title: Altered DNA methylation profiles in blood from patients with sporadic Creutzfeldt-Jakob disease

city: Indianapolis

first: Luke

middle: Child

last: Dabin

state: Indiana

department: Medical and Molecular Genetics

institute: Indiana University

summary: Prion diseases are fatal and transmissible neurodegenerative disorders caused by the misfolding and aggregation of prion protein. Although recent studies have implicated epigenetic variation in common neurodegenerative disorders, no study has yet explored their role in human prion diseases. Here we profiled genome-wide blood DNA methylation in the most common human prion disease, sporadic Creutzfeldt-Jakob disease (sCJD). Our case-control study (n=219), when accounting for differences in cell type composition between individuals, identified 38 probes at genome-wide significance (p < 1.24x10-7). Nine of these sites were taken forward in a replication study, performed in an independent case-control (n=186) cohort using pyrosequencing. Sites in or close to FKBP5, AIM2 (2 probes), UHRF1, KCNAB2, PRNP, ANK1 successfully replicated. The blood-based DNA methylation signal was tissue- and disease-specific, in that the replicated probe signals were unchanged in case-control studies using sCJD frontal-cortex (n=84), blood samples from patients with Alzheimer’s disease, and from inherited and acquired prion diseases. Machine learning algorithms using blood DNA methylation array profiles accurately distinguished sCJD patients and controls. Finally, we identified sites whose methylation levels associated with prolonged survival in sCJD patients. Altogether, this study has identified a peripheral DNA methylation signature of sCJD with a variety of potential biomarker applications.

overall_design: 106 Control and 114 sCJD blood-derived DNA samples were bisulfite converted, sent to UCL Genomics for amplification and hybridization to the Illumina Infinium 450 Beadchip Array. iDAT files were analyzed using ChAMP and one sample (Control 52) was excluded from analysis due to poor detection p-value.

first: Fernando

last: Guntoro

first: Tracy

last: Campbell

first: Tony

last: Bélicard

first: Adam

last: Smith

first: Rebecca

middle: G

first: Rachel

last: Raybould

first: Jonathan

middle: M

last: Schott

first: Katie

last: Lunnon

first: Peter

last: Sarkies

last: Collinge

first: Simon

last: Mead

first: Emmanuelle

last: Viré


title: Chicory – a functional food with multiple effects: cancer-prevention, antimicrobial resistance, glycemia and lipidemia regulation

status: Public on Oct 20 2020

city: Villeneuve d'Ascq

first: Anca

last: Lucau-Danila

address: Cité Scientifique SN2 303

department: Biology

country: France

institute: University of Lille

summary: We experimented on murine model and attempted to point several mechanisms by which the chicory roots acts as a functional food. To this goal, a nutrigenomic analysis was performed.

overall_design: Mice were fed with an aqueous decoction of the roots flour from two selected chicory genotypes (G12 and G35) and with an inulin (I2255 Sigma Aldrich, MO, USA) solution. The mice gavages consisted in a daily force-feeding of 500 µl of stemming solution decoctions of chicory flour or inulin water solution besides the standard chow. As experiments were conducted sequentially for two different periods of time, two control sets were used: first control group (Ctr1) in parallel with G12 and G35 diet and a second control group (Ctr2) in parallel with inulin diet. Three mice for each condition were sacrificed and the central core of the liver left lobe was cubed and frozen at -80 °C for transcriptomics.

first: Céline

last: Pouille


title: Super Enhancer Regulation of Cytokine-Induced Chemokine Production in Alcoholic Hepatitis [ChIP-Seq]

status: Public on Oct 19 2020

city: Rochester

first: Aditya

last: Bhagwate

state: MN

address: 200 1st Street SW

country: USA

institute: Mayo Clinic

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We performed histone modification ChIP-Seq in human liver explants and showed upregulation of multiple CXCL chemokines in AH. ChIP-Seq, chromosome conformation capture assays, and in silico analysis of published data identified a super enhancer for multiple CXCL genes. Targeting this super enhancer by dCas9-KRAB-mediated epigenome editing and Bromodomain and Extraterminal (BET) inhibitors decreased the expression of multiple CXCL genes.

overall_design: In the present study, we utilized ChIP-Seq targeting key histone marks in liver explants of AH patients and normal controls to characterize the transcriptomic and epigenomic changes in AH vs. normal.

first: Vijay

middle: H

last: Shah

first: Sheng

last: Cao

first: Mengfei

last: Liu


title: Interleukin-11 signaling drives vascular smooth muscle phenotypic switching and contributes to aortic remodelling

city: Singapore

first: Eleonora

last: Adami

address: 8 College Road

department: CVMD

country: Singapore

institute: Duke-NUS Medical School

type: Expression profiling by high throughput sequencing

summary: RNA sequencing of primary human aortic or arterial VSMCs after stimulation with transforming growth factor beta-1 (TGFβ1) revealed marked IL11 upregulation. In vitro, IL11 stimulation of VSMCs resulted in phenotypic switching by increased ECM production and migration/invasion. Neutralizing IL11 antibody treatment abolished phenotypic switching in VSMCs. IL11 plays an important and non-redundant role in VSMC phenotypic switching.

overall_design: Primary VSMCs outgrown from Left Internal Mammary Artery (LIMA - 22 samples) and Aortic Button (AB - 10 samples) from a total of  24 patients. Every sample is present as untreated (stimulated with basal M231 medium for 24h) and treated with TGFB )stimulated with 5ng/ml recombinant human TGFB1 in basal M231 medium for 24h)

first: Wei-Wen

last: Lim

first: Benjamin

last: Corden

last: Ng

first: Konstantinos

last: Vanezis

first: Giuseppe

middle: A

last: D'Agostino

first: Anissa

last: Widjaja

first: Wei-Hua

last: Song

first: Chen

last: Xie

first: Liping

last: Su

first: Xiu-Yi

last: Kwek

first: Nicole

last: Tee

first: Jinrui

last: Dong

middle: S

last: Ko

first: Mao

last: Wang

first: Chee

middle: J

last: Pua

first: Muhammed

last: Jamal

first: Beeyong

last: Soh

first: Sivakumar

last: Viswanathan

first: Sebastian

last: Schafer

first: Stuart

last: Cook


title: Hemopexin is a novel tumor suppressor that blocks cancer metastasis by modulating heme:DNA G-quadruplex dynamics to control c-myc expression

city: Boston

first: Mahmoud

middle: Adel

last: Bassal

state: Massachusetts

address: 3 Blackfan Circle

department: Hematology and Oncology

institute: Beth Israel Deaconess Medical Center

summary: Treamtent of PC3 prostate cancer cell line results in enhanced colony growth and c-myc expression. Further, heme promotes tumro growth and metasease in in vivo models of carcinogenesis

overall_design: PC3 cells were treated for 2 and 4 hours with heme and the gene expression was measured by RNA-seq.

first: Giacomo

last: Canesin

first: Annalisa

last: Di Ruscio

first: Mailin

last: Li

first: Andreas

last: Hedblom

first: Reeham

last: Choudhury

first: Agnieszka

last: Krzyzanowska

first: Simone

last: Ummarino

first: Eva

last: Csizmadia

first: Macarena

last: Palominos

first: Anna

last: Stiehm

first: Alexander

last: Ebralidze

first: Shao-Yong

last: Chen

first: Ping

last: Zhao

first: Barry

last: Paw

first: Emanuela

last: Tolosano

first: Laurence

last: Hurley

first: Anders

last: Bjartell

first: Daniel

last: Tenen

first: Barbara

last: Wegiel


title: RNA-Seq transcriptome comparison of microglia and CD11c+ cells sorted from the ischemic brain tissue of parabiotic (female) mice

city: Barcelona

last: PLANAS

state: - If in U.S, Select a State -

address: Rossello 161 planta 6

country: Spain

institute: Spanish Research Council (CSIC)

summary:
RNA-Seq transcriptome comparison of the following cell populations (n=3-4 independent samples per cell population): a) CD11c-eYFP+ cells FACS sorted from brain of female adult mice 4 days after cerebral ischemia, b) CD11c-eYFP+ cells FACS sorted from brain of female parabiotic mice 4 days after cerebral ischemia c) CX3CR1+ microglia sorted from the ischemic brain of female CX3CR1CreERT2-ROSA26 tdTomato mice.
Purpose: The goal of this study is to compare the transcriptome profile (RNA-Seq) of infiltrating cD11c-eYFP+ cells and microglia, both collected from ischemic brains of mice.
Methods: RNA samples were obtained from FACS sorted eYFP+ cells of the ipsilateral brain hemisphere of CD11c-eYFP mice 4 days post-ischemia, the ipsilateral brain hemisphere of CD11c-eYFP/WT parabiotic mice 4 days post-ischemia, and from microglial cells sorted from the ipsilateral brain hemisphere of Cx3cr1CreERT2:ROSA26dTomato mice 4 days post-ischemia. NGS was performed (RNA-Seq) to compare the transcriptome of these populations.
Results: the populations we compared clearly separated the differentially expressed genes in an unsupervised cluster analysis. 1509 genes were overrepresented in microglia and 1183 genes were overrepresented in CD11c-eYFP+ cells in the ischemic brain.
Conclusions: Our study is the first comparative analysis of the transcriptomes of microglia and the infiltrating CD11c-eYFP+ cells derived from the ischemic brain of mice. The results show that the infiltrating CD11c-eYFP cell population in the ischemic brain tissue of parabiotic mice displays overrepresentation of genes typical of dendritic cells, immune functions, and ClassII antigen presentation, amongst others, that are not found represented in microglia.

overall_design: mRNA transcriptome profiles of infiltrating CD11c- eYFP+ cells and microglia cells were compared to find differentially expressed genes specific of each population.

last: Planas

first: Mattia

last: Gallizioli

first: Luca

last: Cozzuto


title: Blood RNA signature predicts recent tuberculosis exposure in mice

city: San Antonio

first: Joanne

last: Turner

state: TX

address: 8715 W Military Dr

institute: Texas Biomedical Research Institute

summary: Knowing when a person was infected with Mycobacterium tuberculosis (M.tb) is critical as recent infection is the strongest clinical risk factor for progression to TB disease in immunocompetent individuals. However, time since M.tb infection is very difficult to determine in routine clinical practice. We determined whether gene expression patterns in blood RNA correlate with time since M.tb infection or exposure to develop a biomarker for recent exposure. As proof of concept, we found an RNA signature that accurately discriminated early and late time periods after experimental infection in mice.

overall_design: Blood was collected from 20 C57BL/6 mice infected with a low dose of M.tb (Erdman), as well as 6 uninfected age-matched control mice. Blood was collected at days 30, 60, 90, 120 and 150 post-infection. Whole blood was subjected to microarray analysis. We identify a gene expression signature that predicts infection time point.

