title: A temporal proteogenomic atlas of HCV-host interactions unravels cell circuits driving viral and metabolic liver disease.

city: Strasbourg

first: Frank

last: Jühling

address: 3 Rue Koeberlé

institute: Université de Strasbourg, Inserm, Institut de Recherche sur Les Maladies Virales et Hépatiques UMR_S1110

summary:
Background and aims: Hepatitis C virus (HCV) infection is a major cause of liver disease including steatosis, fibrosis and liver cancer. Viral cure cannot fully eliminate the risk of disease progression and hepatocellular carcinoma (HCC) in advanced liver disease. The mechanisms for establishment of infection, liver disease progression and hepatocarcinogenesis are only partially understood. To address these questions, we probed the functional proteogenomic architecture of HCV infection within a hepatocyte-model.
Methods: Time-resolved HCV infection of hepatocyte-like cells was analyzed by RNA sequencing, proteomics, metabolomics, and leveraged by integrative genomic analyses. Using differential expression, gene set enrichment analyses, and protein-protein interaction mapping we identified pathways relevant for liver disease pathogenesis that we validated in livers of 216 cirrhotic patients with HCV.
Results: We uncovered marked changes in the protein expression of gene sets involved in innate immunity, metabolism and hepatocarcinogenesis. In infected cells, HCV enhances glucose metabolism and creates a Warburg-like shift of the lactate flux. HCV infection impaired the formation of peroxisomes -organelles required for long-chain fatty acid oxidation- causing intracellular fatty acid accumulation, which is a hallmark of non-alcoholic fatty liver disease (NAFLD). Ex vivo studies confirmed perturbed peroxisomes and revealed an association of hepatic catalase expression with clinical outcomes and phenotypes in HCV-associated cirrhosis, NAFLD and HCC cohorts.
Conclusion: Our integrative analyses uncover how HCV perturbs the hepatocyte cell circuits to drive chronic liver disease and hepatocarcinogenesis. This proteogenomic atlas of HCV infection provides a model for the discovery of novel drivers for viral- and non-viral induced liver disease.

overall_design: mRNA profiles of either mock or HCV-infected Huh7.5.1dif cells, performed in triplicates and collected every day between days 0 and 10 post infection. HCV infection reached plateau at day 7 post infection (pi). After day 7 pi unspecific effects cannot be excluded.

first: Joachim

last: Lupberger


title: Human glioblastoma stem cells (GSCs) differentiation: Undifferentiated cells vs. Differentiated cells

status: Public on Apr 17 2019

city: Beijing

first: Hao

last: Li

address: No.6 Tiantanxili

department: Department of Neurosurgery

country: China

institute: Beijing Tiantan Hospital, Capital Medical University

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

summary: Using four patient-derived GSCs lines and their induced differentiating counterparts, we performed high-throughput microarray analysis to identify the profile changes of lncRNAs and mRNAs.  The differentiation status was determined by Immunofluorescence and qRT-PCR.

overall_design: Two-condition experiment, undifferentiated GSCs vs. differentiated GSCs. Biological replicates: 4 undifferentiated, 4 differentiated GSCs, independently grown and harvested.

first: Yong

last: Cao

first: Jizong

last: Zhao


title: Desmoplasia is associated with carcinoma associated fibroblasts’ heterogeneity in non-small cell lung cancer patients

city: Toronto

first: Ming-Sound

last: Tsao

state: Ontario

address: 101 College St

department: Princess Margaret Cancer Research

country: Canada

institute: University Health Network

summary: Cancer associated fibroblasts (CAFs) are well known to strongly influence tumor development, progression, and metastasis. Their characteristics and prognostic gene signature in non-small cell lung cancer (NSCLC) patients have been recognized. Heterogeneity of CAFs has long been observed, however, the functional heterogeneity of CAFs between patients and their genetic basis are far less known. Here, we report the distinction of two CAF subtypes obtained from primary cultures of CAFs and matched normal fibroblasts (NFs) from 28 resected NSCLC. These 28 pathological NSCLC (82 % adenocarcinoma) were categorized into two types according to the histological properties of the peritumoral stroma: High desmoplasia (HD; n=14), and low desmoplasia (LD; n=14), and the prognostic significance evaluated. This classification seems to align with functional CAFs, as those with HD have higher rate of gel contraction, higher rate of tumor growth and poor prognosis. To demonstrate a gene expression profile specific to CAF activity we used Illumina DASAL Microarray gene expression analysis on extracted RNA from 24 CAF cell lines (12 CAFs-HD and 12 CAFs-LD) that were embedded in collagen gel for 24 hours. From the CAF cohort, the most significant genes that are correlated with the desmoplasia are identified to be enriched in the clinical cohort of 181 NSCLC patients. Overall, our studies showed that in NSCLC, desmoplasia is significantly associated with poor prognosis and is able to significantly subgroup CAF between NSCLC patients.

overall_design: Early passage (passage 2) cultures of 4 LD-CAF (CAF extracted from low desmoplasia (LD) primary non-small cell lung cancer) and 3 HD-CAF  (CAF extracted from high desmoplasia (HD) primary non-small cell lung cancer) were cultured in collagen gel for 24 hours.

first: Ming

middle: S

first: C

middle: Q

last: Zhu

first: Quan


title: Next generation sequencing analysis of mRNA profile in cisplatin-resistant gastric cancer cell line SGC7901

city: Dongguan

first: Libo

address: No.3 Wan Road, Dongguan, Guangdong

department: Department of General Surgery

institute: Dongguan People's Hospital

type: Expression profiling by high throughput sequencing

summary: Cisplatin-resistant gastric cancer (GC) occurs in patients with GC treated with cisplatin-based chemotherapy, which results in disease progression and early recurrence during the treatment. To understand the initiation and developmental mechanism underlying cisplatin-resistant GC, we developed cisplatin resistant SGC7901 cells (SGC7901/DDP) from the parental cells (SGC7901/S) by continuous exposure to increasing concentrations of cisplatin and subjected these two cell lines to RNA sequencing analysis.

overall_design: mRNA profiles of cisplatin resistant SGC7901 cells (SGC7901/DDP) and the parental cells (SGC7901/S) were generated by deep sequencing, using BGISEQ-500.

first: Huohui

last: Ou

first: Dinghua

last: Yang


title: In utero exposure to diesel exhaust particulates is associated with alterations of the neonatal cardiomyocyte transcriptome, metabolic parturbation and a global decrease in DNA methylation. [RNA-Seq]

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

country: USA

institute: University of Washington

summary: Developmental exposure to particulate matter air pollution is harmful to cardiovascular health, but the mechanisms by which this exposure mediates susceptibility to heart disease is poorly understood. We have previously shown, in a mouse model, that gestational exposure to diesel exhaust results in increased cardiac hypertrophy, fibrosis and susceptibility to heart failure in the adult offspring following transverse aortic constriction. In this study, we have analyzed gene expression in neonatal cardiomyocytes after gestational exposure by RNA-sequencing and have identified 300 genes that are dysregulated, including many involved in cardiac metabolism.

overall_design: Female mice were paired with male mice for timed mating in FA. After observation of a vaginal plug, pregnant mice were put into FA or DE with exposures beginning at E0.5 and lasting until E17.5, at which point pregnant mice were transferred from the Northlake facility to the UW Medicine South Lake Union SPF vivarium for neonatal sample collection or weaned and kept until 11-12 weeks for adult sample collection. Upon birth, neonatal hearts were harvested, trimmed of surrounding vascular and atrial tissue, and dissociated as previously described. Dissociation was performed using 1mg/mL Liberase TH (Roche; Pleasanton, CA, USA) in 1X HBSS by incubating hearts at 37 degrees for 5 minutes in solution, with pipetting to release cells after incubation. Media containing released neonatal carciomyocytes (NCMs) was adjusted to 20% FBS-DMEM, and cellular dissociation was continued until the majority of cells were released. Cells were then filtered using a 70um sieve, re-eluted in 20% FBS-DMEM with 20uM Ara-C and incubated at 37 degrees for 1 hour to allow fibroblasts to attach onto the plate. After incubation, media with suspended cardiomyocytes was carefully removed, spun and purified cardiomyocyte pellets were collected and frozen at -80°C.

first: Jamie

middle: M

last: Goodson

middle: W

first: Theo

middle: K

last: Bammler

first: Wei-Ming

last: Chien

first: Michael

middle: T

last: Chin


title: Recurrent chromosomal and epigenetic alterations in oral squamous cell carcinoma and its putative premalignant condition oral lichen planus

city: Ulm

first: Ole

last: Ammerpohl

address: Albert-Einstein-Allee 11

country: Germany

institute: UK Ulm

type: Methylation profiling by genome tiling array

summary: Genome wide DNA methylation profiling of OSCC tissue samples, oral lichen planus tissue samples and normal controls. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 480,000 CpGs. Samples included 15 OSCC, 8 lichen planus and 18 control samples.

overall_design: Bisulphite converted DNA from the 41 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip

first: Volker

last: Gassling


title: Core metabolism shifts of methanol vs. methane growth in the methanotroph Methylomicrobium buryatense 5GB1

first: Mitchell

last: Pesesky

address: 616 NE Northlake Place

summary: Methylomicrobium buryatense 5GB1 is an obligate methylotroph, which grows on methane or methanol with similar growth rates. Core metabolic pathways are similar on both substrates, but recent studies of methane metabolism suggest that growth on methanol might have significant differences from growth on methane. In this study, both a targeted metabolomics approach as well as a 13C tracer approach have been taken to understand core carbon metabolism in M. buryatense 5GB1 during methanol growth, to determine whether such differences occur. Targeted metabolomics analyses were performed on both methane and methanol cultures to identify metabolic nodes with altered fluxes. Several key metabolites showed significant differences in pool size. Noticeably, 2-keto-3-deoxy-6-phosphogluconate (KDPG) showed much larger pools under methanol culture, suggesting the Entner-Doudoroff (ED) pathway was more active. Intermediates in other parts of metabolism also showed differences in pool sizes under methanol growth. A systematic shift of active core metabolism is proposed to explain the changes. In order to distinguish flux partition differences at the C3-C4 node, 13C tracer analysis was also applied to methanol-grown cultures. Using the experimental results as constraints, we applied flux balance analysis to determine the metabolic flux phenotype of M. buryatense 5GB1 growing on methanol. The resulting new insights into core metabolism of this methanotroph provide an improved basis for future strain design.

overall_design: RNA-seq analysis of gene expression of M. buryatense 5GB1 grown in continuous bioreactor culture. Growth parameters were tested with both biological and technical replicates for growth on methane and methanol.

first: Yanfen

last: Fu

first: David

middle: C

last: Beck

first: Mary

middle: E

last: Lidstrom


title: Novel parent-of-origin specific differentially methylated loci on chromosome 16

status: Public on Apr 16 2019

city: Houston

first: Neil

middle: A.

last: Hanchard

state: TX

address: One Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

type: Methylation profiling by high throughput sequencing

summary: To identify parent-of-origin biased DNA methylation, we performed high-resolution bisulfite sequencing of chromosome 16 on peripheral blood and cultured skin fibroblasts from individuals with maternal and paternal UPD(16) as well as lung tissue from patients with 16q24.1 ACDMPV-causative deletions and a normal control. We identified 22 differentially methylated regions (DMRs) with ≥5 consecutive CpG methylation sites and varying tissue-specificity, including the known DMRs associated with the established imprinted gene ZNF597 and DMRs supporting maternal methylation of PRR25, thought to be paternally expressed in lymphoblastoid cells. Lastly, we found evidence of paternal methylation on 16q24.1 near LINC01082 mapping to the FOXF1 enhancer. Using high-resolution bisulfite sequencing to evaluate DNA methylation across chromosome 16, we found evidence of novel candidate imprinted loci on chromosome 16 that would not be evident in array-based assays and could contribute to the birth defects observed in association with UPD(16)mat and in ACDMPV.

