title: RNA profiling of matched pair samples of primary breast cancer vs. lung and pleura metastasis

city: Heidelberg

first: Peter

last: Sinn

address: Im Neuenheimer Feld 224

department: Pathology

institute: University of Heidelberg

summary:
Patient samples were recruited from a series of female patients with metastatic primary breast cancer (PBC) and biopsy-confirmed breast cancer lung or pleural metastasis (BCLPM) at the Department of Thoracic Surgery, Thoraxklinik, Univ. of Heidelberg, Germany. All patients were included who had received lung or pleural metastasis biopsies from 2003 to 2014 and had a prior history of PBC at the Department of Gynaecology and Obstetrics, Univ. Hospital.
Formalin-fixed and paraffin-embedded tissue samples were provided by the Tissue Bank at the National Center for Tumor Diseases (NCT, Heidelberg, Germany) in accordance with the regulations of the Tissue Bank and approval of the Ethics Committee at the Medical Faculty of the Univ. of Heidelberg, approval no. S-716/2018.

overall_design: Retrospective cohort study


title: Adult Born Hippocampal Neurons Mount Unique Translational Changes in Response to Voluntary Running

status: Public on Sep 02 2020

city: Madison

first: Xinyu

last: Zhao

state: Wisconsin

address: 1500 HIghland Ave, Wiasman Center North Tower T513

country: USA

institute: University of Wisconsin Madison

type: Expression profiling by high throughput sequencing

summary: We report the genome-wide gene expression in adult born hippocampal neurons (at three different stages) in dentate gyrus of volentary running mice

overall_design: Examination of translatome of adult born hippocampal neurons in voluntary running mice

first: Yu

last: Gao


title: Transcriptomic profiling of substantia nigra and putamen in Parkinson’s disease

city: Nijmegen

first: Helena

last: Xicoy

address: Geert Grooteplein Zuid 10

country: Netherlands

institute: Radboudumc

summary: We report RNA sequencing results of human substantia nigra and putamen samples from Parkinson's disease patients and controls. Each substantia nigra sample is the result of pooling brain tissue from two individuals with the same , while each putamen sample is the result of pooling brain tissue from three individuals. We found 354 differentially expressed genes (DEGs) in the SN of PD patients compared to age-matched controls, while we observed 261 DEGs in the putamen samples. The top-enriched pathways from the SN were associated with “protein folding” and “neurotransmitter transport”, and the putamen DEGs with “synapse organization”. In summary, our data confirms the key role of protein folding and neuronal degeneration in the pathology of PD, and highlights new genes and pathways that have not yet been explored in the context of PD.

overall_design: RNA sequencing of substantia nigra and putamen samples from Parkinson's disease patients and controls

first: Bé

last: Wieringa

first: Gerard

middle: J

last: Martens


title: Transcriptomic analysis of IRAK4 in murine pancreatic cancer cells (KP2)

city: St. Louis

first: Kian-Huat

last: Lim

state: MO

address: 4566 Scott Avenue, Room 502

department: Internal Medicine/Oncology

institute: Washington University School of Medicine

summary: We perform CRISPR knockout of IRAK4 usig two different sgRNAs in murine KP2 cells, and then reexpressed murine IRAK4 in these two KO cell lines. We performed RNAseq on wild-type, IRAK4 KO and IRAK4 KO/rescue cell lines to investigate pathways contolled by IRAK4.

overall_design: RNAseq analysis of wild-type, IRAK4 KO and IRAK4 KO/rescue KP2 cells

first: Paarth

last: Dodhiawala


title: Signals controlling maintenance and differentiation of embryonic gastric epithelial progenitors

status: Public on Sep 04 2020

city: Mainz

first: Sergi

last: Sayols

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology, Mainz

summary: A dozen of cells expressing various marker genes was defined as adult gastric epithelial stem cells. Do these cells represent different cell types or they are just the same cell with cycling expression of different marker genes? The origin of the adult stem cells could answer this question. Yet, the identity of the embryonic gastric progenitors was not known. We performed single cell RNA-sequencing to characterize cellular composition of the embryonic stomach at the time of initiation of cytodifferentiation.  Our analysis of the scRNA-seq data led to identification of two different embryonic gastric epithelial progenitors. Further, we have defined signals that control their maintenance and differentiation along four main lineages, such as mucous pit, zymogenic, parietal and endocrine cells.

overall_design: Epithelial and mesenchymal cells were FACS isolated from stomachs of 39 mouse embryos at stage E13.5

first: Natalia

last: Soshnikova


title: Light-induced variation in phenolic compounds in Cabernet Sauvignon grapes (Vitis vinifera L.) involves extensive transcriptome reprogramming of biosynthetic enzymes, transcription factors, and phytohormonal regulators

city: Beijing

first: Run-Ze

last: Sun

address: No.20 Nanxincun, Xiangshan, Haidian District

department: Institute of Botany

country: China

institute: Chinese Academy of Sciences

summary: Light environments have long been known to influence grape (Vitis vinifera L.) berry development and biosynthesis of phenolic compounds, and ultimately affect wine quality. Here, the accumulation and compositional changes of hydroxycinnamic acids (HCAs) and flavonoids, as well as global gene expression were analyzed in Cabernet Sauvignon grape berries under sunlight exposure treatments at different phenological stages. Sunlight exposure did not consistently affect the accumulation of berry skin flavan-3-ol or anthocyanin among different seasons due to climatic variations, but increased HCA content significantly at véraison and harvest, and enhanced flavonol accumulation dramatically with its timing and severity degree trend. As in sunlight exposed berries, a highly significant correlation was observed between the expression of genes coding phenylalanine ammonia-lyase, 4-coumarate: CoA ligase, flavanone 3-hydroxylase and flavonol synthase family members and corresponding metabolite accumulation in the phenolic biosynthesis pathway, which may positively or negatively be regulated by MYB, bHLH, WRKY, AP2/EREBP, C2C2, NAC, and C2H2 transcription factors (TFs). Furthermore, some candidate genes required for auxin, ethylene and abscisic acid signal transductions were also identified which are probably involved in berry development and flavonoid biosynthesis in response to enhanced sunlight irradiation. Taken together, this study provides a valuable overview of the light-induced phenolic metabolism and transcriptome changes, especially the dynamic responses of TFs and signaling components of phytohormones, and contributes to the further understanding of sunlight-responsive phenolic biosynthesis regulation in grape berries.

overall_design:
In three consecutive years (2011-2013), eight fruit-zone light exposure levels were established in the vines through artificial leaf removal, half leaf removal, or leaf moving: leaf removal at berry pepper-corn size (LR-PS); leaf removal at véraison (LR-V); leaf removal after véraison (LR-AV); half leaf removal at véraison (HLR-V); half leaf removal after véraison (HLR-AV); leaf moving at véraison (LM-V); leaf moving after véraison (LM-AV); and non-treated control (C). Leaf removal and half leaf removal treatments were carried out by removing the first one to six basal leaves from the main shoots with clusters and three basal leaves from the first, third, and fifth of each shoot with clusters, respectively. For leaf moving treatment, the first one to six basal leaves of each shoot with clusters were moved aside by the use of nylon zipties, in order to increase the sunlight exposure of grape clusters without affecting the photosynthetic carbon assimilation to the fruit. Each treatment was arranged in a completely randomized experimental design with three biological replicates. In each biological replicate, treatment was applied to 15 vines randomly selected from the vineyard's south and north sites. Berries from each treatment and control group were sampled at the following developmental time points: 3 weeks after flowering (waf) (berry pepper-corn size; E-L 29), five waf (berry pea-size, E-L 31), seven waf (berry still hard and green, E-L 33), early-véraison (berries begin to color, E-L 35), mid-ripening stage (berries with intermediate Brix values, E-L 36), end of véraison (berries not quite ripe, E-L 37) and complete ripening stage (E-L 38). Based on biochemical parameters and metabolite profiles, we selected the berries of three developmental stages (E-L 36, 37, and 38) from the LR-V and LM-V treatments and the control group during the 2012 growing season to conduct the transcriptome profiling analysis.

Please note that GSM4762225-GSM4762233 are re-analysis of GSM3727972-GSM3727980 in GSE129916, respectively, and are the duplicated sample records for the convenient retrieval of the complete raw data from SRA.

first: Qiu-Hong

last: Pan

first: Chang-Qing

last: Duan

first: Jun

last: Wang


title: RNA-Seq analysis of Harlequin Ichrthyosis skin, HI 3D model ABCA12 CRISPR-Cas9 KO cell line

city: London

first: Florence

last: Enjalbert

state: London

address: 4 Newark Street

country: United Kingdom

institute: QMUL

summary:
The biology of Harlequin Ichthyosis (HI), a devastating skin disorder, caused by loss of function mutations in the gene ABCA12, is poorly understood and to date no satisfactory treatment has been developed. We sought to investigate pathomechanisms of Harlequin Ichthyosis which could lead to the identification of safe and effective treatments to improve patients' quality of life. RNA-Seq analysis using normal skin (n=5) and HI patient skin (n=4) were performed to define the effects of loss of ABCA12. Functional annotation clustering analysis showed changes in three common groups: epidermal differentiation, lipid metabolism and inflammation (innate immunity and IFNγ signalling). In HI patient skin, gene expression of STAT1, STAT3 and Interleukin 36 (IL-36) A and G cytokines was significantly upregulated compared to normal skin, whereas IL-37, an inhibitor of innate immunity, was downregulated.
RNA-Seq and functional assays were performed to define the effects of loss of ABCA12, using an engineered CRISPR-Cas9 ABCA12 KO 3D model. Functional annotation clustering analysis showed changes in three common groups: epidermal differentiation, lipid metabolism and inflammation.

overall_design:
RNASeq Analysis of Harlequin Ichthyosis patient skin and normal skin
RNA-Seq analysis of HI 3D model ABCA12 CRISPR-Cas9 KO cell line

first: Anton

last: Enright

first: Edel

last: O'Toole


title: Drug screen combining RNA landscape analysis reveals targetable pathways in HIV-1 reactivation

city: New Haven

first: Yang-Hui

last: Yeh

state: CT

address: 295 Congress Ave.

department: Microbial Pathogenesis

institute: Yale University

summary: We invesitgated cellular pathways required for HIV-1 activation using HIV-1-suppressing agents. Despite effective antiretroviral therapy, HIV-1-nfected cells continue to produce viral antigens and induce chronic immune exhaustion. Using a novel dual reporter system and a high-throughput drug screen, we identified FDA-approved drugs which can suppress HIV-1 reactivation in both cell line models and CD4+ T cells from virally suppressed, HIV-1-infected individuals. We identified 11 cellular pathways required for HIV-1 reactivation as druggable targets. Using differential expression analysis, gene set enrichment analysis and exon-intron landscape analysis, we examined the impact of drug treatment on the cellular environment at a genome-wide level.

overall_design: Drugs treatment of HIV-1-infected T cell clones and CD4+ T cells from HIV-1-infected individual under long term suppressive ARTs for 24 hours. Transcriptome analysis was performed on bulk mRNA from treated samples

first: Ya-Chi

last: Ho


title: Genome-wide miRNA and protein coding expression of Danaus plexippus fed on three different hosts.

status: Public on Sep 03 2020

city: irapuato

first: Pablo M.

