title: miRNA sequencing of primary mouse dorsal root ganglia

city: Santa Barbara

first: Kenneth

middle: S.

last: Kosik

address: UC Santa Barbara

department: NRI

institute: UCSB

summary: Peripheral nerve regeneration after injury is a complex process involving a large number of transcriptional changes. How these changes impact the regenerative outcome is though, poorly understood. Here, we take advantage of the genetically based differences in the peripheral and central regenerative capacity of CAST/Ei and C57BL/6j inbred mice to better understand the molecular bases driving superior regeneration in the CAST/Ei mouse strain.

overall_design: 14 samples were analyzed with 3 to 5 biological replicates per sample type

first: Véronique

last: Lisi

first: Bhagat

last: Singh

first: Michel

last: Giroux

first: Elmer

last: Guzman

first: Michio

middle: W

last: Painter

first: Yung-Chih

last: Cheng

first: Eric

last: Huebner

first: Giovanni

last: Coppola

first: Michael

last: Costigan

first: Clifford

last: Woolf


title: Human TFIIH kinase CDK7 regulates transcription-associated epigenetic modification

status: Public on Aug 01 2017

city: Aurora

first: David

middle: L.

last: Bentley

state: CO

department: Biochemistry and Mol. Genetics

country: USA

institute: U. Colorado School of Medicine

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

summary: CDK7 phosphorylates the RNA polymerase II (pol II) CTD and activates the P-TEFb- associated kinase, CDK9, but its regulatory roles remain obscure. Using human CDK7 analog-sensitive (CDK7as) cells, we observed reduced capping enzyme recruitment, increased pol II promoter-proximal pausing, and defective termination at gene 3'-ends upon CDK7 inhibition. We also found that CDK7 regulates chromatin modifications downstream of transcription start sites. H3K4me3 spreading was restricted at gene 5'-ends and H3K36me3 was displaced toward gene 3'-ends in CDK7as cells. Together, these results implicate a CDK7-dependent "CTD code" that regulates epigenetic marks in addition to RNA processing and pol II pausing.

overall_design: WT and analogue sensitive Cdk7as mutant cells were treated with the ATP analogue NM-PP1 that specifically inhibits the Cdk7as mutant kinase. Using ChIP-seq and RNA-seq we tested the effects of Cdk7 inactivation on pol II distribution along genes, CTD Ser2 and Ser5 phosphorylation, capping enzyme recruitment, histone H3K4 and H3K36 methylation and mRNA expression

first: Ben

last: Erickson


title: Viral infection identifies micropeptides differentially regulated in smORF-containing lncRNA

status: Public on Jul 31 2017

city: Berlin

first: Benedikt

last: Obermayer

address: Chariteplatz 1

department: Core Unit Bioinformatics

country: Germany

institute: Berlin Institute of Health

summary: We use genome-wide high-throughput methods to identify potential micropeptides in smORF containing lncRNA involved in the immune response. Using influenza as a viral infection model, we performed RNAseq and ribosome profiling to track expression and translation of putative lncRNAs that encode for peptides and identify tens of potential candidates.

sample_organism: Influenza A virus (A/reassortant/NIBRG-121(California/07/2009 x PR8)(H1N1))

overall_design: RNA-seq and ribosome profiling in A549 cells infected with H1N1 PR8 influenza, PR8dNS1 deletion strain, mock infection, or uninfected, in duplicates

first: Brandon

last: Razooky


title: KRAS-driven miR-29b Expression is Required for Tumor Suppressor Gene Silencing

city: Iowa

first: Charles

last: Brenner

address: Bowen Science Building, Newton Road

department: Biochemistry, Carver College of Medicine

institute: University of Iowa

summary: KRAS activation drives DNA methylation and silencing of specific tumor suppressor genes (TSGs). We previously showed that the ERK pathway induces transcriptional repression of TET1, which results in conversion of TSG promoters from a hydroxymethylated, active state to a hypermethylated and silenced state. Here we identified miR-29b as a KRAS-induced molecule that represses TET1 expression. In KRAS-transformed cells, ectopic miR-29b inhibition restores expression of TET1, thereby reactivating TSGs by reducing methylation and restoring hydroxymethylation. Mining gene expression data of lung cancer cell lines identified additional TSGs suppressed by KRAS signaling whose expression was restored by inhibition of miR-29b and re-expression of TET1. Because KRAS changes TSG promoters from hydroxymethylated to hypermethylated with miR-29b-dependent silencing of TET1, we demonstrate a model in which DNMT1 is present on target promoters prior to KRAS transformation. We also propose miR-29b as a potential circulating biomarker and target for rational treatment of specific malignancies.

overall_design: In order to identify TET1 targeting miRs that are induced by KRAS mutation in a MEK-dependent manner, microRNA profiling was performed on vector versus KRAS transformed HBEC3 cells and DMSO versus PD98059 treated H1299 cells

first: Shilpa

last: Thakur


title: Transcription profiles of WT and CreER-Raptor-flox/flox common myeloid progenitors (CMP), granulocyte-macrophage progenitor (GMP), or lineage negative (Lin-) stimulated with M-CSF for 12 hours

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

summary:
Myelopoiesis is impaired in Raptor-deleted mice (CreER-Rptor-flox/flox). To evaluate the transcriptional changes in myeloid precursors , we isolated CMP (Lin–Sca-1–c-Kit+CD34+FcγRII/IIImid), GMP (Lin–Sca-1–c-Kit+CD34+FcγRII/IIIhigh) and Lin (B220, Ly6C, Ly6G, CD3, Ter-119) negative cells (Lin–) from bone marrow of WT or CreER-Rptor-flox/flox mice. RNA was isolated from CMP and GMP immediately after sorting and Lin- cells were cultured for 12 hours with M-CSF (10 ng/mL) in 10% FBS and 1% P/S DMEM before RNA isolation.
We used microarrays to compare the global transcription profiles of CMP, GMP, or Lin– stimulated with M-CSF for 12 hours from WT and CreER-Raptor-flox/flox mice.

overall_design: We analyzed a total of 20 samples: CMP (6: 3 WT, 3 CreER-Rptor-flox/flox), GMP (6: 3 WT, 3 CreER-Rptor-flox/flox), Lin– + M-CSF (8: 4 WT, 4 CreER-Rptor-flox/flox)

first: Peer

last: Karmaus

first: Yogesh

last: Dhungana

first: Hongbo

last: Chi


title: Evidence for the importance of post-transcriptional regulatory changes in ovarian cancer progression and the contribution of miRNAs

city: Atlanta

first: Mengnan

last: Zhang

state: Georgia

address: 315 Ferst Drive

department: School of Biological Sciences

institute: Georgia Institute of Technology

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

summary:
High-throughput technologies have identified significant changes in patterns of mRNA expression over cancer development but the functional significance of these changes often resets upon the assumption that observed changes in levels of mRNA accurately reflect changes in levels of their encoded proteins.
We systematically compared the expression of genes on the RNA and protein levels between discrete tumor samples collected from the ovary and from the omentum of the same OC patient. The overall correlation between global changes in levels of mRNA and their encoding proteins is low. The majority of differences are on the protein level with no corresponding change on the mRNA level. Indirect and direct evidence indicates that a significant fraction of the differences may be mediated by microRNAs.

platform_organism:
Homo sapiens
synthetic construct

overall_design: Cancer tissues from the right ovary and omental sites were collected from a woman with stage IIIc, grade 2/3 serous adenocarcinoma. Each individual RNA sample was analyzed both for miRNA and mRNA. miRNA profiling analysis was conducted on the GeneChip miRNA 3.0 Array (Affymetrix). mRNA transcriptome analysis was analyzed using GeneChip Human Transcriptome Array 2.0 (Affymetrix). In total, six miRNA and mRNA (two individual samples in triplicate) global expression data sets were generated in this study.

first: Lilya

middle: V

last: Matyunina

first: Lila

middle: D

last: Walker

first: Weixuan

last: Chen

first: Haopeng

last: Xiao

first: Benedict

middle: B

last: Benigno

first: Ronghu

last: Wu

first: John

middle: F

last: McDonald


title: Retinoid X receptor activation alters the chromatin landscape ot commit mesenchymal stem cells to the adipose lineage

city: Irvine

first: Bassem

middle: Merit

last: Shoucri

state: CA

address: 4351 Natural Sciences 2

institute: University of California Irvine

summary:
We set out to study the effects of the endocrine disrupting chemical tributyltin (TBT) on early lineage commitment of primary bone marrow-derived mesenchymal stem cells (MSCs) from the long bones of C57BL/6 mice. We previously showed that prenatal exposure to nanomolar levels of TBT results in increased adiposity in mice. TBT is an agonist of two nuclear receptors, peroxisome proliferator-activated receptor gamma (PPARγ) and retinoid X receptor (RXR), master regulators of adipogenesis. To test if TBT could influence early MSC lineage commitment we treated these cells with 50 nM TBT, 100 nM Rosiglitazone (ROSI, a pure PPARγ agonist), 100 nM AGN194204 (4204, a pure RXR agonist), and vehicle control (0.1% DMSO) for 48 hours prior to differentiation with a standard adipogenic cocktail. This experiment revealed an RXR-dependent commitment to the adipose lineage.
To better understand how TBT induces adipose commimtment, we sequenced RNA from MSCs treated with DMSO (0.1%), ROSI (100 nM), 4204 (100 nM), and TBT (50 nM) for 48 hrs, prior to any differentiation. Unbiased hierarchical clustering analysis showed a clear separation between DMSO and ROSI replicates from 4204 and TBT, strengthening our conclusion that the observed phentype is RXR-dependent. Pathway analysis of differentially expressed genes revealed that TBT and 4204 de-repress targets of the repressive histone modifier Enhancer of zeste 2 (EZH2), the catalytic member of the Polycomb repressive complex 2 (PRC2), which deposits H3K27me3 on histones. We there for preformed ChIP-Seq analysis on MSCs treated with DMSO (0.1%) or TBT (50 nM) for 48 hrs, hypothesizing that TBT would reduce H3K27me3 in proximity to genes that regulate adipose lineage commitment.

overall_design:
We generated RNA-Seq data in undifferentiated MSCs treated with DMSO (0.1%), ROSI (100 nM), 4204 (100 nM), or TBT (50 nM) for 48 hrs. N=6 per treatment.
We also generated H3K4me3 and H3K27me3 ChIP-Seq data in MSCs treated with DMSO (0.1%) or TBT (50 nM). N=4 per treatment, per histone mark, and N=1 input per treatment.

middle: M

first: Toshi

last: Shioda

first: Bruce

last: Blumberg


title: Human virus-derived small RNAs can confer antiviral immunity in mammals

city: Wuhan

first: xi

last: zhou

state: Hubei

address: Luojia Hill

department: State Key Laboratory of Virology, College of Life Sciences

country: China

institute: Wuhan University

type: Non-coding RNA profiling by high throughput sequencing

summary: RNA interference (RNAi) functions as a potent antiviral immunity in plants and invertebrates, however whether RNAi plays antiviral roles in mammals remains unclear. Here, using human enterovirus 71 (HEV71) as a model, we showed HEV71 3A protein as an authentic viral suppressor of RNAi during viral infection. When the 3A-mediated RNAi suppression was impaired, the mutant HEV71 readily triggered the production of abundant HEV71-derived small RNAs with canonical siRNA properties in cells and mice. These virus-derived siRNAs were produced from viral dsRNA replicative intermediates in a Dicer-dependent manner, loaded into AGO, and were fully active in degrading cognate viral RNAs. Recombinant HEV71 deficient in 3A-mediated RNAi suppression was significantly restricted in human somatic cells and mice, whereas Dicer-deficiency rescued HEV71 infection independently of type I interferon response. Thus, RNAi can function as an antiviral immunity, which is induced and suppressed by a human virus, in mammals.

