title: Next Generation Sequencing analysis using splenic CD8 T cells isolated from Wild Type-OT-I (WT) and NIK -CD4Cre-OT-I (KO) mice

status: Public on Oct 02 2020

city: Houston

first: Xiaofeng

last: Zheng

state: TX

address: 7007 Bertner Ave

department: Bioinformatics & Computational Biology

institute: UT MD Anderson Cancer Center

summary: Metabolic reprograming towards aerobic glycolysis is a pivotal mechanism that shapes immune responses. While deregulated T cell metabolism is associated with autoimmune diseases, metabolic deficiency contributes to T cell exhaustion in tumor microenvironment. Here we describe a posttranslational mechanism of glycolysis regulation mediated by the NF-kB-inducing kinase (NIK). NIK deficiency impairs glycolysis induction, rendering CD8 effector T cells hypofunctional with features of exhaustion in tumor microenvironment. Conversely, ectopic expression of NIK promotes CD8 T cell metabolism and prevents exhaustion, thereby profoundly enhancing antitumor immunity and improving the efficacy of T cell adoptive therapy. Interestingly, although NIK is known as a kinase mediating activation of noncanonical NF-kB, NIK regulates T cell metabolism via an NF-kB-independent mechanism that involves stabilization of hexokinase 2 (HK2), a rate-limiting enzyme of the glycolytic pathway. NIK deficiency causes autophagic degradation of HK2, at least in part due to aberrant ROS accumulation. NIK phosphorylates, and maintains the activity of, glucose-6-phosphate dehydrogenase (G6PD), an enzyme mediating production of the antioxidant NADPH required for preventing ROS accumulation and oxidative stress. We provide genetic evidence that the G6PD-NADPH redox system has a vital role in regulating HK2 stability and metabolism in activated T cells. These findings establish NIK as a pivotal regulator of T cell metabolism and highlight a posttranslational mechanism of metabolic regulation involving the G6PD-NADPH redox system.

overall_design: Splenic naïve CD8 T cells cultured with plate-bould anti-CD3 (1ug/ml) plus solube anti-CD28 (1ug/ml) for 24 hours. mRNA profiles of 6 to 8 week old wild type-OT-I (WT) and NIK-CD4Cre-OT-I (KO) mice were generated by deep sequencing, in triplicate

first: Xiaofei

last: Zhou

first: Shao-Cong

last: Sun

first: Jing


title: A unique population of regulatory T cells in heart potentiates cardiac protection from myocardial infarction [scRNA-seq]

status: Public on Oct 03 2020

city: Wuhan

first: Muyang

last: Gu

address: 1277 Jiefang Road, Jianghan District

country: China

institute: Union Hospital, Tongji Medical College, Huazhong   University of Science and Technology

type: Expression profiling by high throughput sequencing

summary:
Purpose: The aims of the study were to identify that heart Tregs were clonally expanded, and single-cell TCR repertoires of heart Tregs were different from spleen Tregs.
Methods: CD4+ T cells from injured hearts and paired spleens of the C57BL/6J mice were double-sorted by magnetic-activated cell sorting (MACS) and fluorescence activated cell sorting (FACS) to generate single cell RNA-sequence and paired V(D)J sequence 7 days after myocaridal infarction (MI).
Results: The characteristics of clonal restriction in heart Tregs were investigated, and there were just a little TCR-sequence sharing between spleen Tregs and heart Tregs.

overall_design: single-cell transcriptome and clonotype of injured heart CD4+ T cells, spleen CD4+ T cells isolated from 8-week-old C57BL/6J mice 7 days post-MI

first: Ni

last: Xia

first: Yuzhi

last: Lu

first: Nana

last: Li

first: Meilin

last: Liu

first: Xiang

last: Cheng


title: Transcriptionnal coregulator GRIP1 differentially modulate myeloid cell-driven neuroinflammation and response to IFN-beta therapy

city: New york

first: Yurii

last: Chinenov

state: New York

address: 535 E 71 str, Hospital for Special Surgery

department: Research Division

country: USA

institute: Hospital for special surgery

summary: Growing evidence are showing a pivotal role of macrophages (MФ) and microglia (MG) in the pathogenesis of Multiple sclerosis (MS). Interferon β (IFN β) and glucocorticoids are front line treatments in MS, and disrupting either type I IFN or GC receptor (GR) pathway in mice aggravates EAE, the mouse model of MS. Here, we evaluated GR Interacting Protein 1 actions in neuroinflammation by subjecting mice conditionally lacking GRIP1 in myeloid cells (cKO) to EAE. We showed that myeloid GRIP1 plays a dual role by promoting the ‘effector’ neuroinflammatory phase of EAE as well as mediating IFN β therapeutic effect. Our sorted MФ/MG transcriptome analysis reveals dramatic changes in inflammatory and IFN-pathway gene expression including potential differences of GRIP1 function in these distinct myeloid cell populations.

overall_design: Analysis of differentially expressed genes in WT and KO myeloid cells isolated from spinal cords of mice with neuroinflammation

first: Sanda

last: Mimouna

first: David

middle: A

last: Rollins

first: Bowranigan

last: Tharmalingam

first: Gayathri

last: Shibu

first: Dinesh

last: Deoshand

first: Xi

last: Chen

first: Inez

last: Rogatsky


title: Total RNA sequencing of IFN-stimulated and HIV-1-infected macrophages

city: Salt Lake City

first: Chris

last: Stubben

state: Utah

address: 2000 Cir of Hope Dr

department: University of Utah

institute: Huntsman Cancer Institute

summary: Monocyte-derived macrophages were stimulated with 25 ng/ml of the indicated IFNs or infected with HIV-1-BaL-HSA. Total RNA was isolated 18 h following stimulation/infection using RNeasy minikit (Qiagen). Intact poly(A) RNA was purified from total RNA samples (100 to 500 ng) with oligo(dT) magnetic beads, and stranded mRNA sequencing libraries were prepared as described using the Illumina TruSeq Stranded mRNA Library Preparation kit (catalog no. RS-122-2101 and RS-122-2102). Purified libraries were qualified on an Agilent Technologies 2200 TapeStation using a D1000 ScreenTape assay (catalog no. 5067-5582 and 5067-5583). The molarity of adapter-modified molecules was defined by quantitative PCR using the Kapa Biosystems Kapa Library Quant kit (catalog no. KK4824). Individual libraries were normalized to 10 nM, and equal volumes were pooled in preparation for Illumina sequence analysis. Sequencing libraries (25 pM) were chemically denatured and applied to an Illumina HiSeq v4 single-read flow cell using an Illumina cBot system. Hybridized molecules were clonally amplified and annealed to sequencing primers with reagents from an Illumina HiSeq SR cluster kit v4-cBot (catalog no. GD-401-4001). Following transfer of the flow cell to an Illumina HiSeq 2500 instrument (HCSv2.2.38 and RTA v1.18.61), a 50-cycle single-read sequence run was performed using HiSeq SBS kit v4 sequencing reagents (catalog no. FC-401-4002).

overall_design: RNA expression profiles of monocyte-derived macrophages 18 hours post-IFN stimulation or HIV-1-BaL infection

first: Matt

last: Szaniawski

first: Vicente

last: Planelles


title: Similar pulmonary toxicity and gene expression changes after short-term inhalation exposure to surface-modified copper oxide nanoparticles

city: Ottawa

first: Sabina

last: Halappanavar

state: Ontario

address: 251 Sir Frederick Banting Driveway, Building 22

country: Canada

institute: Health Canada

summary: This study investigated the pulmonary toxicity of Copper oxide nanoparticles (CuO NPs) surface modified with polyethylenimine (PEI) or ascorbate (ASC), was investigated. Rats were exposed nose-only to a fixed exposure concentration of ASC or PEI coated CuO NPs for 5 consecutive days. On day 6 and day 27 post-exposure, pulmonary toxicity markers in bronchoalveolar lavage fluid (BALF) were analyzed and histopathological evaluation of the lungs was performed, along with microarray analyses on whole lung tissue samples.

overall_design: This experiment examined lung tissues from  8 weeks old male rats (Wistar RjHan:WI, Janvier, France) exposed to 6 hour equivalent doses of 3 and 8.6 mg NPs / m3 of CuO nanomaterials (black material) positively charged coating (PEI) or 6 hour equivalent doses of 3.8 and 10.9 mg NPs / m3 of CuO nanomaterials negatively charged coating (ASC) by nose only inhalation according to the OECD test Guideline 403 for Acute Inhalation Toxicity Test. Rats were exposed to five consecutive days and lung tissues were sampled on day 1 after the last exposure (referrred to as T6) and day 22 post-exposure (referred to as T27). Control animals were exposed to air only. Each treatment group consisted of 5 animals. Exposure and sample collection were conducted at the National Institute for Public Health (RIVM) at Bilthoven, The Netherlands, under permit number 201300190. Experimental procedures were in accordance with the European directive on the protection of animals for scientific purposes (Directive 2010/63/EU).

first: Dongme

last: Wu


title: Loss of the metabolic sensor, PPARA, overcomes differentiation blockade and immune suppression in AML

city: Boston

first: Leinal

middle: Alen

last: Sejour

state: MA

address: 58 Lonsdale St.

department: Pathology

institute: Beth Israel Deaconess medical center

summary:
The hematopoietic system balances self-renewal and differentiation in response to various environmental cues. The nuclear hormone receptor superfamily consists of ligand-activated transcription factors that allow cells to integrate external stimuli with cellular programs regulating differentiation, metabolism, proliferation and survival. We and others have shown that members of this family play central roles in normal, stress and malignant hematopoiesis. Here, we report that expression of PPAR-alpha is elevated in patients with high risk subtypes of acute myeloid leukemia (AML). On this basis, we hypothesized that genetic disruption of the alpha isoform of PPAR would selectively impair AML maintenance while sparing normal hematopoietic stem progenitor cells.  Indeed, Ppara null MLL-AF9 leukemia displayed a relief of its differentiation blockade, a hallmark of acute leukemia. This restored differentiation was accompanied by gene expression patterns indicative of altered metabolic pathways and immune signaling.
By contrast, steady-state and stress myelopoiesis were largely unaffected by the loss of Ppara with the exception of a mild increase in differentiated myeloid cells. Notably, a significant survival advantage was observed in Ppara deleted AML as compared to controls. In contrast, transplantation into Rag2-/- recipients substantially reduced this survival advantage, demonstrating dependence on the adaptive arm of the immune system. These results suggest possible therapeutic implications for immune modulation through pharmacologic targeting of PPARA signaling.  Taken together, our in vivo studies of Ppara in MLL-AF9 AML are consistent with a model in which concomitant regulation of cell-intrinsic programs and modulation of interactions with the leukemic immune microenvironment by PPARA promotes leukemia maintenance.

overall_design: Ppara +/+ and PPARA-/- mice were purchased from The Jackson Laboratory and backcrossed for 10 generations upon arrival. 293T cells were transfected using Lipofectamine 2000 (ThermoFisher catalog # 11668019), pCL-Eco, and MSCV-MLL-AF9-IRES-GFP. Cells were spin-infected with concentrated retrovirus. Following infection, cells were washed twice with PBS before being counted and injected into recipients. Total RNA was extracted from FACS sorted Ppara+/+ and Ppara-/- MLL-AF9 leukemia cells isolated from the bone marrow of secondary recipients. 200 ng of RNA was hybridized to Affymetrix Mouse Gene 2.1 ST arrays at the Beth Israel Deaconess Medical Center Genomics and Proteomics Core.

