associated Fibroblasts are defined by a core set of epigenome changes that contribute to the tumor phenotype [WGBS]


title: Cancer Associated Fibroblasts are defined by a core set of epigenome changes that contribute to the tumor phenotype [Illumina_Omini 2.5-8_SNP]

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array


title: Cancer Associated Fibroblasts are defined by a core set of epigenome changes that contribute to the tumor phenotype [RNA-seq]


title: Glucocorticoid receptor dimers control intestinal STAT1-mediated IFN- and TNF-induced inflammation in mice

status: Public on Apr 26 2018

city: Gent

last: Timmermans

address: Technologiepark 71

institute: VIB-UGent

summary: Tumor Necrosis Factor (TNF) is an important mediator in numerous inflammatory diseases, e.g. in inflammatory bowel diseases (IBD). In IBD, acute increases in TNF production can lead to disease flares. Glucocorticoids (GCs), which are steroids that bind and activate the glucocorticoid receptor (GR), are able to protect animals and humans against acute TNF-induced inflammatory symptoms. Mice with a poor transcriptional response of GR-dimer-dependent target genes were studied in a model of TNF-induced lethal inflammation. In contrast to the GRwt/wt mice, these GRdim/dim mice displayed a significant increase in TNF sensitivity and a lack of protection by the GC dexamethasone (DEX). Unchallenged GRdim/dim mice had a strong interferon-stimulated gene (ISG) signature, along with STAT1 upregulation and phosphorylation. This ISG signature was gut specific and, based on our studies with antibiotics, depended on the gut microbiota. GR dimers directly bound to short DNA sequences in the STAT1 promoter known as inverted repeat negative GRE (IR-nGRE) elements. Poor control of STAT1 in GRdim/dim mice led to failure to repress ISG genes resulting in excessive necroptosis induction by TNF. Our findings support a critical interplay between gut microbiota, interferons, necroptosis and GR in both the basal response to acute inflammatory challenges and in the pharmacological intervention by GCs.

overall_design: 30 samples in 2 sequencing experiments (24 + 6):  24 samples (1-24) in 2 groups with 4 conditions/group and 3 biological replicates/condition  6 samples (25-30) in 2 conditions with 3 biological replicates/condition

first: Marlies

last: Ballegeer

first: Kelly

last: Van Looveren

first: Melanie

last: Eggermont

first: Sofie

last: Vandevyver

first: Fabien

last: Thery

first: Karen

last: Dendocker

first: Jolien

last: Souffriau

last: Vandewalle

first: Lise

last: Van Wyngene

first: Riet

last: De Rycke

first: Nozomi

last: Takahashi

first: Peter

last: Vandenabeele

first: Jan

last: Tuckermann

first: Holger

last: Reichardt

first: Francis

last: Impens

first: Rudi

last: Beyaert

first: Karolien

last: De Bosscher

first: Roosmarijn

middle: E

last: Vandenbroucke

first: Claude

last: Libert


title: Molecular subtype-specific immunocompetent models of high-grade urothelial carcinoma reveal differential neoantigen expression and response to immunotherapy

status: Public on Apr 12 2018

city: Chapel Hill

first: William

middle: Y.

last: Kim

state: NC

address: 450 West Dr.

department: Medicine and Genetics

institute: University of North Carolina at Chapel Hill

summary: We developed a UPPL (Upk3a-CreERT2;p53f/f;Ptenf/f;Rosa26LSL-Luc) mouse model of bladder cancer and compared it with the existing BBN (N-butyl-N-(4-hydroxybutyl)nitrosamine) mouse model of blader cancer. We cultured UPPL and BBN primary tumor cells as cell lines along with MB49 cancer cell lines and KT immortalized normal urothelial cell lines and implanted them back into mice as cell-line derived tumors.

overall_design: RNASeq analysis was performed on 9 UPPL primary tumors, 11 BBN primary tumors, 1 UPPL cell line, 1 BBN cell line, 1 MB49 cell line, 3 KT cell lines, 4 UPPL cell-line derived tumors, 2 BBN cell-line derived tumors, and 4 MB49 cell-line derived tumors

middle: Y


title: Cancer Associated Fibroblasts are defined by a core set of epigenome changes that contribute to the tumor phenotype

first: Ruth

last: Pidsley

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

overall_design: Refer to individual Series


title: Cancer Associated Fibroblasts are defined by a core set of epigenome changes that contribute to the tumor phenotype [Illumina HM450]

first: R

first: L

last: Mitchell


title: Identification of MYB/bHLH proteins required for tissue-specific anthocyanin biosynthesis in inner pericarp of red-centered Actinidia chinensis cv. Hongyang

status: Public on Jan 01 2018

city: Hefei

first: Junyang

last: Yue

state: Anhui

address: Tunxi Road

institute: Hefei University of Technology

summary: In the present study, we employed the high-throughput sequencing technology to profile miRNAs in the inner and outer pericarp of Actinidia chinensis cv. Hongyang. After sequencing and cleaning, the numbers of clean reads generated from these four libraries were 18,203,332, 9,356,430, 11,006,231 and 11,314,375, respectively. Approximately 93.62%, 93.67%, 92.75% and 93.28% clean reads were respectively mapped to the kiwifruit genome with perfect matches. Subsequently, differentially expressed genes were compared between the inner and outer pericarps. Significant differences in both up- and down-regulated genes were identified in inner and outer percarps by comparing expression levels. The results showed that there were significantly 450 up-regulated and 416 down-regulated DEGs in inner pericarp as compared to the outer pericarp.

overall_design: Inner and outer pericarp in two parallel samples of Actinidia chinensis cv. Hongyang

first: Lihuan

last: Wang

first: Wei

last: Tang


title: Transcriptome sequencing reveals candidate NF-κB target genes involved in cocaine sensitization

status: Public on Jan 07 2018

city: BeiJing

first: Wang

last: Yan

address: 16# LinCui Road

institute: Institute of Psychology

summary: NF-κB is an inducible transcription factor complex that is rapidly activated by diverse stimuli. In the current study, we performed next-generation high-throughput sequencing of the prefrontal cortex in a mouse model of cocaine sensitization combined with pharmacological NF-κB inhibition in order to identify NF-κB target genes that mediate cocaine addiction.

overall_design: 1µg of RNA from a pool of 5 animals (200ng each) of each group was sequenced: (1) saline + saline (SS, n=10), (2) DDTC + saline (DS, n=10), (3) DDTC + cocaine (DC, n=10), and (4) saline + cocaine (SC, n=10)

first: Yan

first: Mei

last: Zhao


title: Expression profiles of Brg1-depleted acinar cells during ductal conversion

city: kyoto

first: Motoyuki

last: Tsuda

state: Please Select

address: 54 Kawahara-cho, Shogoin, Sakyo-ku

department: Department of Gastroenterology and Hepatology

country: Japan

institute: Graduate School of Medicine, Kyoto university

summary: Brahma related gene 1 (BRG1), a catalytic ATPase subunit of SWI/SNF chromatin remodeling complexes, is silenced in approximately 10% of human pancreatic ductal adenocarcinomas (PDA). We previously showed that BRG1 inhibits the formation of intraductal pancreatic mucinous neoplasm (IPMN) and IPMN-derived PDA from ductal cells. However, the role of BRG1 in pancreatic intraepithelial neoplasia (PanIN) from acinar cells remains elusive. Here, we investigated the role of BRG1 in PanIN initiation and maintenance and its underlying mechanisms. Exclusive elimination of Brg1 in acinar cells of Ptf1a-CreER; KrasG12D; Brg1f/f (KBC) mice impaired the formation of acinar-to-ductal metaplasia (ADM) and PanIN independent of the presence of p53 mutation. We found that Sox9 expression was down-regulated in both Brg1-depleted acinar cell explants and BRG1-depleted ADMs/PanINs. Sox9 overexpression rescued this PanIN-attenuated phenotype in KBC mice. Furthermore, Brg1-deletion in established PanIN by using an inducible dual recombinase system resulted in regression of the lesions in mice. Finally, expression of BRG1 and SOX9 was also positively correlated in human PanIN-derived PDAs. In summary, BRG1 is critical for both initiation and maintenance of PanIN. Mechanistically, this is mediated through positive regulation of SOX9 expression. Thus, the BRG1/SOX9 axis is a potential target for the prevention of PanIN-derived PDA.

overall_design: Total pooled RNA from three individual acinar cell explants 24 h after Cre-expressing adenovirus infection were used. Mouse genotypes used for analysis were KrasG12D and KrasG12D; Brg1f/f.

first: Akihisa

last: Fukuda


title: Sequential enhancer sequestration dysregulates recombination center formation at the IgH locus

status: Public on Feb 21 2018

first: Supriyo

last: De

summary: We report that Sequential deletion of CTCF binding elements leads to sequential proximal VH utilization.

overall_design: Analysis of VH utilization in different Pro-B cell lines.