last: Gonzalez-De-la-Rosa

state: guanajuato

address: Km. 9.6 Libramiento Norte Carr. Irapuato-León

department: Langebio

country: Mexico

institute: Cinvestav

type: Non-coding RNA profiling by high throughput sequencing

summary: Second instar larvae of the monarch butterfly, Danaus plexippus, from a nonmigratory population in Irapuato, Mexico, were reared for twenty-four hours on three species of milkweed hosts: Asclepias curassavica, A. linaria, and Gomphocarpus physocarpus. The greatest differences in coding gene expression occurred in genes controlling growth and detoxification and were most extreme in comparisons between G. physocarpus and the two Asclepias. MicroRNAs are predicted to be involved as regulators of many of these processes, in particular miR-278 could be an important regulator of growth through Hippo signaling.

overall_design: 9 poly(A) and 9 sRNA libraries were prepared from Danaus pleixppus second instar larvae after feeding for 24 hours on three different hosts to identify genes potentially involved in host specificity.

first: Pablo

middle: M

first: Mariana

middle: R

last: Loustalot-Laclette

first: Cei

last: Abreu-Goodger

first: Therese

middle: A

last: Markow


title: Primary normal human bronchial epithelial cells (NHBE) cultured at air liquid interface with or without macrophage cells (+/- Mac) derived from primary peripheral blood mononuclear cells

city: Richland

first: Natalie

last: Heller

address: 902 Battelle Blvd.

institute: PNNL

summary: The purpose is to obtain samples for mRNA analysis in primary normal human bronchial epithelial cells cultured with or without macrophage cells (+/- Mac) derived from primary peripheral blood monnumclear cells

overall_design: Influenza A/Vietnam/1203/2004 (H5N1, VN1203) or influenza A/California/04/2009 (H1N1, CA04) viral stocks were used to infect NHBE cells at a multiplicity of infection (MOI) of 1. Infections were allowed to progress for 1 hour. Next, 500,000 peripheral blood mononuclear cell (PBMC)-derived macrophages were place onto each apical transwell surface in a final volume of 500 ul to create co cultures. The co-cultures at a ratio of approximately 2 NHBE cells for every PBMC-derived macrophage were allowed to progress for an additional 11, 15 and 23 hours respectively (12, 16, 24 hours post-infection). An n=5 was used for each condition, which included infection with either H1N1, H5N1, or mock uninfected, of either NHBE-only monocultures or NHBE + PBMC-macrophage co-cultures. In total this infection scheme represented a total of 90 samples for microarray analysis. At the specified time points, 1 ml of TRlzol RNA isolation reagent (Thermo Fischer, 15596-016) that lead to inactivation of samples.

first: Josh

last: Powell

first: Katrina

last: Waters

first: Yoshihiro

last: Kawaoka


title: FOXO1 and FOXO3

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

institute: msterdam UMC and University of Amsterdam

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

overall_design: Refer to individual Series


title: Expression data of the human multiple myeloma cell line XG-3 after AKT inhibition in a FOXO3 deficient background

summary:
Forkhead box O transcription factors are important downstream targets of AKT signalling. In the human Multiple Myeloma celline XG-3, AKT inhibtion leads to cell death in a FOXO3 dependent fashion.
We used microarrays to asses which genes are up- or downregulated by FOXO3 after AKT inhibition by MK2206.

overall_design: Crispr Cas9 generated FOXO3 KO or Cas9 only Control clones were generated using the pl-CRISPR.EFS.GFP vector and subsequently sorted (GFP positive) and testing FOXO3 expression by Western Blot. 2 cas 9 only and 2 FOXO3 KO clones were treated O/N with an AKT inhibitor after which gene expression was analyzed.

first: T

last: Bloedjes

first: J

last: Guikema


title: Expression data of the human multiple myeloma cell line MM1.S after AKT inhibition in a FOXO3 deficient background

summary:
Forkhead box O transcription factors are important downstream targets of AKT signalling. In the human Multiple Myeloma celline MM1.S, AKT inhibtion leads to cell death in a FOXO3 dependent fashion.
We used microarrays to asses which genes are up- or downregulated by FOXO3 after AKT inhibition by MK2206.


title: Expression data of the human multiple myeloma cell line LME-1 after AKT inhibition in a FOXO1 deficient background

summary:
Forkhead box O transcription factors are important downstream targets of AKT signalling. In the human Multiple Myeloma celline LME-1 AKT inhibtion leads to cell death in a FOXO1 dependent fashion.
We used microarrays to asses which genes are up- or downregulated by FOXO1 after AKT inhibition by MK2206.

overall_design: Crispr Cas9 generated FOXO1 KO or Cas9 only Control clones were generated using the pl-CRISPR.EFS.GFP vector and subsequently sorted (GFP positive) and testing FOXO1 expression by Western Blot. 2 cas 9 only and 2 FOXO1 KO clones were treated O/N with an AKT inhibitor after which gene expression was analyzed.


title: Glucocorticoids enhance the anti-leukemic activity of FLT3 inhibitors in FLT3 mutant acute myeloid leukemia

city: Hershey

first: Melat

middle: T

last: Gebru

state: PA

address: 95A University Manor East

department: Pediatrics

institute: Penn State University

summary: Utilizing genome wide transcriptome analysis and drug screen we demonstrate that upregulation of inflammatory pathways is a key mechanism of drug tolerance to FLT3 targeted inhibitors in AML

overall_design: Performed RNA-seq after isolating cells that survive treatment with DMSO or quizartinib for 48h or after recovery in drug free media for 13 or 30 days. Another set of RNA-seq was performed using cells that survive treatment with DMSO, dexamethasone, quizartinib or the combination of quizartinib and dexamethasone for 48h or 5 days(in the case of combination tretment for 5days quizartinib was kept for 5 days but dexemethasone was added on Day 3).

first: Hong

middle: G

last: Wang


title: Aurora B phosphorylates hnRNP U/SAF-A to facilitate XIST RNA removal from the inactive X chromosome during mitosis

city: Boston

first: Michael

middle: Demian

last: Blower

state: MA

address: 185 Cambridge St CPZN-7250

department: Molecular Biology

institute: Massachusetts General Hospital

summary: We show that Aurora-B phosphorylates heterogeneous nuclear ribonucleoprotein U (hnRNP U) in the SAP domain to dissociate hnRNP U from chromatin during mitosis. We use RNA-seq to show that hnRNP U associates with hundreds of mRNAs and lncRNAs during interphase and mitosis.

overall_design: Identification of hnRNP U-enriched RNAs using immunoprecipitation and RNA-seq in retinal pigment epithelium (RPE) cells.

first: Judith

last: Sharp


title: Human CXCR5+CD45RA-CD8+ T cells subset in follicular lymphoma

city: Houston

first: Wencai

last: Ma

address: 7455 Fannin st

institute: MD Anderson Cancer Center

summary: We demonstrate that CXCR5+CD8+ T cells are a distinct human T-cell subset that homes to follicles and exerts strong antitumor activity compared with CXCR5-CD8+ T cells. Importantly, this subset is associated with improved outcome in follicular lymphoma patients.

overall_design: Total RNA from FACS-sorted CD45RA+CD8+, CXCR5-CD45RA-CD8+, and CXCR5+CD45RA-CD8+ T cells from human tonsil samples were extracted using Trizol, followed by purification using NucleoSpin RNA XS kit. Tonsils come from tonsillectomy; these patients do not have follicular lymphoma.

first: Fuliang

last: Chu

first: Haiyan

middle: S

last: Li

first: Sattva

last: Neelalpu


title: Gene expression response in human peripheral blood exposed to mixed neutron-photon radiation ex vivo

city: New York

first: Sanjay

last: Mukherjee

state: NY

address: 630 W 168th street

institute: Columbia University

summary: In the current global scenario there is always a possibility that a terrorist group might acquire material to produce a nuclear device. In the likelihood of a detonation of an improvised nuclear device (IND) the prompt radiation would consist of both photons (gamma rays) and neutrons. As neutrons generally have a high Relative Biological Effectiveness (RBE) for most physiological endpoints, it is important to understand the impact that neutrons would have on the biodosimetry methods that are being developed for medical triage purposes. We have previously reported transcriptomic response in human and mouse blood to neutron exposure and determined its RBE compared to photons for gene induction. In this report, we studied the effect of mixed neutron-photon radiation on gene expression in human peripheral blood in order to mimic an IND type radiation   observed increase in number as well as expression level of genes with increasing percentage of neutron in mixed exposures which peaked at 25% neutron exposure which was maximum neutron percentage used for the study.  We identified 156 genes that responded significantly to all the neutron-photon mixed exposures. These genes were found to be mainly involved in p53 signaling and DNA damage response. The 25% neutron exposure also showed maximum enrichment of known neutron associated gene ontology terms reported in the previous studies. Analysis of upstream regulators of gene expression showed strong activation of TP53, SLC29A1, PDCD1 and suppression of ANLN, AURK and ANXA2 across all exposures. While AGT was exclusively activated by neutron specific exposures. We confirmed the expression of genes which showed increased expression as a function of increased neutron percentage using quantitative real-time RT-PCR which matched with the microarray data. Thus, the data in this current study clearly indicates that gene expression can be used to estimate the percentage of the neutron component in mixed neutron-photon exposures.

overall_design: Human blood in Sodium-citrate tube was irradiated to six different neutron-photon mixed exposures to a cumulative dose of 3 Gy with differing percentages of neutrons (0%,5%,15%,25% and maximum neutron)

first: S

last: Amundson


title: Comprehensive analysis of Transcriptome Profiles in Hepatocellular Carcinoma patients

city: Singapore

first: Caroline

last: Lee

address: 12 Science Drive 2

country: Singapore

institute: National University of Singapore

summary:
Purpose: The goal of this study is to get a comprehensive evaluation of the transcriptome profile of HCC patients
Methods:Transcriptome profiles of paired Tumor and adjacent non-tumour from 25 HCC patients were generated by deep sequencing using the Illumina HiSeq 2000 platform. Paired sample T-test was used to identify differentially expressed genes between Tumours and adjacent non-Tumours.
Results: A total of 4462 genes are differentially expressed genes between tumours and adjacent non-tumours
Conclusions: Characterization of the transcriptome profiles of HCC patients reveals key genes and pathways that are deregulated in HCC patients.

first: Yu

last: Jin

first: Wai

middle: Y

first: Soo

last: Toh

first: C

last: Tennakoon

first: Han

middle: C

first: Pierce

middle: K

last: Chow

first: Alexander

last: Chung

first: London

middle: L

last: Ooi

first: W

last: Sung


title: BMPR2 Regulates Hypoxic Exosome Signaling to Maintain Vascular Homeostasis

status: Public on Sep 01 2020

city: Stanford

first: Marlene

last: Rabinovitch

state: California

address: 269 Campus Drive CCSR Building, Room 1215A

institute: Stanford

summary: Endothelial cells (EC) sense stimuli in the circulation and release responsive signaling molecules to coordinate the multicellular adaptations required to maintain vascular homeostasis. The goal of this study were to analyze the transcriptional changes induced by hypoxia in control donor pulmonary arterial endothelial cells and the effect of loss of BMPR2 that is associated with pulmonary arterial hypertension.

overall_design: 24 samples analyzed, 2 biolgoical and 2 technical replicates, siBMPR2 or siControl treated, 3 timepoints of hypoxia treatment (0, 6, 24 hours).

first: James

last: Chappell

first: David

middle: P

last: Marciano

first: Michael

last: Snyder


title: circRNA-sequencing of Chiloscyllium plagiosum liver

city: hangzhou

first: wenjie

last: zhang

address: xuelin street

institute: Zhejiang Sci-Tect University

summary: circRNA sequencing for 1 samples..