overall_design: Comparison of DNA methylation profiles between individuals with UPD(16)mat (n=2), UPD(16)pat (n=2), and normal controls in blood, juxtaposed with UPD(16)mat from fibroblast cultures (n=1), and lung tissue samples from ACDMPV individuals with maternal deletions (n=2) and normal control (n=1).

first: Katharina

middle: V

last: Schulze

first: Przemyslaw

last: Szafranski

first: Harry

last: Lesmana

first: Robert

middle: J

last: Hopkin

first: Aaron

last: Hamvas

first: Jennifer

middle: A

last: Wambach

first: Marwan

last: Shinawi

first: Gladys

last: Zapata

first: Claudia

middle: B

last: Carvalho

first: Qian

last: Liu

first: Justyna

last: Karolak

middle: R

last: Lupski

first: Pawel

last: Stankiewicz


title: In utero exposure to diesel exhaust particulates is associated with alterations of the neonatal cardiomyocyte transcriptome, metabolic parturbation and a global decrease in DNA methylation.

first: James

last: MacDonald

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

overall_design: Refer to individual Series


title: A Cut/cohesin axis altersthe chromatin landscape to facilitate neuroblast death

city: Gainesville

first: Lei

last: Zhou

state: FL

department: Molecular Genetics and Microbiology

institute: University of Florida

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Cut regulates the programmed death of neural stem cells by altering cohesin levels and promoting a more open chromatin conformation to allow cell death gene expression.

overall_design: Histone modification (H3K27Me3 and H3K27Ac) in sorted neuroblast cells was monitored following RNAi KD of Cut.

first: Kristin

last: White


title: Resident Macrophages Reprogram Toward a Developmental State After Acute Kidney Injury

city: Stanford

first: Mark

middle: Emile

last: Pepin

state: CA

address: 870 Quarry Road

department: Cardiovascular Medicine

institute: Stanford University

summary:
Background – Acute kidney injury (AKI) is a devastating clinical condition affecting at least two-thirds of critically ill patients and among these patients is associated with a greater than 60% risk of mortality. Kidney mononuclear phagocytes (MP) are necessary for pathogenesis and healing in mouse models of AKI and thus have been the subject of investigation as potential targets for clinical interventions.
Methods and Results – We have determined that, after injury, F4/80Hi-expressing kidney resident macrophages (KRM) are a distinct cellular subpopulation that does not differentiate from non-resident infiltrating MP.  However, if KRM are depleted using polyinosinic:polycytidylic acid (poly I:C), they can be reconstituted from bone marrow derived precursors. Further, KRM lack major histocompatibility complex class II (MHCII) expression before post-parturition day 7 (P7) but upregulate it over the next 14 days. This MHCII- KRM phenotype reappears after injury. RNA sequencing shows injury causes transcriptional reprogramming of KRM to more closely resemble that found at P7. Post-injury KRM are also enriched in Wingless-type MMTV integration site family (Wnt) signaling, indicating a pathway vital for mouse and human kidney development is active.
Conclusions – These data indicate that mechanisms involved in kidney development may be active after injury in KRM.

overall_design: RNA Sequencing analysis of mononuclear phagocytes isolated from kidneys of 10-wk old male mice after ischemia-reperfusion injury or during healthy state or development.

first: Jeremie

last: Lever

first: Travis

middle: D

last: Hull

first: David

last: Crossman

first: Anupam

last: Agarwal

middle: F

last: George


title: An RNA-centric dissection of host complexes controlling flavivirus infection

first: Ryan

middle: Alexander

last: Flynn

address: 380 Roth Way, Room 265


title: An RNA-centric dissection of host complexes controlling flavivirus infection [irCLIP]

summary: Flaviviruses including dengue virus (DENV) and Zika virus (ZIKV) cause significant human disease. Co-opting cellular factors for viral protein translation and viral genome replication at the endoplasmic reticulum (ER) is a shared replication strategy, despite different clinical outcomes. While the protein products of these viruses have been studied in depth, how the RNA genomes operate inside human cells is poorly understood. Using comprehensive identification of RNA binding proteins by mass spectrometry (ChIRP-MS), we took an RNA-centric viewpoint of flaviviral infection and identified several hundred proteins associated with both DENV and ZIKV genomic RNA inside human cells. Intersection with genome-scale knockout screens assigned putative functional relevance to the RNA-protein interactions. ER RNA binding proteins such vigilin and RRBP1 directly bound viral RNA and each operated at distinct points in the life cycle of flaviviruses. Thus, this versatile strategy can elucidate features of human biology that control pathogenesis of clinically relevant viruses.

overall_design: This experiment was designed to determine what RNAs, both human or viral, direct interact with specific host RNA binding proteins. In particular we characterized the RNA-interactome of RRBP1 and vigilin, two host factors we discovered are important for the flaviviral life cycle.

first: Karim

last: Majzoub

first: Yaw

last: Shin Ooi

first: Carolyn

last: Bertozzi

first: Jan

last: Carette


title: Identifcation of lncRNA MACC1-AS1-associated microRNAs in breast cancer cell line MDA231 using MS2-Tagged RNA Affinity Purification and miRNA-Seq

city: Shantou

first: Zhou

last: Yanchun

state: Guangdong

address: Xinling Road

department: Pathophysiology

institute: Shantou University Medical College

type: Non-coding RNA profiling by high throughput sequencing

summary: LncRNA MACC1-AS1 is the antisense RNA of MACC1 mRNA, which is located on the sixth intronic of MACC1 gene. MACC1-AS1 is an oncogenic lncRNA in colorectal cancer. But the function role of MACC1-AS1 in breast cancer is unknown. In the present study, We used MS2-Tagged RNA Affinity Purification and miRNA-Seq to characterize microRNAs that associated with MACC1-AS1 in breast cancer cell line MDA231.

overall_design: LncRNA MACC1-AS1-MS2 was in vitro transcribed using T7 RNA polymerase transcription system. RNA was incubated with Amylose resin attached MBP-MCP (MS2 coat protein) at 4°C for 3 h with gentle rotation，After incubation, the supernatant was removed by a short centrifugation and the beads were washed three times with wash buffer. Then, cell lysates prepared from cultured MDA231 cells were incubated with RNA conjugated amylose resin at 4°C in the presence of RNase Inhibitor and protease inhibitors. After washed with wash buffer, the Amylose resin complexes  were eluted with 100 μl lysis buffer containing 10 mmol/L maltose. The binding miRNAs were analyzed by miRNA-seq.

first: Y

first: S

last: Chen

first: W

last: Gu


title: Expression data from Pseudomonas aeruginosa +/- 1% ethanol

status: Public on Apr 15 2019

city: Hanover

first: Deborah

middle: Ann

last: Hogan

state: NH

department: Microbiology and Immunology

institute: Geisel School of Medicine

summary: Pseudomonas aeruginosa frequently resides among ethanol-producing microbes, making its response to these microbially-produced concentrations of ethanol relevant to understanding its biology. Transcriptome analysis found that the genes involved in trehalose metabolism were induced by low concentrations of ethanol, and levels of intracellular trehalose increased significantly upon growth with ethanol. The increase in trehalose was dependent on the TreYZ pathway, and not other trehalose metabolic enzymes TreS or TreA. The sigma factor AlgU (AlgT), a homolog of RpoE in other species, was required for increased expression of the treZ gene and trehalose levels, but induction was not controlled by the well-characterized proteolysis of its antisigma factor MucA. Growth with ethanol led to increased (p)ppGpp, synthesized by SpoT, and genetic data suggest that increased (p)ppGpp stimulates AlgU-dependent transcription of treZ and other AlgU-regulated genes through DksA, a (p)ppGpp and RNA polymerase binding protein. Ethanol stimulation of trehalose also required acylhomoserine lactone (AHL)-mediated quorum sensing, as induction was not observed in a ∆lasR∆rhlR strain. A network analysis of publicly available P. aeruginosa transcriptome datasets using eADAGE provided strong support for our model that treZ and co-regulated genes are controlled by both AlgU and AHL-mediated QS. Consistent with (p)ppGpp and AHL-mediated quorum sensing regulation, ethanol, even when added at the time of culture inoculation, only stimulated treZ transcript levels and trehalose production in post-exponential phase cultures. These data highlight the integration of growth and cell density cues in responses to ethanol.

overall_design: We sought to understand the expression profile of wild type Pseudomonas aeruginosa (PA14) in response to growth in the presence of 1% ethanol. We harvested RNA for analysis from colony biofilms grown for 16 h at 37C on tryptone agar plates (1.5% agar) grown without (CTRL) and with (EtOH) 1% ethanol added to the molten agar. We collected duplicate samples of each condition (CTRL and EtOH) for expression analysis.

first: Colleen

last: Harty


title: An RNA-centric dissection of host complexes controlling flavivirus infection [RNA-Seq]

overall_design: This experiment was designed to measure the expression of non-ribosomal RNAs, including viral genomic RNA, from Huh7.5.1 cells using RNA-seq.


title: LKB1 orchestrates dendritic cell metabolic quiescence and anti-tumor immunity

city: Memphis

first: Hongbo

last: Chi

state: TN

address: 262 Danny Thomas Place

department: Immunology

institute: St Jude Children's Research Hospital


title: Expression data from roots of rice sos1 loss-of-function mutant and control plants (azygous) in normal conditions or after 4 days of salt stress

city: Sevilla

first: Javier

last: Perez Hormaeche

state: Sevilla

address: Av. Americo Vespucio

department: IBVF

country: Spain

institute: CSIC

summary: Rice (Oryza sativa) stands among the world's most important crop species and is salt-sensitive. The undue accumulation of sodium ions (Na+) in shoots has the strongest negative correlation with rice productivity under long-term salinity. The plasma membrane Na+/H+ exchanger protein SOS1 is the only Na+ efflux transporter that has to date been genetically characterized and only in dicot plants. Here, the importance of Na+ fluxes governed by the SOS system in the salt tolerance of rice was analyzed by a reverse-genetics approach. A sos1 loss-of-function mutant displayed exceptional salt sensitivity that correlated with excessive Na+ intake and impaired Na+ loading into the xylem. Thus, SOS1 controls net Na+ uptake by roots and the long-distance transport to shoots. The acute Na+ sensitivity of sos1 plants at low NaCl concentrations allowed the inspection of the transcriptional response to sodicity stress, without interference by the osmotic challenge intrinsic to high salinity treatments. The transcriptional response to salt of the sos1 mutant roots involved the preferential down-regulation of stress-related genes compared to the wild-type despite the greater intensity of the stress imposed to the mutant, which suggested impaired stress detection or inability to mount a comprehensive response to salinity.

overall_design: Two-condition experiment: salt stress and control. Three on-chip technical replicates per biological sample were analyzed.

first: Irene

last: Villalta

last: PÃ©rez-Hormaeche

first: Francisco

last: Quintero

first: José

middle: M

last: Pardo


title: Phosphorylation at the S2056 1 cluster of DNA-PKcs is dispensable for lymphocyte development and class switch recombination in mice.