first: Xiang

last: Qiu

first: Gita

last: Kumari

first: Tatiana

last: Gerasimova

first: Hansen

last: Du

first: Lawal

last: Labaran

first: Amit

last: Singh

last: Wood III

first: Kevin

last: Becker

first: Weiqiang

last: Zhou

first: Hongkai

last: Ji

first: Ranjan

last: Sen


title: Improvements in health, not survival, by late-onset metformin treatment

status: Public on Feb 23 2018

summary: The biguanide metformin improves health and survival in male mice; however, it is unclear whether metformin will confer health and lifespan benefits to mice when started late in life. Two year-old mice fed on standard chow were treated with 1% metformin every-other week (EOW) or two consecutive weeks per month (2WM). EOW mice displayed improvements in healthspan reminiscent of mice on caloric restriction. The age-associated histopathological changes in liver and kidney were significantly reduced in EOW compared to 2WM or control mice. Some of the affected gene transcripts and metabolites were found to be risk predictors of metabolic disorder. Neither EOW nor 2WM mice exhibited extension in mean or maximum lifespan compared with control animals. Thus, metformin supplementation had a strong impact on reversing some of the deleterious effects of aging and resulted in an improvement of health in old male mice in the absence of an extension of lifespan.

overall_design: Two-year old mice were fed a standard diet (SD, n=4 biological replicates for microarray), SD+1% metformin, either every other week (EOW, n=5 biological replicates for microarray) or two consecutive weeks per month (2WM, n=4 biological replicates for microarray) for 17 weeks.

first: Irene

last: Alfaras

first: Sarah

last: Mitchell

first: Hector

last: Mora

first: Darisbeth

last: Lugo

first: Alessandra

last: Warren

first: Christopher

last: Hine

first: James

first: David

last: Le Couteur

first: Victoria

middle: C

last: Cogger

first: Michel

last: Bernier

first: Rafael

last: de Cabo


title: Regulation of MIR165/166 by Class II and Class III homeodomain leucine zipper proteins establishes leaf polarity

city: Frederiksberg C

first: Daniel

last: Straub

address: Thorvaldsensvej 40

department: Plant and Environmental Sciences

country: Denmark

institute: University of Copenhagen

summary: ChIP-Seq was used to identify genes bound and regulated by HAT3.

overall_design: A. thaliana HAT3 ChIP-seq with Control

first: Paz

last: Merelo

first: Hathi

last: Ram

first: Monica

last: Caggiano

first: Carolyn

last: Ohno

first: Felix

last: Ott

first: Moritz

last: Graeff

first: Seok

last: Cho

first: Seong

middle: W

last: Yang

first: Stephan

last: Wenkel

first: Marcus

last: Heisler


title: Genome-wide analysis of DNA methylation profile provides clinical implication of Crohn’s Disease

status: Public on Dec 25 2017

city: Cheonan

first: Keunsoo

last: Kang

address: 119 Dandae-ro

institute: Dankook University

summary: Inflammatory bowel disease (IBD) is known to be caused by a genetic predisposition involving multiple genes; however, there is growing evidence that abnormal interaction with environmental, particularly epigenetic, factors can have a significant contribution during the development of IBD. Although many studies, particularly genome-wide association studies (GWAS), have been performed to identify the genetic changes underlying the pathogenesis of Crohn’s disease (CD), the role of epigenetic changes in the development of complications arising from CD is poorly understood. Here, we employed an unbiased approach to define DNA methylation alteration in CD patients using the HumanMethylation450K BeadChip platform. Compared to normal controls, the majority of differential DNA methylation in CD patient samples was in the promoter, intergenic, and gene body regions. The DNA methylation profile in CD revealed 134 probes (23 hypermethylated and 111 hypomethylated probes) that were differentially methylated. We validated the methylation levels of 19 genes that showed hypermethylation in CD patients compared with normal control. Technical validation was performed using quantitative MSP analysis and we finally identified that the Fragile Histidine Triad (FHIT) genes were hypermethylated in a disease-specific manner. Gene network analysis of the hypermethylated candidates suggested putative molecular interactions relevant to IBD pathology. Overall, our DNA methylation profile identifies newly hypermethylated genes in CD, as well as the gene network associated with disease development, which can provide new therapeutic targets.

overall_design: Bisulphite converted DNA from the 11 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip

first: Soo

last: Kim

first: Tae-Oh

first: Joo

last: Yi


title: NAD+ supplementation normalizes key Alzheimer’s features and DNA damage in a new AD mouse model with introduced DNA repair deficiency

status: Public on Feb 26 2018

first: Supriyo

last: De

summary: Emerging findings suggest that compromised cellular bioenergetics and DNA repair contribute to the pathogenesis of Alzheimer's disease (AD), but their role in disease-defining pathology is unclear.  We developed a DNA repair-deficient 3xTgAD/Polb+/- mouse that exacerbates major features of human AD including pTau pathologies, synaptic dysfunction, neuronal death and cognitive impairment.  Here we report that 3xTgAD/Polb+/- mice have reduced cerebral NAD+/NADH ratio indicating impaired cerebral energy metabolism, which is normalized by nicotinamide riboside (NR) treatment.  NR lessened pTau pathology in both 3xTgAD and 3xTgAD/Polb+/- mice, but had no impact on Abeta accumulation.  NR-treated 3xTgAD/Polb+/- mice exhibited reduced DNA damage, neuroinflammation, apoptosis of hippocampal neurons, and increased activity of SIRT3 in the brain.  NR improves cognitive function in multiple behavioral tests, and restored hippocampal synaptic plasticity in 3xTgAD mice and 3xTgAD/Polb+/- mice.  In general, the deficits and the benefits of NR were greater in 3xTgAD/Polb+/- mice than in 3xTgAD mice. Our findings suggest a pivotal role for cellular NAD+ depletion upstream of neuroinflammation, pTau, DNA damage, synaptic dysfunction and neuronal degeneration in AD.  Interventions that bolster neuronal NAD+ levels therefore have potential in AD.

overall_design: Wildtype (WT), Alzheimer's Disease triple transgenic (AD, 3xTgAD), Polymerase beta heterozygote (PolB, Polb+/-), and AD/PolB (ADP) mice were treated with vehicle or nicotinamide riboside (12mM) for six months (four biological replicates per group, using hippocampal and cortical tissues, for a total of 64 samples).

first: Yujun

last: Hou

first: Sofie

last: Lautrup

first: Stephanie

last: Cordonnier

first: Yue

last: Wang

first: Deborah

middle: L

last: Croteau

first: Eduardo

last: Zavala

first: Yongqing

last: Zhang

first: Kanako

last: Moritoh

first: Jennifer

last: O'Connell

first: Beverly

last: Baptiste

first: Tinna

middle: V

last: Stevnsner

first: Mark

last: Mattson

first: Vilhelm

last: Bohr


title: Regulation of HuR structure and function by Dihydrotanshinone-I

status: Public on Dec 20 2017

summary: The Human antigen R protein (HuR) is a RNA-binding protein that recognizes U/AU-rich elements in diverse RNAs through two RNA-recognition motifs, RRM1 and RRM2, and post-transcriptionally regulates the fate of target RNAs.  The natural product Dihydrotanshinone-I (DHTS) prevents the association of HuR and target RNAs in vitro and in cultured cells by interfering with the binding of HuR to RNA.  Here, we report the structural determinants of the interaction between DHTS and HuR and the impact of DHTS on HuR binding to target mRNAs transcriptome-wide. NMR titration and Molecular Dynamic simulation identified the residues within RRM1 and RRM2 responsible for the interaction between DHTS and HuR.  RNA Electromobility Shifts and Alpha Screen Assays showed that DHTS interacts with HuR through the same binding regions as target RNAs, stabilizing HuR in a locked conformation that hampers RNAs binding competitively.  HuR ribonucleoprotein immunoprecipitation followed by microarray (RIP-chip) analysis showed that DHTS treatment of HeLa cells paradoxically enriched HuR binding to mRNAs with longer 3’UTR and with higher density of U/AU-rich elements, suggesting that DHTS inhibits the association of HuR to weaker target mRNAs.  In vivo, DHTS potently inhibited xenograft tumor growth in a HuR-dependent model without systemic toxicity.

overall_design: The influence of DHTS on the interaction of HuR with endogenous mRNAs was analyzed in HeLa cells exposed to either 1 micromolar (1 uM) DHTS or DMSO vehicle for 3 hours, followed by immunoprecipitation (IP) of endogenous ribonucleoprotein complexes, and extraction of  RNA from the IP samples for cDNA microarray analysis or q-RT-PCR validation.

