title: Molecular mechanism of EPC1-PHF1 fusion protein  (Microarray Homo Sapiens)

summary: In this study, we characterize the fusion protein produced by the EPC1-PHF1 translocation in Low Grade Endometrial Stromal Sarcoma (LG-ESS) and Ossifying FibroMyxoid Tumors (OFMT). We express the fusion protein and necessary controls in K562 Cells. The fusion protein assembles a mega-complex harboring both NuA4/TIP60 and PRC2 subunits and enzymatic activities and leads to mislocalization of chromatin marks in the genome, linked to aberrant gene expression.

overall_design: We profiled the gene expression in K562 cells expressing tagged EPC1-PHF1 fusion protein or EPC1(1-581) or PHF1 or tag only. Total RNA was analyzed on Illumina Human HT-12 V4.0 expression beadchip by McGill University and Genome Québec innovation Centre

first: Eric

last: Paquet

first: Jacques

last: Côté


title: LXR target genes in rhesus macaque luteal cells

status: Public on Dec 04 2020

city: Tucson

first: Randy

middle: L

last: Bogan

state: Arizona

address: 1177 E. 4th St, Shantz Building Room 623

department: SACBS

country: USA

institute: University of Arizona

summary: Identify LXR-responsive genes in rhesus macaque luteal cells isolated from CL at 12 days post LH-surge

overall_design: 3 paired biologic replicates. Treated with DMSO or T0901317

first: Jon

middle: D

last: Hennebold


title: Genome-Wide Differentially Methylated Region Analysis to Reveal Epigenetic Differences of Articular Cartilage in Kashin-Beck Disease and Osteoarthritis

status: Public on Dec 03 2020

city: Xi'an

first: Yue

last: Fan

address: Yanta West Road No.76

country: China

institute: Xi'an Jiaotong University

type: Methylation profiling by genome tiling array

summary:
Kashin-Beck disease (KBD) is a degenerative osteoarticular disorder, and displays the significant differences with osteoarthritis (OA) regarding the etiology and molecular changes in articular cartilage.
However, the underlying dysfunctions of molecular mechanisms in KBD and OA remain unclear. Here, we performed the various genome-wide differentially methylated region analyses to reveal the distinct differentially methylated regions (DMRs) and corresponding differentially methylated genes (DMGs), and enriched functional pathways/GO terms for KBD and OA.

overall_design: DNA methylation profiles of 5 KBD patients, 5 OA patients and 5 healthy controls

first: Shiquan

last: Sun

first: Feng

last: Zhang


title: In vitro antifungal activity of myriocin against drug-resistant Candida auris strains

city: Shanghai

first: Jian

last: Bing

address: Songhu Road, Yangpu District

department: School of Life Sciences

institute: Fudan University

type: Expression profiling by high throughput sequencing

summary: Myriocin exhibited very low MIC values (0.016 to 0.4 mg/L) to all C. auris isolates including several multidrug-resistant strains. The yeast-form, filamentous, or aggregating-form cells were all susceptible to the chemical. The antifungal effect was majorly due to the fungistatic activity, although an extended treatment could lead to the fungicidal activity to C. auris cells. Transcriptomic analysis demonstrates that myriocin suppresses the cellular metabolic activity and induces the expression of stress or antifungal response genes.

overall_design: total RNA profiles of Candida auris cells treated with Myriocin and DMSO

first: Guanghua

last: Huang

first: Zhangyue

last: Guan


title: RNA differential expression between OAW42 ovarian cancer cells and its chemoresistant counterpart OAW42-R

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

country: France

institute: Lille University

summary:
We were interested in exploring transcriptional differences between the two cell lines
Transcriptional differences would inform about the process of acquiring resistance to cisplatin, common therapeutic treatment in ovarian cancer

overall_design: Both cell lines were grown in normal and identical conditions

first: Matthieu

last: Meryet-Figuiere

first: Jean-Paul

last: Issartel


title: Transcriptomic analysis of adult zebrafish brain exposed developmentally to 2 concentrations of a persistent organic pollutants (POP) mixture or 2 concentrations of PFOS (0.3, 2.06 mg/L)

city: Utrecht

first: Jorke

last: Kamstra

state: Non United States Or Canada

address: PO Box 80177

department: Faculty of Veterinary Medicine

country: Netherlands

institute: Utrecht University

summary: Complex mixtures of persistent organic pollutants (POPs) are regularly detected in the environment and animal tissues. Often these chemicals are associated with latent effects following early-life exposures, following the developmental origin of health and disease paradigm. We investigated the long-term effects of a human relevant mixture of 29 POPs on adult zebrafish following a developmental exposure, in addition to a single PFOS exposure for comparison, as it was the compound with the highest concentration within the mixture. Zebrafish embryos were exposed from 6 to 96 hours post fertilization to x10 and x70 the level of POP mixture or PFOS found in human blood before being transferred to clean water. We measured growth, swimming performance, and reproductive output at different life stages. In addition, we assessed anxiety behavior of the adults and their offspring, as well as performing a transcriptomic analysis on the adult zebrafish brain, as the POP mixture and PFOS concentrations used are known to affect larval behavior. Exposure to POP mixture and PFOS reduced swimming performance and increased length and weight, compared to controls. No effect of developmental exposure was observed on reproductive output or anxiety behavior. Additionally, RNA-seq did not reveal pathways related to anxiety although pathways related to synapse biology were affected at the x10 PFOS level. Furthermore, pathway analysis of the brain transcriptome of adults exposed as larvae to the low concentration of PFOS revealed enrichment in pathways such as calcium, MAPK, and GABA signaling, all of which are important for learning and memory. Based on our results we can conclude that some effects on the endpoints measured were apparent, but if these effects lead to adversities at population levels remains elusive.

overall_design: The POPs mixture used in this study was base on average leves of chemicals found in blood of the Scandinavian population. The low concentration of POP (POP10) reflected levels x 10 higher of what is found in human blood and the high concentration (POP70) reflected levels x 70. PFOS10 and PFOS70 single exposure were based on the levels of PFOS in the POPs mixture. Zebrafish larvae were exposed from 6 hpf until 96 hpf to either POP10, POP70, PFOS10 or PFOS70 in 4 replicates. We also included a control condition of zebrafish larvae exposed only to the solvent (0.1% DMSO) in 4 replicates. Zebrafish were transferred to clean water and left to grow until adulthood. Sampling of adults was performed at ages 219-240 dpf. Whole brain tissue from 2 females and 2 males per condition and replicate (total 8 females and 8 males per condition) were collected  individually.

first: Maria

last: Christou

first: Erik

last: Ropstad

first: Stephen

last: Brown

middle: H

first: Thomas

middle: W

last: Fraser


title: Regulation and Role of Aryl Hydrocarbon Receptor in Human Embryonic Stem Cells and Their Differentiating Counterparts

city: Tartu

first: Tõnis

last: Org

address: Riia 23

department: Institute of Molecular and Cell Biology

country: Estonia

institute: University of Tartu

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Regulation and Role of Aryl Hydrocarbon Receptor in Human Embryonic Stem Cells and Their Differentiating Counterparts [RNA-Seq]

summary: Aryl hydrocarbon receptor (AHR) is a ligand-activated transcription factor, which mediates the effects of  various environmental contaminants, like polycyclic and halogenated aromatic hydrocarbons, including the most potent agonist 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD),  in multiple tissues. Recent advances in AHR biology have underlined its importance in cells with high developmental potency, including pluripotent stem cells. Nonetheless, there is little data on AHR expression and its role during the initial stages of stem cell differentiation. The purpose of this study was to investigate the temporal pattern of AHR expression during directed differentiation of human embryonic stem cells (hESC) into neural progenitor, early mesoderm and definitive endoderm cells. Additionally, we studied the effect of AHR agonist 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) on gene expression profile in hESCs and differentiated cells by RNA-seq, accompanied by identification of AHR binding sites by ChIP-seq and epigenetic landscape analysis by ATAC-seq. . We show that AHR is differentially regulated in distinct lineages, provide evidence that TCDD impairs differentiation of hESCs and identify novel potential AHR target genes which expand our understanding on the role of this protein in different cell types.

overall_design: ATAC-seq profiles of hESC H9 cells pre-treated with DMSO (control) or 10 nM TCDD in mTESRTM1 medium for 3 days in three biological replicates

first: Indrek

last: Teino

first: Antti

last: Matvere

first: Martin

last: Pook

first: Inge

last: Varik

first: Laura

last: Pajusaar

first: Keyt

last: Uudeküll

first: Helen

last: Vaher

first: Arnold

last: Kristjuhan

first: Toivo

last: Maimets


title: Regulation and Role of Aryl Hydrocarbon Receptor in Human Embryonic Stem Cells and Their Differentiating Counterparts [ChIP-Seq]

overall_design: ChIP-seq profiles of hESC H9 cells and H9 derived endoderm and neural progenitor cells pre-treated with DMSO (control) or 10 nM TCDD at the hESC stage in mTESRTM1 medium for 3 days in three biological replicates


title: Genome-wide analysis of abscisic acid biosynthesis, catabolism, and signaling in Sorghum bicolor under saline-alkali stress

city: Wuhan

first: Ma

last: Siqi

address: No.1,Shizishan Street

institute: Huazhong Agricultural Uinveristy

summary: Sorghum (Sorghum bicolor) is the fifth most important cereal crop in the world. It is an annual C4 crop having a high biomass, used widely, and has a strong resistance to stress. Obviously, there are many benefits of planting sorghum on marginal soils such as saline-alkali land.

overall_design: Total RNA was extracted from wild type Sorghum bicolor BTx623 at the four-leaf-stage under normal conditions, moderate saline-alkali soil stress treatment (3‰ salt content, pH 8.1), severe saline-alkali soil stress treatment (5‰ salt content, pH 8.1), with three biological replicates.

first: Siqi

last: Ma

first: Yiqiang

last: Li


title: Deep sequencing analysis of miRNAs and isomiRs modulated by long-term exposure of human endothelial cells to metformin

city: Ancona

first: Jacopo

last: Sabbatinelli

state: AN

address: Via Tronto 10/A

department: Department of Clinical and Molecular Sciences

country: Italy

institute: Università Politecnica delle Marche

type: Non-coding RNA profiling by high throughput sequencing

summary: Increasing evidence suggest anti-senescence and geroprotective roles for the glucose-lowering drug metformin. In this framework, the ability of metformin to affect the biogenesis of selected microRNAs (miRNAs) was recently suggested. IsomiRs are distinct variations of miRNA sequences, such as addition or deletion of one or more nucleotides at the 5’ and/or 3’ ends of the canonical miRNA sequence. Since no study has comprehensively assessed the miRNA signatures, including isomiR variants, affected by metformin treatment during cellular senescence, we analysed miRNA and isomiR expression in human umbilical vein endothelial cells (HUVECs) undergoing replicative senescence in presence of metformin.

overall_design: MicroRNA and isomiR expression profile obtained from small RNA-sequencing of HUVECs undergoing replicative senescence in absence (SEN, n=3 replicates) or presence (SEN+M, n=3 replicates) of 0.2 μM metformin.