overall_design: Examing 1 liver sample with no replicates

first: Lei

last: Wang

first: Zhengbing

last: Lv


title: Comparative analysis of “Jinyan” and “Hongyang” kiwifruit transcriptomes

city: Jishou

first: Gui-Sheng

last: Li

address: 120 Renmin South Street

institute: Jishou University

summary: to understand molecular mechanism of ripening of kiwifruits, to obtain differentially expressed genes and to acquire the predicted functions

overall_design: using 12 samples to explore differences between two kiwifuits and differences between the fruit periphery and the flesh core


title: Atopic dermatitis displays stable and dynamic skin transcriptome signatures

city: Tampere

first: Lena

last: Möbus

address: Arvo Ylpön katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

summary: To gain a deeper understanding of the atopic dermatitis (AD) skin transcriptome and the effects of systemic treatment with dupilumab and cyclosporine, we conducted a gene expression study of AD using mRNA-Seq data generated from lesional and non-lesional skin biopsies collected from patients included in the TREATgermany registry. We are able to provide deep characterisation of AD skin transcriptomic signatures by using an assortment of bioinformatic approaches such as differential expression, co-expression network and pathway enrichment analysis.

overall_design: We performed mRNA sequencing of 166 skin transcriptomes obtained from 57 patients with moderate to severe AD recruited in the TREATgermany registry between July 2017 and February 2019 at six out of 17 study centres which agreed to participate in the additional and optional bioanalytics module. Intrapersonal lesional (AL) and non-lesional (AN) skin biopsies (4 mm) were collected from 57 patients prior to the initiation of a systemic therapy. Follow-up biopsies 3 months after the initiation of systemic treatment were available from 21 (dupilumab) and 8 (cyclosporine) patients. Non-lesional samples were taken at least 5 cm from the active lesion.

first: Stephan

last: Weidinger

first: Jochen

last: Schmitt

first: Thomas

last: Werfel

first: Elke

last: Rodriguez


title: The Ecdysone Receptor Coactivator Taiman Links Yorkie to Transcriptional Control of Germline Stem Cell Factors in Somatic Tissue

city: Atlanta

first: Bing

last: Yao

address: 615 Michael Street

department: Department of Human Genetics

institute: Emory University

summary: The Hippo pathway is a conserved signaling cas- cade that modulates tissue growth. Although its core elements are well defined, factors modulating Hippo transcriptional outputs remain elusive. Here we show that components of the steroid-responsive ecdysone (Ec) pathway modulate Hippo transcrip- tional effects in imaginal disc cells. The Ec receptor coactivator Taiman (Tai) interacts with the Hippo transcriptional coactivator Yorkie (Yki) and promotes expression of canonical Yki-responsive genes. Tai enhances Yki-driven growth, while Tai loss, or a form of Tai unable to bind Yki, suppresses Yki-driven tissue growth. This growth suppression is not corre- lated with impaired induction of canonical Hippo- responsive genes but with suppression of a distinct pro-growth program of Yki-induced/Tai-dependent genes, including the germline stem cell factors nanos and piwi. These data reveal Hippo/Ec pathway crosstalk in the form a Yki-Tai complex that collabo- ratively induces germline genes as part of a tran- scriptional program that is normally repressed in developing somatic epithelia.

first: Ken

last: Moberg

first: Yangping


title: Myosin 7b is a regulatory long noncoding RNA (lncMYH7b) in the human heart

city: Boulder

first: Lindsey

middle: Joe

last: Broadwell

state: CO

address: 3415 Colorado Avenue, Apt, Suite, Bldg. (optional)

department: Biochemistry

institute: University of Colorado Boulder

summary: We have discovered that the alternative splice form of MYH7b is a regulatory non-coding RNA in the human heart. This dataset contains manipulation of levels of lncMYH7b in human cardiomyocytes.

overall_design: Human induced pluripotent stem cells differentiated to cardiomyocytes and treated with antisense oligonucleotides against MYH7b.


title: RNA-Seq of the different life history stages in Bostrychia moritziana (male gametophyte, female gametophyte, tetrasporophyte)

city: 56, Gongjudaehak-ro, Gongju-si, Republic of Korea

first: EUNYOUNG

last: SHIM

address: Department of Biological Sciences 205

country: South Korea

institute: Kongju National University

summary: Diverse sex determination mechanisms have been reported in eukaryotes, but little is known about the genetic pathways leading to sex determination in red algae. Sex-specific genes that could be involved in sex determination and sexual differentiation were investigated in a red alga Bostrychia moritziana by analyzing the transcriptomes of various phases including males, females and tetrasporophytes. Sex-dominantly-expressed genes which shows >10 fold difference between sexes were isolated using comparative RNA-seq analysis. We found 19 gene homologues, 10 from males and 9 from females, that were found only in one sex in genomic amplification. This suggests that these divergent homologues are on non-recombining, possibly different, chromosomes in their respective sexes. Most of the sex-specific genes are involved in important cellular processes including chromosome segregation, nucleo-cytoplasmic protein shuttling or tRNA modification. Quantitative PCR analysis also showed that some sex-specific genes were differently regulated during critical events of sexual reproduction like fertilization and carposporophyte development. We could also localize the expression of a male-specific gene in spermatia before and after gamete binding using RNA in situ hybridization. Another set of transcripts were found that were sex-dominantly-expressed, but not sex-specific. 19 out of 39 sex-dominantly-expressed transcripts were annotated to transposable elements, but none of them was sex-specific. Our results suggest that sexual differentiation in B. moritziana may be achieved by multi-level regulation of cellular processes, both from genes present only in one sex and differential expression of shared genes.

overall_design: Transcriptomic analysis of various phases in red alga Bostrychia.

first: Gwang

middle: H

last: Kim

first: Eunyoung

last: Shim

first: Giuseppe

last: Zuccarello

first: John

last: West


title: Gene expression profiling of Control and Low BCAA fed aged mouse muscle

city: Madison

first: Nicole

middle: Elise

last: Richardson

state: WI

address: 2500 Overlook Terr VA Hospital C3127 Research 151

department: Medicine

institute: University of Wisconsin Madison

summary: Transcriptome analysis of RNA samples from quadriceps muscle to understand how restricting dietary BCAAs influences muscle gene expression

overall_design: RNA-Seq experiments were conducted on total RNA isolated from quadriceps muscle of aged mice of both sexes fed a Control or Low BCAA diet until 16 months of age

middle: E

first: Dudley

middle: W

last: Lamming


title: Liver-specific knockdown of class IIa HDACs has limited efficacy on glucose metabolism but entails severe organ side effects in mice

city: Frankfurt am Main

first: Daniel

last: Margerie

address: Industrial Park Hoechst, Building H831

department: R&D, Digital Data Sciences

institute: Sanofi-Aventis Deutschland GmbH

summary: Histone deacetylases (HDACs) are important regulators of epigenetic gene modification that are involved in the transcriptional control of metabolism. In particular class IIa HDACs have been shown to affect hepatic gluconeogenesis and previous approaches revealed that their inhibition reduces blood glucose in type 2 diabetic mice. In the present study, we aimed to evaluate the potential of class IIa HDAC inhibition as a therapeutic opportunity for the treatment of metabolic diseases. For that, siRNAs selectively targeting HDAC4, 5 and 7 were selected and used to achieve a combinatorial knockdown of these three class IIa HDAC isoforms. Subsequently, the hepatocellular effects as well as the impact on glucose and lipid metabolism were analyzed in vitro and in vivo. The triple knockdown resulted in a statistically significant decrease of gluconeogenic gene expression in a murine hepatic cell line as well as in human primary hepatocytes. Despite a similar HDAC-induced downregulation of hepatic genes involved in gluconeogenesis in mice using a liver-specific lipid nanoparticle siRNA formulation, the in vivo effects on whole body glucose metabolism were only limited and did not outweigh the safety concerns observed by histopathological analysis in spleen and kidney. Mechanistically, Affymetrix gene chip analysis and gene expression studies provide evidence that class IIa HDACs directly target and thus regulate the expression of HNF4α and FOXP1 in the liver, thereby modifying gene regulatory mechanisms mediating glucose and lipid metabolism and transport.  In conclusion, the combinatorial knockdown of HDAC4, 5 and 7 by therapeutic siRNAs affected multiple pathways in vitro and in vivo leading to the downregulation of genes involved in gluconeogenesis. However, the effects on the gene expression level were not paralleled by a significant reduction of gluconeogenesis in mice, as shown in pyruvate tolerance tests. However, the liver-specific inhibition of these HDAC isoforms was associated with severe adverse effects in vivo, making this approach not a viable treatment option for chronic metabolic disorders like type 2 diabetes.

overall_design: Four different groups of HDAC siRNA treatments with 4 replicate samples each were compared to four replicate LV3 (scrambled siRNA) control samples

last: Ziegler

first: Maximilian

last: Bielohuby

first: Paulus

last: Wohlfart


title: Identification of sites bound by c-Jun and JunB transcription factors in the Karpas 299 ALK+ ALCL cell line

city: Edmonton

first: Robert

middle: J

last: Ingham

state: Alberta

address: Katz Building

department: Medical Microbiology and Immunology

country: Canada

institute: University of Alberta

type: Genome binding/occupancy profiling by high throughput sequencing

summary: In order to identify sites bound by c-Jun/JunB in ALK+ ALCL, we performed ChIP-Seq on the Karpas 299 ALK+ ALCL cell line.

overall_design: Karpas 299 cells grown to exponential phase and cell pellets were sent to Active Motif (Carlsbad, CA) for ChIP-Seq analysis to identify sites bound by the c-Jun and JuNB transcription factors. Sequences were aligned to the hg19 build of the human genome and peak calling was done with MACS 2.1.0.50.

first: Zuoqiao

last: Wu


title: Microarray analysis of Lynx1 modulation in human PDAC cell lines

city: Heidelberg

first: Martin

middle: R

last: Berger

address: INF 581

institute: DKFZ

summary: A microarray was performed in order to screen the changes in gene expression following Lynx1 knockdown in 2 human PDAC cell lines Miapaca and BXPC3 and using two specific siRNA to Lynx1

overall_design: Two different siRNAs (Invitrogen, Germany) were used to modulate  Lynx1 expression. These were siRNALynx1-ORF directed toward the open reading frame tested in both Miapaca and BXPC3 and 3’ prime untranslated region (siRNALynx1-3’UTR) tested in Miapaca cells in comparison to a non targeting siRNA as a control used in the respective cell lines

first: Doaa

middle: M

last: Ali


title: ELAVL1 Primarily Couples mRNA Stability with the 3'UTRs of Interferon Stimulated Genes

city: Nashville

first: Manuel

last: Ascano

state: TN

address: 2215 Garland Avenue

institute: Vanderbilt University

summary: Upon detection of a pathogen, the innate immune system triggers signaling events leading to the transcription of mRNAs that encode for pro-inflammatory and anti-microbial effectors. RNA-binding proteins (RBPs) interact with these functionally critical mRNAs and temporally regulate their fates at the post-transcriptional level. One such RBP is ELAVL1, which is known to bind to introns and 3’UTRs. While significant progress has been made in understanding how ELAVL1 regulates mRNAs, how its target repertoire and binding affinity changes within an immunological context remains poorly understood. Here, we overlap four distinct high-throughput approaches to define its cell-type and context-dependent targets and determine its regulatory impact during immune activation. ELAVL1 overwhelmingly binds to intronic sites in a naïve state, but during an innate immune response, ELAVL1 targets the 3’UTR  binding both previously and newly expressed mRNAs. We find that ELAVL1 mediates the RNA stability of genes that regulate the pathways involved in pathogen sensing and cytokine production. Our findings reveal the importance of examining RBP regulatory impact under dynamic transcriptomic events to best understand their post-transcriptional regulatory roles within specific biological circuitries.