first: Preet

last: Lal

first: Linda

last: Cerofolini

first: Vito

last: D'Agostino

first: Chiara

last: Zucal

first: Carmelo

last: Fuccio

first: Isabelle

last: Bonomo

first: Erik

last: Dassi

first: Danilo

last: Di Maio

first: Sha

middle: N

last: William

first: Vikalp

last: Vishwakarma

first: Rachel

last: Munk

first: Elin

last: Lehrmann

first: Kotb

last: Abdelmohsen

first: Saioa

last: Elezgarai

first: Claudio

last: Luchinat

first: Ettore

last: Novellino

first: Alessandro

last: Quattrone

first: Emiliano

last: Biasini

first: Leonardo

last: Manzoni

first: Piefausto

last: Seneci

first: Myriam

last: Gorospe

first: Dan

last: Dixon

first: Pierfausto

first: Luciana

last: Marinelli

first: Marco

last: Fragai

last: Provenzani


title: miRNA data from extracellular vesicles secreted by Trichuris muris

status: Public on Dec 13 2017

city: Smithfield

first: Javier

last: Sotillo

address: 14-88 McGregor rd

department: AITHM

institute: James Cook University

type: Non-coding RNA profiling by high throughput sequencing

summary: miRNA-Seq analysis of the miRNA present in the extracellular vesicles secreted by the nematode Trichuris muris

overall_design: Analyis of 2 biological replicates of miRNA extracetd from the extracellular vesicles secreted by the nematode Trichuris muris

first: Ramon

last: Eichenberger

first: Matt

last: Field

first: Alex

last: Loukas


title: Nuclear Actin Regulates Inducible Transcription by Enhancing RNA Polymerase II Clustering

status: Public on Dec 01 2017

city: Beijing

first: Ruifeng

last: Li

address: Haidian

institute: Peking University

summary: Nuclear actin dynamics regulate enhanced RNA polymerase II clustering on specific genes upon serum stimulation, thus establishing the serum-induced transcriptional program.

overall_design: We sequenced the transcriptomes of U2OS cells overexpressing actin mutant G13R and those expressing GFP as control, at both normal-growth and serum-stimulation conditions.

first: Mian

last: Wei

first: Xiaoying

last: Fan

first: Yingping

last: Hou

first: Miao

last: Ding

first: Shaoshuai

last: Meng

first: Fuchou

last: Tang

first: Cheng

first: Yujie

last: Sun


title: NAD+ Replenishment Improves Lifespan and Healthspan in Ataxia Telangiectasia Models via Mitophagy and DNA Repair.

city: Baltimore

first: Supriyo

last: De

address: 251 Bayview Blvd

institute: NIA-IRP, NIH

summary: Ataxia telangiectasia (A-T) is a rare autosomal recessive disease characterized by progressive neurodegeneration and cerebellar ataxia. A-T is causally linked to defects in ATM, a master regulator of the response to and repair of DNA double-strand breaks. The molecular basis of cerebellar atrophy and neurodegeneration in A-T patients is unclear. Here we report and examine the significance of increased PARylation, low NAD+, and mitochondrial dysfunction in ATM-deficient neurons, mice, and worms. Treatments that replenish intracellular NAD+ reduce the severity of A-T neuropathology, normalize neuromuscular function, delay memory loss, and extend lifespan in both animal models. Mechanistically, treatments that increase intracellular NAD+ also stimulate neuronal DNA repair and improve mitochondrial quality via mitophagy. This work links two major theories on aging, DNA damage accumulation, and mitochondrial dysfunction through nuclear DNA damage-induced nuclear-mitochondrial signaling, and demonstrates that they are important pathophysiological determinants in premature aging of A-T, pointing to therapeutic interventions.

overall_design: A total of 48 ATM wildtype (WT) and mutated (atm1) C. elegans worm samples (approximately 1000 worms per sample) were used for microarray analysis, divided into three experiments for each of the four treatment conditions: Control (CTR), NAD+ precursor nicotinamide riboside (NR), SIRT1 inhibitor SRT1720 (SRT1720) or PARP1 inhibitor Olaparib, sampled at two time-points (Day 1 and Day 10) after treatment.

first: Evandro

middle: F

last: Fang

first: Henok

last: Kassahun

first: Deborah

last: Croteau

first: Morten

last: Scheibye-Knudsen

first: Krisztina

last: Marosi

first: Huiming

last: Lu

first: Raghavendra

last: Shamanna

first: Sumana

last: Kalyanasundaram

first: Mark

last: Wilson

first: Wendy

last: Iser

first: Bradley

last: Wollman

first: Marya

last: Morevati

first: Jane

last: Tian

first: David

last: Sinclair

last: Mattson

first: Hilde

last: Nilsen

first: Vilhelm

last: Bohr


title: The histone variant H2A.Z and chromatin remodeler BRAHMA act coordinately and antagonistically to regulate transcription and nucleosome dynamics in Arabidopsis

status: Public on Jan 05 2018

city: Atlanta

first: Roger

middle: B

last: Deal

state: GA

address: 1510 Clifton Rd NE

department: Biology

institute: Emory University

type: Genome variation profiling by high throughput sequencing

summary: Plants adapt to changes in their environment by regulating transcription and chromatin organization. The histone H2A variant H2A.Z and the SWI2/SNF2 ATPase BRAHMA have overlapping roles in positively and negatively regulating environmentally responsive genes in Arabidopsis, but the extent of this overlap was uncharacterized. Both have been associated with various changes in nucleosome positioning and stability in different contexts, but their specific roles in transcriptional regulation and chromatin organization need further characterization. We show that H2A.Z and BRM act both cooperatively and antagonistically to contribute directly to transcriptional repression and activation of genes involved in development and response to environmental stimuli. We identified 8 classes of genes that show distinct relationships between H2A.Z and BRM and their roles in transcription. We found that H2A.Z contributes to a range of different nucleosome properties, while BRM stabilizes nucleosomes where it binds and destabilizes and/or repositions flanking nucleosomes. H2A.Z and BRM contribute to +1 nucleosome destabilization, especially where they coordinately regulate transcription. While profiling nucleosomes in arp6 mutants, we discovered that large deletions had accumulated in the arp6 genome. We also found that at genes regulated by both BRM and H2A.Z, both factors overlap with the binding sites of light-regulated transcription factors PIF4, PIF5, and FRS9, and that some of the FRS9 binding sites are dependent on H2A.Z and BRM for accessibility. Collectively, we comprehensively characterized the antagonistic and cooperative contributions of H2A.Z and BRM to transcriptional regulation, and illuminated their interrelated roles in chromatin organization. The variability observed in their individual functions implies that both BRM and H2A.Z have more context-specific roles within diverse chromatin environments than previously assumed.

overall_design: We performed MNase-seq, H2A.Z ChIP-seq, and RNA-seq on 4-5 leaf developmentally-staged, shoot Arabidopsis material from WT, arp6-1, and brm-1. RNA-seq and MNase-seq were also performed on arp6-1;brm-1 mutants. Two biological replicates were generated for H2A.Z ChIP-seq experiments and MNase-seq, and three biological replicates were performed for RNA-seq experiments. The genome of arp6 mutants was also sequenced to identify genomic deletions.

first: E

middle: S

last: Torres


title: Conserved and species-specific molecular denominators in mammalian skeletal muscle aging

status: Public on Sep 20 2017

first: Supriyo

last: De

sample_organism:
Macaca mulatta
Homo sapiens
Mus musculus
Rattus norvegicus


title: The γ2 subunit of AMP-activated protein kinase regulates mammalian heart rate

status: Public on Sep 30 2017

summary: AMP-activated protein 1 kinase (AMPK), a phylogenetically conserved serine/threonine kinase regarded as a key cellular energy sensor, exists in eukaryotes as a heterotrimer comprising a catalytic α and regulatory β and γ subunits. In humans, activating mutations in the gene encoding the γ2 subunit of AMPK (PRKAG2) display a cardiac phenotype of left ventricular hypertrophy (LVH), conduction system disease, ventricular pre-excitation and increased cardiomyocyte glycogen accumulation. While existing transgenic models have elucidated the pathogenesis of several aspects of the disease5-7, the slow heart rate (sinus bradycardia) – a prominent feature of the disease – remains poorly understood. Here, using gene-targeting to generate mice which recapitulate this bradycardia, we demonstrate that γ2 AMPK activation perturbs fundamental mechanisms that determine sinoatrial pacemaker cell function. Reduction in the sarcolemmal hyperpolarization activated (“funny”) current (If) and damping of ryanodine receptor-derived diastolic local subsarcolemmal Ca2+ releases (LCRs)12,13 contribute to reduced sinoatrial cell spontaneous activity and, ultimately, to a lower heart rate. Pharmacological activation of AMPK reversibly reduces the beating rate of murine pluripotent stem cell-derived induced sinoatrial bodies. In contrast, using a mouse knock-out of γ2 AMPK, which exhibits an increased heart rate, we demonstrate a role for γ2 AMPK in physiological heart rate regulation, including an indispensable role in the bradycardic adaptation to endurance exercise. Through regulating the cardiac pacemaker and thereby heart rate, γ2 AMPK by virtue of its energy-sensing role, is a key physiological determinant of overall cardiac energy homeostasis.