first: Fabiola

last: Olivieri

first: Angelica

last: Giuliani

first: Emanuela

last: Mensà

first: Eric

last: Londin


title: Next Generation Sequencing (NGS) Facilitates Quantitative Analysis of Differentially Expressed Genes in Liver Regeneration After Combined Treatment With Ethanol And Carbon Tetrachloride

city: duarte

first: LU

last: YANG

address: 1500 duarte rd

institute: city of hope

summary:
Purpose: The goals of this study are to use NGS-derived liver transcriptome profiling (RNA-seq) and identify differentially expressed genes in regenerating livers that were treated with ethanol and carbon tetrachloride.
Methods: Liver mRNA profiles were generated from ethanol/CCl4-treated floxed homozytoes and Ctgf conditional knockout mice by deep sequencing, in duplicate, using Illumina GAIIx. qRT–PCR validation was performed using SYBR Green assay.
Results: Ctgf deficiency was associated with 220 downregulated genes and 29 upregulated genes whereas Yap1 null livers had 351 downregulated genes and 287 upregulated genes after ethanol/CCl4 induced liver damage
Conclusions: This study provides detailed analysis of liver transcriptomes in absence of Ctgf or Yap1 genes during ethanol/CCl4-induced injury, with biologic replicates, generated by RNA-seq technology.

overall_design: Liverl mRNA profiles of 8-week-old floxed homozygotes versus Ctgf conditional knockouts, and AAV8-GFP treated controls versus AAV8-iCre mediated hepatocyte-specific knockouts of Yap1 were generated by deep sequencing, in duplicate, using Illumina GAIIx.

first: Liya

last: Pi

first: Yang

last: Lu

first: Jinhui

last: Wang


title: Copy Number Variation at 16p11.2 Imparts Transcriptional Alterations in Neural Development in an hiPSC-derived Model of Corticogenesis

city: Stanford

first: Theo

last: Palmer

state: CA

address: 256 Campus Dr., G1141

department: Department of Neurosurgery

institute: Stanford University

summary: Microdeletions and microduplications of the 16p11.2 chromosomal locus are implicated in a collection of  neurodevelopmental disorders and reciprocal physiological conditions such as macro/microcephaly and high/low  body mass index. To facilitate cellular and molecular investigations of these phenotypes, we generated 65 clones  of human induced pluripotent stem cells (hiPSCs) from 13 individuals with 16p11.2 copy number variations  (CNVs) and made each clone available by request from the Simons Foundation Autism Research Initiative  (SFARI). Here we report on pluripotency, vector silencing, CNV breakpoint location, inter-clonal relatedness, and  differentiation capacity for a majority of the available hiPSC clones. Comprehensive demographic and diagnostic  data were collected and tabulated to facilitate investigation across a spectrum of pathologies. We demonstrate a  customizable bioinformatic strategy for enhanced detection of the effects of episomal reprogramming and use this  tool to identify a subset of clones free of off-target effects on neural progenitor gene transcription and phenotypic  variation . With cortical neural progenitor cells (NPCs) derived from these hiPSCs, we identified a set of genes  modulated by 16p11.2 deletion that precede morphological abnormalities reported at more mature developmental  stages. This publicly available resource of 65 human hiPSC clones will serve as a powerful medium for probing  the etiology of developmental disorders associated with 16p11.2 CNVs.

overall_design: 2 or more clones derived from patient iPSCs were analyzed with RNA-Seq for integration status (Integration+ or Integration-) or genotype (DEL or WT). Sequencing data were collected in two different batches. Number of clones and patients varies according to analysis.

first: Kristin

last: Muench

first: Julien

last: Roth


title: Loss of Small-RNA-Directed DNA Methylation in the Plant Cell Cycle Promotes Germline Reprogramming and Somaclonal Variation

city: Versailles

first: Filipe

last: Borges

address: Route de St-Cyr (RD10)

institute: Institut Jean-Pierre Bourgin - INRAE

type: Methylation profiling by high throughput sequencing

summary: 5-methyl cytosine in plant genomes occurs in all sequence contexts, especially in heterochromatin, transposons and other repeats. During replication, nascent cytosines in symmetric contexts (CG) are guided for methylation by hemi-methyl C on the parental DNA strands of both daughter chromatids. However nascent cytosines in the asymmetric CHH context or in symmetric CHG (where H=A, T or C) use modified histones and 24-nt small interfering RNAs to restore methylation to each daughter chromatid. Here, we use fluorescent activated sorting of EdU-labeled nuclei to examine DNA methylation dynamics in dividing cell cultures of Arabidopsis thaliana. We find that CG methylation becomes transiently asymmetric during late S phase, but is rapidly restored during each cell division, while CHG methylation remains asymmetric and is substantially reduced. Levels of mCHH are extremely low in dividing cells, accompanied by a shift from 24-nt to 21-nt epigenetically activated small RNAs (easiRNAs) and a loss of histone lysine-9 methylation. When cell division arrests, RNA-directed CHH methylation is restored, but only at loci that retained 24-nt siRNAs. Comparisons with methylation patterns in pollen suggest that DNA methylation reprogramming in microspores (G2), sperm cells (S phase) and the vegetative nucleus (which is quiescent) reflect their cell cycle stage.  Our results also account for the loss of non-CG methylation in plants micropropagated as clones, which undergo methylation reprogramming in the absence of fertilization.

overall_design: Bisulfite sequencing of Arabidopsis cell culture nuclei

first: Chantal

last: LeBlanc

first: Robert

middle: A

last: Martienssen


summary: 5-methyl cytosine is widespread in plant genomes in both CG and non-CG contexts. During replication, hemi-methylation on parental DNA strands guides symmetric CG methylation on nascent strands, but non-CG methylation requires modified histones and small RNA guides. Here, we used immortalized Arabidopsis cell suspensions to sort replicating nuclei and determine genome-wide cytosine methylation dynamics during the plant cell cycle. We find that symmetric mCG and mCHG are selectively retained in actively dividing cells in culture, while mCHH is depleted. mCG becomes transiently asymmetric during S phase but is rapidly restored in G2, while mCHG remains asymmetric throughout the cell cycle. Hundreds of loci gain ectopic CHG methylation, as well as 24-nt small-interfering RNAs and H3K9me2, without gaining CHH methylation. This suggests that spontaneous epialelles that arise in plant cell cultures are stably maintained by small RNA independently of the canonical RNA-directed DNA methylation pathway. In contrast, loci that fail to produce siRNA are targeted for demethylation when cell cycle arrests. Comparative analysis with methylomes of various tissues and cell types suggests that loss of small RNA-directed non-CG methylation during DNA replication promotes germline reprogramming and epigenetic variation in plants propagated as clones.

overall_design: Small RNA sequencing of Arabidopsis cell cultures


title: Precision rescue of SP140 SNP+/+ Crohn's disease patient peripheral blood mononuclear cells responses to lipopolysaccharide using topoisomerase I or II inhibitors

city: Boston

first: Kate

last: Jeffrey

state: Massachusetts

address: 50 Blossom St, Thier 340

department: Medicine

institute: Massachusetts General Hospital, Harvard Medical School

summary: Peripheral blood-derived mononuclear cells isolated from Crohn's disease patients were pretreated with DMSO control, topotecan and etoposide and stimulated with LPS for 4 hours.

overall_design: Fresh human peripheral blood mononuclear cell (PBMCs) from Crohn disease's patients that are wild-type (SP140 SNP-/-) or homozygous for disease-associated SP140 SNPs (SP140 SNP+/+) were stimulated with LPS with or without Topoisomerase I inhibitor Topotecan (TPT) or Topoisomerase II inhibitor Etoposide (ETO)

first: Hajera

last: Amatullah

first: Ruslan

last: Sadreyev

first: Gracia

last: Bonilla


overall_design: ChIP-seq of Arabidopsis leaves and cell cultures.

first: Milos

last: Tanurdzic


title: PRMT1-dependent histone arginine methylation regulates mature beta cell identity (ATAC-Seq)

city: Daejeon

first: Byoung-Ha

last: Yoon

address: Gwahak-ro, Yuseong-gu, Daejeon 34141, Korea

country: South Korea

institute: KRIBB

summary:
Purpose: Loss of functional β cell mass is an essential feature of type 2 diabetes and recent studies indicate that cell dedifferentiation can result in the loss of functional cell mass. However, the mechanism of cell dedifferentiation has not been elucidated due to the lack of appropriate animal model.
Methods: Prmt1 floxed mice were crossed with Rip2-Cre and Pdx1-CreERT2 mice to generate Prmt1 KO and Prmt1 iKO mice. R26-eYFP mice were crossed for lineage tracing experiments and  cell sorting. All mice were backcrossed and maintained on a C57BL/6J background. Cre recombination for CreERT2 was induced by total 5 times intraperitoneal injections (75 mg/kg) of corn oil dissolved tamoxifen (T5648, Sigma-Aldrich) over 2 weeks.
Results: Deletion of Prmt1 in mature cells resulted in the immediate loss of H4R3me2a which induced cell dedifferentiation and cell selective Prmt1 knock-out mice developed diabetes phenotype. H4R3me2a worked as an active histone code that increased chromatin accessibility at the binding sites for transcription factors including CTCF, NKX6.1, MAFA, PDX1 and NEUROD1.
Conclusions: PRMT1-dependent open chromatin regions showed a strong association with the risk of diabetes in human. In conclusion, PRMT1 plays an essential role in maintaining β cell identity by regulating chromatin accessibility.

overall_design: mRNA profiles, H4R3me2a ChIP-seq, ATAC-seq and CTCF ChIP-seq of wild type (WT) and Prmt1 -/- mice or MIN6 cell line were generated by deep sequencing, in duplicate, using Illumina Hiseq.

first: Hail

last: Kim

first: Mirang

first: Hyunki

first: Chang-Myung

last: Oh


title: PRMT1-dependent histone arginine methylation regulates mature beta cell identity (ChIP-Seq)


title: PRMT1-dependent histone arginine methylation regulates mature beta cell identity (RNA-Seq)


title: Grb10a knockdown in Danio rerio during early life alters growth and cardiometabolic function associated with a remodelled transcriptome

status: Public on Dec 02 2020

city: Manchester

first: Adam

last: Stevens

address: Oxford Road

country: United Kingdom

institute: University of Manchester

summary: Embryonic growth trajectory is a risk factor for chronic metabolic and cardiovascular disorders and influences birth weight and early post-natal weight gain in humans. Grb10 is a negative regulator of the main pathways driving embryonic growth. Grb10 knock-out in mammals increases insulin sensitivity and growth trajectory. This study has now investigated the long-term cardiometabolic consequences and associated transcriptomic profiles of morpholino induced early life disruption in grb10a expression in Danio rerio. Transient knockdown increased embryonic growth (+7 %) and metabolic rate (+25 %), while decreasing heart rate (-50 %) in early life. Juvenile growth and respiratory rate were also elevated (+30 % and 7-fold increase respectively). This was associated with permanent remodelling the transcriptional landscape. Multiple growth-related pathways were dysregulated.  This study indicates that zebrafish are a suitable model for life-long investigation of the link between early growth and later life disease risk.

overall_design: Pooled samples (n=5) were generated to form each treatment group. Treatment group 1 = Standard control oligonucleotide targeting human beta globin [SC] and treatment group 2 =  the knock down (KD) Morpholino- a modified antisense oligonucleotide targeting the splice donor sites of zebrafish grb10a coding exon three (e3i3). All groups were analysed at 5, 10, 15, 20, and 30 days post fertilisation (dpf), with three repeats per group.


title: PRMT1-dependent histone arginine methylation regulates mature beta cell identity


title: Prenatal Androgenization Alters the Development of GnRH Neuron and Preoptic Area RNA Transcripts in Female Mice