overall_design: Four independent high-throughput datasets were integrated to determine the ELAVL1-depedent transcripts during innate immune response. PAR-CLIP, RIP-Seq, and SLAM-Seq samples have two biological replicates; whereas, RNA-Seq has three biological replicates.

first: Katherine

last: Rothamel


title: miRNA profiling of biliary intraepithelial neoplasia reveals step-wise tumorigenesis in distal cholangiocarcinoma via the miR-451a/ATF2 axis

city: Mannheim

first: Carolina

last: Delatorre

address: Theodor-Kutzer-Ufer 1-3

institute: University Heidelberg

summary: Distal cholangiocarcinoma (dCCA) is a biliary tract cancer with dismal prognosis and is often preceded by biliary intraepithelial neoplasia (BilIN) as a non-invasive precursor lesion. We found that miR-451a is downregulated in dCCA. Overexpression of mimic-451a in the CCA cell line SNU478 revealed multiple downregulated genes and potential miR-451a candidate targets.

overall_design: The CCA cell line SNU478 was transfected with AllStars control or mimic-451a miRNA in quadruplicates and cultured for 48 h. Thereafter, cells were harvested and RNA was isolated followed by human Clariom_D microarray analysis.

first: Stephanie

last: Roessler


title: Use of mice defective in interferon signaling to distinguish between primary and secondary pathological pathways in a mouse model of neuronal forms of Gaucher disease

city: Rehovot

first: Ayelet

last: Vardi

state: Hamerkaz

address: Herzl St 234

country: Israel

institute: Weizmann Institute of science

summary: The type 1 interferon (IFN) response is part of the innate immune response and best known for its role in viral and bacterial infection. However, this pathway is also induced in sterile inflammation such as occurs in a number of neurodegenerative diseases, including neuronopathic Gaucher disease (nGD), a lysosomal storage disorder (LSD) caused by mutations in Gba1.  Mice were injected with conduritol B-epoxide, an irreversible inhibitor of acid-beta glucosidase, the enzyme defective in nGD. Quadrat deficient MyTrMaSt mice, where four adaptors of pathogen recognition receptors (PRRs) are deficient, were used to determine the role of the IFN pathway in nGD pathology. Activation of inflammatory and other pathways was analyzed by a variety of methods including RNAseq. Elevation in the expression of PRRs associated with the IFN response was observed in CBE-injected mice. Ablation of upstream pathways leading to IFN production had no therapeutic benefit on the lifespan of nGD mice but attenuated neuroinflammation. Primary and secondary pathological pathways, i.e. those associated or not with mouse lifespan, were distinguished, and a set of ~210 genes including those related to sphingolipid, cholesterol and lipoprotein metabolism, along with a number of inflammatory pathways related to chemokines, TNF, TGF, complement, IL6 and damage associated pathogens were classified as primary pathological pathways, along with some lysosomal and neuronal genes. Although IFN signaling is the top elevated pathway in nGD, we demonstrate that this pathway is not related to mouse viability and is consequently defined as a secondary pathology pathway. By elimination, we defined a number of critical pathways that are directly related to brain pathology in nGD, which in addition to its usefulness in understanding pathophysiological mechanisms may also pave the way for development of novel therapeutic paradigms by targeting such pathways.

overall_design: WT mice brains and MyTrMaSt null brains, injected with conduritol B-epoxide (CBE) to induce Gaucher disease, were examined at 19 days. Brains were compared to WT or MyTrMaSt null brains injected with PBS.

first: Anthony

last: Futerman


title: Bulk RNA-sequencing analysis of isogenic murine Kras/p53 (KP) Brg1 wildtype cells versus Brg1 knockout (KPB) cells

city: Boston

first: Manav

last: Gupta

state: MASSACHUSETTS

address: 1 Blackfan Circle

department: Genetics

institute: Harvard University

summary: The goals of this experiment is to identify transcriptomic changes upon loss of Brg1 in lung adenocarcinoma cells.

overall_design: Kras/p53 lung adenocarcinoma tumor derived cell lines were subjected to CRISRP/Cas9-mediated genome editing using guides against sgTomato (control) or sgBrg1 (sample). Isogenic Kras/p53 mutant lung cancer cell lines with and without Brg1 were derived and used for bulk RNA-sequencing. Experiment was performed in triplicate conditions.

first: Christine

middle: F

last: Brainson

first: Francisco

last: Sanchez-Rivera

first: Arjun

last: Bhutkar


title: Inhibition of histone H3K27 demethylases inactivates brachyury (TBXT) and promotes chordoma cell death (ChIP-seq)

city: Oxford

first: Adam

last: Cribbs

address: Windmill Road

department: NDORMS

institute: University of Oxford

summary: Expression of the transcription factor brachyury (TBXT) is normally restricted to the embryo and its silencing is epigenetically regulated. TBXT promotes mesenchymal transition in a subset of common carcinomas, and in chordoma, a rare cancer showing notochordal differentiation, TBXT acts as a putative oncogene: we hypothesised that TBXT expression could be controlled through epigenetic inhibition to promote chordoma cell death. Screening of five human chordoma cell lines revealed that pharmacological inhibition of the histone 3 lysine 27 demethylases KDM6A (UTX) and KDM6B (JMJD3) leads to cell death. This effect was phenocopied by the dual genetic inactivation of KDM6A/B using CRISPR/Cas9. Inhibition of KDM6A/B using a novel compound, KDOBA67, led to a genome-wide increase in repressive H3K27me3 marks, with concomitant reduction in H3K27ac, H3K9ac and H3K4me3 active marks. We show that TBXT is a KDM6A/B target gene, and that changes in the chromatin at TBXT following KDOBA67 treatment were associated with a reduction in TBXT protein levels in all models tested, including primary patient-derived cultures. KDOBA67 downregulated also the expression of a network of transcription factors critical for chordoma survival, whereas upregulated pathways were dominated by ATF4-driven stress and pro-apoptotic responses in all models. Blocking the AFT4-stress response did not prevent the suppression of TBXT and induction of cell death, but viability was increased by ectopic overexpression of TBXT, therefore implicating TBXT as potential therapeutic target of H3K27 demethylases inhibitors. Our work highlights how knowledge of normal processes in fetal development can provide insight into tumourigenesis and identify novel therapeutic approaches.

overall_design: UCH1 chordoma cell line profiled for H3K27me3, H3K4me3, H3K27ac and H3K9ac binding using spike-in calibrated cross-linked ChIP-seq, in the presence of DMSO or KDOBA67.

first: Adrienne

last: Flanagan

first: Lucia

last: Cottone


title: Transcriptomic signature of fasting in human adipose tissue

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

summary: Little is known about the impact of fasting on gene regulation in human adipose tissue. Accordingly, the objective of this study was to investigate the effects of fasting on adipose tissue gene expression in humans. To that end, subcutaneous adipose tissue biopsies were collected from volunteers 2h and 26h after consumption of a standardized meal. For comparison, epididymal adipose tissue was collected from C57Bl/6J mice after a 16h fast and in the ab-libitum fed state. Transcriptome analysis was carried out using Affymetrix microarrays. We found that, 1) fasting downregulated numerous metabolic pathways in human adipose tissue, including triglyceride and fatty acid synthesis, glycolysis and glycogen synthesis, TCA cycle, oxidative phosphorylation, mitochondrial translation, and insulin signaling; 2) fasting downregulated genes involved in proteasomal degradation in human adipose tissue; 3) fasting had much less pronounced effects on the adipose tissue transcriptome in humans than mi  ce; 4) although major overlap in fasting-induced gene regulation was observed between human and mouse adipose tissue, many genes were differentially regulated in the two species, including genes involved in insulin signaling (PRKAG2, PFKFB3), PPAR signaling (PPARG, ACSL1, HMGCS2, SLC22A5, ACOT1), glycogen metabolism (PCK1, PYGB), and lipid droplets (PLIN1, PNPLA2, CIDEA, CIDEC). In conclusion, although numerous genes and pathways are regulated similarly by fasting in human and mouse adipose tissue, many genes show very distinct responses to fasting in humans and mice. Our data provide a useful resource to study adipose tissue function during fasting.

overall_design:
Microarray analysis was performed on subcutaneous adipose tissue biopsies from the periumbilical area under local anesthesia, two hours after consumption of a standard meal (fed state), and twenty-four hours later and thus 26 hours after consumption of the standard meal (fasted state):
Twenty-four healthy volunteers aged 40-70 years with a BMI of 22-30 kg/m2 were included in the FASTING study. At the start of the study the volunteers consumed a standardized meal until full (ad libitum), consisting of 22 energy% protein, 24 energy% fat, 51 energy% carbohydrate and 476 kJ per 100 gram. After consumption of the standardized meal subjects were not allowed to eat but could drink water for the next 26 hours. Two hours after consumption of the meal, blood samples were taken and a subcutaneous adipose tissue biopsy was collected representing the fed state. Twenty-four hours later and thus 26 hours after consumption of the meal, a second blood sample and subcutaneous adipose tissue biopsy was collected, representing the fasting state. The subcutaneous adipose tissue samples were obtained by needle biopsy from the periumbilical area under local anesthesia.

first: Merel

last: Defour

first: Charlotte

last: Michielsen

first: Lydia

middle: A

last: Afman

first: Sander

last: Kersten


title: Adipose Tissue Macrophage Accrual in Obesity

city: Durham

first: Rana

state: North Carolina

address: Carmichael Building, 300 North Duke St.

department: Duke Molecular Physiology Institute

institute: Duke University

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

overall_design: Refer to individual Series


title: Whole lung gene expression from naïve Bpifb1 WT and KO mice

city: Chapel Hill

first: Samir

last: Kelada

state: NC

address: 120 Mason Farm Road GMB 5007

institute: University of North Carolina at Chapel Hill

summary: We performed RNAsequencing on whole lung tissue from naïve Bpifb1 WT and KO mice.

overall_design: Test for differential expression due to loss of Bpifb1

first: Lauren

last: Donoghue


title: Single-cell sequencing reveals heterogeneity effects of bisphenol A on zebrafish embryonic development

city: Nanjing

first: Chen

last: Ling

address: 163 Xianlin Avenue

institute: Nanjing University

summary: Embryonic period is sensitive window of bisphenol A (BPA) exposure. However, embryonic development is a highly dynamic process with changing cell populations and gene expression profiles. Heterogeneity effects of BPA on fish embryonic development remain not clear. This study applied single-cell RNA sequencing to analyze the impact of BPA exposure on transcriptome heterogeneity of 64683 cells from zebrafish embryos at 8, 12 and 30 hpf. A total of 38 cell populations were identified, and gene expression profiles of 16 cell populations were significantly altered by BPA exposure. The strongest toxic effects of BPA were found at 12 hpf of segmentation stage, which is an active stage of cell differentiation. At 8 hpf, BPA mainly influenced the outer layer cell populations of embryos, such as neural plate border and enveloping layer cells. At 12 and 30 hpf, nervous system formation and heart morphogenesis were disturbed. Differential process of neural plate border, neural crest, and neuron cells was altered, leading to increased neurogenesis. For the forebrain, midbrain, neurons, and optic cells, the altered cell division and DNA replication and repair were identified. Our study for the first time provides the comprehensive understanding of BPA toxicity on fish embryo development at single-cell levels.

overall_design: Single cell RNA sequencing were adopted to learn the transcriptional variation in zebrafish embryonic development following exposure to bisphenol A at different stage (gastrulation, segmentation, and pharyngula).