overall_design: Four mouse SAN tissues were pooled from R299Q γ2 and WT littermate controls and processed together for the extraction of one sample of total RNA for a total of 4 homozygote R299Q γ2, 4 heterozygote R299Q γ2 and 3 WT samples.

first: Arash

last: Yavari

first: Mohamed

last: Bellahcene

first: Annalisa

last: Bucchi

first: Syevda

last: Sirenko

first: Katalin

last: Pinter

first: Neil

last: Herring

first: Julia

middle: J

last: Jung

first: Kirill

last: Tarasov

first: Gabor

last: Czibik

first: Violetta

last: Steeples

first: Sahar

last: Ghaffari

first: Chinh

last: Nguyen

first: Christian

last: Rimmbach

first: Markus

last: Wolfien

first: Yosuke

last: Okamoto

first: Mingyi

last: Wang

first: Bruce

middle: D

last: Ziman

first: Manuel

last: Paina

first: Jack

last: Moen

first: Joonho

last: Lee

first: Jing

last: Zhang

first: Ismayil

last: Ahmet

first: Michael

middle: G

last: Matt

first: Yelena

last: Tarasova

first: Alexander

last: Stockenhuber

first: Dilair

last: Baban

first: Natasha

last: Sahgal

first: Helen

last: Lockstone

first: Rathi

last: Puliyadi

first: Joseph

last: de Bono

first: John

last: Gomes

first: Hannah

last: Muskett

first: Mahon

last: Maguire

first: Matthew

last: Kelly

first: Pedro

last: dos Santos

first: Nicola

last: Bright

first: Angela

last: Woods

first: Katja

last: Gehmlich

first: Henrik

last: Isackson

first: Gillian

last: Douglas

last: Ferguson


title: Conserved and species specific molecular denominators in mammalian aging [human]

first: Supriyo

last: De

summary: Aging is a complex phenomenon involving functional decline in multiple physiological systems. We focused on skeletal muscle to identify pathways that modulate function and healthspan by global expression profiles and specific  mechanisms fundamental to aging processes. Our experimental design integrated comparative analysis of mice, rats, rhesus monkeys and humans and targeted three key time points during their lifespans. Pathways related to oxidative stress, inflammation and nutrient signaling, which function collectively to affect the quality and status of mitochondria, emerged across all species with age. Notably, mitochondrial transcript levels were better preserved in aging human muscle, suggesting an evolution-driven fitness more robust than in other species. The identification of these conserved pathways uncovers common molecular mechanisms intrinsic to health and lifespan, while unveiling of species-specific pathways emphasizes the importance of human studies for devising optimal therapeutic modalities to slow the aging process.

overall_design: RNA extracted from skeletal muscle biopsies of five young, four middle-aged, and seven old human males were analyzed by gene expression microarray analysis.

first: Evi

middle: M

last: Mercken

first: Miriam

last: Capri

first: Bethany

middle: A

last: Carboneau

first: Maria

last: Conte

first: Juliana

last: Heidler

first: Aurelia

last: Santoro

first: Alejandro

last: Martin-Montalvo

first: Marta

last: Gonzalez-Freire

first: Husam

last: Khraiwesh

first: José

last: González-Reyes

first: Ruin

last: Moaddel

first: Yongqing

last: Zhang

first: Kevin

last: Becker

last: Villalba

first: Julie

last: Mattison

first: Ilka

last: Wittig

first: Claudio

last: Franceschi

first: Rafael

last: de Cabo


title: Conserved and species specific molecular denominators in mammalian aging [rhesus monkey]

first: Supriyo

last: De

overall_design: RNA extracted from skeletal muscle biopsies of six young,six middle-aged, and six old rhesus monkey (Macaca mulatta) males were analyzed by gene expression microarray analysis.

first: Evi

last: Mercken

last: Capri


title: Conserved and species specific molecular denominators in mammalian aging [mouse]

overall_design: RNA was extracted from skeletal muscle biopsies of five young, five middle-aged, and five old male C57BL/6 mice and analyzed by gene expression microarray analysis.

first: Miriam

first: Bethany

last: Carboneau

last: Conte

last: Heidler


title: LncRNA OIP5-AS1/cyrano suppresses GAK expression to control mitosis

status: Public on Sep 25 2017

summary: Long noncoding RNAs (lncRNAs) have been found to regulate the expression of mRNAs with which they share partial complementarity.  We sought to identify the mechanism through which the lncRNA OIP5-AS1, which is abundant in the cytoplasm, suppressed cell proliferation.  Silencing of OIP5-AS1 in human cervical carcinoma cells revealed the appearance of many aberrant (monopolar, multipolar, misaligned) mitotic spindles.  By biotin-oligomer affinity pulldown, proteomic, and bioinformatic analyses, we identified a subset of human cell cycle regulatory proteins encoded by mRNAs that were capable of interacting with OIP5-AS1.  Further investigation revealed that GAK mRNA, which encodes a cyclin G-associated kinase important for mitotic progression, was a prominent target of OIP5-AS1.  The interaction between these two transcripts led to a reduction in GAK mRNA stability and GAK protein abundance, as determined in cells in which OIP5-AS1 levels were increased or decreased.  Importantly, the aberrant mitotic cell division seen after silencing OIP5-AS1 was partly rescued if GAK was simultaneously silenced.  These findings indicate that the abnormal mitoses seen after silencing OIP5-AS1 was caused by an untimely rise in GAK levels and suggest that OIP5-AS1 suppresses cell proliferation at least in part by reducing GAK levels

overall_design: RNA from HeLa cell lines was microarrayed after either MS2-pulldown against empty-MS2 (control) or the lncRNA OIP5-AS1/Cyrano-MS2 (Cyrano), or total RNA from siRNA transfection with a control siRNA (Ctl_si) or OIP5-AS1/Cyrano (Cyrano_si). Four biological repeats were examined per group.

first: Jiyoung

last: Kim

first: Ji-Heon

last: Noh

first: Jennifer

last: Martindale

first: Seung-Kyu

last: Lee

first: Alexei

last: Sharov

first: Elin

last: Lehrmann

first: Weidong

last: Wang

first: Kotb

last: Abdelmohsen

first: Myriam

last: Gorospe


title: Conserved and species specific molecular denominators in mammalian aging [rat]

overall_design: RNA extracted from skeletal muscle biopsies of five young, five middle-aged, and five old male Fisher-344 rats was analyzed by gene expression microarray analysis.

first: Maria

first: Juliana

first: Aurelia

last: Santoro

first: Alejandro

last: Martin-Montalvo

first: Marta

last: Gonzalez-Freire

first: Husam

last: Khraiwesh

first: José

last: González-Reyes

first: Ruin

last: Moaddel

first: Yongqing

last: Zhang

first: Kevin

last: Becker

last: Villalba

first: Julie

last: Mattison

last: Wittig

last: Franceschi


title: Genomic binding profiling upon expression of Ubx in S2 cells

status: Public on Aug 31 2017

city: Marseille

first: Andrew

last: Saurin

address: Campus de Luminy

country: France

institute: IBDM / CNRS

summary: We sought to determine the genomic binding profile of the Drosophila Hox protein Ubx in a homogenous cell system. S2-DRSC cells that have no Hox expression were stably transfected with HA-tagged Ubx under the control of a metallothionein promoter. Upon Ubx expression, we identified high enrichment of Ubx at a large number transcription start sites that colocalises with the GAGA and M1BP.

overall_design: S2-DRSC cells are stably transfected with HA-tagged Ubx (S2-DRSC:Ubx).S2-Ubx cells are analysed for genomic binding of HA-Ubx

first: Amel

last: Zouaz

first: Ankush

last: Auradkar

first: Marie

last: Delfini

first: Meiggie

last: Macchi

first: Marine

last: Barthez

first: Serge

last: Akoa

first: Leila

last: Bastianelli

first: Stuart

last: Levine

first: Yacine

last: Graba


title: MicroRNAs Modulate Oxidative Stress in Hypertension through PARP-1 Regulation

status: Public on Aug 11 2017

first: Supriyo

last: De

summary: Oxidative stress is thought to contribute to aging and age-related diseases, such as cardiovascular and neurodegenerative diseases. Here we report that the Poly-(ADP-ribose) polymerase 1 (PARP-1), a DNA damage sensor protein involved in DNA repair and other cellular processes, is upregulated with hypertension in African American women. To further explore this mechanism, we identified two microRNAs, miR-103a-2-5p and miR-585-5p that are differentially-expressed with hypertension and were predicted to target PARP-1. Overexpression of these two miRNAs downregulated PARP-1 mRNA and protein levels in primary endothelial cells. Using heterologous luciferase reporter assays, we demonstrate that miR-103a-2-5p and miR-585-5p regulate PARP-1 through binding to sites in the coding region.  Given the important role of PARP-1 in DNA repair, we assessed whether overexpression of miR-103a-2-5p or miR-585-5p affected DNA damage and cell survival. Overexpression of these miRNAs enhanced DNA damage and decreased both cell survival and colony formation. These findings highlight the role for PARP-1 in regulating oxidative DNA damage in hypertension and identify important new regulators of PARP-1 expression, miR-103a-2-5p and miR-585-5p. Additionally, these insights may provide additional avenues to understand hypertension health disparities

overall_design: Primary human endothelial aortic cells (HAECs) were transfected with either pre-miR miRNA precursors for hsa-miR-103a-2-5p, miR-585-5p, or scrambled negative control (Control), and the transcriptional changes examined by gene expression microarray analysis using three biological repeats of each experimental condition.