city: New Yprk

first: Zhengping

last: Shao

state: New York

address: 1130 St. Nicholas Ave

department: ICG

institute: Columbia University Medical Center

summary: The classical non-homologous end-joining (cNHEJ) pathway is a major DNA double-strand break repair pathway in mammalian cells and is required for lymphocyte development and maturation. The DNA-dependent protein kinase (DNA-PK) is a cNHEJ factor that encompasses the Ku70-Ku80 (KU) heterodimer and the large catalytic subunit (DNA-PKcs). In mouse models, loss of DNA-PKcs (DNA-PKcs-/-) abrogates end-processing (e.g., hairpin-opening), but not end-ligation, while expression of the kinase-dead DNA-PKcs protein (DNA-PKcsKD/KD) abrogates end-ligation, suggesting a kinases-dependent structural function of DNA-PKcs during cNHEJ. Lymphocyte development is abolished in DNA-PKcs-/- and DNA-PKcsKD/KD mice due to the requirement for both hairpin-opening and end-ligation during V(D)J recombination. DNA-PKcs itself is the best-characterized substrate of DNA-PK. The S2056-cluster is the best characterized auto-phosphorylation site on human DNA-PKcs. Here we show that radiation can induce phosphorylation of murine DNA-PKcs at the corresponding S2053 and generated knockin mouse models with alanine- (DNA-PKcsPQR) or phospho-mimetic aspartate (DNA-PKcsSD) substitutions at the S2053 cluster.  Despite moderate radiation sensitivity in the DNA-PKcsPQR/PQR fibroblasts and lymphocytes, both DNA-PKcsPQR/PQR and DNA-PKcsSD/SD mice retain normal kinase activity, and undergo efficient V(D)J recombination and class switch recombination, indicating that phosphorylation at the S2053-cluster of mouse DNA-PKcs (corresponding to S2056 of human DNA-PKcs), although important for radiation resistance, is dispensable for the end-ligation and hairpin-opening function of DNA-PK essential for lymphocyte development.

overall_design: HTGTS analyzes thousands of CSR junctions between the 5’ of Sμ and its joining partner genome wide, including both internal deletion (Sμ-Sμ) and potentially productive switching (Sμ-Sγ1). We also used HTGTS to uncover a prominent shift to MH, extensive erosion within switch region, and relative increase of inversion in DNA-PKcs-/- B cells with only moderate CSR defects. So we performed HTGTS analyses of CSR junctions from DNA-PKcsPQR/PQR B cells along with control DNA-PKcs-/- B cells.  While the results confirmed S region erosion and increased MH usage in DNA-PKcs-/- B cells, no alteration in MH usage and Sµ junction distribution is noted in DNA-PKcsPQR/PQR B cells.

first: Xiaobin

middle: S

last: Wang

first: Jennifer

middle: L

last: Crowe

first: Brian

last: Lee

first: Shan

last: Zha


title: BCL6 de-repression induces the fasting transcriptome and protects from steatosis (ChIP-Seq I)

city: Chicago

first: Grant

middle: D.

last: Barish

state: IL

address: 303 E Superior Street

department: Medicine

institute: Northwestern University

summary: Here, we find that the B cell lymphoma 6 (BCL6) repressor is enriched upon feeding and converges genome-wide with PPARs to opposingly control lipid metabolism.

overall_design: Identification of BCL6, PPARa, PPARd, and H3K27ac binding sites in fasted and fed livers.

first: Meredith

last: Sommars


title: Bovine liver gene expression database of Polish-HF, Polish-Red and Hereford cattle breeds.

city: Torun

first: CHANDRA

middle: SHEKHAR

last: PAREEK

state: Kuj. Pom.

address: ul. Wilenska 4

department: Centre for Modern Interdisciplinary Technologies

country: Poland

institute: Nicolaus Copernicus University

summary: We reported the bovine liver gene expression database of Polish-HF, Polish-Red and Hereford cattle breeds.

overall_design: Examination of bovine liver gene expression in Polish-HF, Polish-Red and Hereford cattle breeds.

first: Chandra

last: Shekhar Pareek

first: Dibyendu

last: Kumar


title: Layered ontogeny and in situ perinatal priming of tissue ILC2s

city: San Francisco

first: Jinwoo

address: 513 Parnassus Ave

institute: UCSF

summary: The perinatal period is a critical window for the distribution of innate tissue-resident immune cells to developing organs. Despite epidemiologic evidence implicating early life environment in risk for allergy, temporally controlled lineage-tracing of ILC2s during this period has not been done.  Using complementary fate-mapping approaches and fluorescent reporters of ILC2 activation, we demonstrate that ILC2s appear in multiple organs during late gestation similar to tissue macrophages, but unlike the latter, a majority of peripheral ILC2 pools are generated de novo during a postnatal window. This period was accompanied by systemic ILC2 priming and acquisition of tissue-specific expression profiles.  Although perinatal ILC2s are variably replaced with age, the dramatic increases in tissue ILC2s following helminth infection are mediated through local expansion independent of de novo generation by BM hematopoiesis.  We provide the first comprehensive temporally controlled fate-mapping of an innate lymphocyte subset with notable nuances as compared to tissue macrophage ontogeny

overall_design: single-cell mRNA profiles of ILC2s sorted from neonatal (14-day-old) mouse lung and skin tissues

first: Richard

last: Locksley


title: Ketogenesis-generated β-hydroxybutyrate is an epigenetic regulator of CD8+ T cell memory development

status: Public on Apr 13 2019

first: Bo

last: Huang

address: #5 Dong Dan San Tiao

institute: Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences

summary: Elucidation of metabolic flux and switch is fundamental for understanding of CD8+ memory T (Tm) cell development. Glycogen, an intracellular carbon reservoir, has long been functionally considered as the use of energy metabolism. However, our recent study indicated that glycogen metabolism, directed by a cytosolic phosphoenolpyruvate carboxykinase (Pck1), controls the formation and maintenance of CD8+ Tm cells through regulating the redox homeostasis1. This unusual metabolic program raises the question of how Pck1 is upregulated in CD8+ Tm cells. Here, we show that mitochondrial acetyl-CoA is shunted to ketogenesis, which indirectly regulates Pck1 expression. Mechanistically, ketogenesis-derived β-hydroxybutyrate (BHB) is stocked in CD8+ Tm cells, which epigenetically modifies H3K9 of FoxO1 and PGC-1α with β-hydroxybutyrylation so to upregulate these genes expression. As a result, FoxO1 and PGC-1α cooperatively upregulates Pck1 expression, thus directing the carbon flow along the gluconeogenic pathway to glycogen and the pentose phosphate pathway. These results unveil that the ketogenesis acts as an unusual metabolic pathway in CD8+ Tm cells, linking epigenetic modification required for memory development.

overall_design: H3K9bhb CHIP-seq done  in CD8+ Tm cells treated with BHB

first: Huafeng

last: Zhang

first: Li

last: Zhou

first: Jiadi

last: Lv

first: Jincheng

last: Liu


title: An RNA-centric dissection of host complexes controlling flavivirus infection [LAM-PCR]

first: Ryan

last: Flynn

overall_design: This experiment was designed to assess, in a genome-wide manner, what human genes are required for the Zika virus to infect HAP1 cells. Genes were disrupted with lentiviral gene trap technology.

first: Karim

last: Majzoub

first: Yaw

last: Shin Ooi

first: Carolyn

last: Bertozzi

first: Jan

middle: E

last: Carette


title: Comparative multi-omic analyses of Trichinella Pseudospiralis based on a new genome assembly by long-read sequencing

city: Shenzhen

first: Desheng

last: Gong

address: No.7 PengFei road

institute: Agricultural Genomes Institute at Shenzhen

summary: Genome assemblies can form the basis of comparative analyses fostering insight into the evolutionary genetics. Genome evolution influences a parasite’s pathogenicity, host–pathogen interactions, environmental constraints and invasion biology. Comparative genomics and epigenomics analyses will provide deep understanding of parasitism biology for future diagnosis and prevention of trchinellosis. We provide a near-complete new T.p reference genome using SMRT technology, first time confirmed and characterized T.p DNA methylome, enabling full annotation. Based on this new version, we show repetitive sequences play important role in genome expansion, in synergy with DNA methylation during evolution. We further portrait the genomic and epigenomic regulation on E-S products in relation with their parasitism differences, especially for two super-families, including DNase II and EGF-like domain proteins.

overall_design: We generated single-base resolution maps of DNA methylation using whole-genome bisulﬁte sequencing and gene expression pattern by RNA-seq for three life stages(adults (Ad), muscle larvae (ML) and newborn larvae (NBL)).

first: Fei

last: Gao

first: Xiao


title: Effect of p38 SAPK activation on HeLa cells

city: barcelona

first: BELEN

last: MINANA

state: barcelona

address: dr aiguader 88

department: GENE REGULATION, STEM CELLS AND CANCER

institute: Center for genomic regulation

summary:
HeLa cells were treated with 100 mM NaCl during 2h versus untreated. HeLa cells treated with 100 mM NaCl during 2h versus  HeLa cells treated with 100 mM NaCl during 2h after pre-treatment with 10 μM SB203580 for 30 min.
Alternative splicing is a crucial mechanism for gene regulation that is modulated in response to a wide range of extracellular stimuli. Stress-activated protein kinases (SAPKs) play a key role in controlling several steps of mRNA biogenesis. Here, we show that osmostress has a major impact on the regulation of alternative splicing (AS), which is partly mediated through the action of the p38 SAPK.

overall_design: Three biological replicates were labeled in direct and dye-swap microarray experiments and hybridized onto an Agilent custom splicing-sensitive microarray platform

first: Caterina

last: Carbonell

first: Claudia

last: Vivori

first: Arnau

last: Ulsalmer

first: Panagiotis

last: Papasaikas

first: René

last: Böttcher

first: Manel

last: Joaquin

first: Belén

last: Miñana

first: Juan

last: Tejedor

first: Eulàlia

last: de Nadal

last: Valcárcel

first: Francesc

last: Posas


title: Genomic expression analysis of K562 cells expressing shRNA targeting lncRNA-IIRX and control cells

city: Beijing

first: Xuefei

last: Wang

state: Beijing

address: NO.1 West Beichen Road, Chaoyang District, Beijing 100101, China

institute: nstitute of Microbiology, Chinese Academy of Sciences (CAS)

summary: LncRNA-IIRX plays critical role in Bcr-Abl-induced tumorigenesis. To discover its mechanisms underlying cellular transformation by Bcr-Abl oncogene, genome-wide mRNA expression was measured by RNA-seq in K562 cells expressing shRNA targeting lncRNA-IIRX and control cells. We identified many genes with differential expression in K562 cells after knocking down lncRNA-IIRX.

overall_design: RNA samples from K562 cells expressing shRNA targeting lncRNA-IIRX and control cells were collected. Six total RNA samples from three independent experiments were extracted and used for RNA-seq.

first: Jilong

last: Chen


title: BCL6 de-repression induces the fasting transcriptome and protects from steatosis

first: Grant

last: Barish

overall_design: Refer to individual Series


title: RNA_Seq-based global transcriptome analysis of Streptococcus pyogenes M1T15448 lacking Spy_1476/SP-TyK

city: Columbus

first: Vijay

last: Pancholi

state: OH

address: 420W 12th Ave, TMRF-288

department: Pathology

institute: Ohio State University

summary: We report the mRNA expression profile of Streptococcus pyogenes M1T15448 strain-derived mutant lacking the spy_1476/sp-tyk gene encoding tyrosine kinase/GTP-ATP hydrolase

overall_design: Measuring transcriptome profiling in S.pyogenes M1T1DTyK mutants vs M1T1-WT  wild-type strains


title: Transcriptome profile of Carrizo citrange roots in response to Phytophthora parasitica infection

city: Apopka

first: Zunaira

last: Afzal

address: 2725 S Binion Road

department: Plant pathology

summary: Phytophthora parasitica is one of the most widespread Phytophthora species, which is known to cause root rot, foot rot/gummosis and brown rot of fruits in citrus. In this study, we have analyzed the transcriptome of a commonly used citrus rootstock Carrizo citrange in response to P. parasitica infection using the RNA-seq technology. In total, we have identified 6692 differentially expressed transcripts (DETs) among P. parasitica-inoculated and mock-treated roots.  Of these, 3960 genes were differentially expressed at 24 hours post inoculation and 5521 genes were differentially expressed at 48 hours post inoculation. Gene ontology analysis of DETs suggested substantial transcriptional reprogramming of diverse cellular processes particularly the biotic stress response pathways in Carrizo citrange roots.  Many R genes, transcription factors, and several other genes putatively involved in plant immunity were differentially modulated in citrus roots in response to P. parasitica infection. Analysis reported here lays out a strong foundation for future studies aimed at improving resistance of citrus rootstocks to P. parasitica.