first: Bing

last: Wu

first: Ling

last: Chen


title: BAF250a Gdf9-cre knockout mice GV and MII stage oocyte transcriptome compared with control mice.

city: beijing

first: Qian

last: Zhou

state: china

address: Chao Yang Qu,  Zhong Guo Ke Xue Yuan Da Xue

institute: institute of zoology, Chinese academy of sciences

summary: GV and MII stage oocyte transcriptome of control and BAF250aGKO mice.

overall_design: 5-10 oocytes were collected for RNA-seq per sample.

first: Qing-Ren

last: Meng


title: Expression analysis using 4 x 44K micro array in Arabidopsis

city: Nagakute

first: Hidenori

last: Tanaka

state: Aichi

address: 41-1 Yokomichi

department: Genome Engineering Program

country: Japan

institute: Toyota Central R&D Labs., Inc

summary:
Gene expression analysis of Arabidopsis cDNA comprising control diploid wild type (col) with progeny of Ex-TAQing treaded (Ex-TAQed) diploid strain.
Ex-TAQed plant was introduced of MseI restriction enzyme gene and activation of MseI by heat treated for 3 hours at 33ºC.

overall_design: Analysis of gene expression using 8 diploids progenies after activation of  Ex-TAQing system.

first: Nobuhiko

last: Muramoto


title: Genomic copy number variation analysis using 4 x 180K tiling array

type: Genome variation profiling by genome tiling array

summary:
CGH analysis of Arabidopsis genome comprising control diploid wild type (col) with progeny of Ex-TAQing treaded (Ex-TAQed) diploid strain.
Ex-TAQed plant was introduced of MseI restriction enzyme gene and activation of MseI by heat treated for 3 hours at 33ºC.

overall_design: Analysis of copy number variation using 16 diploids progenies after activation of  Ex-TAQing system.


title: Single Cell Analysis Reveals NUPR1 Promotes Docetaxel Resistance in Prostate Cancer

city: Ann Arbor

first: Evan

middle: T

last: Keller

state: MI

address: 2800 Plymouth Rd

institute: University of Michigan

summary: The majority of prostate cancer (PCa) patients treated with docetaxel develop resistance to it.  In order to better understand the mechanism behind the acquisition of resistance, we conducted single cell total RNA sequencing (sctotal RNA-seq) of docetaxel sensitive and resistant variants of DU145 and PC3 PCa cell lines.  Overall, sensitive and resistant cells clustered separately.  However, for both cell lines we identified rare sensitive cells that clustered with the resistant cells indicating resistant cells pre-exist in the sensitive population.  Differential gene expression analysis between resistant and sensitive cells revealed 182 differentially expressed genes common to both PCa cell lines.  A subset of these genes gave a gene expression profile in the resistant-like sensitive cells similar to the resistant cells.  Exploration for functional gene pathways identified 218 common pathways between the two cell lines.  Protein ubiquitination was the most differentially regulated pathway and was enriched in the resistant cells.  Transcriptional regulator analysis identified potential 321 regulators across both cell lines.  One of the top regulators identified was nuclear protein 1 (NUPR1).  In contrast to the single cell analysis, bulk analysis of the cells did not reveal NUPR1 as a promising candidate.  Knockdown and overexpression of NUPR1 in the PCa cells demonstrated that NUPR1 confers docetaxel resistance in both cell lines.  Collectively, these data demonstrate the utility of sctotal RNA-seq to identify regulators of drug resistance.  Furthermore, NUPR1 was identified as a mediator of PCa drug resistance, which provides the rationale to explore NUPR1 and its target genes to for reversal of docetaxel resistance.

overall_design: Single cell sequencing of DU145 and PC3 sensitive and docetaxel resistant cell lines

first: Patricia

last: Schnepp

first: Greg

last: Shelley

first: Nicole

last: Wakim

first: Hui

last: Jiang

first: Atsushi

last: Mizokami


title: Lupus susceptibility gene Esrrg regulates TREG development and suppressive function through mitochondrial metabolism

city: Gainesville

first: Minghao

last: Gong

state: Florida

address: 1395 Center Drive, D6-18c

department: Pathology

institute: University of Florida

summary: To investigate insight into how Esrrg regulates the TREG transcriptional program, we performed high-throughput RNA sequencing (RNA-seq) analysis of CD4+Foxp3-YFP+ from splenic cells of WT and KO female mice (2-3 months old). We show that the Esrrg-deficient Treg cells presented increased transcript related to oxidative phosphoration, cell cycle, proteasome, and antigen-presenting, suggesting Esrrg plays an essential role in mitochondral metabolism and it is associated with antigen-presenting and processing. Finally, Esrrg-deficient Treg displayed decreased Erbb and ribosome pathway, which may also related to TREG function. Our data suggest an critical role of lupus susceptibility gene Esrrg in regulating Treg cell function through mitochondrial metabolism.

overall_design: CD4+Foxp3-YFP+ TREG cells from B6N.Foxp3YFP-Cre (WT, n = 5) or EsrrgNf/f.Foxp3YFP-Cre mice (KO, n = 4) at the matched ages of 2-3 months old were sorted for RNA-seq analysis.

first: Gong

last: Minghao

first: Li

last: Wei

first: Morel

last: Laurence


title: Adenosine A2A Receptor Null Chondrocyte Transcriptome Resembles that of Human Osteoarthiris Chodnrocytes

city: New York

first: Zhi

last: Li

address: 435 East 30th St, 9th Floor  New York, NY 10016

institute: NYU School of Medicine

summary: Osteoarthritis (OA) is a highly prevalent and morbid disease affecting over 30 million Americans. Effective drugs and treatments to halt the progression or reverse OA pathogenesis are not available, creating a need for translational research in the field. The A2AR null mouse is an important animal model for the understanding of disease pathogenesis and the development of novel therapies. We have previously shown that these mice develop OA spontaneously by age 16 weeks and that liposomal adenosine is able to reverse established OA in animal models of post-traumatic OA and overbearing/overweight OA. We here illustrate how the A2ARKO transcriptome shows early compromise of cell viability and compares to that of human OA chondrocytes.

overall_design: A2ARKO and WT primary neonatal chondrocytes were isolated and submitted for RNA sequencing with subsequent KEGG pathway analysis to characterize drivers of OA. oPOSSUM and the flatiron database were used for transcription factor binding enrichment and tissue specific network analyses.

first: Cristina

last: Castro

first: Carmen

last: Corciulo

first: Benjamin

last: Friedman

first: Samson

last: Jacob

first: David

last: Fenyo

first: Bruce

middle: N

last: Cronstein


title: RNA-seq of human gut bacterial isolates grown on seaweed polysaccharides

first: Eric

last: Martens

address: 1150 W. Medical Center Dr.

summary:
Purpose: Examining the transcriptome of human gut bacteria that grow on seaweed polysaccharides as a sole carbon source
Methods: Strains were grown on 5 mg/ml seaweed polysaccharides (carrageenan, agarose and/or poprhyran respective to strain) or galactose as a sole carbon source in vitro. Fold change was calculated as seaweed polysaccharide over galactose with n=2 biological replicates.  Once cells reached an optical density corresponding to mid-log phase growth, RNA was isolated and rRNA depleted. Samples were multiplexed for sequencing on the Illumina HiSeq platform at the University of Michigan Sequencing Core. Data was analyzed using Arraystar software (DNASTAR, Inc.) Genes with significant up- or down-regulation were determined by the following criteria: genes with an average fold-change >10-fold and with both biological replicates with a normalized expression level >1% of the overall average RPKM expression level. READS WERE ANALYZED .......GABRIEL FILL IN
Results: We identified novel polysaccharide utiilization loci in 5 strains of human gut bacteria

sample_organism:
Bacteroides thetaiotaomicron
Faecalicatena contorta
Faecalicatena fissicatena
Bacteroides xylanisolvens

overall_design: rRNA-depleted, mRNA profiles of human gut bacteria on respective seaweed polysaccharides run on Illumina Hi-Seq platform.

first: Nicholas

last: Pudlo

first: Gabriel

middle: V

last: Pereira


title: Activation of a collaborative innate-adaptive immune response suppresses metastatic breast and ovarian cancer in mice

city: Guangzhou

first: Bodu

last: Liu

state: State...

address: School of Life Sciences, Sun Yat-sen U East Camp, High. Edu. Meg. Cntr.

institute: Sun Yat-sen University

summary: Many cancers recruit monocytes/macrophages and polarize them into tumor-associated macrophages (TAMs). TAMs promote tumor growth and metastasis and inhibit cytotoxic T cells, preventing immune control of the cancer. However, macrophages polarized by lipopolysaccharide (a bacteria-derived toll-like receptor 4 [TLR4] agonist) and interferon gamma (IFNγ) instead kill cancer cells. They do so via nitric oxide (NO), generated by inducible NO synthase (iNOS). Altering the polarization of macrophages might therefore be a strategy for controlling tumors. Here, we show that monophosphoryl lipid A (MPLA, a TLR4 agonist used as a vaccine adjuvant)- and IFNγ-activated human macrophages from metastatic breast cancers to kill the same patients’ cancer cells in vitro. Excitingly, intratumoral injection of MPLA with IFNγ not only controlled local tumor growth but also led to reduced metastasis in mouse models of metastatic luminal and triple negative breast cancers. Furthermore, intraperitoneal administration of MPLA and IFNγ reprogrammed peritoneal macrophages and suppressed metastasis in ID8-p53-/- ovarian tumor-bearing mice. We found that the combination of MPLA and IFNγ reprogrammed the immunosuppressive microenvironment to be immunostimulatory by recruiting leukocytes, stimulating type I interferon signaling, reprogramming tumor-associated (CD206+) macrophages to tumoricidal (iNOS+) macrophages, and activating cytotoxic T cells through macrophage-secreted IL12 and TNFα. Both macrophages and T cells, including memory T cells (CD44+CD62L-), were critical for the anti-metastatic effects of MPLA and IFNγ. MPLA and IFNγ are used individually in humans, so our strategy to engage the anti-tumor immune response, which requires no knowledge of unique tumor antigens, may be ready for near-future clinical testing.

overall_design: Expression profile of MMTV-PyMT mammary gland tumor treated with MPLA, IFNg, alone or combined

first: Lijuan

last: Sun

first: Tim

last: Kees

first: Ana

middle: S

last: Almeida

first: Xue-Yan

last: He

last: Ng

last: Spector

first: Iaian

last: McNeish

first: Sylvia

last: Adams

first: Mikala

last: Egeblad


title: Single cell RNA-sequencing of inguinal adipose tissue Pdgfrβ+ cells

first: Rana

middle: K

last: Gupta

summary: We previously derived a doxycycline-inducible (Tet-On) lineage-tracing model that allows for the indelible labeling of Pdgfrb-expressing perivascular cells in adipose tissue of adult mice (PdgfrbrtTA; TRE-Cre; Rosa26RmT/mG; herein, MuralChaser mice). Prior to exposing animals to doxycyline, all cells within the stromal-vascular fraction (SVF) of adult inguinal WAT (iWAT) express membrane tdTomato from the Rosa26 locus. Following 9 days of exposure to doxycycline-containing chow diet, Cre-mediated excision of the loxP-flanked tdTomato cassette occurs in Pdgfrb-expressing cells, and membrane-bound GFP (mGFP) expression is constitutively activated. We set out to test the hypothesis that Pdgfrb-expressing perivascular cells in inguinal WAT of adult mice are heterogeneous, with subpopulations harboring functionally distinct phenotypes. To this end, we performed single cell RNA-sequencing of mGFP+ cells isolated from iWAT of lean (chow fed) 8 weeks-old male MuralChaser mice following 9 days of doxycycline exposure.

overall_design: We pooled tdTomato- GFP+ cells from inguinal white adipose tissue (WAT) from 5 MuralChaser mice. Single cell library preparation was performed using the 10X Genomics Single Cell 3 v2 according to the manufacturers instructions.

first: Mengle

last: Shao

first: Gervaise

last: Henry


title: RNA-sequencing of airway epithelial cells from individuals with cystic fibrosis; with and without infection with human rhinovirus and treatment with CFTR corrective therapy

city: Crawley, Perth

first: Emma

last: de Jong

state: WA

address: 35 Stirling Hwy

country: Australia

institute: University of Western Australia

summary:
Background: Respiratory viruses including rhinovirus can cause pulmonary exacerbations in cystic fibrosis (CF). Aberrant responses by the CF airway epithelium during rhinovirus infection, particularly interferon production, may underly the clinical observations. Whether CFTR modulators affect antiviral responses by CF epithelia is presently unknown. We tested the hypothesis that treatment of CF epithelial cells with Ivacaftor or ivacaftor/lumacaftor (Orkambi) would improve control of rhinovirus infection.