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan


title: Prenatal Androgenization Alters the Development of GnRH Neuron and Preoptic Area RNA Transcripts in Female Mice (II)

summary: Translating Ribosome Affinity Purification results in non specific RNA binding to the immunoprecipitation matrix, even in mice not expressing cell specific GFP labelled ribosomal protein L10a. This creates false positive enriched transcripts in our datasets. To determine which RNA transcripts bind non specifically to the immunoprecipitation matrix, preoptic area punches were collected from young and adult mice that do not express L10a-GFP. Also, included was a positive control (GnRH CRE x floxed L10a-GFP mice) to ensure that the TRAP procedure was enriching for GnRH neuron specific transcripts as previously described. Four GnRH depleted supernatant RNA samples from the previous study were also included to aid comparison of the two sequencing runs.

overall_design: There are 16 new RNA samples, 122429-122440. All except samples 122433 and 122438 are from L10a GFP negative mice and therefore negative control samples. 122432 and 122438 are from GnRH CRE-L10a GFP mice, therefore ribsomes in GnRH neurons are GFP labelled. This positive control biological replicate was included to ensure that the technique worked as it should. Samples 122441-122444 are technical replicates from the other data set (GSE155314).  122441 = 95718(GSM4698966), 122442 =95722(GSM4698970), 122443 = 95731(GSM4698979) and 122444 = 95734(GSM4698982).

first: Laura

last: Burger

first: Sue

last: Moenter


title: Genome wide map of chromatin state during early development of TrkC neurons of the DRG

city: Rehovot

first: Tsviya

last: Olender

address: 234 Herzl St.

department: Molecular Genetics

country: Israel

institute: The Weizmann Institute

summary: We isolated E11.5 TrkC neurons and profiled ATAC and H3K27ac genomic regions

overall_design: Isolation of GFP expressing TrkC neurons from E11.5 embryos and performing ATAC-seq and H3K27ac ChIP-seq.

first: Elena

last: Appel

first: Kira

last: Orlovsky

first: Ditsa

last: Levanon

first: Yoram

last: Groner


title: A genome-wide transcription analysis of the ∆ohkA and ∆orrA mutants in comparion with the wild type strain M145

first: Yinhua

last: Lu

address: 100 Guilin Road

department: College of Life Sciences

institute: Shanghai Normal University

summary: We conducted a genome-wide transcription profiling experiment using Agilent GeneChip S. coelicolor DNA microarrays (custom-specific design) to determine whether OhkA and OrrA function in the same pathway. From the complete transcriptome data, we observed that, totally, 981 and 1242 genes had significantly altered transcription levels (with at least two-fold increases or decreases) in the mutants of ΔohkA and ΔorrA, respectively, compared with the wild-type strain M145. Importantly, among the genes differentially expressed in the ΔohkA and ΔorrA mutants, 877 genes were similarly affected in these two mutants, in which 427 were downregulated and 450 were upregulated; moreover, none showed an opposite transcription alteration.The large number of genes with similar transcription alterations identified in the ΔohkA and ΔorrA mutants is in good agreement with the speculation that OhkA and OrrA function in the same signaling pathway.

overall_design: Total RNA samples were isolated from cultures of M145, the ΔohkA and ΔorrA mutants, which were grown on MS agar plates covered with plastic cellophanes for 48 h. As one custom-designed DNA array (8×15 K) only contains eight microarrays, here we tested eight RNA samples from three independent replicates for both mutants (ΔohkA and ΔorrA) and two independent replicates for the wild-type strain M145. Significantly regulated genes (ΔohkA/M145 or ΔorrA/M145) were selected according to the fold-change (linear=<0.5 or >=2) in combination with a T-test p-value <0.05.

first: Guosong

last: Zheng

first: Panpan

last: Liu

first: Wenyan

last: He

first: Hengnuo

last: Tao

first: Zhen

last: Yang

first: Weihong

last: Jiang

first: Wenfang

last: Wang


title: MeDIP-seq of genome-wide methylation state in M-SCT floxed and M-SCT KO inguinal white adipose tissue

city: Wuxi

first: Li

last: Yan

institute: Jiangnan University

summary: We analysed the DNA methylation patterns of inguinal white adipose tissue in M-SCT floxed and M-SCT KO, the results indicated a significant widepread hypermethylation modification in M-SCT floxed which contributed to the increased obesity susceptibility of M-SCT floxed

overall_design: DNA methylation petterns of Inguinal white adipose tissue in M-SCT floxed and M-SCT KO mice

first: Xue

last: Lamei

first: Wang

last: Li


title: Integrator-PP2A complex dephosphorylates the C-terminal repeat domain of RNA Polymerase II

first: Xuan

last: Cao

address: 320 Yueyang Road

institute: Shanghai Institute of Nutrition and Health,  Chinese Academy of Sciences

summary: The phosphorylation and dephosphorylation of transcription machinery are essential for the precise control of gene expression. A non-canonical protein phosphatase 2A (PP2A) holoenzyme (denoted INTAC), in which the 14-subunit Integrator recruits RNA polymerase II (Pol II) and the PP2A core enzyme dephosphorylates the C-terminal repeat domain (CTD) of Pol II at Serine-5 and Serine-2.

overall_design: We have finished the ChIP-seq and nascent-seq to investigate the role of integrated phosphatase and endonuclease activities in this Integrator-PP2A complex and its function in regulating Pol II phosphorylation and transcription.

first: Xavier

middle: F

last: Chen


title: Gene expression profile of supernumerary type II neuroblasts transiently overexpressing Insb

first: Bioinformatics

last: Core

summary: Genes that positively regulate neuroblast functional identity shoud be expressed in type II neuroblasts and become repidly downregulated in immature INPs in wild-type brains while genes that suppress neuroblast functional idnetity should be upregulated in immature INPs. The goal of this study is to identify genes involved in regulation of type II neuroblast functional identity.

overall_design: mRNA profiles of brat mutant brain without Insb overexpression (0-hr) and brat mutant brains following 9 and 18 hours of Insb overexpression (9-hr and 18-hr) were generated by deep sequencing, in triplicate

first: Noemi

last: Rives-Quinto

first: Hideyuki

last: Komori

first: Cheng-yu

last: Lee


title: Transcriptome map of cancerous and para-cancerous tissues in patients with liver hepatocellular carcinoma

city: Guangzhou

first: Ke

state: Guangdong

address: 466 Xingangdong Road, Guangzhou

summary: To validate CXCL12 and IL7R expression between cancerous and paracancerous, five cancer and five paracancerous tissues，wihch were obtained from five LIHC patients undergoing liver cancer surgery at the Guangdong Second Provincial General Hospital，were performed RNA-seq. The RNA-seq data showed a significant difference in CXCL12 expression between cancerous and paracancerous tissues (p =0.04), as well as the IL7R expression (p<0.01). There was also a significant difference between cancerous and paracancerous samples in NK cells (resting) (p = 0.0014), M1 macrophages (p = 0.0058), CD8+ T cells (p = 0.0026), and Tregs (p = 0.0015) in the immunocyte infiltration analysis.

overall_design: Examination of differences in transcriptome expression levels between cancerous and para-cancerous tissues of liver hepatocellular carcinoma patients

first: Shuai

first: Guoan

last: Xiang

first: Meixiao

last: Zhan


title: ALC1 and PARP activities coordinate chromatin accessibility and viability in homologous recombination deficient cells  (ATAC-seq)

city: Philadelphia

first: Robert

middle: Babak

last: Faryabi

state: Pennsylvania

address: Room 553 BRB II/III, 421 Curie Boulevard

department: Pathology

institute: University of Pennsylvania

summary: The response to Poly (ADP-ribose) polymerase inhibitors (PARPi) is dictated by homologous recombination (HR) DNA repair mechanisms and the abundance of lesions that trap PARP enzymes on chromatin. It remains unclear, however, if the established role of PARP in promoting chromatin accessibility impacts viability in these settings. Using a CRISPR based screen, we identify the PAR-binding Snf2-like ATPase, ALC1 as a key determinant of PARPi toxicity in HR-deficient cells. ALC1 loss reduced viability of BRCA mutant cells and enhanced their sensitivity to PARPi by up to 250-fold, while overcoming several known resistance mechanisms. ALC1 loss was not epistatic to other repair pathways that execute the PARPi response. Instead, ALC1 deficiency reduced chromatin accessibility concomitant with a decrease in the association of repair factors. This resulted in an accumulation of replication associated DNA damage and a reliance on HR. These findings establish PAR-dependent chromatin remodeling as a mechanistically distinct aspect of PARPi responses, implicating ALC1 inhibition as a new approach to overcome therapeutic resistance in HR-deficient cancers.

overall_design: ATAC seq profiles of DLD1 BRCA2-/- cells  and UWB1.29 cells expressing either sgRNA for a Negative control (ctrl) or for ALC1. DLD1 cells were also treated with either DMSO or 5uM Olaparib(PARPi) for 4hrs. UWB1.289 cells were treated with either DMSO or 1uM talizoparib (PARPi) for 4 hours

first: Yeqiao

last: Zhou

first: Priyanka

last: Verma

middle: B

first: Roger

last: Greenberg


title: Massively multiplex single-molecule oligonucleosome footprinting

city: San Francisco

first: Colin

last: McNally

address: 600 16th Street

department: Biochemistry and Biophysics

institute: University of California, San Francisco

summary: SAMOSA is a single-molecule oligonucleosome footprinting technology, which can be employed to reveal nucleosome patterns (nucleosome positioning, nucleosome repeat length) at transcription factor binding sites and epigenomic domains.

sample_organism:
Homo sapiens
unidentified plasmid

platform_organism:
Homo sapiens
unidentified plasmid

overall_design: Single-molecule chromatin profiling with m6A methyltransferase footprinting and SMRT long-read sequencing.

first: McNally

last: Colin

first: Abdulhay

last: Nour

first: Ramani

last: Vijay


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type (WT) and E4BP4 Overexpressed Liver Transcriptomes

city: Ube, Yamaguchi

first: Yasuharu

last: Ohta

address: 1-1-1, Minami Kogushi

department: Endocrinology, Metabolism, Hematological Science and Therapeutics

country: Japan

institute: Yamaguchi University Scool of Medicine

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to evaluate the effects of liver-specific E4BP4 overexpression under mouse albumin promoter on the liver glucose and lipid metabolism.
Methods: We generated transgenic mice (TG) with liver-specific E4BP4 overexpression. Livers were isolated at Zeitgeber Time (ZT) 2 or 14 from transgenic mice and WT littermates and total RNA was extracted. Liver RNA profiles were generated by deep sequencing for four groups with three mouse samples each.
Results: Compared with the livers from the WT mice, those from Transgenic mice featured 290 differentially expressed genes (DEGs) (106 at ZT2, 134 at ZT14, and 14 at both times).
Conclusions:  Lipid metabolism might be altered in the transgenic liver.