overall_design: Small RNA profile of virus infected HEK 293T cells

first: Yang

last: Qiu

first: Yanpeng

last: Xu

first: Yao

first: Hui

last: Zhou

first: Yong-Qiang

last: Deng

first: Xiao-Feng

last: Li

first: Meng

last: Miao

first: Qiang

first: Bo

last: Zhong

first: Yuanyang

last: Hu

first: Fu-Chun

first: Ligang

first: Cheng-Feng

last: Qin

first: Xi


title: SMAD4 impedes conversion of NK cells into ILC1-like cells by curtailing non-canonical TGFb signaling (mouse data sets)

city: San Francisco

first: Victor

middle: S

last: Cortez

address: 513 Parnassus Avenue

department: Medicine

institute: University of California, San Francisco

summary:
Among the features that distinguish type 1 innate lymphoid cells (ILC1s) from NK cells is a gene signature indicative of TGFb-family cytokine imprinting. To assess the impact of TGFb family cytokines on ILC1 differentation, we examined SMAD4- a transcription factor that facilitates the signaling pathway common to all TGFb family cytokines-was specifically ablated in ILCs and NK cells. While SMAD4 deficiency did not affect ILC1 differentation, NK cells paradoxically aquired an ILC1-like gene signature and were incapable of controlling tumor metastasis and viral infection.
We used microarray to  define the transcriptional differences between splenic NK cells from WT and SMAD4F/F x Ncr1-Cre mice.

overall_design: Splenic NK cells (NK1.1+CD49b+CD3-CD19-) were sorted to purity for RNA extraction and hybridization on Affymetrix microarrays.

first: V

first: M

last: Cella

last: Colonna


title: Molecular analysis of high-grade serous ovarian carcinoma with and without associated serous tubal intra-epithelial carcinoma [RNA-Seq]

city: Baltimore

first: leslie

last: cope

state: MD

address: 550 N. Broadway

institute: leslie cope

summary: Many high-grade serous carcinomas (HGSCs) of the pelvis are thought to originate in the distal portion of the fallopian tube.  Serous tubal intraepithelial carcinoma (STIC) lesions are the putative precursor to HGSC and identifiable in ~50% of advanced stage cases. To better understand the molecular etiology of HGSCs, we report a multi-center integrated genomic analysis of advanced stage tumors with and without STIC lesions and normal tissues. The most significant focal DNA SCNAs were shared between cases with and without STIC lesions. RNA sequence and miRNA data did not identify any clear separation between cases with and without STIC lesions.  HGSCs had molecular profiles more similar to normal fallopian tube epithelium than ovarian surface epithelium or peritoneum. The data suggest that the molecular features of HGSCs with and without associated STIC lesions are mostly shared, indicating a common biologic origin, likely to be the distal fallopian tube among all cases.

overall_design: In this study, 96 previously untreated high-grade serous carcinoma samples were selected to have half with STIC lesions and half without.  Molecular assays were performed that included RNAseq, microRNA expression, and copy number variation.

first: Douglas

last: Levine

first: Leslie

last: Cope


title: SMAD4 impedes conversion of NK cells into ILC1-like cells by curtailing non-canonical TGFb signaling

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Enhanced neuronal regeneration in the CAST/Ei mouse strain is linked to expression of differentiation markers after injury

first: Kenneth

last: Kosik

state: California


title: ARS2 is a general suppressor of pervasive transcription

city: Macclesfield

first: Muhammad

middle: Ahmad

last: Maqbool

address: Alderley Park

department: Cancer Research UK Manchester Institut

country: United Kingdom

institute: University of Manchester

summary: Termination of transcription is important for establishing gene punctuation marks. It is also critical for suppressing many of the pervasive transcription events occurring throughout eukaryotic genomes and coupling their RNA products to efficient decay. In human cells, the ARS2 protein has been implicated in such function as its depletion causes transcriptional read-through of selected gene terminators and because it physically interacts with the ribonucleolytic nuclear RNA exosome. Here, we study the role of ARS2 on transcription and RNA metabolism genome-wide. We show that ARS2 depletion negatively impacts levels of promoter-proximal RNA polymerase II (RNAPII) at protein-coding (pc) genes, Moreover, our results reveal a general role of ARS2 in transcription termination-coupled RNA turnover at short transcription units like snRNA-, replication dependent histone (RDH)-, promoter upstream transcript (PROMPT)- and enhancer RNA (eRNA)-loci. Depletion of the ARS2 interaction partner ZC3H18 mimics the ARS2 depletion, although to a milder extent, whereas depletion of the exosome core subunit RRP40 selectively impacts RNA abundance post-transcriptionally. Interestingly, ARS2 is also involved in transcription termination events within first introns of pc genes. Our work therefore establishes ARS2 as a general suppressor of pervasive transcription with the potential to regulate protein-coding gene expression.

overall_design: This study was performed in a human Hela cell line. It contains ChIP-seq data for RNA Pol II. All sequencing was performed in paired-end sequencing runs.

first: Claudia

last: Iasillo

first: Manfred

last: Schmid

first: Yousra

last: Yahia

middle: A

first: Nicolas

last: Descostes

first: Edouard

last: Bertrand

first: Jean-Christophe

last: Andrau

first: Torben

middle: H

last: Jensen


title: Enhancer reprogramming promotes pancreatic cancer progression and metastasis [RNA-seq]

city: Seoul

first: Jae Seok

last: Roe

address: Yonsei-ro, 50

country: South Korea

institute: Yonsei University

summary: Pancreatic ductal adenocarcinoma (PDA) is one of the most lethal human malignancies, owing in part to its propensity for metastasis. Here, we used an organoid culture system to investigate how transcription and the enhancer landscape become altered during each stage of PDA progression. This approach revealed that the metastatic transition is accompanied by massive, and recurrent alterations in enhancer activity. We implicate the transcription factors FOXA1 and GATA5 as drivers of enhancer activation in this system, a mechanism that we show renders PDA cells more invasive and less anchorage-dependent for growth in vitro, as well as more metastatic in vivo. FOXA1 and GATA5 were found to activate a foregut endoderm transcriptional program in PDA cells, without altering genes associated with the epithelial-to- mesenchymal transition. Collectively, our study implicates FOXA1/GATA5 upregulation, enhancer reprogramming, and a novel retrograde developmental transition in PDA progression and metastasis.

overall_design: RNA-Seq of mouse and/or human PDA organoids and/or cell lines

first: Jae-Seok

first: Christopher

middle: R

last: Vakoc


title: Enhancer reprogramming promotes pancreatic cancer progression and metastasis [ATAC-seq]

overall_design: ATAC-Seq of mouse PDA organoids


title: ARS2 is a general suppressor of pervasive transcription [RNAseq]

city: Aarhus

first: Evdoxia

last: Karadoulama

address: C.F. Møllers Alle 3

department: Molecular Biology and Genetics

country: Denmark

institute: Aarhus University

summary: Termination of transcription is important for establishing gene punctuation marks. It is also critical for suppressing many of the pervasive transcription events occurring throughout eukaryotic genomes and coupling their RNA products to efficient decay. In human cells, the ARS2 protein has been implicated in such function as its depletion causes transcriptional read-through of selected gene terminators and because it physically interacts with the ribonucleolytic nuclear RNA exosome. Here, we study the role of ARS2 on transcription and RNA metabolism genome-wide. We show that ARS2 depletion negatively impacts levels of promoter-proximal RNA polymerase II (RNAPII) at protein-coding (pc) genes, Moreover, our results reveal a general role of ARS2 in transcription termination-coupled RNA turnover at short transcription units like snRNA-, replication dependent histone (RDH)-, promoter upstream transcript (PROMPT)- and enhancer RNA (eRNA)-loci. Depletion of the ARS2 interaction partner ZC3H18 mimics the ARS2 depletion, although to a milder extent, whereas depletion of the exosome core subunit RRP40 only impacts RNA abundance post-transcriptionally. Interestingly, ARS2 is also involved in transcription termination events within first introns of pc genes. Our work therefore establishes ARS2 as a general suppressor of pervasive transcription with the potential to regulate protein-coding gene expression.

overall_design: RNA from HeLa cells was analysed by next generation sequencing upon depletion of EGFP(control), ARS2(SRRT), ZC3H18 and CBP80. Total RNA was collected for each condition in triplicates.


title: Maturation of Human iPSC-derived Astrocytes in 3D Cortical Spheroids

first: Steven

last: Sloan

state: GA

address: 615 Michael Street, Whitehead Building Room 375

department: Human Genetics

institute: Emory University

summary:
Single-cell RNA-seq: We used single-cell RNAseq to investigate the maturation of astrocytes within human cortical spheroids

Bulk RNA-seq: Bulk sequencing from astrocytes and neurons purified (via immunopanning) from iPSC-derived coritical spheroids at varying in vitro differentiation states

overall_design:
Single-cell RNA-seq: Examination of neurons and glia from dissociated hCS at varying in vitro differentiation stages

Bulk RNA-seq: Transcriptomic profiling of iPSC-derived human astrocytes and neurons from 3D cultures

first: Spyros

last: Darmanis

first: Sergiu

last: Pasca

first: Ben

last: Barres


title: KMT1A (SUV39H1) prevents somatic cell nuclear transfer (SCNT) mediated reprogramming

city: Yangling

first: Jingcheng

last: Zhang

address: Taicheng Road NO.3

institute: Northwest A&F University

summary: KMT1A (also known as SUV39H1)was involved in improving reprogramming efficiency during inducing pluripotent stem cells (iPSC). However, the knowledge about KMT1A regulating somatic cell nuclear transfer (SCNT) mediated reprogramming was limited. To understand the role of KMT1A during SCNT embryos in vitro development; we performed based transcriptome profiling in SCNT embryos at 8-cell stages and KMT1A knockdown 8-cell SCNT embryos. The data show the mRNAs regulated after KMT1A was down-regulated.

overall_design: Here we perform transcriptome profiling in SCNT embryos at 8-cell stages and KMT1A knockdown 8-cell SCNT embryos with duplicates.

first: Yong

first: Xin

last: Liu

first: Pengxiang

last: Qu

first: Chuan

last: Zhou

first: Xiaonan

last: Ma


title: Enhancer reprogramming promotes pancreatic cancer progression and metastasis


title: Expression data in HCT-116 colon cancer cell treated with SCD1 inhibitor or in SCD1 knocked out HCT-116 cell

city: Fujisawa

first: Akito

last: Ono

address: Muraoka-higashi 2-26-1

country: Japan

institute: Takeda Pharmaceutical company

summary: To understand molecular mechanisms underlying the growth inhibitory ativity of Stearoyl-CoA desaturase-1 (SCD1) inhibitor, we performed microarray analysis using HCT-116 colorectal cancer cells, in which SCD1 was pharmacologically blocked or genetically ablated.

overall_design: HCT-116 cells treated with DMSO or SCD1 inhibitor, and SCD1 knocked-out cells were harvested for RNA extraction and hybridization on Affymetrix microarray (n = 1 each). The DMSO-treated sample was used as a control.