first: Douglas

last: Dluzen

first: Yoonseo

last: Kim

first: Paul

last: Bastian

first: Elin

last: Lehrmann

first: Nicole

last: Noren Hooten

first: Michele

middle: K

last: Evans


title: Tomatidine enhances lifespan and healthspan in C. elegans through mitophagy induction via the SKN-1/Nrf2 pathway.

status: Public on Aug 21 2017

summary: Aging is a major international concern and brings with it formidable socioeconomical and healthcare challenges. An attainable approach to improve general health in humans is using small molecules. Tomatidine, a natural compound abundant in unripe tomatoes, inhibits aging-related skeletal muscle atrophy in mice. Here we show that tomatidine extends lifespan and healthspan in the aging animal model C. elegans, which shares many major longevity pathways with those of mammals. Tomatidine improves behaviors related to healthspan, including increased pharyngeal pumping and swimming movement, and also reduces deterioration of muscle cells in worms. Microarray, imaging, and behavioral analysis reveal that tomatidine maintains mitochondrial homeostasis through mitochondrial biogenesis and PINK-1/DCT-1-dependent mitophagy. Mechanistically, tomatidine induces mitochondrial hormesis by mildly inducing ROS production, which in turn activates the cellular antioxidant response SKN-1/Nrf2 pathway, followed by increased mitophagy in worms, primary rat neurons, and human cells. Our data suggest that tomatidine may delay some physiological aspects of aging, and points to new approaches for pharmacological interventions towards diseases of aging.

overall_design: N2 worms from L4 stage were exposed to either vehicle (DMSO) or 25 μM tomatidine, and four independent experiments for each condition were collected on adult Day 7.

first: Evandro

last: Fang

first: Tyler

last: Waltz

first: Henok

last: Kassahun

first: Qiping

last: Lu

first: Jesse

last: Kerr

first: Marya

last: Morevati

first: Elayne

last: Fivenson

first: Bradley

last: Wollman

first: Krisztina

last: Marosi

first: Mark

last: Wilson

first: Wendy

last: Iser

first: D

last: Eckley

first: Yongqing

last: Zhang

first: Ilya

last: Goldberg

first: Morten

last: Scheibye-Knudsen

middle: P

last: Mattson

first: Hilde

last: Nilsen

first: Vilhelm

last: Bohr

first: Kevin

last: Becker


title: The transcriptome of human oocytes is related to age and ovarian reserve.

status: Public on Aug 29 2017

city: Barcelona

first: Montse

last: BARRAGAN

state: Select One

address: Baldiri Reixac, 15

country: Spain

institute: Clinica EUGIN

summary: Although it is well established that the ovarian reserve diminishes with increasing age, and that a woman’s age is correlated to lower oocyte quality, the interplay of a diminished reserve and age on oocyte developmental competence is not clear. After maturation, oocytes are mostly transcriptionally quiescent, and developmental competence prior to embryonic genome activation (EGA) relies on maternal RNA and proteins.  Age and ovarian reserve both affects oocyte developmental competence, however, their relative importance in this process are difficult to tease out, as ageing is accompanied by a decrease in ovarian reserve.  Oocytes store large quantities of RNA, including several noncoding transcripts (ncRNAs) involved in early development transcription and translation modulation. Despite the central role of ncRNAs in maternal to zygote transition, no characterization of the ncRNA transcriptome in human oocytes has been reported. This study aims at identifying how the human oocyte transcriptome changes across reproductive ages and ovarian reserve levels, with the goal of identifying candidate markers of developmental competence, and to assess the independent relevance of age and ovarian reserve in the changes of the transcriptome

overall_design: A total of 36 vitrified/warmed MII oocytes from 30 women undergoing oocyte donation were included in this study, processed and analyzed individually. Oocytes were divided in 4 groups, each including 9 oocytes, according to the woman´s age and antral follicular count (AFC) (mean ± SD): Young with High AFC (YH; age 21 ± 1 years and 24 ± 3 follicles)? Old with High AFC (OH; age 32 ± 2 years and 29 ± 7 follicles)? Young with Low AFC (YL; age 24 ± 2 years and 8 ± 2 follicles)? Old with Low AFC (OL; age 34 ± 1 years and 7 ± 1 follicles). Total RNA from each oocyte independently was isolated, amplified, labeled, and hybridized on HTA 2.0 arrays (Affymetrix). One sample from group Young with Low AFC (YL) was excluded due to apparent data quality issues. Remaining data were analyzed using TAC software and qPCR was performed to validate arrays.

first: Montserrat

last: Barragán

first: Jose

middle: I

last: Pons

first: Anna

last: Ferrer-Vaquer

first: Anthony

last: Schweitzer

first: Jason

last: Hubbard

first: Herbert

last: Auer

first: Annie

last: Rodolosse

first: Rita

last: Vassena


title: KSRP specifies monocytic and granulocytic differentiation through regulating miR-129 biogenesis and RUNX1 expression

status: Public on Aug 01 2017

first: Jia

last: Yu

address: Dong Dan San Tiao 5, Dongcheng District

institute: Peking Union Medical College

summary: We used CD34-positive cells isolated from cord blood to differentiate to granulocytic and monocytic lineages, respectively. Poly A-enriched RNA-seq was performed on the day 5, 10 and 15 samples of both granulocytic and monocytic lineages.

overall_design: We forcused on the RNA binding proteins involved in granulocytic and monocytic lineage differentiation.

first: Hongmei

last: Zhao

first: Xiaoshuang

last: Wang

first: Ping

last: Yi

first: Dong

first: Fang


title: Genomic deletion of GIT2 induces a premature age-related thymic dysfunction and systemic immune system disruption.

first: Supriyo

last: De

summary: Recent research has proposed that GIT2 (G protein-coupled receptor kinase interacting protein 2) acts as an integrator of the aging process through regulation of ‘neurometabolic’ integrity. One of the commonly accepted hallmarks of the aging process is thymic involution. At a relatively young age, 12 months of age, GIT2-/- mice present a prematurely distorted thymic structure and dysfunction compared to age-matched 12 month-old wild-type control (C57BL/6) mice. Disruption of thymic structure in GIT2-/- (GIT2KO) was associated with a significant reduction in the expression of the cortical thymic marker, Troma1 (cytokeratin 8). Double positive (CD4+CD8+) and single positive CD4+ T cells were also markedly reduced in 12 month-old GIT2KO mice compared to age-matched control wild-type mice. Coincident with the premature (12 months of age) thymic disruption in GIT2KO mice was the unique generation of a novel cervical ‘organ’, i.e. novel ‘parathymic lobes’. These novel organs did not exhibit classical peripheral lymph node-like characteristics but expressed high levels of T cell progenitors that were reflexively reduced in GIT2KO thymi. Using signaling pathway analysis of GIT2KO thymus and parathymic lobe transcriptomic data we found that the molecular signaling functions lost in the dysfunctional GIT2KO thymus were selectively reinstated in the novel parathymic lobe – suggestive of a compensatory effect for the premature thymic disruption. Broader inspection of high-dimensionality transcriptomic data from GIT2KO lymph nodes, spleen, thymus and parathymic lobes revealed a systemic alteration of multiple proteins (Dbp, Tef, Per1, Per2, Fbxl3, Ddit4, Sin3a) involved in the multidimensional control of cell cycle clock regulation, cell senescence, cellular metabolism and DNA damage. Altered cell clock regulation across both immune and non-immune tissues therefore may be responsible for the premature ‘aging’ phenotype of GIT2KO mice.

overall_design: RNA from spleen, thymus, and lymph nodes (extra, inguinal and mesenteric) from homozygote GIT2 knock-out (N=3/tissue) and C57BL/6 WT (N=3/tissue) mice were compared.