first: Pier

middle: P

last: Pandolfi

first: Lourdes

last: Mendez

first: Ryan

last: Posey

first: Moussa

last: Diolombi

first: Anish

last: Sharda

first: Ming

first: Sanjana

last: Thosar

first: Jacqueline

last: Fung

first: Jiangwen

last: Zhang

first: Olga

last: Pozdnyakova

first: Jonathan

last: Lee

first: Daphna

last: Nachmani

first: Assaf

last: Bester

first: John

last: Clohessy


title: Formation of the CenH3-deficient holocentromere in Lepidoptera avoids actie chromatin

city: Paris

first: Ines Anna

last: Drinnenberg

address: 26 Rue d'Ulm

country: France

institute: Institut Curie

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Despite the essentiality for faithful chromosome segregation, centromere architectures are diverse among eukaryotes and embody two main configurations: mono- and holocentromeres, referring respectively to localized or unrestricted distribution of centromeric activity. Of the two, some holocentromeres offer the curious condition of having arisen independently in multiple insects, most of which have lost the otherwise essential centromere-specifying factor CenH3 (first described as CENP-A in humans). The loss of CenH3 raises intuitive questions about how holocentromeres are organized and regulated in CenH3-lacking insects. Here, we report the first chromatin-level description of CenH3-deficient holocentromeres by leveraging recently-identified centromere components and genomics approaches to map and characterize the holocentromeres of the silk moth Bombyx mori, a representative lepidopteran insect lacking CenH3. This uncovered a robust correlation between the distribution of centromere sites and regions of low chromatin activity along B. mori chromosomes. Transcriptional perturbation experiments recapitulated the exclusion of B. mori centromeres from active chromatin. Based on reciprocal centromere occupancy patterns observed along differentially-expressed orthologous genes of Lepidoptera, we further found that holocentromere formation in a manner that is recessive to chromatin dynamics is evolutionarily conserved. Our results help us discuss the plasticity of centromeres in the context of a role for the chromosome-wide chromatin landscape in conferring centromere identity rather than the presence of CenH3. Given the co-occurrence of CenH3 loss and holocentricity in insects, we further propose that the evolutionary establishment of holocentromeres in insects was facilitated through the loss of a CenH3-specified centromere.

sample_organism:
Bombyx mori
Trichoplusia ni

platform_organism:
Bombyx mori
Trichoplusia ni

overall_design: Mapping and molecular characterization of holocentromeres in Bombyx mori and Trichoplusia ni.

first: Aruni

last: Senaratne

first: Héloïse

last: Muller

first: Kelsey

last: Fryer

first: Munetaka

last: Kawamoto

first: Susumu

last: Katsuma

first: Ines


title: Histone deacetylase 5 regulates Interleukin 6 secretion and insulin action in skeletal muscle

city: Duesseldorf

first: Birgit

last: Knebel

address: Auf'm Hennekamp 65

department: Cinical Biochemistry and Pathobiochemistry

country: Germany

institute: German Diabetes Center

summary: Physical exercise training is associated with increased glucose uptake in skeletal muscle and improved glycemic control. Histone Deacetylases (HDACs) are divided into three structurally defined subclasses and are critical for transcriptional regulation, cell cycle progression, and developmental events. HDAC5, a class IIa histone deacetylase regulates transcription of the insulin-responsive glucose transporter GLUT4 in cultured muscle cells. Interleukin-6 (IL-6) is a prototypical cytokine featuring functional redundancy and pleiotropy. Under healthy conditions the serum level of IL-6 is less than 4 pg/ml. The cytokine IL-6 was the first myokine found to be secreted into bloodstream in response to muscle contractions. Exercise intervention induce secretion of muscle-derived IL-6, leading to an acute and rebuses increase of systemic IL-6 up to 100-fold higher than basal levels a far greater increase than that of any other cytokine that has been measured. HDAC5 depletion in skeletal muscle lead to increased glucose uptake that was driven by IL-6 and p-AKT signaling. We specifically revealed that HDAC5 binds to the IL-6 promoter to regulate its transcription. These effects were facilitated by exercise and muscle contractions. In summary, we identified HDAC5 as a negative regulator of IL-6 synthesis and release in skeletal muscle. HDAC5 may exert beneficial effects through two different mechanisms, transcriptional control of genes required for glucose disposal and utilization, and HDAC5-dependent IL-6 signaling in order to improve glucose uptake in muscle in response to exercise.

overall_design: We used microarrays, to find out the global evidence and role of HDAC5 in regulation of IL-6 transcription and IL-6 regulated gene in HDAC5 KO mice (McKinsey, T.A. et al.. Nature. 2000 Nov 2;408(6808):106-11) compared to WT littermate.

first: Oleksiy

last: Klymenko

first: Tim

last: Brecklinghaus

first: Hadi

last: Al-Hasani

first: Dhiraj

middle: G

last: Kabra


title: Identifying improved sites for heterologous gene integration using ATAC-seq

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

institute: Koch Institute

summary: We analyzed the chromatin accessibility and nucleosome positioning by ATAC-seq of both null and transgene-expressing strains of Komagataella phaffii (Pichia pastoris) under different growth conditions. These data enabled identification of the features that determine performance of various integration sites for transgene expression. Understanding chromatin accessibility and nucleosome positioning can provide further clarity into gene regulation and expression broadly in this organism.

overall_design: ATAC-seq was performed on Komagataella phaffii NRRL Y-11430 after 24h growth on glycerol-containing medium as well as after an additional 24h growth on methanol-containing medium. Four strains were analyzed: 1 null (wild-type) strain and 3 transgene-expressing strains with modified pPICZA (Invitrogen) vectors integrated upstream of the AOX1, DAS2, or OLE1 genes. For all samples, accessibility peaks and nucleosome positioning were determined.

first: Joseph

middle: R

last: Brady

first: J

middle: C

last: Love


title: Genome-wide effects of the antimicrobial peptide apidaecin on translation termination

city: Chicago

first: Kyle

last: Mangano

state: Illinois

address: 900 S Ashland Ave, MBRB Rm 3056

institute: University of Illinois at Chicago

summary: The proline-rich antimicrobial peptide apidaecin (Api) inhibits bacterial protein synthesis in a distinctive way. In vitro biochemical and structural studies showed that Api binds in the nascent peptide exit tunnel of a ribosome that has completed translation of a gene and traps the release factors on the ribosome. By analyzing the distribution of ribosomes on mRNAs in Api-treated cells using Ribo-seq, we uncovered a range of effects that stem from the unique mechanism of Api action. Exposure of bacterial cells to Api results in arrest of ribosomes at stop codons, likely in a post-release state due to direct Api action, as well as in a pre-release state due to the depletion of available release factors. In addition, Api action leads to a pronounced queuing of translating ribosomes behind those arrested at stop codons. One of the major consequences of Api action is a dramatically increased level of stop codon bypass by ribosomes paused in a pre-release state, leading to an accumulation of proteins with C-terminal extensions, as confirmed by whole-cell proteomics analysis. Stop codon bypass occurs either in 0-frame, by misincorporation of a near-cognate aminoacyl-tRNA at the stop codon, or via frameshifting, allowing for a fraction of the translating ribosomes to reach the 3’ ends of mRNA transcripts. The pervasive stalling of pre-release ribosomes at the stop codons and at the RNA transcripts ends triggers activation of the cellular ribosome rescue systems which, likely due to Api action as well, remain ineffective. Understanding the unique mode of Api action as translation termination inhibitor in the cell can advance the development of treatments for infection and genetic diseases as well as new research tools for genome exploration.

overall_design: Ribosome profiling and RNA-seq were performed on Escherichia coli dosed with apidaecin and compared to non-treated cells (2 biological replicates each). Additionally, the lysate of one Api replicate and one control replicate were treated with the antibiotic puromycin in an attempt to clear ribosomes from the mRNAs.

first: Tanja

last: Florin

first: Xinhao

last: Shao

first: Irina

last: Chelysheva

first: Dorota

last: Klepacki

first: Zoya

last: Ignatova

first: Yu

last: Gao

first: Alexander

middle: S

last: Mankin

first: Nora

last: Vázquez-Laslop


title: Transcriptional response of rat skeletal muscle to prolonged fasting

city: Strasbourg

first: Fabrice

last: Bertile

address: 25 rue Becquerel

department: Analytical Sciences

institute: CNRS, IPHC

summary:
Prolonged fasting-induced changes in rat tibialis anterior muscle transcriptome
Skeletal muscle is of primary importance for metabolism, thermogenesis and locomotion.  However, muscle integrity is inevitably challenged throughout life, and muscle atrophy occurs in various situations, being associated with development of metabolic diseases. There is virtually no fully effective countermeasure today to fight the loss of muscle mass. It is therfore needed to understand in depth how muscle mass is regulated in wasting conditions. The aim of this study was to decipher the transcriptional regulations involved in prolonged fasting-induced muscle wasting during the phase of protein sparing (P2) and the late phase of increased body protein mobilization (P3). The main findings show that gene expression changes reflect well the intense use of lipids as fuels during P2 and increased use of muscle proteins during P3.  Changes in muscle transcriptome for downstream signaling of anabolic and catabolic hormones (Smad, NFKB, EiF2alpha-ATF4, autophagy, ubiquitin-proteasome, Foxo, AMPK, PI3K/AKT, and mTOR pathways) and for the response to oxidative stress, transcription and translation processes, and myogenesis are generally consistent with increased muscle protein degradation and repressed synthesis, in a more marked manner during P3 than P2 compared to the fed state. Nevertheless, several changes appeared to be in favour of muscle protein synthesis during fasting, notably at the level of PI3K/AKT and mTOR pathways, transcription and translations processes, and the response to oxidative stress. They could constitute mechanisms that promote protein sparing during P2 and anticipate refeeding during P3 for restoration of the protein compartment. Future studies should examine validity of such targets for improving nitrogen balance during catabolic diseases.

overall_design: We analyzed tibialis anterior muscle (TIB) from 9 male Sprague Dawley rats randomly divided into 3 groups (3 fed3 4 fasted until phase 2 of fasting [P2], and 3 fasted until phase 3 of fasting [P3]) using the Affymetrix Rat Gene 1.0 ST platform. Array data was processed by Affymetrix GCOS v1.4 and Expression Console v1.1. No techinical replicates were performed.

first: Marianne

last: Ibrahim

first: Thierry

last: Wasselin

first: Etienne

last: Challet

first: Alain

last: Van Dorsselaer

first: Yvon

last: Le Maho

last: Raclot


title: Molecular investigation of Breast Cancer xenograft model exposed to proton radiations

city: Cefalù

first: Valentina

last: Bravatà

address: Contrada Pietrapollastra Pisciotto

country: Italy

institute: IBSBC CNR

summary: Specific Breast Cncer (BC) subtypes are associated with a bad prognosis due to the absence of successful treatment plans. Moreover, the triple negative breast cancer (TNBC) subtype, with estrogen (ER), progesterone (PR) and human epidermal growth factor-2 (HER2) negative receptors status, were characterized by unsuccessful therapies, makes it a clinical challenge for oncologists. In addition, Proton RadioTherapy (PRT) represents an effective treatment also against conventional radiotherapy (RT) resistant cancers, and a promising therapeutically choice for TNBC. Our study aimed at analyze the in vivo molecular response induced by PRT in a MDA-MB-231 triple negative Breast Cancer xenograft model, focusing on gene expression profile (GEP) analyses. Our results demonstrate the multiple advantages of xenograft tissue microarrays for preclinical signature characterization of PRT to understand the molecular mechanism activated and to discover new molecular targets.

overall_design: Proton-induced gene expression changes in MDA-MB-231 Breast Cancer xenograft model after 2, 6 and 9Gy of IR doses, were analyzed as two-color hybridizations using Agilent Technologies whole human genome 4x44K microarrays. Samples were named as follow: MDA-MB-231 xenograft mouse exposed to 2Gy PRT; MDA-MB-231 xenograft mouse exposed to 6Gy PRT; MDA-MB-231 xenograft mouse exposed to 9Gy PRT.