first: Ken-ichi

last: Kazetani

first: Hidehisa

last: Iwata


title: Enhancer reprogramming promotes pancreatic cancer progression and metastasis [ChIP-seq]

first: Jae Seok

overall_design: H3K27ac, H3K4me1, Foxa1 ChIP-Seq of mouse and/or human PDA organoids and/or cell lines


title: Trypanosoma cruzi mini-exon based mRNA amplification technique

city: Curitiba

first: Christian

middle: Macagnan

last: Probst

state: PR

address: Rua Professor Algacyr Munhoz Mader, 3775

country: Brazil

institute: Instituto Carlos Chagas

summary: We have developed a method of mRNA amplification based on T7 polymerase, where T7 promoter is attached to a oligonucleotide containing the mini-exon sequence, which will hybridize with cDNA molecules containing the anti-ME sequence

sample_organism:
Trypanosoma cruzi
Homo sapiens

platform_organism:
Trypanosoma cruzi
Homo sapiens

overall_design: The method was tested on two different stages of T. cruzi (epimastigotes, Epi and cell-derived trypomastigotes, Trp) and for each one we have two biological replicates (A and B). Each mRNA sample was processed in three distinct ways: poly-A purification (polA), oligo-dT T7 (dT) amplification and oligo-ME T7 (ME) amplification. For the other analyzes, one biological replicate of epimastigotes (EpiA) was selected and processed for the following series of experiments:  mRNA quantity (100ng, 50ng, 25ng, 12.5ng, 6.25ng and 3.125ng); mixed sample with human mRNA (mRNA from HeLa cells, in the following masses (T. cruzi / Human): 100ng/0ng (100%), 100ng/900ng (10%), 10ng/990ng (1%), 5ng/4995ng (0.1%), 10ng/9990ng (0.1%). For the majority of the mixed sample series, Pfx was used as enzyme for 2nd strand synthesis. EpiB was used for mRNA extraction after cell sorting. All samples were processed in two technical replicates (1 and 2). For the cell sorting, there is three technical replicates. There is no technical replicates for the Poly-A samples

first: Rafael

middle: L

last: Kessler


title: PHF6 regulates B-cell identity in acute lymphoblastic leukemia [ATAC-Seq]

city: Cambridge

first: Michael

last: Hemann

state: Massachusetts

address: 500 Main St, Building 76 Room 301

department: Koch Institute

institute: Massachusetts Institute of Technology

summary: Inactivating mutations in the zinc finger gene PHF6 are seen in approximately 40% of adult T-cell acute lymphoblastic leukemias (T-ALLs) and 3% of adult acute myeloid leukemias (AMLs). The absence of PHF6 mutations in B-cell lineage malignancies has led to the hypothesis that PHF6 may act as a lineage-specific tumor suppressor gene. Here, we demonstrate that PHF6 plays a critical role in regulating B-cell identity in the context of B-cell precursor acute lymphoblastic leukemia (preB-ALL). Transplantation of Phf6 knockout preB-ALL cells (hereafter referred to as Phf6KO cells) into immunocompetent syngeneic recipients resulted in the development of a fully penetrant lymphoma-like disease. Strikingly, the resulting lymphomas showed robust up-regulation of the canonical T-cell marker CD4, suggesting that Phf6KO cells adopt a T-cell program in the context of leukemogenesis. RNA sequencing analysis revealed numerous differentially expressed (DE) genes in Phf6WT and Phf6KO cells, including a significant down-regulation of genes and gene sets involved in pathways important for B-cell development. Chromatin immunoprecipitation followed by high-throughput sequencing analysis revealed that PHF6 co-localizes with H3K27ac signals close to the transcription start sites (TSSs) and enhancer regions of a significant proportion of DE genes. Notably, regions flanking the TSS of DE genes showed significant enrichment for binding sites of several well-described master regulators of B-cell development, including PU.1, EGR-1, EBF-1, NF-kB, TCF3 and TCF12. We found that PHF6 and TCF12 physically interact in preB-ALL cells, suggesting that these factors act synergistically in the establishment and maintenance of B-cell identity. In addition, we found that a human PHF6 mutant T-ALL cell line has an incompletely rearranged IGH locus, strongly suggesting that T-ALL can have a B-cell origin. These findings reveal an essential role for PHF6 in the establishment and maintenance of B-cell identity in preB-ALL by directly activating genes that are crucial for B-cell lineage commitment and maintenance. Collectively, these results indicate that loss of function of PHF6 in preB-ALL leads to an unstable cellular state in which cells acquire alternate developmental programs (such as the T-lineage program) to survive, potentially explaining the apparent absence of PHF6 mutations in human B cell-lineage malignancies.

overall_design: ATAC-seq is performed on 2 and 3 biological replicates of PHF6 wildtype and knockout cells respectively

first: Yadira

last: Soto-Feliciano

middle: T


title: Genetic Background-Dependent Role of Egr1 for Eyelid Development

status: Public on Jul 30 2017

city: Bethesda

first: Peng

last: Li

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

summary: EGR1 is an early growth response zinc finger transcription factor with broad actions, including in differentiation, mitogenesis, tumor suppression, and neuronal plasticity. Here we demonstrate that Egr1-/- C57BL/6-background mice have normal eyelid development, but back-crossing to BALB/c background for 4-5 generations resulted in defective eyelid development by embryonic day E15.5, at which time EGR1 was expressed in eyelids of WT mice. Defective eyelid formation correlated with profound ocular anomalies evident by post-natal days 1-4, including severe cryptophthalmos, microphthalmia or anophthalmia, retinal dysplasia, keratitis, corneal neovascularization, cataracts, and calcification. The BALB/c albino phenotype-associated Tyrc tyrosinase mutation appeared to contribute to the phenotype, as crossing the independent Tyrc-2J allele to Egr1-/- C57BL/6 mice also produced ocular abnormalities, albeit less severe than those in Egr1-/- BALB/c mice. Thus, EGR1 in a genetic background-dependent manner plays a critical role in mammalian eyelid development and closure, with subsequent impact on ocular integrity.

overall_design: RNA-Seq analyses using total RNA from eyes of newborn and adult Egr1-/- BALB/c mice, and total RNA from each eye of three 3-day old Egr1-/- mice with unmerged eyelids as well as Egr1+/- littermate controls

first: Jangsuk

last: Oh

first: Yujuan

last: Wang

first: Shida

last: Chen

first: Ning

last: Du

first: Zu-Xi

last: Yu

first: Donna

last: Butcher

first: Tesfay

last: Gebregiorgis

first: Erin

last: Strachan

first: Ordan

last: Lehmann

first: Brian

middle: P

last: Brooks

first: Chi-Chao

last: Chan

first: Warren

middle: J

last: Leonard


title: Rps26 directs mRNA-specific translation by recognition of Kozak sequence elements

city: Jupiter

first: Katrin

last: Karbstein

state: FL

address: 130 Scripps Way, Mail Code 2C2

institute: The Scripps Research Institute

summary: The “Kozak sequence”, immediately upstream of the start codon, regulates the translational efficiency of an mRNA. Nevertheless, how this sequence is recognized remains unexplored. Here, we describe a novel approach to separate two ribosome populations from the same cells and use this method, and RNA-seq, to identify the mRNAs bound to ribosomes with and without Rps26, a protein linked to the pathogenesis of Diamond Blackfan Anemia (DBA). These analyses reveal that Rps26 contributes to recognition of the Kozak sequence in well-translated mRNAs, and that Rps26-deficient ribosomes preferentially translate mRNA from select stress response pathways. Surprisingly, we demonstrate that exposure of cells to these stresses leads to the formation of Rps26-deficient ribosomes and to the translation of their targets. Thus, Rps26-deficient ribosomes play aberrant pathogenic roles in DBA as well as physiological roles in augmenting the well-characterized stress transcriptional response with a heretofore unknown translational stress response, thereby creating a feed forward loop in gene-expression.

overall_design: Comparison of the mRNA bound to two classes of ribosomes in three biological replicates.

first: Max

last: Ferretti

first: Homa

last: Ghalei

first: Ethan

last: Ward

first: Elizabeth

last: Potts


title: Expression profile from mouse lung treated with B[a]P and LPS

status: Public on Jul 29 2017

city: Maastricht

first: Quan

last: Shi

state: Limburg

address: Universiteitssingel 50

department: Pharmacology and Toxicology

country: Netherlands

institute: Maastricht University

summary:
Patients with inflammatory lung diseases are often additionally exposed to polycyclic aromatic hydrocarbons like B[a]P and B[a]P-induced alterations in gene expression in these patients may contribute to the development of lung cancer. Mice were intra-nasally treated with lipopolysaccharide (LPS, 20 μg/mouse) to induce pulmonary inflammation and subsequently exposed to B[a]P (0.5 mg/mouse) by intratracheal instillation
We used RNA microarrays to detail the global gene expression change after each treatment. Meanwhile, compared the up- and down-regulated gene between the LPS&BaP and BaP in order to identify the role of inflammation on BaP induced carcinogenesis

overall_design: 15 mouse lung were analyzed, including 3 control, 4 LPS, 4 BaP and 4 LPS&BaP. All lung samples were collected after 72 hours and RNA were extracted and hybridized on Affymetrix RNA microarrays.

first: Rianne

last: Fijten

first: Domenico

last: Spina

first: Yanira

last: Riffo-Vasquez

first: Volker

last: Arlt

first: Roger

middle: W

last: Godschalk

first: Frederik-Jan

last: Van Schooten


title: Omics-based identification of the combined effects of idiosyncratic drugs and inflammatory cytokines on the development of drug-induced liver injury

first: Jian

last: Jiang

address: Maastricht University

department: Toxicogenomics

summary: To unravel the underlying mechanisms of inflammation-related idiosyncratic drug toxicity

overall_design: HepG2 cells were exposed to 3 idiosyncratic and 3 non-idiosyncratic compounds with or without the cytokine mix (TNF 100 ng/ml + IFNγ 100 ng/ml + IL-1α 20 ng/ml + IL-6 20 ng/ml + LPS 10 µg/ml)as described previously (Cosgrove et al., 2009) for 6, 12 or 24 h.

first: Karen

last: Mathijs

first: Leen

last: Timmermans

first: Sandra

last: Claessen

first: Audrey

last: Hecka

first: Jos

last: Weusten

first: Ron

last: Peters

first: Joost

last: van Delft

middle: C

last: Kleinjans

first: Danyel

middle: G

last: Jennen

first: Theo

last: de Kok


title: SMAD4 impedes conversion of NK cells into ILC1-like cells by curtailing non-canonical TGFb signaling (human data sets)

first: Victor

last: Cortez

summary:
Among the features that distinguish type 1 innate lymphoid cells (ILC1s) from NK cells is a gene signature indicative of TGFb-family cytokine imprinting. To assess the impact of TGFb family cytokines on ILC1 differentation, we examined SMAD4- a transcription factor that facilitates the signaling pathway common to all TGFb family cytokines-was specifically ablated in ILCs and NK cells. While SMAD4 deficiency did not affect ILC1 differentation, NK cells paradoxically aquired an ILC1-like gene signature and were incapable of controlling tumor metastasis and viral infection.
We used microarray to compare the transcriptional differences between human blood NK cells. NK cells from a patient with a deleterious SMAD4 mutation or control NK cells were cultured overnight with either IL-2 alone or TGFb1 and IL-2.

overall_design: Sort purified blood NK cells (CD56+CD3-CD19-) from a patient with a deleterious SMAD4 mutation or a healthy control patient were expanded in cultured. Cells were then cultured overnight with either IL-2 alone or TGFb1 and IL-2.