first: Russell

middle: C

last: Ault

first: Colwyn

last: Headley

middle: E

last: Hare

first: Bridget

last: Carruthers

first: Asuncion

last: Mejias


title: CD11c+ cells in the inflamed brain derive from proliferating microglia and invading dendritic cells that comprise beneficial cDC1 subsets

first: Anna

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

overall_design: Refer to individual Series


title: RNA-Seq transcriptome comparison of microglia and CD11c+ cells sorted from the ischemic brain tissue of (male) mice

summary:
RNA-Seq transcriptome comparison of the following cell populations (n=4 independent samples per cell population): a) CD11c-eYFP+ cells FACS sorted from brain of adult mice 4 days after cerebral ischemia, b) CX3CR1+ microglia sorted from the ischemic brain of CX3CR1CreERT2-ROSA26 tdTomato mice; c) CD11c-rYFP+ cells sorted from the spleen of control mice; d) CX3CR1+ microglia sorted from the brain of control mice.
Purpose: The goal of this study is to compare the transcriptome profile (RNA-Seq) of cD11c-eYFP+ cells and microglia, both collected from ischemic brains of mice, and with reference cell populations, i.e. Steady-stated microglia from brain of corresponding control mice and steady-state CD11c-eYFP cells sorted from the spleen of control mice.
Methods: RNA samples were obtained from FACS sorted eYFP+ cells of the ipsilateral brain hemisphere of CD11c-eYFP mice 4 days post-ischemia, the spleen of control CD11c-eYFP mice, and from microglial cells sorted from control brain and the ipsilateral brain hemisphere 4 days post-ischemia of Cx3cr1CreERT2:ROSA26dTomato mice. NGS was perfomed (RNA-Seq) to compare the transcriptome of these populations.
Results: the populations we compared clearly separated the differentially expressed genes in an unsupervised cluster analysis. 950 genes were overrepresented in microglia and 1469 genes were overrepresented in CD11c-eYFP+ cells in the ischemic brain.
Conclusions: Our study is the first comparative analysis of the transcriptomes of microglia and the infiltrating CD11c-eYFP+ cells derived from the ischemic brain of mice. The results show that the infiltrating CD11c-eYFP cell population in the ischemic brain tissue of parabiotic mice displays overrepresentation of genes typical of dendritic cells, immune functions, and ClassII antigen presentation, amongst others, that are not found represented in microglia.


title: A comprehensive RNA handling and transcriptomics guide for high-throughput processing of Plasmodium blood-stage samples.

first: Zbynek

last: Bozdech

state: Select if applicable

department: Molecular Genetics&Cell Biology

institute: Nanyang Technological University

summary: Here we have designed a full processing pipeline of P. falciparum RNA that innclues RNA preservation, extraction, cDNA synthesis and amplification, globin depletion and final transcriptome readout. To validate the protocol we have analyzed transcriptomes of  P. falciaprum samples derived from filed studies as well as 3D7 lab strains. This dataset have been used to establish the best conditions for whole transcriptome amplification protocol. Additionally it inclues the validation of bead extraction protocol. It also contains field samples used for validation of the entire protocol.

overall_design: Samples were extracted using high-throughput techniques adied by automatics liquid handlers, cDNA was amplified and resulted transcriptomes were analyzed and validated using microarray platform.

first: Grennady

last: Wirjanata

first: Jaishree

last: Tripathi

first: Michal

last: Kucharski

first: Sourav

last: Nayak

first: Lei

last: Zhu


title: Genome wide gene-expression and mRNA splicing profile in human cardiomyocytes differentiated from Wt and QKI mutant embryonic stem cells

first: Weinian

last: Shou

state: IN

department: Pediatrics

summary: We sequenced mRNA from cardiomyocytes derived from hESCS in vitro.  By using the Cas9n, we generated the QKI null hESCs. The gene expression level and alternative splicing events were compared between 4 control and 4 QkI KO samples.  Here, we applied a widely used cardiomyocyte differentiation protocol  that was reported to produce a population of more than 90% cardiac troponin T (TNNT2)-positive cardiomyocytes. And we are able to demonstrate that QKI is indespensible to cardiac sarcomerogenesis and cardiac function through its regulation of alternative splicing in genes involved in Z-disc formation, such as ACTN2, NEBL, ABLIM1, and PDLIM5.

overall_design: Compare potential altered RNA processing in normal and QKI mutant hESCs-differentiated hCMs at D15 of differention and alternative RNA splicing changes.

first: Ying

last: Liu

first: Xinyun

last: Cheng

first: Chen

last: Xu


title: Plant microRNAs in WT and SIDT1 KO mice liver

city: Nanjing

first: Zhen

last: Zhou

state: Jiangsu

address: 22th,Hankou Road

department: School of Lifesciences

country: China

institute: Nanjing University

type: Non-coding RNA profiling by high throughput sequencing

summary: Animal microRNAs (which lack 2'-O-methyl modification) can be broken down at the terminal nucleotide by oxidation, while plant microRNAs (with 2'-O-methyl modification) are not affected. To gain additional sight into the role of SIDT1 in exogenous plant microRNAs absorption, we profiled oxidized smalll RNAs of liver from SIDT1 deficient mice and their wild type couterparts.

overall_design: Profiling of known plant microRNA in the liver samples from WT and SIDT1 KO mice.

first: Qun

last: Chen

first: Qipeng

last: Zhang


title: Cell-free DNA Methylation and Transcriptomic Signature Prediction of Pregnancies with Adverse Outcomes [RNA-seq]

city: Los Angeles

first: Giorgia

last: Del Vecchio

address: 610 Charles E Young Dr S, Room 5146

institute: University of California Los Angeles

summary: Although analysis of maternal plasma cell-free content has been employed for screening of genetic abnormalities within a pregnancy, limited attention has been paid to its use for the detection of adverse pregnancy outcomes (APOs) based on placental function. We investigated the cell-free RNA content of 102 maternal, 25 cord plasma samples and 7 non pregnant women as control. using cell-free RNA sequencing, APOs revealed seventy-one differentially expressed genes early in pregnancy. We noticed the upregulation of S100A8, MS4A3 and MMP8 that have been already associated with APOs but also the upregulation of BCL2L15 and the downregulation of ALPL that have never been associated with APOs. We constructed a classifier with a positive predictive ability (AUC) of 0.91 for APOs, 0.86 for preeclampsia alone and 0.64 for GDM. We conclude that placenta-specific cell-free nucleic acids during early gestation provide the possibility of predicting APOs prior to the emergence of characteristic clinical features.

overall_design: cell-free RNA profile from plasma of pregnant women with normal pregnancies or with adverse pregnancy outcomes (APOs) such as gestational diabetes, preeclampsia or gestational hypertension. The samples have been collected at 1st, 2nd and 3rd trimester during pregnancy and again at delivery. The cord blood has been collected as well.  We analyzed the cell-free RNA content of 102 maternal, 25 cord plasma samples and 7 non pregnant women as control.

first: Qingjiao

last: Li

first: Wenyuan

first: Shanthie

last: Thamotharan

first: Anela

last: Tosevska

first: Marco

last: Morselli

first: Kyunghyun

last: Sung

first: Carla

last: Janzen

first: Xianghong

first: Matteo

last: Pellegrini

first: Sherin

middle: U

last: Devaskar


title: Deciphering Primate Retinal Aging at Single-Cell Resolution

city: Shanghai

first: Yuxuan

last: Zheng

address: 825 Zhangheng Rd.

institute: Fudan University

summary: The retina is a light-sensitive highly-organized tissue, which is vulnerable to aging and age-related retinal diseases. However, the effects of aging on retinal cell types including those present in neural retina and retinal pigment epithelium (RPE), as well as cell types in choroid layer remain largely unknown. Here, we established the single-cell transcriptomic atlas of the retina and adjacent choroid in young and aged non-human primates (NHPs), identifying 15 cell types with distinct gene expression signatures and finding several novel markers. Our analysis reveals that oxidative stress is a major aging feature of the cells in the neural retinal layer, whereas an enhanced inflammatory response is that of RPE and choroidal cells. We also found that the RPE cell is the cell type most susceptible to aging in retina, as evidenced by the decreased cell density as well as the highest numbers of differentially expressed genes overlapping with genes underlying aging and aging-related retinal diseases, along with aberrant cell-cell interactions with its two adjacent layers. Altogether, our study provides the roadmap for understanding retinal aging in a NHP model at single-cell resolution, enabling the identification of new diagnostic biomarkers and potential therapeutic targets for age-related human retinal disorders.

overall_design:
We collected 7,461 single cells from the whole retinas of 8 young and 8 aged monkeys and performed single-cell RNA-seq sequencing.
[Correspondences between file labels and monkey individuals]
CE01: YF1, CE07: YF2, CE08: YF3, CE14: YF4
CE04: YM1, CE05: YM2, CE06: YM3, CE15: YM4
CE09: OF1, CE10: OF2, CE13: OF3, CE16: OF4
CE03: OM1, CE11: OM2, CE12: OM3, CE17: OM4

first: Si

last: Wang

first: Qingqing

first: Xiaojun

last: He

first: Ruotong

last: Ren

first: Weiqi

first: Moshi

last: Song

first: Huifang

last: Hu

first: Feifei

first: Guoqiang

last: Sun

first: Shuhui

first: Zunpeng

first: Yang

last: Yu

first: Piu

last: Chan

first: Guo-Guang

last: Zhao

first: Qi

first: Guang-Hui

first: Fuchou

last: Tang

first: Jing

last: Qu


title: ATACSeq and genome-wide binding profile of EBF1 and Pax5 to unravel molecular networks driving leukemia in Ebf1+/-Pax5+/- (dHet) B-ALL mice.

city: Freiburg

first: Senthilkumar

last: Ramamoorthy

address: Stübeweg 51

department: Cellular & Molecular Immunology

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

summary: ATACSeq, EBF1 ChIPSeq and Pax5 ChIPSeq of dHet B-ALL, dHet proB and wt proB cells.

overall_design: ATACSeq, EBF1 ChIP and Pax5 ChIP were performed on the pro-B cell lines and dHet B-ALL cell lines. The pro-B cell lines were established by culturing c-Kit+ fetal liver cells of Ebf1+/+ Pax5+/+ Rag2-/- or Ebf1+/-Pax5+/-Rag2-/- cells.  Ebf1+/-Pax5+/- dHet B-ALL cell lines were established using bone marrow CD19+AA4.1hi cells.

first: Sören

last: Boller

first: Kohei

last: Kometani

first: Rudolf

last: Grosschedl


title: Gene expression profifile during osteogenic differentiation of hPDLSCs was analyzed using microarray

city: Guangzhou

first: Zhao

last: Chen

state: Guangdong

address: Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, P.R. China

department: Department of Stomatology

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

summary: The roles of lncRNAs and mRNAs in osteogenic differentiation of human periodontal ligament stem cells (hPDLSCs) remain largely unexplored. In this study, the underlying molecular mechanism of osteogenic differentiation in hPDLSCs is investigated using microarray profiling.

overall_design: Gene expression of hPDLSCs at differentiated group were cultured with an odontogenic differentiation medium containing 50 mg/mL ascorbic acid, 10 ng/mL dexamethasone, and 10 mmol/L β-glycerolphosphate (Sigma, St Louis, MO, USA) for 14 days in 6-well plates. hPDLSCs at undifferentiated group were cultured in 10 % FBS in DMEM with no supplements.

first: Fuchun

last: Fang

first: Qian


title: miRNA expression profifile during osteogenic differentiation of hPDLSCs was analyzed using microarray

institute: Nanfang Hospital, Southern Medical University

summary: The roles of miRNA in osteogenic differentiation of human periodontal ligament stem cells (hPDLSCs) remain largely unexplored. In this study, the underlying molecular mechanism of osteogenic differentiation in hPDLSCs is investigated using microarray profiling.

overall_design: miRNA expression of hPDLSCs at differentiated group were cultured with an odontogenic differentiation medium containing 100 nM dexamethasone, 10 mmol/L β-glycerophosphate, and 50 mg/mL ascorbic acid. (Sigma, St Louis, MO, USA) for 14 days in 6-well plates. hPDLSCs at undifferentiated group were cultured in 10 % FBS in DMEM with no supplements.

