summary: The first trimester is a critical window of maternal-fetal communication for pregnancy. Using single cell RNA-sequencing to dissect placenta heterogeneity, we identified five major cell types (trophoblasts, stromal cells, hofbauer cells, antigen presenting cells and endothelial cells). We identified seven unique trophoblast subclusters, including new subtypes that transition into the terminal cell types, extra-villous trophoblasts and syncytiotrophoblasts. As fetal sex impacts pregnancy, we analyzed sex differences in each cell type and identified differences in immune cell function. TGFβ1, β-estradiol, and dihydrotestosterone emerge as upstream regulators of sexually dimorphic genes in a cell type specific manner. Thus, the fetal contribution at the maternal-fetal interface is cell and sex specific.

overall_design: Examination of transcriptomic profiles at the single cell level in the primary tissues from first trimester human placenta. In total, 6 placental tissues were utilized, of which 3 were from female conceptions and 3 were from male conceptions.

first: Tianyanxin

first: Tania

last: Gonzalez

last: Deng

first: Rosemarie

last: DiPentino

first: Ekaterina

last: Clark

first: Bora

last: Lee

first: Jie

last: Tang

first: Yizhou

first: Barry

last: Stripp

first: Changfu

last: Yao

first: Hsian-Rong

last: Tseng

first: Subbian

last: Karumanchi

first: Alexander

middle: F

last: Koeppel

first: Stephen

last: Turner

first: Charles

last: Farber

last: Rich

first: Erica

middle: T

first: John

last: Williams III


title: Kinetically controlled competition between NusA and σ70 yields functionally diverse transcription elongation complexes

status: Public on Aug 20 2020

city: Waltham

first: Jeff

last: Gelles

state: MA

address: 415 South Street

department: Biochemistry

country: USA

institute: Brandeis University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: In all organisms, the multi-subunit RNA polymerases (RNAPs) that synthesize messenger RNAs bind multiple accessory proteins to regulate transcript elongation rate, transcriptional pausing, and termination. However, the dynamics of regulatory protein association/dissociation and how different regulators influence one another’s function is unclear. We used single-molecule multi-wavelength fluorescence colocalization techniques to directly observe the dynamics of the elongation regulators NusA and σ70 with E. coli RNAP in vitro. Contrary to previous proposals, NusA was observed to repeatedly bind to and release from elongation complexes (ECs) during synthesis of a single RNA.  However, elongation complexes that retained bound σ70 did not bind NusA and the EC-bound σ70 was largely retained even in the presence of physiological (µM) concentrations of competing elongation factors NusA and/or NusG. Factor occupancy of elongation complexes was non-equilibrium, with substantial amounts of σ70ECs even in the absence of free σ70, because composition was controlled by slow σ70 dissociation from σ70ECs. The experiments show that at steady state the same gene is transcribed by two distinct types of elongation complexes that are (ECs) or are not (σ70ECs) capable of binding NusA. Consistent with the known regulatory effects of NusA, the two types are observed to have different elongation rates, pausing dynamics, and efficiency of termination at an intrinsic terminator. During cellular transcription, these non-equilibrium populations of ECs are predicted to cause selective EC loss at intergenic transcriptional attenuators, traffic jams and altered pausing. This is an example of a potentially general “two-body” mechanism in which a functionally silent protein fine-tunes gene expression by modulating a second, functionally consequential regulator.

overall_design: ChIP-seq datasets (four) in Esherichia coli.

first: M

last: Chamberlain

first: R

last: Landick

first: J


title: TRIBE editing reveals specific mRNA targets of eIF4E-BP in Drosophila and in mammals

city: Beijing

first: Hua

last: Jin

state: Choose a State or Province

address: Rm 225-1, Bldg Qiushilou, Beijing Institute of Technology,

country: China

institute: Beijing Institute of Technology

type: Expression profiling by high throughput sequencing

summary: 4E-BP (eIF4E-BP) represses translation initiation by binding to the 5’cap-binding protein eIF4E and inhibiting its activity. Although 4E-BP has been shown to be important in growth control, stress response, cancer, neuronal activity and mammalian circadian rhythms, it is not understood how it preferentially represses a subset of mRNAs. We successfully used hyperTRIBE (Targets of RNA-binding proteins identified by editing) to identify in vivo 4E-BP mRNA targets in both Drosophila and mammals under conditions known to activate 4E-BP. The protein associates with specific mRNAs, and ribosome profiling data show that mTOR inhibition changes the translational efficiency of 4E-BP TRIBE targets compared to non-targets. In both systems, these targets have specific motifs and are enriched in translation-related pathways, which correlate well with the known activity of 4E-BP and suggest that it modulates the binding specificity of eIF4E and contributes to mTOR translational specificity.

sample_organism:
Drosophila melanogaster
Homo sapiens

platform_organism:
Drosophila melanogaster
Homo sapiens

overall_design: We used hyperTRIBE (Targets of RNA-binding proteins identified by editing) to identify in vivo 4E-BP mRNA targets in both Drosophila S2 cells and human prostate cancer cell PC3 under conditions known to activate 4E-BP. We also carried out ribosome profiling after mTOR inhibition.

