title: Temporal alterations in the HSAEC transcriptome following infection by virulent and attenuated strains of Rift Valley Fever Virus

city: Manassas

first: Catherine

middle: Elizabeth

last: Campbell

state: VA

address: 10650 Pyramid Place, MS 1J5

department: National Center for Biodefense and Infectious Diseases

country: USA

institute: George Mason University

summary: Rift Valley fever virus (RVFV) causes major outbreaks among livestock, characterized by “abortion storms” in which spontaneous abortion occurs in almost 100% of pregnant ruminants. Humans can also become infected with mild symptoms that can progress to more severe symptoms, such as hepatitis, encephalitis, and hemorrhagic fever. The goal of this study was to use RNA-sequencing (RNA-seq) to analyze the host transcriptome in response to RVFV infection. G2/M DNA damage checkpoint, ATM signaling, mitochondrial dysfunction, regulation of the antiviral response, and integrin-linked kinase (ILK) signaling were among the top altered canonical pathways with both the attenuated MP12 strain and the fully virulent ZH548 strain. Although several mRNA transcripts were highly upregulated, an increase at the protein level was not observed for the selected genes, which was at least partially due to the NSs dependent block in mRNA export.  Inhibition of ILK signaling, which is involved in cell motility and cytoskeletal reorganization, resulted in reduced RVFV replication, indicating that this pathway is important for viral replication.  Overall, this is the first global transcriptomic analysis of the human host response following RVFV infection, which could give insight into novel host responses that have not yet been explored.

overall_design: The study included triplicate samples of HSAEC cells infected with Mock, MP12, or ZH548 strains of RVFV, and collected at 3, 9, and 18 hourse post-infection. There are a total of 27 samples.

first: Aarthi

last: Narayanan

first: Aura

last: Garrison

first: Bibha

last: Dahal

first: Brett

last: Beitzel

first: Chelsea

last: Pinkham

first: Connie

last: Schmaljohn

first: Cynthia

middle: L

last: de la Fuente

first: Gustavo

last: Palacios

first: Kylene

last: Kehn-Hall

first: Michael

last: Linquidst

first: Nicole

last: Bracci


title: Loss of a mammalian circular RNA locus causes miRNA deregulation and affects brain function

status: Public on Aug 11 2017

city: Berlin

first: Petar

last: Glazar

address: Robert Rössle Str. 10 (H. 87)

department: Systems Biology of Gene Regulatory Elements

country: Germany

institute: Max Delbrück Center for Molecular Medicine

type: Expression profiling by high throughput sequencing

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Expression data from invasive breast cancer patient

city: Taipei

first: Hung-Chun

last: Cheng

state: Taiwan

address: 125 Lih-Der Road, Peitou District

department: Research

country: Taiwan

institute: Koo Foundation SYS Cancer Center

summary: We aimed to validate an 18-gene classifier (GC) initially developed to predict local/regional recurrence (LRR) after mastectomy in estimating distant metastasis risk.

overall_design: There were 683 breast cancer samples to be analyzed.

first: Skye

middle: H

first: Tzu-Ting

last: Huang

first: Yu-Hao

first: Tee

middle: B

last: Tan

first: Chen-Fang

last: Horng

first: Yong

middle: A

last: Wang

first: Nicholas

middle: S

last: Brian

first: Li-Sun

last: Shih

first: Ben-Long

last: Yu


title: microRNA expression profiling in diffuse malignant peritoneal mesothelioma

city: Milan

first: Paolo

last: Gandellini

address: Via Amadeo 42

department: Department of Applied Research and Technological Development

country: Italy

institute: Fondazione IRCCS Istituto Nazionale Tumori

summary: Diffuse malignant peritoneal mesothelioma (DMPM) is a rapidly lethal malignancy. The comprehension of the molecular and cellular features of DMPM is of utmost importance for the fruitful management of the disease, especially in patients who fail standard treatments and have a poor prognosis due to the lack of effective alternative therapeutic options. In this context, we previously found that telomerase activity (TA), which accounts for the limitless proliferative potential of cancer cells, is prognostic for disease relapse and cancer-related death in DMPM patients. Consequently, the identification of factors involved in telomerase activation/regulation may pave the way towards the development of novel therapeutic interventions for the disease. In the present study, miRNA expression profiling was carried out in a series of DMPM tissue specimens, previously characterized for the occurrence of TA, in order to possibly identify miRNAs that may play a role in the establishment/regulation of such a telomere maintenance mechanism in this malignancy and consequently furnish a biological rationale for the possible future development of miRNA-based telomerase-targeted therapeutic approaches.

overall_design: microRNA expression profiling was carried out on a series of 51 frozen surgical specimens of diffuse malignant peritoneal mesothelioma (DMPM), 5 normal peritoneum samples, 1 normal mesothelial cell line (MES-F) and 1 cell line derived from the tumor of a DMPM patient.

first: Marco

last: Folini


title: Endotoxin preconditioning reprograms S1 tubules and macrophages to protect the kidney

status: Public on Aug 10 2017

city: Indianapolis

first: Takashi

last: Hato

state: IN

address: 950 W. Walnut St. R2 202

department: Medicine

institute: Indiana University

summary: Preconditioning with a small dose of endotoxin confers unparalleled protection against otherwise lethal models of sepsis. The mechanisms of preconditioning have been investigated extensively in isolated immune cells such as macrophages. However, the role of tissue in mediating the protective response to preconditioning remains unknown. Using the kidney as a model organ, we identify the essential role of the renal epithelial cell in mediating the full expression of protective preconditioning. The protective phenotype is characterized by the clustering of macrophages around S1 segments of proximal tubules, which forms a functional unit mediating protection. To investigate the molecular pathways, we laser microdissected S1 segments from the following: 1) Non-preconditioned mice subjected to single-dose 5 mg/kg lipopolysaccharide (0111:B4, LPS) intraperitoneally for 24 hours. 2) Preconditioned mice subjected to 0.25 mg/kg LPS followed 24 hour later by 5 mg/kg LPS (LPS/LPS). 3) Control mice (saline vehicle).

overall_design: S1 proximal tubular segments from control, LPS-treated (non-preconditioned) and preconditioned C57BL/6J male mice.

first: Pierre

middle: C

last: Dagher


title: Smooth muscle cell mineralocorticoid receptor regulation of vascular mRNAs with aging

city: Boston

first: Seung

middle: Kyum

last: Kim

state: MA

address: 15 Kneeland st.

department: Molecular Cardiology Research Institute

institute: Tufts Medical Center

summary:
We used a smooth muscle cell-specific mineralocorticoid receptor knockout mouse to generate young and aged MR-intact and SMC-MR-KO aortic mRNA to examine the effect of age on vascular mRNA alterations in the presence and absence of SMC-MR.
For more information about the mouse model see: McCurley, A et al. Direct regulation of blood pressure by smooth muscle cell mineralocorticoid receptors. Nat Med. 2012 Sep;18(9):1429-33

overall_design: Total mRNA was extracted from young (3-4 mo) and aged male (12mo) MR-intact and SMC-MR-KO mice to investigate aging-induced alterations in vascular mRNA expression

first: Iris

middle: Z

last: Jaffe

middle: K

first: Amy

middle: T

last: McCurley


title: Distinct cellular mechanisms underlie anti-CTLA-4 and anti-PD-1 checkpoint blockade

city: Houston

first: Spencer

last: Wei

state: TX

address: 7455 Fannin St.

department: Immunology

institute: MD Anderson Cancer Center

type: Genome variation profiling by high throughput sequencing


title: Distinct cellular mechanisms underlie anti-CTLA-4 and anti-PD-1 checkpoint blockade [WES]

summary: Immune checkpoint blockade is able to achieve durable responses in a subset of patients, however we lack a satisfying comprehension of the underlying mechanisms of anti-CTLA-4 and anti-PD-1 induced tumor rejection. To address these issues we utilized mass cytometry to comprehensively profile the effects of checkpoint blockade on tumor immune infiltrates in human melanoma and murine tumor models. These analyses reveal a spectrum of tumor infiltrating T cell populations that are highly similar between tumor models and indicate that checkpoint blockade targets only specific subsets of tumor infiltrating T cell populations. Anti-PD-1 predominantly induces the expansion of specific tumor infiltrating exhausted-like CD8 T cell subsets. In contrast, anti-CTLA-4 induces the expansion of an ICOS+ Th1-like CD4 effector population in addition to engaging specific subsets of exhausted-like CD8 T cells. Thus, our findings indicate that anti-CTLA-4 and anti-PD-1 checkpoint blockade induced immune responses are driven by distinct cellular mechanisms.

overall_design: Mouse cell lines B16BL6 and MC38 were analyzed using whole exome sequencing

first: Jacob

last: Levine

first: Alexandria

middle: P

last: Cogdill

first: Yang

last: Zhao

first: Nana-Ama

last: Anang

first: Miles

last: Andrews

first: Padmanee

last: Sharma

first: Jing

first: Jennifer

last: Wargo

first: Dana

last: Pe’er

first: James

last: Allison

first: Louis

last: Ramagli


title: RNA transcriptome analysis of floral buds of male-fertile and male-sterile tomato

city: Seoul

first: Koeun

last: Han

address: Gwanak-ro 1

country: South Korea

institute: Seoul National University

summary: To compare the global gene expression between male sterile line (ms1035) and fertile line (T-1082), RNA-seq was performed using different tstages of floral buds. A strand-specific RNA-seq library was constructed and sequence using Illumina Hiseq 2500. Differentailly expressed genes were identified using CLC Genomics Workbench 6.0 and DESeq tool of R.

overall_design: 3 biological replicates of 3 developmental stages of floral buds.

first: Hee-Jin

last: Jeong

first: Byoung-Cheorl

last: Kang


title: Variation in single-nucleotide sensitivity of eCLIP derived from reverse transcription conditions

city: La Jolla

first: Gene

last: Yeo

state: CA

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

institute: UCSD

summary: Crosslinking and immunoprecipitation (CLIP) followed by high-throughput sequencing identifies the binding sites of RNA binding proteins on RNAs. The covalent RNA-amino acid adducts produced by UV irradiation can cause  premature reverse transcription termination, which may decrease overall cDNA yield but is exploited in state of the art CLIP methods to identify these crosslink sites at single-nucleotide resolution. Here, we show the ratio of read-through versus termination is highly dependent on the identity of the reverse transcriptase enzyme as well as on buffer conditions used. Commonly used enzymes, including Superscript III and AffinityScript, show high termination rates in standard magnesium buffer conditions, but show a single base difference in the position of termination for TARDBP motifs. In contrast, manganese-containing buffer promoted read-through at the adduct site. These results validate the use of standard enzymes and suggest that alternative enzyme and buffer choices for particularly challenging samples that contain extensive RNA adducts or other modifications that inhibit standard reverse transcription.