Methods: Nineteen CF epithelial cultures (CFTR Class 2: 10 homozygous for p.Phe508del, CFTR Class 3: 9 p.Phe508del/p.Gly551Asp) were infected with rhinovirus 1B at multiplicity of infection 12 for 24 hours. Culture RNA and supernatants were harvested to assess gene and protein expression respectively.

Results: RNA-seq analysis comparing rhinovirus infected cultures to control identified 796 and 629 differentially expressed genes for Class 2 and Class 3, respectively. This gene response was highly conserved when cells were treated; all infected cultures (+/- treatment) were associated with the same top three over-represented biological pathways associated with interferon signalling, and were predicted to be driven by the same interferon-pathway transcriptional regulators (IFNA, IFNL1, IFNG, IRF7, STAT1). Direct comparisons between treated and untreated infected cultures did not yield any differentially expressed genes for Class 3, and only 68 genes for Class 2, related to cell metabolic pathways. In addition, CFTR modulators did not affect viral copy number, or levels of pro-inflammatory cytokines produced post-infection.

Conclusions: Though long term clinical data is not yet available, results presented here suggest CFTR modulators do not interfere with core airway epithelial responses to rhinovirus infection.

overall_design: Airway epithelial cells (nasal and tracheal) were obtained from eleven individuals with cystic fibrosis; five with a class 2 mutation, six with a class 3 mutation. Cells were cultured for 24 hours alone, or with HRV +/- CFTR corrective therapy (orkambi or ivacaftor).

first: Luke

last: Garratt

first: Kevin

last: Looi

first: Stephen

last: Stick

first: Anthony

last: Kicic


title: Methylation and Hydroxymethylation profile of zebrafish tet2 mutant

city: North York

first: Vinothkumar

last: Rajan

state: ON

address: 2075 Bayview Ave, Room # M7-413

department: Biological Sciences

institute: Sunnybrook Research Institute

type: Methylation profiling by high throughput sequencing

summary: Zebrafish hematopoietic cells from kidney marrow from zebrafish tet2 mutants were compared to wild-type

overall_design: MeDIP and hmeDIP  performed across three biological replicates and 2 genotypes

first: Sergey

last: Prykhozhij

first: Jason

last: Berman

first: Martin

last: Hirst

first: Annaick

last: Carles

first: Michelle

last: Moksha


title: Gene expression profile of zebrafish tet2 mutant

overall_design: RNAseq in three biological replicates and 2 genotypes


title: Maternal Vitamin D deficiency induces transcriptomic changes in newborn rat lungs

city: Austin

first: James

middle: C

last: Fleet

state: TX

address: 1400 Barbara Jordan Blvd

department: Nutritional Sciences

institute: University of Texas at Austin

summary:
Transcriptomic analysis of lungs from newborn rats born to vitamin D adequate and vitamin D deficient mothers
Vitamin D deficiency during pregnancy is common and is related to several maternal and fetal morbidities. Past studies suggest that vitamin D  plays a role in normal lung development and we have shown that vitamin D regulates lung alveolar and vascular growth and preserves lung structure in experimental bronchopulmonary dysplasia (BPD) through improved pro-angiogeneic signaling.  In addition, maternal vitamin D deficiency causes abnormal airway, alveolar, and vascular growth, as well as impaired lung function and airway hyper-reactivity in newborn rats. However, the mechanisms responsible for these physiologic effects are unknown. To gain insight into the role that maternal vitamin D status has on fetal lung development we used an unbiased transcriptomic approach to identify pathways altered in the lungs of offspring from vitamin D deficient dams.

overall_design: We collected lungs from newborn pups born to mothers with adequate or deficient vitamin D nutritional status (n=4 per group).  To generate the mothers for our experiments, 4-week-old female rats were obtained from Charles River Laboratories (Wilmington, MA) then maintained in room air at Denver altitude (1,600 m; barometric pressure 630 mmHg; inspired oxygen tension 122 mmHg). Rats were housed in ultraviolet (UV) light-free surroundings using UV A/B blocking films on all light fixtures and they were exposed to a 12 h day- 12 h night cycle. UV A/B levels were verified to be less than 1 W/m2 with Sper Scientific UV A/B light meter. Rats were randomized to be fed ad libitum with semi-purified AIN93G diets containing adequate (1000 IU/kg diet) or no added vitamin D (0 IU/kg diet, VDD); both diets contained 0.5% calcium, and 0.4% phosphorus (Research Diets Inc. New Brunswick NJ). At 8 weeks of age serum 25-OHD levels were determined from blood obtained via the tail vein. If 25-OHD levels were <10 ng/ml, the female mice were mated with vitamin D–replete males. Pups from control and VDD dams were allowed to spontaneously deliver at term.

first: Erica

last: Mandell


title: Single cell RNA-seq of bioprinted human kidney organoid

city: Parkville

first: Kynan

middle: Thomas

last: Lawlor

state: VIC

address: Murdoch Children's Research Institute, Flemington Road

institute: Murdoch Children's Research Institute

summary: These files represent single cell RNA-Seq data generated on a 10x Chromium genomics platform from bioprinted iPSC-derived human kidney organoids differentiated according to our published protocol (Takasato et al., Nature Protocols 2016). The data contains >2000 cells that passed our QC. Data was used to confirm that bioprinted organoids contain a similar cellular composition as standard manually produced organoids - See https://www.biorxiv.org/content/10.1101/505396v1.

overall_design: Comparing the cellular composition of organoids generated using different methods. This set was generated using a 3D extrusion bioprinter. Data was generated in parallel with single cell libraries from manually generated organoids (GEO GSM3149442) and micro-organoids (GSE117211).

first: Jessica

last: Vanslambrouck

first: Alexander

last: Combes

first: Melissa

last: Little


title: Generation of functional hepatocytes from extended pluripotent stem cells

city: Beijing

first: Qiming

last: Wang

address: No.5 Yiheyuan Road Haidian District

institute: School of Life Sciences, Peking University

summary: We established efficiently differentiation protocol of human extented pluripotent stem (EPS) cells to functional hepatocytes (EPS-Heps) by simply adding a pre-treatment step before applying the directed differentiation protocol for conventional human pluripotent stem cells. Importantly, compared to hepatocytes derived from conventional human pluripotent stem cells, EPS-Heps transcriptionally more resemble primary human hepatocytes.

overall_design: Examination of mRNA expression pattern of EPS cells, primed pluripotent stem cells, differentiated cells and freshly isolated fetal liver and freshly isolated primary hepatocytes (F-PHHs).

first: Hongkui

last: Deng


title: Expression data from murine caecal tissue

city: Frederiksberg

first: Laura

last: Myhill

address: Dyrlægevej 100

country: Denmark

institute: University of Copenhagen

summary: We aimed to determine the effect of inulin and Trichuris muris infection on mucosal immune pathways in mice.

overall_design: Mice were fed either a control or inulin supplemented diet, then either infected with Trichuris muris or left uninfected. Caecal tissue was dissected at day 21 post infection for microarray analysis.


title: Neuropeptides modulate local astrocytes to regulate adult hippocampal neural stem cells and neurogenesis

city: Atlanta

first: Feiran

last: Zhang

state: GA

address: 615 Michael St NE

department: Human Genetics

institute: Emory University

summary: It has been well established that parvulbumin (PV) interneurons in the adult dentate gyrus (DG) regulate radial-glia like neural stem cells (rNSCs) through tonic GABA signaling. However, several major local interneuron subtypes co-release GABA and neuropeptides. Virtually nothing is known about whether and how endogenous neuropeptides regulate rNSCs. Here we demonstrate an unprecedented role of endogenous CCK in regulating rNSCs and hippocampal neurogenesis through distinctive states of the local astrocytes. Specifically, stimulating CCK release leads to increased Ca2+ transients in local astrocytes, and the subsequent astrocytic glutamate release promotes rNSC proliferation and neurogenesis via glutamate receptor mediated MAPK/ERK signaling cascade. In contrast, suppression of CCK synthesis switches resident astrocytes to a reactive state, which leads to decreased proliferation of rNSCs by regulating a gene network that negatively regulates rNSC proliferation. These findings have broad implications in multiple neuropathological conditions associated with altered CCK level, neuroinflammation, and impaired hippocampal neurogenesis.

overall_design: Gene expression analyses were performed on mRNA samples isolated from the dentate gyrus (right side) of adult mice treated with shScrambled or shCCK.

first: Peng

last: Jin


title: Genome-wide analysis of a transcriptional network of the Sterol Regulatory Element Binding Protein, Sre1, in the human fungal pathogen Cryptococcus neoformans

city: Seoul

first: Yong-Joon

last: Cho

address: 1 Gwanak-ro, Gwanak-gu

institute: Seoul National University

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

overall_design: Refer to individual Series


title: COPZ1 depletion in thyroid tumor cells triggers type I IFN response and immunogenic cell death.