title: The Association between Poverty and Gene Expression within Immune Cells in a Diverse Baltimore City Cohort

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: Socioeconomic status (SES), living in poverty, and other social determinants of health contribute to health disparities in the United States. African American (AA) men living below poverty in Baltimore City have a higher incidence of mortality when compared to either white males or AA females living below poverty. Previous studies in our laboratory and elsewhere suggest that environmental conditions are associated with differential gene expression (DGE) patterns in white blood cells, and this may contribute to the onset of diseases in the immune or cardiovascular systems. DGE have also been associated with hypertension and cardiovascular disease (CVD) and correlate with race and gender. However, no studies have investigated how poverty status associates with DGE between male and female AAs and whites living in Baltimore City. We examined DGE in 52 AA and white participants of the Healthy Aging in Neighborhoods of Diversity across the Life Span (HANDLS) cohort, who were living above or below 125% of the 2004 federal poverty line at time of sample collection. We performed a microarray to assess DGE patterns in peripheral blood mononuclear cells (PBMCs) from these participants. AA males and females living in poverty had the most genes differentially-expressed compared with above poverty controls. Gene ontology (GO) analysis identified unique and overlapping pathways related to the endosome, single-stranded RNA binding, long-chain fatty-acyl-CoA biosynthesis, toll-like receptor signaling, and others within AA males and females living in poverty and compared with their above poverty controls. We performed RT-qPCR to validate top differentially-expressed genes in AA males. We found that  KLF6, DUSP2, RBM34, and CD19 are expressed at significantly lower levels in AA males in poverty and KCTD12 is higher compared to above poverty controls. This study serves as initial link to better understand the biological mechanisms of poverty status with health outcomes and disparities.

overall_design: Total RNA from peripheral blood mononuclear cells (PBMCs) from 52 African-American (AA) and White female (F) and male (M) individuals 125% above or below the 2014 federal poverty line (N = 6-7 for each ethnicity, gender and poverty status group) were used to examine differential gene expression profiles  by microarray analysis.

first: Nicole

last: Arnold

last: Noren Hooten

first: Yongqing

last: Zhang

first: Elin

last: Lehrmann

first: William

last: Wood III

first: Wendy

last: Nunez

first: Roland

middle: J

last: Thorpe

first: Michele

middle: K

last: Evans

first: Douglas

middle: F

last: Dluzen


title: Polar infection of Echovirus 30 causes differential barrier affection and gene regulation at the blood-CSF barrier

city: Mannheim

first: Marie

last: Wiatr

address: Theodor-Kutzer-Ufer 1-3

department: University Children's Hospital Mannheim

institute: Medical Faculty Mannheim, Heidelberg University

summary: Among the non-polio enterovirus (NPEV) Echovirus-30 (E-30) is responsible for extensive global outbreaks of meningitis in children. To gain access to the central nervous system (CNS), E-30 first have to cross one of the two main barriers, the epithelial blood-cerebrospinal fluid (CSF) barrier (BCSFB) or the endothelial blood-brain barrier (BBB). Previously it has been shown that several meningitis causing bacteria preferentially infect human choroid plexus papilloma cells (HIBCPP) in a polar fashion from the basolateral cell side. Here, we investigated the polar infection with E-30 of HIBCPP cells. Both, apical and basolateral infections caused a significant decrease of the transepithelial resistance (TEER) of HIBCPP cells in a dose-dependent manner. However, to reach the same TEER decrease the multiplicity of infection (MOI) of the apical infection had to be 20 times higher than the basolateral infection. In line with this finding the number of infected cells at respective time-points after basolateral infection was significantly higher compared to apical infection. Cytotoxic effects of E-30 on HIBCPP cells during basolateral infection were observed following prolonged infection, and appeared more drastically compared to the apical infection. Evaluation of massive analysis of cDNA ends (MACE) RNA data comparing basolateral versus apical infection, revealed a distinct pattern of up- and down-regulated genes depending on the side of infection. Especially, the down-regulation of ITGα5 upon basolateral infection can be correlated with a more drastic impact of E-30 on the HIBCPP cells when compared to apical infection, leading to structural changes. Also, type 3 interferon genes might be a factor involved in the polar effect of E-30 on HIBCPP. Altogether, the data highlights the polar effect of E-30 in HIBCPP cells as an important factor for an efficient infection.

overall_design: 15 samples were analysed by genome-wide gene expression profiling of human choroid plexus papilloma cells (HIBCPP) after apical (MOI 0.7) and basolateral (MOI 0.7 and 20) infections with Echovirus-30 (E-30) and respective controls (3 biological replicates per condition).

first: Ricardo

last: Figueiredo

first: Peter

last: Winter

first: Carolin

last: Stump-Guthier

first: Hiroshi

last: Ishikawa

first: Ortwin

last: Adams

first: Christian

last: Schwerk

first: Horst

last: Schroten

first: Henriette

last: Rudolph

first: Tobias

last: Tenenbaum


title: Morphological and physiological factors contributing to stronger early vigor in the elite rice cultivar 9311 compared to Huanghuazhan (HHZ)

city: Shanghai

first: Faming

last: Chen

address: 320 Yue Yang Road

department: CAS-MPG Partner Institute for Computational Biology

institute: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

summary: Huanghuazhan (HHZ) and 9311 are two elite rice cultivars in China. They have achieved high yield through quite different mechanisms. One of the major features that gives high yield capacity to 9311 is its strong early vigor, i.e., faster establishment of its seedling as well as its better growth in its early stages. To understand the mechanistic basis of early vigor in 9311, as compared to HHZ the cultivar, we have examined, under controlled environmental conditions, different morphological and physiological traits that may contribute to its early vigor. Our results show that the fresh weight of the seeds, at germination, not only determined the seedling biomass at 10 days after germination (DAG), but was also responsible for ~ 80% of variations in plant biomass between the two cultivars even up to 30 DAG. Furthermore, the 9311 cultivar had a larger root system, which led to its higher nitrogen uptake capacity. Other noteworthy observations about 9311 being a better cultivar than HHZ are : (i) Ten out of 15 genes involved in nitrogen metabolism were much more highly expressed in its roots; (ii) it had a higher water uptake rate, promoting better root-to-shoot nitrogen transfer; and (iii) consistent with the above, it had higher leaf photosynthetic rate and stomatal conductance. All of the above identified features explain, to a large extent, why the 9311, as compared to HHZ, exhibits much more vigorous early growth.

overall_design: At 50 days after germination (DAG), plants were transferred to NH4NO3-free solution for 2 days. Then, plants were transferred back to normal culture solution (containing 1 mM NH4NO3) for 3 hours. Then roots were sampled and frozen in liquid nitrogen immediately. Three replications were used. We used the PureLink RNA Mini Kit (Life Technologies Corporation) for RNA extraction from roots. To do this, we firstly grinded the root sample with liquid nitrogen, then followed the manufacture’s protocol for RNA extraction.

first: Zai

last: Shi

first: Tian-Gen

last: Chang

first: Xin-Guang

last: Zhu


title: Characterization of histone acetylation in intestinal epithelial cells

city: Cincinnati

first: Theresa

last: Alenghat

state: OH

address: 240 Albert Sabin Way, S5.409

department: Division of Immunobiology

institute: Cincinnati Childrens Hospital Medical Center

summary: We compare global H3K9Ac enrichment in intestinal epithelial cells from germ-free, E.coli mono-associated, and conventionally-housed mice. Microbiota colonization resulted in significant genome-wide differences in H3K9Ac levels in epithelial cells.

overall_design: ChIP-seq was performed for H3K9Ac in intestinal epithelial cells harvested from intestine of germ-free, E.coli mono-associated or conventional C57BL/6 mice. Replicates: 2 germ-free, 2 E.coli-monoassociated, 2 conventionally-housed.

first: Vivienne

last: Woo


title: Anaerobic fermentative metabolism of Corynebacterium glutamicum is hampered by a functional oxidative pentose phosphate pathway

city: Lyngby

first: Jing

last: Shen

address: Kemitorvet Building 201

country: Denmark

institute: Technical University of Denmark

summary: Previous findings have demonstrated that the NADH/NAD+ ratio has a strong impact on the glycolytic flux in C. glutamicum under anaerobic conditions in the absence of external electron acceptors. During an attempt to rewire anaerobic metabolism to achieve high yield formation of ethanol, we inactivated the malate dehydrogenase and lactate dehydrogenase in a C. glutamicum strain expressing pyruvate decarboxylase and alcohol dehydrogenase, to eliminate formation of the by-products succinate and lactate, respectively. This modification increased the yield of ethanol but had a negative effect on glycolysis, which we found to correlate with an elevated NADH/NAD+ ratio. The pyruvate dehydrogenase (PDH) of C. glutamicum is active under anaerobic conditions, and can potentially exacerbate the negative effect on glycolysis, due to NADH formation. To reduce PDH activity under anaerobic conditions, we decided to replace the gene encoding the E3 subunit of PDH with its Escherichia coli counterpart, as E. coli PDH has been reported to be functional under aerobic conditions only. The resultant strain JS133 produced far less acetate with a further increased ethanol production, however, the glycolytic flux was still low. After observing differences in glycolytic flux for JS133 on glucose and fructose, we speculated that the pentose phosphate pathway (PPP) might be involved in the reduced flux on glucose. To prove this, we deleted the zwf gene, encoding glucose-6-phosphate dehydrogenase, which is the entry point into PPP, and immediately observed a stimulating effect on glycolysis. Subsequent characterization revealed a direct correlation between the intracellular NADH/NAD+ and NADPH/NADP+ ratios under anoxic conditions. Based on these findings we managed to re-channel the metabolism of C. glutamicum successfully towards either to ethanol or D-lactate with 92% and 98% of the theoretical yield respectively, which is the highest yields for D-lactate production thus far reported in the literature.

overall_design: Examination of gene expression before/after deletion of zwf under anoxic conditions

first: Jun

last: Ruhdal Jensen

last: Solem


title: Gene expression profiles of matched pre- and post-treatment melanoma metastasis from seven patients treated with BRAF inhibitors (BRAFi)

city: Milan

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

institute: IRCCS Ospedale San Raffaele

summary: Pre- and post-BRAFi melanoma FFPE samples were macrodissected for enrichment of tumor cellularity and analyzed for gene expression to identify transcriptional changes related to resistance to BRAFi therapy

overall_design: Paired pre- and post-BRAFi FFPE samples from seven metastatic melanoma patients were profiled for gene expression using the Illumina HumanHT-12 WG-DASL V4.0 R2 platform

first: Monica

last: Rodolfo

first: Elisabetta

last: Vergani

first: Loris

last: De Cecco


title: Transcriptomic changes upon overexpression of S. cerevisiae Ppz1 protein phosphatase

city: CERDANYOLA DEL VALLES

first: JOAQUIN

last: ARINO

state: Barcelona

address: ED. IBB

department: Biochemistry & Mol. Biol.

country: Spain

institute: UNIVERSITAT AUTONOMA BARCELONA

summary: Overexpression of the protein phosphatase Ppz1 is toxic for yeast cells as it blocks cell cycle progression from G1 to S phase. To identify relevant changes caused by Ppz1 overexpression we have constructed a strain (ZCZ01) in wich the PPZ1 promoter has been replaced by the GAL promoter. Cell grown on raffinose were shifted to galactose and samples were taken after 30, 120 and 240  min and changes in mRNA levels analyzed by RNA-seq.

overall_design: Six different samples were analyzed. Three were controls (wild type strain) taken 30, 120 and 240 min after shifting cells to galactose, and three were the equivalent samples from the ZCZ01 (GAL1:PPZ1) strain.

first: Joaquín

last: Arino


title: Body temperature-dependent microRNA expression analysis in rats

city: Kitakyushu

first: Takahiro

last: Umehara

address: 1-1 Iseigaoka Yahatanishiku

country: Japan

institute: University of Occupational and Environmental Health

summary: We made rat models of mild, moderate and severe hypothermia, and performed body temperature-dependent microRNA expression analysis in illiopsoas muscle.