first: Yilin

last: Hao


title: Global hyperactivation of enhancers stabilizes human and mouse naïve pluripotency [RNA-Seq 2]

city: Madrid

first: Cian

last: Lynch

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Molecular Oncology

institute: Spanish National Cancer Research Centre (CNIO)

summary: The transition of pluripotent stem cells (PSCs) from primed to naïve states constitutes a prototypical example of cellular plasticity.  The naïve state can be stabilized by defined chemical cocktails that block extracellular signals, notably including the MEK pathway. However, little is known regarding the underlying transcriptional mechanisms.  Here, we report that the transcriptional landscape of the naïve state can be mimicked in mouse and human PSCs by stimulating transcriptional enhancers.  This is attained by inhibiting the CDK8 and CDK19 kinases, which are negative regulators of Mediator, a critical component of enhancer function.  Mechanistically, CDK8/19i triggers a global increase in the recruitment of RNA Pol II at promoters and enhancers, hyperactivating enhancers and their target genes.  Lastly, the emergence of naïve pluripotency in the pre-implantation epiblast coincides with a marked reduction in CDK8/19 activity, and CDK8/19i blocks its subsequent developmental progression.  These findings suggest that naïve pluripotency during development includes hyperactivation of enhancers and can be captured in vitro, either by blunting extracellular signaling, or by stimulating enhancer-driven transcription.  These principles may apply to other cellular transitions.

overall_design: We performed RNA-seq in human PSCs adapted to culture media containing small molecule inhibitors.

first: Raquel

last: Bernad

first: Ana

last: Martínez-Val

first: Marta

last: Shahbazi

first: Sandrina

last: Nóbrega-Pereira

first: Isabel

last: Calvo

first: Carmen

last: Blanco

first: Laia

last: Richart-Ginés

first: Osvaldo

last: Graña-Castro

first: Gonzalo

last: Gómez-Lopez

first: Sagrario

last: Ortega

first: Irene

last: Aksoy

first: Susana

last: Prieto

first: Agustin

middle: F

last: Fernandez

middle: I

last: Zapico

first: Mario

last: Fraga

first: Joaquin

last: Pastor

first: Pierre

last: Savatier

first: Daniel

last: Fisher

first: Javier

last: Muñoz

first: Magdalena

last: Zernicka-Goetz

first: Manuel

last: Serrano


title: RNASeq analysis to unravel molecular networks driving leukemia in Ebf1+/-Pax5+/- (dHet) B-ALL mice

first: Senthilkumar

last: Ramamoorthy

summary: To profile gene expression changes in  Ebf1+/-Pax5+/- (dHet) leukemic mice, we performed RNASeq analysis in dHet B-ALL, dHet proB and wt proB cells.

overall_design: Leukemic cells derived from the lymph node of three dHet B-ALL mice (686,713 and 760), a short term culture of proB cells derived from dHet pre-leukemic mice and wt proB cells were used for the RNASeq analysis.

first: Marc

last: Bayer

first: Kohei

last: Kometani

first: Sören

last: Boller

first: Rudolf

last: Grosschedl


title: Single-cell RNASeq analysis to unravel molecular networks driving leukemia in Ebf1+/-Pax5+/- (dHet) B-ALL mice

summary: Here, we report that EBF1 and Pax5 collaborate in a  dose-dependent manner to regulate the IL-7-STAT5 signaling  pathway and one-carbon metabolism, whereby  we found both diminished and enhanced binding of  EBF1 and Pax5 to target genes in compound heterozygous  mutant mice. Moreover, single-cell RNA sequencing  analysis identified a small subset of wild-type pro-B cells  on the trajectory to pre-B cells that share gene expression  signatures with leukemic Ebf1+/−Pax5+/− pro-B cells.  Thus, a normal expression level of EBF1 and Pax5 is required  for safeguarding a potentially vulnerable pro-Bcell  subset from a transformation to B-ALL.

overall_design: Single cells from the bone marrow, spleen or blood were sorted into 384-well plates and processed using a modified version of the CEL-Seq2 protocol (Hasimshony et al. 2016, Genome Biology, DOI: 10.1186/s13059-016-0938-8).

first: Josip

last: Herman

first: Joy

last: Edwards-Hicks

first: Haribaskar

last: Ramachandran

first: Rui

last: Li

first: Ramon

last: Klein-Geltink

first: Erika

middle: L

last: Pearce

first: Dominic

last: Grün


title: RNA-sequencing with human liver organoids derived from human induced pluripotent stem cells

status: Public on Oct 18 2020

city: Tokyo

first: Norikazu

last: Saiki

address: 1-5-45 Yushima, Bunkyo-ku

department: Institute of Research

country: Japan

institute: Tokyo Medical and Dental University

summary: We established a human liver organoid (HLO) based screening model for analyzing DILI pathology at organoid resolution. HLO contains polarized immature hepatocytes with bile canaliculi-like architecture, establishing the unidirectional bile acid transport pathway. Single cell RNAseq profiling identified diverse and zonal hepatocytic populations that in part emulate primary adult hepatocytes. By developing a 384 well based high-speed live imaging platform, we successfully developed a Liver organoid-based Toxicity screen (LoT) with multiplexed readouts measuring viability, cholestatic and/or mitochondrial toxicity. We functionally validated LoT with 238 marketed drugs at 4 different concentrations. LoT positively predicts genomic predisposition (CYP2C9*2) for Bosentan-induced cholestasis. Thus, LoT is a high-fidelity model for drug safety with a cost-effective platform, facilitating compound optimization, mechanistic study, and precision medicine as well as drug screening applications.

overall_design: Examination of mRNA expression profile in human liver organoid derived from human induced pluripotent stem cells.

first: Takanori

last: Takebe

first: Tadahiro

last: Shinozawa

first: Masaki

last: Kimura


title: Microarray analysis to unravel molecular networks driving leukemia in Ebf1+/- Pax5+/- (dHet) B-ALL mice

summary: To profile gene expression changes in  Ebf1+/-Pax5+/- (dHet) B-ALL mice, we performed microarray analysis in dHet B-ALL, dHet proB and wt proB cells

overall_design: Leukemic cells derived from the lymph node of three dHet B-ALL mice (686,713 and 760), a short term culture of proB cells derived from dHet pre-leukemic mice and wt proB cells were used for the microarray analysis.


title: EBF1 and Pax5 safeguard leukemic transformation by limiting IL-7 signaling, Myc expression and folate metabolism


title: Global hyperactivation of enhancers stabilizes human and mouse naïve pluripotency

first: Cian

last: Lynch

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

first: Osvaldo

last: Graña


title: Mitochondrial Potentiation Ameliorates Age Related Heterogeneity in Hematopoietic Stem Cell Function [MMPhigh and MMPlow HSCs]

city: Lund

first: Shamit

last: Soneji

address: Solvegatan 19

country: Sweden

institute: BMC

summary:
introduction: Ageing is associated with reduced fitness and increased myeloid bias of the hematopoietic stem cell (HSC) compartment, causing increased risk of immune compromise, anemia and malignancy
results: We show that mitochondrial membrane potential (MMP) can be used to prospectively isolate chronologically old HSCs with transcriptional features and functional attributes characteristic of young HSCs, including a high rate of transcription and balanced lineage-affiliated programmes. Strikingly, MMP is a stronger determinant of the quantitative and qualitative transcriptional state of HSCs than chronological age and transcriptional consequences of manipulation of MMP in HSCs within their native niche suggest a causal relationship.  Accordingly, we show that pharmacological enhancement of MMP in old HSCs in vivo increases engraftment potential upon transplantation and reverses myeloid-biased peripheral blood output at steady state.
conclusion: Our results demonstrate that MMP is a source of heterogeneity in old HSCs and its pharmacological manipulation can alter transcriptional programs with beneficial consequences for function.

overall_design: RNA seq of MMPhigh and MMPlow sorted HSCs from either young or old mice

first: Els

last: Mansell

first: Chela

last: James

first: Elitza

last: Deltcheva

first: John

last: Brown

first: T

last: Enver


title: Super Enhancer Regulation of Cytokine-Induced Chemokine Production in Alcoholic Hepatitis

first: Aditya

last: Bhagwate


title: Super Enhancer Regulation of Cytokine-Induced Chemokine Production in Alcoholic Hepatitis [RNA-Seq]

summary: Super enhancer in liver propagates inflammatory signaling by super enhancer-mediatedinducing chemokine expression and is the therapeutic potential of BET inhibition in Alcoholic hepatitis(AH) treatment.

overall_design: For human liver RNA-Seq and ChIP-Seq analyses, human liver explants from 6 patients with AH were procured at the time of liver transplant surgery. 4 control patients with no history of chronic liver diseases undergoing liver resection for other causes were obtained to serve as controls.

first: Vijay

last: Shah

first: Sheng

last: Cao

first: Mengfei

last: Liu


title: Single-Cell sequence profile in human cardiomyocytes differentiated from Wt and QKI mutant embryonic stem cells

first: Weinian

last: Shou

summary: Transcriptomic profiling of WT and QKI KO hESC derived cardiomyocyte on Day 6 and 15 via Single cell RNA-seq.

overall_design: To gain insight into the role of QKI on cardiac lineage commitment,we applied a widely used cardiomyocyte differentiation protocol  that was reported to produce a population of more than 90% cardiac troponin T (TNNT2)-positive cardiomyocytes. Following, we performed single-cell RNA-sequencing (scRNA-seq) on over 6,500  cells captured across two key time points (Day 6 and 15) during in vitro cardiac differentiation of human ESCs. When comparing the overall distribution of differentiated cells derived from QKI null hESCs and normal control hESCs at Day-6 and -15, we did not observe a major defect in terms of different cell lineages, suggesting that the lineage specification and determination towards cardiomyocytes were well preserved in hESCs-QKIdel. When we compared the expression profiles of these clusters, we did find the expression of 13 genes which involved in sarcomere formation was significantly altered. These downregulation of sarcomere genes may lead to the dimished contractile function of hESCs-QKIdel derived cardiomyocytes.

first: Ying

first: Xinyun

last: Chen

first: Chen

last: Xu


title: Cell-free DNA Methylation and Transcriptomic Signature Prediction of Pregnancies with Adverse Outcomes

first: Giorgia

last: Del Vecchio

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Cell-free DNA Methylation and Transcriptomic Signature Prediction of Pregnancies with Adverse Outcomes [WGBS]

summary: Although analysis of maternal plasma cell-free content has been employed for screening of genetic abnormalities within a pregnancy, limited attention has been paid to its use for the detection of adverse pregnancy outcomes (APOs) based on placental function. Here we investigated cell-free DNA and RNA content of 102 maternal and 25 cord plasma samples. Employing a novel deconvolution methodology, we found that during the first trimester, placenta-specific DNA increased prior to the subsequent development of gestational diabetes with no change in patients with preeclampsia while decreasing with maternal obesity. Moreover, using cell-free RNA sequencing, APOs revealed seventy-one differentially expressed genes early in pregnancy. We noticed the upregulation of S100A8, MS4A3 and MMP8 that have been already associated with APOs but also the upregulation of BCL2L15 and the downregulation of ALPL that have never been associated with APOs. We constructed a classifier with a positive predictive ability (AUC) of 0.91 for APOs, 0.86 for preeclampsia alone and 0.64 for GDM. We conclude that placenta-specific cell-free nucleic acids during early gestation provide the possibility of predicting APOs prior to the emergence of characteristic clinical features.

overall_design: cell-free DNA deconvolution analysis from plasma of pregnant women with normal pregnancies or with adverse pregnancy outcomes (APOs) such as gestational diabetes, preeclampsia or gestational hypertension. The samples have been collected at 1st, 2nd and 3rd trimester during pregnancy and again at delivery. The cord blood has been collected as well.  We analyzed the cell-free WGBS content of 102 maternal, 25 cord plasma samples and 7 non pregnant women as control.