first: V

first: M

last: Cella

last: Colonna


title: Expression data from rat endosalpinx at 3 hours after mating

city: Antofagasta

first: Lidia

middle: M.

last: Zuniga

state: Antofagasta

address: Av. Universidad de Antofagasta 02800

department: Instituto Antofagasta

country: Chile

institute: Universidad de Antofagasta

summary:
In the mammalian oviduct, mating regulates sperm storage, egg transport, fertilization, early embryonic development and estradiol metabolism. However, the main molecules responsible for these processes are poorly understood.
Herein, we used Affymetrix microarrays to conduct a transcriptomic analysis of the endosalpinx at 3 h after mating and used Qiagen´s Ingenuity Pathway Analysis to perform network modeling to identify the main mating-activated cellular processes in the endosalpinx and the possible upstream regulators of the mating-induced transcriptional response.

overall_design:
Females in pro-estrus were kept isolated (unmated rats) or were caged with fertile males at 2200 h of pro-estrus. Thirty minutes after caging with males, the presence of spermatozoa in the vaginal smear or a vaginal plug was verified. Females with spermatozoa or a vaginal plug were designated mated rats and remained caged with the males until 0130 h of estrus, 3 h after mating.
Under our environmental and experimental conditions, at 3 h after mating, sperm would have arrived in the oviduct, and ovulation would have occurred approximately 5 h later. Unmated and mated rats were sacrificed at 0130 h of estrus or 3 h after mating. Then, the endosalpinx was isolated from the oviducts and stored in TRIZOL reagent until processing.
We used six chips to hybridize six individual samples; 3 of them were samples from unmated rats, and 3 were samples from mated rats (N = 3 per group). We follow the manufacturer’s instructions.

last: Zúñiga

first: Horacio

middle: B

last: Croxatto

first: Rodrigo

last: Gutiérrez


title: SERPINA3- a novel keratinocyte differentiation promotor mediates epidermal barrier repair response in psoriatic lesion

city: Canton

first: Leqing

last: Zhu

state: Guangdong Province

address: East of Huangpu street 601

department: Biology

institute: Jinan University

summary: To excavate the genes regulated by SERPINA3, We profiled SERPINA3 silenced differentiated KC versus control using a RNA-seq approach. The genes down regulated in SERPINA3 silenced cells represent targets that are positively regulated by SERPINA3.

overall_design: mRNA profiles of differentiated keratinocytes which are SERPINA3-silenced by 3 different siRNA and Scramble siRNA transfected differentiated keratinocytes were generated by deep sequencing.


title: Deletion of 11q in neuroblastomas drives sensitivity to PARP inhibition

status: Public on Jul 28 2017

city: Valencia

first: Jaime

last: Font de Mora

address: Avenida Fernando Abril Martorell, 106; Torre A,  5-07

country: Spain

institute: Instituto de Investigación Sanitaria La Fe

type: Genome variation profiling by high throughput sequencing

overall_design: Refer to individual Series


title: Deletion of 11q in neuroblastomas drives sensitivity to PARP inhibition [SEQ]

summary: SNP arrays were combined with next generation sequencing (NGS) to precisely define the deleted region in 17 primary 11q-loss neuroblastomas and identify allelic variants in genes relevant for neuroblastoma aetiology. We assessed PARP inhibitor olaparib in combination with other chemotherapy medications using both in vitro and in vivo models.

overall_design: Next generation sequencing of genes relevant for neuroblastoma aetiology and cancer

first: Elena

last: Sanmartín


title: HDACi Delivery Reprograms Tumor-infiltrating Myeloid Cells to Eliminate Antigen-loss Variants

city: Hamilton

first: Yonghong

last: Wan

state: ON

address: 1280 Main St W

country: Canada

institute: McMaster University

summary: Immune recognition of tumor-expressed antigens by cytotoxic CD8+ T lymphocytes is the foundation of adoptive T-cell therapy. However, therapy-induced selective pressure can sculpt the antigenicity of tumors resulting in the outgrowth of variants that have lost the target antigen. Interestingly, tumor relapse resulting from adoptive memory T cell transfer and boosting oncolytic viral vaccination can be prevented using Class I histone deacetylase inhibitor, MS-275. We demonstrate that concomitant drug delivery subverts the phenotype and suppressive function of tumor-infiltrating myeloid cells and reprograms them with the cytotoxic capacity to directly eliminate antigen-negative tumor cells. By enhancing the production of IFNγ within the tumor microenvironment, our data suggest that MS-275 modifies the local cytokine landscape in favor of antitumor myeloid cell polarization.

overall_design: Total RNA (n=4 per group) obtained from tumors subjected to gp33-specific Tm + VSV-gp33 +/- MS-275 compared to untreated control tumors.

first: Andrew

last: Nguyen

first: Louisa

last: Ho


title: Comparisonof  kPSCs versus cMSC

city: Leiden

first: Danielle

last: Leuning

address: Albinusdreef 2

department: Nephrology

institute: LUMC

summary:
expression profiles kPSCs versus cMSC
Here we compare human kidney derived perivascular stromal cells  (hkPSCs) with kidney capsule derived MSCs (cMSC)

overall_design: hkPSCs were isolated from human kidneys based on plastic adherence and NG2 expression. cMSCs were isolated from the kidney capsule by outgrowth culture

first: D

first: T

last: Rabelink


title: DNA bisulfite sequencing of Invader 4 LTRs in Drosophila

city: Vienna

first: Schaefer

last: Matthias

state: AT

address: Schwarzspanierstrasse 17-I

department: Cell and Developmental Biology

country: Austria

institute: Medical University Vienna, Center for Anatomy & Cell Biology

type: Methylation profiling by high throughput sequencing

summary: It has been claimed previously that loss of (cytosine-5) DNA methylation in Dnmt2 mutant embryos affected the establishment of silent chromatin at Invader4 LTRs (Phalke et al., 2009). The inability of Dnmt2 mutants to control TE expression after heat shock (GSE40432) raised the possibility that DNA methylation could be required for control of Invader 4 during the heat shock response. We used DNA bisulfite sequencing at Inv4 LTRs that were previously suggested to be methylated (Phalke et al., 2009).

overall_design: 8 samples examined: genomic DNA from wild type controls and Dnmt2 mutant adult flies under standard, heat shock and recovery conditions

first: Zeljko

last: Durdevic

first: Matthias

last: Schaefer


title: Immunomodulatory Effects of Yeast Cell Wall Compounds on mouse BMDM

city: TOULOUSE

first: Gilles

last: Foucras

state: Haute Garonne

address: 23 chemin des capelles

department: JRU1225 IHAP

country: France

institute: ENVT-INRA

summary:
Since few years, yeast cell wall components and especially beta-glucans (BG) have been identified as potential stimulators of the innate immune system in murine and human species. A large screening of crude and BG-enriched components from Saccharomyces cerevisiae has been performed on murine macrophages. A priming effect with bacterial ligands was revealed in terms of pro-inflammatory cytokines release. To further characterize the responsiveness of bone marrow derived-macrophages which express high levels of dectin-1, the major receptor of BG, transcriptional analysis would provide more hypotheses about the genes and signaling pathways triggered by yeast cell wall compounds in macrophages.
Gene expression profiling was performed in murine BMDM pretreated with a set of three BG-containing cell wall compounds and then stimulated with LPS. Conditions with BG-enriched pretreatment clustered together in contrast to the crude compound and mock pretreatment conditions that remained separated whatever the time point analyzed, with a greater number of differentially-expressed genes following the crude compound treatment compared to BG-enriched pretreatment. BG-enriched pretreatment induced a specific set of genes in mouse macrophages, involving the PI3K/AKT signaling pathway. Among them, the two main upregulated genes by BG-enriched priming condition were considered for further analysis and their associated-protein production were consistently increased in BMDM pretreated with BG-enriched compound. Microarray results were confirmed using RT-qPCR on a different set of samples.

overall_design: Gene expression was measured in murine BMDM pretreated with ScCW (A), BG65 (C) and BG75 (D), or mock controls for 8 h, and further stimulated with LPS for 4 and 8 h. Four independent experiments were performed at each time using 4 individuals for each experiment.

first: Sarah

last: Walachowski

first: Claire

last: Naylies

first: Yannick

last: Lippi


title: ChIP-seq for GABPα in T cells

city: Pittsburgh

first: Hatice

middle: Ulku

last: Osmanbeyoglu

state: PA

address: 5117 Centre Ave

institute: University of Pittsburgh

summary: Ets family transcription factor GA-binding protein (GABP) regulates gene expression in T cells.

overall_design: GABPα binding sites in CD4 T cells from wild-type C57BL/6 mice were determined by chromatin immunoprecipitation coupled to high-throughput sequencing (ChIP-seq) experiments.

middle: U

first: Chong

last: Luo


title: GABP-dependent gene regulation in T cells

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


title: Gene expression in GABPα-sufficient and -deficient T cells

summary:
Ets family transcription factor GA-binding protein (GABP) regulates gene expression in CD4 and CD8 T cells.
We used microarray to examine genes differentially expressed in GABP-sufficient (WT) and GABP-deficient (KO) CD4 and CD8 T cells

overall_design: Naive CD4+ and CD8+ T cells were purified from spleen and lymph nodes of Gabpaf/f (WT) and CD4CreGabpaf/f  (KO) mice by FACS sorting. Naive T cells were either subjected to RNA extraction directly  (0-hour), or stimulated with α-CD3/28 and IL-2 for 18 hours before RNA extraction (18-hour).


title: Metabolic, Epigenetic, and Transgenerational Effects of Gut Bacterial Choline Consumption

city: Madison

first: Federico

last: Rey

state: WI

address: 1550 Linden Dr.

institute: University of Wisconsin-Madison

summary: Abstract: Choline is an essential nutrient and methyl donor required for epigenetic regulation.  Here, we assess the impact of gut microbial choline metabolism on bacterial fitness and host biology by engineering a microbial community to lack a single choline-utilizing enzyme. Our results indicate that choline-utilizing bacteria compete with the host for this nutrient, significantly impacting plasma and hepatic levels of methyl-donor metabolites recapitulating biochemical signatures of choline deficiency. Mice harboring high levels of choline-consuming bacteria show increased susceptibility to metabolic disease.  Furthermore, bacterially-induced reduction of methyl-donor availability alters global DNA methylation patterns in both adult mice and their offspring in utero and engenders anxious behavior. Altogether, our results reveal an underappreciated aspect of bacterial choline metabolism (i.e., methyl-donor depletion) that is linked to alterations in metabolism, epigenetics, and behavior. More broadly, this work suggests that interpersonal differences in microbial metabolism should be considered when determining optimal levels of nutrient intake.

overall_design: 8 samples in total (biological n=4 per for each defined community; 9kw old female C57BL/6 mouse liver; 2 weeks of colonization and maintenance on 1% choline diet; 4hours of fasting prior to sacrifice)

first: Kymberleigh

last: Romano

first: Ana

last: Martinez del Campo

first: Kazuyuki

last: Kasahara

first: Carina

last: Chittim

first: Eugenio

middle: I

last: Vivas

first: Daniel

last: Amador-Noguez

first: Emily

last: Balskus

middle: E


title: Gene expression analysis of two elite breeding barley lines with distinct tolerance to abiotic stress

city: Gatersleben

first: Andreas

last: Graner

address: Corrensstrasse 3

institute: Leibniz Institute of Plant Genetics and Crop Plant Research

summary: To investigate the differences in gene expression during germination time course of two elite breeding barley lines (LP104 and LP106), an Agilent oligo microarray was applied. A total of 5320 and 4271 genes were found to be significantly up- and down-regulated, respectively, in LP104 compared to LP106. The highest number of differentially expressed genes (DEGs) was identified after 24h of germination (2260); stages 0h, 2h, 48h, 96h, 120h and 144h were of a lesser magnitude ranging from 929 to 1169 DEGs, and at 72h only 826 DEGs were identified. Analysis of DEGs according to their biological functions revealed that major enriched functional categories among DEGs included RNA, protein, stress, transport and development.