overall_design: Twelve male wistar rats (Pathogen-free 9-week-old) were divided into 4 groups (control, mild, moderate and severe hypothermia), which were belonged 3 rats, and were anesthetized with intraperitoneal. After 30 minutes, they were treated at cold (ambient temperature: 4 °C), and chronologically measured rectal temperature (Ret). Control was euthanized by cervical dislocation at 30 minutes after anesthesia. Mild hypothermia was done by cervical dislocation when the Ret reached 30°C. Similarly, moderate and severe hypothermia also was done when the Ret did 22°C and 12°C, respectively. Total RNA from iliopsoas muscle was extracted using miRNeasy Mini kit (QIAGEN GmbH, Hilden, Germany) according to the manufacturer's instructions. RNA integrity was assessed by on-chip capillary electrophoresis using an Agilent RNA 6000 Nano kit and Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA, USA). Microarray analysis was performed on a total of 12 samples (each group n=3) using Rat_miRNA_V21.0_Microarray.


title: Comparative transcriptome analysis reveals differential transcription in heat-resistant and heat-sensitive jujube cultivars under heat stress

city: WuHan

first: Guosong

last: Jiang

state: Hubei Province

address: Jiefang Road, No. 1277

department: Department of Urology

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

summary: Jujube (Ziziphus jujuba Mill.) is an economically and agriculturally significant fruit crop and is widely cultivated throughout the world. Heat stress has recently become one of the major abiotic stresses limiting plant growth and productivity. However, there are few studies on the transcriptome profiling of jujube subjected to heat stress. In this study, we analyzed the physiological and transcriptomic changes of heat-resistant jujube cultivar ‘HR’ and heat-sensitive cultivar ‘HS’ caused by high temperature stress. We statistically determined 984, 1468, 1727 and 2098 differentially expressed genes (DEGs) between ‘HR’ and ‘HS’ after 0, 1, 3, 5 d of heat stress, respectively. Gene Ontology (GO) enrichment analysis indicated that Aa great deal of heat-responsive genes were identified in these DEGs by Gene Ontology (GO) enrichment analysis. It suggests the distinct molecular mechanism of jujube response to heat stress. Furthermore, we validated the expression profiles of 12 candidates using qRT-PCR to further confirm the accuracy of the RNA-seq data. These results will advance our knowledge of the genes involved in the complex regulatory networks of heat stress and provide genetic resources for further improving the heat tolerance in jujube.

overall_design: Transcriptome analysis for  a  jujuebe heat-sensitive cultivar under  heat stress,in triplicate, using Illumina  HiSeq X-ten.

first: Juan

last: Jin

first: Qing

last: Hao


title: Silencing of ZFP36L1 using siRNA

city: Singapore

first: Pushkar

last: Dakle

address: 14 Medical Drive, #12-01,

country: Singapore

institute: Cancer Science Institute of Singapore

summary: ZFP36L1 is a tandem zinc-finger RNA-binding protein that recognizes conserved Adenylate-Uridylate-rich Elements (AREs) located in 3' untranslated regions (UTRs) to mediate RNA decay. We hypothesized that ZFP36L1 is a negative regulator of a post-transcriptional hub involved in the RNA half-life regulation of cancer-related transcripts. Forced expression of ZFP36L1 in cancer cells markedly reduced cell proliferation in vitro and in vivo; whereas silencing of ZFP36L1 enhanced tumor cell growth. To identify direct downstream targets of ZFP36L1, systematic screening using RNA pull-down of wildtype and mutant ZFP36L1 as well as whole transcriptome sequencing of bladder cancer cells ± tet-on ZFP36L1, was performed.  A network of 1,410 genes was identified as potential direct targets of ZFP36L1, including HIF1A, CCND1, and E2F1. ZFP36L1 specifically bound to the 3' UTRs of these targets for RNA degradation, thus suppressing their expression. Collectively, our findings reveal an indispensable role of ZFP36L1 as a post-transcriptional safeguard against aberrant hypoxic signaling and abnormal cell cycle progression.

overall_design: mRNA profiles of ZFP36L1 knockdown cells were generated by deep sequencing using BGISEQ-500.

first: Xin-Yi

last: Loh

first: Qiao-Yang

last: Sun

first: Ling-Wen

last: Ding

first: Anand

last: Mayakonda

first: Nachiyappan

last: Venkatachalam

first: Mei-Shi

last: Yeo

first: Tiago

last: Silva

first: Jin-Fen

last: Xiao

first: Ngan

middle: B

last: Doan

first: Jonathan

middle: W

last: Said

first: Xue-Bin

last: Ran

first: Si-Qin

last: Zhou

first: Pavithra

last: Shyamsunder

first: Angele

last: Koh

first: Ruby

middle: Y

last: Huang

first: Benjamin

last: Berman

first: Soo-Yong

last: Tan

first: Henry

last: Yang

first: De-Chen

last: Lin

first: H

last: Koeffler


title: Tet-ZFP36L1 in 6 hours and 24 hours

first: Pushkar

last: Dakle

overall_design: mRNA profiles of tet-ZFP36L1 overexpressing cells (treated in 0, 6 hours and 24 hours of Doxycycline) were generated by deep sequencing using BGISEQ-500.

first: Xin-Yi

last: Loh

first: Qiao-Yang

last: Sun

first: Ling-Wen

last: Ding

first: Anand

last: Mayakonda


title: Universal NicE-seq for high resolution accessible chromatin profiling for native and formaldehyde fixed cells and tissues

city: Ipswich

first: Sriharsa

last: Pradhan

address: 240 County Road

institute: New England Biolabs

summary: Accessible chromatin plays a central role in gene expression and chromatin architecture. Current accessible chromatin approaches depend on limited digestion/cutting and pasting adaptors at the accessible DNA, thus requiring additional materials and time for optimization.  Universal NicE-seq (UniNicE-seq) is an improved accessible chromatin profiling method that negate the optimization step and is suited to a variety of mammalian cells and tissues. Addition of 5-methyldeoxycytidine triphosphate during accessible chromatin labeling and an on-bead library making step substantially improved the signal to noise ratio while protecting the accessible regions from repeated nicking in cell lines, mouse T cells, mouse kidney, and human frozen and FFPE tissue sections. These refinements allowed reliable mapping of accessible chromatin for high resolution genomic feature studies.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Open-chromatin profile of various samples from cultured cancer cell lines, mouse tissue and human tissue section using nicking enzyme, NtCviPII based NicE-seq library were generated and sequenced. Depending on the experiments some samples were sequenced once, in duplicate or triplicate.

first: Hang

last: Chin

first: Zhiyi

first: Christina

last: Hao


title: Intrahepatic lipocalin 2 promotes liver fibrosis in alcoholic hepatitis [array]

city: Pittsburgh

first: Ramon

last: Bataller

state: PA

address: 200 Lothrop St

institute: Pittsburgh Liver Research Center

summary: Our project is to explore the molecular subtypes for targeted therapies in Alcoholic Hepatitis (AH). We have found that LCN2 gene expression is markedly induced in AH patients and correlated to the disease severity including portal hypertension. Animal data from microarray experiments show that compared with the wild mice, LCN2 knockout mice are protected from CCl4-induced liver fibrosis. The focus of our current study is to investigate the effect of overexpression of LCN2 on functional changes in hepatocytes. To this end, HepG2 cells and human primary hepatocytes (HPH) were overexpressed human LCN2 gene and samples were analyzed through RNA-sequencing.

overall_design:
To dissect the molecular mechanisms that mediate LCN2 fibrogenic effects in the injured liver, we performed transcriptome profiling analysis of Lcn2–/– and WT mice treated with CCl4.
Liver tissue was collected from BALB/c WT and Lcn2-/- mice treated with CCl4 or corn oil for 4 weeks.


title: Ca2+ release-activated Ca2+ entry is a potent host innate immune defence against influenza A virus

city: Loughborough

first: Kin-Chow

last: Chang

state: Select State

address: College Street,, Sutton Bonington

department: School of Veterinary Medicine and Science

country: United Kingdom

institute: University of Nottingham

summary: Gene expression was determined for normal human bronchial epithelial (NHBE) cells incubated with DMSO or TG immediately prior to infection with USSR H1N1 virus for 12 hours. All of the NHBE cell stocks were obtained from QIAGEN.

overall_design: Normal human bronchial epthelial cells  mRNA profiles were generated by deep sequencing, in quadruplicate (two donors and two replicates per donor), using Illumina HiSeq 3000

first: Kin-chow

first: Leah

last: Goulding


title: Intrahepatic lipocalin 2 promotes liver fibrosis in alcoholic hepatitis [RNA-Seq]

overall_design: Immunofluorescence staining showed that the receptor of LCN2 expression was not detected in normal hepatocytes but markedly expressed in the liver with AH.  To explore the effect of LCN2 on hepatocytes expression profile, we used adenovirus overexpressing LCN2 in human primary hepatocytes and HepG2 cells and ran RNA-sequencing.


title: Intrahepatic lipocalin 2 promotes liver fibrosis in alcoholic hepatitis

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

overall_design: Refer to individual Series


title: microRNA expression profiling of melanoma cell lines with acquired resistance to the BRAF inhibitor PLX4032 compared to the parental sensitive counterparts

first: Matteo

last: Dugo

summary: microRNA expression profiles show altered  patterns in cell lines with acquired resistance  to the BRAF inhibitor  compared to the parental cell lines, and common miRNAs regulated in the resistant variants

overall_design: microRNA profiling of six paired resistant (R)/sensitive cell lines (12 samples) was performed using NanoString platform

first: Vergani

last: Elisabetta


title: An intact heterotrimeric G-Protein complex is required for the N-acylethanolamine-induced, transcriptionally-mediated chloroplast response in developing Arabidopsis seedlings

city: Denton

first: Ashley

middle: Elisabeth

last: Cannon

address: 1155 Union Circle #305220

department: Biological Sciences

institute: The University of North Texas

summary:
Purpose: Using RNA-seq and differential expression analysis, we examined the NAE 18:3-induced and AGB1-dependent and -independent transcriptional responses involved in transducing early signals into downstream physiological changes involved in Arabidopsis seedling growth.
Methods: Seedling mRNA profiles of 4-day-old Arabidopsis seedlings treated with DMSO or 40 µM NAE 18:3 for 1 h or 3 h were generated by deep sequencing, in triplicate, using the Illumina Next-Seq 500 system. The sequence reads that passed quality filters were analyzed using STAR followed by DESeq2. qRT–PCR validation was performed using SYBR Green assays.
Results: We show that the activity of N-linolenoylethanolamine (NAE 18:3) requires an intact G-protein complex; specifically, genetic ablation of the Gβ dimer or loss of the full set of atypical G⍺ subunits strongly attenuates an NAE 18:3 de-greening of cotyledons in Arabidopsis seedlings. This effect involves, at least in part, transcriptional regulation of chlorophyll synthesis gene expression. In addition, there is feedforward transcriptional control of G-protein signaling components and G-protein interactors.
Conclusions: These results are consistent with NAE 18:3 being a lipid signaling molecule in plants with a requirement for G-proteins to mediate signal transduction, a situation similar, but not identical, to the action of NAE endocannabinoids in animal systems.

overall_design: Seedling mRNA profiles of 4-day-old Arabidopsis Col-0 and agb1 seedlings treated with DMSO or 40 µM NAE 18:3 for 1 h or 3 h were generated by deep sequencing, in triplicate, using the Illumina Next-Seq 500 system.