overall_design: eCLIP-seq in HeK293T Cells

first: Eric

last: Van Nostrand

first: Alexander

last: Shishkin

first: Gabriel

last: Pratt

first: Thai

last: Nguyen


title: Receptor quaternary organization explains G protein-coupled receptor family structure.

city: Oxford

first: Simon

last: Davis

address: MRC Weatherall Institute of Molecular Medicine

department: Radcliffe Department of Medicine

country: United Kingdom

institute: University of Oxford

summary:
Purpose: To investigate the quaternary structures of Rhodopsin-family GPCRs.
Method: Analyzed 60 receptors from HEK 293T cells.
Results: 1) Most of these receptors are monomers. 2) The phylogenetic distribution of dimers suggests that monomers have an evolutionary advantage due to constraints imposed by dimerization on rates of receptor diversification.

overall_design: To investigate the quaternary structures of 60 Rhodopsin-family GPCRs expressed in HEK 293T cells using type-1 and -3 BRET assays.

last: Felce

first: Sarah

last: Latty

first: Rachel

middle: G

last: Knox

first: Susan

middle: R

last: Mattick

first: Yuan

last: Lui

first: Steven

middle: F

last: Lee

first: David

last: Klenerman

middle: J


title: Genome-wide Maps of Alkylation Damage, Repair, and Mutagenesis in Yeast Reveal Mechanisms of Mutational Heterogeneity

city: Pullman

first: John

middle: J.

last: Wyrick

state: WA

address: Biotechnology Life Sciences 241

department: School of Molecular Biosciences

institute: Washington State University

summary: DNA base damage is an important contributor to genome instability, but how the formation and repair of these lesions is affected by the genomic landscape is unknown. Here we describe genome-wide maps of DNA base damage, repair, and mutagenesis at single nucleotide resolution in yeast treated with the alkylating agent methyl methanesulfonate (MMS). Analysis of these maps revealed that base excision repair (BER) of alkylation damage is significantly modulated by chromatin, with faster repair in nucleosome free regions, and slower repair and higher mutation density within strongly positioned nucleosomes. Both the translational and rotational settings of lesions within nucleosomes significantly influence BER efficiency; moreover, this effect is asymmetric relative to the nucleosome dyad and is regulated by histone modifications. Our data also indicate that MMS-induced A mutations are significantly enriched on the non-transcribed strand (NTS) of yeast genes, particularly in BER-deficient strains, due to higher damage formation on the NTS and transcription-coupled repair of the transcribed strand (TS). These findings reveal the influence of chromatin on repair and mutagenesis of base lesions on a genome-wide scale, and suggest a novel mechanism for transcription-associated mutation asymmetry, which is frequently observed in human cancers.

overall_design: MMS lesion mapping data was analyzed for WT or mag1∆ yeast cells treated with 0.2% MMS or 0.4% MMS and allowed to repair for 0hr, 30 minutes, 1 hour, or 2 hours.

first: Peng

last: Mao


title: Co-overexpression of the constitutively active form of OsbZIP46 and ABA-activated protein kinase SAPK6 improves drought and temperature stress resistance in rice

city: Wuhan

first: Yu

last: Chang

state: Hubei

address: No.1, Shizishan Street, Hongshan District

department: National Key Laboratory of Crop Genetic Improvement

country: China

institute: Huazhong Agricultural University

summary: Drought is one of the major abiotic stresses threatening rice (Oryza sativa) production worldwide. Drought resistance is controlled by multiple genes, and therefore, a multi-gene genetic engineering strategy is theoretically useful for improving drought resistance. However, the experimental evidence for such a strategy is still lacking. In this study, a few drought-responsive genes from rice were assembled by a multiple-round site-specific assembly (MISSA) system, and the constructs were introduced into the rice cultivar KY131 via Agrobacterium-mediated transformation. The transgenic lines of the multi-gene and corresponding single-gene constructs were pre-evaluated for drought resistance. We found that the co-overexpression of two genes, encoding a constitutively active form of a bZIP transcription factor (OsbZIP46CA1) and a protein kinase (SAPK6) involved in the abscisic acid (ABA) signaling pathway, showed significantly enhanced drought resistance compared with the single-gene transgenic lines and the negative transgenic plants. Single-copy lines of this bi-gene combination (named XL22) and the corresponding single-gene lines were further evaluated for drought resistance in the field using agronomical traits. The results showed that XL22 exhibited greater yield, biomass, spikelet number, and grain number under moderate drought stress conditions. The seedling survival rate of XL22 and the single-gene overexpressors after drought stress treatment also supported the drought resistance results. Furthermore, expression profiling by RNA-Seq revealed that many genes involved in the stress response were specifically up-regulated in the drought-treated XL22 lines and some of the stress-related genes activated in CA1-OE and SAPK6-OE were distinct, which could partially explain the different performances of these lines with respect to drought resistance. In addition, the XL22 seedlings showed improved tolerance to heat and cold stresses. Our results demonstrate that the multi-gene assembly in an appropriate combination may be a promising approach in the genetic improvement of drought resistance.

overall_design: Transcriptome analysis of XL22, CA1-OE, and SAPK6-OE plants under both severe drought stress and normal growth conditions.

first: Lizhong

last: Xiong


title: Transcriptional effects of motor neuron autophagy inhibition

city: New York

first: Paolo

last: Guarnieri

state: NY

address: 1130 St. Nicholas Avenue

department: Systems Biology

institute: Columbia University

summary: To investigate the role of motor neuron autophagy in ALS, we generated mice in which the critical autophagy gene Atg7 was specifically disrupted in motor neurons (Atg7 cKO). We also bred these mice to the SOD1G93A mouse model of ALS. Then we performed RNA sequencing on lumbar spinal cords from these mice to determine how motor neuron autophagy inhibition altered gene expression.

overall_design: RNA-seq of lumbar spinal cords from four biological replicates each of 150 day-old Atg7 cWT, Atg7 cWT; SOD1G93A, Atg7 cKO and Atg7 cKO; SOD1G93A mice

first: Noam

middle: D

last: Rudnick

first: Tom

last: Maniatis


title: Genome-wide analysis of gene expression by E2F3 L430Q knock-in mutation in MEF cells in normal proliferation and serum starvation conditions

status: Public on Aug 09 2017

city: Chicago

first: Yang

last: Liao

state: IL

address: 929 East 57th Street

institute: The University of Chicago

summary: Analysis of E2F3 L430Q knock-in mutation in gene expression level. The hypothesis tested was gain-of-function of E2F3 L430Q mutation would induce particular gene expression. Results help to identify novel E2F3 targeted genes.

overall_design: Total RNA were extracted from E2F3 L430Q MEF cells compared to wild type MEF cells in proliferation or serum starvation conditions.

first: Wei

last: Du


title: Early life exposure to low levels of AHR agonist 3,3’,4,4’,5-pentachlorobiphenyl (PCB126) reprograms gene expression in adult brain.

city: Woods Hole

first: Neelakanteswar

last: Aluru

address: 45 Water Street

department: Biology

institute: Woods Hole Oceanographic Institution

summary: There is growing evidence from epidemiological and experimental studies suggesting that early life exposure to environmental chemicals can have long-term consequences that are seen in adults and not apparent early in life. We recently demonstrated that developmental exposure of zebrafish embryos to low, non-embryotoxic levels of PCB126 did not affect larval behavior but caused changes in adult behavior (Glazer et al., 2016, NeuroToxicology 52:134-143). Zebrafish embryos were exposed to either vehicle (DMSO) or low concentrations of PCB126 (0.3, 0.6, 1.2 nM) for 20 h (4–24 h post fertilization), and then reared to adulthood in clean water. Locomotor activity of the larvae at 7 and 14 days post fertilization (dpf) was not affected by PCB126. In contrast, adult fish (4 months old) tested in novel tank and shoaling assays showed impaired habituation to a novel environment. In order to investigate the underlying molecular basis of these phenotypes, we determined the transcriptional profiles in whole embryos (48 hpf), larvae (5 dpf) and adult brain (4 mo) using strand-specific RNA-sequencing. Our results show that 0.3 nM PCB126 exposure induced cyp1a transcript levels 12.5-fold in 48-hpf embryos but there was no induction in 5-dpf larvae, suggesting transient activation of aryl hydrocarbon receptor during early development. No significant induction of cyp1a was observed in the brains of adults exposed as embryos to PCB126. However, we observed significant changes in gene expression profiles in the adult brain samples. A total of 2209 and 1628 genes were differentially expressed in 0.3 nM and 1.2 nM PCB126-exposed groups, respectively. KEGG pathway analysis of differentially expressed genes in the brain suggest enrichment of genes involved in oxidative phosphorylation, neurodegenerative diseases, circadian rhythm and calcium signaling pathways. We are currently investigating the role of these genes in altered behavior observed in the adults. Overall, our results suggest that PCB exposure during sensitive periods of early development alters normal development of the brain by reprogramming gene expression patterns. [Funded by NIH P01ES021923 and NSF OCE-1314642].

overall_design: A total of 24 samples were sequenced. It includes 3 different time points and 2 or 3 different treatments. Each treatment had 3 biological replicates.

first: Lilah

last: Glazer

first: Mark

middle: E

last: Hahn


title: EZH2 enables germinal center formation through epigenetic silencing of CDKN1A and an Rb-E2F1 positive feedback loop

first: Matt

last: Teater

address: 445 E 69th St

institute: Weill Cornell Medical College

summary: The EZH2 histone methyltransferase is required for B cells to form germinal centers (GCs). Here we show that EZH2 mediates GC formation through repression of cyclin-dependent kinase inhibitor CDKN1A (p21Cip1). Deletion of Cdkn1a rescued the GC reaction in Ezh2 knockout mice. To study the effects of EZH2 in primary GC B cells we generated and validated a 3D B cell follicular organoid system that mimics the endogenous GC reaction. Using this system we found that depletion of EZH2 suppressed G1 to S phase transition of GC B cells in a Cdkn1a dependent manner. GC B cells of Cdkn1a;Ezh2 double knockout mice exhibited high levels of phospho Rb, indicating that loss of Cdkn1a allows progression of cell cycle. Moreover, we show that the transcription factor E2F1 plays a major role in inducing EZH2 upregulation during the GC reaction. E2F1 deficient mice manifest impaired GC responses, which was rescued by restoring EZH2 expression, thus defining a positive feedback loop whereby EZH2 controls GC B cell proliferation by suppressing CDKN1A, allowing cell cycle progression with a concomitant phosphorylation of Rb and release of E2F1.