first: Qingjiao

last: Li

first: Wenyuan

first: Shanthie

last: Thamotharan

first: Anela

last: Tosevska

first: Marco

last: Morselli

first: Kyunghyun

last: Sung

first: Carla

last: Janzen

first: Xianghong

last: Zhou

first: Matteo

last: Pellegrini

first: Sherin

last: Devaskar


title: Global hyperactivation of enhancers stabilizes human and mouse naïve pluripotency [RNA-seq]

first: Cian

last: Lynch

overall_design: We performed two RNA-seq experiments in mouse PSCs treated with small molecule inhibitors, where the cells were cultured in Serum/LIF or KSR/LIF (serum-free) conditions.

first: Raquel

last: Bernad

first: Ana

last: Martínez-Val

first: Marta

last: Shahbazi

first: Sandrina

last: Nóbrega-Pereira

first: Isabel

last: Calvo

first: Carmen

last: Blanco

first: Laia

last: Richart-Ginés

first: Osvaldo

last: Graña-Castro

first: Gonzalo

last: Gómez-Lopez

first: Sagrario

last: Ortega

first: Irene

last: Aksoy

first: Susana

last: Prieto

first: Agustin

last: Fernandez

last: Zapico

first: Mario

last: Fraga

first: Joaquin

last: Pastor

first: Pierre

last: Savatier

first: Daniel

last: Fisher

first: Javier

last: Muñoz

first: Magdalena

last: Zernicka-Goetz

first: Manuel

last: Serrano


title: Two faces of bivalent domain regulate VEGFA responsiveness and angiogenesis

status: Public on Oct 17 2020

city: Minhang

first: bing

last: zhang

state: Shanghai

address: 800 Dong Chuan Road

department: Shanghai Center for Systems Biomedicine

institute: Shanghai Jiao Tong University

summary: The bivalent domain at promoter region is a unique epigenetic feature poised for activation or repression during cell differentiation in embryonic stem cell. However, the function of bivalent domains in already differentiated cells remains exclusive. By profiling the epigenetic landscape of endothelial cells during VEGFA stimulation, we discovered that bivalent domains are widespread in endothelial cells and preferentially marked genes responsive to VEGFA. The bivalent domains responsive to VEGFA have more permissive chromatin environment comparing to other bivalent domains. The initial activation of bivalent genes depends on RNAPII pausing release induced by EZH1 rather than removal of H3K27me3. The later suppression of bivalent gene expression depended on KDM5A recruitment by its interaction with PRC2. Importantly, EZH1 promoted both in vitro and in vivo angiogenesis by upregulating EGR3, whereas KDM5A dampened angiogenesis. Collectively, this study demonstrated a novel dual function of bivalent domains in endothelial cells to control VEGF responsiveness and angiogenesis.

overall_design: Our model system consisted of human umbilical vein endothelial cells that were cultured overnight in low serum and no VEGFA, and then stimulated for 12 hours with 50 ng/ml VEGFA. Samples were collected at 0 (unstimulated), 1, 4, and 12 hours. ChIP-seq of corresponding factors or histone markers were sequenced.

first: Jiahuan

last: Chen

first: Xiaodong

last: Liang

first: Shasha

last: Zhang

first: Shiyan

last: Wang

first: Sara

middle: P

last: Garcia

first: Pengyi

last: Yan

first: Huijing

last: Yu

first: Zixuan

last: Li

first: Li

last: Liu

first: Weiting

last: Wei

first: Huangying

last: Le

first: Yan

first: Guo-cheng

last: Yuan

first: Sun

first: Yingwei

first: Kun

last: Sun

first: William

middle: T

last: Pu

first: Bing


title: Global hyperactivation of enhancers stabilizes human and mouse naïve pluripotency [ChIP-seq]

first: Cian

last: Lynch

summary: We perform ChIP-seq for RNA Pol II total and phosphorylated forms, in mouse ES cells, and in three culture conditions

overall_design: We investigated global regulation of RNA Pol II abundance on chromatin by ChIP-seq in mouse ES cells (E14, BL6/129 mixed background) cultured in three conditions: serum/LIF, 2i, or CDK8/19i.  Similar to published resources of Pol II ChIP-seq in mouse ES cells (ENCODE: https://www.encodeproject.org/; Marks H et al., 2012, Cell; Rahl PB et al., 2010, Cell), we found RNA Pol II, both total and Ser5-phosphorylated, enriched at known transcriptional start sites (TSS) in all three conditions.  ChIP-Seq METHODS: ChIP-seq for RNA Pol II was performed as described by Young and colleagues (Rahl PB et al., 2010, Cell).  Briefly, cells were fixed using 1% formaldehyde, scrape-harvested, resuspended in ChIP lysis buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl, pH 8.1) and sonicated using Covaris water bath sonicator to generate fragments of 150 to 500 bp. Soluble chromatin was diluted 10 fold in ChIP Dilution buffer (1% Triton X-100, 2 mM EDTA pH 8.0, 150 mM NaCl) precleared with Agarose Protein A/G beads (Santa Cruz), and then incubated with antibody specific for total RNA Pol II (N-20, sc-899x, Santa Cruz) or specific for the RNA Pol II Ser5P-phoshorylated form (Abcam #ab5131).  After incubation, immunocomplexes were collected with Agarose Protein A/G beads (Santa Cruz). Next, the immunocomplexes were washed sequentially with Low Salt Wash Buffer (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris-HCl, pH 8.1, 150mM NaCl), High Salt Wash Buffer (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris-HCl, pH 8.1, 500mM NaCl), LiCl Wash Buffer (0.25M LiCl, 1% NP40, 1% deoxycholate-Na, 1mM EDTA, 10mM Tris-HCl, pH 8.1) and washed twice with TE (10 mM Tris-HCl pH7.5, 1mM EDTA).  Immunocomplexes were eluted in ChIP elution buffer (1%SDS, 0.1M NaHCO3) and the crosslinking was reverted by incubation at 65 ºC for 8 hrs with 200 mM NaCl. Samples were treated with Proteinase K and RNase A, and DNA was extracted using Phenol-Chloroform.  DNA precipitation was in 100% ethanol with 0.1 M NaAcetate ph5.2 and 2 uLs glycogen (Roche).  The DNA pellet was washed with 70% ethanol, and resuspended in ddH2O. Purified chromatin was used for library construction.  For ChIP-seq the amount of DNA used was ~5 ng from each sample (as quantitated by fluorometry). Samples were processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq DNA Sample Preparation Guide" (part # 15005180 Rev. C). Adapter-ligated libraries were completed by limited-cycle PCR with Q5 High-Fidelity DNA Polymerase (NEB) and Illumina PE primers (15 cycles), and further purified with a double-sided SPRI size selection to obtain a size distribution in the range of 230-500bp. Libraries were applied to an Illumina flow cell for cluster generation (TruSeq cluster generation kit v5) and sequenced on the Illumina HiSeq4000 with SBS TruSeq v5 reagents by following manufacturer's protocols, to 20-25 million reads per replicate, to a total of >60 million reads per condition.  BIOINFORMATIC METHODS: Sequencing quality for ChIP-seq samples was analyzed with FastQC (Andrews, 2011).  Reads were aligned with Bwa 0.7.5a (Li and Durbin, 2009) to the mouse reference genome (NCBIm37/mm9) using the default seed length (32) and allowing 1 mismatch in the seed.  SAMtools 0.1.16 (Li et al., 2009b) was used to convert the output alignment SAM files to the BAM file format, sort the alignments and eliminate duplicated reads.  BEDTools 2.23.0 (Quinlan, 2014) was used to convert the resulting files to the BED format.  All ChIP and input samples were randomly normalized to the same number of reads.  Peak calling was performed with MACS 2.0.10.20130712 (Feng et al., 2012) using the input sample as control for each one of the ChIP samples.  BigWig files were obtained with bedGraphToBigWig (Kent et al., 2010) from the BedGraph files generated with MACS.  Resulting peaks were annotated with PeakAnalyzer 1.4 (Salmon-Divon et al., 2010) and the distribution of peaks was plotted with SeqMiner 1.3.3e (Ye et al., 2014).

first: Osvaldo

last: Graña


title: Impact of acute noise trauma on the gene expression profile of the hippocampus

city: Seongnam

first: So Young

last: Kim

address: Yatapro 59

country: South Korea

institute: CHA University

summary: To investigate the early changes in the hippocampus following noise-induced hearing loss, the gene expression profile of the hippocampus was evaluated using microarray analyses immediately after exposure to intense noise stimuli.

overall_design: rats were divided into control and noise groups.  Immediately after the 3 days of noise exposure, hippocampi were used for microarray analysis.

first: Chang

last: Lee

first: Kyung

middle: W

first: So

middle: Y


title: Analysis of epigenome reprogramming and  pre-malignant transformation in bronchial epithelial cell lines

city: Albuquerque

first: Steven

last: Belinsky

state: NM

address: 2425 Ridgecrest Dr SE

department: Lung Cancer Program

institute: Lovelace Respiratory Research Institute

summary: An in vitro model of pre-malignancy was used to evaluate the role of double-strand break DNA repair capacity in transformation of hTERT/CDK4 immortalized human bronchial epithelial cells and reprogramming of the epigenome. Remove probes on X and Y chromosomes, detection p-value >0.01 and/or outside TSS1500-1st Exon genomic region.  Analysis was restricted to probes for genes found to be methylated in TCGA lung cancer tumors and change in beta values was assessed in transformed clones compared to vehicle treated control cell lines.

overall_design: Bisulphite converted DNA from the 8 samples were hybridized to the Illumina  MethylationEPIC Beadchip

first: Maria

last: Picchi

first: Ivo

last: Teneng


title: Analysis of transcriptome and epigenome reprogramming and pre-malignant transformation in bronchial epithelial cell lines

type:
Expression profiling by array
Methylation profiling by array


title: Transcriptional profiling of paired ccRCC patient CD8+ and CD19+ lymphocytes isolated from tumors, normal tissues, and circulating peripheral blood

city: Montreal

first: Anne

last: Monette

state: Quebec

address: Centre de recherche du CHUM (CRCHUM), 900 rue St-Denis

country: Canada

institute: University of Montreal

summary: Tumor infiltrating lymphocytes are widely associated with positive outcomes, but are still markers of a systemic failed immune response against unresolved cancer. Cancer immunotherapies can reverse their tolerance phenotypes, while preserving tumor-reactivity and neoantigen-specificity shared with circulating immune cells. We performed comprehensive transcriptomic analyses to identify gene signatures common to circulating and tumor infiltrating lymphocytes in the context of clear cell renal cell carcinoma. Modulated genes also associated with disease outcome were validated in other cancer types. Using bioinformatics we identified practical diagnostic markers and actionable targets of the failed immune response. On circulating lymphocytes, three genes could efficiently stratify patients from healthy control donors. From their associations with resistance to cancer immunotherapies as well as viral and bacterial infections, we have uncovered not only pan-cancer, but pan-pathology failed immune response gene signatures.

overall_design: CRCHUM kidney biobank consented, TNM stages I-III clear cell renal cell carcinoma (ccRCC) patients underwent resection at the CHUM, Montreal, Quebec from 2013 to 2017. Microarray analysis was performed on paired patient (pt) CD8+ T cells and CD19+ B cells isolated from ccRCC tumors (TIL, TIL-B), normal tumor-adjacent tissue infiltrating immune cells (TIIC), peripheral blood mononuclear cells (PBMC) from patients (ptPBL), and from age-matched healthy control donors (cdPBL).