sample_organism:
Phytophthora nicotianae
Citrus sinensis x Citrus trifoliata

overall_design: To determine the transcriptional changes in Carrizo citrange roots in response to Phytophthora parasitica

first: Naveed

last: Zunaira

first: Ali

last: Gul


title: Transcriptional profiling of growing and senescent WT and IL-1R-depleted IMR90 cells

city: New York

first: Lena

last: Lau

address: 550 1st Ave, MSB417

institute: NYU School of Medicine

summary: Senescent cells no longer divide, but remain metabolically active and secrete an array of cytokines, growth factors, and proteases termed the senescence-associated secretory phenotype (SASP). Previous studies have indicated that the SASP factor IL-1α may be an upstream regular of the SASP. We show here that knockdown of the IL-1α receptor IL-1R results in a sizable reduction of SASP expression late in senescence induction. Our results suggest that targeting the IL-1 signaling pathway is a reliable method to dissociate the SASP from cell-cycle exit.

overall_design: Cells were induced to senesce via activation of oncogene Ras. Samples were collected at day 0 (growing phase), day 4 (beginning of SASP induction) and day 10 (senescent phase) of Ras induction. Samples were collected from control cells expressing a scramble shRNA and samples expressing 1 of 2 independent shRNAs against IL-1R. Two replicates were collected per condition per timepoint for a total of 12 samples.

first: Gregory

last: David


title: BCL6 de-repression induces the fasting transcriptome and protects from steatosis (RNA-Seq)

overall_design: Identification of BCL6, Fasting, and PPARa-regulated genes in mouse liver

first: Meredith

last: Sommars


title: Strigolactones activate defense against the stem-boring weevil Trichobaris mucorea via their interactions with jasmonates and auxin

city: Jena

first: Klaus

last: Gase

address: Hans-Knoell-Strasse 8

department: Molecular Ecology

institute: Max-Planck-Institute for Chemical Ecology

summary: The aim of this study is to identify genes in the pith of Nicotiana attenuata stems that are regulated by the F-box protein MAX2. Functional enrichment based on differentially expressed genes will indicate possible candidate genes.

overall_design:
Gene expression in pith of root-shoot-junction of Nicotiana attenuata empty vector (EV) and ir-max2 plants.Four biological replicates were performed with both wild type and  ir-max2 plants. In total 12 microarrays were hybridized.
Ir-max2 plants 107 and 136 represent two independently transformed Nicotana attenuata lines both carrying a single T-DNA insertion from the binary plant transformation vector pRESC8MAX at different positions of the genome. The use of the two independent lines is necessary to avoid false positive results due to position effects of the T-DNA insertions.

first: Suhua

last: Li


title: Expression data from a staygreen mutant of citrus and its wild type

status: Public on Apr 14 2019

city: Wuhan

first: Feng

last: Zhu

address: No.1,Shizishan Street

department: College of Horticulture & Forestry Sciences

institute: Huazhong Agricultural University

summary: The fruits color is one of the most important appearance qualities of citrus fruits. To illuminate the potential regulation of the color formation process of citrus fruits, the present study compared the different genes expression pattern between a spontaneous stay-green mutant and its wild type.

overall_design: The flavode of the citrus were collected at 170 days after flowering for RNA extraction and hybridization on Affymetrix microarrays.

first: Yunjiang

last: Cheng


title: MicroRNA expression profile of bovine monocyte derived macrophages infected with Mycobacterium avium subsp. Paratuberculosis

city: Changchun

first: zi

last: wang

address: Xincheng Street No.#2888

institute: Jilin Agricultural University

summary: In order to gain a better understanding of MAP infection in immature macrophages, high-throughput sequencing technology was used to perform an analysis of miRNAs profiles of bovine monocyte derived macrophages upon MAP infection.The total numbers of raw reads collected from the MAP-infected and control MDM cells were 14.3 and 17.0 million raw reads per library.The length distribution of the clean reads was focused on 21–24 nt in length and read counts of 22 nt were highest.A total of 510 mature miRNAs were identified, among these a total of 433 miRNAs were homologous to bovine, while 77 were predicted as novel miRNAs that not homologous to any species.The analyses of differential expression revealed 21 DE miRNAs in MDM challenged with MAP compared to the control MDM, Among the DE miRNAs, 14 were upregulated and 7 were downregulated.Furthermore, The GO and KEGG pathway enrichment of these miRNA targets were performed.

overall_design: miRNA-sequencing analysis was performed on an Illumina Hiseq 2500 (LC Sciences, USA) following the vendor's recommended protocol

first: Zi

first: Bo-Yan

last: Jia


title: An RNA-centric dissection of host complexes controlling flavivirus infection [GeCKO]

city: Stanford

first: Ryan

last: Flynn

address: 380 Roth Way, Room 265

institute: Stanford University

summary: Flaviviruses including dengue virus (DENV) and Zika virus (ZIKV) cause significant human disease. Co-opting cellular factors for viral protein translation and viral genome replication at the endoplasmic reticulum (ER) is a shared replication strategy, despite different clinical outcomes. While the protein products of these viruses have been studied in depth, how the RNA genomes operate inside human cells is poorly understood. Using comprehensive identification of RNA binding proteins by mass spectrometry (ChIRP-MS), we took an RNA-centric viewpoint of flaviviral infection and identified several hundred proteins associated with both DENV and ZIKV genomic RNA inside human cells. Intersection with genome-scale knockout screens assigned putative functional relevance to the RNA-protein interactions. ER RNA binding proteins such vigilin and RRBP1 directly bound viral RNA and each operated at distinct points in the life cycle of flaviviruses. Thus, this versatile strategy can elucidate features of human biology that control pathogenesis of clinically relevant viruses.

overall_design: This experiment was designed to assess, in a genome-wide manner, what human genes are required for the dengue virus to infect Huh7.5.1 cells. Genes were disrupted with CRISPR/Cas9 technology.

first: Karim

last: Majzoub

first: Yaw

last: Shin Ooi

first: Carolyn

last: Bertozzi

first: Jan

last: Carette


title: RNA-seq for sf3b-1 alleles

status: Public on Apr 12 2019

city: Hospitalet de Llobregat

first: Julián

last: Cerón

state: Barcelona

address: Gran via 199, Hospital Duran i Reynals, planta 3

department: Cancer and Human Molecular Genetics

institute: IDIBELL

summary: RNA-seq for sf3b-1 alleles

overall_design: To study the transcriptional consequences of the K718E mutation, we used two homozygous mutant lines (CER218 and CER220) derived from two independent CRISPR/Cas9 events (cer3 and cer7 alleles, respectively), and the corresponding wild-type siblings (CER217 and CER221). Synchronized L4 animals were collected in M9 after growing for 41 hours at 20oC and total RNA was isolated using TRI Reagent and the PureLink® RNA Mini Kit, following the manufacturer’s instructions. sftb-1(cer6) homozygous larvae were obtained by automatically sorting non-red animals from a synchronized CER191 population grown at 20C for 23 hours, using a the COPAS worm sorter system.Two CER276 (cer39 allele) biological replicates were collected independently without sorting, after growing for 23 hours at 20C. Total RNA from the six samples was extracted using TRI Reagent, followed by aqueous and organic phase separation using 1-Bromo-3-chloropropane, and RNA was precipitated with 2 propanol. After treatment with TURBO DNase, RNA was purified following a phenol/chloroform extraction protocol.   In all cases, total RNA was quantified by Qubit® RNA BR Assay kit (Thermo Fisher Scientific) and the integrity was checked by using RNA 6000 Nano Bioanalyzer 2100 Assay (Agilent).

first: Xènia

last: Serrat


title: A subset of type I conventional dendritic cells control cutaneous bacterial infections through VEGFa-mediated recruitment of neutrophils [single-cell RNA-seq]

city: Singapore

first: Florent

last: Ginhoux

address: 8A Biomedical Grove, Immunos Building, Level 3

country: Singapore

institute: Singapore Immunology Network (SIgN), A*STAR

summary: Skin conventional dendritic cells (cDC) exist as two distinct subsets, cDC1 and cDC2, which maintain the balance of immunity to pathogens and tolerance to self and microbiota. Here we examined the roles of dermal cDC1 and cDC2 during bacterial infection, notably Propionibacterium acnes (P. acnes). cDC1, but not cDC2, regulated the magnitude of the immune response to P. acnes in the murine dermis by controlling neutrophil recruitment to the inflamed site and survival and function therein. Single-cell mRNA sequencing revealed that this regulation relied on secretion of the cytokine VEGFα by a minor subset of activated EpCAM+CD59+Ly6D+ cDC1. Neutrophil recruitment by dermal cDC1 was also observed during S. aureus, BCG or E. coli infection, as well as in a model of bacterial insult in human skin. Thus, skin cDC1 are essential regulators of the innate response in cutaneous immunity, with roles beyond classical antigen presentation.

overall_design: Single-cell gene expression of cDC1s (CD103+DC) in P. acnes-infected skin.

first: Baptiste

last: Janela

first: Amit

last: Patel

first: Mai

middle: C

first: Chi

last: Goh

first: Rasha

last: Msallam

first: Wan

middle: T

last: Kong

first: Michael

last: Fehlings

first: Sandra

last: Hubert

first: Josephine

last: Lum

first: Yannick

last: Simoni

first: Benoit

last: Malleret

first: Francesca

last: Zolezzi

first: Jinmiao

last: Chen

last: Poidinger

first: Ansuman

last: Satpathy

first: Carlos

last: Briseno

first: Christian

last: Wohn

first: Bernard

last: Malissen

first: Kenneth

last: Murphy

first: Alexander

last: Maini

first: Leen

last: Vanhoutte

first: Martin

last: Guilliams

first: Emmanuel

last: Vial

first: Laurent

last: Hennequin

first: Evan

last: Newell

first: Lai

middle: G

last: Ng

first: Philippe

last: Musette

first: Simon

last: Yona

first: Feriel

last: Hacini-Rachinel


title: Deletion of adrenocortical Bmal1 results in sex-biased gene expression.

city: Bern

first: Emanuele

last: Pignatti

address: Freiburgstrasse 15

country: Switzerland

institute: University of bern

summary: We report that deletion of BMAL1 from adrenocortical cells using a SCC(Cyp11a1)-Cre driver reults in elevated plasma corticosterone in female, but not in male mice, following submaximal stress stimulation. RNA sequencing of adrenal glands from control and experimental animals was adopted to identify sex-dependent differences in gene expression that may explain the augmented corticosterone response specifically in female mice.

overall_design: Examination of the effect of BMAL1 inactivation in female and male adrenals.