overall_design: gene expression profiles of murine B cells

first: W

last: Beguelin

first: Olivier

last: Elemento

first: Ari

middle: M

last: Melnick


title: lncRNA profiles in colorectal cancer

status: Public on Aug 08 2017

city: Guangzhou

first: Jiaxin

last: Lin

state: Guangdong

address: 651 Dongfeng East Road

institute: Sun Yat-sen University Cancer Center

summary: Long noncoding RNAs (lncRNAs) have been shown to play critical roles in the biology of various cancers. However, their expression patterns and biological functions in human colorectal cancer (CRC) remain largely unknown. The aim of this study was to explore lncRNA profiles in CRC and investigate key lncRNAs involved in CRC tumourigenesis and progression.

overall_design: 6 CRC tissues and matched normal tissues

first: Xin

last: Tan

first: Lin

last: Qiu

first: Long

last: Huang

first: Yi

last: Zhou

first: Zhizhong

last: Pan

first: Ranyi

last: Liu

first: Shuai

last: Chen

first: Rong

last: Geng

first: Jiangxue

last: Wu

first: Wenlin


title: Permissive zones for the centromere-binding protein ParB on the Caulobacter crescentus chromosome

city: Norwich

first: Tung

middle: Ba  Khanh

last: Le

state: Norfolk

address: Colney Lane

department: Department of Molecular Microbiology

institute: John Innes Centre

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Proper chromosome segregation is essential in all living organisms if daughter cells are each to inherit a full copy of genetic information. In Caulobacter crescentus, the ParA-ParB-parS system is required for proper chromosome segregation and cell viability. The bacterial centromere-like parS DNA locus is the first to be segregated following chromosome replication. parS is recognized and bound by ParB protein, which in turn interacts with ParA to partition the ParB-parS nucleoprotein complex to each daughter cell. In this study, we investigated the genome-wide distribution of ParB on the Caulobacter chromosome using a combination of in vivo chromatin immunoprecipitation (ChIP-seq) and in vitro DNA affinity purification with deep sequencing (IDAP-seq). We confirmed two previously identified parS sites and discovered at least three more sites that cluster ~8 kb from the origin of replication. We showed that Caulobacter ParB nucleates at parS sites, then associates non-specifically with flanking DNA to form a high-order nucleoprotein complex that occupies an extensive ~10 kb DNA segment on the left chromosomal arm. Lastly, using transposon mutagenesis coupled with deep sequencing (Tn-seq), we identified a ~500 kb region surrounding the origin of replication and a ~100 kb region surrounding the terminus of the Caulobacter chromosome that are tolerable to the insertion of a second parS cluster without severely affecting cell viability. Our results demonstrate that the genomic distribution of the bacterial centromere-like parS is highly restricted and is crucial for chromosome segregation in Caulobacter.

sample_organism:
Escherichia coli
Caulobacter vibrioides

platform_organism:
Escherichia coli
Caulobacter vibrioides

overall_design: Chromatin-immunoprecipitation with deep sequencing experiments (ChIP-seq) were performed on exponential-growing Caulobacter crescentus and Escherichia coli (see the supplementary Materials and Methods for the exact treatment that were applied to each strain). In vitro affinity purification with deep sequencing (IDAP-seq) were performed using sonication-fragmented genomic DNA from Caulobacter crescentus and purified ParB-His6 (or no protein in the case of a negative control). Random transposon mutagensis with deep sequencing (Tn5-seq) were performed for wild-type (WT) and Δsmc Caulobacter crescentus. Half a million to a million of single colonies of WT and Δsmc Caulobacter crescentus were collected from PYE plates, pooled together and their genomic DNA were extracted for Tn5-seq.

first: Ngat

last: Tran

first: Clare

last: Stevenson

first: Nicolle

last: Som

first: Anyarat

last: Thanapipatsiri

first: Adam

last: Jalal

middle: B


title: E. coli BW25113 azide treated vs untreated cells

city: Birmingham

first: Damon

last: Huber

address: Edgbaston

department: School of Biosciences

institute: University of Birmingham

summary: Transcriptional profiling of mid-log phase (OD600 ~ 0.8) E. coli BW25113 cells grown treated with 2 mM NaN3 for 10 minutes

platform_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: 2-condition experiment, untreated v. treated, 2 biological replicates


title: Biological and RNA Regulatory Function of MOV10 in Mammalian Germ Cells

city: Nanjing

first: Suwen

last: Tian

address: 101Longmian Avenue

institute: Nanjing Medical University

summary:
Background: RNA regulation by RNA-binding proteins (RBPs) involve extremely complicated mechanisms. MOV10 and MOV10L1 are two homologous RNA helicases implicated in distinct intracellular pathways. MOV10L1 participates specifically in Piwi-interacting RNA (piRNA) biogenesis and protects mouse male fertility. In contrast, the functional complexity of MOV10 remains incompletely understood, and its role in the mammalian germline is unknown. Here we report a study of the biological and molecular functions of the RNA helicase MOV10 in mammalian male germ cells.

Results: MOV10 is a nucleocytoplasmic protein mainly expressed in spermatogonia. Knockdown and transplantation experiments show that MOV10 deficiency has a negative effect on spermatogonial progenitor cells (SPCs), limiting proliferation and in vivo repopulation capacity. This effect is concurrent with a global disturbance of RNA homeostasis and downregulation of factors critical for SPC proliferation and/or self-renewal. Unexpectedly, microRNA (miRNA) biogenesis is impaired due partially to decrease of miRNA primary transcript levels and/or retention of miRNA via splicing control. Genome-wide analysis of RNA targetome reveals that MOV10 binds preferentially to mRNAs with long 3'-UTR, and also interacts with various non-coding RNA species including those in the nucleus. Intriguingly, nuclear MOV10 associates with an array of splicing factors, particularly with SRSF1, and its intronic binding sites tend to reside in proximity to splice sites.

Conclusions: These data expand the landscape of MOV10 function and highlight a previously unidentified role initiated from the nucleus, suggesting that MOV10 is a versatile RBP involved in a broader RNA regulatory network.

overall_design: Triplicate identification of transcripts associated with MOV10 in mice testes, triplicate mRNA profiles and miRNA profile of Mov10 knockdown and control in spermatogonial progenitor cells were generated  by deep sequencing.

first: Kaiqiang

last: Fu

first: Huanhuan

first: Caifeng

last: Wang

first: Hanben


title: RNA Sequencing of Novel HIV RNA TAR-gag and Host Genome of EVs from HIV-1 Infected Cells

city: Manassas

first: Fatah

last: Kashanchi

address: 10900 University Blvd

institute: George Mason University

summary: We performed a 3' RACE of a novel HIV RNA TAR-gag in order to determine the sequence of the RNA at the 3' end.  Our data had shown that TAR-gag was potentially a noncoding RNA and our hypothesis was that TAR-gag ended somewhere prior to the end of the gag region of the HIV genome.  The 3' RACE experiment showed that TAR-gag actually consists of four different RNA clusters, the longest of which ends at 615 bases from the transcription start site; this is in the middle of the p17 region of the gag gene. In addition, we sequenced all host RNAs in the EVs.

overall_design:
RNA from J1.1 and U1 exosomes was isolated and converted to cDNA.  Sequencing libraries of the cDNA were made and a 3' RACE was perforemed to determine how long TAR-gag RNA is.
Please note that the clustering analysis (published in PMID 28536264) was done only on the unfragmented samples (i.e. *-U samples).

first: Jeffrey

middle: S

last: Chu


title: Characterization of microRNAs of Beta macrocarpa and their responses to Beet necrotic yellow vein virus infection [miRNA array]

status: Public on Aug 07 2017

city: Beijing

first: Junying

state: Beijing

address: yuan ming yuan weat road

department: Plant Pathology

institute: China Agricultural University

summary: Plant microRNAs (miRNAs) are a class of non-coding RNAs that play important regulatory roles in plant development, defense and abnormal disease symptom formation. Here, 547 known miRNAs, representing 129 miRNA families, and 282 potential novel miRNAs were identified in Beta macrocarpa using small RNA deep sequencing. Through a differential expression analysis, miRNAs responding to Beet necrotic yellow vein virus (BNYVV) infection were identified and confirmed using a microarray analysis. In total, 103 known miRNAs, representing 38 miRNA families, and 45 potential novel miRNAs were differentially regulated, with at least a two-fold change, in BNYVV-infected plants compared with the mock-inoculated control. These differentially expressed miRNAs were involved in hormone biosynthesis and signal transduction pathways, and enhanced axillary bud development and plant defenses. This work is the first to describe miRNAs of the plant genus Beta and may offer a reference for miRNA research in other species in the genus. It provides valuable information on the pathogenicity mechanisms of BNYVV.

overall_design: MicroRNAs of Beta macrocarpa and their responses to Beet necrotic yellow vein virus infection was investigated using systemic leaves of BNYVV-inoculated B. macrocarpa (15 dpi) as the experimental group and healthy plants as the control group by Two-condition experiment.

first: Jun-ying

first: Yongliang

last: Zhang


title: Characterization of microRNAs of Beta macrocarpa and their responses to Beet necrotic yellow vein virus infection

last: Liu

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

overall_design: Refer to individual Series


title: Enhanced Inflammatory Transcriptome in the Granulosa Cells of Women With Polycystic Ovarian Syndrome

first: JoAnne

last: Richards

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

summary: Context: Polycystic ovarian syndrome (PCOS), the most common endocrine disorder of reproductive-  aged women, is associated with systemic low-grade inflammation.  Objective: We propose that increased or altered intrafollicular inflammatory reactions also occur  in periovulatory follicles of PCOS patients.  Design: Gene profiling and quantitative PCR (qPCR) analyses in granulosa-lutein cells (GCs) collected  from PCOS and non-PCOS women undergoing in vitro fertilization were compared with  serum and follicular fluid (FF) levels of cytokines and chemokines.  Setting: This was a university-based study.  Patients: Twenty-one PCOS and 45 control patients were recruited: demographic, hormone, body  mass index, and pregnancy outcomes were abstracted from patient data files.  Interventions:GCcytokine/chemokinemRNAswere identified and analyzed by gene-chip microarrays/  qPCR before and after culture withhumanchorionic gonadotropin, DHT, IL-6, or IL-8; serum/FF  cytokine levels were also analyzed.  Main Outcome Measures: Relative serum/FF cytokine levels and GC cytokine expression before and  after culture were compared and related to body mass index.  Results: The following results were found: 1) PCOS GCs express elevated transcripts encoding  cytokines, chemokines, and immune cell markers, 2) based on gene profiling and qPCR analyses,  obese PCOS patients define a distinct PCOS disease subtype with the most dramatic increases in  proinflammatory and immune-related factors, and 3) human chorionic gonadotropin and DHT  increased cytokine production in cultured GCs, whereas cytokines augmented cytokine and vascular  genes, indicating that hyperandrogenism/elevated LH and obesity in PCOS women augment  intrafollicular cytokine production.  Conclusions: Intrafollicular androgens and cytokines likely comprise a local regulatory loop that  impacts GC expression of cytokines and chemokines and the presence of immune cells; this loop is  further enhanced in the obese PCOS subtype.