first: Daxiang

first: Wei

last: Song

first: Michael

last: Rosbash


title: Sexually dimorphic crosstalk at the maternal-fetal interface

city: Los Angeles

first: Margareta

middle: D

last: Pisarska

state: CA

address: 8700 Beverly Blvd

department: OB/GYN, Div REI

institute: Cedars Sinai Medical Center

summary: The first trimester is a critical window of maternal-fetal communication for pregnancy. RNA-sequencing of matched maternal decidua (4) and placenta (4) identified 91 sexually dimorphic receptor-ligand pairs across the maternal-fetal interface, 32 in females and 59 in males.

overall_design: Matched decidua (4) and placenta (4) samples from first trimester singleton healthy pregnancies included 2 female conceptions and 2 male conceptions.

first: Tianyanxin

last: Sun

first: Tania

middle: L

last: Gonzalez

last: Deng

first: Rosemarie

last: DiPentino

first: Ekaterina

last: Clark

first: Bora

last: Lee

first: Jie

first: Yizhou

last: Wang

first: Barry

middle: R

first: Hsian

first: S

middle: A

middle: S


title: Gene expression analysis of murine 4T1 breast cancer cells derived from primary tumor, lung metastasis and brain metastasis

city: Fribourg

first: Girieca

last: Lorusso

state: Fribourg

address: Route A. Gockel, 1

department: Medicine, Pathology

country: Switzerland

institute: University of Fribourg

summary:
We recently established an orthotopic breast cancer model of brain metastasis based on the injection of murine breast cancer cell lines into the mammary fat pad. This model is based on the use of 4T1 murine breast carcinoma cells. 4T1-derived tumors recapitulate the main steps of human breast cancer progression, including epithelial-to-mesenchymal transition and metastases to lung and lymph nodes.
Bioluminescence imaging revealed the appearance of secondary lesions to the lung and lymph nodes and sporadically to the brain. Brain metastases were confirmed by macroscopic and microscopic evaluation of the brains at necropsy. We then isolated brain metastatic cells, re-injected them orthotopically in syngeneic (BALB/c) mice and isolated again cell lines from brain metastatic lesions for two rounds of selection. We obtained a cell line metastasizing to the brain with 100% penetrance (named 4T1-BM2 for Brain Metastasis, 2nd generation). In parallel we derived after two rounds of in vivo growth tumor cell lines from primary tumors (4T1-T2) and from lung metastases (4T1-LM2).

overall_design: Primary, lung and brain metastasis tumors from 4T1 murine breast carcinoma cells were re-derived from nine independent mice (three mice per cell line). The cell lines were expanded and frozen as independent lines. For RNA extraction, the nine cell lines were thawed at the same time and cultured in parallel, under identical conditions. Samples were also processed at the same time by RNAeasy mini kit (Qiagen) and subsequently RNA content and quality were determined by NanoDrop spectrophotometer.

first: Curzio

last: Ruegg


title: Endothelial stromal cells enhance lung-tumor cell migration through TNFα and SDF-1α secretion

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

country: Germany

institute: University of Lübeck

summary: Recent studies have noted the tumor-stroma interaction as an integral  part of tumor growth and spread as well as novel  avenues for effective treatment.  However, the details by which tumor and stroma cells communicate remain poorly understood.  Here we show that the migration speed of the non-small-cell lung tumor  cell line H838 is significantly increased under the influence of  human pulmonary endothelial cells, HPAEC, in a transfilter co-culture system.    To elucidate the effect of cell communication on the increased tumor  cell migration, we record the H838 transcriptome response after the induction of migration  in a hetero- and homogenous co-culture conditions. Gene Set enrichment analysis indicates a migration response  of H838 in heterogenous co-culture system. Moreover, computationally transcription factor analysis relates the  specific gene expression response to the cytokine-induced up-stream receptor activity and subsequently linking these factors  to the upstream receptors via shortest paths across a directed protein-protein interaction network.  This analysis predicted TNF- and SDF-1 signaling as well as multiple receptors  upstream of Stat3 as putative mediators of the transcriptome response.  To close the signaling information path from transcription factors to the possible receptor activation, we determine secretome quantification using a cytokine array. The latter  revealed the predicted TNFa, SDF-1a signaling molecules as well as other known migration cytokines, like IL8 and IL6, as possible candidates for increased migration. Addition through the recombinant proteins or respected inhibitions reveal TNFa as well as SDF-1a as an immediate and early-late secreted factors that cause the increase in H838 migration. Interestingly, both factors were not regulated on the gene level of the H838 in heterogenous co-culture conditions, consequential HPAEC produce TNFa and SDF1a as shown by qPCR technique.    Concluding, our combined computational and experimental approach  revealed a holistic overview on the migration enhancement of lung tumor cells due to endothelial  derived factors. Increase in migration is caused by an early TNFa induced  inflammation response followed by a SDF-1a activity to sustaining the phenotype of migration.  This tumor-endothelial-communication give a new insight for tumor migration.