first: Chengshi

last: Yan

middle: E

first: Jantana

last: Keereetaweep

first: Bibi

last: Khan

first: Alan

middle: M

last: Jones

first: Elison

last: Blancaflor

first: Rajeev

last: Azad

first: Kent

middle: D

last: Chapman


title: Fermentation product with new equol-producing Lactobacillus paracasei as a probiotic candidate for prevention of skin and intestinal disorder (RNA-Seq)

city: Ulsan

first: jaewon

last: lim

address: 50, UNIST-gil

country: South Korea

institute: ulsan national institute of science and technology

summary: Equol is one of major isoflavones with an affinity to endoplasmic reticulum and has an estrogen-like biological activity. Equol-producing bacteria have been isolated and characterized, however fermentation has been performed in an anaerobic condition with soybean-based products as substrates. Pueraria lobata has been reported as a plant with a higher content of isoflavones, such as daidzein, daidzin, and puerarin.

overall_design: L. paracasei JS1 growth with and without P. lobata extrection. Then do RNA-seq to analize expression level of each genes.

first: Jeong

last: Kwon

first: Jaewon

last: Lim

first: Inhye

last: Kim

first: Donghyuk

first: Se

last: Kang


title: CpG islands shape the epigenome landscape.

city: ILLKIRCH-GRAFFENSTADEN

first: Christophe

last: Papin

address: 1 rue Laurent Fries

institute: IGBMC - CNRS UMR 7104 - Inserm U 964

type: Methylation profiling by high throughput sequencing

summary: Epigenetic modifications and nucleosome positioning play an important role in modulating gene expression. However, how the patterns of epigenetic modifications and nucleosome positioning are established around promoters is not well understood. Here, we have addressed these questions in a series of genome-wide experiments coupled to a novel bioinformatic analysis approach. Our data reveal a clear correlation between CpG density, promoter activity and accumulation of active or repressive histone marks. CGI boundaries define the chromatin promoter regions that will be epigenetically modified. CpG-rich promoters are targeted by histone modifications and histone variants, while CpG-poor promoters are regulated by DNA methylation. CGIs boundaries, but not transcriptional activity, are essential determinants of H2A.Z positioning in vicinity of the promoters, suggesting that the presence of H2A.Z is not related to transcriptional control. Accordingly, H2A.Z depletion has no impact on gene expression of arrested mouse embryonic fibroblasts. Therefore, the underlying DNA sequence, the promoter CpG density and, to a lesser extent, transcriptional activity, are key factors implicated in promoter chromatin architecture.

overall_design:
We have generated genome-wide ChIP-seq and MeDIP-seq for the following main epigenetic marks: H2A.Z, H3.3, H3K4me1, 5mC and 5hmC in mouse embryonic fibroblasts (MEFs).
We also measured the impact of H2A.Z depletion on gene transcription of arrested MEFs. We derived MEFs from our mouse cKO H2A.Z-1flox/flox : H2A.Z-2flox/flox lines and grew them until confluency to reach the G0 phase of the cell cycle. This allows to dissociate the role of H2A.Z from its implication in replication. H2A-Z.1flox/flox : H2A-Z.2flox/flox MEFs were infected with control adenovirus or adenovirus expressing Cre recombinase to generate control (WT) or double KO (dKO) cell lines.

first: Stéphanie

last: Le Gras

first: Ali

last: Hamiche


title: RNA pull down assay of GST-ZFP36L1 (wildtype and mutant)

first: Pushkar

last: Dakle

overall_design: RNA profiles of RNA pull-down by GST, wildtype ZFP36L1 and ZFP36L1-Ala mutant were generated by deep sequencing using BGISEQ-500.

first: Xin-Yi

last: Loh

first: Qiao-Yang

last: Sun

first: Ling-Wen

last: Ding

first: Anand

last: Mayakonda

first: Nachiyappan

last: Venkatachalam

first: Mei-Shi

last: Yeo

first: Tiago

last: Silva

first: Jin-Fen

last: Xiao

first: Ngan

last: Doan

first: Jonathan

last: Said

first: Xue-Bin

last: Ran

first: Si-Qin

last: Zhou

first: Pavithra

last: Shyamsunder

first: Angele

last: Koh

first: Ruby

last: Huang

first: Benjamin

last: Berman

first: Soo-Yong

last: Tan

first: Henry

last: Yang

first: De-Chen

last: Lin

first: H

last: Koeffler


title: Genome-wide analysis of VlbZIP30-targeted genes involved in drought responses in grapevine (Vitis vinifera)

status: Public on Oct 01 2020

city: Yangling

first: Xianhang

last: Wang

state: Shaanxi

address: No.3 Taicheng Road

department: State Key Laboratory of Crop Stress Biology in Arid Areas

institute: Northwest A&F University

summary: Drought stress dramatically affects the growth and development of grapevine (Vitis vinifera) in many areas of the world, and identifying the mechanisms responsible for drought stress responses is therefore of great interest. The transcription factor, VlbZIP30 has been reported to enhance drought resistance in grapevine, however, the regulatory mechanisms mediated by VlbZIP30 remain poorly understood. Here, we performed chromatin immunoprecipitation (ChIP)-seq and RNA-seq analyses to identify the direct VlbZIP30 target genes at a genome-wide scale. The ChIP-seq analysis determined that VlbZIP30 binds to DNA sequences containing an ACGTG core motif, termed a G-box. By combining the ChIP-seq and RNA-seq results, we identified 48 VlbZIP30-induced target genes, related mainly to the gene ontology (GO) terms: nucleic acid-templated transcription, plant hormone and abiotic stimulus. Through ChIP-qPCR analysis, we confirmed that VlbZIP30 binds directly to the promoters of four of the target genes (VvNAC26, VvDHN1, VvGRAS17 and VvVQ6) containing a G-box motif. In addition, overexpression of VlbZIP30 led to less H2O2 accumulation compared with the wild type under drought conditions in both Arabidopsis thaliana and grapevine, indicating a role for VlbZIP30 in reactive oxygen species (ROS) scavenging. In summary, we report that VlbZIP30 promotes the activity of ROS scavenging by directly regulating the expression of downstream target genes, thereby conferring drought resistance. We also reveal that VlbZIP30 directly regulates the expression of a number of target genes (such as VvDHN1, VvGRAS17 and VvVQ6) to improve plant drought resistance.

overall_design: ChIP-seq assay of 4-month-old overexpression VlbZIP30 transgenic grape grown under drought stress for 20 days

first: Mingxing

last: Tu

first: Xiping


title: The SDHB Arg230His mutation causing familial paraganglioma alters glycolysis in a new Caenorhabditis elegans model

city: Budapest

first: István

last: Likó

address: Üllői út 26.

country: Hungary

institute: Semmelweis University

summary: The conserved B-subunit of succinate dehydrogenase (SDH) participates in the TCA cycle and mitochondrial electron transport.  The Arg230His mutation in SDHB causes heritable pheochromocytoma/paraganglioma (PPGL). In C. elegans, we generated an in vivo PPGL model (SDHB-1 Arg244His; equivalent to human Arg230His) which manifests delayed development, shortened lifespan, attenuated ATP production and reduced mitochondrial number. Although succinate is elevated in both missense and null sdhb-1(gk165) mutants, transcriptomic comparison suggests very different causal mechanisms that are supported by metabolic analysis where only Arg244His (not null) worms elevate lactate/pyruvate levels, pointing to a missense-induced, ‘Warburg’-like aberrant glycolysis. In silico predictions of the SDHA-B dimer structure demonstrate that Arg230His modifies the catalytic cleft despite the latter’s remoteness from the mutation site. We hypothesise that Arg230His SDHB mutation rewires metabolism, reminiscent of metabolic reprogramming in cancer. Our tractable model provides a novel tool to investigate the metastatic propensity of this familial cancer and our approach may illuminate wider SDH pathology.

overall_design: Transcriptomic analysis of sdhb-1 deletional and R244H point mutant worms versus stage-specific wild-type and transgenic controls.

first: Éva

last: Saskői

first: Gábor

last: Nyírő

first: Attila

last: Patócs

first: Anil

last: Mehta

first: Krisztina

last: Takacs-Vellai


title: Effect of exogenous apo-transferrin on erythropoiesis in Hbbth-1 (th1/th1) mice, a model of beta-thalassemia intermedia

city: New York

first: Christopher

last: Mason

address: 1305 York Ave

department: Physiology and Biophysics

institute: Weill Cornell Medical College

summary: We aimed to evaluate changes in expression in control and th1/th1 mice treated with PBS and apo-transferrin to understand the effect(s) of exogenous apo-transferrin on normal and ineffective erythropoiesis

overall_design: sorted bone marrow erythroblasts from PBS and apo-transferrin treated WT and th1/th1 mice (n=3 per group)

first: Yelena

last: Ginzburg

first: Huiyong

last: Chen


title: Integrative genomic strategies applied to a lymphoblast cell line model reveal specific transcriptomic signatures associated with clozapine response [expression]

city: Los Angeles

last: Ori

state: Verenigde Staten van Amerika

address: 695 Charles E Young Drive South

department: Center for Neurobehavioral Genetics

institute: University of California, Los Angeles

summary: In vitro genomic analyses of clozapine response. Genome wide gene expression profiling was performed across several experimental conditions of clozapine exposure. LCLs were exposed for 24 hours to 1x, 10x, 50x and 100x clinical concentration (2μM, 20μM,100μM,200 μM clozapine) and vehicle (DMSO); each concentration was measured in 4 cell lines.

overall_design: Lymphoblast cells were lysed and RNA extracted using column-based extraction methods from Qiagen according to manufacturer’s instructions. Gene expression profiling was carried out using Illumina HumanHT- 12 v4 Expression BeadChip technology.

first: Sera

last: de With

first: Roel

middle: A

last: Ophoff


title: Integrative genomic strategies applied to a lymphoblast cell line model reveal specific transcriptomic signatures associated with clozapine response

type:
Expression profiling by array
Methylation profiling by array


title: STAT3 phosphorylation at Ser727 and Tyr705 differentially regulates the EMT-MET switch and cancer metastasis

city: Hsinchu

first: Jia-Lin

last: Lee

address: 101, Sec. 2, Kuang Fu Road

country: Taiwan

institute: National Tsing Hua University

summary: Epithelial-mesenchymal transition (EMT)/mesenchymal-epithelial transition (MET) processes are proposed to be a driving force of cancer metastasis. By studying metastasis in bone marrow-derived mesenchymal stem cell (BM-MSC)-driven lung cancer models, microarray time-series data analysis by systems biology approaches revealed BM-MSC-induced signaling triggers early dissemination of CD133+/CD83+ cancer stem cells (CSCs) from primary sites shortly after STAT3 activation but promotes proliferation towards secondary sites. The switch from migration to proliferation was regulated by BM-MSC-secreted LIF and activated LIFR/p-ERK/pS727-STAT3 signaling to promote early disseminated cancer cells MET and premetastatic niche formation. Then, tumor-tropic BM-MSCs circulated to primary sites and triggered CD151+/CD38+ cells acquiring EMT-associated CSC properties through IL6R/pY705-STAT3 signaling to promote tumor initiation and were also attracted by and migrated towards the premetastatic niche. In summary, STAT3 phosphorylation at tyrosine 705 and serine 727 differentially regulates the EMT-MET switch within the distinct molecular subtypes of CSCs to complete the metastatic process.

overall_design: We obtained quantified time-course gene expression profiles for A549 lung cancer cells cultured both with and without human BM-MSC-CM. Microarray profiles for the BM-MSC-treated and control cells were obtained at eight time points (2, 4, 8, 16, 24, 48, 72, and 96 hours post treatment) in triplicate samples.