overall_design: Liver mRNA profiles of 8-week old wild type mice and transgenic mice with  liver-specific E4BP4 overexpression

first: Akihiko

last: Taguchi

first: Yukio

last: Tanizawa

first: Yoichi

last: Mizukami

first: Kenji

last: Watanabe


title: Evolution of heterochromatin and heterochromatin genes in the Oryza genomes reveals a new heterochromatin-euchromatin boundary [bisulfite-Seq]

city: Beijing

first: Lei

last: Li

state: Beijing

address: 1 Beichen West Road, Chaoyang District, Beijing 100101, P.R.China

institute: INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES

summary: How heterochromatin genes evolve as ‘gene islands’ to fit into the repressive chromatin environment in plants are poorly understood. To address this question, we performed a comprehensive epigenetic profiling in the genus Oryza with high quality BAC-assembled regional sequences and near gap-free genomes. Comparative analyses of a heterochromatin knob demonstrated the dynamics of chromatin states (heterochromatin versus euchromatin) among the Oryza species in a phylogenetic context. LTR (long-terminal repeat) retrotransposons are the main contributor (~99%) to heterochromatin diversity. Heterochromatin genes are distributed as ‘gene islands’ in heterochromatin, but heterochromatin hardly projects expression disturbance to them. Heterochromatin genes are almost free of H3K9me2 histone modifications in exons, and have similar gene structure and transposon invasion rate in introns to its orthologous euchromatin counterparts. Analyses of the rice HiC data verified the topological existence of ‘gene islands’ and demonstrated that ‘gene islands’ are less spatially co-localized with heterochromatin. By examining evolutionarily recent inserted genes in the Oryza species, we found that the active promoters of six inserted genes can elevate CHH (H=A, C, T) methylation at the insertion sites. Our results reveals that heterochromatin genes evolve as heterochromatin-insulated ‘gene islands’ to escape the repressive influence of heterochromatin, contrasting to the ‘integration’ model in Drosophila. We suggest that active gene promoters may contribute to this insulation by acting as an important heterochromatin-euchromatin boundary in plants.

overall_design: We conducted a comprehensive heterochromatin study among close-related species with high quality sequences and near-gap free genomes. To achieve this, we generated twenty-six new epigenetic datasets in this study including the heterochromatin hallmark H3K9me2 in six species and DNA methylation of Oryza brachyantha, two siRNA libraries of O. sativa and O.brachyantha.

first: Meijiao

last: Wang

first: Mingsheng

last: Chen


title: Regulation and Role of Aryl Hydrocarbon Receptor in Human Embryonic Stem Cells and Their Differentiating Counterparts [ATAC-seq]

city: Tartu

first: Tõnis

last: Org

address: Riia 23

institute: University of Tartu

summary: Aryl hydrocarbon receptor (AHR) is a ligand-activated transcription factor, which mediates the effects of  various environmental contaminants, like polycyclic and halogenated aromatic hydrocarbons, including the most potent agonist 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD),  in multiple tissues. Recent advances in AHR biology have underlined its importance in cells with high developmental potency, including pluripotent stem cells. Nonetheless, there is little data on AHR expression and its role during the initial stages of stem cell differentiation. The purpose of this study was to investigate the temporal pattern of AHR expression during directed differentiation of human embryonic stem cells (hESC) into neural progenitor, early mesoderm and definitive endoderm cells. Additionally, we studied the effect of AHR agonist 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) on gene expression profile in hESCs and differentiated cells by RNA-seq, accompanied by identification of AHR binding sites by ChIP-seq and epigenetic landscape analysis by ATAC-seq. . We show that AHR is differentially regulated in distinct lineages, provide evidence that TCDD impairs differentiation of hESCs and identify novel potential AHR target genes which expand our understanding on the role of this protein in different cell types.

overall_design: ATAC-seq profiles of hESC H9 cells pre-treated with DMSO (control) or 10 nM TCDD in mTESRTM1 medium for 3 days in three biological replicates

first: Indrek

last: Teino

first: Antti

last: Matvere

first: Martin

last: Pook

first: Inge

last: Varik

first: Laura

last: Pajusaar

first: Keyt

last: Uudeküll

first: Helen

last: Vaher

first: Arnold

last: Kristjuhan

first: Toivo

last: Maimets


title: Sex specific gene expression patterns in cortico-limbic structures associate with psychiatric disorders

city: Verdun

first: Nicholas

last: O'Toole

state: QC

address: 6875 Boulevard Lasalle

country: Canada

institute: Douglas Mental Health University Institute

summary: In humans there are sex-specific differences in the prevalence and symptomology of psychiatric disorders. However, preclinical animal models have primarily used males. As such, the molecular mechanisms underlying sex-specific differences in mental illness are not well established. In this study, we compared transcriptome-wide gene expression profiles in male and female rats within the corticolimbic system, including the cingulate cortex, nucleus accumbens medial shell (NAcS), ventral dentate gyrus and the basolateral amygdala. We found a considerable number of differentially expressed genes (DEGs) between males and females across all brain regions. However, 84.9% of all DEGs were found in the NAcS (> 5000 genes; p < 0.01, FDR < 0.01). Relating these DEGs to genome wide association studies (GWAS) revealed an enrichment for loci associated with major depressive disorder (Psychiatric Genomics Consortium 2019). We compared the DEGs in the NAcS to an analgous human dataset (Labonte, 2017), and found 587 common DEGs which were enriched for genes associated with both anxiety (neuro genetics study, 2016) and broad depression (UK biobank, 2018). Our data provide comprehensive evidence of sex molecular profiles in the NAcS. Importantly these differences associate with anxiety and depression, suggesting an intrinsic molecular basis for sex-based differences in disease prevalence and presentation.

overall_design: RNA sequencing of brain regions of male and female rats

last: O’Toole

first: Tieyuan

last: Zhang


title: Defining a critical Nanog enhancer using chromatin-focused approaches identifies RNAPII recruitment as required for expression [CUT&Tag]

status: Public on Dec 07 2020

city: Milwaukee

first: Sridhar

last: Rao

state: WI

address: 8727 Watertown Plank Road

department: Blood Research Institute

institute: BloodCenter of Wisconsin

summary: Transcriptional enhancers have been defined by their ability to operate independent of distance and orientation in plasmid reporters rather than native chromatin. We employed a combination of approaches to investigate the Nanog locus in mouse embryonic stem cells (ESCs) and an associated cis regulatory element (CRE) which may operate as either a super-enhancer (SE) or alternative promoter. We establish this element is a SE within chromatin using distance- and orientation-independence as criteria, and that it regulates Nanog by recruiting and/or initiating RNA Polymerase II. Our work highlights that enhancers can regulate gene expression through a diverse set of mechanisms.

overall_design: CUT&Tag of 2 conditions, 3 replicates of each

first: Puja

last: Agrawal


title: Gene expression of human angiosarcoma and correlation with treatment outcomes

status: Public on Dec 01 2020

city: Singapore

first: Jason

middle: Yongsheng

last: Chan

address: 30 Hospital Blvd

country: Singapore

institute: National Cancer Centre Singapore

summary: Gene expression profiling of human angiosarcoma samples was performed using the NanoString Human nCounter PanCancer IO 360 Panel

overall_design: A series of human angiosarcomas was profiled using the NanoString PanCancer IO 360 panel and the data was correlated with treatment and survival outcomes


title: Viral N6-methyladenosine upregulates replication and pathogenesis of human respiratory syncytial virus: m6A-seq of vesicular stomatitis virus

city: CHICAGO

first: Zijie

state: IL

department: Chemistry

institute: University of Chicago

summary: N6-methyladenosine (m6A) is the most abundant internal RNA modification catalyzed by host RNA methyltransferases. As obligate intracellular parasites, many viruses acquire m6A methylation in their RNAs. However, the biological functions of viral m6A methylation are poorly understood. Here, we found that viral m6A methylation serves as a molecular marker for host innate immunity to discriminate self from nonself RNA and that this novel biological function of viral m6A methylation is universally conserved in non-segmented negative-sense (NNS) RNA viruses. Using m6A methyltransferase (METTL3)-knockout cells, we produced m6A-deficient virion RNA from the representative members of the families Pneumoviridae, Paramyxoviridae, and Rhabdoviridae and found that these m6A-deficient viral RNAs triggered significantly higher levels of type I interferon compared to the m6A-sufficient viral RNAs, in a RIG-I dependent manner. Reconstitution of the RIG-I pathway revealed that m6A-deficient virion RNA induced higher expression of RIG-I, bound to RIG-I more efficiently, enhanced RIG-I ubiquitination, and facilitated RIG-I conformational rearrangement and oligomerization. Furthermore, the m6A binding protein YTHDF2 sequesters m6A-sufficient virion RNA which suppresses type I interferon signaling pathway. Collectively, our results suggest that NNS RNA viruses acquire m6A in viral RNA as a common strategy to evade host innate immunity.

overall_design: A few other (NNS) RNA viruses including RSV and hMPV has been sequenced and published before by us. Here, we performed m6A-seq of vesicular stomatitis virus (VSV). VSV virions were purified from supernatants of VSV-infected Hela cell lines. Virus derived mRNA as well as host mRNA were purified from total RNA, which were extracted from VSV infected cells.

first: Mijia

last: Lu

first: Jianrong

last: Li


title: Single cell RNAseq for human female ESCs

first: Kyoung Jae

last: Won

address: 3400 Civic Center Blvd

department: Genetics

summary: Sigle cell RNAseq for human female embryonic stem cells and the differentiated cells by BMP4 treatment

overall_design: RNAseq for HUES-9 hESCs.  BMP4 treatment for HUES-9 cells and collected after day 2

first: Kyoung-Jae

first: Montserrat

last: Anguera


title: The comprehensive analysis of total expression profiles in initial diagnosed multiple myeloma by genetic microarray

first: yuan

middle: jiu

last: yun

address: Beijing xizhimen station

institute: Company

summary:
Long non-coding RNA (lncRNA) plays a vital role in Multiple Myeloma. Nevertheless, the exact expression features and functions of lncRNAs are still obscure.To investigate aberrantly expressed lncRNAs and mRNAs in MM, we screened the crucial differentially expressed lncRNA and mRNA in mononuclear cells from bone marrow of multiple myeloma patients and normal donors.These differentially expressed lncrnas are likely to play a key role in the development of MM, and may be used as a novel  biomarker for the diagnosis or therapy of MM.
We used microarrays to screen the candidate differentially expressed lncRNAs and mRNAs in mononuclear cells from bone marrow of multiple myeloma patients and normal donors .Subsequently,the candidate differentially expressed lncRNAs and mRNAs were verified by qRT-PCR.

overall_design: We selected BM mononuclear cells from 10 multiple myeloma patients and 10 normal donors for total RNA extraction and Clariom D Assay (human,Affymetrix) analysis. At the same time, in order to deeply understand the relationship between differential lncRNA and mRNA, we carried out in-depth analysis, including GO Enrichment Analysis,Hierarchical Clustering,Enrichment Analysis,co-expression network and ceRNA network analysis under the basic analysis. We are trying to find out an novel marker which is of guiding significance for the diagnosis and therapy of Multiple Myeloma.

first: Yuqin

last: He

first: Wenming

last: Chen


title: Evolution of heterochromatin and heterochromatin genes in the Oryza genomes reveals a new heterochromatin-euchromatin boundary [ncRNA-Seq]

first: Lei

sample_organism:
Oryza sativa
Oryza brachyantha

platform_organism:
Oryza sativa
Oryza brachyantha

overall_design: we conducted a comprehensive heterochromatin study among close-related species with high quality sequences and near-gap free genomes. To achieve this, we generated twenty-six new epigenetic datasets in this study including the heterochromatin hallmark H3K9me2 in six species and DNA methylation of Oryza brachyantha, two siRNA libraries of O. sativa and O.brachyantha.