first: Nadia

last: Al-Banna

first: Louise

last: Rousseau

first: Jean-Baptiste

last: Lattouf

first: Jean-Pierre

last: Routy

first: Réjean

last: Lapointe


title: Long non-coding RNA CAR10 promotes lung adenocarcinoma metastasis via miR-203/30/SNAI axis

city: Changsha

first: Zheng

last: Li

state: Hunan

address: 110 Xiangya Road

institute: Central South University

summary:
Long noncoding RNAs (lncRNAs) are a class of transcripts longer than 200 nucleotides with limited protein coding potential. Long non-coding RNAs (lncRNAs) play an important role in lung adenocarcinoma (LUAD) metastasis.
In this study, we profiled matched tissue from LUAD patients with HTA 2.0 microarray analysis and identified lncRNA- chromatin-associated RNA 10 (CAR10) as obviously clearly overexpressed in LUAD tissues.  we demonstrated that CAR10 accelerates tumor growth and promotes metastasis in lung adenocarcinoma. CAR10 was shown to promote epithelial-to-mesenchymal transition (EMT) translation of LUAD cells through sponging miR-30/203, leading to upregulation of SNAI1/2 expression.

overall_design: A coding and non-coding gene expression analysis was performed on a cohort of 3 patients. We used 3 tumor, 3 paired metastatic and 3 paired normal lung tissue samples. We analyzed these 9 samples using human transcriptome microarray Affymetrix® HTA 2.0.

first: Xiaolu

last: Ge

first: Gui-yuan

first: Lin

last: Jiang

first: Liqing

last: Jia

first: Zhezhe

last: Zhang

first: Xiaoling

first: Ranran

last: Wang

first: Ming

last: Zhou

first: Yanhong

first: Zhaoyang

last: Zeng

first: Juanjuan

last: Xiang


title: Analysis of transcriptome reprogramming and  pre-malignant transformation in bronchial epithelial cell lines

first: Steven

last: Belinsky

summary: An in vitro model of pre-malignancy was used to evaluate the role of double-strand break DNA repair capacity in transformation of hTERT/CDK4 immortalized human bronchial epithelial cells and reprogramming of the epigenome

overall_design: Total RNA isolated from DNA-PKC deficient HBECS or empty vector controls compared to vehicle or Bleomycin treated HBECs, respectively

first: Maria

last: Picchi

first: Ivo


title: Transcriptome analysis of G. oxydans 621H  in response to L-arabinose

status: Public on Oct 16 2020

city: Juelich

first: Tino

last: Polen

state: NRW

address: Wilhelm-Johnen-Str 1

department: IBG-1: Biotechnology

institute: Forschungszentrum Jülich GmbH

summary: DNA microarray analysis was performed to check whether the addition and/or oxidation of L-arabinose to the growth medium of G.oxydans 621H possibly affects short-term global gene expression.

platform_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: Addition of 1% (w/v) L-arabinose supplemented in the mid-exponential growth phase to G. oxydans 621H cells cultured in 4% (w/v) mannitol medium were compared to the respective control culture where water was added instead of L-arabinose.

first: Philipp

last: Moritz Fricke

first: Michael

last: Bott


title: Overexpression of an ethylene-forming ACC Oxidase (ACO) gene precedes the Minute Hilum seed coat phenotype in Glycine max

city: Urbana

first: Lila

middle: O.

last: Vodkin

state: IL

address: 1201 W. Gregory Dr.

department: Crop Sciences

institute: University of Illinois

summary:
Background: To elucidate features of seed development, we investigated the transcriptome of a soybean isoline from the germplasm collection that contained an introgressed allele known as minute hilum (mi) which confers a smaller hilum region where the seed attaches to the pod and also results in seed coat cracking surrounding the hilum region.
Results: RNAs were extracted from immature seed from an extended hilum region (i.e., the hilum and a small ring of tissue surrounding the hilum in which the cracks form) at three different developmental stages:10-25, 25-50 and 50-100 mg seed fresh weight in two independent replicates for each stage. The transcriptomes of these samples from both the Clark isoline containing the mi allele (PI 547628, UC413, ii R t mi G), and its recurrent Clark 63 parent isoline (PI 548532, UC7, ii R T Mi g), which was used for six generations of backcrossing, were compared for differential expression of 88,648 Glyma models of the soybean genome Wm82.a2. The RNA sequence data obtained from the 12 cDNA libraries were subjected to padj value <0.05 and at least two-fold expression differences to select with confidence genes differentially expressed in the hilum-containing tissue of the seed coat between the two lines. Glyma.09G008400 annotated as encoding an ethylene forming enzyme, ACC oxidase (ACO), was found to be highly overexpressed in the mi hilum region at 165 RPKMs (reads per kilobase per million mapped reads) compared to the standard line at just 0.03 RPKMs. Evidence of changes in expression of genes downstream of the ethylene pathway included those involved in auxin and gibberellin hormone action and extensive differences in expression of cell wall protein genes. These changes are postulated to determine the restricted hilum size and cracking phenotypes.
Conclusions: We present transcriptome and phenotypic evidence that substantially higher expression of an ethylene-forming ACO gene likely shifts hormone balance and sets in motion downstream changes resulting in a smaller hilum phenotype and the cracks observed in the minute hilum (mi) isoline as compared to its recurrent parent.

overall_design: 20 total samples representing the indicated stages of development and soybean genetic isolines described in the samples

first: Gracia

last: Zabala

first: Anupreet

last: Kour


title: Type 2 Diabetes reduces the enteroendocrine GLP-1 cell lineage in human obesity:  characterization in enriched human enteroendocrine cells

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

institute: IBENS

summary: Obesity and type 2 diabetes (T2D) can be associated with altered secretion of enterohormones in condition that remains to be understood in depth. Here, we aimed to decipher the mechanisms by which a major enterohormone GLP-1, is decreased in human obese patients according to their diabetic status.

overall_design: Patient candidates for bariatric surgery were phenotyped and pieces of jejunum were gathered. Jejunum epithelial samples from non-obese, obese and obese-diabetic patients were collected. Samples were assayed for enteroendocrine cell (EEC) densities and RNA for transcription factors known to drive EEC lineage. EEC enrichment was performed and transcriptional profile was established by RNA sequencing to identify unknown factors in relation with GLP-1 production and secretion in another group of 14 obese and 13 obese-diabetic patients

first: Céline

last: Osinski

first: Léa

last: Le Gléau

first: Christine

last: Poitou

first: Juan

last: de Toro-Martin

first: Laurent

last: Genser

first: Magali

last: Fradet

first: Hédi

last: Soula

first: Armelle

last: Leturque

first: Corinne

last: Blugeon

last: Joudren

first: Edwige

last: Hubert

first: Karine

last: Clément

first: Patricia

last: Serradas

first: Agnès

last: Ribeiro


title: RNA seq of mammary epithelial cells with loss-of-function Pten mutations

city: Clayton

first: David

middle: Richard

last: Powell

state: VIC

address: Wellington Road

department: Bioinformatics Platform

country: Australia

institute: Monash University

summary: The PTEN tumor suppressor controls cell death and survival by regulating functions of various molecular targets. Whilst the role of PTEN lipid-phosphatase activity on PtdIns(3,4,5)P3 and inhibition of PI3K pathway is well characterized, the biological relevance of PTEN protein-phosphatase activity remains undefined. Using knock-in (KI) mice harbouring cancer-associated and functionally relevant missense mutations, we show that although loss of PTEN lipid-phosphatase function cooperates with oncogenic PI3K to promote rapid mammary tumorigenesis, the additional loss of PTEN protein-phosphatase activity triggered an extensive cell death response evident in early and advanced mammary tumors. Omics and drug-targeting studies revealed that PI3Ks act to reduce glucocorticoid receptor (GR) levels, which are rescued by loss of PTEN protein-phosphatase activity to restrain cell survival. The dual regulation of GR by PI3K and PTEN functions as a rheostat that can be exploited for the treatment of PTEN-loss driven cancers.

overall_design: 4 biological replicates of RNA samples from mammary epithelial cells (luminal and basal) of Pten KI mice

first: Antonella

last: Papa

first: Hon

last: Yip


title: Identification of HSF1- target genes involved in thermal stress in the Pacific oyster Crassostrea gigas by ChIP-seq

city: Qingdao

first: Youli

last: Liu

address: Nanhai Road No. 7

institute: Institute of Oceanology

summary: The Pacific oyster Crassostrea gigas, a commercially important species inhabiting the intertidal zone, can tolerate temperature fluctuations. Heat shock transcription factor 1 (HSF1) plays an important role in the process of resistance of thermal stress. However, HSF1 has not been fully characterized in the Pacific oyster. C. gigas with an expansion of heat shock protein (HSP) 70. In this study, we analyzed genes regulated by HSF1 in response to heat shock by Chromatin immunoprecipitation followed sequencing (ChIP-seq), determined the expression patterns of target genes by qRT-PCR, and validated the regulatory relationship between one HSP70 and HSF1. We found 916 peaks corresponding to specific binding sites of HSF1, and peaks were annotated to nearest genes. In Gene Ontology analysis, HSF1 target genes was related to signal transduction, energy production, and response to biotic stimulus. Four HSP70 genes, two HSP40 genes, and one small HSP gene exhibited binding to HSF1. One HSP70 with a binding site in the promoter region was validated to be regulated by HSF1 under heat shock. These results provide a basis for future studies aimed at determining the mechanisms underlying thermal tolerance and provide insights into gene regulation in the Pacific oyster.

overall_design: Examination of two samples for HSF1-regulated gene detection

first: Qihui

last: Zhu


title: Characterization of immune responses and the lung transcriptome in a murine model of instanasal IL-33 challenge

status: Public on Oct 15 2020

city: Burnaby

first: Travis

last: Blimkie

state: British Columbia

address: 8888 University Drive

department: MBB

institute: Simon Fraser University

summary: We provide a comprehensive assessment of the cellular, immunological, physiological and transcriptomic responses in an IL-33-challenged murine model.

overall_design: A total of ten murine lung tissue samples were analyzed, comprising two groups of five: untreated controls, and IL-33-challenged mice.

first: Hadeesha

last: Piyadasa

first: Dylan

last: Lloyd

first: Amy

middle: H

last: Lee

first: Anthony

last: Altieri

first: Mahadevappa

last: Hemshekar

first: Natasah

last: Osawa

first: Sujata

last: Basu

first: Reza

last: Falsafi

first: Andrew

last: Halayako

first: Robert

last: Hancock

first: Neeloffer

last: Mookherjee


title: The TyrR regulon of Enterobacter ludwigii UW5

city: Fredericton

first: Cheryl

middle: L.

last: Patten

state: New Brunswick

address: 10 Bailey Drive

department: Biology

institute: University of New Brunswick

summary: The TyrR transcription factor controls the expression of genes for the uptake and biosynthesis of aromatic amino acids in Escherichia coli. In the plant-associated and clinically significant proteobacterium Enterobacter ludwigii UW5, the TyrR orthologue was previously shown to regulate genes that encode enzymes for synthesis of the plant hormone indole-3-acetic acid and gluconeogenesis, indicating a broader function for the transcription factor. This study aimed to delineate the TyrR regulon of E. ludwigii by comparing the transcriptomes of the wild-type and a tyrR deletion strain. Our data show that TyrR regulates the expression of over 150 genes positively or negatively. The findings suggest that the E. ludwigii TyrR regulon has diverged from that of E. coli to include genes for survival in the diverse environments that this bacterium inhabits, and illustrate the expansion and plasticity of transcription factor regulons.

overall_design: RNA expression profiles were analyzed from quadruplicate cultures of wild-type and tyrR deletion mutant of Enterobacter ludwigii UW5.