title: Melatonin Enhances Osteoblastogenesis from Senescent Mesenchymal Stem Cells via MMSET Mediated Chromatin Remodeling[ChIP-Seq]

city: Tianjin

first: Liu

last: Zhiqiang

address: 22 Qxiangtai Rd

institute: Tianjin Medical University

summary: Functional crosstalk between histone modifications and chromatin remodeling has emerged as a key regulatory mode of transcriptional control during cell fate decisions, but the underlying mechanisms are not fully understood. Here we demonstrate that RUNX2 and SP7 osteogenic genes coordinate histone H3 lysine 36 dimethylation (H3K36me2) and transcriptional elongation factor Pol II to regulate chromatin dynamic and gene transcription during osteogenesis. Mechanistically, melatonin favored osteogenic differentiation via the MMSET-mediated modification of H3K36me2 on the promoters of osteogenic driver genes in MSCs.

overall_design: Examination of histone modification in MSCs treated with melatonin.

first: Ying

last: Xie

last: Han

first: Feng

last: Li

first: Xuelei

last: Wei


title: Differential expression profiles of tsRNAs in myocardial ischemic rats with/without caloric restriction

city: Yantai

first: Defang

address: No. 346 Guanhai, Laishan District

institute: Binzhou Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary: We report the application of high-throughput RNA sequencing technology to examine expression profiling of transfer RNA (tRNA)-derived small RNAs (tsRNAs) in a normal control group (Norm group), isoproterenol (ISO)-induced myocardial ischemic group (MI group), and CR-pretreatment plus ISO-induced myocardial ischemic group (CR+MI group). A total of 714 precisely matched tsRNAs were identified in the myocardial tissues from the three groups of rats (701 in Norm, 708 in MI, and 712 in CR+MI). We find that 302 tsRNAs were identified to be notably dysregulated in the MI group: 166 tsRNAs were upregulated while 136 tsRNAs were downregulated compared with those in the Norm group. After CR pretreatment, we identified 136 tsRNAs that were significantly altered compared with those in the MI group: 45 were upregulated while 91 were downregulated. This study provides new ideas for future research on elucidating the mechanisms of CR pretreatment through regulating tsRNAs levels in myocardial ischemic injury.

overall_design: Examination of different expression profiling of tsRNAs in in ISO-induced myocardial ischemic rats with/without caloric restriction.

first: Yang

last: Liu

first: Qiusheng

last: Zheng

first: Wenjing


title: Expression data in primary osteoblasts (OBs) obtained from women with osteoporotic fracture or severe osteoarthritis.

city: Valencia

first: Miguel Angel

last: Garcia Perez

state: Comunidad Valenciana

address: Av. Menéndez Pelayo, 4 accesorio

department: Research Unit

institute: INCLIVA Health Research Institute

summary:
Osteoporosis and bone fragility fracture are multifactorial pathologies whose genetic component is still poorly characterized. The present experiment aims to identify genes differentially expressed in the bone-forming cell; the osteoblast. To do this, we obtain primary osteoblasts from bone explants of women undergoing hip replacement to later obtain RNA. The cases are women with a fragility bone fracture of the hip. The controls are women with severe osteoarthritis.Microarray analysis yielded 2542 differentially expressed transcripts belonging to 1798 annotated genes, of which 45.6% (819) were overexpressed, and 54.4% (979) underexpressed (fold-change between -7.45 and 4.0). Among the most represented pathways indicated by transcriptome analysis were chondrocyte development, positive regulation of bone mineralization, BMP signaling pathway, skeletal system development and Wnt signaling pathway. Then, we selected SNPs in genes related to epigenetic mechanisms to study their association with bone mass in a cohort of 1028 Spanish women.
We used microarrays to compare the overall gene expression between primary osteoblasts from women with fragility fracture with that of control women undergoing hip replacement due to severe osteoatritis.

overall_design: This study compares gene expression in primary osteoblasts obtained from women undergoing hip replacement due to osteoporotic fracture or due to severe osteoarthritis.

first: Layla

last: Panach

first: Clara

last: Pertusa

first: Beatriz

last: Martínez-Rojas

first: Álvaro

last: Acebrón

first: Damián

last: Mifsut

first: Juan

last: Tarín

first: Antonio

last: Cano

first: Miguel

last: García-Pérez


title: Developmental, cellular, and behavioral phenotypes in a mouse model of congenital hypoplasia of the dentate gyrus

city: Baltimore

first: Amir

last: Rattner

state: MD - Maryland

address: 725 North Wolfe St.

institute: Johns Hopkins University

summary: We studied conditional knockout mice in which the vast majority of dentate granule cells (DGCs) fail to develop – including nearly all DGCs in the dorsal hippocampus – secondary to eliminating Wntless (Wls) in a subset of cortical progenitors with Gfap-Cre.

overall_design: Bulk RNA-seq and single nuclei RNA-seq were preformed on hippocampi from adult control, Gfap-Cre;Wlsfl/+, and mutant, Gfap-cre;Wlsfl/- mice.

first: Chantelle

last: Terrillion

first: Claudia

last: Jou

first: Tina

last: Kleven

first: Shun

last: Hu

first: John

last: Williams

first: Zhipeng

last: Hou

first: Manisha

last: Aggarwal

first: Susumu

last: Mori

first: Gloria

last: Shin

first: Loyal

last: Goff

first: Menno

last: Witter

first: Mikhail

last: Pletnikov

first: André

last: Fenton

first: Jeremy

last: Nathans


title: Exploitable, highly context-specific astrocytes

first: Xinzhu

last: Yu

state: CA

address: 10833 Le Conte Ave, CHS 53-359

institute: University of California Los Angeles

summary: To investigate the functional heterogeneity of astrocytes from a defined brain region, we performed single cell RNA-seq of striatal cells from adult mice (8-9 weeks old). From the analyses, we have identified context-specific changes of striatal astrocytes.

overall_design: Total 3 samples from 3 adult mice were used in this data set. Single cell suspension was prepared according to the protocol of Act-seq.

first: Jun

last: Nagai

first: Joselyn

last: Soto

first: Maria

last: Marti

first: Giovanni

last: Coppola

first: Madan

last: Babu

first: Baljit

last: Khakh


title: Overlapping activities of ELAV/Hu family RNA binding proteins specify the extended neuronal 3' UTR landscape in Drosophila [L1 CNS RNA-seq]

first: Seungjae

last: Lee

state: NY

address: 430 East 67th St.

department: Department of Developmental Biology

institute: Sloan-Kettering Institute

summary: The goals of this study are to perform quantitative comparison of whole transcriptome of Drosophila melanogaster 1st instar larvae central neural system (L1CNS) from three genotypes: Canton-S, elav5 single mutant, and elav5/fne double mutant; and the global 3'-end features of Drosophila melanogaster 1st instar larvae central neural system from three genotypes: Canton-S, elav5 single mutant. Total RNAs were extracted from dissected L1CNS of Drosophila melanogaster Canton-S, elav5 single mutant, and elav5/fne double mutant; total RNA-seq libraries were prepared using Illumina TruSeq Stranded Total RNA Sample Prep kit with replicates for each genotype; final cDNA libraries were sequenced on Illumina HiSeq-1000 sequencer with PE-100 mode. Total RNA-seq data were mapped to the corresponding UCSC genome assemblies: Drosophila melanogaster (dm6), HISAT2 aligner was used for the alignment with default parameters. We found that L1CNS from Canton-S expresses neural specific 3' UTR extensions like head, while in L1CNS from elav5 single mutant, global neural specific 3' UTR extensions are not significantly lost, but in elav5/fne double mutant L1CNS, there is a dramatic loss of neural specific 3' UTR extensions. We reported for the first time demonstration of trans-acting factors that globally maintain this very distinctive tissue-specific APA landscape.

overall_design: RNA-seq profiles from dissected Drosophila melanogaster 1st instar larvae central neural system from three genotypes: Canton-S (WT), elav5 single mutant, and elav5/fne double mutant. Elav5 and fne mutants are deletion KO alleles.

first: Lu

last: Wei

first: Sonali

last: Majumdar

first: Binglong

last: Zhang

first: Piero

last: Sanfilippo

first: Brian

last: Joseph

first: Pedro

last: Miura

first: Matthias

last: Soller

first: Eric

last: Lai


title: Overlapping activities of ELAV/Hu family RNA binding proteins specify the extended neuronal 3' UTR landscape in Drosophila

overall_design: Refer to individual Series


title: Overlapping activities of ELAV/Hu family RNA binding proteins specify the extended neuronal 3' UTR landscape in Drosophila [L1 CNS 3'seq]

summary: The goal of this study is to perform quantitative comparison of transcriptome-wide 3'-end features of Drosophila melanogaster 1st instar larvae central neural system (L1CNS) from three genotypes: Canton-S, elav5 single mutant, and elav5/fne double mutant; Total RNAs were extracted from dissected L1CNS of Drosophila melanogaster Canton-S, elav5 single mutant, and elav5/fne double mutant; 3'-end sequencing libraries were prepared using Lexogen QuantSeq 3′ mRNA-Seq Library Prep Kit REV for Illumina with replicates for each genotype; final cDNA libraries were sequenced on Illumina HiSeq-1000 sequencer with SE-50 mode. 3'-end sequencing data were mapped onto the corresponding UCSC genome assemblies: Drosophila melanogaster (dm6) and 3′ end clusters were derived and quantified within a 25 bp window. We found that L1CNS from Canton-S expresses neural specific 3' UTR extensions like head, while in L1CNS from elav5 single mutant, global neural specific 3' UTR extensions are not significantly lost, but in elav5/fne double mutant L1CNS, there is a dramatic loss of neural specific 3' UTR extensions. We reported for the first time demonstration of trans-acting factors that globally maintain this very distinctive tissue-specific APA landscape.

overall_design: 3'-end sequencing profiles from dissected Drosophila melanogaster 1st instar larvae central neural system from three genotypes: Canton-S, elav5 single mutant, and elav5/fne double mutant.  Elav5 and fne mutants are deletion KO alleles.


title: Overlapping activities of ELAV/Hu family RNA binding proteins specify the extended neuronal 3' UTR landscape in Drosophila [S2 3-seq]

summary: The goals of this study are to establish a cell line based analysis platform to unbiasedly evaluate the capabilities of Elav/Hu family RNA binding proteins in regulating neural specific 3' UTR extension; and perform quantitative analysis of global 3' UTR extension regulated by individual Elav/Hu family RNA binding protein. We reported that in non-neural tissue context such as S2R+ cells, with the overexpression of wildtype Elav, Rbp9 and Fne, we observed global 3' UTR extensions for hundreds of genes, whose 3' UTR extension corespond with those detected in head; also, RNA rocognition motif mutant versions of Elav, Rbp9 and Fne loss the ability to regulate the generation of neural specific 3' UTR extension. We reported here for the first time, we show quantitative comparison between Elav/Hu family RNA binding proteins in regulating neural specific 3' UTR landscape and imply the overlapping activities of Elav/Hu family RNA binding proteins specifying neural 3' UTR landscape in Drosophila.

overall_design: 3'-end sequencing profiles from S2R+ cells with the overexpression of wildtype,  Elav, Rbp9, Fne and RRM mutant versions of Elav, Rbp9, Fne.


title: Plant breeding involving genetic engineering does not result in unacceptable unintended effects in rice relative to conventional cross-breeding

city: Xinyang

first: Qingsong

last: Liu

state: Henan

address: No. 237, Nanhu road

institute: Xinyang Normal University

summary: Advancements in -omics techniques provide powerful tools to assess potential effects in composition of a plant at the RNA, protein and metabolite levels. These technologies can thus be deployed to assess whether genetic engineering causes changes in plants that go beyond the changes introduced by conventionally plant breeding. Here, we compare the extent of transcriptome and metabolome modification occurring in leaves of four GE rice lines expressing Bacillus thuringiensis (Bt) genes that developed by genetic engineering and seven rice lines developed by conventional cross-breeding. The results showed that both types of crop breeding methods can bring changes at transcriptomic and metabolic levels, but the differences were comparable between the two methods, and were less than those between conventional non-GE lines. Metabolome profiling analysis found several new metabolites in GE rice lines when compared to the closest non-GE parental lines, but these compounds were also found in several of the conventionally bred rice lines. Functional analyses suggest that the differentially expressed genes and metabolites caused by both genetic engineering and conventional cross-breeding do not involve detrimental metabolic pathways. The study successfully employed RNA-sequencing and HPLC-MS technology to assess the unintended changes in new rice varieties, and the results suggest that genetic engineering does not cause unintended effects that go beyond conventional cross-breeding in rice.