overall_design: The human NSCLC cell line  H838 was propagated in DMEM with 10% fetal calf serum and 50,000 U/ml Penicillin/Streptomycin. HPAEC was propagated in Endothelial cell growth medium 2 (Promocell) including 2% fetal calf serum with supplements.  H838 and HPAEC cells were applied to polycarbonate transwell culture inserts. The filters were placed to the corresponding well plates and allowed to propagate until confluence was reached. H838 cells were cultivated together with HPAEC cells (heteroenous co-culture) or together with the same h838 cell line (homogenous co-culture) serving as controls. Confluent H838 monolayers from wither the heterogenous or homogenous transfilter system were scratched multiple times to induce tumor cell migration. H838 cells were lysed  at time points 0, 0.5, 1, 2, 3, 4, 5, 10, 15 and 24 hours after scratching. The samples at 0 and 24 hours were taken in duplicates.

last: Bao

first: Dennis

last: Dauscher

first: Melanie

last: Boerries

first: Sophia

last: Depner

first: Margaretha

last: Müller


title: Genome-wide microRNAs analysis of peripheral blood mononuclear cells reveals elevated miR-142-3p expression as a potential biomarker for secondary syphilis

status: Public on Aug 19 2020

first: sheng

middle: zhu

last: yang

address: No. 1 Dongjiaomin Lane, Dong Cheng District

institute: Beijing Tongren Hospital

summary: Treponema pallidum subspecies pallidum (T. pallidum) infection induces significant immune responses, resulting in tissue damage. Gene expression plays an essential role in regulating the progression of syphilis infection. However, little is known about the regulatory role of miRNAs in the immune response to T. pallidum infection. Here, we analyze the differential expression of miRNAs in peripheral blood mononuclear cells (PBMCs) between secondary syphilis (SS) patients and healthy controls and study the correlation between miRNAs expression and clinical features with bioinformatics.

overall_design: RNA extraction and Affymetrix microarray analysis were performed on peripheral blood mononuclear cells from healthy and secondary syphilis patients. In order to reduce the interference factors caused by treatment, we selected syphilis subjects who had not been treated before the collection of specimens. To this end, we compared the differential expression of miRNAs in peripheral blood mononuclear cells of healthy and secondary syphilis patients.

first: Zhu-Sheng

last: Yang

first: Wei

last: Liu

first: Chao-Zeng

last: Si

first: Liang

last: Yuan

first: Xiu-Min

first: Zhao-Yan

last: Gan


title: Expression data from in vitro differentiated MDSC

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

summary: MDSC (myeloid-derived suppressor cells) can be differentiated in vitro using IL-6 and GM-CSF. To identify the specific role of IL-6 in this process, we used microarray to compare MDSC differentiated with IL-6 and GM-CSF to MDSC differentiated with GM-CSF alone. We have found genes and pathways that are up- or downregulated when IL-6 is present.

overall_design: Total RNA was isolated from MDSC after in vitro differentiation with IL-6 and GM-CSF or GM-CSF only and hybridized to Affymetrix microarrays. To generate biological replicates MDSC were differentiated from the bone marrow of three different mice.

first: Rebekka

last: Weber


title: TNFAIP8 promotes AML chemoresistance by activating ERK signaling pathway through interaction with Rac1

city: Jinan

first: Yihua

last: Pang

address: Wenhuaxi road

institute: Qilu hospital

summary: The tumor necrosis factor induced protein 8 (TNFAIP8), a novel anti-apoptotic molecule, has been implicated in chemoresistance of several types of neoplasms, but its role in AML remains to be elucidated. In this study, upregulated TNFAIP8 expression was found in human AML patients and cell lines. E74 like ETS transcription factor 1 (ELF1) was identified to contribute to its aberrant expression. Forced expression of TNFAIP8 protected cells from apoptosis induced by chemotherapeutic agents and increased drug resistance. Importantly, the leukemia-promoting action of TNFAIP8 was mediated by sustaining activity of the extracellular signal-regulated kinase (ERK) signaling pathway through an interaction with Rac family small GTPase 1 (Rac1). In vivo experiments showed that TNFAIP8 suppression lowered leukemia infiltration and improved survival. Taken together, our data provide a molecular basis for the role of TNFAIP8 in chemoresistance and progression of AML and highlight the unique function of TNFAIP8 as an attractive therapeutic target.

overall_design: Gene expression analysis by RNA-seq of K562/A02 cells with or without lentivirus-mediated knockdown of TNFAIP8

first: Fei

last: Lu

first: Yanan

last: Zhao

first: Yan

last: Wang

first: Xinlu

first: Ruiqing

first: Peng

last: Li

first: Min

last: Ji

first: Jingjing

last: Ye

first: Tao

last: Sun

first: Jingxin

first: Daoxin

last: Ma

first: Chunyan


title: A Long Non-Coding RNA (Lrap) Modulates Brain Gene Expression and Levels of Alcohol Consumption in Rats

city: Aurora

first: Laura

middle: Maren

last: Saba

state: CO

address: 12850 East Montview Blvd.