overall_design: A direct comparison of human granulosa cells from six different pooled sample groups that were distinct for PCOS status, BMI, and cytokine profile.

first: Jaye

last: Adams

first: Zhilin

first: Yi

middle: A

last: Ren

first: Wan-Song

last: Wun

first: Wei

last: Zhou

first: Shlomit

last: Kenigsberg

first: Clifford

last: Librach

first: Cecilia

last: Valdes

first: William

last: Gibbons


title: Genome analysis of gene expression by THP-1 macrophage during Brucella abortus wild type and mutant strains infection

status: Public on Aug 05 2017

first: Soojin

last: Shim

address: Kwan-ak ro

summary: Brucella abortus (B. abortus), an intracellular bacterium, is the causative agent of Brucellosis. This organism invades into macrophages and then survives through its abilities to modulate host cells functions. The biggest problem caused by B. abortus is that it prevents macrophage elimination and makes it difficult to remove B. abortus from the host body. Therefore, it is essential to identify the bacterial genes involved in virulence factor as a first step to understanding the bacterial pathogenicity and controlling Brucellosis. To identify these genes, B. abortus mutant strains were generated using transposon mutagenesis and transcriptomic profile during macrophage infection were analyzed.  The gene expression level was analyzed using total RNA obtained from THP-1 cells infected with B. abortus wild type and mutant strains and cellular immunity during the infections were compared to wild type infected cell to identify the role of genes in B. abortus pathogenicity. Transcriptomic profiling showed that two mutant strains having disrupted genes related to 4-hydrobenzoate 3-monooxygenase (PHBH) of C1 strain and heme exporter protein cytochrome C (CcmC) of C10 strain, induced suppression of cytokine expression during infection in human macrophages. Conversely, two other mutant strains of exopolyphosphatase (PPX)of C27 and Peptidase M24 of C32 induced activation of cytokine expression in the THP-1 macrophage cells.

overall_design: Total RNA obtained from THP-1 cells after stimulation with B. abortus mutant strains was compared to RNA from THP-1 cells infected with B. abortus wild type. All of RNA was obtained at 24 hours after stimulation.

first: Han

last: Yoo


title: Hit-and-run epigenetic editing prevents senescence entry in primary breast cells from healthy donors [EPIC methylation]

city: London

first: Emily

last: Saunderson

address: Charterhouse Square

institute: Barts Cancer Institute

type: Methylation profiling by genome tiling array

summary: Aberrant promoter DNA hypermethylation is a hallmark of cancer; however, whether this is sufficient to drive cellular transformation in the absence of genetic mutations is not clear. To investigate this question, we use a CRISPR/dCas9 based epigenetic editing tool, where an inactive form of Cas9 is fused to DNMT3A and its regulator DNMT3L. Using this system, we show simultaneous de novo DNA methylation of genes commonly methylated in cancer, CDKN2A, RASSF1, HIC1 and PTEN in primary myoepithelial cells isolated from healthy human breast tissue. We find that promoter methylation is maintained in this system, even in the absence of the fusion construct and results in sustained repression of CDKN2A and RASSF1 transcripts which prevents cells from entering senescence. The phenotype is associated with retuned expression of a subset of genes to levels in early passage cells; however, the outgrowing myoepithelial cells are not immortal but proliferate for 25-30 population doublings before cell cycle arrest. Finally, we show that the key driver of this phenotype is repression of CDKN2A transcript p16, but prolonged proliferation is enhanced by combined hypermethylation and repression of both CDKN2A transcripts p16 and p14. This work demonstrates that hit-and-run epigenetic events can prevent senescence entry, a potential first step in the disease process.

overall_design: EPIC array data for n=3 samples, primary myoepithelial cells from donor 1 transfected with either dCas9 3A3L or dCas9 3A3L delta and 26x gRNAs targeting genes of interest in cancer, and harvested 10 days after transfection. N=1 early passage myoepithelial cells from donor 2 and n=1 for cells from donor 2 38 days after transfection with dCas9 3A3L.

first: Gabriella

last: Ficz


title: Hit-and-run epigenetic editing prevents senescence entry in primary breast cells from healthy donors [EPIC methylation 2]

overall_design: EPIC array data for n=1 early passage myoepithelial cells from donor 1 and n=1 for cells from donor 1 37 days after transfection with dCas9 3A3L.


title: Different molecular complexes that mediate transcriptional induction and repression by FoxP3

city: Boston

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: ChIP-seq profile of WT or mutant FoxP3 in CD4+ T cells

overall_design: Activated CD4+FoxP3 retrovirally transduced with WT or mutant FoxP3 were single sorted based on Thy1,1 and ChIP-seq profiling was perfomed.

first: HoKeun

last: Kwon

first: Diane

last: Mathis

first: Christophe

last: Benoist


title: Lineage-specific transcription factors regulate DNA methylation dynamics during hematopoietic development [ChIP-Seq]

city: Yokohama

first: Takahiro

last: Suzuki

state: Kanagawa

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

department: Center for Integrative Medical Sciences

country: Japan

institute: RIKEN

summary: DNA methylation is a major epigenetic modification for gene silencing and is dramatically altered spatiotemporally during cellular development. However, the roles of DNA methylation dynamics and regulation in cellular development remain unclear. The present analyses of DNA methylome dynamics during hematopoietic development suggest that DNA demethylation pre-defines the gene expression potential of terminal differentiation-specific genes at the progenitor cell stage and is regulated by lineage-specific transcription factors (TFs). Demethylation of majority of hypo-methylated CpGs in terminally differentiated cells occurs during the progenitor cell stage and is associated with rapid upregulation of terminal differentiation-specific genes. Accordingly, TF overrepresentation analyses indicated that lineage-specific TFs regulate DNA demethylation. The present experiments show that RUNX1 induces site-directed active DNA demethylation by recruiting DNA demethylation enzymes. Collectively, the present data indicate an integrated system of DNA methylation and gene expression during cellular development.

overall_design: RUNX1 and TET2 binding site profiling.

first: Yuri

last: Shimizu

first: Erina

last: Furuhata

first: Shiori

last: Maeda

first: Mami

last: Kishima

first: Hajime

last: Nishimura

first: Yoshihide

last: Hayashizaki

first: Harukazu


title: Hit-and-run epigenetic editing prevents senescence entry in primary breast cells from healthy donors


title: Lineage-specific transcription factors regulate DNA methylation dynamics during hematopoietic development


title: Combined analysis of oligonucleotide microarray data from transgenic and knockout mice identifies direct SREBP target genes [MG_U74Cv2]

city: Research Triangle Park

first: Christopher

last: Corton

state: NC

address: 109 TW Alexander Dr.

institute: US-EPA

summary: The synthesis of fatty acids and cholesterol is regulated by three membrane-bound transcription factors: sterol regulatory element-binding proteins (SREBP)-1a, -1c, and -2. Their function in liver has been characterized in transgenic mice that overexpress each SREBP isoform and in mice that lack all three nuclear SREBPs because of gene knockout of SREBP cleavage-activating protein (SCAP) required for nuclear localization of SREBPs. Here, we use oligonucleotide arrays hybridized with RNA from livers of three lines of mice (transgenic for SREBP-1a, transgenic for SREBP-2, and knockout for SCAP) to identify genes that are likely to be direct targets of SREBPs in liver. Application of stringent combinatorial criteria to the transgenic/knockout approach allows identification of genes whose activities are likely controlled directly by the SREBPs.

overall_design: Transgenic mice that overexpress transcriptionally active nuclear forms of human SREBP-1a (TgSREBP-1a) or SREBP-2 (TgSREBP-2) and mice that lack SCAP (Scap–/–) in liver were used. Studies included five 12- to 16-wk-old male TgSREBP-1a and TgSREBP-2 mice and five male littermate wild-type controls. Mice were fed a high protein/low carbohydrate diet for 2 weeks before liver removal to elicit high-level expression of the nSREBPs. Studies using liver-specific Scap–/– mice included five 10- to 12-wk-old male Scap–/–;MX1-Cre and corresponding wild-type mice that received four i.p. injections of polyinosinic-polycytidylic acid to induce the Cre recombinase. Mice were fed Teklad chow and livers removed 14 days after the last injection. Liver RNA was prepared using RNA STAT-60 (Tel-Test, Friendswood, TX). Equal aliquots of total RNA from each of five mice per group were pooled (total, 20 μg) and used for biotin labeling as described in the Affymetrix technical bulletin. Hybridization, washing, scanning, and analysis of the Affymetrix GeneChip Murine Genome MU74A, -B, and -C version 2 arrays (Affymetrix, Santa Clara, CA) were carried out. Duplicate hybridizations were performed with each RNA sample and data processed with MICROARRAY SUITE 5.0 (Affymetrix) software.

first: Jay

last: Horton

first: Nila

last: Shah

first: Janet

last: Warrington

first: Norma

middle: N

last: Anderson

first: Sahng

middle: W

last: Park

first: Michael

last: Brown

first: Joseph

middle: L

last: Goldstein


title: Transcriptome profiling of ozone responses of Arabidopsis thaliana natural accessions Col-0 and Cvi-0, and a near-isogenig line Col-S with Cvi-0's ozone sensitivity introgressed into Col-0

city: Helsinki

first: Mikael

last: Brosché

address: Viikinkaari 1

department: Department of Biosciences

country: Finland

institute: University of Helsinki

summary: Many Arabidopsis thaliana accession show sensitvity to the air pollutant ozone,  including the accession Cvi-0 from the Cape Verde Islands. To understand and assist in genetic mapping of loci causing the ozone sensitvity of Cvi-0, transcript profiling was performed in Cvi-0, the tolerant Col-0, and a near isogenic line (Col-S) where ozone sensitivity was introgressesed from Cvi-0 to Col-0 through eight rounds of backcrossing.

overall_design: The near isogenic line Col-S and its parents Col-0 and Cvi-0 were grown for three weeks and treated with 350 ppb ozone for two hours. The whole rosettas were harvested from controls and and ozone treated plants. Three separate biological repeats used for RNA-seq analysis.