overall_design: Gene expression in germinating grains of two barley lines was measured at 0-144 hours after imbibition. Three biological replications, eight  germination stages.

first: Christiane

last: Seiler

first: Andriy

last: Kochevenko

first: Nese

last: Sreenivasulu


title: Lethality of MalE-LacZ hybrid protein shares mechanistic attributes with oxidative component of antibiotic lethality

first: Jason

last: Yang

state: MA

address: 415 Main St, Rm 2017

department: Biological Engineering

institute: MIT / Broad Institute

summary: This study examines stress responses following lethal induction of a MalE-LacZ hybrid protein

sample_organism: Escherichia coli str. K-12 substr. MC4100

overall_design: E coli MC4100 cells bearing a MalE-LacZ hybrid protein under a maltose promoter (MM18) were grown in M63 medium and induced with 0.2% maltose. Cells were incubated for at 37C with shaking and sampled hourly over 5 hr for RNA extraction.

first: Noriko

last: Takahashi

first: Charley

last: Gruber

first: James

last: Collins

first: Graham

last: Walker


title: RNA-sequencing of Scr or miR-99 KD L-GMPs from MLL-F9 AML secondary recipients

status: Public on Jul 27 2017

city: NEW YORK

first: WENHUO

last: HU

email: huwenhuo@gmail.com, huw@mskcc.org

state: NEW YORK

address: 1275 YORK AVENUE

department: HOPP

institute: MEMORIAL SLOAN KETTERING CANCER CENTER

summary: We FACS purified L-GMP cells (GFP+ tdTom+ c-Kit+ Sca-1+ CD16/32+ CD34+)  from mice transplanted with post-transformed Scr or miR-99 KD MLL-AF9 bone marrow and performed RNA-sequencing, demonstrating miR-99 KD results in induction differentiation and enrichment for a normal GMP gene expression signature

overall_design: FACS purification of Scr and miR-99 KD L-GMPs from 2 mice in each group

first: Mona

last: Khalaj

first: Christopher

middle: Y

last: Park


title: Gene expression data from African Americans and European Americans with non-small cell lung cancer

city: Rockville

first: Khadijah

middle: A

last: Mitchell

address: 37 Convent Drive, Building 37, Room 3060

department: Laboratory of Human Carcinogenesis

institute: National Cancer Institute

summary:
Translational Relevance
Historically, African Americans have been underrepresented in clinical cancer research. Diversity helps to ensure equal access to new cancer therapies and better treatment for everyone. Cancer research is increasingly focused on classifying patients according to molecular profiles for particular groups. We provide a detailed molecular analysis from paired NSCLC tissues that identified differential coding and noncoding RNA expression in NSCLC from African Americans (AA) and European Americans (EA). Similar to other tumor types, we determined that race-enriched gene and microRNA expression signatures suggest a more aggressive disease in African Americans. Based on predicted drug resistance to adjuvant chemotherapies, AA may not equally benefit from the same range of clinical drugs as EA. Our findings provide a rationale for integrating coding and noncoding transcriptome profiles, along with clinical, demographic, and genomic data, when determining treatment options.
Abstract
Purpose: To determine if racial differences in gene and microRNA expression translates to differences in lung tumor biology with clinical relevance in African Americans (AA) and European Americans (EA).
Experimental Design: The NCI-Maryland Case Control Study includes seven Baltimore City hospitals and is overrepresented with AA patients (~40%). Patients that underwent curative NSCLC surgery between 1998 and 2014 were enrolled. Comparative molecular profiling used mRNA (n = 22 AAs and n = 19 EAs) and microRNA (n = 42 AAs and n = 55 EAs) expression arrays to track differences in paired fresh frozen normal tissues and lung tumor specimens from AA and EA. Pathway enrichment, predicted drug response, tumor microenvironment infiltration, cancer immunotherapy antigen profiling, and microRNA target enrichment were assessed.
Results: AA-enriched differential gene expression was characterized by stem-cell and invasion pathways. Differential gene expression in lung tumors from EA were primarily characterized by cell proliferation pathways. Population-specific gene expression was partly driven by population-specific miRNA expression profiles. Drug susceptibility predictions revealed a strong inverse correlation between AA resistance and EA sensitivity to the same panel of drugs. Statistically significant differences in M1 and M2 macrophage infiltration was observed in AA (P <0.05), however, PD-L1, PD-L2 expression was similar between both.
Conclusions: Comparative transcriptomic profiling revealed clear differences in lung tumor biology between AA and EA. Increased participation by AA in lung cancer clinical trials are needed to integrate, and leverage, transcriptomic differences with other clinical information to maximize therapeutic benefit in both AA and EA.
GSEA, Connectivity Map, CIBERSORT, cancer immunotherapy antigen profiling, and hypergeometric testing for overlapping miRNA targets were performed.

overall_design:
We used microarrays to detail differential gene expression in African Americans and European Americans with non-small cell lung cancer.
Patient characteristics for the mRNA cohort (n = 22 AAs and n = 19 EAs). The mRNA cohort included 11 matched pairs and 5 unmatched pairs from AA, and 14 matched pairs and 2 unmatched pairs from EA.

first: Brid

middle: M

last: Ryan


title: DNMT3B overexpression contributes to aberrant DNA methylation and MYC-driven tumor maintenance in T-ALL and Burkitt’s lymphoma

city: Augusta

first: Jan

last: van Riggelen

address: 1410 Laney Walker Blvd.

institute: Augusta University

summary: We performed methylation profiling using RRBS-seq to investigate the role of DNMT3B in MYC-driven tumor maintenance. Comparing tumor cells before and upon DNMT3B knock-down revealed genome-wide changes in the DNA methylation pattern.

overall_design: Samples used in this study correspond to T-cell acute lymphoblastic leukemia (T-ALL) cell lines derived from EμSRα-tTA;tet-o-MYC mice.

first: Candace

last: Poole


title: Molecular signature of response to preoperative radiotherapy in locally advanced breast cancer

city: Belgrade

first: Miljana

last: Tanic

address: Pasterova 14

department: Experimental Oncology

country: Serbia

institute: Institute for Oncology and Radiology of Serbia (IORS)

summary:
gene expression profiling of locally invasive breast carcinomas treated with preoperative radiotherapy
the purose of this study was to establish molecular signature associated with response to radiotherapy using radiotherapy-naïve biopsies of locally advanced breast cancer

overall_design: single color experiments in a pairwise comparison design

first: Ana

last: Krivokuca

first: Jasmina

last: Mladenovic

first: Milena

last: Cavic

first: Sinisa

last: Radulovic

first: Snezana

last: Susnjar

first: Radmila

last: Jankovic


title: Differentially Expressed Genes in PPARγ-deficient MSCs

first: Xing-Ming

last: Shi

address: 1120 15th Street

summary: Peroxisome proliferator-activated receptor gamma (PPARγ) is a key regulator of adipogenesis. It is also a central player in energy metabolism, inflammation and immunity. As an important nuclear transcription factor, PPARγ can regulate the expression and function of genes or biological processes directly or indirectly via association with other factors and modulate their activities. To exploit the impact of PPARγ on global gene expression profile, we report in this study the bioinformatics data analysis results revealing the changes of genes and pathways in the absence of PPARγ. In brief, we performed RNA deep sequencing (RNA-Seq) analysis using RNA samples isolated from multipotent mesenchymal stromal cells (MSCs) of PPARγ knockout and wild type control mice. The RNA-Seq data sets were then subjected to bioinformatics analyses from different angles to reveal the scale and depth of PPARγ in different biological processes. Our results not only recapitulated the known functions of PPARγ, it also revealed new genes and networks influenced by PPARγ and shed new lights on our current understanding of this nuclear receptor in health and disease. microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis

overall_design: Expression profile of genes in PPARγ-deficient and PPARg-floxed MSCs were analyzed by RNA-Seq on a HiSeq2000 sequencing machine.

first: Yun

last: Su

first: Xiaona

last: Shen

first: Jie

last: Chen

first: M

last: Isales

first: Jing

last: Zhao


title: miR-99 regulates normal and malignant hematopoietic stem cell self-renewal

first: WENHUO

last: HU


title: RNA-sequencing of stably engrafted miR-99 KD LSKs

summary: We FACS-purified GFP+ LSK cells from mice transplanted with stably engrafted miR-99 KD and Scr HSCs and performed RNA-sequencing, demonstrating miR-99 KD results in significant depletion of hematopoietic stem cell gene expression signature and induces a differentiated progenitor gene expression signature.

overall_design: FACS purification of Scr and miR-99 KD LSKs from 2 mice in each group

first: Mona

last: Khalaj

first: Christopher

last: Park


title: Ectopic application of the repressive histone modification H3K9me2 establishes postzygotic reproductive isolation in Arabidopsis thaliana

city: Uppsala

first: Juan

last: Santos-González

state: Uppsala

address: Almas Allé 5

department: Department of Plant Biology and Forest Genetics

country: Sweden

institute: SLU

summary: Hybrid seed lethality as a consequence of interspecies or interploidy hybridizations is a major mechanism of reproductive isolation in plants. This mechanism is manifested in the endosperm, a dosage sensitive tissue supporting embryo growth. Deregulated expression of imprinted genes like ADMETOS (ADM) underpin the interploidy hybridization barrier in Arabidopsis thaliana, however, the mechanisms of their action remained unknown. In this study we show that ADM interacts with the AT-hook domain protein AHL10 and the SET domain-containing SU(VAR)3-9 homolog SUVH9 and ectopically recruits the heterochromatic mark H3K9me2 to AT-rich transposable elements (TEs), causing deregulated expression of neighboring genes. Several hybrid incompatibility genes identified in Drosophila encode for heterochromatin-interacting proteins, which has led to the suggestion that hybrid incompatibilities evolve as consequence of interspecies divergence of selfish DNA elements and their regulation. Our data showing that imbalance of dosage-sensitive chromatin regulators underpins hybrid incompatibility in Arabidopsis strongly support this view, demonstrating that reproductive isolation as a consequence of epigenetic regulation of TEs is a conserved feature in animals and plants.

overall_design: 54 genome-wide ChIP sequencing libraries and 6 genome-wide cytosine methylation libraries. All libraries derive from INTACT purified endosperm from seeds at 4 days after pollination from the cross of maternal 2x Col-0 with paternal 2x Col-0 and the mutant backgrounds osd1-1, osd1-1 adm-2, adm-2, 2x suvh2-2 suvh9-1, 4x suvh2-2 suvh9-, 2x ahl10-1, 4x ahl10-1, and osd1-2.