department: Pharmaceutical Sciences

institute: University of Colorado Anschutz Medical Campus

type: Non-coding RNA profiling by high throughput sequencing

summary: LncRNAs are important regulators of quantitative and qualitative features of the  transcriptome. We have used QTL and other statistical analyses to identify a gene coexpression module associated with the phenotype of alcohol consumption. The “hub gene” of this module, Lrap (Long non-coding RNA for alcohol preference), was an unannotated transcript resembling a lncRNA. We used partial correlation analyses to establish that Lrap is a major contributor to the integrity of the coexpression module. Using CRISPR/Cas9 technology, we disrupted an exon of Lrap in Wistar rats. The genetically modified rats were assessed for alcohol consumption and brain RNA expression levels were evaluated using RNASeq. Measures of alcohol consumption in wild type, heterozygous and knockout rats demonstrated that disruption of Lrap produced increases in alcohol consumption/alcohol preference. The disruption of Lrap also produced changes in expression of over 700 other transcripts. Furthermore, it became apparent that Lrap may have a function in alternative splicing of the affected transcripts. More than 20% of the differentially expressed isoforms exhibited evidence for novel alternative splicing between Lrap+/+ and Lrap-/- rats. The GO category of “Response to Ethanol” emerged as one of the top candidates in an enrichment  analysis of the differentially expressed transcripts. We validate the role of Lrap as a mediator of alcohol consumption by rats, and also implicate Lrap as a modifier of the expression and splicing of a large number of brain transcripts. A defined subset of these transcripts significantly impacts alcohol consumption by rats (and possibly humans).

overall_design: RNA expression levels were examined in 9 male rat whole brain samples. Rats were genetically modified using CRISPR/Cas9 to remove a 618 bp region of the genome that codes for Lrap, a novel potentially long non-coding transcript (Crl:WI-Lrapem1Geh). 3 rats were heterozygous for the knockout, 3 rats were homozygous for the knockout, and 3 were wild type controls (Wistar from Charles River).

first: Boris

last: Tabakoff

first: Paula

last: Hoffman

middle: M

first: Gregg

last: Homanics


title: BI-3406, a potent and selective SOS1::KRAS interaction inhibitor, is effective in KRAS-driven cancers through combined MEK inhibition

city: Vienna

first: Daniel

last: Gerlach

address: Dr.-Boehringer-Gasse 5-11

department: Global Computational Biology and Digital Sciences

country: Austria

institute: Boehringer Ingelheim RCV GmbH & Co KG

summary: KRAS is the most frequently mutated driver of pancreatic, colorectal, and non-small cell lung cancers. Direct KRAS blockade has proven challenging and inhibition of a key downstream effector pathway, the RAF-MEK-ERK cascade, has shown limited success due to activation of feedback networks that keep the pathway in check. We hypothesized that inhibiting SOS1, a KRAS activator and important feedback node, represents an effective approach to treat KRAS-driven cancers. We report the discovery of a highly potent, selective and orally bioavailable small-molecule SOS1 inhibitor, BI-3406, that binds to the catalytic domain of SOS1 thereby preventing the interaction with KRAS. BI-3406 reduces formation of GTP-loaded RAS and limits cellular proliferation of a broad range of KRAS-driven cancers. Importantly, BI-3406 attenuates feedback reactivation induced by MEK inhibitors and thereby enhances sensitivity of KRAS-dependent cancers to MEK inhibition. Combined SOS1 and MEK inhibition represents a novel and effective therapeutic concept to address KRAS-driven tumors.

overall_design: In-vivo biomarker experiments were conducted using MIA PaCa-2 in a cell line derived xenograft experiment. Groups included an untreated control group at T=0, Natrosol treated control groups, as well as BI-3406 compound treated groups. A daily b.i.d dosing treatment schema was used, with a delta of 6h between treatments. Tumor material was extracted at 4h, 10h, 24h post-first treatment, followed by RNA isolation. Samples were then subjected to QuantSeq 3' mRNA sequencing for RNA quantification. All groups comprised 5-6 animals, however some samples were excluded from the analysis due to low quality of input RNA and sequencing.

first: Christoph

last: Albrecht

first: Marco

middle: H

last: Hofmann

first: Onur

last: Kaya

first: Fabio

last: Savarese

first: Norbert

last: Schweifer


title: Lionheart LincRNA Alleviates Cardiac Systolic Dysfunction under Pressure Overload

city: Cincinnati

first: Yasuhide

last: Kuwabara

state: Ohio

address: 240 Albert Sabin Way, Building S

department: Molecular Cardiovascular Biology

institute: Cincinnati Children's Hospital Medical Center

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

summary: to screen upregulated lincRNAs in pressure overloaded hearts, we conducted microarray analysis

overall_design: To identify transcribed intergenic regions that yield upregulated lincRNAs during cardiac remodeling, we performed a screen using total RNA extracted from mouse hearts subjected to transverse aortic constriction (TAC) surgery. In this screen, we assessed two time points at 2 weeks and 8 weeks after TAC surgery for the hypertrophic response and the heart failure phase, respectively.