first: Lauri

last: Vaahtera

first: Enjun

last: Xu


title: Combined analysis of oligonucleotide microarray data from transgenic and knockout mice identifies direct SREBP target genes [MG_U74Bv2]


title: Gene expression profiles of mice BMDCs treated with Nitidine Chloride or vehicle following LPS stimulation

city: Shanghai

first: niao

last: Yang

address: 325 Guohe Road

institute: Second Military Medical University,

summary:
Nitidine Chloride(NC) were found to enhance IL-10 production in LPS-stimulated Bone-marrow dendritic cells(BMDCs ) ,while at the same time inhibit pro-inflammatory cytokines production, such as TNF- α and IL-6. BMDCs were treated with NC or vehicle following LPS stimulation to find out the influence of NC on BMDCs that regulate cytokines expression.
This study indicated that NC regulate numerous gene expression, thus influence IL-10 and pro-inflammatory cytokines production in LPS-treated BMDCs.

overall_design: We produced the gene expression profiles of mice BMDCs in four groups. BMDCs were incubated with vehicle or the of NC for 12 h and then stimulated with vehicle or LPS 1 μg/ml for 12 h.

first: Niao

first: Rongcai

last: Yue

first: Chao

last: Lv

first: Ping

last: Li

first: Wencai

first: Yizhi

last: Yu

first: Weidong

last: Zhang


title: Combined analysis of oligonucleotide microarray data from transgenic and knockout mice identifies direct SREBP target genes [MG_U74Av2]

first: Christopher

last: Corton

first: Jay

first: Nila


title: Combined analysis of oligonucleotide microarray data from transgenic and knockout mice identifies direct SREBP target genes


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

status: Public on Aug 04 2017

city: Rockville

first: Khadijah

last: Mitchell

state: MD

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.

overall_design:
We used microarrays to detail differential microRNA expression in African Americans and European Americans with non-small cell lung cancer.
Patient characteristics for the miRNA cohort (n = 42 AAs and n = 55 EAs). The miRNA cohort included 38 matched pairs and 2 unmatched pairs from AA. All the EA samples were matched. Differential expression and hypergeometric testing for overlapping mRNA targets were performed.
This submission includes data for 39 AA patients and 52 EA patients.

first: Brid

last: Ryan


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

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


title: Microarray data from e4.5 mouse trophectoderm on high fat vs control diet

city: PHILADELPHIA

first: Tami

last: Stuart

state: PA

address: 421 Curie Blvd, BRB II/III, CRRWH Rm 1341

department: Pediatrics

institute: CHOP

summary:
Maternal obesity can lead to altered outcomes for offspring, and it is believed that the placenta plays a role in this fetal programming.
We sought to examine the effects on maternal diet-induced obesity on changes in gene expression at the earliest stages of placenta development using microarray

overall_design: e4.5 blastocyts were flushed from female mice exposed to a control or high fat diet.  The trophectoderm was removed, and the trophectoderm from 5 blastocyts was pooled to produce a single sample.  RNA was isolated  from 4 replicates each from control or high fat diet mice.  cDNA was generated and samples were hybridized to an Affymetrix array

first: Isaac

last: Sasson


title: Regulation of gene expression by HIF-2alpha in multiple myeloma

city: Adelaide

first: Andrew

last: Zannettino

state: SA

address: SAHMRI, North Terrace

department: Faculty of Health and Medical Sciences

country: Australia

institute: University of Adelaide

summary: Proliferation of neoplastic plasma cells within the bone marrow leads to reduced oxygen availability. In response to hypoxia, the transcription factor hypoxia-inducible factor-2alpha (HIF-2α) is activated and stabilised. We hypothesise that activation of HIF-2α is a central driver of multiple myeloma disease progression, leading to the induction of transcription of genes associated with angiogenesis, osteoclast activation and cell migration. In this study we assessed the affects of HIF-2α overexpression on gene expression in the human myeloma cell line LP-1.

overall_design: 2 samples: LP-1 cell line stably overexpressing HIF-2α (LP-1-HIF2A) and empty vector control cells (LP-1-pRUF)

middle: C

first: Peter

last: Diamond

first: Kate

last: Vandyke


title: Gene expression signatures associated with Perineural Invasion in pancreatic ductal adenocarcinoma

first: Yongwei

last: Sun

address: 160 Pujian Rd

department: Department of Biliary-Pancreatic Surgery

institute: Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University

summary: Perineural invasion (PNI) is a prominent characteristic of pancreatic ductal adenocarcinoma (PDAC) and indicates poor prognosis. The invasion of the surrounding nerves by pancreatic cancer cells not only provides route for metastasis but also contributes to neural remodeling and changes in the neuronal milieu that can profoundly influenced the microenvironment of pancreatic cancer. To investigate the downstream molecules associated with PNI, the experiment analyzed mRNA expression of 50 pairs of pancreatic ductal adenocarcinoma tissue and paired adjacent non-tumor tissue, among which 28 pairs of cases diagnosed with PNI by experienced pathologist. Results provide new insight into molecular basis for the influence of PNI on the microenvironment of pancreatic cancer.

overall_design: The aim of our work was to characterize downstream molecules influenced by the perineural invasion of pancreatic cancer. For this purpose, we generated and compared expression profiles of PDAC tissue from patients diagnosed with PNI (n=28) and PDAC tissue from patients without PNI (n=22).

first: Zhigang

first: Jing

last: Xue


title: The effect of obestatin contained in the breast milk on the structural and functional development of the offspring in the early postnatal period

city: Jablonna

first: Monika

last: Słupecka-Ziemilska

address: Instytucka 3

department: Animal Physiology

country: Poland

institute: The Kielanowski Institute of Animal Physiology and Nutrition, Polish Academy of Sciences

summary: Recent studies indicated that obestatin may play a regulatory role in the development of gastrointestinal track in the early postnatal period. The project aimed to understand the effect of obestatin in the development of structure and function ot he small intestine in the early postnatal period. Results shown that enteral administration of obestatin to suckling rats significanlty effects on activity of brush border enzymes, morphometry of intestinal wall as well as small intestinal epithelial renewal. The effect of observed changes was dependent on the segment of intestine studied. Significant changes in the transcriptomic gene profile were founded both in the middle part of intestine and stomach

overall_design: The study was conducted on suckling Wistar rats which were administrated either obestatin (NOH, 250 nmoles/ kg b.wt) or saline solution (NC) twice a day starting from the 14th day of life till the 21st day of life which was the day when all animals were euthanised.

last: Słupecka

first: Jarosław

last: Woliński

first: Magdalena

last: Hulanicka

first: Alicja

last: Majewska

first: Michał

last: Jank


title: Spatially varying cis-regulatory divergence in Drosophila embryos elucidates cis-regulatory logic

city: Stanford

middle: Acuña

last: Combs

address: Gilbert Rm 309, 371 Serra Mall

institute: Stanford University

summary: Both cis- and trans-acting changes could accumulate and participate in complex interactions, so to isolate the cis-regulatory component of patterning evolution, we measured allele-specific spatial gene expression patterns in Drosophila melanogaster × D. simulans hybrid embryos. RNA-seq of cryosectioned slices revealed 55 genes with strong spatially-varying allele-specific expression, and several hundred more with weaker but significant spatial divergence.  Combined with mathematical modeling and regulatory locus editing, we determine the SNP responsible for the allele-specific expression observed in the gene hunchback.

sample_organism: Drosophila melanogaster x Drosophila simulans

overall_design: Embryonic mRNA profiles of mid-stage 5 hybrid and parental embryos were generated using RNA-seq

first: Hunter

last: Fraser


title: Transcriptome profiling of microRNA-induced neurons, microRNA-induced motor neurons, and starting fibroblasts [array]

city: Saint Louis

first: Matthew

middle: James

last: McCoy

state: MO

address: 4523 Clayton Ave, MCD SCI 361

department: Developmental Biology

institute: Washington University in St. Louis

summary: Neuronal microRNAs miR-9/9* and miR-124 (miR-9/9*-124) direct cell-fate conversion of adult human fibroblasts to post-mitotic neurons and work in concert with additional transcription factors to enable the generation of discrete neuronal subtypes. Previously, the molecular events underlying the neurogenic switch mediated by microRNAs during neuronal reprogramming were unknown. Here, we systematically dissected the neurogenic state induced by miR-9/9*-124 alone. We found that miR-9/9*-124 surprisingly stimulate reconfiguration of chromatin accessibility, DNA methylation and mRNA levels, leading to the generation of functionally excitable neurons that are not yet biased towards a particular subtype-lineage. Further subtype identity can be programmed through additional transcription factors. As such, we show ISL1 and LHX3 selectively commit conversion to a highly homogenous population of human spinal cord motor neurons. Taken together, our study reveals a modular synergism between microRNAs and transcription factors that allows lineage-specific neuronal reprogramming, providing a platform for generating distinct subtypes of human neurons.

overall_design: Gene expression was examined in starting human fibroblasts, microRNA-induced neurons (miNs), and microRNA-induced motor neurons (moto-miNs) after 35 days of miR-9/9*-124 and transcription factor expression, in duplicate.

last: Yoo

first: Daniel

middle: G

last: Abernathy


title: Transcriptome profiling at day 30 of microRNA-mediated neuronal reprogramming [RNA-seq d30]

summary: Neuronal microRNAs, miR-9/9* and miR-124 (miR-9/9*-124), exert reprogramming activities to direct cell-fate conversion of adult human fibroblasts to post-mitotic neurons and enable the generation of discrete neuronal subtypes with additional transcription factors. Previously, the molecular events underlying the neurogenic switch mediated by microRNAs during neuronal reprogramming were unknown. Here, we systematically dissected the neurogenic state induced by miR-9/9*-124 alone and reveal the surprising capability of miR-9/9*-124 in coordinately stimulating the reconfiguration of chromatin accessibilities, DNA methylation and transcriptome, leading to the generation of functionally excitable neurons, yet unbiased towards a particular subtype-lineage. We show that the microRNA-induced neuronal state enables additional transcription factors, ISL1 and LHX3, to selectively commit conversion to a highly homogenous population of human spinal cord motor neurons. Taken together, our study reveals a modular synergism between microRNAs and transcription factors that allows lineage-specific neuronal reprogramming, providing a platform for generating distinct subtypes of human neurons.

overall_design: Human fibroblasts were reprogrammed by microRNAs miR-9/9* and miR-124 (miNs). To profile transcriptome of the reprogrammed cells, mRNA were isolated from miNs day 30 and starting fibroblasts.

first: W

middle: K

last: Kim

first: A


title: Genome-wide profiling of DNA methylation by MRE-seq during microRNA-mediated neuronal reprogramming [MRE-seq]

type: Methylation profiling by high throughput sequencing

overall_design: Neonatal human fibroblasts were reprogrammed by microRNAs miR-9/9* and miR-124. DNA was collected at days 10, 20 and 30 into reprogramming for reprogrammed samples (9124), as well as for samples transduced with a non-specific microRNA control (NS). Libraries were prepared for methylation-sensitive restriction enzyme sequencing (MRE-seq).