first: Hua

last: Jiang

first: Jordi

last: Moreno-Romero

first: Geert

last: De Jaeger

first: Kris

last: Gevaert

first: Eveline

last: Van De Slijke

first: Claudia

last: Köhler


title: Epigenome analysis of normal breast samples

city: Columbus

first: Daniel

middle: Yui

last: Weng

state: OH

address: 420 W. 12th Ave. Room 390

department: Comprehensive Cancer Center

institute: The Ohio State University

type: Methylation profiling by genome tiling array

summary: Despite known age-related DNA methylation (aDNAm) changes in breast tumors, little is known about aDNAm in normal breast tissues. Breast tissues from a cross-sectional study of 121 cancer-free women, were assayed for genome-wide DNA methylation. mRNA expression was assayed by microarray technology. Analysis of covariance was used to identify aDNAm’s. Altered methylation was correlated with expression of the corresponding gene and with DNA methyltransferase protein DNMT3A, assayed by immunohistochemistry. Publically-available TCGA data were used for replication. 1,214 aDNAm’s were identified; 97% with increased methylation, and all on autosomes. Sites with increased methylation were predominantly in CpG lslands and non-enhancers. aDNAm’s with decreased methylation were generally located in intergenic regions, non-CpG Islands, and enhancers. Of the aDNAm’s identified, 650 are known to be involved in cancer, including ESR1 and beta-estradiol responsive genes. Expression of DNMT3A was positively associated with age. Two aDNAm’s showed significant associations with DNMT3A expression; KRR1 (OR 6.57, 95% CI: 2.51-17.23) and DHRS12 (OR 6.08, 95% CI: 2.33-15.86). A subset of aDNAm’s co-localized within vulnerable regions for somatic mutations in breast cancer. Expression of C19orf48 was inversely and significantly correlated with its methylation level. In the TCGA dataset, 84% and 64% of the previously identified aDNAm’s were correlated with age in both normal-adjacent and tumor breast tissues, with differential associations by histological subtype. Given the similarity of findings in the breast tissues of healthy women and breast tumors, and the effects on gene expression, aDNAm’s may be one pathway for increased breast cancer risk with age.

overall_design: Bisulphite converted DNA from the 121 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchips

first: Min-Ae

last: Song

first: Catalin

last: Marian

first: Peter

last: Shields


title: RNA-sequencing of GFP+ cells 2 days post-transduction of LSK cells with Scr or miR-99 KD lentiviral vectors

summary: We FACS purified GFP+ cells 2 days post-transduction of LSK (Lin-Negative c-Kit+ Sca1+) cells with miR-99 KD and Scr lentiviral vectors and performed RNA-sequencing; this allowed us to identify potential miR-99 target genes for inclusion in the shRNA library

overall_design: FACS purification of Scr and miR-99 KD GFP+ cells 2 days after infection, with two to three replicates per experimental group


title: Metabolic Stress Induces Modifications in the Epigenetic Program of Preimplantation Bovine Embryos

city: Québec City

first: Marc-André

last: Sirard

state: Quebec

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

institute: Université Laval

summary: we induced an energetic stress on in vitro embryos to observe the epigenetic response associated with metabolic stress. Embryos were created with slaughterhouse cows oocytes and then exposed to an elevated glucose concentration (5mM vs 0.2mM for the control embryos) for the first 3 days post fecundation and then cultivated in normal media until blastocyst stage. Blastocysts were collected from 4 different weeks of culture. Genome-wide DNA methylation analysis was performed by micro array using EDMA platform.

overall_design: Two condition experiment, control at 0.2 uM glucose and treatment at 5 uM glucose.  4 pools of 5 blastocysts

first: R

last: Tremblay

first: I

last: Dufort


title: KK-Ay mice gene expression profile

city: Taichung

first: Yng-Tay

last: Chen

address: No 2 Yude road

department: Department of medical research

country: Taiwan

institute: China Medical University Hospital

summary: Mouse gene express was using Mouse Gene 1.0 ST Array.

overall_design: In total 12 samples, 6 T2D mice and 6 control mice were selected for Mouse gene expression status was tested."  T2D: 6Y-1, 6Y-2, 16Y-1, 16Y-2, 42Y-1, 42Y-2 , Control: 1-3, 1-5, 6K-1, 6K-2, 42WKKA, 42WKKB

first: Fuu-Jen

last: Tsai


title: A ‘Synthetic-Sickness’ Screen for Senescence Re-engagement Targets in Mutant Cancer Backgrounds

city: Glasgow

first: W. Nicol

last: Keith

address: Wolfson Wohl Translational Cancer Research Centre

department: Institute of Cancer Science

institute: University of Glasgow

summary: Senescence is a universal barrier to immortalisation and tumorigenesis.  As such, interest in the use of senescence-induction in a therapeutic context has been gaining momentum in the past few years; however, senescence and immortalisation remain underserved areas for drug discovery owing to a lack of robust senescence inducing agents and an incomplete understanding of the signalling events underlying this complex process.  In order to address this issue we undertook a large-scale morphological siRNA screen for inducers of senescence phenotypes in the human melanoma cell line A375P.  Following rescreen and validation in a second cancer cell line, HCT116 colorectal carcinoma, a panel of 16 of the most robust hits were selected for further validation based on significance and the potential to be targeted by drug-like molecules.  Using secondary assays for detection of senescence biomarkers p21, 53BP1 and senescence associated beta-galactosidase (SA?Gal) in a panel of HCT116 cell lines carrying cancer-relevant mutations, we show that partial senescence phenotypes can be induced to varying degrees in a context dependent manner, even in the absence of p21 or p53 expression. However,  proliferation arrest varied among genetic backgrounds with predominantly toxic effects in p21 null cells, while cells lacking PI3K mutation failed to arrest. Furthermore, we show that the oncogene ECT2 is a robust inducer of senescence in all mutant backgrounds tested and highlight a dependence on activating KRASG13D for growth suppression and a complete senescence response, suggesting a potential mechanism to target mutant KRAS signalling through ECT2 in cancers that are reliant on activating KRAS mutations and remain refractory to current treatments.

overall_design: HCT116 colorectal cancer cells with heterozygous KRAS mutation and KRAS+/- cells in which the mutation is knocked out were reverse transfected with 50nM siRNA against ECT2 or scrambled control. 5 days post transfection, cells were harvested for RNA extraction.

first: C

last: Cairney

first: L

middle: S

last: Godwin

first: A

last: Bilsland

first: S

last: Burns

first: K

middle: H

last: Stevenson

last: McGarry

first: J

last: Revie

middle: D

last: Moore

last: Wiggins

last: Collinson

last: Mudd

first: E

last: Tsonou

first: M

last: Sadaie

first: D

last: Bennet

last: Narita

last: Torrance

first: W

middle: N


title: Gene expression of  young, middle-aged and old Drosophila melanogaster exposed to different levels of larval and adult diet

city: Wageningen

first: Christina

last: May

state: Gelderland

address: Droevendaalsesteeg 1

institute: Wageningen University

summary:
Many studies have addressed the effects of adult diet on gene expression in Drosophila melanogaster, however, little is known about how developmental diet influences adult gene expression, and how this interacts with adult dietary conditions.
We found that developmental and adult diet exert largely independent effects on gene expression, with the effect of adult diet being considerably larger.We did find effects of developmental diet on the transcriptome that persist into middle and old-age. Most of the genes affected show no correlation with the observed phenotypic effects of larval diet on lifespan, however, in each sex we identified a cluster of ribosome, transcription, and translation-related genes whose expression was altered across the lifespan and negatively correlated with lifespan.

overall_design: We raised flies as larvae on three different diets and switched them across these same diets as adults, using a fully factorial design (3 larval * 3 adult diets = 9 treatments in total). We measured gene expression in both sexes at 1 day post-eclosion, middle-age (10% cohort mortality) and old-age (90% cohort mortality).

first: Bas

middle: J

last: Zwaan


title: A single TCF transcription factor, regardless of its activation capacity, is sufficient for effective trilineage differentiation of ES cells

city: Hamilton

first: Bradley

last: Doble

state: Ontario

address: 1280 Main Street West

department: Biochemistry and Biomedical Sciences

institute: McMaster University

summary: Co-expression and cross-regulation of the four TCF/LEFs render their redundant and unique functions ambiguous. Here, we describe quadruple-knockout (QKO) mouse ES cells lacking all full-length TCF/LEFs and cell lines rescued with TCF7 or TCF7L1. QKO cells self-renew, despite gene expression patterns that differ significantly from WT, and display delayed, neurectoderm-biased, embryoid body (EB) differentiation. QKO EBs have no contracting cardiomyocytes and differentiate poorly into mesendoderm, but readily generate neuronal cells. QKO cells and TCF7L1-rescued cells cannot efficiently activate TCF reporters, whereas TCF7-rescued cells exhibit significant reporter responsiveness. Surprisingly, despite dramatically different transactivation capacities, re-expression of TCF7L1 or TCF7 in QKO cells restores their tri-lineage differentiation ability, with similar lineage marker expression patterns and beating cardiomyocyte frequencies observed in EBs. Both factors also similarly affect the transcriptome of QKO cells. Our data reveal that a single TCF, regardless of its activation capacity, is sufficient for effective trilineage differentiation of ES cells.

overall_design: Total RNA was isolated from mouse ES cells lacking all full-length TCF/LEFs (Quadruple Knock Outs) and QKOs rescued with a single copy of TCF7 or TCF7L1 compared to wildtype E14TG2a mouse ES cells, cultured for 48 hours in 15% serum + LIF.

first: Steven

middle: F

last: Moreira

middle: W


title: Effect of Selective Androgen Receptor Degraders (SARDs) on Androgen Receptor (AR) Function in LNCaP Cells

city: Memphis

first: Daniel

middle: Lee

last: Johnson

state: Tennessee

address: 71 S Manassas

department: Molecular Informatics Core

country: USA

institute: UTHSC

summary: LNCaP cells were maintained in charcoal-stripped serum containing medium for 48 hours and treated with vehicle or 10 uM of UT-69, UT-155, R-UT-155, or enzalutamide. Twenty four hours after treatment, the cells were harvested, RNA was isolated and expression of genes was measured using microarray (Affymetrix Clarion S)

overall_design: n=1/treatment from n=3/treatment RNA pooled

first: Ramesh

last: Narayanan


title: Neat1 is a p53-inducible lincRNA essential for transformation suppression

city: Stanford

first: Stephano

last: Spano Mello

state: CA

address: 269 Campus Drive

institute: Stanford University

summary: p53 is a transcriptional activator that induces myriad target genes. However, those p53-inducible genes most critical for tumor suppression remain elusive. Here, we identify Neat1, a ncRNA constituent of paraspeckles, as a p53 target gene induced by mouse and human p53 in different cell types and by diverse stress signals. Using fibroblasts derived from Neat1-/- mice, we examine the functional role of Neat1 in the p53 pathway. We find that Neat1 is dispensable for cell-cycle arrest and apoptosis in response to genotoxic stress, but plays a crucial role in suppressing transformation in response to oncogenic signals. To determine the effects of Neat1 deficiency on cells, we used E1A;HRasV12-expressing  wild-type and Neat1-/- mouse embryonic fibroblasts (MEFs) for RNA-sequencing analysis. This analysis revealed that  Neat1 deficiency impacts the regulatory networks involved in nervous system development and axon guidance programs, as well as genes of the SWI/SNF complex  and components of the pancreas development network. These findings suggest that the ability of Neat1 to globally regulate gene expression, with effects on diverse transcriptional programs, provides a potential mechanism for how Neat1 acts to suppress transformation and tumor initiation.

overall_design: RNA-seq was performed to determine the differentially expressed genes in  E1A;HRasV12-expressing  wild-type and Neat1-/- mouse embryonic fibroblasts (MEFs) .