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

summary:
Thyroid carcinoma (TC) is generally associated with good prognosis, nevertheless no effective treatments are available for aggressive forms not cured by current therapies. We previously identified the coatomer protein complex zeta 1 (COPZ1) as a new putative therapeutic target for TC, since its depletion impairs the viability of tumor cells, leads to abortive autophagy, ER stress, unfolded protein response and apoptosis, and reduces the tumor growth of TC xenograft models.
By combining genomic, proteomic and functional approaches, we now provide evidence that COPZ1 silencing stimulates a type I IFN-mediated viral mimicry response, boosts the production of several inflammatory molecules and induces immunogenic cell death, which in turn promotes dendritic cell maturation and T cell activation. Collectively, our findings indicate that COPZ1 targeting could be exploited as a new strategy to kill cancer cells while stimulating anti-tumor T cell responses.

overall_design: Total RNA samples from Nthy-ori 3–1 (SV-40 immortalized normal human thyroid follicular cells) and TPC-1 (papillary thyroid carcinoma) cell lines that were transfected with siRNA oligos directed to COPZ1 gene (siCOPZ1) or siRNA Universal Negative Control (non-targeting: siNT). All experiments were performed in triplicate wells for each condition.

first: Tiziana

last: Di Marco

first: Francesca

last: Bianchi

first: L

last: Sfondrini

first: Katia

last: Todoerti

first: Italia

last: Bongarzone

first: Elisa

last: Maffioli

first: Gabriella

last: Tedeschi

first: Mara

last: Mazzoni

first: Sonia

last: Pagliardini

first: Sandra

last: Pellegrini

first: Antonino

last: Neri

first: MariaChiara

last: Anania

first: Angela

last: Greco


title: Genome-wide analysis of a transcriptional network of the Sterol Regulatory Element Binding Protein, Sre1, in the human fungal pathogen Cryptococcus neoformans (ChIP-seq)

summary:
Purpose: Defining the regulatory role of the transcription factor Sre1 in C. neoformans.
Methods: Chromatin immunoprecipitation followed by high-throughput sequencing was performed using chromatin immunoprecipitated DNA from the strain Flag-Sre1 grown in low- and high-iron media under normoxia and hypoxia condition.
Results: Sre1 directly bind to the promoter region of the genes involved in ergosterol biosynthetic pathway and iron acquisition in C. neoformans.

overall_design: The enriched binding peaks of Sre1 were compared with the input DNA (control).

first: Won

last: Jung

first: Eunsoo

last: Do

first: James

last: Kronstad


title: Perivascular Mesenchymal Cells Control Adipose Tissue Macrophage Accrual in Obesity

city: Durham

first: Rana

last: Gupta

address: Carmichael Building, 300 North Duke St.

institute: Duke University

summary: Chronic low-grade visceral white adipose tissue (WAT) inflammation is a hallmark of metabolic syndrome in obesity. Here, we demonstrate that a subpopulation of adipose tissue perivascular (PDGFRb+) cells, termed “fibro-inflammatory progenitors” (FIPs), activate pro-inflammatory signaling cascades shortly after the onset of high-fat diet feeding of mice and regulate pro-inflammatory macrophage accumulation in WAT in a TLR4-dependent manner. FIPs activation in obesity is mediated by the downregulation of ZFP423, identified here as a transcriptional co-regulator of NFkB. Biochemical analysis of ZFP423-protein complexes and ChIP-seq analysis reveal that ZFP423 suppresses the DNA-binding capacity of the p65 subunit of NFkB by inducing a p300 to NuRD co-regulator switch. Doxycycline-inducible expression of Zfp423 in PDGFRb+ cells suppresses inflammatory signaling in FIPs and attenuates metabolic inflammation of visceral WAT in obesity. Inducible inactivation of Zfp423 in PDGFRb+ cells increases FIP activity, exacerbates adipose macrophage accrual, and promotes WAT dysfunction. These studies implicate perivascular mesenchymal cells as important regulators of chronic adipose tissue inflammation in obesity and identify ZFP423 as a transcriptional break on NFkB signaling.

overall_design: Bulk RNA-seq experiment to analyze gene expression profile in FIPs and APCs of gonadal white adipose tissue of Mural-Zfp423TG mice and Control animals under HFD feeding.

first: Mengle

last: Shao


title: Mural Cell ZFP423 Controls Adipose Tissue Macrophage Accrual in Obesity [ChIP-seq]

summary: Chronic low-grade visceral white adipose tissue (WAT) inflammation is a hallmark of metabolic syndrome in obesity. Here, we demonstrate that a specific subpopulation of adipose tissue perivascular (PDGFRb+) stromal cells, termed “fibro-inflammatory progenitors” (FIPs), activate  pro-inflammatory signaling cascades shortly after the onset of high-fat diet feeding of mice and control the accumulation of pro-inflammatory macrophages in WAT. The activation of FIPs is mediated by the downregulation of ZFP423, identified here as a transcriptional co-regulator of  NFkB. Biochemical analysis of ZFP423-protein complexes and ChIP-seq analysis reveal that  ZFP423 suppresses the DNA-binding capacity of the p65 subunit of NFkB by inducing  a co-regulator switch. Doxycycline-inducible expression of Zfp423 in PDGFRb+ cells  suppresses inflammatory signaling in FIPs and attenuates macrophage accumulation within  visceral WAT of obese mice. Conversely, inducible inactivation of Zfp423 in PDGFRb+ cells increases FIP activity, exacerbates adipose macrophage accrual, and promotes WAT  dysfunction in obese mice. These studies implicate mural cells as sentinels and gatekeepers of adipose tissue inflammation in obesity.

overall_design: We performed NFKB p65 subunit binding sites (using ChIP-seq) of FIPs (pooled samples, ~5,000,000 cells per genotype) isolated from both control and Mural-Zfp423TG mice after 2 hours of  LPS (100ng/mL) treatment.


title: mRNA sequencing time course of C. elegans samples at time point 1 hours until time point 16 hours at room temperature

city: Basel

first: Helge

last: Grosshans

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedriche Miescher Institute for Biomedical Research (FMI)

summary: We find gene expression oscillations which arise after a time lag of around 7 hours.

overall_design: Examination of gene expression profiles over time (1-16 hours after plating L1 arrested C. elegans larvae) using high throughput mRNA sequencing.

first: Gert-Jan

last: Hendriks


title: Transcriptional control of influenza-specific CD4+ tissue-resident memory T cell generation

first: Donna

middle: L

last: Farber

state: NY

address: 650 West 168th Street, BB1701

department: Surgery

institute: Columbia University

summary: Tissue-resident memory T cells (TRM) are a non-circulating subset of memory that are maintained at sites of pathogen entry and mediate optimal protection against reinfection. Lung TRM can be generated in response to respiratory infection or vaccination, however, the molecular pathways involved in CD4+TRM establishment have not been defined. Here, we performed transcriptional profiling of influenza-specific lung CD4+TRM following influenza infection to identify pathways implicated in CD4+TRM generation and homeostasis. Lung CD4+TRM displayed a unique transcriptional profile distinct from spleen memory, including up-regulation of a gene network induced by the transcription factor IRF4, a known regulator of effector T cell differentiation.

overall_design: Transcriptional profiling by RNA-Seq of lung-resident and spleen influenza-specific mouse CD4+ T cells. Project includes four and five biological replicates of each sample type, respectively.

first: Filip

last: Cvetkovski

first: Mark

last: Snyder


title: Inhibition of histone H3K27 demethylases inactivates brachyury (TBXT) and promotes chordoma cell death [RNA-Seq III]

city: Oxford

first: Adam

last: Cribbs

address: Windmill Road

institute: University of Oxford

summary: The expression of transcription factor brachyury (TBXT) is normally restricted to embryonic development and its silencing after mesoderm development is epigenetically regulated. In chordoma, a rare tumour of notochordal differentiation, TBXT acts as a putative oncogene, and we hypothesised that its expression could be contolled through epigenetic inhibition. Screening of five chordoma cell lines revealed that inhibitors of the histone 3 lysine 27 demethylases KDM6A (UTX) and KDM6B (Jmjd3) reduce TBXT expression and lead to cell death, findings validated in primary patient-derived culture systems. Pharmacological inhibition was phenocopied by genetic inactivation of KDM4/B using CRISPR/Cas9. Transcriptional profiles in response to a novel KDM6A/B inhibitor, KDOBA67, revealed downregulation of critical genes and transcription factor networks for chordoma survival pathways, characterised by paired and homeobox genes, whereas upregulated pathways are dominated by stress, cell cycle and pro-apoptotic response pathways. This study supports previous data showing that the function of TBXT is essential for maintaining notochord cell fate and function and provides further evidence that TBXT is an oncogenic driver in chordoma. The data suggest that TBXT can potentially be targeted therapeutically by modulating epigenetic control mechanisms such as H3K27 demethylases.

overall_design: Examination of gene expression differences in 3 chordoma cell lines in the presence of DMSO or KDOBA67

middle: P

first: Udo

last: Oppermann


title: Genes associated with Gabarapl1-KD in LNCaP

city: Shenzhen

first: Chongwei

last: Xie

address: Futain,Shenzhen

institute: Shenzhen Hospital

summary: We want to find genes who's expression are regulated by or associated with Gabarapl1. For this purpose, we knocked down Gabarapl1 gene. Samples were prepared for microarray and data processing were performed by Shanghai Biotechnology Corporation.

overall_design: Gabarapl1 expression was knocked down in LNCap gab_2 sample comparing to LNCap plko sample(control). shRNA targetting Gabarapl1 was used to knock down Gabarapl1. Non-targetted shRNA was used as a negative control (LNCap plko sample). RNA extraction, construction of libraries, and microarray using human gene expression 4x44K microarray (Agilent Technologies, Santa Clara, CA, USA) were performed by Shanghai Biotechnology Corporation (Shanghai, China).


title: Genome-wide methylation analysis of T-cells using Infinium HumanMethylation BeadChip

city: Saga

first: Tatsuro

last: Watanabe

state: Saga

address: 5-1-1 Nabeshima, Saga

institute: Saga University

type: Methylation profiling by genome tiling array

summary: DNA methylation in T-cells.

overall_design: A picture of epigenetic alterations in T-cells with and without HTLV-1 infection was characterized.

first: Satoshi

last: Yamashita

first: Hideaki

last: Nakamura

first: Akemi

last: Sato

first: Shinya

last: Kimura

first: Eisaburo

last: Sueoka

first: Toshikazu

last: Ushijima


title: Inhibition of histone H3K27 demethylases inactivates brachyury (TBXT) and promotes chordoma cell death [RNA-Seq II]


title: Identification of regulators of vascular proliferation

first: Peter

last: Etchells

address: Durham University

department: Department of Biosciences

institute: Durham University

summary: Vascular tissue transports water and nutrients throughout the plant body and is consequently essential for growth and development. In Arabidopsis, the vascular tissue is initiated at the centre of the embryo.  During embryogenesis it is found in a characteristic diarch pattern with a central file of xylem cells with an adjacent layer of procambium on either side. Phloem poles are present on the outside of the procambium layers. Following germination a series of cell divisions results in the reorganisation of the vascular tissue which transitions to a radially symmetric structure. The RNA-seq data associated with this submission captures those early events. In 7-day old seedlings, wild type hypocotyl s have begun the process of change towards radial symmetry. In pxy mutants this process is stalled, and in 35S::CLE41 lines, radial expansion occurs prematurely. In root tissue of this age there is little evidence of the transition to radial symmetry in any of the genotypes tested. The RNA-seq dataset submitted will thus provide insight into the changes required to reorganise Arabidopsis vascular tissue as it transitions from primary to secondary growth.

overall_design: There are 6 groups made up of 4 biological replicates each (24 Samples in total). Each sample has 2 technical replicates. Samples are taken from either the root or the shoot and there is a control group for both root and shoot groups (designated WT)

first: J

first: David

last: Dolan

first: Siobhan

last: Brady


title: Eumyc and WT NK cells

city: Esch-sur-Alzette

first: Takumi

last: Kobayashi

address: 29, rue Henri Koch

department: Department of Infections and Immunity

country: Luxembourg

institute: Luxembourg Institute of Health

summary: Eumyc lymphoma was inoculated i.v. into C57BL/6J mice. Spleens were harvested from healthy or Emyc lymphoma-bearing mice at day 14 post-inoculation, and splenic NK cells were purfied using flow cytometry.

overall_design: Eumyc and WT NK cells


title: Inhibition of histone H3K27 demethylases inactivates brachyury (TBXT) and promotes chordoma cell death


title: Genome-wide analysis of a transcriptional network of the Sterol Regulatory Element Binding Protein, Sre1, in the human fungal pathogen Cryptococcus neoformans (RNA-seq)

first: Yong-Joon

last: Cho

summary:
Purpose: Understanding the regulatory role of Sre1 in Cryptococcus neoformans.
Methods: The transcriptome profiles of the wild-type and sre1 mutant were generated by RNA-seq using Illumina Hiseq. The transcriptome profile of the sre1 mutant was compared with that of the wild-type strain.
Results: The Sterol Regulatory Element Binding Protein, Sre1 is a major regulator for the genes involved in ergosterol biosynthetic pathway and iron acquisition in C. neoformans.