first: Sana

last: Siddiqui

first: Ana

last: Lustig

first: Arnell

last: Carter

first: Mathavi

last: Sankar

first: Caitlin

last: Daimon

first: Richard

middle: T

last: Premont

first: Harmonie

last: Etienne

first: Jaana

last: van Gastel

first: Abdelkrim

last: Azmi

first: Jonathan

last: Janssens

first: Yongqing

last: Zhang

first: William

last: Wood

first: Elin

last: Lehrmann

first: James

last: Martin

first: Bronwen

first: Dennis

last: Taub

first: Stuart

last: Maudsley


title: Genomic binding profiling upon expression of AbdA in S2 cells

first: Andrew

last: Saurin

summary: We sought to determine the genomic binding profile of the Drosophila Hox protein AbdA in a homogenous cell system. S2-DRSC cells that have no Hox expression were stably transfected with HA-tagged AbdA under the control of a metallothionein promoter. Upon AbdA expression, we identified high enrichment of AbdA at a large number transcription start sites that colocalises with the GAGA and M1BP. Genes targeted by GAGA and M1BP contain paused RNA polymerase II and show enrichment of PcG proteins. Upon AbdA binding at M1BP-target sites, a significant reduction in PcG protein binding is observed  with a concomitant reduction in RNA Pol II pausing. These data suggest that AbdA targets both GAGA- and M1BP-controlled genes, and at M1BP-controlled genes, AbdA binding is sufficient to release PcG-mediated RNA Pol II pausing to induce gene transcription.

overall_design: S2-DRSC cells are stably transfected with HA-tagged AbdA (S2-DRSC:AbdA). S2 and S2-AbdA cells are analysed for genomic binding of HA-AbdA, Poised RNA Pol II (Rpb3), Elongating RNA Pol II (PolII_phosphoSer2), M1BP, GAGA factor, dRing, E(z), in the absence (S2-DRSC) and presence (S2-DRSC-HA::AbdA) of AbdA

first: Amel

last: Zouaz

first: Ankush

last: Auradkar

first: Marie

middle: C

last: Delfini

first: Meiggie

last: Macchi

first: Marine

last: Barthez

first: Serge

middle: E

last: Akoa

first: Leila

last: Bastianelli

last: Levine

first: Yacine

last: Graba


title: transferred T helper cell sorted from mice

status: Public on Aug 10 2017

city: cleveland

first: Yong

last: Lu

address: 9500 euclid avenue, NB40

institute: Cleveland Clinic

summary: Mice were injected s.c. in the front of the abdomen with 1 × 106  B16-OVA tumor cells. At 10 days after tumor injection, mice (5/group) were treated with adoptive transfer of 2.5 × 106 Th1, Th9 or Th17 cells, followed by i.v. injection of 2.5 × 105 peptide-pulsed BMDC. Total RNA was extracted with RNeasy Mini kit (Qiagen) from CD45.1+CD4+ Th cells sorted from spleens of tumor-bearing mice 12 days after transfer.

first: Qing

last: Yi


title: Effect of hyperglycemia on the transcriptional profile of primary human macrophages

status: Public on Jul 12 2017

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

summary: Hyperglycemia is an essential factor leading to micro- and macrovascular diabetic complications. Macrophages are key innate immune regulators of inflammation that undergo 2 major directions of functional polarization: classically (M1) and alternatively (M2) activated macrophages. The aim of the study was to examine the effect of hyperglycemia on transcriptional activation of M0, M1 and M2 human macrophages.

overall_design: Monocytes were isolated from buffy coats by magnetic cell sorting using CD14 beads and cultivated in the presence of 5mM (NG) and 25mM (HG) glucose for 6 days under stimulation with IFNg (M1), IL4 (M2) or without cytokine (M0). M0, M1 and M2 macrophages from 4 individual donors were used

first: Kondaiah

last: Moganti

first: Julia

last: Kzhyshkowska


title: Interferon-γ drives T reg fragility to promote anti-tumor immunity

status: Public on May 22 2017

city: Pittsburgh

first: Maria

last: Chikina

state: PA

address: 3501 5th ave

institute: University of Pittsburgh

summary: Regulatory T cells (Tregs) are a barrier to effective anti-tumor immunity. Neuropilin-1 (Nrp1) is required to maintain intratumoral Treg stability and function but is dispensable for peripheral immune homeostasis, Treg-restricted Nrp1 deletion in mice results in profound tumor resistant due to Treg functional fragility.  Drivers of Treg fragility, the mechanistic basis of Nrp1 dependency, and the relevance of these processes for human cancer and immunotherapy remain unknown.  NRP1 expression on human Tregs in melanoma and HNSCC was highly heterogeneous and correlated with prognosis.  Using a mouse model of melanoma in which mutant Nrp1-deficient (Nrp1–/–) and wild type (WT) Tregs could be assessed in a competitive environment, we found that a high proportion of intratumoral Nrp1–/– Tregs produce interferon-γ (IFNγ), which in turn drove the fragility of surrounding WT Tregs, boosting anti-tumor immunity and facilitating tumor clearance. We also show that IFNγ-induced Treg fragility is required for an effective response to PD1 immunotherapy, suggesting that cancer therapies promoting Treg fragility may be efficacious .

overall_design: Tregs from B16 tumors and non-draining lymph nodes NDLN  from WT, Nrp-1 deficient homozygous and heterozygous mice


title: Altered learning, memory, and social behavior in type 1 taste receptor subunit 3 knock-out mice are associated with neuronal dysfunction.

status: Public on May 17 2017

first: Supriyo

last: De

summary: The type 1 taste receptor member 3 (T1R3) is a G protein-coupled receptor involved in sweet-taste perception. Besides the tongue, the T1R3 receptor is highly expressed in brain areas implicated in cognition, including the hippocampus and cortex. As cognitive decline is often preceded by significant metabolic or endocrinological dysfunctions regulated by the sweet-taste perception system, we hypothesized that a disruption of the sweet-taste perception in the brain could have a key role in the development of cognitive dysfunction. To assess the importance of the sweet-taste receptors in the brain, we conducted transcriptomic and proteomic analyses of cortical and hippocampal tissues isolated from T1R3 knock-out (T1R3KO) mice. The effect of an impaired sweet-taste perception system on cognition functions were examined by analyzing synaptic integrity and performing animal behavior on T1R3KO mice. Although T1R3KO mice did not present a metabolically disrupted phenotype, bioinformatic interpretation of the high-dimensionality data indicated a strong neurodegenerative signature associated with significant alterations in pathways involved in neuritogenesis, dendritic growth, and synaptogenesis. Furthermore, a significantly reduced dendritic spine density was observed in T1R3KO mice together with alterations in learning and memory functions as well as sociability deficits. Taken together our data suggest that the sweet-taste receptor system plays an important neurotrophic role in the extralingual central nervous tissue that underpins synaptic function, memory acquisition, and social behavior.

overall_design:
All animal procedures were approved by the Animal Care and Use Committee (ACUC) of the National Institute on Aging (NIA). T1R3 knockout mice (T1R3KO) were kindly provided by Dr. Charles Zuker (Columbia University) and were cross bred with wild type (WT) C57BL/6J mice (Jackson Laboratory) for at least 4 generations. All animals were kept in a 12 h light/dark cycle and received food (standard Harlan-Teklad chow: LM-485) and water ad libitum. A total of 10 to 20 mice (4-5 months of age) in each  group were employed for behavioral, histological and protein expression analyses. 4-5month old animals were used in the experiments and euthanized right after the experiments. For post mortem tissue  extraction, animals were humanely euthanized with isoflurane: specific organs/tissues were then carefully dissected, snap-frozen and stored at -80˚ C until further analysis
RNA was isolated from cortical, hypothalamic, and hippocampal brain tissues from wildtype and T1R3 knockout (T1R3KO) C57BL/6J mice and used for transcriptomic analyses (N=3/group, 18 animals total).

first: Bronwen

last: Martin

first: Rui

last: Wang

first: Wei-Na

last: Cong

first: Caitlin

last: Daimon

first: Wells

middle: W

last: Wu

first: Bin

last: Ni

first: Kevin

last: Becker

first: Elin

last: Lehrmann

first: William

middle: H

last: Wood III

first: Yongqing

last: Zhang

first: Etienne

last: Harmonie

first: Jaana

last: van Gastel

first: Abdelkrim

last: Azmi

first: Jonathan

last: Janssens

last: Maudsley


title: Differentiation of human embryonic stem cells towards hepatocytes

status: Public on Apr 28 2017

city: Shenzhen

first: Andrew

last: Hutchins

address: 1088 Xueyuan Rd

department: Bioinformatics

institute: Southern University of Science and Technology

summary: To understand in detail the molecular phases that occur during the differentiation of human embryonic stem cells to hepatocyte-like cells we performed an RNA-seq time course of the stages of differentiation across the 21 day differentiation time course. We used a chemically defined (serum-free) protocol, modified from Si-Tayeb et al., 2010 and Song et al., 2009. We describe acquisition of definitive endoderm characteristics at day 3, followed by hepatoblast charcter at day 7-13 and then maturation to hepatocyte-like cells at day 21.

overall_design: Time course of differentiation of human embryoic stem cells to hepatocyte-like cells over 21 days, using an adapted chemically defined protocol of Song et al., 2009; Cell Research

first: Duanqing

last: Pei

first: Xiaodong

last: Shu


title: Sav1 Loss Induces Senescence and Stat3 Activation Coinciding with Tubulointerstitial Fibrosis

status: Public on Apr 26 2017

middle: Y.