first: M

middle: J

first: X

last: Xing

first: D

last: Li

first: T

last: Wang


title: Genome-wide profiling of DNA methylation by MeDIP-seq during microRNA-mediated neuronal reprogramming [MeDIP-seq]

overall_design: Neonatal human fibroblasts were reprogrammed by microRNAs miR-9/9* and miR-124. DNA was collected at days 10, 20 and 30 into reprogramming for reprogrammed samples (9124), as well as for samples transduced with a non-specific microRNA control (NS). Libraries were prepared for methylated DNA-immunoprecipitation sequencing (MeDIP-seq).


title: Genome-wide profiling of chromatin accessibility during microRNA-mediated neuronal reprogramming [ATAC-seq]

overall_design: Human fibroblasts were reprogrammed by microRNAs miR-9/9* and miR-124 (miNs) or transduced with a non-specific microRNA control (Ctrl). To profile chromatin accessibility during neuronal reprogramming, samples were collected at Ctrl day 10, miNs day 10 and miNs day 20. For Brg1 knockdown in reprogrammed cells, miNs were transduced with shBRG1 or shEGF and samples were collected at shBRG1 day 20 and shEGFP day 20. ATAC-seq was performed as previously described (Buenrostro et al., 2013).


title: Dynamic epigenetic remodeling underlies microRNA-mediated transdifferentiation of human adult fibroblasts into neuronal subtypes

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

overall_design: Refer to individual Series


title: Myc regulates chromatin decompaction and nuclear architecture during B cell activation

city: bethesda

first: Seolkyoung

last: Jung

address: 10 Center Dr

department: NIAMS

institute: NIH

summary: 50 years ago, Vincent Allfrey and colleagues discovered that lymphocyte activation triggers massive acetylation of chromatin. However, the molecular mechanisms driving epigeneticaccessibility are still unknown. We here show that stimulated lymphocytes decondense chromatin by three differentially regulated steps. First, chromatin is repositioned away from the nuclear periphery in response to global acetylation. Second, histone nanodomainclusters decompact into mononucleosome fibers through a mechanism that requires Mycand continual energy input. Single-molecule imaging shows that this step lowers transcription factor residence time and non-specific collisions during sampling for DNA targets. Third, chromatin interactions shift from long range to predominantly short range, and CTCF-mediated loops and contact domains double in numbers. This architectural change facilitates cognate promoter-enhancer contacts and also requires Myc and continual ATPproduction. Our results thus define the nature and transcriptional impact of chromatin decondensation and reveal an unexpected role for Myc in the establishment of nuclear topology in mammalian cells.

overall_design: Chip-Seq of 36 histone modifications, Gro-Seq, Mnase-Seq, ATAC-seq and Hi-C from mouse resting, activated B cells and various conditions on B cells

first: Kyong-Rim

last: Kieffer-Kwon

first: Keisuke

last: Nimura

first: Suhas

last: Rao

first: Jianliang

last: Xu

first: Aleksandra

last: Pekowska

first: Marei

last: Dose

first: Evan

last: Stevens

first: Ewy

last: Mathe

first: Peng

last: Dong

first: Su-Chen

last: Huang

first: Maria

last: Ricci

first: Laura

last: Baranello

first: Ying

last: Zheng

first: Francesco

last: Ardori

first: Wolfgang

last: Resch

first: Diana

last: Stavreva

first: STeevenson

last: Nelson

first: Michael

last: McAndrew

first: Adriel

last: Casellas

first: Elizabeth

last: Finn

first: Charles

last: Gregory

first: Steven

last: Johnson

first: Wendy

last: Dubois

last: Cosma

first: Eric

last: Batchelor

first: David

last: Levens

first: Rovert

last: Phair

first: Tom

last: Misteli

first: Lino

last: Tessarollo

first: Gordon

last: Hager

first: Melike

last: Lakadamyali

first: Zhe

last: Liu

first: Monique

last: Floer

first: Hari

last: Shroff

first: Erez

last: Lieberman-Aiden

first: Rafael


title: Repression by PRDM13 is critical for generating precise neuronal identity

city: Dallas

first: Jane

address: 5323 Harry Hines Blvd

department: Neuroscience

institute: UT Southwestern Medical Center


title: Human HCT-116 cells: Control vs CDK2 knockout, NU6102 treated and resistant cells

status: Public on Aug 03 2017

city: Montpellier

first: Daniel

last: Fisher

address: 1919 Route de Mende

department: IGMM

country: France

institute: CNRS

summary: Transcriptional profiling of isogenic human colorectal cancer cell line HCT-116, comparing parental cells, CDK2 knockout cells, cells treated with the CDK2-selective inhibitor NU6102 and cells resistant to 50µM NU6102. The aim was to compare effects of loss of CDK2 gene or kinase activity and determine potential mechanisms of inhibitor-resistance

overall_design: Four condition experiment. 2 biological replicates of each condition

first: Katarina

last: Bacevic


title: Indole from commensal bacteria impact the aging transcriptome of C. elegans

city: GA

first: Robert

last: Sonowal

state: Atlanta

address: 144 Whitehead Bldg., 615 Michael St.

department: Pathology & Laboratory Medicine

institute: Emory University

summary:
We report here that in C. elegans, indole induces a gene expression profile in aged animals reminiscent of that seen in the young, but which is distinct from that
associated with normal aging. Moreover, in older animals, indole induces genes associated with oogenesis, and, accordingly, extends fecundity and reproductive span.

overall_design:
Whole animal trnascriptomic profile of old (12 day old adult) C. elegans growing on indole-positive E.coli, K12 or indole-negative mutant of K12, K12tnaA was obtained using RNA-Seq with Illumina Trueseq and
was compared with the profile of their younger (2 day old adult)  counterparts
-------------------------------------------
RNA was prepared from 12 day old adult (LATE) wild type worms (N2) grown on E.coli K12tnaA (tnaA) containing a deletion of
tryptophanase (necessary for indole production)
N2K12 means worms were grown in E coli K12 bacteria which is indole positive
EARLY means RNA was prepared from 2 day old adults.
AHRK12 means ahr-1(ia3) which has loss of function mutaion of ahr-1 gene was grown on K12 condition

last: Kalman

first: Ayush

last: Ranawade

first: Anusmita

last: Sahoo


title: mRNA content of extracellular vesicles, microvesicles and exosomes derived from human H9 embryonic stem cells in culture

city: Los Angeles

first: Debora

last: Farber

state: California

address: 100 Stein Plaza

department: Ophthalmology, Stein Eye Institute

institute: University of California Los Angeles

summary: Extracellular vesicles released from cultured H9 cells were fractionated by differential ultracentrifugation and their total RNA were isolated for microarray analysis.

overall_design: H9 hESC-derived hESEVs were fractionated into microvesicles (MVs) and exosomes (EXOs) by differential centrifugation. The total RNA was extracted from MVs, EXOs and non-fractionated hESEVs and hybridized to Affymetrix microarrays. We expected to see differences in the mRNA contents of MVs and EXOs.

first: Yingqian

last: Peng


title: Repression by PRDM13 is critical for generating precise neuronal identity (ChIP-Seq)

last: Johnson

state: TX

summary: The mechanisms that activate some genes while silencing others are critical to ensure precision in lineage specification as multipotent progenitors become restricted in cell fate. During neurodevelopment, these mechanisms are required to generate the wide variety of neuronal subtypes found in the nervous system. Here we report interactions between basic helix-loop-helix (bHLH) transcriptional activators and the transcriptional repressor PRDM13 that are critical for these processes during specification of dorsal spinal cord neurons. PRDM13 inhibits gene expression programs for the excitatory neuronal lineages in the dorsal neural tube while also suppressing a battery of genes that determine ventral neural tube fates including Olig1, Olig2 and Prdm12. PRDM13 does this via recruitment to chromatin by multiple neural bHLH factors to restrict gene expression in specific neuronal lineages. Together these findings highlight the function of PRDM13 in repressing bHLH transcriptional activators that together are required to achieve precise neuronal specification during development.

overall_design: ChIP-seq performed on mouse (ICR) embryonic day 11.5 (E11.5) neural tubes using a Johnson Lab generated antibody (PA6659, rabbit anti-PRDM13). The antigen was a bacterially expressed C-terminal domain of mouse PRDM13 including amino acids 622 to 755.

first: Ana

last: Uruena

first: Bishakha

last: Mona

first: Rahul

last: Kollipara

first: Zhenzhong

last: Ma

first: Mark

last: Borromeo


title: Genomic architecture of biomass heterosis in Arabidopsis

city: Beijing

first: Xuncheng

last: Wang

address: 5 Yiheyuan Road

institute: Peiking University

summary: Heterosis is most frequently manifested by the substantially increased vigorous growth of hybrids compared with their parents. Investigating genomic variations in natural populations is essential to understand the initial molecular mechanisms underlying heterosis in plants. Here, we characterized the genomic architecture associated with biomass heterosis in 200 Arabidopsis hybrids. The genome-wide heterozygosity of hybrids makes a limited contribution to biomass heterosis, and no locus shows an obvious overdominance effect in hybrids. However, the accumulation of significant genetic loci identified in genome wide association studies (GWAS) in hybrids strongly correlates with better-parent heterosis (BPH). Candidate genes for biomass BPH fall into diverse biological functions, including cellular, metabolic, and developmental processes and stimulus-responsive pathways. Important heterosis candidates include WUSCHEL, ARGOS, and some genes that encode key factors involved in cell cycle regulation. Interestingly, transcriptomic analyses in representative Arabidopsis hybrid combinations reveal that heterosis candidate genes are functionally enriched in stimulus-responsive pathways, including responses to biotic and abiotic stimuli and immune responses. In addition, stimulus-responsive genes are repressed to low-parent levels in hybrids with high BPH, whereas middle-parent expression patterns are exhibited in hybrids with no BPH. Our study reveals a genomic architecture for understanding the molecular mechanisms of biomass heterosis in Arabidopsis, in which the accumulation of the superior alleles of genes involved in metabolic and cellular processes improve the development and growth of hybrids, whereas the overall repressed expression of stimulus responsive genes prioritizes growth over responding to environmental stimuli in hybrids under normal conditions.

overall_design: First leaf mRNA profiles of 14-day old A.thaliana Ak-0 and Col-0×Ak-1 were generated by deep sequencing, in duplicate, using Illumina Hiseq 2500.