first: Meijiao

last: Wang

first: Mingheng


title: The differentially expressed circular and long non-coding RNAs in the prefrontal cortex of Nrf2-knockout mice

city: Shijiazhuang

address: Hebei Medical University, No. 361, Zhongshan East Road, Chang'an District

institute: Heibei Medical University

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

summary: Circular RNAs (circRNAs), long non-coding RNAs (lncRNAs) and mRNAs have displayed dysregulated expression in the prefrontal cortex of Nrf2-knockout mice.

overall_design: prefrontal cortex_wild and prefrontal cortex_nrf2 knockout

first: Shaoguang

last: Sun


title: Evolution of heterochromatin and heterochromatin genes in the Oryza genomes reveals a new heterochromatin-euchromatin boundary [ChIP-Seq]

sample_organism:
Oryza brachyantha
Oryza punctata
Oryza glaberrima
Sorghum bicolor
Oryza sativa Japonica Group
Leersia perrieri

first: Mingsheng


title: Differential gene expression analysis of eys+/-; lrp5+/- zebrafish eye by microarray

city: Indianapolis

first: Yoshikazu

last: Imanishi

state: Indiana

address: 1160 W Michigan Street

department: Department of Ophthalmology

institute: Indiana University School of Medicine

summary: Vision is essential for vertebrates including humans. Sustained vision is accomplished by retinoid metabolism, the ‘visual cycle’, where all-trans retinol (atROL) is incorporated into the retinal pigment epithelium (RPE) from photoreceptors presumably through decade-long missing receptor(s). Here, we show that the LDL-related receptor-5 (Lrp5) protein is linked to the retinol binding protein 1a (Rbp1a), the transporter of atROL in the visual cycle, by generating and analyzing the digenic eyes shut homolog+/-; lrp5+/- zebrafish, the same form of gene defect detected in a human case of inherited retinal degeneration. Global gene expression analysis followed by genetic study clarified that rbp1a played a role downstream of lrp5. Rbp1a protein was colocalized with Lrp5 protein at microvilli of RPE cells. Furthermore, Rbp1a directly bound to the C-terminal intracellular region of Lrp5 in vitro. Collectively, these results strongly suggest that Lrp5 is a potent candidate of the receptor of atROL in the visual cycle.

overall_design: Grobal gene expression was compared between eys+/-; lrp5+/-, eys-/- or lrp5-/- eyes and wildtype eyes at 3.5 months post-fertilisation (3.5 mpf) zebrafish using Affymetrix microarray

first: Shimpei

last: Takita

first: Yuko

last: Seko


title: Comparing mRNA expression of Myc/NrasG12V and Myc/Akt1 driven liver tumors

city: Tübingen

first: Omelyan

last: Trompak

state: BW

address: Otfried-Müller-Straße 14

department: Internal Medicine VIII

country: Germany

institute: University Hospital of Tübingen

summary: To analyze mRNA expression of Myc/NrasG12V and Myc/Akt1 driven liver tumors (HCC), we generated HCCs with elevated MYC expression and activated Raf-MEK-ERK or Akt1 signaling. To trigger tumor development, we co-delivered transposable elements encoding for Myc and oncogenic NrasG12V or myristoylated Akt1 via hydrodynamic injection into the hepatocytes of C57BL/6 wildtype mice and analyzed the transcriptomes of the developed tumors.

overall_design: mRNA expression of Myc/NrasG12V and Myc/Akt1 driven liver tumors was compared via mRNAseq analysis

first: Daniel

last: Dauch

first: Lars

last: Zender

first: Ramona

last: Rudalska

first: Thales

last: Kronenberger


title: Comparing mRNA expression between carrier treated and sorafenib treated Myc/NrasG12V liver tumors

summary: To profile determinants of sensitivity and resistance towards the multikinase inhibitor sorafenib in liver cancer (HCC), we generated HCCs with elevated MYC expression and activated Raf-MEK-ERK signaling. To trigger tumor development, we co-delivered transposable elements encoding for Myc and oncogenic NrasG12V via hydrodynamic injection into the hepatocytes of C57BL/6 wildtype mice. To characterize the response of Myc/NrasG12V HCCs towards sorafenib, we analyzed their transcriptomes after three weeks of sorafenib or carrier treatment.

overall_design: mRNA expression of carrier treated and sorafenib treated Myc/NrasG12V liver tumors was compared via mRNAseq analysis


title: Histone deacetylase inhibitor givinostat alleviates liver fibrosis by regulating hepatic stellate cell activation

city: shanghai

first: heming

last: huang

address: 1665 Kongjiang Road

institute: Xinhua Hospital, School of Medicine, Shanghai Jiaotong University

summary: Hepatic fibrosis, a common pathological manifestation of chronic liver injury, is generally considered to be the end result of an increase in extracellular matrix produced by activated hepatic stellate cells (HSCs). Targeting the mechanisms underlying HSC activation may provide a powerful therapeutic strategy for the prevention and treatment of liver fibrosis. A high-throughput screening assay was established, and the histone deacetylase inhibitor givinostat was identified as a potent inhibitor of HSC activation in vitro. Givinostat significantly inhibited HSC activation in vivo, ameliorated carbon tetrachloride-induced mouse liver fibrosis and lowered plasma aminotransferases. Transcriptomic analysis revealed the most significantly regulated genes in the givinostat treatment group in comparison with those in the solvent group, among which, Dmkn, Msln and Upk3b were identified as potential regulators of HSC activation. Givinostat significantly reduced the mRNA expression of Dmkn, Msln and Upk3b in both a mouse liver fibrosis model and in HSC-LX2 cells. Knocking down any of the aforementioned genes inhibited the TGF-β1-induced expression of α-smooth muscle actin and collagen type I, indicating that they are crucial for HSC activation. In summary, using a novel strategy targeting HSC activation, the present study identified a potential epigenetic drug for the treatment of hepatic fibrosis and revealed novel regulators of HSC activation.

overall_design: RNA-sequencing analysis of liver tissue extracted from CCl4 (n=3) and CCl4 + givinostat-treated mice (n=2).

first: He-ming

last: Huang

first: Xiao-ru

last: Zhou

first: Yan-jun

last: Liu

first: Shi-jie

last: Fan

first: Li-ping

last: Liao

first: Jing

first: Cui-cui

last: Shi

first: Liang

last: Yu

first: Jin-jin

last: Pen

first: Cheng

last: Luo

first: Yuan-yuan

last: Zhang

first: Guang-ming


title: Radiation dose-fractionation effects on immune modulation in murine mammary tumors

city: Melbourne

first: Joseph

last: Sia

address: 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

summary: Radiation therapy (RT) induces pleiotropic effects on the tumor immune microenvironment, but how these changes are modulated by radiation dose-fractionation is not well understood. Our in vivo data murine data suggests that while changes evoked by RT in the tumor immune compartment are largely concordant between radiation regimens, several key immunological processes are differentially regulated by radiation dose-fractionation.

overall_design: Wildtype female C57BL/6 mice were injected with AT3-OVA triple negative mammary tumor cells orthotopically into the mammary fat pad and received local RT to the tumors using either the 3x4Gy regimen or the 1x20Gy regimen. Tumors were harvested at days 5 and 13 post completion of RT, processed into single cell suspensions and stained for the pan-leukocyte marker CD45.2. CD45.2+ immune cells were sorted by fluorescence-activated cell sorting (FACS) and underwent RNA extraction. Only samples with an RNA integrity number (RIN) of greater than 8.5 were processed for library preparation. Mock-irradiated tumors from mice anaesthetized as per their irradiated counterparts were used as controls (3x0 Gy and 1x0 Gy, respectively).

first: Jim

last: Hagekyriakou

first: Ioana

last: Chindris

first: Niko

last: Thio

first: Nicole

last: Haynes


title: Methamphetamine increases the proportion of SIV-infected microglia/macrophages, alters metabolic pathways, and elevates cell death pathways: a single-cell analysis

city: OMAHA

first: Meng

last: Niu

state: NE

address: 42nd and Emile

department: Department of Neurological sciences

institute: University of Nebraska Medical Center

summary: Both drugs abuse and HIV infection continue to affect many indiviiduals. Both have untoward effects on the brain, and the two conditions often co-exist. In the brain, macrophages and microglia are infectable by HIV, and these cells are also targets for the effects of drugs of abuse such as the psychostimulant methamphetamine. In order to determine the interaction of HIV and methamphetamine we isolated microglia and macrophages from the brains of SIV-infected rhesus monkeys treated with methamphetamine and from SIV-infected monkeys who did not receive methamphetamine. Cells were subjected to single cell RNA sequencing and results analyzed by statistical and bioinformatic analysis. In the animals treated with methamphetamine, a significantly increased proportion of cells were infected by SIV. In addition, genes encoding functions in cell death pathways were increased, and the brain-derived neurotropic factor pathway was inhibited. The gene expression patterns in infected cells did not cluster separately from uninfected cells, but clusters comprised of cells from methamphetamine-treated animals differed in neuroinflammatory and metabolic pathways from those comprised of cells from untreated animals. Methamphetamine increases CNS infection by SIV and has adverse effects on both infected and uninfected microglia and brain macrophages, highlighting the dual and interacting harms of HIV infection and drug abuse on the brain.

overall_design: Microglia/Macrophages were isolated from the brains of 2 saline-treated (control), and 2 Methamphetamine treated (experimental), SIV-infected rhesus monkeys with encephalitis and cryopreserved. They were subsequently thawed, purified immunomagnetically for CD11b+ and then by flow cytometry for CD11b+ and Live cells, and then captured by the 10xGenomics platform subjected to single cell RNA sequencing

first: Brenda

last: Morsey

first: Benjamin

middle: G

last: Lamberty

first: Katy

last: Emanuel

first: Fang

first: Rosiris

last: León-Rivera

first: Joan

last: Berman

first: Peter

middle: J

last: Gaskill

first: Stephanie

middle: M

last: Matt

first: Pawel

middle: S

last: Ciborowski

first: Howard

last: Fox


title: ALC1 and PARP activities coordinate chromatin accessibility and viability in homologous recombination deficient cells  (RNA-seq)

city: PHILADELPHIA

first: Zhendong

last: Cao

state: PA

address: BRB Rm620, 421 Curie Blvd

department: Cancer biology

institute: university of pennsylvania

summary: The response to Poly (ADP-ribose) polymerase inhibitors (PARPi) is dictated by  homologous recombination (HR) DNA repair mechanisms and the abundance of lesions  that trap PARP enzymes on chromatin. It remains unclear, however, if the established  role of PARP in promoting chromatin accessibility impacts viability in these settings.  Using a CRISPR based screen, we identify the PAR-binding Snf2-like ATPase, ALC1 as  a key determinant of PARPi toxicity in HR-deficient cells. ALC1 loss reduced viability  of BRCA mutant cells and enhanced their sensitivity to PARPi by up to 250-fold, while  overcoming several known resistance mechanisms. ALC1 loss was not epistatic to other  repair pathways that execute the PARPi response. Instead, ALC1 deficiency reduced  chromatin accessibility concomitant with a decrease in the association of repair factors.  This resulted in an accumulation of replication associated DNA damage and a reliance on  HR. These findings establish PAR-dependent chromatin remodeling as a mechanistically  distinct aspect of PARPi responses, implicating ALC1 inhibition as a new approach to  overcome therapeutic resistance in HR-deficient cancers.