overall_design: Transcriptome of the sre1 mutant vs. Transcriptome of the wild-type

first: Won

middle: H

last: Jung

first: Eunsoo

last: Do

first: James

last: Kronstad


title: Transcriptome dynamics of oral polymorphonuclear neutrophils during experimental gingivitis

city: Zeist

first: Lars

last: Verschuren

address: Utrechtseweg 48

department: Microbiology and Systems Biology

institute: TNO

summary: Oral polymorphonuclear neutrophils (oPMNs) are essential for the maintenance of oral health. Functionally active oPMNs have been described in oral health, gingivitis and periodontitis. Interestingly, recent evidence showed that oPMNs from chronic periodontitis patients have a similar functional and reactivity pattern compared to oPMNs from healthy subjects. However, it remains unknown whether oPMNs respond to the initiation and resolution of gingival inflammation. Therefore, this study aimed to evaluate the oPMNs’ transcriptional responses during the initiation and resolution of an experimentally induced gingivitis.     Oral rinses were obtained from 8 subjects at 4 different time points during the experiment for the isolation of oPMNs; day 0 (baseline), day 9 (during gingivitis challenge), day 14 (end of the challenge) and day 21 (resolution). Transcriptome of oPMNs was determined by RNAsequencing. Differentially expressed genes (DEGs) was selected at P<0.01 level, and evaluated for pathway regulation at different time points using Ingenuity Pathway Analysis suite.     During the gingivitis challenge, dental plaque levels and gingival bleeding levels were significantly increased at day 14 compared to baseline. Transcriptome analysis indicate four major clusters of DEGs, which consisted of a group of 256 initial response DEGs (day 9 only), 221 late response DEGs (day 14 only), 53 persistent response DEGs (consistent at day 9 and day 14), and a group of 524 DEGs showing response only after the gingivitis challenge (day 21 only). Pathway analysis of the initial response DEGs showed their involvement in many immune regulatory pathways (interleukin signaling, reactive oxygen species processes and granulocyte adhesion and diapedesis). Late responding DEGs mainly showed activation of signaling pathways and phagosome formation as part of the phagocytosis process, whereas DEGs at day 21 were involved in epithelial adherence signaling and other miscellaneous related signaling pathways.    This study showed that oPMNs have specific expression profiles during the development and resolution of experimental gingivitis. Even though, the specific observed pathways were not identical within each time point, the altered pathways indicate PMN responses in general and suggests an immunomodulatory role for the oPMNs. The oPMNs may therefore play a co-controlling part in the initiation and resolution of gingival inflammation.

overall_design: Time course study in which 8 healthy individuals were asked to refrain from any form of oral hygiene for a period of 2 weeks. Data were derived from samples taken at start (day 0), day 9, and day 14. After this timepoint the habitual oral hygiene routine was re-established by each participant. At the end of the study (day 21) a final sample was collected from all participants.

first: Patrick

last: Rijkschroeff

first: Ton

last: Schoenmaker

first: Martien

last: Caspers

first: Bart

last: Keijser

first: Elena

last: Nicu

first: Bruno

middle: G

last: Loos


title: Macrophage Syk-PI3Kγ-HIF axis controls tumor immune suppression

city: La Jolla

first: Dylan

middle: Derik

last: Skola

state: CA

address: 9500 Gilman Dr.

department: Cellular and Molecular Medicine

country: USA

institute: UCSD

summary:
Macrophages (MΘs) play a critical role in tumor growth, immunosuppression and inhibition of adaptive immune responses in cancer. Hence, targeting signaling pathways in MΘs that promote tumor immunosuppression will provide therapeutic benefit. PI3Kγ has been recently established by our group and others as a novel immuno-oncology target. Herein, we report that macrophage Syk drives polarization of immunosuppressive macrophages which establish an immunosuppressive tumor microenvironment in in vivo syngeneic tumor models. Genetic or pharmacological blockade of Syk in MΘs promotes a pro-inflammatory MΘ phenotype, restores CD8+ T cell activity, destabilizes HIF under hypoxia, and stimulates antitumor immune response. Moreover, we have developed in silico the “first in class” dual Syk/PI3K inhibitor, SRX3207, for the combinatorial inhibition of Syk and PI3K in one small molecule to activate anti-tumor immunity in vivo.  This chemotype shows great efficacy in various tumor models and represents a new therapeutic approach to treat devastating cancers.
Significance: Our data indicate a central role of Syk in macrophage transcriptional programming leading to inhibition of adaptive immune responses. Furthermore, SRX3207 blocks macrophage expression of immunosuppressive factors and activates anti-tumor immune responses, validating the concept of combined Syk and PI3K inhibition as an effective approach to treat macrophage driven cancers.

overall_design: Examination of effects of SykKO and a dual Syk/PI3K inhibitor on tumor progression, immune cell populations, protein levels and gene expression.

first: Shweta

last: Joshi

first: Kevin

middle: X

last: Liu

first: Muamera

last: Zulcic

first: Alok

last: Singh

first: Christopher

last: Glass

first: Phillip

last: Sander

first: Andrew

last: Sharabi

first: Guillermo

last: Morales

first: Joe

last: Garlich

first: Donald

last: Durden


title: Mining of scab resistance R-genes from different cultivars of apple and Introducing Scab resistance in commercially important varieties of apple grown in Kashmir valley through cisgenesis

city: Srinagar

middle: Z.

last: Masoodi

state: Jammu and Kashmir

address: Shalimar Campus

department: Division of Plant BiotechnologyDivision of Plant Biotechnology

country: India

institute: Sher-e-Kashmir University of Agricultural Sciences & Technology of Kashmir

summary: Identification of scab resistant genes in apple varieties. The research was funded by SERB.

overall_design: Identification of scab resistant genes from various apple cultivars

first: Khalid

middle: Z

first: Mudasir

last: Mir

first: Nazeer

last: Ahmed


title: Stem Cell-Derived Matrices Provide Improved Isolation and Maintenance of hMSC Characteristics

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

summary: Adult human mesenchymal stem cells (hMSCs) have shown promise as a valuable new therapeutic tool in a wide range of diseases.  hMSCs from bone marrow stroma are currently isolated by their adherence to tissue culture treated polystyrene (TCP) and passaged multiple times on the same plastics until they are able to produce enough cells to be useful for research or clinical therapeutic trials.  However, evidence in the literature has shown that culture on TCP can negatively alter hMSC function.  Our aim was to expand hMSCs in an in vitro environment more closely resembling that of the hMSCs' native microenvironment to maximize proliferation while retaining therapeutic potential.  We used decellularized hMSC-derived extracellular matrix (hMSC-ECM) to test hMSCs' maintenance of stem cell properties during in vitro expansion.  We found that hMSC-ECM was able to increase hMSC proliferation while retaining the stem cells‘ immature state and increasing differentiation potential.  In addition, the hMSC-ECM could be covalently cross-linked to polymer substrates and was effective in the isolation and expansion of hMSCs in the presence of fetal bovine serum and human serum.  Using proteomics and transcriptomics, we were able to determine the mechanism behind the hMSCs’ increased proliferation was due to their ability to downregulate their otherwise required gene expression for ECM proteins by on hMSC-ECM.  The effects of hMSC-ECM were largely hMSC specific and were not found with several other types of human cells.  Providing a pre-formed in vitro niche for hMSCs can provide the cells with the critical components required for hMSC function during in vitro expansion.

overall_design: Three replicates of hMSC cells cultured on Tissue Culture Plastic Alone, Tissue Culture Plastic plus Crosslinker, hMSC Depositied ECM plus Crosslinker, hMSC Depositied ECM Plus Crosslinker and Fibronectin or hMSC Depositied ECM alone.

first: Benjamin

last: Larson

first: Héloïse

last: Ragelle

first: Miralem

last: Prijic

first: Fangheng

last: Zhou

first: Kathryn

middle: M

last: Luly

first: Robert

last: Langer

first: Daniel

last: Anderson


title: Alteration of miRNome and transcriptome by recombinant ncRNA agents

city: Sacramento

first: Pui Yan

last: Ho

address: 2700 Stockton Blvd., Rm2120B

institute: UC Davis

overall_design: Refer to individual Series


title: Inhibition of histone H3K27 demethylases inactivates brachyury (TBXT) and promotes chordoma cell death [RNA-Seq I]

first: Adam

last: Cribbs

first: Udo

last: Oppermann


title: Alteration of transcriptome by recombinant ncRNA agents

summary:
Purpose: Identify whether recombinant ncRNAs are recognized by mammalian cells and processed into mature microRNAs, thus leading to the alteration of downstream target genes. In addition, we also explored whether the alteration of known or novel target genes are Dicer dependent.
Methods: HEK293T (Dicer-WT) and 424 (Dicer-KO) cell lines were treated with 20nM of control tRNA (MSA), nCAR/miR-34a-5p, or nCAR/miR-34a-3p in triplicate.
Results: Read counts of known mRNAs were analyzed using a RSEM-EdgeR workflow. Sequence reads were mapped to the human reference genome (hg19) by BWA, read counts for individual genes were computed using RSEM, and EdgeR was used to analyze significant (log2FC > 1.2 or log2FC < 0.8. P-value < 0.05 and log2CPM > 5) differentially expressed mRNAs.
Conclusions: Upon transfection of recombinant RNA agents in mammalian cells, known and novel target genes were regulated in a Dicer dependent manner (nCAR/miR-34a-5p) and also in a Dicer independent manner (nCAR/miR-124a-3p).

overall_design: A total of 18 samples were analyzed. Three biological replicates in each group were subjected to treatment with control tRNA (MSA), nCAR/miR-34a-5p, or nCAR/miR-124a-3p. Therefore, each cell line had a total of 9 samples and the transcriptome was explored in two different cell lines for a total of 18 samples.

first: Pui

first: Aiming

last: Yu

first: Zihua

last: Hu


title: Splicing regulation by USP39 deubiquitinase is essential for KRAS-driven cancer

city: Oviedo

first: Jose

last: Freije

state: Asturias

address: C/ Fernando Bongera s/n

department: Bioquimica y Biologia Molecular

country: Spain

institute: Universidad de Oviedo

summary: KRAS is the most frequently mutated oncogene in human cancer, but its therapeutic targeting remains challenging. Here, we report a synthetic lethal screen with a library of deubiquitinases and identify USP39, which encodes an essential splicing factor, as a critical gene for the viability of KRAS-dependent cells. We show that the essentiality of USP39 for these cells is based on its critical role in splicing regulation, as splicing fidelity inhibitors also decrease preferentially the proliferation rate of KRAS-active cells. Moreover, depletion of DHX38, an USP39-interacting splicing factor, also reduces the viability of these cells. Furthermore, we show that USP39 is upregulated in lung and colon carcinomas and its expression correlates with KRAS levels and poor clinical outcome, supporting the oncogenic role of this deubiquitinase. Accordingly, our work provides critical information for the development of splicing-directed antitumor treatments and supports the potential of USP39-targeting strategies for the development of anticancer therapies.

overall_design: RNA from control (transduced with empty pLKO-1 vector) and USP39-silenced A549 and H358 lung cancer cells was extracted and transcriptional profiling was obtained with GeneChip Human Exon 1.0 ST Arrays.

first: Julia

last: Fraile

first: Carlos

last: Lopez-Otin