first: Mei

last: Yang

first: Guangming

last: He

first: Xing

last: Deng


title: miRNA expression profile of GT1-7 exposed to 500 nM MC-LR for 24 h

city: Nanjing

first: Yabing

last: Chen

address: No. 22 Hankou Rd., Gulou District, Nanjing, Jiangsu

institute: Nanjing University

summary: Using miRNA microarray, we screened 42 up-regulated miRNAs and 59 down-regulated miRNA in MC-LR-treated GT1-7 cells.

overall_design: In this study, GT1-7 cells were treated with or without 500 nm MC-LR for 24 h. RNA was extracted and miRNA microarray was used to screened the differentially expressed miRNA in GT1-7 cells.

first: Jing


title: DNA methylation profiles in sibling pairs discordant for intrauterine exposure to maternal gestational diabetes

city: Seongnam

first: Hak Chul

last: Jang

address: 82, Gumi-ro 173beon-gil, Bundang-gu

department: Department of internal medicine

institute: Seoul National University Bundang Hospital

summary: Intrauterine exposure to hyperglycemic environment is reported to confer increased metabolic risk in later life, supporting the “developmental origins of health and disease” hypothesis. Epigenetic alterations are suggested as one of the possible underlying mechanisms. We measured DNA methylation using Infinium HumanMethylation450 BeadChip in siblings discordant for maternal gestational diabetes mellitus (GDM), which may allow possible genetic and environmental confounding effects to be reduced. Of the 465,447 CpG sites analyzed, 12 showed differential methylation (false discovery rate < 0.15), including markers within genes associated with monogenic diabetes (HNF4A) or obesity (RREB1). The overall methylation at the HNF4A gene region showed inverse correlations with mRNA expression levels though non-significant. In a gene set enrichment analysis, differentially methylated CpGs-associated genes were involved in metabolism and signal transduction pathways. Our findings implicate epigenetic mechanisms in relation to prenatal exposure to maternal hyperglycemia.

overall_design: A discordant sibship design with whole blood samples of 18 maternal GDM-exposed siblings and 18 GDM-unexposed sibling controls assayed

first: E

last: Kim

first: S

middle: H

last: Kwak

first: H

last: Cung

first: J

last: Ohn

last: Bae

last: Choi

first: K

last: Park

last: Hong

last: Sung


title: Affect of growth on cantaloupe at 10°C on the transcriptome of Listeria monocytogenes

city: Laurel

first: Atin

last: Datta

address: 8301 Muirkirk Rd

department: CFSAN/DVA

institute: FDA

overall_design: A strain isolated from the 2011 cantaloupe outbreak was used to determine what changes in transcription are observed in the organism after reaching stationary phase growth on cantaloupe versus BHI broth.

first: Jihun

last: Kang

middle: R

first: Laurel

last: Burall


title: Major satellite repeat RNA stabilize heterochromatin retention of Suv39h enzymes by RNA-nucleosome association and RNA:DNA hybrid formation

city: Freiburg

first: Thomas

last: Jenuwein

address: Stuebeweg 51

institute: Max Planck Institute of Immunobiology and Epigenetics

summary: Molecular definition of an RNA-mediated mechanism that stabilizes association of the Suv39h enzymes at mouse heterochromatin.

overall_design: Chromatin-associated and nucleoplasmic RNA-seq in mouse ES cells

first: Oscar

last: Velazquez Camacho

first: Carmen

last: Galan

first: Kalina

last: Swist-Rosowska

first: Reagan

last: Ching

first: Michael

last: Gamalinda

first: Fethullah

last: Karabiber

first: Inti

last: De La Rosa-Velazquez

first: Bettina

last: Engist

first: Birgit

last: Koschorz

first: Nicholas

last: Shukeir

first: Megumi

last: Onishi-Seebacher

first: Suzanne

last: van de Nobelen


title: Whole Genome Bisulfite Sequencing  of Longissimus Dorsi Muscles between Japanese Black (Wagyu) and Chinese Red Steppes Cattle

city: Changchun

first: Xibi

last: Fang

address: No. 5333 Xian Road

institute: Jilin University

summary: We performed a comparative genome-wide methylation analysis of longissimus dorsi muscles between the Japanese Black (Wagyu) and Chinese Red Steppes cattle, which exhibit significant differences in meat quality traits. This will allow us to better understand the correlation between DNA methylation variants and meat quality traits.

overall_design: Comparative Genome-wide Methylation between three longissimus muscle (LM) tissue samples of Japanese black cattle (28 months old) and three LM samples of Chinese Red Steppes cattle (28 months old)

first: Zhihui

last: Zhao


title: Human memory CD8 T-cell effector-potential is epigenetically preserved during in vivo homeostasis

city: memphis

first: yiping

last: fan

state: tn

address: 262 Danny Thomas Place

institute: st jude children's hospital

summary: Maintenance of memory CD8 T cell effector function is coupled to stability ofeffector DNA methylation programs during homeostatic proliferation

overall_design: Human naïve and memory CD8 T cell subsets were sorted for Whole genome bisulfite sequencing analyses

first: Hossam

last: Abdelsamed

first: Adriana

last: Moustaki

first: Yiping

last: Fan

first: Pranay

last: Dogra

first: Hazem

middle: E

last: Ghoneim

first: Caitlin

last: Zebley

first: Brandon

last: Triplett

first: Rafick-Pierre

last: Sekaly

first: Ben

last: Youngblood


title: p53 binding during the DNA double-strand break response

status: Public on Aug 02 2017

city: Bethesda

first: Eric

last: Batchelor

department: LP/CCR/NCI

institute: National Institutes of Health

summary: We used ChIP-seq to assess where p53 binds in the human genome and how that binding changes during the DNA double-strand break response. In particular, we considered the 1-Mb-wide window centered on the MYC locus. Contrary to previous reports, we found no evidence of p53 binding at the MYC promoter. Rather, we identified three locations downstream of MYC at which p53 was bound; binding at each of these regions increased during the DNA double-strand break response.

overall_design: Examination of p53 binding in cells with/without DNA double-strand breaks.

first: Joshua

last: Porter

first: Laura

last: Baranello


title: Androgen receptor variants mediate DNA repair after prostate cancer irradiation

first: Ganesh

middle: V

last: Raj

department: Department of Urology

institute: UT SOUTHWESTERN MEDICAL CENTER

summary: We employ ChIP- seq methodology, to study the effect of ionizing radiation  treatment in genome wide binding of RNA pol-II and AR

overall_design: ChIP-seq using RNApol-II and AR antibodies was conductd in R1-D567 irradiated cells with non radiated cells as control

first: Yi

last: Yin

first: Susmita

last: Ramanand

first: Yunpeng

last: Gao

first: Mohammed

last: Kanchwala

first: Chao

last: Xing

first: Ram

last: Mani


title: p53-dependent effects of DNA double-strand breaks on chromatin accessibility

summary: We used ATAC-seq to detect changes in chromatin accessibility and nucleosome positioning around the MYC gene during the DNA double-strand break response in human cells and the dependence of these changes on p53. We found that, in the region ~50 kb downstream of MYC where p53 binds strongly, chromatin accessibility as measured by ATAC-seq fragment density increased during the DNA DSB response, corresponding to the removal of a single nucleosome. These results are consistent with increased accessibility of a distal regulatory element at this locus that is dependent on DNA damage and p53 expression. At the MYC promoter region there is a p53-dependent decrease in chromatin accessibility in response to DSBs, even in the absence of a direct p53 binding site near the region. While both the P1 and P2 promoters of MYC are relatively free of nucleosomes in MCF-7 sh-p53 cells, both promoters are occluded in cells expressing WT levels of p53, with an increase of nucleosomal occlusion in response to DNA damage. This supports the hypothesis that MYC repression during the DNA DSB response results from nucleosomal occlusion of both the P1 and P2 promoters.

overall_design: Examination of chromatin accessibility and nucleosome positioning in cells with/without p53 and with/without DNA double-strand breaks.


title: Expression data from normal breast tissues

status: Public on Aug 01 2017

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

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.
Obesity is a risk factor for breast cancer, but the underlying mechanisms for this are only partially understood, and there has been only limited study of breast tissues molecularly before cancer develops. Breast tissues from healthy women undergoing reduction mammoplasty and epidemiologic interviews (n=121) were profiled for the whole genome transcriptome (Affymetrix Human Transcriptome Arrays) and genome-wide DNA methylation (Infinium HumanMethylation 450 BeadChip array). After adjusting for confounding by age and race, 12,210 CpG dinucleotides with altered methylation levels correlated with body mass index (BMI) (10,808 positive correlations and1,402 negative correlations, FDR<0.05). Among them 4,170 BMI-associated hypermethylated CpG dinucleotides (-1.5 kb from transcription start site, 1st Exon, and 5’UTR) and 443 BMI-associated hypomethylated CpG dinucleotides were located in promoter regions. By integrating DNA methylation and mRNA expression data, we identified 310 methylated genes that correlated with gene expression (FDR<0.05). Of these, 242 genes had higher methylation status showing concurrent down-regulation in obese women, and 68 genes had lower methylation status showing concurrent up-regulation in obese women. Among the affected genes involved in diseases and disorders for inflammatory response, hereditary disorder, and immunological disease. This study provides evidence that obesity epigenetically deregulates genes potentially involved in breast cancer that have functional relationships to gene expression.

overall_design: Gene expression in normal breast tissues from 114 women patients undergoing reduction mammoplasty was analyzed by Affymetrix arrays

middle: Y

first: Min-Ae

last: Song

first: Peter

last: Shields


title: Early transcriptome profiling of microRNA-mediated neuronal reprogramming [RNA-seq timecourse]

first: Matthew

last: McCoy

summary: Neuronal microRNAs, miR-9/9* and miR-124 (miR-9/9*-124), exert reprogramming activities to direct cell-fate conversion of adult human fibroblasts to post-mitotic neurons and enable the generation of discrete neuronal subtypes with additional transcription factors. Previously, the molecular events underlying the neurogenic switch mediated by microRNAs during neuronal reprogramming were unknown. Here, we systematically dissected the neurogenic state induced by miR-9/9*-124 alone and reveal the surprising capability of miR-9/9*-124 in coordinately stimulating the reconfiguration of chromatin accessibilities, DNA methylation and transcriptome, leading to the generation of functionally excitable neurons, yet unbiased towards a particular subtype-lineage. We show that the microRNA-induced neuronal state enables additional transcription factors, ISL1 and LHX3, to selectively commit conversion to a highly homogenous population of human spinal cord motor neurons. Taken together, our study reveals a modular synergism between microRNAs and transcription factors that allows lineage-specific neuronal reprogramming, providing a platform for generating distinct subtypes of human neurons.