first: Thomas

last: Coulson

first: René

middle: M

last: Malenfant


title: Circadian clocks drive regeneration of pancreatic β-cells in mice

city: Geneva

first: Cedric

last: Howald

state: Geneva

address: Campus Biotech, Chemin des Mines 9

country: Switzerland

institute: Health2030 Genome Center

summary: We aimed to understand the functional roles of islet cellular oscillators under diabetic conditions and during β-cell regeneration. We assessed diurnal regulation of β-cell proliferation and the transcriptional landscape in α- and residual β-cells following β-cell ablation in Insulin-rtTA/TET-DTA mice that simultaneously expressed α- and β-cell specific fluorescent reports. The mouse pancreatic islets were isolated over 24-h with 4-h interval, followed by separation of α- and β- cells using FACS sorting, RNA extraction and RNA sequencing. Acute hyperglycemia and loss of β-cell mass perturbed absolute expression levels and temporal transcriptome profiles in residual β-cells, whereas in neighboring α-cells only changes in temporal profiles were observed. Strikingly, compensatory regeneration of β-cells exhibited circadian rhythmicity. In arrhythmic Bmal1 deficient mice, massive β-cell ablation led to aggravated hyperglycemia, hyperglucagonemia and a fatal diabetes. No compensatory proliferation of β-cells was observed in arrhythmic mice, suggesting an essential role of circadian clocks in β-cell regeneration.

overall_design: Massive β-cells ablation was induced in ProGcg-Venus/RIP-Cherry/PER2::Luc/Insulin-rtTA/TET-DTA mice by administering 300 mg of doxycycline (DOX) in the drinking water supplemented with 2% sucrose. The control group received only water supplemented with 2 % sucrose. All the experiments were done in mice aged 6-8 weeks, under standard animal housing conditions with ad libitum access to food and water and under 12 h light/12 h dark cycles (LD). For the islet isolation experiments, male mice were subjected to night-restricted feeding 10 days prior to the experiments, and during the entire period of DOX treatment and sample collection. For the islet isolation across 24 h period, half of the animals were entrained by inverted LD and feeding cycles for 2 weeks preceding the experiments.   Islets of Langerhans were isolated by standard procedure based on collagenase (Type XI, Sigma) digestion of pancreas followed by Ficoll purification (Petrenko et al., 2017a). Islet cells were gently dissociated by 0.05% trypsin (GIBCO) treatment, re-suspended in KRB solution (pH 7.4, supplemented with 0.3 % free fatty acid bovine serum albumin (BSA; Sigma), 1.4 mM glucose and 0.5 mM EDTA). α- and β-cell populations were separated by flow cytometry fluorescence activated cell sorting (FACS; Astrios sorter (Beckman Coulter)) based on fluorescence wavelength and intensity, cell singlet nature, size and viability as described previously (Petrenko et al., 2017b).

first: Volodymyr

last: Petrenko

first: Charna

last: Dibner

first: Miri

last: Stolovich-Rain

first: Bart

last: Vandereycken

first: Laurianne

last: Giovannoni

first: Kai-Florian

last: Storch

first: Yuval

last: Dor

first: Simona

last: Chera


title: Functional interrogation of immature β-cells reveals their role in insulin release

city: birmingham

first: ildem

last: akerman

address: BR Tower, 3rd Floor, Room 333, Edgbaston,

department: IMSR

country: United Kingdom

institute: University of Birmingham

summary: Immature β-cells are present in adult islets. However, their contribution to insulin release is not fully understood. Here we show that specific loss of immature β-cells induces failure throughout the β-cell complement. Functional mapping of the β-cell population in rodent and human loss-of-immaturity islets revealed defects in metabolism, ionic fluxes and insulin secretion. At the transcriptomic level, loss of immature β-cells led to dysregulation of gene pathways involved in glucose and carbohydrate-derivative metabolic processes. Using a chemogenetic disruption strategy, immature β-cells were found to depend on the islet signaling network for their phenotype. During metabolic stress, islet function could be restored by redressing the balance between immature and mature β-cells. We thus unveil immature β-cells as a critical component in islet operation. Preserving immature β-cells might be important for islet engineering efforts and more broadly the treatment of type 1 and type 2 diabetes.

overall_design: RIP7rtTA+/-;TetO-M3C+/- mice possess a gene cassette comprising of the mouse Pdx1, Mafa, Ngn3, and mCherry genes under the control of the Tet-On system. Upon addition of doxycycline these genes are overexpressed in β-cells leading to an increase in the ratio of mature/immature cells. Gene expression changes in these mice compared with littermate controls was assessed using RNA-sequencing of islets isolated from these mice.

first: Daniela

last: Nasteska

first: Nicholas

last: Fine

first: Ildem

last: Akerman

first: David

last: Hodson


title: A whole-genome CRISPRa screening metformin resistance related gene in prostate cancer

status: Public on Oct 14 2020

city: Huizhou

first: Chen

middle: Jia

last: hong

address: 41 erling North Road, Huicheng District, Huizhou City, Guangdong Province

department: Department of Urology

institute: Huizhou Municipal Central Hospital

summary: Metformin is a classic type II diabetes drug which has possessed anti-tumor properties for various cancers. However, different cancers do not respond to metformin with the same effectiveness or acquire resistance. Thus, searching for vulnerabilities of metformin-resistant prostate cancer is a promising strategy to improve the therapeutic efficiency. A genome-scale CRISPR-Cas9 activation library targeting 23430 genes is conducted to identify the genes that confer resistance to metformin in prostate cancer cells.

overall_design:
Examination of the genes that confer resistance to metformin in DU145 cells
22.5 μg of the human CRISPR/Cas9 SAM pooled library was transfected into 7.5×10^6 HEK293 T cells for 24 h. Viral supernatant was harvested, and DU145 cells were transduced at a calculated multiplicity of infection (MOI) of 0.4 followed by selection with hygromycin B (YEASEN, 60225ES03) and blasticidin (MDBio, D0120601) for 15 days. The DU145 cells were  treated three rounds with metformin (100 mM) for 24 h .


title: Assessing biosimilarity of Trastuzumab monoclonal antibody therapeutics using RNA sequencing

city: Waterloo

first: Karsten

last: Rinas

state: ON

address: 200 University Ave W

institute: University of Waterloo

summary: Patents of some therapeutic monoclonal antibodies (mAb) used for cancer treatment are ending soon, allowing for the entry of similar analogs (biosimilars) onto the market. To have a biosimilar approved by health agencies, the manufacturer must typically demonstrate functional and physicochemical similarity between the biosimilar and the approved reference product. Functional similarity is often validated with cell-based assays, but the information gained is limited. In contrast, RNA-seq methods enable a sensitive transcriptomic analysis, providing detailed information on pathways and cellular responses. Trastuzumab inhibits signaling of the cell-surface receptor HER2, which is overexpressed in approximately 30% of all breast cancer patients. Here, we compare the functional effect of the mAb Trastuzumab and a corresponding biosimilar.   The BT-474 breast cancer cell line was treated with the reference product, Trastuzumab (Herceptin®), or a proposed biosimilar (ApoTras), and the cellular transcriptomes were analyzed by RNA-seq. Functional similarity was assessed using two statistical contrasts. One contrast evaluated the mechanism of action by comparing treated samples (Her and ApoTras, n = 19) vs. untreated controls (n = 10), which identified 2623 differentially expressed genes (DEG) at a minimum fold change of 1.25. The other contrast directly compared ApoTras (n = 9) vs. Her (n = 10) to determine differences in expression between treatments and identified 24 DEG using a 1.25 fold- change threshold. This low DEG number reveals a very high similarity of effect of both mAb treatments on the cancer cells. A gene set overrepresentation analysis of DEG for mAb treatments revealed mechanisms of action, which were consistent with known trastuzumab effects. Supporting the small number of changes between both treatments, a post-hoc power analysis for the between-treatment comparison estimated power of 0.88 to detect a gene expression fold-changes of 2.0. To summarize these data, we introduce an overall similarity index (SI) to quantify treatment similarity based on changes in gene expression.   Using statistical contrasts with RNA-seq analysis provides a powerful tool for the comparison of biological effects of biosimilar and originator compounds and can be broadly used for functional comparisons of drug treatments.

overall_design: We compared changes in gene expression of mRNAs in BT-474 cells untreated or treated with Herceptin or a biosimilar of it by RNA-seq.  Paired-End Sequencing of samples with Illumina HiSeq Sequencing

first: Brendan

last: McConkey

first: Steve

last: Mooney


title: Profiling of post-mortem brain microRNA in Alzheimer’s disease

city: Brasília

first: Otavio

middle: T.

last: Nobrega

state: DF

address: RUA 3 SUL - EDIFICIO NETUNO - APTO 301, AGUAS CLARAS, 301, lote 08

department: Medicine Faculty

country: Brazil

institute: University of Brasilia

summary:
Non-coding RNA profiling by microarray in an Affymetrix® miRNA Array, version 4.1 (Santa Clara, CA, USA), commercially available by Thermo Fisher Scientific (Waltham, MA)
We aimed to profile the expression of the entire population of annotated small non-coding RNAs in the Temporal Cortex (TC) of Alzheimer diseased (AD) individuals compared to age-matched controls.

overall_design: The microarray expression platform chosen was the Affymetrix® miRNA Array, version 4.1, targeting coverage of miRBase v20 that encompasses 2,578 mature and 2,025 imature (pre-miRNA) human probe sets. Samples obtained from post-mortem TC of 16 cases, 8 from AD patients (Braak stage III or above) and 8 control individuals without neuropathological lesions or neurological signs.

first: Nóbrega

last: Otávio

first: Henriques

last: Adriane


title: Transcriptomic analysis of mouse preimplantation embryo development and nutrient provision

city: Los Angeles

first: Utpal

last: Banerjee

state: California

address: Charles E. Young Drive

institute: University of California, Los Angeles

summary:
Purpose:  The goals of this study are to define transcriptome (RNA-seq) of mouse preimplantation embryos at different stages of development under a range of different environmental conditions.
Methods: Mouse preimplantation embro transcriptional profiles were generated using embryos at several different developmental stages using Smart-seq2.
Results: RNA-seq analysis finds that there is a highly dynamic pattern of gene expression during the preimplantation period. The sensitiivty to nutrient conditions varies markedly at different stages of development, with 2C embryos more sensitive to pyruvate omission than later stage embryos.
Conclusions: Our study represents a comprehensive analysis of the mouse preimplantation development transcriptome, and how pyruvate provision impacts different developmental stages.

overall_design: mRNA analysis of mouse preimplantation embryos at different stages of development

first: Fangtao

last: Chi


title: Parallel analysis of H3K9ac reveals Dux-dependent 2C activation deficiency in mouse SCNT embryos

city: Shanghai

first: Gran

last: Young

state: --- Select a state ---

address: 1239th, Siping Road, Yangpu district

institute: Tongji University

summary: Somatic cell nuclear transfer (SCNT) enables gaining of totipotency by reprogramming nuclei of terminally differentiated donor cell. Recent studies have clearly demonstrated that intervention of epigenetic networks can significantly elevate both in vitro and in vivo development potential of NT embryos. Specifically, trichostatin A (TSA), a kind of histone deacetylase inhibitors (HDACi), was proved to functionally works during cloning in various mammal systems. However, how it modulates histone acylation lacks careful illustration. Here, we systematically evaluate the effect and limitation of TSA during SCNT embryo development by generating genome-wide H3K9ac maps. In addition, a Dux-dependent 2-cell (2C) activation deficiency is observed in SCNT embryos as compared with their natural fertilized counterparts. Strikingly, a refined Dux supplement can successfully assist SCNT embryos in overcoming the 2C activation defect and further promotes the overall cloning efficiency. Together, our study for the first time reveals the regulation mechanism of histone marker H3K9ac in SCNT and provides the new insight of Dux during embryogenesis.

overall_design: Examination of H3K9ac in IVF/NF and SCNT mouse preimplantation embryos.