last: Kim

address: 450 West Dr.

institute: University of North Carolina at Chapel Hill

summary: Our mouse model (Ksp-CreER/Sav1fl/fl ) offers novel insights into molecular events that are linked to fibrosis development from Sav1 loss.

overall_design: RNAseq analysis was performed on cortex tissue from mouse kidneys with and without Sav1 loss.

middle: Y


title: Novel RNA-binding activity of NQO1 promotes SERPINA1 mRNA translation

first: Supriyo

last: De

summary: NAD(P)H:quinone Oxidoreductase (NQO1) is essential for cell defense against reactive oxidative species, cancer, and metabolic stress.  Recently, NQO1 was found in ribonucleoprotein (RNP) complexes, but NQO1-interacting mRNAs and the functional impact of such interactions are not known.  Here, we used ribonucleoprotein immunoprecipitation (RIP) and microarray analysis to identify comprehensively the subset of NQO1 target mRNAs in human hepatoma HepG2 cells.  One of its main targets, SERPINA1 mRNA, encodes the serine protease inhibitor α-1-antitrypsin, A1AT, which is associated with disorders including obesity-related metabolic inflammation, chronic obstructive pulmonary disease (COPD), liver cirrhosis and hepatocellular carcinoma.  Biotin pulldown analysis indicated that NQO1 can bind the 3’ untranslated region (UTR) and the coding region (CR) of SERPINA1 mRNA.  NQO1 did not affect SERPINA1 mRNA levels; instead, it enhanced the translation of SERPINA1 mRNA, as NQO1 silencing decreased the size of polysomes forming on SERPINA1 mRNA and lowered the abundance of A1AT.  Luciferase reporter analysis further indicated that NQO1 regulates SERPINA1 mRNA translation through the SERPINA1 3’UTR.  Accordingly, NQO1-KO mice had reduced hepatic and serum levels of A1AT and increased activity of neutrophil elastase, one of the main targets of A1AT.  We propose that this novel mechanism of action of NQO1 as RNA-binding protein may help to explain its pleiotropic biological effects.

overall_design: NQO1 RIP in HepG2 cells

first: Andrea

last: Di Francesco

first: Clara

last: Di Germanio

first: Amaresh

last: Panda

first: Phu

last: Huynh

first: Robert

last: Peaden

first: Ignacio

last: Navas-Enamorado

first: Paul

last: Bastian

first: Alberto

last: Diaz-Ruiz

first: David

last: Ross

last: Siegel

first: Jennifer

middle: L

last: Martindale

first: Michel

last: Bernier

first: Myriam

last: Gorospe

first: Kotb

last: Abdelmohsen

first: Rafael

last: de Cabo


title: Near-tetraploid cells exhibit chromosome instability triggered by replication stress and enhanced invasive capabilities [aCGH]

status: Public on May 10 2017

first: Jordi

last: Camps

state: Catalonia

address: c/Rosselló 149-153 4th floor, Center Esther Koplowitz

department: Gastroenterology

institute: IDIBAPS / Hospital Clinic

type: Genome variation profiling by genome tiling array

summary: A considerable proportion of tumors exhibit aneuploid karyotypes, likely resulting from the loss of chromosomes following whole genome duplication. Here, by using isogenic diploid and near-tetraploid clones derived from the same parental cell line, we aimed at exploring how polyploidization affects cellular functions and how tetraploidy generates chromosome instability. Gene expression profiling in near-tetraploid clones revealed a significant enrichment of genes involved in replication stress. This increased level of replication stress resulted in DNA damage, greater sensitivity to S-phase checkpoint inhibitors, and impaired proliferation caused by a cell cycle delay during S-phase. Additionally, replication stress promoted higher levels of intercellular heterogeneity and ongoing genomic instability, which we observed in the form of abnormal anaphases and prometaphase events. Finally, our data unveiled that near-tetraploid cells displayed increased migratory and invasive capacities, both in vitro and in primary colorectal tumors, thus providing physiological advantages to the cancer cell.

overall_design: Single-cell clones were generated from the parental colorectal cell line DLD-1 to produce isogenic diploid and tetraploid clones.

first: Darawalee

last: Wangsa

first: Isabel

last: Quintanilla

first: Keyvan

last: Torabi

first: Maria

last: Vila-Casadesús

first: Amaia

last: Ercilla

first: Greg

last: Klus

first: Zeynep

last: Yuce

first: Claudia

last: Galofré

first: Míriam

last: Cuatrecasas

first: Juan

last: Lozano

first: Neus

last: Agell

first: Antoni

last: Castells

first: Thomas

last: Ried


title: Near-tetraploid cells exhibit chromosome instability triggered by replication stress and enhanced invasive capabilities [expression]


title: MYC activation cooperates with Vhl and Ink4a/Arf loss to induce clear cell renal cell carcinoma

status: Public on Apr 12 2017

first: William

last: Kim

summary: We present three mouse models of kidney cancer that recapitulate the genomic alterations found in human papillary (pRCC) and clear cell RCC (ccRCC), the most common RCC subtypes.  MYC activation results in highly penetrant pRCC tumors (MYC), while MYC activation, when combined with Vhl and Cdkn2a (Ink4a/Arf) deletion (VIM), produce kidney tumors that approximate human ccRCC.

overall_design: Kidney tumor tissue and cell lines from three GEMM models (M,VM and VIM) and normal tissue.  Cells lines were assessed on/off dox.


title: Near-tetraploid cells exhibit chromosome instability triggered by replication stress and enhanced invasive capabilities

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

overall_design: Refer to individual Series


title: High-purity circular RNA isolation method (RPAD) reveals vast collection of intronic circRNAs (IcircRNAs)

status: Public on May 03 2017

first: Supriyo

last: De

summary: High-throughput RNA sequencing methods coupled with specialized bioinformatic analyses have recently uncovered tens of thousands of unique circular (circ)RNAs, but their complete sequences, genes of origin, and functions are largely unknown.  Given that circRNAs lack free ends and are thus relatively stable, their association with microRNAs (miRNAs) and RNA-binding proteins (RBPs) can influence gene expression programs.  While exoribonuclease treatment is widely used to degrade linear RNAs and enrich circRNAs in RNA samples, it does not efficiently eliminate linear RNAs.  Here, we describe a novel method for the isolation of highly pure circRNA populations involving RNase R treatment followed by Polyadenylation and poly(A)+ RNA Depletion (RPAD), which removes linear RNA to near completion.  High-throughput sequencing of RNA prepared using RPAD from human cervical carcinoma HeLa cells and mouse C2C12 myoblasts led to two surprising discoveries: (1) many circRNA isoforms share an identical backsplice sequence but have different body sizes and sequences, and (2) thousands of novel intronic circular RNAs (IcircRNAs) are expressed in cells, including many IcircRNAs that do not follow gt/ag splicing patterns.  In sum, isolating high-purity circRNAs using the RPAD method can enable quantitative and qualitative analyses of circRNA types and sequence composition, paving the way for the elucidation of circRNA functions.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: The method we report here, which we termed 'RPAD' begins with RNase R digestion, but then includes polyadenylation of any undigested linear RNA in the sample followed by the depletion of poly(A)+ RNA using oligo-dT beads.

first: Amaresh

last: Panda

first: Ioannis

last: Grammatikakis

first: Rachel

last: Munk

first: Yulan

last: Piao

first: Dawood

middle: B

last: Dudekula

first: Kotb

last: Abdelmohsen

first: Myriam

last: Gorospe


title: Small RNAs in stv-1 mutant

status: Public on Mar 06 2017

city: Lincoln

first: Chi

last: Zhang

state: NE

address: 1901 Vine Street

institute: University of Nebraska - Lincoln

summary: MiRNAs are key regulators of gene expression. They are processed from primary miRNA transcripts (pri-miRNAs), most of which are transcribed by DNA-dependent polymerase II (Pol II). MiRNA levels need to be precisely controlled to maintain various biological processes. In this manuscript, we report a discovery that STV1, a conserved ribosomal protein, acts in miRNA biogenesis in Arabidopsis. A portion of STV1 localizes at the nucleus and binds pri-miRNAs. Using pri-miR172b as a reporter, we show that STV1 binds the stem-loop with a short 5’ flanking sequencing within pri-miRNAs. Lack of STV1 in stv1-1 reduced the association of pri-miRNAs with their processing complex. These data suggest that STV1 promotes miRNA biogenesis through facilitating the recruitment of pri-miRNAs to their processing complex. Furthermore, we show that STV1 indirectly influence the occupancy of Pol II at the promoters of miRNA coding genes (MIR) and MIR promoter activities.  Based on these results, we propose that STV1 refines the accumulation of miRNAs through its combined effects on pri-miRNA processing and transcription. This study uncovers an extra-ribsomal function of STV1.