last: Mello

first: Laura

last: Attardi


title: Expression profiling of peripheral blood mononuclear cells in normal controls and patients with Parkinson's disease

city: Hirosaki

first: Shuji

last: Shimoyama

state: Aomori

address: 5 Zaifu-cho

department: Department of Neurophysiology

institute: Hirosaki University Graduate School of Medicine

summary: Autophagy is a highly conserved degradation pathway whereby not only cytosolic components but also aberrant proteins are sequestered within double-membraned vesicles. Parkinson's disease (PD) is pathologically characterized by accumulation of  phosphorylated α-synuclein in the neuronal cytoplasm and its accumulation occurs in the peripheral autonomic nervous system as well as the central nervous system. In the brains of patients with PD, abnormal autophagy is known to occur and be involved with neurodegeneration. To investigate abnormal autophagy in peripheral blood mononuclear cells (PBMC) in the patients with PD, we performed whole transcriptome analysis of PBMC obtained from 9 normal controls and 10 patients with PD.

overall_design: PBMC in 9 normal controls and 10 patients with PD were isolated by Ficoll-paque plus (GE Healthcare, 17144002) centrifugation of heparinized blood and frozen at -80 degrees Celsius until microarray or qRT-PCR.

first: Yasuo

last: Miki


title: Continuous suppression of Mek1/2 impairs the developmental potential of mouse embryonic stem cells (H2A.X pattern)

city: New Haven

first: Andrew

middle: Zhuo

last: Xiao

state: CT

address: 10 Amistad St

department: Genetics

institute: Yale Stem Cell Center

summary: Simultaneous inhibition of Gsk3α/β and Mek1/2 signaling in the presence of LIF (2i/L) induces a naïve state in mouse embryonic stem cells (ESCs) that resembles the inner cell mass (ICM) of the pre-implantation embryo. Since the ICM exists only transiently in vivo, it remains unclear how continuous propagation of naïve ESCs in vitro affects their stability and functionality. Here, we show that extended culture of male ESCs in 2i/L results in the progressive erosion of genomic imprints, loss of H2A.X binding, and accumulation of chromosomal aberrations. Consistent with these observations, we find that ESCs propagated in 2i/L have an impaired developmental potential. Mechanistically, we demonstrate that Mek1/2 inhibition is predominantly responsible for these effects, in part through downregulation of DNA methyltransferases. We further provide evidence that female ESCs cultured in conventional serum/LIF media phenocopy male ESCs cultured in 2i/L, including the aforementioned epigenetic and developmental abnormalities. Finally, we show that replacement of the Mek1/2 inhibitor with a Src inhibitor preserves the epigenetic and genomic integrity as well as developmental potential of ESCs. Taken together, our data suggest that, while suppression of Mek1/2 in ESCs maintains an ICM-like epigenetic state, continuous suppression results in irreversible changes that compromise their developmental potential.

overall_design: Detect and analyze different H2A.X deposition pattern in ESCs under different culture conditions

first: Jiho

last: Choi

first: Aaron

last: Huebner

first: Kaixuan

last: Lin

first: Konrad

last: Hochedlinger


title: Fire salamander gene expression data from field samples in Israel

status: Public on Jul 26 2017

city: Braunschweig

last: Goedbloed

address: Mendelssohnstrasse 4

country: Germany

institute: TUBS

summary: Goal of the study was to compare gene expression patterns between sites and habitats

overall_design: Salamandra infraimmaculata tail-tip tissue was collected from different field sites, used for whole RNA extraction and analyzed using an Agilent microarray

first: Till

last: Czypionka


title: Parallel habitat acclimatization is realized by the expression of different genes in two closely related salamander species (genus Salamandra)

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

sample_organism:
Salamandra salamandra
Salamandra infraimmaculata

overall_design: Refer to individual Series


title: Scope and mechanism of eIF4F-independent mRNA translation

city: Hangzhou

first: Yuanhui

last: Mao

state: Zhejiang

address: 1369 West Wenyi Road

country: China

institute: Zhejiang University

summary: In eukaryotic cells, protein synthesis typically begins with the binding of eIF4F to the 7-methylguanylate (m7G)cap found on the 5’ end of the majority of mRNAs. Surprisingly, overall translational output remains robust under eIF4F inhibition. The sustained protein synthesis has been largely attributed to cap-independent translation mediated by internal ribosome entry sites (IRES). However, the IRES-driven translation is substrate-specific and largely incompatible with the broad spectrum of eIF4F-resistant translatomes.Here, we report that N6-methyladenosine (m6A)-mediated translation prevails on capped mRNAs and is resistant to eIF4F inactivation.Depletion of the methyltransferase METTL3 selectively inhibits translation of mRNAs bearing 5’UTR methylation, but not mRNAs with 5’ terminal oligopyrimidine (TOP) elements. Mechanistically, we identify ABCF1 as a critical mediator of m6A-promoted translation under both stress and physiological conditions. Supporting the role of ABCF1 in m6A-mediated cap-independent translation, ABCF1-sensitive transcripts largely overlap with METTL3-responsible mRNA targets. By illustrating the scope and the mechanism of translation initiation that is neither cap- nor IRES-dependent, these findingsreshape our current perceptions of cellular translational pathways

overall_design: Ribo-seq and RNA-seq in Scramble, ABCF1 and METTL3 knockdown.

first: Xiao-min

last: Liu

first: Shu-Bing

last: Qian


title: Acute Exercise Bout Effects on GH and IGF1 in Prediabetic and Healthy African Americans

city: Washington

first: Monica

last: Hubal

state: DC

address: 111 Michigan Ave NW

department: Integrative Systems Biology

institute: Children's National Medical Center

summary: The incidence of pre-diabetes (PD) and Type-2 Diabetes Mellitus (T2D) is a worldwide epidemic. African American (AA) individuals are disproportionately more likely to become diabetic than other ethnic groups. Over the long-term, metabolic complications related to diabetes result in significant alterations in growth hormone (GH) and insulin-like growth factor-1 (IGF-1). Considering the limited exercise-related studies in the area of gene expression changes with disease progression, the objective of this study was to examine differences in exercise-induced gene expression related to the GH and IGF-1 pathways in peripheral blood mononuclear cells (PBMCs) of healthy (CON) and PD AA individuals. Design: Ten subjects [5 PD (age=35±9.3 yr, BMI=32.1±4.0, FBG=101.8±1.3 mg/dl) and 5 CON (age=31±9.4 yr, BMI=29.4±5.2, FBG=82.8±9.7 mg/dl)] had blood drawn for RNA isolation prior to exercise (Pre), immediately following acute moderate intensity exercise on a treadmill (Post-1), 6-hours post (Post-6), and 24-hours post (Post-24). Isolation of mRNA from PBMCs was performed using ficoll separation, while the profiling of mRNA expression was performed using beadchip arrays that were scanned and analyzed by a gene expression module. Scan results were statistically analyzed for a specific list of genes related to GH and IGF-1. GH and IGF-1 protein levels were also assessed in each sample. To address issues of normality, all GH and IGF-1 data were log-transformed prior to analysis. Statistical significance was set at p<0.05. Results: Group differences for GH2 variant 2 (p=0.070) and GH2 variant 3 (p=0.059) were coupled with significant alterations in IGF-1 mRNA over time (p=0.024). A significant interaction between group and time was observed for GHRH mRNA (p=0.008). No group differences were observed in GH AUC (p=0.649), ∆GH (p=0.331), GHrec (p=0.294), or IGF-1 AUC (p=0.865), representing a similar exercise-induced GH and IGF-1 response for both groups.  Conclusions: Analysis of GH and IGF-1 related-gene expression indicates that mild elevations in fasting blood glucose and exercise-induced alterations in gene expression are impacted by the prediabetic state.

overall_design: Group*time (exercise); Illumina gene expression data; 5 subjects per group * 2 groups; each subject's pre-exercise expression serves as intrasubject control; healthy group is control vs pre-diabetic group; quantile norm

first: Laurie

last: Gold


title: A Shared Runx1-bound Zbtb16 Enhancer Directs Innate and Innate-Like Lymphoid Lineage Development

city: Chicago

first: Aiping

state: IL

address: 929 East 57th street

department: Pathology

institute: University of Chicago

summary: Combined with CRISPR/Cas9 and ATAC-seq approach, we identified open chromatin sites critical for PLZF expression in ILC and NKT innate lineages. Runx1 is bound to multiple open chromatin sites and is essential for PLZF expression.

overall_design: ATAC-seq was performed in NKT cells vs CD4SP thymocytes, ILCP vs CLP. Runx1 ChIP-seq was performed in NKT cells.

first: Albert

last: Bendelac


title: IL-12 and type I IFN response of neonatal myeloid DC to human CMV infection

city: Gosselies

first: Baharak

last: Hooshiar Kashani

state: Charleroi

address: Rue Adrienne Bolland 8

department: Institute for Medical Immunology

country: Belgium

institute: Université Libre de Bruxelles

summary: Transcriptional profiles of HCMV or Mock infected neonatal and adult were anayzed

overall_design: Dendritic cells were HCMV infected for 6 and 16 hours and were compared to mock infected cells at 16 hours

first: Arnaud

last: Marchant


title: Gene CNVs genetically mapped and linked to adaptation in spruce

city: Quebec

first: Julien

last: Prunier

state: QC

address: 1030 av. de la medecine

department: Forestry

summary:
Following previous work, we extend the use of a reliable detection method to a wide progeny in white spruce in order to genetically map a maximum of inherited gene CNVs and linked those to phenotypic traits related to adaptation. We selected probes targeting 3911 genes likely in CNV in this progeny and performed genetic mapping for those harboring a 1:1 segregation. In addition, the link between gene CNVs and phenotypic variation was tested using budburst, budset and growth data for the same samples.
Results: We genetically mapped 82 gene CNVs inherited from the previous generation and harboring the expected segregation ratio. This mapping allowed to delineate a few hotspots of CNV that are likely shared with other conifer species. In addition, individual-specific gene CNVs likely representing de novo variation supported the hypothesis of a purifying selection against copy losses. Finally, 29 gene CNVs were significantly associated to adaptive trait variation; 13 were located on the genetic map, including 4 located within hotspots of CNVs.

overall_design: A total of 114 spruce descendants coming from a controlled cross were hybridized at the time with their 'mother' on a CGH array. In addition, the other parent was also compared to the 'mother'.

first: Manuel

last: Lamothe

first: John

last: MacKay

first: Sylvie

last: Blais

first: Nathalie

last: Isabel

first: Jean

last: Bousquet

first: Sébastien

last: Caron


title: Integrated metabolic models for xenobiotic induced mitochondrial toxicity in skeletal muscle

city: Leicester

first: Karl

middle: Eric

last: Herbert

address: Glenfield Hospital

department: Cardiovascular Sciences

country: United Kingdom

institute: University of Leicester


title: Integrated metabolic models for xenobiotic induced mitochondrial toxicity in skeletal muscle (compound 197 experiments)

summary: There is a need for robust in vitro models to sensitively capture skeletal muscle adverse toxicities early in the research and development of novel xenobiotics. To this end, an in vitro rat skeletal muscle model (L6) was used to study the translation of transcriptomics data generated from an in vivo rat model. Novel sulfonyl isoxazoline herbicides were associated with skeletal muscle toxicity in an in vivo rat model. Gene expression pathway analysis on skeletal muscle tissues taken from in vivo repeat dose studies identified enriched pathways associated with mitochondrial dysfunction, oxidative stress, energy metabolism, protein regulation and cell cycle. Mitochondrial dysfunction and oxidative stress were further explored in an in vitro L6 model. This model demonstrated that the sulfonyl isoxazoline compounds induced mitochondrial dysfunction, mitochondrial superoxide production and apoptosis. These in vitro findings accurately concurred with the in vivo transcriptomics data, thereby confirming the ability of the L6 skeletal muscle model to identify relevant in vivo mechanisms of xenobiotic-induced toxicity. Moreover, these results highlight the sensitivity of the L6 galactose media model to study mitochondrial perturbation associated with skeletal muscle toxicity; this model may be utilised to rank the potency of novel xenobiotics upon further validation.