overall_design: Time series RNA-seq of miRNA-mediated neuronal reprogramming at post-induction day (PID) 0, 3, 6, 10, and 20.

first: M

first: D

last: Abernathy

first: A

middle: S

last: Yoo


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

city: Baltimore

first: leslie

last: cope

address: 550 N. Broadway

institute: leslie cope

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

overall_design: Refer to individual Series


title: A comprehensive, cell specific microRNA catalogue of human peripheral blood

city: Kiel

first: Matthias

last: Hübenthal

state: SH

address: Rosalind-Franklin-Str. 9

department: Dermatology, Venereology and Allergy

institute: University Hospital Schleswig-Holstein

overall_design: miRNomes from seven distinct blood cell populations namely, CD4, CD8, CD14, CD15, CD19, CD56 and CD235a of 43 healthy individuals using smallRNA-seq. Additionally examination of miRNA profiles from 77 whole-blood samples and 38 exosome and serum samples.

first: Simonas

last: Juzenas

first: Geetha

last: Venkatesh


title: A diet enriched with low or high molecular weight oat beta-glucans on blood inflammatory and oxidative stress status in rats with LPS-induced enteritis

city: Warsaw

first: Dariusz

last: Kamola

address: Nowoursynowska 159

department: Faculty of Veterinary Medicine

institute: Warsaw University of Life Sciences

summary: The aim of this study was to evaluate the ability of a diet enriched with two types of oat beta-glucans on inflammatory and oxidative stress status in blood cells in rats with LPS-induced enteritis

overall_design: The aim of the study was to investigate the protective effect of low and high molecular weight beta-glucans on chosen immunological parameters, markers of antioxidative potential in rats blood ceels. Experiment was carried out on 72 8-week old male Sprague-Dawley rats: control (n=36) and experimental (n=36). In half of the animals from each group enteritis was induced by LPS (10 mg/kg). Rats from experimental group were divided into two groups receiving high (GI) or low (GII) molecular weight beta-glucans for 6 consecutive weeks. RNA from blood cells were hybridized to Agilent two color microarrays with a common reference. Then, the transcriptomic profile of these cells were compared to the transcriptomic profile of rats received the same control diet and diet enriched with low and high molecular weight beta-glucans.

first: Jacek

last: Wilczak

first: Katarzyna

last: Blaszczyk

first: Joanna

last: Gromadzka-Ostrowska


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

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: MT1-MMP (MMP14)-dependent gene expression in APOE-null vascular smooth muscle cells (VSMCs)

city: ANN ARBOR

first: Tae-Hwa

last: Chun

state: MI

address: 2800 PLYMOUTH RD, NCRC B10-A186, NCRC B10-A186

department: Internal Medicine

institute: University of Michigan

summary:
VSMC-specific MT1-MMP gene targeting in APOE-null mice promotes atherosclerosis and iliac artery aneurysm formation. To determine the MT1-MMP-dependent regulation of VSMC function, whole-genome transcriptomes of wild-type and MT1-MMP-null APOE-null VSMCs were determined.
We used microarray-based transcriptome analysis to detect MT1-MMP-dependent regulation of VSMC function under atherogenic conditions.

overall_design: VSMCs were isolated from two independent pairs of SM22α-Cre(−)Mmp14(fl/fl)Apoe(−/−) and SM22α-Cre(+)Mmp14(fl/fl)Apoe(−/−) mice fed Western diet for 3 months. Total RNA was extracted and used for hybridization with Mouse Gene ST 2.1 Strip.

first: Craig

last: Johnson

first: Yibin

last: Jiang

first: Richard

last: Barnes


title: Worldwide patterns of human epigenetic variation

city: Philadelphia

first: Oana

last: Carja

state: Pennsylvania

address: 204K Lynch Labs, 433 S University Ave

department: Biology

institute: University of Pennsylvania

summary: DNA methylation is an epigenetic modification, influenced by both genetic and environmental variation, that plays a key role in transcriptional regulation and many organismal phenotypes. Although patterns of DNA methylation have been shown to differ between human populations, it remains to be determined how epigenetic diversity relates to the patterns of genetic and gene expression variation at a global scale. Here we measured DNA methylation at 485,000 CpG sites in five diverse human populations, and analyzed these data together with genome-wide genotype and gene expression data. We found that population-specific DNA methylation mirrors genetic variation, and has greater local genetic control than mRNA levels. We estimated the rate of epigenetic divergence between populations, which indicates far greater evolutionary stability of DNA methylation in humans than has been observed in plants. This study provides a deeper understanding of worldwide patterns of human epigenetic diversity, as well as initial estimates of the rate of epigenetic divergence in recent human evolution.

overall_design: This cohort consist of genomic DNA extracted from 34 individuals representing 5 populations, bisulphite converted and hybridized to the Illumina Infinium HumanMethylation450 Beadchip for genome wide DNA methylation profiling


title: Transcriptome of neonatal preBötzinger Complex neurons in Dbx1 reporter mice

city: Williamsburg

first: Maria Cristina

last: Picardo

state: VA

address: 540 Landrum Dr

department: Applied Science, ISC 3

institute: College of William and Mary

summary: We sequenced the transcriptome of brainstem interneurons in the specialized respiratory rhythmogenic site dubbed preBötzinger Complex (preBötC) from newborn mice. To distinguish molecular characteristics of the core oscillator we compared preBötC neurons derived from Dbx1-expressing progenitors that are respiratory rhythmogenic to neighbouring non-Dbx1-derived neurons, which support other respiratory and non-respiratory functions.

overall_design: RNA-seq gene expression profile for preBötC neurons in newborn mice

first: John

middle: A

last: Hayes*

first: Andrew

last: Kottick*

first: Maria

last: Picardo*

middle: D

last: Halleran

first: Ronald

last: Smith

first: Gregory

first: Margaret

last: Saha

first: Christopher

last: Del Negro


title: Deriving mature Schwann cells from human BMSCs

city: Hong Kong

first: Sally

last: Cai

address: Sassoon Road

institute: The University of Hong Kong

summary: A protocol was established for the derivation of Schwann cell-like cells from human BMSCs. The commitment to the Schwann cell fate was acquired by Schwann cell-like cells in co-culture with rat DRG neurons. Microarray analysis provided evidence that the human BMSC-derived Schwann cells were functionally mature.

overall_design: Microarrays was used to compare the gene expression profiles of human BMSCs, Schwann cell-like cells, human BMSC-derived Schwann cells and adult human Schwann cells.

first: Sa


title: DNMT3A haploinsufficiency predisposes hematopoietic cells to myeloid malignancies

city: St Louis

first: Timothy

last: Ley

address: 660 S Euclid Avenue

institute: Washington University School of Medicine

summary: DNMT3A (which encodes a de novo DNA methyltransferase) is one of the most frequently mutated genes in AML genomes. Point mutations at position R882 have been shown to cause a dominant negative loss of DNMT3A methylation activity, but 15% of DNMT3A mutations are predicted to produce truncated proteins, which could either have dominant negative activities, or cause loss-of-function and haploinsufficiency. We demonstrate that three of these mutants produce truncated, inactive proteins that do not dimerize with wild-type DNMT3A, strongly supporting the haploinsufficiency hypothesis. We therefore evaluated hematopoiesis in mice heterozygous for a constitutive null Dnmt3a mutation: unmanipulated mice developed myeloid skewing over time, and their stem/progenitor cells exhibited a long-term competitive transplantation advantage. Dnmt3a+/- mice spontaneously developed transplantable myeloid malignancies after a long latent period, and three of 12 tumors tested had cooperating mutations in the Ras- MAPK pathway. The residual Dnmt3a allele was neither mutated nor downregulated in tumors. The bone marrow cells of Dnmt3a+/- mice had a subtle but significant DNA hypomethylation phenotype that was not associated with gene dysregulation. These data demonstrate that haploinsufficiency for DNMT3A alters hematopoiesis, and predisposes mice (and probably humans) to myeloid malignancies by a mechanism that is not yet clear.

overall_design: Mouse Microarray

last: Cole

first: David

last: Russler-Germain

first: Shamika

last: Ketkar


title: Gene expression data from lineage negative c-kit positive sca-1 positive hematopoietic stem cells (LSK, Lin-Sca-1+c-kit+) isolated from  Jak2VF/+ vector and Jak2VF/+ Hmga2 mice

city: Syracuse

first: Golam

last: Mohi

state: New York

address: 766 Irving Avenue

department: Pharmacology

institute: SUNY Upstate Medical University

summary: The JAK2V617F mutation has been detected in ~50% cases of MF. Elevated expression of high mobility group AT hook 2 (HMGA2) also has been frequently observed in patients with MF. Interestingly, upregulation of HMGA2 expression has been found in association with the JAK2V617F mutation in significant cases of MF.  However, the contribution of HMGA2 in the pathogenesis of MF remains elusive. To determine the effects of concurrent expression of HMGA2 and JAK2V617F mutation in hematopoiesis, we transduced bone marrow cells from Jak2V617F knock-in mice with lentivirus expressing Hmga2 and performed bone marrow transplantation. In order to assess the effects of Hmga2 overexpression on gene expression, we performed RNA sequencing analysis for the LSK from  Jak2VF/+ vector and Jak2VF/+ Hmga2mice.

overall_design: Bone marrow cells from 5-fluorouracil-primed Mx1Cre; Jak2V617F/+ (referred as Jak2VF/+)  mice were transduced with lentiviruses expressing vector alone or Hmga2 by two rounds of spin infection. Transduced bone marrow cells (1X106) were injected into retro-orbital veins of lethally irradiated (2X 550 cGy) C57BL/6 recipient mice. BM cells were harvested at 32 weeks after BMT. RNA sequencing analysis from  Jak2VF/+ vector and Jak2VF/+ Hmga2 mice were performed for LSK cells sorted from BM cells. There are three biological replicates for each genotype and six samples in total.

first: Avik

last: Dutta


title: Transcriptome Profiling in KY1005-treated NHP HCT-recipients

city: Seattle

first: Victor

last: Tkachev

state: Washington

address: 1100 Olive way, suite 100

institute: Seattle Children's Research Institute Ben Towne Center for Childhood Cancer Research

summary: Graft versus host disease (GVHD) is the most common complication of hematopoietic stem cell transplant (HCT). However, our understanding of the molecular pathways that cause this disease remains incomplete, leading to inadequate treatment strategies. To address this, we measured the gene expression profile of non-human primate (NHP) T cells during acute GVHD.  In this study we specifically interrogated the transcriptional signatures of animals treated with KY1005 monotherapy and KY1005/Sirolimus combination therapy

overall_design: Series of n=102 arrays taken from animal from the post transplant period including arrays from n=46 untransplanted healthy controls

first: Leslie

last: Kean