overall_design: mRNA profiles of  delp53-/- del BRCA1-/- RPE1 and BRCA2-/- DLD1 cells expressing a Negative control sgRNA or sgRNA for ALC1

first: Priyanka

last: Verma

first: Junwei

last: Shi

first: Roger

last: Greenberg


title: Expression data from cultured cell line (Caco-2)

city: changzhou

first: jiang

last: wei

address: juqian street

institute: Soochow University

summary:
ApoM may be a crucial regulator of colorectal cancer progression, but its role in colorectal cancer has not been elucidated. Bioinformatic analysis of the microarray data revealed unique transcriptomes under different apoM expression.
We used microarrays to detail the global programme of gene expression underlying different apoM genetypes and identified distinct classes of regulated genes

overall_design: Caco-2 cells with different apoM expression were selected for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain different expression levels of genes under different apoM expression levels

first: Qinfeng

last: Mu

first: Miaomei

last: Yu


title: Epigenetic gene-expression links heart failure to memory impairment [smallrna_after_saha]

city: Goettingen

first: Md Rezaul

last: Islam

address: von siebold str. 3a

institute: DZNE

summary: In current clinical practice care of diseased patients is often restricted to separated disciplines. However, such an organ-centered approach is not always suitable. For example, cognitive dysfunction is a severe burden in heart failure patients. Moreover, these patients have an increased risk for age-associated dementias. The underlying molecular mechanisms are presently unknown and thus corresponding therapeutic strategies to improve cognition in heart failure patients are missing. Using mice as model organisms we show that heart failure leads to specific changes in hippocampal gene-expression, a brain region intimately linked to cognition. These changes reflect increased cellular stress pathways which eventually lead to loss of neuronal euchromatin and reduced expression of a hippocampal gene cluster essential for cognition. Consequently, mice suffering from heart failure exhibit impaired memory function. These pathological changes are ameliorated via the administration of a drug that promotes neuronal euchromatin formation. Our study provides first insight to the molecular processes by which heart failure contributes to neuronal dysfunction and point to novel therapeutic avenues to treat cognitive defects in heart failure patients.

overall_design: Analysis of smallRNAseq data from 3 months old CamkdeltaC mice CA1 hippocampal region after 4 weeks Vorinostat/vehicle treatment

first: Islam

last: Rezaul

first: Fischer

last: Andre


title: Epigenetic gene-expression links heart failure to memory impairment [rnaseq_after_saha]

overall_design: Analysis of RNAseq data from 3 months old CamkdeltaC mice CA1 hippocampal region after 4 weeks Vorinostat/vehicle treatment


title: Master regulators and cofactors of human neuronal cell fate specification identified by CRISPR gene activation screens [DualFactor_RNAseq]

city: Durham

first: Charles

last: Gersbach

state: NC

address: 101 Science Drive

department: Biomedical Engineering

institute: Duke University

summary: Technologies to reprogram cell-type specification have revolutionized the fields of regenerative medicine and disease modeling. Currently, the selection of fate-determining factors for cell reprogramming applications is typically a laborious and low-throughput process. Due to the diversity of neuronal subtypes governed by a variety of distinct regulators, methods for the programmed specification of neurons would particularly benefit from a systematic understanding of the transcriptional codes that define the neuronal phenotype. Therefore, we used high-throughput pooled CRISPR activation (CRISPRa) screens to map human neuronal cell-fate regulators. We utilized dCas9-based activation to target 1,496 putative transcription factors in the human genome. Using a reporter of neuronal commitment, we profiled the neurogenic activity of these transcription factors in human pluripotent stem cells, leading to a curated set of neuronal factors. Activation of pairs of transcription factors revealed neuronal cofactors, including E2F7, RUNX3 and LHX8, that improve conversion efficiencies and influence gene expression programs related to subtype-specificity and maturation of neuronal cell types. Finally, using multiplexed gene regulation with orthogonal CRISPR systems, we demonstrated improved neuronal differentiation with concurrent activation and repression of target genes, underscoring the power of CRISPR-based gene regulation for programming complex cellular phenotypes.

overall_design: TUBB3-2A-mCherry iPS cells were transduced with a cDNA encoding the indicated transcription factor and assessed for neuronal differentiation with RNA-sequencing

first: Joshua

last: Black

first: Sean

middle: R

last: McCutcheon

first: Shataakshi

last: Dube

first: Alejandro

last: Barrera

first: Tyler

last: Klann

first: Grayson

last: Rice

first: Shaunak

last: Adkar

first: Scott

last: Soderling

first: Timothy

middle: E

last: Reddy


title: Master regulators and cofactors of human neuronal cell fate specification identified by CRISPR gene activation screens [CAS_TF_sgNGN3_Screen_AmpliconSeq]

overall_design: TUBB3-2A-mCherry dCas9-2xVP64 iPS cells were transduced with a CRISPRa gRNA library targeting 1,496 transcription factors in combination with sgNGN3 and sorted into mCherry-expressing bins after five days of culture.


title: Epigenetic gene-expression links heart failure to memory impairment [chipseq_tg_wt_3m]

overall_design: Analysis of H3K4me3 Chipseq data from 3 months old CamkdeltaC transgenic mice CA1 hippocampal region


title: Epigenetic gene-expression links heart failure to memory impairment [rnaseq_tg_vs_wt_3m]

overall_design: Analysis of RNAseq data from 3 months old CamkdeltaC mice CA1 hippocampal region


title: Master regulators and cofactors of human neuronal cell fate specification identified by CRISPR gene activation screens

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

overall_design: Refer to individual Series


title: Epigenetic gene-expression links heart failure to memory impairment [rnaseq_tunicamycin_6h]

overall_design: Analysis of RNAseq data from hippocampal neurons exposed to ER stress


title: Master regulators and cofactors of human neuronal cell fate specification identified by CRISPR gene activation screens [CAS_TF_sgASCL1_Screen_AmpliconSeq]

overall_design: TUBB3-2A-mCherry dCas9-2xVP64 iPS cells were transduced with a CRISPRa gRNA library targeting 1,496 transcription factors in combination with sgASCL1 and sorted into mCherry-expressing bins after five days of culture.


title: p53 directly represses human LINE1 transposons

city: Dallas

first: John

last: Abrams

state: TX

address: 5323 Harry Hines Blvd

department: Cell Biology

institute: University of Texas Southwestern Medical Center

summary: p53 is a potent tumor suppressor and commonly mutated in human cancers. Recently, we demonstrated that p53 genes act to restrict retrotransposons in germ line tissues of flies and fish but whether this activity is conserved in somatic human cells is not known. Here we show that p53 constitutively restrains human LINE1s by cooperatively engaging sites in the 5’UTR and stimulating local deposition of repressive histone marks at these transposons. Consistent with this, the elimination of p53 or the removal of corresponding binding sites in LINE1s, prompted these retroelements to become hyperactive. Concurrently, p53 loss instigated chromosomal rearrangements linked to LINE sequences and also provoked inflammatory programs that were dependent on reverse transcriptase produced from LINE1s. Taken together, our observations establish that p53 continuously operates at the LINE1 promoter to restrict autonomous copies of these mobile elements in human cells. Our results further suggest that constitutive restriction of these retroelements may help to explain tumor suppression encoded by p53, since erupting LINE1s produced acute oncogenic threats when p53 was absent.

overall_design: RNA sequencing of a crispr cas9 generated p53 knockout A375 cell line together with the parental line.


title: Master regulators and cofactors of human neuronal cell fate specification identified by CRISPR gene activation screens [SingleFactor_RNAseq]


title: Master regulators and cofactors of human neuronal cell fate specification identified by CRISPR gene activation screens [CAS_TF_Orthogonal_RNAseq]

overall_design: TUBB3-2A-mCherry iPS cells were transduced with two gRNAs from different CRISPR species to enable orthogonal gene regulation assessed by RNA-sequencing


title: Master regulators and cofactors of human neuronal cell fate specification identified by CRISPR gene activation screens [CAS_TF_SingleFactor_Sublibrary_Screen_AmpliconSeq]

overall_design: TUBB3-2A-mCherry dCas9-2xVP64 iPS cells were transduced with a CRISPRa gRNA library targeting 109 transcription factors and sorted into mCherry-expressing bins after five days of culture.


title: Master regulators and cofactors of human neuronal cell fate specification identified by CRISPR gene activation screens [CAS_TF_SingleFactor_Screen_AmpliconSeq]

overall_design: TUBB3-2A-mCherry dCas9-2xVP64 iPS cells were transduced with a CRISPRa gRNA library targeting 1,496 transcription factors and sorted into mCherry-expressing bins after five days of culture.


title: Exosomes differentiate mouse embryonic fibroblasts to beta-like cells

city: Suwon-si

first: Paulami

last: Mandal

state: Gyeonggi-do

address: 2066, Seobu-ro, Jangan-gu, Room 6317, School of Medicine

department: Molecular Cell Biology

institute: Sungkyunkwan University

summary: Diabetes is a concerning health malady worldwide. Islet or pancreas transplantation is the only long-term treatment available; however, the scarcity of transplantable tissues hampers this approach. Therefore, new cell sources and differentiation approaches are required. Apart from the genetic- and small molecule-based approaches, exosomes could induce cellular differentiation by means of their cargo, including miRNA. We developed a chemical-based protocol to differentiate mouse embryonic fibroblasts (MEFs) into β-like cells and employed mouse insulinoma (MIN6)-derived exosomes in the presence or absence of specific small molecules to encourage their differentiation into β-like cells. We further performed miRNA sequencing to identify the miRNAs present in the exosomes that could mediate the differentiation process. The miRNA sequencing study found some of the miRNAs to be highly upregulated in the exosomes, some in the parent MIN6 cells, and some other were present in almost equal representation. Some of the miRNAs were investigated for their role in mediating the differentiation process to β-like cells . These miRNAs were able to differentiate the exocrine cells too.

overall_design: Examination of MIN6-derived exosomes compared to MIN6 cells in terms of their miRNA repertoire by using miRNA-sequencing in duplicate samples.

first: Kyeong

last: Kim


title: Mechanical Regulation of Stem Cell Proliferation and Fate Decisions by their Differentiated Daughters

first: Terry

last: Lechler

summary: RNAseq analysis of suprabasal cells in the epidermis of control and K10rtTA;TRESpastin (which depolymerize microtubules) at E16.5 were performed. We observed the premature differentiation of the barrier and increased actomyosin contractility in suprabasal differentiated cells upon microtubule disruption compared to control, and proved the increased actomyosin contractility caused by microtubule depolymerization leads to basal stem cell hyperproliferation during epidermal development.

overall_design: mRNA profiles of suprabasal differentiated cells in the epidermis of control and K10rtTA;TREspastin at E16.5

first: Wenxiu

last: Ning


title: Microarray study of aldosterone-producing adenomas (APA) and their adjacent normal adrenal glands

city: Cheras

first: Elena

middle: AB

last: Azizan

state: Wilayah Persekutuan Kuala Lumpur

address: PPUKM, Jalan Yaacob Latif, Bandar Tun Razak

department: Department of Medicine

country: Malaysia

institute: The National University of Malaysia

summary: Aldosterone-producing adenomas (APA) are heterogeneous. The objectives of this study were to compare the transcriptional profiles in APA and normal adjacent adrenal gland (AAG).  This was done through the Illumina beadchip analysis of RNA from eight paired APA-AAG. Other tissues (phaeochromocytoma, cushing, and hyperplastic adrenals) were included as controls.