overall_design: We compare the extent of transcriptome and metabolome modification occurring in leaves of four GE rice lines expressing Bacillus thuringiensis (Bt) genes that developed by genetic engineering and seven rice lines developed by conventional cross-breeding.

first: Yunhe

last: Li


title: Single-cell sequencing reveals heterogeneity effects of arsenic or/and 2,2-dichloroacetamide on zebrafish liver

city: Nanjing

first: Chen

last: Ling

address: 163 Xianlin Avenue

institute: Nanjing University

summary: Arsenic and DBPs has been found to be one of the major risk in many regions of the world. However, current understanding of thier combined toxicities are unclear. Here we used single-cell RNA sequencing to provide the transcriptome heterogeneity of 13563 liver cells obtained from zebrafishes exposed to 100μg/L arsenic, 300μg/L dichloroacetanilide (DCAcAm) and co-exposure for 23 days. Five liver cell populations were identified. We found that the hepatocytes and macrophages were the main target of arsenic and DCAcAm exposure. And the hepatocytes of male and female showed a huge difference, when expsoure to arsenic and DCAcAm).

overall_design: Single-cell RNA sequencing were adopted to learn the transcriptional variation in zebrafish liver exposure to arsenic and DCAcAm.

first: Bing

last: Wu

first: Ling

last: Chen


title: Dual RNAseq analysis of THP1 macrophages infected by AIEC LF82 bacteria

city: Paris

first: Olivier

last: Espeli

address: 11 place Marcelin Berthelot

department: CIRB

institute: College de France

summary: AIEC are crohn disease related bacteria, they can survive and growth within macrophages mature lysosomes. To characterise the Human and bacterial pathways involved in this adaptation we performed Dual RNAseq

sample_organism:
Homo sapiens
Escherichia coli LF82

platform_organism:
Homo sapiens
Escherichia coli LF82

overall_design: Examination of bacterial and Human transcriptomes 1h and 6h post infection. Examination of bacterial and macrophage transcriptomes in the absence of infection

last: Espéli

first: Gaelle

last: Demarre

first: Maxime

last: Wery

first: Antonin

last: Morillon


title: Exposure to tert-butylphenyl diphenyl phosphate, an organophosphate ester flame retardant and plasticizer, alters hedgehog signaling in ex vivo murine limb bud cultures

city: Montreal

first: Barbara

middle: F.

last: Hales

state: QC

address: 3655 Prom. Sir William Osler, room 110

department: Pharmacology and Therapeutics

institute: McGill University

summary: Organophosphate esters (OPEs) have become widely used as flame retardants since the global phase out of polybrominated diphenyl ethers (PBDEs). Previously, we demonstrated that some OPEs, such as tert-butylphenyl diphenyl phosphate (BPDP), were more detrimental to endochondral ossification in ex vivo murine limb bud cultures than one of the major PBDEs that they replaced, 2,2',4,4'-tetrabromodiphenyl ether (BDE-47). Here we used a transcriptomic approach to elucidate the mechanism of action of BPDP in the developing limb. Limb buds collected from gestation day 13 CD1 mouse embryos were cultured for 3 or 24 hours in the presence of vehicle, 1 μM, or 10 μM BPDP. RNA sequencing (RNA-seq) analyses revealed that exposure to 1 µM BPDP for 24 hours increased the expression of 5 transcripts, including Ihh, and decreased 14 others, including Gli1, Ptch1, Ptch2, and other targets of Hedgehog (Hh) signaling. Pathway analysis inferred the inhibition of Hh signaling. Attenuation of Hh signaling activity began earlier and reached a greater magnitude after exposure to 10 µM BPDP. Since this pathway is part of the regulatory network governing endochondral ossification, we used a known Hh agonist, purmorphamine, to determine the contribution of Hh signaling inhibition to the negative impact of BPDP on endochondral ossification. Co-treatment of limbs with purmorphamine rescued the detrimental morphological changes in the cartilage template induced by BPDP exposure though it did not restore the expression of key transcription factors, Runx2 and Sp7, to control levels. These data highlight Hh signaling as a developmentally important pathway vulnerable to environmental chemical exposures.

overall_design: Forelimb buds collected from gestation day 13 CD1 mouse embryos were cultured for 3 or 24 hours in the presence of vehicle (DMSO), 1 μM, or 10 μM BPDP; n = 4.

first: Yan

last: Han


title: RNA-seq analysis in residual pancreatic β-cells of Bmal1KO/DTA mice following massive ablation

city: Geneva

first: Celine

last: Delucinge

address: 1 rue Michel Servet

department: iGE3 Genomics Platform

country: Switzerland

institute: University of Geneva

summary: We aimed to fill the gap in understanding functional roles of the islet cellular oscillators under diabetic conditions following massive β-cell ablation, and during β-cell regeneration. We assessed diurnal regulation of β-cell proliferation and transcriptional landscape in separated α- and residual β-cells -utilizing rtTA/TET-DTA mouse model that bears α- and β-cell specific labeling. Acute hyperglycemia and loss of β-cell mass perturbed absolute expression levels and temporal transcriptome profiles in residual β-cells, whereas in neighboring α-cells only changes in temporal profiles were observed. Strikingly, compensatory regeneration of β-cells exhibited circadian rhythmicity. In arrhythmic BMAL1 knockout mice, massive β-cell ablation led to aggravated hyperglycemia, hyperglucagonemia and a fatal non-compensated diabetes. No activation of β-cell regeneration via entry into cell-cycle was observed in arrhythmic mice, suggesting essential role of functional circadian clocks in this process.

overall_design: mRNA from FACS-sorted residual β-cells from Bmal1KO/DTA and Bmal1+/-DTA mice following massive β-cell ablation induced by 10-day Doxycycline administration

first: Volodymyr

last: Petrenko

first: Charna

last: Dibner


title: Gene expression changes in NRASG12D, NUP98-NSD1 and NUP98-NSD1+NRASG12D transformed mouse bone marrow  cells (in vitro).

city: Halle

first: Razif

last: Gabdoulline

state: Sachsen-Anhalt

address: Ernst-Grube-Straße 40

department: Innere Medizin IV Haematologie und Onkologie

institute: Universitätsklinikum Halle

summary: NUP98-NSD1 positive Acute myeloid leukemia (AML) frequently occurs within the pediatric karyotypic normal(CN)-AML cohort. It is often associated with mutations in genes like FLT3, NRAS, WT1 and MYC. Here we have studied the role of NUP98-NSD1 fusion and NRASG12D in leukemia initiation and progression.

overall_design: After 4 days of treatment with 150 mg 5-fluorouracil/kg, bone marrow cells were harvested from mice. Cells were stimulated for 48 hours in Dulbecco’s modified Eagle medium (DMEM) (STEM cell Technologies, Cologne, Germany) supplemented with 15% fetal bovine serum (FBS) (Sigma-Aldrich, Munich, Germany), 10 ng/mL human interleukin-6 (hIL-6), 6 ng/mL murine interleukin-3 (mIL-3), and 20 ng/mL murine stem cell factor (mSCF; all from PeproTech, Hamburg, Germany). Retrovirus producing Phoenix packaging cells were transfected with the required vectors and viral supernatant was used to transduce mouse bone marrow cells using 5 μg/mL protamine sulfate (Sigma-Aldrich, Seelze, Germany). After cells were expanded, they were sorted for the respective fluorochrome expression.Total RNA was isolated and sent for sequencing.

first: Sagarajit

last: Mohanty

first: Michael

last: Heuser


title: m7G Trac-Seq analysis in LNZ308  METTL1 knockdown cells

city: Boston

first: Qi

last: Liu

state: MASSACHUSETTS

address: Boston, 02115.USA

institute: Boston Children's Hospital

summary: The RNA methyltransferase METTL1 catalyzes the N7-methylguanosine (m7G) modification of certain tRNAs, mRNAs, and miRNA precursors. However, the role of METTL1 and its cofactor WDR4 in cancer remains largely unexplored. Here we reveal the oncogenic role of METTL1/WDR4. METTL1 is frequently amplified and overexpressed in cancers and correlates with poor patient survival. METTL1 depletion in human cancer cells causes decreased abundance of m7G-modified tRNAs, altered cell cycle, and inhibits oncogenicity. Strikingly, METTL1/WDR4 overexpression induces oncogenic transformation and carcinogenesis. Mechanistically, we find increased abundance of a subset of m7G-modified tRNAs including tRNA-Arg(TCT), and increased translation of mRNAs enriched in the corresponding AGA codon including cell cycle regulators. Accordingly, expression of tRNA-Arg(TCT) is significantly elevated in many cancer types, correlates with patient survival, and overexpression of this tRNA enhances reporter gene expression and cell transformation. Thus, METTL1/WDR4-mediated m7G tRNA modification drives oncogenic transformation, thereby highlighting METTL1 as a promising cancer therapeutic target.

overall_design: Examination of  m7G modification in METTL1 silenced LNZ308 human glioblastoma cells  compared to shGFP control cells, in duplicate, using Trac-Seq  techique. Input samples were used for abundance determination and cleaved samples for m7G modification analysis.

first: Esteban

last: Orellana

first: Richard

middle: I

last: Gregory


title: Ribosome Footprinting (RiboSeq) analysis of mRNA translation in MEF Wt cells overexpressing  METTL1+WDR4

overall_design: Examination of translatome in MEF Wt cells overexpressing METTL1+WDR4 compared to empty vector control, in duplicate, using Ribo-Seq  techique.


title: METTL1-mediated m7G tRNA modification drives oncogenic transformation

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


title: Functional precision medicine identifies new therapeutic candidates for medulloblastoma (methylation dataset)

city: La Jolla

first: Edwin

middle: Francisco

last: Juarez

address: 9500 Gilman Dr

institute: University of California San Diego

type: Methylation profiling by genome tiling array

summary: Medulloblastoma (MB) is among the most common malignant brain tumors in children. Recent studies have identified at least four subgroups of the disease that differ in terms of molecular characteristics and patient outcomes. Despite this heterogeneity, most MB patients receive similar therapies, including surgery, radiation and intensive chemotherapy. Although these treatments prolong survival, many patients still die from the disease, and survivors suffer severe long-term side effects from therapy. We hypothesize that each MB patient is sensitive to different therapies, and that tailoring therapy based on the molecular and cellular characteristics of patients’ tumors will improve outcomes. To test this, we have assembled a panel of orthotopic patient-derived xenografts (PDXs) and subjected them to DNA sequencing, gene expression profiling and high-throughput drug screening. Analysis of DNA sequencing suggests that most MBs do not have actionable mutations that point to effective therapies. In contrast, gene expression and drug response data provide valuable information about potential therapies for every tumor. For example, drug screening demonstrates that actinomycin D – which is used for treatment of sarcoma but rarely for MB – is active against PDXs representing Group 3 MB, the most aggressive form of the disease. Finally, we show that functional analysis of tumor cells can be used in a clinical setting to identify more treatment options than sequencing alone. These studies suggest that it should be possible to move away from a one-size-fits-all approach and begin to treat each patient with therapies that are effective against their tumor.

overall_design: 30 samples were profiled on IlluminaHumanMethylation450k arrays: 20 PDOX models and 10 matching human tumors.