first: William

last: Engeland

first: David

last: Breault


title: The Oncogenic Transcription Factor RUNX1/ETO Corrupts Cell Cycle regulation to Drive Leukemic Transformation  [ChIP]

city: Birmingham

first: Salam

middle: Adli

last: Assi

address: IBR

department: Institute for Cancer and Genomic Sciences

country: United Kingdom

institute: University of Birmingham

summary: Oncogenic transcription factors such as the leukaemic fusion protein RUNX1/ETO constitute cancer-specific but highly challenging therapeutic targets, whose functions depend on pharmacologically tractable downstream pathways. Here we interrogated the transcriptional network of RUNX1/ETO in an in vitro/in vivo RNAi screen and identified Cyclin D2 (CCND2) as a crucial transmitter of RUNX1/ETO-driven leukemic propagation. RUNX1/ETO drives CCND2 expression by binding to a regulatory element upstream of the CCND2 promoter.  Both knockdown of CCND2 and treatment with the CDK4/6 inhibitor palbociclib inhibited leukemic expansion patient-derived AML cells and impaired engraftment of immunodeficient murine hosts. Our data demonstrate that RUNX1/ETO drives leukaemia by directly promoting cell cycle progression and establish inhibition of G1 CCND-CDK complexes as a promising therapeutic strategy for RUNX1/ETO-driven AML.

overall_design: ChIP-seq exprement before and after RUNX1/ETO knock-down is used in this study

first: Natalia

last: Martinez-Soria

first: Lynsey

last: McKenzie

first: Julia

last: Draper

first: Anetta

last: Ptasinska

first: Helen

middle: J

last: Blair

first: Sirintra

last: Nakjang

first: Anna

last: Pickin

first: Paulynn

last: Chin

first: Sandeep

last: Potluri

middle: A

first: Daniel

last: Coleman

first: Victoria

last: Forster

first: Hasan

last: Issa

first: Asmida

last: Isa

first: Ricky

last: Tirtakusuma

first: Philip

last: Berry

first: Dorothee

last: Mueller

first: Deepali

last: Pal

first: Alex

last: Elder

first: Gareth

last: Veal

first: Peter

middle: N

last: Cockerill

last: Wichmann

first: Josef

last: Vormoor

first: Georges

last: Lacaud

first: Constanze

last: Bonifer

first: Olaf

last: Heidenreich


title: The Oncogenic Transcription Factor RUNX1/ETO Corrupts Cell Cycle regulation to Drive Leukemic Transformation [HiC]

first: Salam

last: Assi

overall_design: Capture HiC experiment before and after RUNX1/ETO knock-down is used in this study

first: Natalia

last: Martinez-Soria

first: Lynsey

last: McKenzie

first: Julia

last: Draper

first: Anetta

last: Ptasinska

first: Helen

last: Blair

first: Sirintra

last: Nakjang

first: Anna

last: Pickin

first: Paulynn

last: Chin

last: Potluri

first: Christian


title: mRNA degradome analysis indicating miRNA regulation in muscle mass development

city: Kraków

first: Tomasz

last: Szmatoła

address: Komuny Paryskiej, 4

institute: National Reseach Institute of Animal Production

summary: The search of the molecular process associated with development and metabolism of muscle mass is still actual, what in humans is related to muscle modification after endurance training exercises. In turn in farm animals, the high meat content in carcasses delivers higher economic benefit. Over a few recent years, scientists using next-generation-sequencing (NGS) methods attempted to indicate proteins/genes engaged in muscle mass development. The aim of the present study was to show mRNA degradome signals that could be characteristic for molecular processes associated with muscle development in pigs and indicate the miRNA regulation controlling this process based using also NGS technology. The preliminary results exhibited that the huge amount of miRNAs regulate gene expression at the different molecular level than mRNA degradation. Moreover, the study found significant differences between investigated pig breeds. The results often were opposite for Pietrain breed that could be related to differences in muscle fibre composition and their microstructure. The present study showed an interesting dependence between miRNA and their targets - the most of transcripts found as being degraded, were associated with controlling muscle mass development such as ENO3, CKM, CRYAB and ADAM19. In turn, performed PAREsnip analysis showed that only a small percentage of identified degraded transcripts was associated with miRNA regulation, what suggested a different mechanism of mRNA degradation. Nevertheless, the complete view of miRNA regulation could be obtained in the more advanced study, which would employ miRNA transfection procedure in muscle tissue cell culture that could be a subject of further research.

overall_design: Examination of mRNA levels between chicken groups differing in age and growth rate. The study was supported by statutory activity of National Research Institute of Animal Production (no. 01-013.1) and National Multidisciplinary Laboratory of Functional Nanomaterials NanoFun nr POIG.02.02.00-00-025/09 (Innovative Economy Operational Programme, Priority Axis 2: R&D Infrastructure, Action 2.2: Support of Formation of Common Research Infrastructure of Scientific Units.

first: K

last: Piórkowska

first: T

first: Klaudia

last: Pawlina-Tyszko

first: A

last: Gurgul

last: Ropka-Molik


title: Lasting expression changes in tomato after tomato psyllid (Bactericera cockerelli) infestation

status: Public on Apr 11 2019

city: Lincoln

first: Kyle

last: Harrison

state: Nebraska

address: 1700 E Campus Mall

department: Entomology

institute: USDA-ARS

summary:
Purpose: The tomato psyllid, Bactericera cockerelli Šulc (Hemiptera: Triozidae), is a pest of tomato (Solanum lycopersicum) and potato (S. tuberosum) in the U.S. and vectors the disease-causing pathogen ‘Candidatus Liberibacter solanacearum’. Plants undergo physiological, transcriptomic, or epigenetic changes in order to mount a stronger, faster response against secondary challenges by previously perceived threats. This is called defense ‘priming’ and it likely has an impact on vectored disease transmission. Currently, it is still unknown whether or not psyllid infestation has any lasting consequences for tomato gene expression or defense. To characterize the genes potentially involved in tomato priming against psyllids, RNA was extracted from psyllid-primed and uninfested tomato (Moneymaker) leaves three weeks after infestation.
Methods: RNA was extracted and sequenced from plants three weeks after psyllid infestation. Plants were either left alone (Control or C) or infested with psyllids (Primed or J1). Libraries were developed using the TruSeq RNA Library Prep Kit v2. Sequencing was performed on the Illumina PE HiSeq 2500 v4 platform. Processed sequences were uploaded to the CyVerse Discovery Environment computational infrastructure where bioinformatic analysis was performed using the Tuxedo Suite 2 workflow.
Results: Illumina HiSeq sequencing of tomato cDNA libraries produced 132,428,443 total reads that met FastQC quality control criteria. 94.6% of all reads mapped to vSL3.0 of the S. lycopersicum genome. CuffDiff2 analysis identified 310 differentially expressed genes (DEGs) between control and psyllid-primed plants (q-value <0.01).
Conclusions: A week-long infestation by a small number of B. cockerelli had lasting consequences for gene expression in tomato plants. Homologs of the DEGs were associated with 1) defense against abiotic and biotic stress, 2) growth and development, and 3) components of plant biology indirectly involved in plant growth and development such as homeostasis, transcription/translation, and molecular transport.

overall_design: FPKM values of control and psyllid-primed tomato leaf transcriptomes were generated by Illumina PE HiSeq 2500 v4 sequencing.

first: Azucena

last: Menoza

first: Cecilia

last: Tamborindeguy

first: Julien

last: Levy


title: Long noncoding RNA ELIT-1 acts as a Smad3 cofactor to facilitate TGF-β/Smad signaling and promote epithelial-mesenchymal transition

city: Hamamatsu

first: Tatsuya

last: Ohhata

state: Shizuoka

address: Higashi-ku Handayama 1-20-1

department: Department of Molecular Biology

country: Japan

institute: Hamamatsu University School of Medicine

summary: TGF-β is involved in various biological processes, including development, differentiation, growth regulation, and epithelial-mesenchymal transition (EMT). In TGF-β/Smad signaling, receptor-activated Smad complexes activate or repress their target gene promoters. Smad cofactors are a group of Smad-binding proteins that promote recruitment of Smad complexes to these promoters. Long noncoding RNAs (lncRNAs), that behave as Smad cofactors have thus far not been identified. Here, we characterize a novel lncRNA EMT-associated lncRNA induced by TGF-β-1(ELIT-1). ELIT-1 was induced by TGF-β-stimulation via the TGF-β/Smad pathway in TGF-β-responsive cell lines. ELIT-1-depletion abrogated TGF-β-mediated EMT progression and expression of TGF-β target genes including Snail, a transcription factor critical for EMT. A positive correlation between high expression of ELIT-1 and poor prognosis in lung adenocarcinoma and gastric cancer patients suggests that ELIT-1 may be useful as a prognostic and therapeutic target. RIP assays revealed that ELIT-1 bound to Smad3, but not Smad2. In conjunction with Smad3, ELIT-1 enhanced Smad-responsive promoter activities by recruiting Smad3 to the promoters of its target genes including Snail, other TGF-β-target genes, and ELIT-1 itself. Collectively, these data show that ELIT-1 is a novel trans-acting lncRNA that forms a positive feedback loop to enhance TGF-β/Smad3 signaling and promote EMT progression.

overall_design: To identify the genes induced by HBV replication, HBV genome containing episomal vectors (Ae, Bj35, Bj56) or its empty vector (pEB) were transfected in liver carcinoma cell line Huh7. After puromycin screening, the transfectants were subjected to purify its total RNA and followed by microarray analysis.

first: Satoshi

last: Sakai

first: Masatoshi

last: Kitagawa


title: Expression data from whole blood of RRMS patients initiating treatment with intramuscular IFN-β1a (Avonex®) obtained immediately prior to treatment.

city: Cleveland

first: Mark

middle: R

last: Chance

address: 10900 Euclid Ave

institute: Case Western Reserve University School of Medicine

summary: Interferon beta (IFN-β) is a first line treatment for patients with relapsing forms of MS, but response to the drug varies and to date there are no biomarkers associated with individual patient response. Whole blood gene expression data from a clinical study of patients initiating treatment with intramuscular IFN-β1a (Avonex®) was comprehensively analyzed for gene signatures distinguishing between good vs. poor responders where the latter were defined by increases in number and size of observed lesions in quantitative imaging over a 6-month period. We observed signatures related to B-cell activation in subject gene expression prior to treatment while T-cell and interleukin signatures were observed in the same subjects immediately after treatment. These signatures form a basis for developing predictors of IFN-β1a response in patients both prior to and after IFN-β1 treatment.

overall_design: Whole blood was obtained from 85 RRMS/CIS immediately prior to injection of intramuscular IFN-β1a (Avonex®) at an initial (characteristic: time point=T0) and 6-month visit (characteristic: time point=T6). Clinical response was measured by quantifying new and enlarging brain lesions on T2-weighted MRI scans at 6 months (T6) compared to baseline (T0). Based on pre-defined MRI criteria, a group of 15 poor responders (characteristic: response=Poor) with 3 or more new or enlarging lesions was identified, and compared with a group of 15 good responders (characteristic: response=Good) selected from the full patient cohort. The remaining patients (characteristic: response=Indeterminate) were not used for the analysis.


title: Effects of IKKβ inhibition on NF-κB transcription

city: AUSTIN

first: Meghan

last: Bloom

address: 107 W DEAN KEETON ST

institute: THE UNIVERSITY OF TEXAS - AUSTIN

summary: Nuclear factor kappa B (NF-kB) is a well-studied transcription factor that plays a  key role in a number of diseases. Here, we present an RNA TagSeq dataset consisting of 164 samples, including four biological replicates, collected over six hours from populations of murine 3T3 fibroblasts that were treated with four concentrations of an IKK inhibitor (SC-514) and perturbed with two inflammatory stimuli that activate NF-kB—interleukin 1 beta (IL-1β) and tumor necrosis factor alpha (TNF-α).