first: Koh

last: Ono


title: Zfp281 functions as a barrier in embryonic stem cells to extraembryonic endoderm stem cells differentiation [ChIP-seq]

city: New York

first: Jianlong

last: Wang

state: New York

department: Department of Medicine

institute: Columbia University Irving Medical Center

summary: Cell-fate decisions and lineage commitment in early embryonic development are governed by comprehensive gene-regulatory programs. However, the molecular details leading to initial segregation of different lineages remain unclear. In the second cell-fate decision, epiblast (EPI) and primitive endoderm (PrE) lineages are formed from the pluripotent inner cell mass (ICM) cells at blastocyst stage. Here, we demonstrated that the pluripotency transcription factor Zfp281 is a barrier in embryonic stem cells (ESCs) to PrE lineage differentiation. Zfp281 is expressed in extraembryonic endoderm cells (XENs), the ex vivo derivatives of PrE. But knockdown of Zfp281 doesn’t affect either maintenance or expression of the PrE master regulators in XENs. Using an in vitro differentiation protocol, we revealed that knockout of Zfp281 significantly increased the efficiency of ESC to XEN derivation. Using a Zfp281 rescue line for the knockout cells, we further confirmed that effects of elevated efficiency of XEN derivation is specifically due to loss of Zfp281. Mechanistically, we revealed that Zfp281 interacts with components in the polycomb repressive complex 2 (PRC2), and recruits PRC2 to promoters of PrE master regulators GATA4 and GATA6 for transcriptional and epigenetic repression. Taken together, our results demonstrated a novel role of Zfp281 in second cell-fate decision in embryonic stem cell differentiation.

overall_design: Genome binding/occupancy profiling of Zfp281 and Suz12 in mouse embryonic stem cells (ESCs) and extraembryonic endoderm stem cells (XENs) by ChIP sequencing.

first: Xin

last: Huang


title: Genome wide H3k27ac modification changes in Wild Type PC9 cells and  MED13L knocking-down PC9 cells [H3K27ac ChIP-seq]

first: Nasha

last: Zhang

state: Shandong

address: No. 440 Jiyan Road

department: Cancer Research Center

institute: Shandong Cancer Hospital and Institute

summary: Silencing of MED13L impairs Mediator-regulated chromatin H3K27ac modification in NSCLC. Here, we performed H3K27ac ChIP-seq to investigate impacts of miR-4497 or  knocking-down MED13L on chromatin H3K27ac modification in NSCLC PC9 cells.

overall_design: Four samples were examined: PC9 cells transfected with miR-4497 mimics, si13L-1, si13L-2 or negtive control RNA.

first: Ming

last: Yang


title: Epigenome analysis of low-grade neuroepithelial tumors with FGFR1 alterations

city: Stanford

first: David

middle: A.

last: Solomon

address: 300 Pasteur Dr, Lane L216

department: Pathology

institute: Stanford University School of Medicine

type: Methylation profiling by genome tiling array

summary: Genome-wide DNA methylation profiling of 30 low-grade neuroepithelial tumors with FGFR1 alterations including rosette-forming glioneuronal tumor, pilocytic astrocytoma, dysembryoplastic neuroepithelial tumor, and extraventricular neurocytoma. The Illumina Infinium EPIC 850k Human DNA Methylation Beadchip was used to obtain DNA methylation profiles across approximately 850,000 CpG sites of genomic DNA extracted from formalin-fixed, paraffin-embedded tumor tissue of 30 low-grade neuroepithelial tumors with FGFR1 alterations including kinase domain tandem duplication, in-frame fusion with TACC1, and hotspot missense mutation within the intracellular tyrosine kinase domain.

overall_design: Bisulfite converted genomic DNA extracted from the 30 tumor samples was hybridized to Illumina Infinium EPIC 850k Human DNA Methylation Beadchip


title: Optimized adapter:DNA ratios for efficient ChIP-seq library preparation from low input samples

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

summary: The goal of this study was to titrate the amount of adapters for picogram amounts of ChIP DNA to determine the optimal conditions for library generation.  H3K4me3 ChIP DNA from human Raji cells was diluted to the indicated amount and sequencing libraries generated using a range of adapter concentrations.  The optimal adapter:DNA ratios were sequenced in technical duplicate to determine the reproducibility at each starting ChIP DNA amount.  Additionally, for two samples we altered the number of cycles during the PCR amplification to determine the effect of PCR on library complexity and read duplicates.

first: Christopher

first: Jeremy

last: Boss


title: Identification of radiation-induced miRNAs in NSCLC cells

summary: To identify radiation-induced miRNAs, we initially profiled human miRNA expression in NSCLC A549 and H1299 cells treated with X-ray radiation using miRNA microarrays. Indeed, we observed multiple dysregulated miRNAs following radiation in NSCLC cell lines.


title: Defining effects of in utero arsenic exposure on immune cells in lungs of adult mice exposed to Influenza A with single cell RNA sequencing

city: Lebanon

first: Britton

middle: C

last: Goodale

state: NH

address: 1 Medical Center Drive

department: Dartmouth Cancer Center

institute: Geisel School of Medicine at Dartmouth

summary: Our recent studies have shown that adult mice exposed to inorganic arsenic exclusively in utero (100 ppb via maternal drinking water) exhibit greater lung damage and inflammation following infection with  IAV (Influenza A virus, H1N1) than control mice not exposed in utero.  We employed an unbiased single cell RNA sequencing approach to conduct a high resolution molecular analysis of recruited immune cells and their transcriptional activities in the lungs of arsenic-exposed and control mice at day 3 after IAV infection. Transcriptional profiling of single immune cells from 6 mice (3 As, 3 Con, all exposed to IAV) revealed evidence of an enhanced inflammatory response mediated by dysregulation of innate immune functions of monocyte derived macrophages, neutrophils and alveolar macrophages.