first: Guang

last: Yang

first: Linfeng

last: Zhang


title: A critical role for STING signaling in limiting pathogenesis of Chikungunya virus

city: Farmington

first: Tingting

last: Geng

state: CT

address: 263 Farmington Avenue

department: Department of Immunology

institute: Uconn Health

summary: The stimulator-of-interferon-gene (STING) pathway controls both DNA and RNA virus infection. STING is essential for induction of innate immune responses during DNA virus infection, while its mechanism against RNA virus remains largely elusive. We show that STING signaling is crucial for restricting Chikungunya virus infection and arthritis pathogenesis. Sting-deficient mice (Stinggt/gt) had elevated viremia throughout the viremic stage and viral burden in the feet transiently, along with a normal type I IFN response.  Stinggt/gt mice presented much greater foot swelling, joint damage and immune cell infiltration than WT mice. Intriguingly, expression of interferon gamma and its induced Cxcl10 was continuously upregulated by ~7-10-fold, and further elevated in Stinggt/gt mice synchronously with arthritis progression. However, expression of chemoattractants for and activators of neutrophils, Cxcl5, Cxcl7 and Cxcr2 was suppressed in Stinggt/gt joints. These results demonstrate that STING deficiency leads to an aberrant chemokine response that promotes pathogenesis of CHIKV arthritis.

overall_design: Bone-marrow-derived macrophages from three individual WT/Sting gt/gt mice were infected by CHIKV at a multiplicity of infection of 5 for 12 hrs or not infected (mock). The whole genome transcriptome was analyzed by RNAseq.

first: Penghua

last: Wang


title: TBK1-METTL3 axis facilitates antiviral immunity [RNA-seq: Brain from WT and Mettl3 heterozygous kd]

city: beijing

first: fuping

last: you

address: xueyuan street

institute: Peking University Health Science Center

summary: mRNA m6A modification is involved in regulation of immune system. However, its function in antiviral immunity is controversial, and how immune responses regulate m6A modification is unknown. We here found TBK1, a key kinase of antiviral pathways, phosphorylated the core m6A methyltransferase METTL3 at Serine 67. The phosphorylated METTL3 interacted with translational complex and enhanced proteins translation, including IRF3, and facilitated antiviral responses. TBK1 also promoted METTL3 activation and m6A modification, which is required for stabilizing IRF3 mRNA. Type I IFN induction was severely impaired in METTL3 deficient cells. Mettl3flfl-lyz2-Cre mice were significantly more susceptible to IAV-induced lethality than control mice. Consistently, Ythdf1-/- mice cannot control viral infection and showed higher mortality than control mice due to decreased IRF3 expression. Together, we demonstrated that innate signals activated METTL3 via TBK1, and METTL3 and m6A modification secured antiviral immunity by promoting mRNA stability and protein translation.

overall_design: Brain mRNA profiles of 7-week old wild type (WT) and Mettl3+/- (Heterozygote) mice infected with HSV-1 at 3 dpi (days postinfection)

first: Jingxuan

last: Chen

first: Xuemei

last: Wei

first: Xiao

first: Fuping

last: You


title: Effect of amyloid beta-protein on SH-SY5Y cell

city: Kyoto

first: Akira

last: Hirasawa

state: Kyoto

address: 46-29 Yoshida Shimoadachi-cho, Sakyo-ku

department: Genomic Drug Discovery Science

institute: Kyoto University Graduate School of Pharmaceutical Sciences

summary: Using human neuroblastoma SH-SY5Y cells, cytotoxic mechanisms of Ab during its aggregation process were examined by microarray under conditions in which both oligomeric Ab (6-h incubation) and fibrillar Ab (24-h incubation) were formed.

overall_design: RNA from human SH-SY5Y cells was extracted and processed for hybridization on Affymetrix microarrays.

first: Eri

last: Takada

first: Yoshiaki

last: Yano

first: Katsumi

last: Matsuzaki

first: Keiko

last: Iida


title: Base editing improvement

city: shanghai

first: Tian-Lin

last: Cheng

state: I am not in the U.S. or Canada

address: Dong An Road, No. 131

institute: Fudan University

summary: We examined the off-targets of new base editing tools at RNA level

overall_design: cells transfected with different base editing tools or GFP were cultured for 48 hours and total RNA was purified for transcriptome analysis

first: Zilong

last: Qiu


title: Dynamic Properties of the Reissner Fiber and Implications on Scoliosis II

city: Saint Louis

first: Bo

state: Missouri

address: 4515 McKinley Research Bldg 03212

department: Developmental Biology

institute: Washington University School of Medicine

summary: Background: Whole genome sequencing (stl297) and whole exome sequencing (stl300) of scospondin hypomorphic mutants and their wild type siblings

overall_design: Scospondin hypomorphic mutants and their wild type siblings

first: Ryan

middle: S

last: Gray

first: Paul

last: Gontarz

first: Lilianna

last: Solnica-Krezel


title: Transcriptome analysis of w1118 and miR-210 mutant adult fly heads

city: Hangzhou

first: Wanzhong

last: Ge

state: Zhejiang

address: Yuhangtang Road 866

institute: Zhejiang University

summary: We report the genome-wide RNA profiling of adult fly heads upon miR-210 mutation

overall_design: mRNA expression profiles of three replicates of w1118 and three replicates of miR-210 mutant adult fly heads


title: Dynamic Properties of the Reissner Fiber and Implications on Scoliosis

last: Zhang

summary: Background: RNASeq of a scospondin hypomorphic mutant at differnet time points


title: Irradiation of healthy brain alters expression of genes involved in cell motility and invasiveness of glioblastoma

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

summary:
Traumatic brain injury is known to cause proliferation and migration of astrocytic and neuronal cells. To find out whether irradiation may influence migration of intracranial tumors, we performed expression profiling of orthotopically implanted glioblastomas following irradiation to the contralateral (non-diseased) hemisphere.
Microarrays were used to identify differentially expressed genes associated with glioblastoma-malignancy in distinct tumor compartments following irradiation of brain tissue of contralateral (non-diseased) hemisphere. Differentially expressed genes were the object to functional network analysis with Ingenuity pathway analysis software

overall_design: We orthotopically implanted 2.5x10^6 cells of the human glioblastoma cell line U87 MG into immunodeficient NSG mice. Following tumor detection in serial imaging, fractionated irradiation with 3 x 5 Gy was applied to the contralateral hemisphere. Non-irradiated tumor-bearing mice served as control group. Following snap-freezing of brains, tumor cores and peripheries were separated using laser-capture microdissection (LCM) and subjected to RNA isolation and Affymetrix microarray hybridisation. We sought to separately compare gene expression profiles following contralateral irradiation within the two tumor compartments.

first: Marianne

middle: R

last: Hahn

first: Stefanie

last: Kirschner


title: Transcriptome analysis of dNKAP knockdown and control wing imaginal discs

summary: We report the genome-wide profiling of wing imaginal discs upon dNKAP knockdown

overall_design: mRNA expression profiles of three replicates of control wing imaginal discs (MS1096-Gal4) and three replicates of dNKAP knockdown wing discs (MS1096-Gal4>dNKAP RNAi)


title: KANSL1 CHIP-sequence analysis in HeLa cells

status: Public on Oct 13 2020

city: Beijing

first: Ting

last: Li

address: Taiping Road 27

institute: National Center of Biomedical Analysis

summary: We report the application of CHIP-sequence in HeLa cells. By obtaining over fifty million bases of sequence from chromatin immunoprecipitated DNA for each sample, we generated genome-wide chromatin-state maps of HeLa cells.

overall_design: Examination of KANSL1 target genes in HeLa cells.


title: RNA sequencing (RNA-SEQ) of RECQL4 knockdown by siRNA in ovarian cancer cells

city: Qingdao

first: Li

last: Guo

state: China

address: N0.1 jiaozhou road

institute: Qingdao Municipal Hospital

summary: The high frequency of somatic copy number alterations, as opposed to point mutations, is considered a unique feature of high-grade serous ovarian carcinoma (HGSOC). Amplification-dependent overexpression of RECQL4, which participates in DNA replication and repair, mediates the development of various cancers, but its pathobiological and clinical roles are poorly understood. Here, using bioinformatics analysis, RECQL4 amplification was found to occur in 27% of HGSOC samples in the TCGA cohort. RECQL4 was found to be upregulated and associated with a poor prognosis based on the immunohistochemistry staining of HGSOC. Functionally, RECQL4 overexpression increased proliferation and invasion of ovarian cancer cells both in vitro and in vivo. RECQL4 silencing had the opposite effects. In addition, RECQL4 knockdown enhanced the sensitivity of ovarian cancer cells to cisplatin and PARP inhibitor (PARPi). Further mechanistic investigations revealed that MAFB was a downstream target of RECQL4. The oncogenic effect of RECQL4 was attenuated after MAFB knockdown. Moreover, RECQL4 overexpression was negatively regulated by the tumour suppressor miR-10a-5p. Collectively, these findings indicate that genomic amplification and low expression of miR-10a-5p contribute to RECQL4 overexpression in ovarian cancer. This is the first study to reveal the oncogenic functions and clinical significance of RECQL4 in ovarian cancer.

overall_design: The assay was performed on three biological triplicates as well as three experimental triplictes of RECQL4 knockdown and control cells.

first: Yingwei


title: Expression data from epithelial cells of nasal mucosa

first: Wei

last: Xian

address: 150 Jimo Road, Pudong New Area, Shanghai

institute: East Hospital Affiliated to Tongji University

summary:
As the first defense line to contact respiratory allergens, epithelial cells play an extremely critical role in the occurrence of allergic rhinitis, and the mechanism is realized by the regulation of the expression of co-expressed mRNA which is controlled by lncRNA.
We used microarrays to screen gene expression profiles in nasal mucosal epithelial cells of allergic rhinitis, and predicted the relationship between lncRNA and mRNA by bioinformatics analysis.

overall_design: Patients who need the operation of nasal septal correction were selected, part of the inferior turbinate mucosa was taken as experimental samples during the operation. According to the diagnosis guidelines of allergic rhinitis, the samples were divided into AR group and non-AR group, and 3 samples were selected for microarray analysis in each group.Then we analyzed the function of differentially expressed genes.

first: Weihua

last: Wang

first: Xian

last: Wei

first: Chao

first: Shengjian

last: Fang

first: Yu


title: The cellular basis of distinct thirst modalities

city: Dallas

first: Allan-Hermann

last: Pool

state: TX

address: 6000 Harry Hines Blvd

department: Department of Neuroscience, Peter O'Donnell Brain Institute, Department of Anesthesia and Pain Management

institute: University of Texas Southwestern Medical Center

summary: We performed single-cell RNA-seq (10x Chromium 3' v.2) on dissociated single cell suspensions from mouse (C57BL/6) osmosensory brain nuclei - subfornical organ (SFO) and organum vasculosum lamina terminalis (OVLT) to determine transcriptomic cell types in each structure. We identified 12 and 13 major cell classes as well as 8 neuron types in each for SFO and OVLT respectively. Furthermore, we studied how different types of thirst signals (osmotic thirst, hypovolemic thirst, chronic water deprivation) engage this cellular diversity by performing single cell RNA-seq based (10x Chromium 3' v.3.0) stimulus to cell-type mapping, where dissociation related transcriptional artifacts were suppressed through a modified tissue preparation protocol involving a transcriptional blocker and dissociation at room temperature. This approach revealed the endogenous immediate early gene expression triggered by distinct thirst stimuli in SFO and OVLT cells. By analyzing immediate early gene expression that is driven by changes in neural activity (Fos) we identified excitatory neuron types in SFO and OVLT that are uniquely tuned to distinct thirst states.