overall_design: Total RNA obtained from isolated thigh skeletal muscle obtained from Han Wistar rats fed 150ppm sulfonyl isoxazoline 197 compounds for 28 days (repeat dose), n=4, compared to n-4 control rats fed standard lab chow.

first: William

last: Dott


title: DNAm profiling of healthy cord whole blood

city: Vancouver

first: Michael

middle: S.

last: Kobor

state: BC

address: 950 West 28th Avenue

department: Medical Genetics

institute: Centre for Molecular Medicine and Therapeutics / University of British Columbia

summary: DNAm profiles of control cord whole blood was obtained for 6 samples using the Illumina 450K platform.

overall_design: Cord blood was initially collected from neonates delivered by elective cesarean section in the absence of labor at the Children’s & Women’s Health Centre of BC (Vancouver, Canada). Cells from these samples were separated by FACS and used for characterizing the effect of nucleated red blood cells on genomic assays (PMCID: PMC4567832, GEO: GSE68456). These are healthy cord whole blood samples that have been used as controls/references for independent projects, as well as methods for identifying maternal contamination of cord blood.

first: O

last: de Goede

first: E

last: Price

first: H

middle: R

last: Razzaghian

first: M

first: W

middle: P

last: Robinson

first: P

last: Lavoie

last: Jones

first: J

middle: L

last: MacIsaac

first: A

last: Morin


title: Integrated metabolic models for xenobiotic induced mitochondrial toxicity in skeletal muscle (compound 177 experiments)

overall_design: Total RNA obtained from isolated thigh skeletal muscle obtained from Han Wistar rats fed 150ppm sulfonyl isoxazoline compound 177 for 28 days (repeat dose), n=4, compared to n-4 control rats fed standard lab chow.


title: overexpression of a newly truncated FMRP isoform with 297 amino acid

city: Fuzhou

first: Yang

last: wenjing

address: 156 Xierhuan Road

institute: Fuzhou General Hospital

summary:
RNA microarray was used to analyze the differentialy expressed genes between stably transfected HEK293T cells of the overexpression of the new FMRP isoform with 297 amino acid and stably transfected HEK293T cells of empty lentiviral vector.
we constructed the lentiviral vector of exons 1-9 together with the sequence of 140bp fragment of human FMR1 gene to overexpress the truncated FMRP with 297 amino acid, and transfected cells with the void plasmid pLEX-MCS were regarded as control group.

overall_design: stably transfected HEK293T cells of empty lentiviral vector and the overexpression of the new FMRP isoform were for RNA extraction and hybirdization on Affymetrix microarrays.

last: Wenjing

first: Lan

last: Fenghua


title: Neural Precursor Cell-Derived Pleiotrophin Mediates Glioma Invasion of the Subventricular Zone

first: Michelle

last: Monje

address: 265 Campus Drive, SIM1 G3035

summary: The lateral ventricle subventricular zone (SVZ) is a frequent and consequential site of pediatric and adult glioma spread, but the cellular and molecular mechanisms mediating this are poorly understood. We demonstrate that neural precursor cell (NPC):glioma cell communication underpins this propensity of glioma to colonize the SVZ through secretion of chemoattractant signals toward which glioma cells home. Biochemical, proteomic, and functional analyses of SVZ NPC-secreted factors revealed the neurite outgrowth-promoting factor pleiotrophin, along with required binding partners SPARC/SPARCL1 and HSP90B, as key mediators of this chemoattractant effect. Pleiotrophin expression is strongly enriched in the SVZ, and pleiotrophin knockdown starkly reduced glioma invasion of the SVZ in the murine brain.  Pleiotrophin, in complex with the binding partners and signaling through the receptor PTPRZ1, activated glioma Rho/ROCK signaling, and ROCK inhibition decreased invasion toward SVZ NPC-secreted factors. These findings demonstrate a pathogenic role for NPC:glioma interactions and potential therapeutic targets to limit glioma invasion.

overall_design: RNA-seq in patient-derived DIPG cell cultures in two replicates. Libraries were sequenced on Illumina NextSeq 500, 1x75.

first: Surya

last: Nagaraja


title: A FTH1 gene:pseudogene:miRNA network regulates tumorigenesis in prostate cancer

city: Singapore

first: Henry

last: Yang

address: 28 Medical Drive

country: Singapore

institute: Cancer Science Institute of Singapore

summary: Pseudogenes, non-coding homologs of protein-coding genes, were once considered non-functional evolutional relics. Recent studies have shown that pseudogene transcripts can regulate their parental transcripts by sequestering shared microRNAs, thus acting as competing endogenous RNAs (ceRNAs). In this study, we utilize an unbiased screen to identify the ferritin heavy chain 1 (FTH1) transcript and multiple FTH1 pseudogenes as targets of several oncogenic miRNAs in prostate cancer. We characterize the critical role of this FTH1 gene:pseudogene:microRNA network in regulating tumorigenesis in prostate cancer, and show that impairing microRNA binding and subsequent ceRNA crosstalk results in complete phenotype rescue. Our results also demonstrate that pseudogenes are able to regulate intracellular iron levels, which are crucial for multiple physiological and pathophysiological processes. In summary, we describe a novel and extensive gene:pseudogene ceRNA network comprising multiple microRNAs and multiple pseudogenes derived from a single parental gene, which regulates iron storage and tumorigenesis in prostate cancer.

overall_design: Biotinylated microRNA-638 and microRNA-17 pulldown was performed using human prostate cancer cell line DU145 with two non-targeting controls (NC1 and NC2). DU145 cells with non-targeting controls (NC1 and NC2) or microRNA-638 mimic overexpression were used for RNA extraction and hybridization on Affymetrix microarrays.

first: Jia

last: Chan

first: Zhi

last: Kwok

first: Xiao

last: Chew

first: Gina

last: DeNicola

first: Yvonne

last: Tay


title: The role of FAM46C in myeloma cells

city: Rochester

first: Xuewei

last: Wang

address: 200 1st street

institute: Mayo Clinic


title: ATAC-seq profiling of open chromatin in the root tips of four plant species (Arabidopsis thaliana, Medicago truncatula, Solanum lycopersicum, and Oryza sativa) and two Arabidopsis thaliana cell types (root hair and non-hair epidermal cells)

city: Atlanta

first: Roger

middle: B

last: Deal

state: GA

address: 1510 Clifton Rd NE

department: Biology

institute: Emory University

summary: The transcriptional regulatory structure of plant genomes remains poorly defined relative to that of animals. It has been unclear how many cis-regulatory elements generally exist in plant genomes, where these elements lie in relation to their target promoters, and how these features are conserved across species. We employed the Assay for Transposase-Accessible Chromatin with sequencing (ATAC-seq) in four different plant species (Arabidopsis thaliana, Medicago truncatula, Solanum lycopersicum, and Oryza sativa) to delineate open chromatin regions and transcription factor (TF) binding sites across each genome. Despite a ~10-fold variation in intergenic space among species, the majority of open chromatin regions consistently lie within 3 kb upstream of a transcription start site (TSS) in all four species. Nearly 70% of genes in Arabidopsis, Medicago, and Rice have a single putative regulatory region upstream of the TSS, while a similar percentage of tomato genes have 2-5 such elements. Despite variation in the location and number of regulatory elements within orthologous gene sets, transcriptional regulatory networks appear to be largely conserved across species. Profiling of open chromatin in the Arabidopsis root hair and non-hair epidermal cell types indicated that while the open chromatin landscapes of these two cell types were largely indistinguishable on a global scale, thousands of relatively subtle, quantitative cell-specific differences could be found. Analysis of TF binding sites in these differentially accessible regions led to the discovery of a MYB-driven transcriptional regulatory module unique to the hair cell type, which appears to control both hair cell fate regulators and abiotic stress responses. Our cross-species and cross-cell type analyses revealed common transcriptional regulatory principles among species and shed light on the mechanisms that produce cell type-specific transcriptomes during development.

sample_organism:
Arabidopsis thaliana
Medicago truncatula
Solanum lycopersicum
Oryza sativa

overall_design: ATAC-seq was performed on nuclei isolated from 1 cm root tips of Arabidopsis thaliana, Medicago truncatula, Solanum lycopersicum, and Oryza sativa plants grown vertically on nutrient agar plates. Plants of all species were transgenics constitutively expressing the INTACT transgenes (UBQ10p:NTF/ACT2:BirA) such that all root tip nuclei could be affinity purified using streptavidin beads. ATAC-seq was also performed on Arabidopsis thaliana root tip nuclei prepared by sucrose sedimentation (crude purification). Root hair and non-hair cell nuclei of Arabidopsis thaliana affinity purified from INTACT transgenics (ADF8p:NTF/ACT2p:BirA and GL2p:NTF/ACT2p:BirA, respectively) were also used in ATAC-seq. All ATAC-seq experiments were performed in two biological replicates. ATAC-seq was also performed on purified Arabidopsis thaliana genomic DNA as a control.


title: Helicobacter pylori sabA gene is associated with iron deficiency anemia (IDA) in childhood and adolescence

status: Public on Jul 25 2017

city: Mitaka

first: Takako

last: Osaki

state: Tokyo

department: Department of Infectious Diseases

country: Japan

institute: Kyorin University School of Medicine

summary: Background  Gastric Helicobacter pylori colonization leads to iron deficiency anemia (IDA), especially in children and adolescents. However the pathogenesis is poorly understood.   Objective  We sought to identify specific H. pylori genes involved in IDA development, by comparing bacterial genome-wide expression profiling in patients affected or not.   Methods   H. pylori were isolated from four children with IDA and four from matched controls without IDA. Based on these isolates, cDNA microarrays under iron-replete or depleted conditions were systematically performed to compare gene expression profiles at the whole genome level. Real-time reverse-transcription (RT-) PCR and protein assays were performed for further assessing the profile differentiation of the identified H. pylori IDA-associated genes.   Results  We identified 29 and 11 genes with significantly higher or lower expression in the IDA isolates compared to non-IDA isolates, respectively. Especially notable were higher expression of sabA gene encoding sialic acid-binding adhesin in the IDA isolates, which was confirmed by real-time RT-PCR study. Moreover, iron-depletion in vitro led to up-regulation of fecA1 and frpB1 genes and down-regulation of pfr, as predicted. Known iron-regulated genes such as fur, pfr, fecA, and feoB did not significantly differ between both groups. The IDA isolates had significantly higher expression of vacuolating cytotoxin gene vacA than non-IDA isolates, consistent with the results of VacA protein assays. There were no significant differences in bacterial growth value between IDA and non-IDA isolates.   Conclusions  It is likely that H. pylori carrying high expression of sabA causes IDA, especially in children and adolescents who have increased daily iron demand. In addition, it is possible that several host-interactive genes, including vacA, may play a synergistic role for sabA in IDA development.

overall_design: The four H. pylori strains isolated from the IDA patients and 4 strains from other gastric disorder patients were analysed by DNA micro array. In addition, two samples from IDA patients and two control samples were treated with DFM.

first: Seiichi

last: Kato

first: Shigeru

last: Kamiya

first: Xue-Song

last: Zhang

first: Martin

last: Blaser