overall_design: Evaluation of IKKβ selective inhibition on NF-κB gene transcription to two different stimuli, IL-1β and TNF-α. SRA: SRP163157, BioProject:PRJNA494428

first: Sachit

middle: D

last: Saksena


title: Role of Nampt-Sirt6 axis in renal proximal tubules in extracellular matrix deposition in diabeteic nephropathy.

status: Public on Apr 10 2019

city: Tokushima

first: Kazuhiro

last: Hasegawa

address: 3-18-15 Kuramoto-cho

department: Department of Nephrology

institute: Tokushima University Graduate School of Biomedical Sciences

summary:
PT-specific Nampt knockout (CKO) mice exhibited TBM thickening and collagen deposition.
Renal fibrotic changes in CKO mice are associated with the upregulation of the profibrogenic gene TIMP-1.

overall_design: Mice in the control and Nampt CKO groups were sacrificed and their whole kidneys were harvested for microarray analysis using the SurePrint G3 Mouse GE 8x60K Microarray according to the Agilent standard protocols.


title: Improved SALP-seq method for construct next-generation sequencing library of cell free DNA

city: NanJing

first: Jian

last: Wu

state: Jiangsu

address: Sipailou 2#, Sipailou 2#

institute: Southeast University

summary: Cell free DNA (cfDNA) in human plasma carries abundant information on physiological condition, especially in cancer patients such as esophageal cancer. Next-generation sequencing (NGS) as a rapidly developed technology could decode the information effectively. As a key step of NGS, using existing methods to construct cfDNA sequencing libraries is limited by several shortcomings. In this study, we developed a new NGS library construction method for highly degraded DNA, cfDNA as example, based on Single strand Adaptor Library Preparation (SALP). With the high ligation efficiency of single strand adaptor (SSA) which overhangs 3 random bases at 3' end of a double-strand DNA, the new method could construct the sequencing library with high sensitivity without using specific enzymes except T4 DNA ligase and Taq polymerase. With the special designed barcode T adaptor (BTA), multiple libraries constructed from different samples can be amplified in unbiased strategy and facility to compare. Using this method, this study successfully sequenced and compared totally 20 cfDNA samples derived from esophageal cancer patients and healthy people in whole genome scale. This study also compared the chromatin state between cancer patients and healthy people using cfDNA, identified the significant difference between different health condition. Our findings extend the application of cfDNA beyond the analysis with degraded DNA fragments itself, to the transcription regulation level, which also provide an important clue for biopsy of esophageal cancer and other diseases.

overall_design: The cell free DNA of 20 samples were sequenced with adapted SALP-seq.

first: Wei

last: Dai

first: Lin

first: Xinyi

last: Xia

first: Jinke

last: Wang


address: 1-20-1 Handayama, Higashi-ku

department: Virology and Parasitology

overall_design: Liver carcinoma cell line Huh7 samples were transfected with each siRNA (siCtrl #2 scramble, #3 scramble, siELIT-1 #2, or siELIT-1 #3). At 24 h after the first transfection, cells were transfected with these siRNAs, again. At 6 h after the second transfection, cells were treated with or without 10 ng/mL TGF-b for 48 h. Total RNA was isolated from cultured cells using RNeasy Mini Kit and followed by microarray analysis.


title: Analysis of gene expression in Tgif mutant mouse colon tumors.

city: Charlotesville

first: David

last: Wotton

department: Biochemistry and Molecular Genetics

institute: University of Virginia

summary: Colon tumors in mice were generated by deleting one allele of the Apc gene, or both alleles of Tgif1 and Tgif2, together with a single Apc allele. Gene expression was compared by RNA-seq analysis of wild type colon, Apc mutant tumors or Apc mutant colon tumors with deletion of both Tgif1 and Tgif2. Comparison of Apc tumors to Apc;Tgif1;Tgif2 tumors was used to identify Tgif-dependent gene expression changes associated with intestinal tumorigenesis.

overall_design: Tissues were isolated from 12 week old mice. Three groups were analyzed: 1. Wild type colon tissue from three female and two male mice. 2. Colon tumors from Apc mutant mice (generated using Villin-Cre to delete one allele of the Apc gene), with individual tumors isolated from three female and four male mice. 3. Colon tumors from Apc mutant mice with deletion of both Tgif1 and Tgif2 (generated using Villin-Cre to delete one allele of the Apc gene and both alleles each of Tgif1 and Tgif2), with single tumors isolated from three female and four male mice. RNA-seq was used to compare gene expression profiles between wild type colon and the two different geneotype colon tumors.


title: Treanscriptomes of emering nodules, mature nodules, emerging lateral roots, and young lateral roots in soybean

city: Brookings

first: Sen

last: Subramanian

state: SD

address: 1390 College Avenue

department: Agronomy, Horticulture, and Plant Science

institute: South Dakota State University

summary: Symbiotic legume nodules and lateral roots arise away from the root meristem via dedifferentiation events. While these organs share some morphological and developmental similarities, whether legume nodules are modified lateral roots is an open question. We dissected emerging nodules (EN), mature nodules (MN), emerging lateral roots (ELR) and young lateral roots (YLR), and constructed strand-specific RNAseq libraries using polyA-enriched RNA preparations. Root sections above and below these organs devoid of any lateral organs were used to construct respective control tissue libraries (ABEN, ABMN, ABELR, ABYLR respectively). High sequence quality, predominant mapping to coding sequences, and consistency between replicates indicated that the RNAseq libraries were of very high quality. We identified genes enriched in emerging nodules, mature nodules, emerging lateral roots and young lateral roots in soybean by comparing global gene expression profiles between each of these organs and adjacent root segments. Potential uses for this high quality transcriptome data set include generation of global gene regulatory networks to identify key regulators; metabolic pathway analyses and comparative analysis of key gene families to discover organ-specific biological processes; and identification of organ-specific alternate spliced transcripts. When combined with other similar datasets especially from leguminous plants these analyses can help answer questions on the evolutionary origins of root nodules and relationships between the development of different plant lateral organs.

overall_design: Three replicate samples were harvested for each of the eight tissue types for the preparation of twenty four RNAseq libraries.

first: Sajag

last: Adhikari

first: Suresh

last: Damodaran

first: Senthil


title: Expression profiles of human cumulus cells from GV-stages COCs

city: hangzhou

first: long

last: cui

address: xueshi Rd1#

institute: women's hospital school of medicine,zhejiang university

summary:
The present study was designed to investigate the effect of Endothelin-1 (ET-1) on human GV-stage oocyte maturation and explore the mechanism of ET-1 induced resumption of meiosis.
Adding ET-1 to the culture medium may enhance the occurrence rate of germinal vesicle breakdown (GVBD) in cumulus cell-enclosed human oocytes. We used whole-genome transcriptome microarray to analysis the differential expression gene in cumulus cells

overall_design: Two samples were analyzed.  Cumulus cells from GV-stages COCs cultured in G-IVF medium for 18 hours, with or without 100ng/ml ET-1. As a better control, we harvest cells at the same time. The sample 18Hmean GV-stages cumulus cells treated with ET-1 medium for 18 hours. The sample 0H mean  GV-stages cumulus cells treated without ET-1 medium for 18 hours.

first: Yinghui

last: Ye

first: Long

last: Cui


title: Bmi1 suppresses adipogenesis in the hematopoietic stem cell niche: ChIP-Seq

city: Houston

first: Daisuke

last: Nakada

state: Texas

address: One Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

summary: Bone marrow mesenchymal stromal cells (MSCs) that express high levels of stem cell factor (SCF) and CXC chemokine ligand 12 (CXCL12) are one crucial component of the hematopoietic stem cell (HSC) niche. While the secreted factors produced by MSCs to support HSCs have been well described, little is known regarding the transcriptional regulators controlling the cell fate of MSCs and thus indirectly maintaining HSCs. Bmi1 is a polycomb group protein that regulates HSCs both cell intrinsically and extrinsically, but it is unknown in which cell type and how Bmi1 functions to maintain HSCs extrinsically. Here we show that Bmi1 maintains HSCs by preventing adipogenic differentiation of MSCs. Bmi1 is highly expressed in MSCs but becomes downregulated upon adipogenic differentiation and during aging. Deleting Bmi1 from MSCs increased marrow adipocytes, induced HSC quiescence and depletion, and impaired hematopoiesis. We found that Bmi1 repressed multiple developmental programs in MSCs by safeguarding the repressive epigenetic marks histone H2A ubiquitylation and H3 lysine 27 trimethylation. We identified a novel adipogenic program governed by Pax3, which Bmi1 repressed in MSCs. Our results establish Bmi1 as a critical regulator of MSC cell fate that suppresses marrow adipogenesis to create a supportive niche for HSCs.

overall_design: Histone ChIP-seq using two antibodies (H2Aubi, H3K27me3) on each of two treatments (WT, KO), with three replicates per treatment, and a matching set of ‘Input’ samples.

first: Kevin

last: Hoegenauer

first: Tianyuan

last: Hu


title: Gene expression profile between ARID1A knockdown SAS cells and mock SAS cells

status: Public on Apr 09 2019

city: Gifu City

first: Katsuaki

last: Bunai

state: Gifu

address: 1-1 Yanagido

institute: Gifu University Graduate School of Medicine

summary: The aim of the study was to elucidate the character of ARID1A by a comprehensive gene expression analysis.

overall_design: Total RNA from human oral cancer SAS cell line and ARID1A knockdown SAS cell line was hybridized on Affymetrix® GeneChip Human Gene 2.0 ST arrays. siRNAs were transfected into SAS cell line using Lipofectamine RNAiMAX.

first: T

last: Takeuchi

first: K


title: Differential gene expression upon priming of Neural Crest Stem Cells (NCSCs)

city: Zurich

first: Luis

last: Zurkirchen

state: Zurich

address: Winterthurerstrasse 190

department: Institute of Anatomy

institute: University of Zurich

summary:
The aim was to identify a NCSC transcriptional program
In this study we included a total of 16 data sets including gene expression from migratory NCSCs and primed couterparts

overall_design: Differential gene expression between migratory NCSCs and NCSCs primed to differentiation by exposure to instructive growth factors.

first: Sandra

last: Varum

first: Lukas

last: Sommer


title: Gene expression profile of HeLa cells with stable inducible expression of DOCK10

city: Murcia

first: Antonio

last: Parrado

address: Ctra. Madrid-Cartagena, s/n

institute: Hospital Clinico Universitario Virgen de la Arrixaca

summary: The goal of this study was to identify changes in the gene expression profile (GEP) of HeLa cells in response to induction of expression of DOCK10 during 24 hours.