overall_design: To determine transcriptomic cell types in the SFO and OVLT we used 8 and 12 male mice respectively. For stimulus to cell-type mapping experiments we used 12 animals per condition. Both male and female animals were used in equal measure. All animals were 7.5-8 weeks of age. Prior to tissue extraction, animals were subjected to one of the following experimental treatments: a) wated satiation: ad libitum access to food and water); b) osmotic thirst: intraperitoneal (i.p.) injection of 2 M NaCl (5 μl/g bodyweight) followed by sacking 1 hour after injection; c) hypovolemic thist: i.p. injection of furosemide at a dose of 50 mg/kg bodyweight followed by sacking 4 hours after injection; d) chronic water deprivation: 36H water deprivation with food.

first: Yuki

last: Oka


title: Kidney GATA3+ regulatory T cells play roles in the  convalescence stage after antibody-mediated renal injury

city: Fukuoka

first: Minako

last: Ito

address: 3-1-1 Maidashi, Higashi-ku

institute: Kyushu University

summary: FoxP3+ regulatory T cells (Tregs) play crucial roles in peripheral immune tolerance. In addition, Tregs that reside or accumulate in nonlymphoid tissues, called tissue Tregs, exhibit tissue-specific functions and contribute to the maintenance of tissue homeostasis and repair. In an experimental mouse model of crescentic glomerulonephritis induced by an anti-glomerular basement membrane antibody, Tregs started to accumulate in the kidney on day 10 of disease onset and remained at high levels (~30–35% of CD4+ T cells) during the late stage (days 21–90), which correlated with stable disease control. Treg depletion on day 21 resulted in the relapse of renal dysfunction and an increase in Th1 cells, suggesting that Tregs are essential for disease control during the convalescence stage. The Tregs that accumulated in the kidney showed tissue Treg phenotypes, including high expression of GATA3, ST2 (the IL33 receptor subunit), amphiregulin (Areg), and PPARγ. Although T-bet+ Tregs and RORγt+ Tregs were observed in the kidney, GATA3+ Tregs were predominant during the convalescence stage, and a PPARγ agonist enhanced the accumulation of GATA3+ Tregs in the kidney. To understand the function of specific genes in kidney Tregs, we developed a novel T cell transfer system to T cell-deficient mice. This experiment demonstrates that ST2, Areg, and CCR4 in Tregs play important roles in the accumulation of GATA3+ Tregs in the kidney and in the amelioration of renal injury. Our data suggest that GATA3 is important for the recruitment of Tregs into the kidney, which is necessary for convalescence after renal tissue destruction.

overall_design: Tregs (CD45+CD3e+CD4+FoxP3-hCD2+ T cells) from renal tissue were isolated on day 28 after cGN induction. Total RNA was isolated using a TRIzol LS reagent (Invitrogen).Disease severity was depended on variation among lots of anti-GBM antibodies in this experiments. To improve the quality of this analysis, we used the two lots of anti-GBM antibodies, M and I.

first: Ryota

last: Sakai


title: Pharmacological blockade of high-risk MYCN driven neuroblastoma using an orally-bioavailable CDK2/9 inhibitor

city: Houston

first: Tong

last: Liang

address: One Baylor Plaza

institute: Baylor College of Medicine

summary: The undruggable nature of oncogenic Myc transcription factors poses a therapeutic challenge in neuroblastoma, a paediatric cancer in which MYCN amplification is strongly associated with unfavourable outcome. Here, we show that CYC065, a clinical inhibitor of CDK2 and CDK9, selectively targets MYCN-amplified neuroblastoma via blockade of CDK9-dependent, MYCN-driven transcriptional elongation and CDK2-dependent proliferation. CYC065 also targets nascent transcription of short half-life genes including MYCN and MCL-1 leading to downregulation of MYCN-driven ‘adrenergic’ gene expression programs, growth inhibition, and apoptosis in vitro and in vivo. These data highlight the clinical potential of CDK2/9 inhibition in the treatment of MYCN-amplified neuroblastoma.

overall_design: RNA-seq in SHEP and SHEP MYCN neuroblastoma cell lines.  SHEP MYCN cell lines exogenously expressed MYCN or its mutants in SHEP parental cells. MYCN T58A and S62A are MYCN double mutant alleles.

first: Evon

last: Poon

first: Charles

last: Lin

first: Louis

last: Chesler


title: eRNAs and super-enhancer lncRNAs are functional in human prostate cancer

first: xiaona

last: zhang

address: No.151 Libing Road

institute: Shanghai Biochip Corporation

summary: Prostate cancer (PCa) is one of the most commonly diagnosed cancers in males worldwide. lncRNAs (long non-coding RNAs) play a significant role in the occurrence and development of PCa. eRNAs (enhancer RNA) and SE-lncRNAs (super-enhancer lncRNA) are important elements of lncRNAs, but the role of eRNAs and SE-lncRNAs in PCa remains largely unclear. In this work, we identified 681 eRNAs and 292 SE-lncRNAs that were expressed differentially in PCa using a microarray. We constructed a transcriptional regulation network that eRNA related enhancer and the target genes shared the same TF binding motifs. Further, we investigated whether CTCF played a role in mediating the transcriptional regulation network. eRNAs, especially those that regulate androgen response genes, may be candidates for prognostic biomarkers and therapy targets. Our work provide a new perspective for developing medical treatments and therapies for prostate cancer.

overall_design: In the study presented here, three prostate tumors and corresponding adjacent normal  prostate tissues was used to acquire expression profiles of a total of 18793 coding genes and  72002 lncRNAs, leading to the successful construction of supervised

first: Xiaona

last: Zhang

first: Junsong

last: Han


title: Profiling of 8-oxoG RNA modifications reveals strong functional network relationships in bronchial epitheilium following exposure to formaldehyde

city: Austin

first: Lydia

last: Contreras

address: 200 E Dean Keeton St,

department: Chemical Engineering

institute: University of Texas at Austin

summary: Recent studies have highlighted the association between oxidative stress-inducing chemicals and diseases such as Alzheimer’s disease and cancer. While chemicals like formaldehyde are known causative agents of disease and overall negatively impact human health, their mechanisms of action remain unclear. Recent development of antibodies that target oxidized RNA nucleotides and advances in RNA-sequencing technology enable the isolation and identification of differentially oxidized transcripts. In this study, oxidation-specific immunoprecipitation is combined with RNA-sequencing to detect transcripts that are enriched in oxidized nucleotides following direct exposure of 1 ppm formaldehyde to human BEAS-2B lung cells using an air-liquid interface exposure system. Results from this analysis suggest a functional role of the oxidized transcripts in signaling pathways regulating cellular proliferation, migration, and programmed cell death. By combining direct cell-exposure systems, oxidized-RNA immunoprecipitation, RNA-sequencing technologies, and network analyses, detection of specifically oxidized molecular markers could be used to further characterize biological responses to external stressors and identify targets for drug development toward therapies for complex diseases.

overall_design: Examination of transcript abundance from two biological replicates of lung cell RNA isolated by immunoprecipitation relative to total RNA following exposure to either clean air or 1ppm formaldehyde for two hours

first: Juan

middle: C

last: Gonzalez

first: Mark

last: Sherman

first: Dongyu

first: Jamie

last: Chuvalo-Abrahm

first: Lea

last: Hildebrandt Ruiz


title: Microarray profiling analysis of lncRNAs expression in glioma cells

city: Shenyang

first: Wei

last: Wang

state: Liaoning

address: 155 Nanjing North Street

department: Department of Neurosurgery

institute: the First Affiliated Hospital of China Medical University

summary:
Tremendous studies have found that the abnormality of long noncoding RNA (lncRNA) contributed to cancer initiation, progression, and recurrence via multiple signaling cascades. Nevertheless, the possible underlying mechanisms of lncRNA in temozolomide (TMZ)-resistant glioma were not well understood, hindering the improvement of TMZ-based therapies against glioma. The present study illustrated that the lncRNA KCNQ1OT1 increased in TMZ-resistant gliomas cells compared to the parental cells. Introduction of KCNQ1OT1 boosted glioma cell viability, clonogenicity and rhodamine 123 efflux while hampered apoptosis post-exposure to TMZ. Consistent with bioinformatic prediction, KCNQ1OT1 directly sponged miR-761, which was downregulated in TMZ-resistant glioma cell lines. Overexpression of miR-761 attenuated glioma cell viability and clonogenicity while triggered apoptosis and rhodamine 123 cellular accumulation post-exposure to TMZ, leading to rehabilitated glioma TMZ-sensitivity, which was against the function of KCNQ1OT1. miR-761 bound to 3’-untranslated region of PIM1, a proto-oncogene with constitutive serine/threonine kinase activity, attenuated PIM1-mediated signaling cascades. Furthermore, stable knockdown of KCNQ1OT1 by small hairpin RNA amplified the TMZ-induced tumor regression in TMZ-resistant U251 mouse models. Briefly, the present study evaluated KCNQ1OT1 conferred TMZ resistance by sponging miR-761 and releasing PIM1 expression, resulting in activation of PIM-mediated MDR1/c-Myc/Survivin signaling pathways. The findings mentioned above extended the knowledge of lnRNA KCNQ1OT1 in the regulation of chemoresistance in glioma and provided a promising therapeutic target for TMZ-resistant glioma patients.
Long noncoding RNA profiling by array

overall_design: Three U251 clones and three U251 temozolomide-resistant (U251TR) clones were generated in the present study. LncRNA expression profiles were obtained with Qiagen custom RT2 PCR Arrays.

first: Di

last: Wu


title: Sprr2f protects against renal injury by decreasing the level of reactive oxygen species in female mice

city: Stanford

first: George

middle: Edward

last: Marti

state: CA

address: 318 Campus Dr., E300

department: MCP

institute: Stanford University

summary: Renal injury leads to chronic kidney disease for which women are not only more likely to be diagnosed with than men but also have poorer outcomes as well. We have previously shown that expression of Sprr2f, a member of the Small Proline Rich Region (Sprr) gene family, is increased several hundred fold after renal injury using a unilateral ureter obstruction (UUO) mouse model. To better understand the role of Sprr2f in renal injury, we generated a Sprr2f knockout (Sprr2f-KO) mouse model using CRISPR-Cas9 technology. To identify genes that are differentially expressed in Sprrf2f-KO mice after UUO, we performed gene expression profiling by RNA-seq on kidney tissues harvested from Sprr2f-KO mice at time 0 (n=4) and after 5 days (n=3), a time known to show dramatic changes in gene expression. Compared to day 0, expression levels of 162 genes were significantly changes with 121 up-regulated and 41 down-regulated 5 days after obstruction. Enrichment analysis using PANTHER Classification System  identified 12 and 2 pathways enriched in genes that are upregulated or downregulated after UUO respectively. Eleven out of the 12 pathways enriched in the genes upregulated after UUO are related to metabolism such as drug metabolic process, consistent with a profound role of kidney as a major clearance organ of the body responsible for the elimination of many xenobiotics and prescription drugs. Interestingly, the only pathway not related to metabolism enriched in genes upregulated by UUO is oxidation-reduction, suggesting a potential role of oxidative stress in renal damage after UUO in Sprr2-KO animals. This phenotype is not observed in Sprr2f-WT animals after UUO in our previous gene expression profiling study, suggesting that Sprr2f function is sufficient to protect kidney from oxidative damage after UUO in Sprr2f-WT animals.

overall_design:
To identify genes that are differentially expressed in Sprrf2f-KO mice after UUO, we performed gene expression profiling by RNA-seq on kidney tissues harvested from Sprr2f-KO mice at time 0 (n=4) and after 5 days (n=3), a time known to show dramatic changes in gene expression.
Total RNA was isolated from fresh frozen kidney tissues and delivered to Novogene for next generation sequencing using Illumina Hiseq system. Raw data were analyzed in house using STAR and HTSeq.

first: Kieu

last: Huynh

first: Anny

last: Wong

first: Bo

first: Marc

last: Horschman

first: Hongjuan

last: Zhao

first: James

middle: D

last: Brooks