first: Jessica

last: Rusert

first: Sebastiam

last: Brabetz

first: Marcel

last: Kool

first: Jill

middle: P

last: Mesirov

first: Robert

last: Wechsler-Reya


title: Functional precision medicine identifies new therapeutic candidates for medulloblastoma


title: The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2’-O-Me sites

city: Copenhagen

first: Nicolai

last: Krogh

address: Blegdamsvej 3B

department: Department of Cellular and Molecular Medicine

institute: University of Copenhagen

summary: A sequencing-based profiling method (RiboMeth-seq) for ribose methylations was used to study methylation patterns during Zebrafish (Danio rerio) development

overall_design: All samples were analyzed in biological triplicates, except for adult tail (trunk) that was in duplicate.

first: Sowmya

last: Ramachandran

first: Tor

last: Jørgensen

first: Steinar

last: Johansen

first: Henrik

last: Nielsen

first: Igor

last: Babiak


title: Transcriptomic responses of hornyhead turbot (Pleuronichthys verticalis) to environmentally relevant doses of polybrominated diphenyl ethers or polychlorinated biphenyls

city: Costa Mesa

first: Alvine

middle: C

last: Mehinto

address: 3535 Harbor Blvd, Suite 110

institute: Southern California Coastal Water Research Project

summary: Hornyhead turbot (Pleuronichthys verticalis), a sentinel flatfish species, were intraperitoneally injected with environmentally relevant mixtures of polybrominated diphenyl ethers (PBDEs) or polychlorinated biphenyls (PCBs). After 96 h, fish were sacrificed and liver tissue was collected for gene expression analysis using a custom-designed microarray.

overall_design: Hornyhead turbot (Pleuronichthys verticalis), a sentinel flatfish species, were intraperitoneally injected with a low or high dose of environmentally relevant mixtures of polybrominated diphenyl ethers (PBDEs) (0.5 or 5 µg/g body weight) or a low or high dose of polychlorinated biphenyls (PCBs) (1 or 10 µg/g body weight). After 96 h, fish were sacrificed and liver tissue was collected for chemical and gene expression analyses. Gene expression analysis was performed using a custom-designed Agilent 8 x 15K microarray (n = 5-7 fish/treatment group).

first: Leah

last: Thornton Hampton

first: Doris

last: Vidal-Dorsch

first: Natàlia

last: Garcia-Reyero

first: Mark

last: Arick II

first: Keith

last: Maruya

first: Wenjian

last: Lao

first: Christopher

last: Vulpe

first: Marianna

last: Brown-Augustine

first: Alex

last: loguinov

first: Steven

last: Bay


title: Transcriptional profiling of mouse prefrontal cortex and nucleus accumbens under chronic jet lag

city: Wuhan

first: Qian

last: Gao

state: hubei

address: Luoyu Road 1037 Huazhong University of Science and Technology

department: College of Life Science and Technology

summary: Chronic jet lag (CJL) induced by shifting light-dark cycles repeatedly is a commonly used protocol to mimic the environmental light/dark changes encountered by shift workers. We conducted RNA sequencing using prefrontal cortex (PFC) and nucleus accumbens (NAc) tissues from these animals, which are brains regions strongly implicated in the pathology of various neurological and psychiatric conditions. Our results reveal the alterations of brain activities and systematic reprogramming of gene expression in brain tissues under CJL, building hypothesis for how CJL increases the susceptibility to neurological and psychiatric diseases.

overall_design: 8-week-old male C57BL/6J mice purchased from Model Animal Research Center of Nanjing University were assigned to different cages randomly with approximately 5 animals per cage. Animals were housed in light-tight cabinets with time-controlled illumination. Food and sterilized water were accessible ad libitum. The mice were housed under 12 hour light: 12 hour dark (12L12D) for 2 weeks for entrainment prior to CJL treatment. For CJL group, lights on and off times were advanced by 6 hours every 2 days whereas for control group they remain unchanged. On CJL Day 10, PFC and NAc were harvested from 3 control and 3 CJL treated animals at Zeitgeber Time 1 (ZT1, 1 hour after lights on; ZT0 is defined as the time of lights on) and ZT13, respectively.

first: Suliman

last: Khan

first: Luoying

last: Zhang


title: Chromatin accessibility changes of Fli1ko vs WT in CD8 T cells

city: Philadelphia

first: E

middle: JOHN

last: WHERRY

address: 421 Curie Blvd,354 BRB II/III

department: Systems Pharmacology       and Translational Therapeutics,Institute for Immunology

institute: University of Pennsylvania

summary: Genetic deletion of Fli1 enhanced CD8 Effector responses

overall_design: Biological replicates were analyszed for WT and the KO genotypes

first: Zeyu

last: Chen

last: Wherry


title: Cut and Run chipseq of Fli1 in CD8 post Cl13 infection

summary: Genetic deletion of Fl1 enhanced CD8 Effector responses

overall_design: Biological replicates were analyzed for WT and the KO genotypes

middle: J


title: Fli1 as transcriptional safeguard that restrains effector CD8 T cell differentiation

overall_design: Refer to individual Series


title: m7G Trac-Seq analysis in MEF Wt cells overexpressing  METTL1+WDR4

first: Qi

last: Liu

overall_design: Examination of  m7G modification in MEF Wt cells overexpressing METTL1+WDR4 compared to empty vector control, in duplicate, using Trac-Seq  techique. Input samples were used for abundance determination and cleaved samples for m7G modification analysis.

first: Esteban

last: Orellana

first: Richard

last: Gregory


title: In vivo CRISPR screening identifies Fli1 as transcriptional safeguard that restrains effector CD8 T cell differentiation [RNA-seq]


title: RNAseq analysis of gene expression in colorectal tumors of wild-type and Nlrp12-/- mice

city: Dallas

first: Hasan

last: Zaki

address: 6000 Harry Hines Blvd

department: Pathology

institute: UT Southwestern Medical Center

summary:
Background: NLRP12 is a cytosolic pattern recognition receptor in the family of NOD-like receptor. NLRP12 has been shown to suppress colorectal tumorigenesis. However, the precise mechansim of NLRP12-mediated regualtion of colorectal cancer is unknown.
Results:  RNAseq data demonstrate higher expression of oncogenes, matrix degrading enzymes such as matrix metaloproteinases (MMPs), and genes involved in tumor invasion in Nlrp12-/- compared to wild-type tumors. Notably, several of the genes highly induced in Nlrp12-/- tumors are regulated by the Wnt/b-catenin pathway.
Conclusion: NLRP12 negatively regualtes the Wnt/b-catenin pathway to suppress colorectal cancer progression and invasion.

overall_design: Methods: Colorectal tumors were induced in wild-type and Nlrp12-/- mice with a single injection (i.p.) of azoxymethane followed by 3 cycles of 2.5% dextran sodium sulphate administration for 5 days in each cycle. Tumors were collected 12 weeks post azoxymethane treatment. RNA was isolated from tumors and analyzed by RNAseq.

first: Shahanshah

first: Yunpeng


title: SHP2 Inhibition Abrogates Adaptive Resistance to KRAS-G12C-Inhibition and Remodels the Tumor Microenvironment of KRAS-Mutant Tumors

city: New York

first: Igor

last: Dolgalev

state: New York

address: 550 1st Ave

institute: NYU Grossman School of Medicine

summary: KRAS is the most frequently mutated oncogene in human cancer, and KRAS inhibition has been a longtime goal. Recently, inhibitors (G12C-Is) that bind KRAS-G12C-GDP and react with Cys-12 were developed. Using new affinity reagents to monitor KRAS-G12C activation and inhibitor engagement, we found that SHP2 inhibitors (SHP2-Is) increased KRAS-GDP occupancy, enhancing G12C-I efficacy. SHP2-Is abrogated feedback signaling by multiple RTKs and adaptive resistance to G12C-Is in vitro, in xenografts, and in syngeneic KRAS-G12C-mutant pancreatic ductal adenocarcinoma (PDAC) and non-small cell lung cancer (NSCLC) models. The combination of SHP2-I and G12C-I evoked favorable changes in the immune microenvironment, decreasing myeloid suppressor cells, increasing CD8+ T cells, and sensitizing tumors to PD-1 blockade. Experiments using an inhibitor-resistant SHP2 mutant showed that SHP2 inhibition in PDAC cells is required for tumor regression and remodeling of the immune microenvironment, but SHP2-Is also had direct effects on angiogenesis. Our results demonstrate that SHP2-I/G12C-I combinations confer a substantial survival benefit in PDAC and NSCLC and identify additional potential combination strategies. G12C-Is show significant, but limited, efficacy as single agents, in part because of “adaptive resistance”. We find that combining G12C-Is with SHP2-Is abrogates adaptive resistance and results in favorable changes in the immune microenvironment that potentiate PD-1 blockade in KRAS-mutant malignancies. SHP2-Is also can have direct, context-dependent, effects on tumor vasculature.

overall_design: Trascriptomic analysis of tumors or cell line after treatment with Vehicle, SHP099, ARS1620 or SHP099+ARS1620

first: Carmine

last: Fedele

first: Benjamin

middle: G

last: Neel


title: H3.3G34W promotes growth and impedes differentiation of osteoblast-like mesenchymal progenitors in Giant Cell Tumour of Bone [ChIP-Seq]

first: Nada

last: Jabado

state: Québec

address: 1001 Décarie Boulevard

department: Department of Pediatrics

summary: Glycine 34 to tryptophan (G34W) substitutions in H3.3 arise in ~90% of giant cell tumour of bone (GCT). Here, we show H3.3G34W is necessary for tumour formation. Profiling the epigenome, transcriptome and secreted proteome of patient samples and tumour-derived cells CRISPR/Cas9-edited for H3.3G34W shows that H3.3K36me3 loss on mutant H3.3 induces a shift of the repressive H3K27me3 mark from intergenic to genic regions, beyond areas of H3.3 deposition. This promotes the redistribution of antagonistic chromatin marks and aberrant downregulation of contractile myofibroblast-associated genes altering cell fate in mesenchymal progenitors. Single-cell transcriptomics reveals that H3.3G34W stromal cells recapitulate a neoplastic trajectory from an SPP1+ osteoblast progenitor-like population towards an ACTA2+ myofibroblast population, which secretes extracellular matrix ligands predicted to recruit and activate osteoclasts. Our findings suggest that H3.3G34W leads to GCT by sustaining a transformed state in osteoblast-like progenitors which promotes neoplastic growth, pathological recruitment of giant osteoclasts, and bone destruction.

overall_design: We performed ChIP sequencing of isogenic unedited H3.3G34W and isogenic clones where the mutant allele was KO or repaired to WT by CRISPR/Cas9 from two patient-derived cell lines.  We performed ChIP-seq of H3.3, H3.3G34W, H3K27ac, H3K27me3, H3K36me2, H3K36me3, H3K9me3, SUZ12.

first: Sima

last: Khazaei

first: Nicolas

last: De Jay

first: Shriya

last: Deshmukh

first: Liam

last: Hendrikse

first: Wajih

last: Jawhar

first: Carol

first: Leonie

last: Mikael

first: Damien

last: Faury

first: Dylan

last: Marchione

first: Joel

last: Lanoix

first: Éric

last: Bonneil

first: Takeaki

last: Ishii

first: Siddhant

middle: U

last: Jain

first: Kateryna

last: Rossokhata

first: Tianna

last: Sihota

first: Robert

last: Eveleigh

first: Véronique

last: Lisi

first: Ashot

middle: S

last: Harutyunyan

first: Sungmi

last: Jung

first: Jason

last: Karamchandani

first: Brendan

last: Dickson

last: Turcotte

first: Jay

last: Wunder

first: Pierre

last: Thibault

first: Peter

last: Lewis

last: Garcia

first: Stephen

last: Mack

first: Michael

last: Taylor

first: Livia

last: Garzia

first: Claudia

middle: L

last: Kleinman