overall_design: non coding RNA deep sequencing

first: B

last: Yu

first: C


title: Aplysia Pleural Ganglia 24 Hours After Long-Term Sensitization Training

status: Public on Mar 03 2017

city: River Forest

first: Robert

middle: J

last: Calin-Jageman

state: IL

address: 7900 West Division

department: Psychology

institute: Dominican University

summary: We used a custom-designed microarray and qPCR to characterize the persistent transcriptional response to long-term sensitization training in the marine mollusk Aplysia californica.  Aplysia were exposed to a 1-day unilateral LTS training protocol (4 rounds of noxious shock at 30 min intervals, each shock 10s of 1/2s off 1/2on 90mA 60-hz biphasic square-wave shock).  Training produced robust sensitization in all animals (measured as an increase in T-SWR response from baseline to 24h after training).  Immediately after 24h post-tests, pleural ganglia was harvested.  Samples from a left-trained and right-trained animal were combined to smooth out lateralized gene expression.  The pleural ganglia contains the VC nociceptors, which are thought to play a primary role in expressing LTS memory.

overall_design: Within-subjects comparison.  Each array is a two-color approach hybridized to a matched trained and untrained set of samples (with each sample containing tissue from a left- and right-trained animal).  Conducted with 8 biological replicates, meaning 8 arrays, each comparing paired trained and untrained samples.

first: Irina


title: Epigenome-Wide Methylation Profile in Normal Human Kidney: Sex, Age, and Ethnic Differences

status: Public on Mar 10 2017

city: Jefferson

first: Stancy

last: Joseph

state: Ar

address: 3900 NCTR Road

department: Biochemical Toxicology

institute: FDA/NCTR

summary: Epienome-wide DNA methylation profiling of normal human kidney tissue samples. The Illumina HumanMethylation450K Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in normal human kidney samples. Samples included 15 male and 16 female normal human kidney samples tissue.

overall_design: Bisulphite converted DNA from the 31 samples were hybridized to the Illumina Infinium HumanMethylation450K Beadchip

first: Biridgett

last: Green-Knox

first: Nysia

last: George

first: Beverly

last: Lyn-Cook


title: Induced Pluripotent Stem Cell Differentiation Provides an Approach for Functional Validation of GWAS Variants in Metabolic Disease

status: Public on Apr 01 2017

city: Cambridge

first: Curtis

middle: Robert

last: Warren

state: Massachusetts

address: 7 Divinity Ave

department: Stem Cell And Regenerative Biology

institute: Harvard University

summary: Genome-wide association studies (GWAS) have highlighted a large number of genetic variants with potential disease association, but functional analysis and validation remains a challenge.  Here we describe an approach to functionally validate these variants through the differentiation of induced pluripotent stem cells (iPSCs) to study cellular pathophysiology.  We collected peripheral blood cells from Framingham Heart Study participants and reprogrammed them to iPSCs.  We then differentiated 68 iPSC lines into hepatocytes and adipocytes to investigate the effect of the 1p13 rs12740374 variant on cardiometabolic disease phenotypes via transcriptomics and metabolomic signatures. We observed a clear association between rs12740374 and lipid accumulation and gene expression changes in differentiated hepatocytes, in particular expression of SORT1, CELSR2 and PSRC1, consistent with previous analysis of this variant using other approaches.  Initial investigation of additional SNPs also highlighted correlations with gene expression.  Thus, iPSC-based population studies seem promising for further development as a tool for the functional validation of GWAS variants.

overall_design: 68 Induced Pluripotent Stem Cell Lines derived from 34 Participants Differentiated into white adipocytes and hepatocyte like cells

first: Chad

last: Cowan

first: Christopher

last: O'Donnell


title: TT-seq captures simultaneous activation of eRNAs and promoters during T cell activation

status: Public on Mar 01 2017

city: Göttingen

first: Carina

last: Demel

address: Am Fassberg 11

institute: Max-Planck Institute for biophysical Chemistry

summary: Jurkat T cells were activated with PMA and ionomycin. Total and Labeled fragmented RNA was extracted every 5 minutes during a time course up to 15min after activation. Biological duplicates of all samples were sequenced on a HiSeq 1500

first: Margaux

last: Michel

first: Benedikt

last: Zacher

first: Björn

last: Schwalb

first: Stefan

last: Krebs

first: Helmut

last: Blum

first: Julien

last: Gagneur

first: Patrick

last: Cramer


title: Gene expression analysis of Influenza vaccine response in Young and Old - Year 3 - PBMC

city: New Haven

first: Hailong

last: Meng

state: CT

address: 300 George Str

institute: Yale University

summary: We profiled gene expression of PBMC from a stratified cohort of subjects to define influenza vaccine response in Young and Old

overall_design: Differential gene expression by human PBMCs from Healthy Adults receiving Influenza Vaccination (Fluvirin, Novartis). Healthy adults (older >65, younger 21-30 years) were recruited at seasonal Influenza Vaccination clinics organized by Yale University Health Services during 2012 - 2013 seasons. With informed consent, healthy individuals were recruited as per a protocol approved by Human Investigations Committee of the Yale University School of Medicine. Each subject was evaluated by a screening questionnaire determining self-reported demographic information, height, weight, medications and comorbid conditions. Participants with acute illness two weeks prior to vaccination were excluded from study. Blood samples were collected into BD Vacutainer Sodium Heparin tube at four different time points, once prior to administration of vaccine and three time points after vaccination on days 4, 7 and 28. Peripheral Blood Mononuclear Cells (PBMC) were isolated from heparinized blood using Histopaque 1077 in gradient centrifugation. About 1.0x10^7 freshly isolated PBMC were lysed in Triso and immediately stored in -800C. Total RNA in aqueous phase of Trisol - Chloroform was isolated in an automated QiaCube instrument using miRNeasy according to manufacturer's instructions. Integrity of RNA samples were assessed by Agilent 2100 BioAnalyser Samples were processed for cRNA generation using Illumina TotalPrep cRNA Amplification Kit and subsequently hybridized to Human HT12-V4.0 BeadChip at Yale Center for Genomic Analysis (YGCA).

first: Albert

last: Shaw

first: Subhasis

last: Mohanty

first: Samit

middle: R

last: Joshi

first: Ikuyo

last: Ueda

first: Jean

last: Wilson

first: Juilee

last: Thakar

first: Steven

last: Kleinstein

first: Sui

last: Tsang


title: Metformin Induces Dicer via Regulation of the RNA-binding protein AUF1

status: Public on Feb 14 2017

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary:
Metformin has been commonly used for decades to treat type 2 diabetes. Recent data indicates that mice treated with metformin live longer and healthier lives. Here, we show that chronic metformin exposure in mice and diabetics taking metformin have higher levels of the microRNA processing protein, Dicer. Examination of how metformin affects Dicer expression revealed that metformin alters binding of the AUF1 RNA-binding protein to DICER1 mRNA, which leads to stabilization of DICER1 mRNA. We found differential changes in microRNA expression in mice treated with metformin or caloric restriction, a proven life extending intervention.  Several of these microRNAs are important for regulating cellular senescence and lifespan in model organisms. Consistent with this observation, treatment with metformin decreased cellular senescence in a Dicer-dependent manner. These data lead us to hypothesize that changes in Dicer levels may be important for organismal aging and that interventions that upregulate Dicer expression (e.g., metformin) may offer new therapeutic approaches to combat or prevent age-related diseases.
Key words:  diabetes mellitus, metformin, senescence, miRNA, RNA-binding proteins

overall_design: Groups of one-year old male B6C57/J mice were maintained on ad libitum AIN-93G SD diet, a 40% caloric restriction of the AIN-93G SD diet, or an ad libitum AIN-93G diet supplemented with 0.1% w/w metformin for the rest of their lives. Five mice from each of these 3 groups were selected and total RNA including miRNAs was isolated from the liver using the Absolutely RNA miRNA Kit (Agilent). Quality and quantity of the samples was checked with the Agilent 2100 bioanalyzer using RNA 6000 Nano chips.   The Agilent miRNA Complete Labeling and Hyb Kit was used to generate fluorescently-labeled miRNA. This method involves the ligation of one Cyanine 3-pCp molecule to the 3' end of the RNA molecules.   Arrays were hybridized to Agilent Mouse miRNA Microarray Release 15.0, 8x15K arrays using the entire labeled RNA product at 55 degrees C for at least 20 hours.  The arrays were washed, and the bound miRNA was scanned in the Agilent scanner at 5um resolution.  The data was extracted using Agilent's Feature Extractor Version 11.5.1.1, and this data was analyzed after z-score normalization. The natural log of all scores were used to find the avg and std of each array and the z-score normalization was calculated.  Z-score = (raw value - avg)/std

first: Nicole

last: Noren Hooten

first: Alejandro

last: Martin-Montalvo

first: Yongqing

last: Zhang

first: Douglas

middle: F

last: Dluzen

first: Michel

last: Bernier

first: Alan

last: Zonderman

first: Kevin

middle: G

last: Becker

first: Rafael

last: de Cabo

first: Michele

last: Evans