overall_design: Cervical cancer epithelial HeLa cells, growing adherently as monolayers, were cultured in Dulbecco’s MEM supplemented with 10 % FCS, 50 U/ml penicillin, 50 U/ml streptomycin, 2,5 µg/ml amphotericin B, and 2 mM L-glutamine. At subconfluency, HeLa cells were transfected using lipofectamine with pUHD-15-1-Puro vector and, after treatment with 1 µg/ml puromycin during 2-3 weeks, a stable doxycycline (dox)-regulatable tTA-expressor clone was selected (HeLa-tTA). The HeLa-tTA clone was transfected using lipofectamine with pJAG4-HA-DOCK10.1 plasmid and, after treatment with 0.5 mg/ml G418 during 2-3 weeks, a stable dox-regulatable HA-DOCK10.1-expressor clone was selected (C33), as well as an HA-DOCK10.1-non-expressor clone (C23). The parental HeLa-tTA clone, the non-expressor HeLa-C23 clone, and the HA-DOCK10.1-expressor HeLa-C33 clone were washed free of dox and cultured for 24 h in the presence (dox+) and absence of dox (dox–). Only HeLa-C33-dox– expressed HA-DOCK10.1. Following detachment of cells with 0.05%-EDTA 0.02% in PBS, total RNAs were isolated using the miRNeasy Mini Kit (Qiagen). HeLa-C33-dox+/HeLa-C33-dox–, performed twice from biological replicates, were used as reference/test pairs, respectively, and these experiments were designated as HeLa-DOCK10. HeLa-tTA-dox+/HeLa-tTA-dox– and HeLa-C23-dox+/HeLa-C23-dox–, were used as controls for dox withdrawal, and were designated as HeLa-CTRL. References were labeled with cyanine-3-CTP, and tests with cyanine-5-CTP. The labeled cRNAs were mixed together and hybridized onto Agilent SurePrint G3 Human Gene Expression 8×60K v2 Microarrays targeting 50,599 biological features (technology 39494), using the Agilent Gene Expression Hybridization kit. After hybridization, the microarray slides were washed and scanned in an Agilent G2565CA DNA Microarray Scanner using the Agilent Scan Control software. Images were analyzed with the Agilent Feature Extraction software, which computes log ratios (test vs reference) following normalization correction by linear and Lowess methods.


title: Defining the Activated Fibroblast Population in Lung Fibrosis Using Single Cell Sequencing

city: New York

first: Lori

last: Morton

state: NY

address: 777 old saw mill river road

institute: Regeneron Pharmaceuticals

summary: In brief, we have applied a novel and unbiased approach to identify distinct and dynamic cell populations, including an in-depth analysis of the fibroblast population, in lung fibrosis. We found that while fibroblast number did not increase after injury, a population of activated fibroblasts can be identified in the fibrotic mouse lung. Using expression profiles of 1,945 lung fibroblasts we redefine the molecular characteristics of activated fibroblasts, finding that they are not a separate population but rather exhibit a similar, yet amplified, gene expression pattern to non-activated cells.

overall_design: A bolus of Bleomycin (2.8 U/kilogram (kg); 1.75 milligram (mg)/kg) or 0.9% sterile saline at 2ml/kg volume was dosed into mouth of each C57BL/6 male mouse (12-13 weeks) near the larynx to induce lung fibrosis.  3 Groups: Saline Control, Bleomycin, and Bleomycin+60mg/kg Nintedanib treatment was started concomitantly with the administration of bleomycin and single cell isolations were performed on day 11.

first: Rebecca

last: Peyser

first: Scott

last: MacDonnell

first: Yinglin

last: Gao

last: Cheng

first: Yong

last: Kim

first: Theodore

last: Kaplan

first: Qin

last: Ruan

first: Yi

last: Wei

first: Min

last: Ni

first: Christina

last: Adler

first: Wen

last: Zhang

first: Kishor

last: Devalaraja-Narashimha

first: Justin

last: Grindley

first: Gabor

last: Halasz


title: Targetable vulnerabilities in T- and NK-cell lymphomas identified through preclinical models

city: Boston

first: Samuel

last: Ng

state: MA

address: 450 Brookline Avenue

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: We report the expression profiles of 21 T- and NK-cell lymphomas to provide a platform for further investigation of targetable vulnerabilities in diseases represented by these cell lines

overall_design: RNA-seq analysis of 21 different cell lines in cuture media

middle: Y

first: Noriaki

last: Yoshida

first: David

last: Weinstock

first: Raphael

last: Koch


title: Expression data from whole blood of RRMS patients initiating treatment with intramuscular IFN-β1a (Avonex®) obtained exactly 12 hours after treatment.

first: Mark

last: Chance

overall_design: Whole blood was obtained from 85 RRMS/CIS precisely 12 hours after injection of intramuscular IFN-β1a (Avonex®) at an initial (characteristic: time point=T0) and 6-month visit (characteristic: time point=T6). Clinical response was measured by quantifying new and enlarging brain lesions on T2-weighted MRI scans at 6 months (T6) compared to baseline (T0). Based on pre-defined MRI criteria, a group of 15 poor responders (characteristic: response=Poor) with 3 or more new or enlarging lesions was identified, and compared with a group of 15 good responders (characteristic: response=Good) selected from the full patient cohort. The remaining patients (characteristic: response=Indeterminate) were not used for the analysis.


title: Targeting Pyrimidine Synthesis Accentuates Molecular Therapy Response in Glioblastoma Stem Cells

city: San Diego

first: Jeremy

last: Rich

state: CA

address: 9500 Gilman Drive #0695

institute: University of California, San Diego

summary: Glioblastoma stem cells (GSCs) reprogram glucose metabolism by hijacking high-affinity glucose uptake to survive in a nutritionally dynamic microenvironment. Here, we trace metabolic aberrations in GSCs to link core genetic mutations in glioblastoma to dependency on de novo pyrimidine synthesis. Targeting the pyrimidine synthetic rate-limiting step enzyme CAD (carbamoyl-phosphate synthetase 2, aspartate transcarbamyolase, dihydroorotase) or the critical downstream enzyme, DHODH (dihydroorotate dehydrogenase) inhibited GSC survival, self-renewal, and in vivo tumor initiation through the depletion of the pyrimidine nucleotide supply. Mutations in EGFR or PTEN generated distinct CAD phosphorylation patterns to activate carbon influx through pyrimidine synthesis. Simultaneous abrogation of tumor-specific driver mutations and DHODH activity with clinically approved inhibitors demonstrated sustained inhibition of metabolic activity of pyrimidine synthesis and GSC tumorigenic capacity. Higher expression of pyrimidine synthesis genes portend poor prognosis of glioblastoma patients. Collectively, our results demonstrate a novel therapeutic approach of precision medicine through targeting the nexus between driver mutations and metabolic reprogramming in cancer stem cells.

overall_design: Four H3K27ac ChIP-seq experiments were performed. One replicate was used for each glioma stem cell model analyzed

first: Xiuxing

last: Wang


title: The Oncogenic Transcription Factor RUNX1/ETO Corrupts Cell Cycle regulation to Drive Leukemic Transformation

city: Birmingham

first: Salam

last: Assi

address: IBR

institute: University of Birmingham

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

overall_design: Refer to individual Series


title: OncoScan analysis of breast carcinomas from the Swedish haemangioma cohort

city: Gothenburg

first: Jana

last: Biermann

address: Medicinaregatan 1F

country: Sweden

institute: University of Gothenburg

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

summary: The Swedish haemangioma cohort consists of 17,200 women treated with radium-226 for skin haemangioma at an early age (<1.5 years of age) between 1920 and 1965. A total of 877 breast cancer cases were reported by December 2009, estimating an excess relative and absolute risk at the age of 50 years of 0.48 Gy^(−1) and 10.4 (10^4 PYR Gy)^(−1), respectively. We screened 31 primary breast carcinomas for genetic alterations using the OncoScan CNV Plus Assay to assess genomic instability.

overall_design: Copy number analysis of Affymetrix OncoScan CNV Plus arrays was performed on 31 formamid-fixed paraffin-embedded breast tumours.

first: Britta

last: Langen

first: Szilárd

last: Nemes

first: Erik

last: Holmberg

first: Toshima

middle: Z

last: Parris

first: Anikó

last: Kovács

first: Khalil

last: Helou

first: Per

last: Karlsson


title: Single-cell Transcriptomics Resolves Intermediate Glial Progenitors and Uncovers a Pivotal Determinant of Cell Fate and Gliomagenesis

city: Cincinnati

first: Richard

last: Lu

address: 3333 Burnet Ave

department: CBDI

institute: Cincinnati Children's Hospital Medical Center

summary: The identity and heterogeneity of glial progenitors and their contributions to brain tumor malignancy remain elusive. By applying lineage-targeted single-cell-transcriptomics, we uncover an unanticipated diversity of glial progenitor pools with unique molecular identities in developing brain. Our analysis identifies distinct transitional intermediate states and their divergent developmental trajectories in astroglial and oligodendroglial lineages. Moreover, intersectional analysis uncovers analogous intermediate progenitors during brain tumorigenesis, wherein lineage-restricted oligodendrocyte-progenitor intermediates are abundant, hyper-proliferative and progressively reprogrammed towards a stem-like state susceptible to further malignant transformation. Similar actively cycling intermediate progenitors are prominent components in human gliomas with distinct driver mutations. We further unveil lineage-driving networks underlying glial fate specification and identify Zfp36l1 as necessary for oligodendrocyte-astrocyte lineage transition and glioma growth. Together, our results resolve the dynamic repertoire of common and divergent glial progenitors during development and tumorigenesis and highlight Zfp36l1 as a molecular nexus for balancing glial cell-fate decision and controlling gliomagenesis.

overall_design:
scRNA-seq:Individual cells were sampled from mice cortices of PDGFRa-GFP and hGFAP-GFP strains and mouse glioblastoma tissues.

ATAC-seq:ATAC-seq sampled from E14.5 and P5 PDGFRa-GFP cells

first: Qinjie

last: Weng

first: Jincheng

first: Jiajia

first: Danyang

last: He

first: Lingli

last: Xu

first: B

last: Aronow

first: Q


title: Impact of a pre-operative exercise intervention on breast cancer proliferation and gene expression

first: Rinath

last: Jeselsohn

state: MD

address: 450 Brookline Ave, D728

institute: DFCI

summary: RNAseq analysis of primary breast cancer samples

overall_design: Inactive women with newly diagnosed breast cancer were randomized to an exercise intervention or mind-body control group, and participated in the study between enrollment and surgery (mean 29.3 days). Tumor were collected at baseline and surgery.

first: Jennifer

last: Ligibel


title: Transcriptional landscape of human myogenesis reavels a key role of TWIST1 in maintenance of skeletal muscle progenitors

city: Baltimore

first: Gabsang

last: Lee

address: 733 North Broadway, Suite 747

department: Department of Neurology and Neuroscience

institute: Institute for Cell Engineering, Johns Hopkins University

summary: Derivation of human skeletal muscle in vitro with human pluripotent stem cells (hPSCs) opens new avenues for deciphering essential, but poorly understood aspects of transcriptional regulation in myogenic specification and relevance to rare genetic diseases. We characterized the transcriptional landscape of distinct human myogenic stages, including OCT4::EGFP+ PSCs, MSGN1::EGFP+ presomites, PAX7::EGFP+ skeletal muscle progenitors, MYOG::EGFP+ myoblasts, and multinucleated myotubes. We defined signature gene expression profiles from each population with unbiased clustering analysis, which provided unique insights into the transcriptional dynamics of human myogenesis from undifferentiated hPSCs to fully differentiated myotubes. Using knock-out strategy, we identified TWIST1 as a critical factor in maintenance of human PAX7::EGFP+ putative skeletal muscle progenitors,  providing an explanation for the musculoskeletal symptoms of a rare genetic disease, Saethre-Chotzen syndrome. We have established a foundation for future studies to identify regulators of human myogenic ontogeny.

overall_design: To systematically investigate the transcriptional blueprint of developing human skeletal muscle cells and to gain comprehensive insights into the molecular signatures of putative skeletal muscle stem/progenitors, we conducted step-wise isolations of stage-specific cellular subtypes during muscle differentiation in vitro and performed global gene expression analysis. Using our human genetic reporter PSC lines and a newly devised method for myotube enrichment, we isolated five distinct cell types in human embryonic myogenesis, including OCT4::EGFP+ embryonic stem cells, MSGN1::EGFP+ presomite cells, PAX7::EGFP+ putative skeletal muscle stem/precursor cells, MYOG::EGFP+ myoblast cells, and multinucleated myotubes.