overall_design:
RNA samples from eight primary hyperaldosteronism patients, each with a paired aldosterone-producing adenoma (APA) and normal adjacent adrenal gland (AAG) were used for this microarray analysis as published (https://doi.org/10.1210/jc.2011-2965).
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Authors state "we have not been able to locate the raw data".

first: Morris

last: Brown


title: DNA methylation in airway and parenchymal fibroblasts isloated by from individuals with and without asthma

city: nottingham

first: Rachel

last: Clifford

address: Biodiscovery Institute 3

institute: University of Nottingham

summary: Background: Mesenchymal fibroblasts are ubiquitous cells that maintain the extracellular matrix of organs. Within the lung, airway and parenchymal fibroblasts are crucial for lung development and are altered with disease, but it has been difficult to understand their roles due to the lack of distinct molecular markers.

overall_design: We studied DNA methylation and gene expression in airway and parenchymal lung fibroblasts from healthy and asthmatic donors, to identify a molecular marker and to determine if they are molecularly distinct in asthma.

middle: L


title: Epigenetic gene-expression links heart failure to memory impairment [rnaseq_hypoxia_4h]

first: Md Rezaul

last: Islam

overall_design: Analysis of RNAseq data from hippocampal neurons exposed to 4 hour of hypoxic condition.

first: Islam

last: Rezaul

first: Fischer

last: Andre


title: RNA-seq of human gut Bacteroides xylanisolvens and Bacteroides ovatus isolates grown on mucin O-linked glycans compared to glucose

city: Ann Arbor

first: Eric

last: Martens

address: 1150 W. Medical Center Dr.

institute: University of Michigan

summary:
Purpose: Examining the transcriptome of human gut bacteria (Bacteroides xylanisolvens/Bacteroides ovatus) that grow on mucin O-linked glycans as a sole carbon source
Methods: Strains were grown on 10 mg/ml mucin O-linked glycans (MOG) or 5 mg/ml glucose as a sole carbon source in vitro. Fold change was calculated as MOG over glucose. Once cells reached an optical density corresponding to mid-log phase growth, RNA was isolated and rRNA depleted. Samples were multiplexed for sequencing on the Illumina HiSeq platform at the University of Michigan Sequencing Core. Data was analyzed using Arraystar software (DNASTAR, Inc.) Genes with significant up- or down-regulation were determined by the following criteria: genes with an average fold-change >10-fold and biological replicates with a normalized expression level >1% of the overall average RPKM expression level.
Results: We identified genes activated in response to mucin O-linked glycans from Bacteroides xylanisolvens/Bacteroides ovatus strains

sample_organism:
Bacteroides ovatus
Bacteroides xylanisolvens

overall_design: rRNA-depleted, mRNA profiles of human gut bacteria grown on mucin O-linked glycans run on Illumina Hi-Seq platform.

first: Nicholas

last: Pudlo

first: Karthik

last: Urs

middle: C


title: Differential gene expression in the tumorigenic liver of Nod2-/- and wild type mice

city: GARY

first: Dipika

last: Gupta

state: IN

address: 3400 BROADWAY

institute: INDIANA UNIV SCHOOL MEDICINE-NORTHWEST

summary: We report that Nod2, a pattern recognition receptor, protects from high fat diet-dependent liver malignancy and this protection is accompanied by changes in gene expression for cell proliferation, inflammation and steroid biosynthesis.

overall_design: We compared RNA populations in the liver from WT and Nod2-/- mice treated with a carcinogen and maintained on high fat diet for 30 weeks.

first: Serdar

last: Gurses

first: Roman

last: Dziarski


title: Epigenetic gene-expression links heart failure to memory impairment [rnaseq_from_MI_experiment]

overall_design: Analysis of CA1 hippocampal RNAseq data from MI vs Sham mice


title: Stimulation of soluble guanylate cyclase exerts anti-inflammatory actions in the liver through a VASP/NF-kB/NLRP3 inflammasome circuit

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

summary: Soluble guanylate cyclase (sGC) catalyzes the conversion of GTP into cyclic guanosine-3',5’-monophosphate (cGMP), a key second messenger in cell signaling and tissue homeostasis. We and others recently demonstrated that sGC stimulation is associated with a remarkable anti-inflammatory effect in the liver of mice experimentally induced to nonalcoholic steatohepatitis (NASH). Here, we investigated the mechanisms of action underlying the anti-inflammatory effect of the sGC stimulator praliciguat (PRL) in the liver. Therapeutic administration of PRL exerted anti-inflammatory and anti-fibrotic actions in mice fed with choline-deficient L-amino acid-defined high-fat diet (CDAHFD), an optimized experimental model of NASH. The anti-inflammatory effect of PRL was associated with lower F4/80- and CX3CR1-positive macrophage infiltration into the liver in parallel with lower Ly6CHigh- and higher Ly6CLow-expressing monocytes in peripheral circulation. The PRL anti-inflammatory effect was also associated with a remarkable suppression of hepatic levels of IL-1β, NLPR3, ASC and active cleaved-Caspase-1, which are components of the NLRP3 inflammasome. In vitro, in Kupffer cells challenged with the classical inflammasome model of LPS plus ATP, PRL inhibited the priming (expression of Il1b and Nlrp3) and blocked the release of mature IL-1β. Mechanistically, PRL induced the PKG-mediated phosphorylation of the VASP Ser239 residue, which in turn, reduced NF- κB activity and Il1b and Nlrp3 gene transcription. PRL also reduced active cleaved-Caspase-1 levels independently of pannexin-1 activity. These data indicate that sGC stimulation with PRL exerts anti-inflammatory actions in the liver through mechanisms related to a PKG/VASP/NF-kB/NLRP3 inflammasome circuit.

overall_design: Transcriptomic analysis from 8 control mouse (C) and 8 samples from nonalcoholic steatohepatitis (NASH) mouse model (CD)

first: R

last: Flores R

first: J

last: Clarià


title: The effect of MPC EV on myotubes

city: Lexington

first: Kevin

last: Murach

state: KY

address: 900 South Limestone CTW 445

department: Physical Therapy

institute: University of Kentucky

platform_organism:
Mus musculus
synthetic construct


title: Endogenous miRNA-200b/c activity and regulation explored by a functional dual fluorescence reporter

first: Irfan

last: Asangani

address: 421 Curie Bld.

department: Cancer Biology

institute: University of Pennsylvania

summary: Since their discovery, microRNAs (miRNA)s have been widely studied in almost every field of biology and medicine, leading to the identification of important gene regulation circuits and cellular mechanisms. However, investigations are generally focused on the analysis of their downstream targets and biological functions in overexpression and knockdown approaches, while miRNAs endogenous levels and activity remain poorly investigated. Here, we used the cellular plasticity-regulating process of epithelial-to-mesenchymal transition (EMT) as a model to show the efficacy of a plasmid-based fluorescent sensor to separate cells with distinct EMT signatures, based on miR-200b/c activity. The system was further combined with a CRISPR-Cas9 screening platform to unbiasedly identify miR-200b/c upstream regulating genes. The sensor allows to infer miRNAs fundamental biological properties, as profiling of sorted cells indicated miR-200b/c as a molecular switch between EMT differentiation and proliferation, and suggested a role for metabolic enzymes in miR-200/EMT regulation. Analysis of miRNAs’ endogenous levels and activity could lead to a better comprehension of their biological role in physiology and disease.

overall_design: Gene expression analysis by RNAseq in colorectal carcinoma cell line HCT116 sorted for high and low activity of miR-200b/c

first: Paolo

last: Ceppi

first: Ram

last: Natesan


title: MPC EVs onto Myotubes

summary: Extracellular vesicles (EVs) from proliferating primary myogenic progenitor cells (MPCs) were incubated on myotubes for 12 and 24 hours

overall_design: Primary myogenic progenitor cells from C57BL6/J mice were differentiated into myotubes, MPC EVs were incubated with the myotubes, then the myotubes underwent RNA-sequencing to assess the effect of MPC EVs on gene expression

first: Charlotte

last: Peterson


title: Genome-wide identification of Argonautes in Solanaceae with emphasis on potato

city: Uppsala

first: Kristian

middle: Erik

last: Persson Hodén

address: Almas allé 5

department: Plant Biology

country: Sweden

institute: Swedish University of Agricultural Sciences

summary: Regulatory small RNAs (sRNAs) play important roles in many fundamental processes in plant biology such as development, fertilization and stress responses. The AGO protein family has here a central importance in gene regulation based on their capacity to associate with sRNAs followed by mRNA targeting in a sequence-complementary manner. The present study explored Argonautes (AGOs) in the Solanaceae family, with emphasis on potato, Solanum tuberosum (St). A genome-wide monitoring was performed to provide a deeper insight into gene families, genomic localization, gene structure and expression profile against the potato late blight pathogen Phytophthora infestans. Among 15 species in the Solanaceae family we found a variation from ten AGOs in Nicotiana obtusifolia to 17 in N. tabacum. Comprehensive analyses of AGO phylogeny revealed duplication of AGO1, AGO10 and AGO4 paralogs during early radiation of Solanaceae. Fourteen AGOs were identified in potato. Orthologs of AGO8 and AGO9 were missing in the potato genome. However, AGO15 earlier annotated in tomato was identified. StAGO15 differs from the other paralogs having residues of different physico-chemical properties at functionally important amino acid positions. Upon pathogen challenge StAGO15 was significantly activated and hence may play a prominent role in sRNA-based regulation of potato defense.

sample_organism:
Solanum tuberosum
Phytophthora infestans

overall_design: 13 RNAseq samples are included in the analysis. Potato cv. Sarpo Mira was innoculated with H2O, P infestans  strains 88069 and 11388. 3 replicates for each of these samples. Also  88069 and 11388 Mycelia samples were included, 2 replicates each.

first: Zhen

last: Liao

middle: P

last: Hodén

first: Ravi

middle: K

last: Singh

first: Christina

last: Dixelius


title: Persistent viral activity, cytokine storm and lung fibrosis in severe COVID-19

city: Shenzhen

first: Zheng

last: Zhang

address: No. 29, Bulan Road

institute: Shenzhen 3rd People's Hospital

summary: Severe COVID-19 may progress into acute respiratory distress syndrome (ARDS) with high mortality risk. Its exact pathological mechanism, therapeutic obstacles and the clinical sequelae are critical and unresolved issues. Here, we reported a representative COVID-19 induced ARDS case experienced initially stable, then suddenly deteriorating up to final respiratory failure courses, until his death despite of lung transplantation. His lung pathology showed necrosis of parenchymal tissues, extensive immune cell infiltration and lung fibrosis. Single-cell RNA sequencing revealed various immune cell populations were largely expanded in his lung, and manifested inflammatory/activated functions. We also showed that cell-crosstalk between lung macrophages and fibroblasts promoted pulmonary fibrosis through IL-1B and TGF-Β signaling pathways. Although SARS-CoV-2 RNA remained undetectable in his respiratory tract specimens including BALF at the later stage of his disease, the presence of SARS-CoV-2 was definitely confirmed in his lung tissues. Thus, this case indicates the pathological mechanism of severe COVID-19 includes pulmonary SARS-CoV-2 persistence, deranged inflammation and the extensive lung fibrosis which set the barriers for effective treatments and indicate potential health complications for severe COVID-19 patients.