overall_design: Dams were exposed to 100ppb sodium arsenite or control drinking water from cervical plug formation until pups were born. Arsenic was removed from drinking water and F1 offspring were allowed to mature to adulthood (7-8 weeks). Three F1 adult female mice from each treatment group were randomly selected and infected with 0.5 LD50 of influenza A/PR8/34. Whole lung homogenate was collected at day 3 of infection, and CD45+ immune cells isolated for single cell RNA sequencing (10X Genomics).

first: Kevin

last: Hsu

first: Kenneth

last: Ely

first: Thomas

last: Hampton

first: Bruce

last: Stanton

first: Richard

middle: I

last: Enelow


title: Transcriptome alteration of cultured SCC23 cells

first: Cunyu

address: 10833 Le Conte Ave

department: School of Dentistry

institute: university of California, Los Angeles

summary: To Test whether BMI1 Inhibition Induces Expression of Effector T Cell Attracting Chemokines

overall_design: We performed RNA-Seq in SCC23 treated with PTC209, DMSO, and transfected with shBMI1 or shCtrl.

first: Lingfei

last: Jia


title: RUNX transciption factor mediated control of breast cancer stem cells

city: Burlington

first: Jonathan

middle: AR

last: Gordon

state: VT

address: 89 Beaumont Ave Given E209

institute: University of Vermont

summary: Cancer stem cells (CSC) are postulated to be capable of initiating tumor formation, growth, and are resistant to therapies thereby causing tumor recurrence. We flow sorted breast cancer stem cells using CD24 (a negative marker) and CD44 (a positive marker) and performed RNAseq to determine what genes and pathways are altered in the CD24 low/ CD44 high subpopulation relative to CD24high/CD44+ subpopulation.

overall_design: three replicates (each) of FACS sorted cells (CD24low/CD44high and CD24high/CD44+)

first: Fritz

last: Andrew

first: Boyd

last: Joseph


title: Gene expression and pathway enrichment associated with psychomotor slowing in patients with depression

first: Mandakh

last: Bekhbat

address: 1365 Clifton Rd NE, Room 5204

department: Psychiatry and Behavioral Sciences

summary: Analysis of genes and pathways related to psychomotor retardation symptoms in patients with major depressive disorder. Results indicate that psychomotor slowing is associated with enrichment of inflammatory and metabolic pathways in unmedicated patients with depression.

overall_design: Whole blood samples collected at baseline on the morning of psychomotor testing.


title: Pseudohyphal differentiation in Komagataella phaffii: investigating the FLO gene family (FAIRE-seq)

first: Nadine

middle: Elpida

last: Tatto

address: Muthgasse 18

department: Department of Biotechnology

institute: University of Natural Resources and Life Sciences

summary: The protein production host Komagataella phaffii has possess the ability to differentiate into pseudohyphal form when cultivated at slow growth rates (µ=0.05 h-1) in glucose-limited chemostats. In this study, we investigated the K. phaffii FLO gene family in the context of pseudohyphae formation. Transcriptional analysis helped us identify 3 possible responsible genes, FLO11, FLO400 and FLO5-1, all of which are under control of Flo8, a transcription factor whose disruption prevents pseudohyphae formation. Knocking out FLO11 revealed that this is not the sole protein responsible for this phenotype. Strikingly, the expression of FLO400 and FLO5-1 was negatively correlated with pseudohyphae formation, and shown to be under epigenetic control by FAIRE-Seq analysis. Knock outs of these two genes completely inhibited the appearance of pseudohyphal cells and prevented the expression of FLO11. Even though the    mechanism is unclear at present, we propose that in K. phaffii Flo400 and/or Flo5-1 act as upstream signals that lead to the induction of FLO11 expression upon severe glucose limitation in chemostats at slow growth rate, and that the expression of FLO400 and FLO5-1 is controlled by epigenetic silencing, which acts independently from the general activation of FLO gene expression by the transcriptional regulator Flo8.