first: Jooheon

last: Shin

first: In

last: Choi


title: Global gene expression analysis of neutrophils from Periparturient Holstein Cows

city: Greensboro

first: Mulumebet

last: Worku

state: North Carolina

address: 1601 E market Street

department: Animal Sciences

institute: North Carolina Agricultural and Technical State University

summary: This study aimed at evaluating the global gene expression of blood-derived neutrophils from periparturient cows. Blood was collected from Holstein Friesian periparturient cows (N=3) at −14 d relative to expected calving date and 7 d relative to actual calving date. Neutrophils were isolated and subsequently used for transcriptional profiling using the Agilent bovine (v2) 4 × 44 K array. Calculation of fold change in gene expression and pathway analysis was conducted using the GeneSpring GX software 13.0. Periparturient period impacted global gene expression and resulted in 249 genes that were differentially expressed (FC≥2, p<0.05.); 162 were upregulated post-calving 87 of these were downregulated. Genes that code for proinflammatory receptors (CD58, GLRX3), chemokines  (CMKLR1), and transcriptional regulation (MTA) were upregulated. Concurrently, genes that code for cellular adhesion and migration (ADRM1 and THY1), and immune induction (CATHL2) and homeostasis were downregulated gene. Pathway analysis revealed that 118 pathways are affected in bovine neutrophils during the periparturient period (p<0.05). These pathways included the Wnt signaling, one carbon Metabolism, TLR, inflammation response, Oxidative Stress, T-Cell Receptor signaling, adipogenesis, and MAPK Signaling Pathways.

overall_design: Blood was sampled from the jugular vein of three Holstein Friesian periparturient cows at -14 d relative to expected calving date and at 7 d relative to actual calving date. Extracted RNA from isolated neutrophils were used for transcriptional profiling .

first: Emmanuel

middle: K

last: Asiamah

first: Sarah

last: Adjei-Fremah

first: Kingsley

last: Ekwemalor


title: Estimating Genome-wide Off-Target Effects for Pyrrole-Imidazole Polyamide Binding by a Pathway-Based Expression Profiling Approach (SiHA cells)

city: Chiba

first: Jason

last: Lin

state: Chiba

address: 666-2 Nitona-cho, Chuo-ku

institute: Chiba Cancer Center Research Institute

summary: Side and off-target effects remain a difficult issue in the search of pharmaceutical leads, especially with DNA-binding molecules or genome editing methods where the issue becomes particularly thorny. A particular case is the investigations into the off-target effects of N-methylpyrrole-N-methylimidazole polyamides, a naturally inspired class of DNA binders that discriminately access the minor groove with strong affinity and sequence specificity but the relatively short motif of < 20 bases often imply possible non-unique genomic binding. Multiple binding sites may translate to binding at non-intended loci, potentially leading to off-target effects, issues that very few approaches are able to address to-date.  We here report an analytical method of inferring off-target binding from expression profiling based on the relative impact to various biochemical pathways, as well as an accompanying side effect prediction engine to allow candidate polyamides to be systematically screened. This method marks the first attempt in PI polyamide research to identify elements in various biochemical pathways sensitive to the treatment of a candidate polyamide to infer possible off-target effects. Expression changes were then considered for their possible effect on outward phenotypic changes, manifested as side effects, should the same PI polyamide candidate be administered clinically. We also performed a series of animal experiments to validate some of these effects, and found some corroboration in certain side effect manifestations, such as changes in the level of aspartate transaminase in ICR and nude mice after injection of some of the candidate polyamides in this study.

overall_design: O(4) to O(5) cells per condition were plated in a 6-well microtiter plate for overnight attachment prior to treatment of candidate polyamides or 0.05% DMSO. After RNA extraction with RNeasy Plus Mini Kit (Qiagen), labelled with RNA Spike-In Kit and analyzed on SurePrint G3 Human GE 8x60K V2 microarrays.

first: Sakthisri

last: Krishnamurthy

first: Takatori

last: Atsushi


title: Quantitative variation in m.3243A>G mutation produce discrete changes in energy metabolism

city: Roanoke

first: Sarika

last: Srivastava

state: Virginia

address: 2 Riverside Circle

department: Fralin Biomedical Research Institute

institute: Virginia Tech Carilion

summary: Mitochondrial DNA (mtDNA) 3243A>G tRNALeu(UUR) heteroplasmic mutation (m.3243A>G) exhibits clinically heterogeneous phenotypes. While the high mtDNA heteroplasmy exceeding a critical threshold causes mitochondrial encephalomyopathy, lactic acidosis with stroke-like episodes (MELAS) syndrome, the low mtDNA heteroplasmy causes maternally inherited diabetes with or without deafness (MIDD) syndrome. How quantitative differences in mtDNA heteroplasmy produces distinct pathological states has remained elusive. Here we show that despite striking similarities in the energy metabolic gene expression signature, the mitochondrial bioenergetics, biogenesis and fuel catabolic functions are distinct in cells harboring low or high levels of the m.3243A>G mutation compared to wild type cells. We further demonstrate that the low heteroplasmic mutant cells exhibit a coordinate induction of transcriptional regulators of the mitochondrial biogenesis, glucose and fatty acid metabolism pathways that lack in near homoplasmic mutant cells compared to wild type cells. Altogether, these results shed new biological insights on the potential mechanisms by which low mtDNA heteroplasmy may progressively cause diabetes mellitus.

overall_design: Total RNA was extracted from the 143B wild type osteosarcoma cells (WT) and the osteosarcoma-derived cybrid cells harboring either a low (ML) or  high (MH) level of m.3243A>G mutation. 4 wild type samples, 4 low mutant samples, and 4 high mutant samples.

first: Ryan

middle: P

last: McMillan

first: Sidney

last: Stewart

first: James

last: Budnick

first: Clayton

last: Caswell

first: Matthew

middle: W

last: Hulver

first: Konark

last: Mukherjee


title: Chromatin remodeling mediated by ARID1A is indispensable for normal hematopoiesis in mice (ATAC-Seq)

city: Singapore

first: Pushkar

last: Dakle

address: 14 Medical Drive, #12-01,

institute: Cancer Science Institute of Singapore

summary: ARID1A is a component of the mammalian SWI/SNF complex involved in chromatin remodeling. A functional SWI/SNF complex is required for diverse physiological processes including hematopoiesis, however, the precise role played by ARID1A in hematopoietic development is unclear. Here we utilize hematopoietic cell-specific deletion of Arid1a in mice to uncover its role during adult hematopoiesis. We demonstrate that ARID1A is essential for maintaining the frequency and function of hematopoietic stem cells and its loss impaired the differentiation of both myeloid and lymphoid lineages. ARID1A deficiency led to a global reduction in open chromatin and ensuing transcriptional changes affected key genes involved in hematopoietic development. We also observed that silencing of ARID1A affected ATRA-induced differentiation of NB4 cells, suggesting its role in granulocytic differentiation of human leukemic cells. Overall, our study provides a comprehensive elucidation of its function in hematopoiesis and establishes ARID1A as a major regulator of chromatin dynamics in hematopoietic cells.

overall_design: Study of chromatin accessibility in WT and ARID1A KO Lin-Kit+ BM cells

first: Lin

last: Han

first: Vikas

last: Madan

first: Anand

last: Mayakonda

first: Weoi

last: Teoh

first: Pavithra

last: Shyamsunder

first: Hazimah

middle: M

last: Nordin

first: Cao

last: Zeya

first: Janani

last: Sundaresan

first: Ienglam

last: Lei

first: Zhong

last: Wang

first: H

last: Koeffler


title: Expression data from whole blood of RRMS patients initiating treatment with intramuscular IFN-β1a (Avonex®)

city: Cleveland

first: Mark

last: Chance

address: 10900 Euclid Ave

institute: Case Western Reserve University School of Medicine


title: The effect of PGC-1α adenovirus on gene expression in mouse primary hepatocytes

city: Oulu

first: Jukka

last: Hakkola

address: Aapistie 5

department: Research Unit of Biomedicine

country: Finland

institute: University of Oulu

summary: The effect of PGC-1α overexpression using adenovirus (PGC-1α-Ad) on hepatic gene expression was studied in mice primary hepatocytes.

overall_design: The effect of PGC-1α-Ad was studied in male 9-week-old C57BL/6 mouse primary hepatocytes. Cells were treated with PGC-1α-Ad (MOI 1) for 36 h, GFP-Ad (MOI 1) was used as a control. Three parallel RNA samples were pooled in both groups. DNA microarrays were used for gene expression profiling.

first: Sanna

last: Aatsinki

first: Marcin

last: Buler


title: Characterization of the transcriptomes of Atoh1-induced hair cells in the mouse cochlea

city: Shanghai

first: Luo

last: Guo

address: 83# fenyang road, 9# building, room 613

institute: Fudan University

summary: Mammalian cochlea hair cells can be regenerated from the adjacent supporting cells in many ways, however, the newly hair cells are immature and without hearing function almost. The expression of Atoh1 is an important maker of the appearance of newly hair cells, many approaches of inner ear hair cells’ regeneration are concerned with the transcription factor Atoh1. However, most new HCs are immature HCs, and they do not have the function of mature HCs and eventually die a few weeks after regeneration. Thus promoting the maturation and survival of new HCs is the primary focus of HC regeneration field. We used RNA-Seq analysis to compare the differences between the transcriptomes of Atoh1 overexpression-induced new HCs and the original HCs, and to define the factors that might help to promote the maturation and survival of new HCs.

overall_design: We used transgenic mice in the C57BL/6J background to perform this assay. Sox2-CreER mice (JAX number 008875) and Rosa26-tdTomato mice (JAX number 007914) were ordered from the Jackson Laboratory. Atoh1-eGFP (enhanced green fluorescent protein) mice were provided by Jane Johnson (University of Texas Southwestern Medical Center, Dallas, TX, USA), and CAG-loxP-stop-loxP-Atoh1-HA+ mice (Atoh1-HA+ mice) were the kind gift of St. Jude Children's Research Hospital. Postnatal day (P) 0 was defined as the day of birth. Both male and female mice were used for all experiments. Tamoxifen (Sigma-Aldrich) diluted in corn oil was injected intraperitoneally at the late stage of P3 at 0.20 mg/g bodyweight, and the control group was injected only with corn oil. Sox2-CreER+/Atoh1-HA+/Atoh1-eGFP+/tdTomato+ fourth positive mice were sacrificed at P7, and the cochlear epithelium was dissected and trypsinized with pre-warmed 0.25% trypsin/EDTA (Invitrogen) at 37°C for 5 min. Soybean trypsin inhibitor (Worthington Biochem) was added to terminate the reaction followed by mechanical trituration with blunt tips and pipetting up and down ~100 times. Suspended cells were percolated through a 40 µm cell strainer (BD Biosciences) before FACS. The original HCs were labeled with enhanced green fluorescent protein (eGFP+ cells), new HCs were co-labeled with enhanced green fluorescent protein and tdTomato red fluorescent protein (eGFP+/tdTomato+ cells), and SCs were labeled with tdTomato red fluorescent protein (tdTomato+ cells). The original HCs, new HCs, and SCs were sorted on a BD FACS Aria III (BD Biosciences) using the tdTomato and GFP channels.  The samples are prepared for the following experiments including PCR and RNA sequence analysis.

first: Liman

last: Liu

first: Lingjie

last: Wu

first: Yan

last: Chen

first: Huawei

last: Li