overall_design: Using 10x genomics to measure single-cell RNA sequence (scRNA-seq) to comprehensively characterize the lung microenvironment in 4 lung tissues from the same COVID-19 severe patient.

first: Gang

last: Xu

first: Yang

last: Liu

first: Mingfeng

first: Jizhou

last: Gou

first: Xin

last: Wang

first: Jing

last: Yuan

first: Weilong

first: Guangde

last: Zhou

first: Shuye

first: Lei


title: Impact of mothers' early life exposure to low or high folate on progeny outcome and DNA methylation patterns

city: Montreal

first: Jacquetta

last: Trasler

state: Quebec

address: 1001 Decarie Boul, Block E, ES1.4380

department: Pharmacology & Therapeutics; Human Genetics

institute: McGill University

summary: The dynamic patterning of DNA and histone methylation during oocyte development presents a potentially susceptible time for epigenetic disruption due to early life environmental exposure of future mothers. We investigated whether maternal exposure to folic acid deficient (FD) and supplemented (FS) diets starting in utero could affect oocytes and cause adverse developmental and epigenetic effects in next generation progeny. Female BALB/c mice (F0) were placed on one of four amino acid defined diets for 4 weeks before pregnancy and throughout pregnancy and lactation: folic acid control (rodent daily recommended intake or DRI; Ctrl), 7−fold folic acid deficient (7FD), 10−fold folic acid supplemented (10FS) or 20−fold folic acid supplemented (20FS) diets. F1 female pups were weaned onto Ctrl diets, mated to produce the F2 generation, and the F2 offspring were examined at E18.5 for developmental and epigenetic abnormalities. Resorption was increased and litter sizes decreased amongst F2 E18.5 day litters in the 20FS group. Increases in abnormal embryo outcomes were observed in all three FD and FS groups. Subtle genome-wide DNA methylation alterations were found in the placentas and brains of F2 offspring in the 7D, 10FS and 20FS groups; in contrast, global and imprinted gene methylation were not affected.  The findings show that early life female environmental exposures to both low and high folate prior to oocyte maturation can compromise oocyte quality, adversely affecting offspring of the next generation, in part by altering DNA methylation patterns.

overall_design: Eight-week old BALB/c female mice (F0) were exposed for 4 weeks to folic acid control (FCD; 2mg/kg), folic acid deficient (7FD; 0.3mg/kg), 10-fold folic acid supplemented (10FS; 20mg/kg) or a 20-fold folic acid supplemented (20FS; 40mg/kg) diets. Following these 4 weeks, they were then mated to BALB/c male mice on regular chow diets.  Throughout mating, gestation and lactation, the females were fed their respective diets and the F1 female offspring were then weaned at postnatal day 20 onto FCD.  At 8-10 weeks of age, F1 females, representative of 10 Ctrl, 11 FD, 10 10FS, and 9 20FS different original F0 litters per diet group, were mated with 10 week old male BALB/c mice fed regular mouse chow.  Throughout mating and gestation, the F1 females were fed the FCD (2mg/kg).  Embryonic tissues from E18.5 embryos were collected (placenta and cortex), flash frozen and kept at -80oC until use for DNA methylation analyses (i.e. RRBS)

first: Lundi

last: Ly

first: Donovan

last: Chan

first: Mylene

last: Landry

first: Camille

last: Angle

first: Josee

last: Martel


title: MPC EV miRNA Microarray

first: Kevin

last: Murach

country: USA

summary: Extracellular vesicles (Evs) from proliferating myogenic progenitor cells (MPCs) were isolated and RNA was profiled via miRNA microarray

overall_design: C57BL6/J MPCs were expanded on mutliple plates in vitro, EVs were isolated using a polymer-based methods, and ~70 ng of total RNA was used for miRNA microarray analysis

first: Charlotte

last: Peterson


title: Impact of LDOC1 on gene expression profiling of a human oral keratinocyte cell line CGHNK2

city: Zhunan Miaoli County

first: Chia

middle: Huei

last: Lee

address: 35, Keyan Rd.

department: National Institute of Cancer Research

country: Taiwan

institute: Taiwan National Health Research Institute

summary: Previous studies demonstrated that LDOC1 as a tumor suppressor which epigenetically silenced by cigarette exposure, but the mechanisms through which LDOC1 suppresses tumorigenesis are not well understood. To investigate the moloecular mechanism involved in the LDOC1-mediated tumor suppressing activity, we established a LDOC1-knockdown subline derived from an untransformed human oral keratinocyte cell line CGHNK2, named CGHNK2-shLDOC1, and its corresponding control subline CGHNK2-shCtrl. These two cell lines were subjected to cDNA microarray analysis in order to identified the genes and signaling pathways regulated by LDOC1.

overall_design: Total RNA was harvested from CGHNK2-shLDOC1 and CGHNK2-shCtrl cell lines after serum starvation for 16 hours. These RNA samples were subjected to cDNA microarray analysis to explore the genes and signaling pathways regulated by LDOC1 in human oral cells.

first: Chia-Huei

first: Pin-Feng

last: Hung

first: Ji-Rui

last: Yang


title: Non-templated oligo-adenylation of small RNAs in the parasite Entamoeba

city: Stanford

first: Gretchen

middle: Marie

last: Ehrenkaufer

state: CA

address: Grant S-143, 300 Pasteur Dr.

department: Microbiology and Immunology

institute: Stanford Uninversity

summary: we found a new population of 31nt sRNAs that results from the addition of a non-templated 3-4 adenosine nucleotides at the 3´-end of the 27nt sRNA populations. We sequenced various sRNA libraries including both total RNAs and IP-ed RNAs of EhAgo proteins.

sample_organism:
Entamoeba histolytica
Entamoeba invadens

overall_design: sRNA library from size-selected (30-45nt)  total RNA of E. histolytica trophozoites; from size-selected (30-45nt)  total RNAs of development of E. invadens; from IP-ed RNAs of EhAgo proteins and mutant.

first: Hanbang

last: Zhang

first: Neil

last: Hall

first: Upi

last: Singh


title: T-cell receptor repertoire in uterine and ovarian carcinosarcoma

city: Koto-ku

first: Osamu

last: Gotoh

state: Tokyo

address: Ariake 3-8-31

institute: Japanese Foundation For Cancer Research

summary: Carcinosarcoma of the uterus or ovary is a rare, biphasic tumor comprising epithelial and mesenchymal elements, and exhibits aggressive clinical features. Four molecular subtypes of carcinosarcoma (POLE, MSI, CNH, and CNL) were recently established and shown to be associated with multiple clinicopathological parameters including patient outcomes. Immune microenvironment analyses on CS samples was performed using immune cell profiling with T-cell receptor repertoire assay. Carcinoma and sarcoma elements from CS samples were also assessed separately.

overall_design: T-cell receptor repertoire was analyzed using total RNA from each tumor (Bulk tumors: 59 uterine and 8 ovarian; Differential analyses of carcinoma and sarcoma elements: 5 uterine), according to the manufacturer’s instructions.

first: Seiichi

last: Mori


title: N6-methyladenosine (m6A) profiling and translatome of human trophoblast

city: Wuhan

first: Hanyang

last: Hu

state: Please Select

address: School of Basic Medical Sciences, Wuhan University

country: China

institute: Wuhan University

summary: To investigate the role of METTL3-mediated m6A modification and mRNA translation, we performed m6A-sequencing and Ribosome-nascent chain (RNC)-RNA sequencing in high glucose treated control or METTL3 knockdown HTR8/SVneo cells.

overall_design: m6A-seq and Ribosome-nascent chain complex-RNA sequencing of the METTL3 knockdown and control HTR8/SVneo cells with treatment of 30 mM glucose for 24 hours

first: Lulu

last: Ji


title: Glutamine addicted myeloma cells inhibits osteoblastic differentiation of bone marrow mesenchymal stromal cells limiting asparagine availability.

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

institute: IRCCS Istituto Nazionale dei Tumori

summary: Osteolytic lesions with suppression of osteoblastic (OB) differentiation are hallmarks of multiple myeloma (MM). Most recently, Gln availability has been found to be essential to sustain bone mass formation in murine models. On the other hand, MM cells are Gln-addicted and consume huge amounts of the amino acid, leading to a partial Gln depletion in the bone marrow (BM) plasma. We hypothesize that MM-dependent Gln depletion contributes to the defective OB differentiation characteristic of MM. Conversely, GLS (both KGA and GAC isoforms) and SLC38A2, the gene for the concentrative Gln transporter SNAT2, were induced. Consistent with this conclusion, the activity of SNAT2 was absent in undifferentiated hMSCs but well detectable after 14 days of OB differentiation, when total Gln uptake was also increased. Under the same conditions, OB differentiation markers (RUNX2, COL1A1, ALPL expression and ALPL activity or staining) were significantly induced but their expression was blunted by incubation in low-Gln (0.4 mM) medium or in the presence of the SNAT2 inhibitor MeAIB. The incubation in Gln-free D-MEM suppressed the induction of GLS and SLC38A2 along with OB differentiation, which was restored by the supplementation of Non-Essential Amino Acids (NEAA). Among NEAA, only asparagine (Asn) was able to rescue OB differentiation in the absence of Gln. The determination of intracellular amino acids with MS indicated that OB differentiation was associated with the increase of cell Asn, without significant changes of Gln, glutamate (Glu) or aspartate (Asp). Asparagine Synthetase (ASNS), the Gln-dependent enzyme that accounts for Asn synthesis, was also found induced during OB differentiation of hMSCs.   Gene Expression Profiles of primary BM hMSCs and OBs from bone biopsies of both healthy donors and MM patients indicated that GLS, ASNS, and SLC38A2 are more expressed in OBs, while the expression of GLUL, the gene for GS, is higher in undifferentiated hMSCs from healthy donors.   Overall, these results indicate that (1) OB differentiation of hMSCs is Gln-dependent; (2) the partial Gln depletion, imposed by Gln-addicted MM cells in the BM microenvironment, contributes to the impairment of osteoblastic differentiation of hMSCs; (3) hindrance of differentiation may depend on the limited availability of intracellular Asn derived from Gln-dependent ASNS. These results support the evidence that Gln addiction of MM cells affects bone microenvironment leading to the inhibition of OB differentiation and, consequently, to the development of MM bone disease.

overall_design: Osteogenic differentiation was inducted for two weeks in hTERT-MSCs in presence or absence of 2 mM Gln, and in absence of Gln with 380 µM Asparagine (Asn). Total RNA was extracted from three independent experiments and analyzed on GeneChip ClariomD array. hTERT-MSCs in presence of 2mM Gln were compared to hTERT-MSCs in absence of 2 mM Gln and with hTERT-MSCs in absence of Gln with 380 µM Asn to find specific differentially expressed genes in each experimental condition.

first: Martina

last: Chiu

first: Denise

last: Toscani

first: Valentina

last: Marchica

first: Giuseppe

last: Taurino

first: Federica

last: Costa

first: Massimiliano

last: Bianchi

first: Roberta

last: Andreoli

first: Laura

last: Notarfranchi

first: Benedetta

last: Della Palma

first: Paola

last: Storti

first: Michael

last: Kilberg

first: Jixiu

last: Shan

first: Giovanna

last: D'Amico

first: Erica

last: Dander

first: Giancarlo

last: Pruneri

first: Antonino

last: Neri

first: Ovidio

last: Bussolati

first: Nicola

last: Giuliani