overall_design: To investigate possible changes in chromatin accessibility that occur at a genome-wide level of fast and slow growing K. phaffii, we carried out Formaldehyde Assisted Isolation of Regulatory Elements (FAIRE-Seq) analysis of samples collected during glucose-limited chemostat cultivation after 5 residence times at different growth rates; fast (µ=0.1 h-1), slow (µ=0.05 h-1) and finally again switching back to the fast (µ=0.1 h-1) growth rate. The cultivation was carried out for both wild-type CBS7435 as well as the CBS7435 strain with a disrupted FLO8 gene. In both cases samples were taken in biological replicates, except for the Δflo8 sample at the slow growth rate and after switching back to the fast growth rate, where due to technical problems the chemostat had to be terminated and only one sample was available for these time points. An input control sample was used which was a formaldehyde fixed sample which was decrosslinked overnight before carrying out the phenol/chloroform extraction

first: Sonakshi

last: De

first: Corinna

last: Rebnegger

first: Josef

last: Moser

middle: E

first: Diethard

last: Mattanovich

first: Brigitte

last: Gasser


title: Pseudohyphal differentiation in Komagataella phaffii: investigating the FLO gene family

overall_design: Comparison of transcript levels of FLO genes of Komagataella phaffii (wild-type strain) when cultivated in a glucose-limited chemostat at fast (µ=0.1 h-1), slow (µ=0.05 h-1) and then switched back to fast (µ=0.1 h-1) growth rates. Samples were taken after 5 residence times at each growth rate, in triplicates. A similar cultivation was carried out for the K. phaffii strain with disrupted FLO8 gene to identify the FLO genes under the control of the Flo8 transcription factor.  In this case samples were taken at the fast (µ=0.1 h-1) and the slow (µ=0.05 h-1) growth rates.


title: Cis-Regulatory Accessibility Directs Muller Glial Development and Regenerative Capacity

city: Seattle

last: Reh

state: WA

address: 1959 NE Pacific St

department: Biological Structure

institute: University of Washington

summary: Diseases and damage to the retina lead to losses in retinal neurons and eventual visual impairment. Although the mammalian retina has no inherent regenerative capabilities, fish have robust regeneration from Müller glia (MG). Recently, we have shown that driving expression of Ascl1 in adult mouse MG stimulates neurogenesis similar to fish regeneration. The regeneration observed in the mouse is limited in the variety of neurons that can be derived from MG; Ascl1-expressing MG primarily generate bipolar cells. To better understand the limits of MG-based regeneration in mouse retinas, we used ATAC- and RNA-seq to compare newborn progenitors with MG. Our analysis demonstrated striking similarities between MG and progenitors, with losses in regulatory motifs for neurogenesis genes. Young MG were found to have intermediate expression profiles and accessible DNA, which is mirrored in the ability of Ascl1 to direct bipolar neurogenesis in young MG. When comparing what makes bipolar and photoreceptor cells distinct from glial cells, we find that bipolar-specific accessible regions are more frequently linked to bHLH motifs and Ascl1 binding, indicating that Ascl1 preferentially binds to bipolar regions. Overall, our analysis indicates a loss of neurogenic gene expression and motif accessibility during glial maturation that may prevent efficient reprogramming.

overall_design: Examination of MG development from progenitors using ATAC and RNA-seq

first: VandenBosch

last: Leah S

first: Wohl

last: Stefanie G

first: Wilken

last: Matthew S

first: Kox

last: Kristen

first: Chipman

last: Laura


title: RNA-sequencing of glioma and adjacent tissue

city: chengdu

first: qian

last: bu

address: gaopeng street

institute: sichuan university

summary: RNA-sequencing for 10 samples

overall_design: examining 2 conditions, each with 5 replicates

first: Qian

last: Bu


title: Hypoxia regulates cytokine synthesis and lipid droplet-associated protein in SZ95 sebocytes.

city: Seoul

first: KeunOh

last: Choi

address: Chungmugwan 602, 209, Neungdong-ro, Gwangjin-gu, Seoul

country: South Korea

institute: Sejong University

summary: The differential gene expression in SZ95 sebocytes under hypoxia include 256 genes, among them several lipid droplet-associated proteins. We detected 93 inflammatory mediators been regulated under hypoxia.

overall_design: 4 each cells were incubated under hypoxia for 0h, 8h, 24h, 48h.

first: Keunoh

first: Youngjoo

last: Lee


title: High-resolution mapping of multiway enhancer promoter interactions regulating pathogen detection

status: Public on Aug 18 2020

city: Worcester

first: Pranitha

last: Vangala

address: 55 Lake Avenue North

institute: University of Massachussets Medical School

summary: We developed an adaptation to Split-Pool Recognition of Interactions by Tag Extension (SPRITE) called SPRITE-immunoprecipitation (SIP), which enables us to map genome-wide higher-order interactions that are coupled with the protein of interest. In this study we generated SIP data fo H3K4me3 and pan-promoter mark.  We generated SIP maps in two mammalian cell types – mouse embryonic stem cells (mES) and mouse bone marrow derived dendritic cells.

overall_design: Mapping enhancer promoter interactions in mESC and bone marrow derived dendritic cells

first: Manuel

last: Garber


title: miRNAs expression profile in goat peripheral blood mononuclear cells (PBMCs) infected with Nigeria 75/1 vaccine virus

city: Yangling

first: Xuefeng

last: Qi

state: Shaanxi

address: Taicheng Road

institute: Northwest A&F University

overall_design: Peripheral blood mononuclear cells of goat were subjected to analysis.Peripheral blood mononuclear cells were infected with Nigeria 75/1 vaccine virus for 24h.


title: Effects of lipid-specific antibodies (sulphatide, O4) on dissociated myelinating cultures

city: Glasgow

first: Chris

last: Linington

address: 120 University Avenue

department: Institute of Infection, Immunity and Inflammation

country: United Kingdom

institute: University of Glasgow

summary: Analysis of the effects of sulphatide specific antibody (O4, 20microg/ml) on myelinating cultures generated from dissociated embryonic rat spinal cord after 24 hours treatment to give insights into effects of lipid-specific antibodies and its implication in demyelinating diseases.

overall_design: Dissociated myelinating cultures were generated from neurosphere derived astrocytes (generated from striata of P1 Sprague-Dawley rats) and spinal cord cells from E15.5 Sprague-Dawley(SD) embryos. The effect of O4 (anti sulphatide, 20microg/ml) antibody in the presence or absence of 2% rabbit serum as a source of complement on these in vitro myelinating cultures was investigated by adding O4 (with or without serum), serum only or IgM isotype control to the culture media after 24 days in vitro (DIV). The effects of each factor were analysed using three independent cultures treated for 24hrs.

first: Tiia

last: Semenoff

first: Katja

last: Thuemmler

first: Christopher


title: Transcriptional Regulation by Cullin Ubiquitin Ligases

city: Houston

first: Andre

last: Catic

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

summary: We determined the genomic location of ubiquitin and CUL1 by chromatin-immuno precipitation.

overall_design: We performed ChIP-sequencing with 3F-tagged ubiquitin and CUL1 in HeLa cells.


title: Overexpression of wild type or a Q311E mutant MB21D2 promotes a pro-oncogenic phenotype in HNSCC

city: Kaohsiung

first: Daniel

middle: Esguerra

last: Gracilla

state: Taiwan

address: Institution of Biomedical Sciences, National Sun Yatsen University, Kaohsiung, TAIWAN

department: Biomedical Science

country: Taiwan

institute: National Sun Yat Sen University

summary: This study aims to determine the regulation mediated by Q311E and WT form of MB21D2 in cancer.

overall_design: Comparison on the transcriptome level regulation between Q311E and WT form of MB21D2

first: Praveen

middle: K

last: Korla

first: Wen-Shiung

last: Liou

first: Ming-Tsung

last: Lai

first: An-Jen

last: Chiang

first: Jim

middle: J

last: Sheu


title: Role of c-Myc haploinsufficiency in the maintenance of HSCs

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

department: Medicine

institute: University of Viginia

summary: Here we report a dosage effect of c-Myc on hematopoiesis and its distinct role in mediating the Wnt/b-catenin pathway in hematopoietic stem cell (HSC) and bone marrow niche cells. We showed that c-Myc haploinsufficiency led to ineffective hematopoiesis by inhibiting HSC self-renewal and quiescence, and promoting its apoptosis. We have identified Nr4a1, Nr4a2 and Jmjd3, which are critical for the maintenance of HSC functions, as previously unrecognized downstream targets of c-Myc in HSCs. c-Myc directly binds to the promoter regions of Nr4a1, Nr4a2 and Jmjd3 and regulates their expression. Our results revealed that Nr4a1 and Nr4a2 mediated the function of c-Myc in regulating HSC quiescence while all three genes contribute to the function of c-Myc in the maintenance of HSC survival. Adenomatous polyposis coli (Apc) is a negative regulator of the Wnt/b-catenin pathway. We have provided the first evidence that Apc haploinsufficiency induced a blockage of erythroid lineage differentiation through promoting expression and secretion of IL6 in bone marrow endothelial cells. We found that c-Myc haploinsufficiency failed to rescue defective function of Apc-deficient HSCs in vivo but it was sufficient to prevent the development of severe anemia in Apc heterozygous mice, and to significantly prolong survival of such mice. Furthermore, we showed that c-Myc mediated Apc loss-induced IL6 secretion in endothelial cells, and c-Myc haploinsufficiency reversed the negative effect of Apc deficient endothelial cells on erythroid cell differentiation. Our studies indicate that c-Myc has a context-dependent role in mediating the function of Apc in hematopoiesis.

overall_design: c-Mycfl/fl mice1, obtained from the Jackson Laboratory, were crossed with Mx1-Cre mice23 to generate c-Mycfl/+ (WT) and c-Mycfl/+Mx1Cre (HET) mice. c-Myc deletion was induced by injection of 6 mg/kg poly(I:C) i.p. every other day for three times. The LT-HSCs (Lin-Sca1+c-Kit+CD48-CD150+) were sorted from c-Mycfl/+ and c-Mycfl/+Mx1Cre mice (deletion was induced by PIPC) by MoFlo Astrios cell sorter (Beckman Coulter). RNA-seq was performed by UCLA Clinical Microarray Core (Los Angeles, CA).

first: Yue

last: Sheng

first: Zhijian

last: Qian


title: miR-34a is upregulated in AIP mutated pituitary adenomas and induces octreotide-resistant cell proliferation and growth hormone secretion

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

summary: Pituitary adenomas (PAs) are intracranial tumors associated with significant morbidity due to hormonal dysregulation, mass effects and heavy treatment burden. Growth hormone (GH)-secreting PAs (somatotropinomas) cause acromegaly-gigantism. Genetic forms of somatotropinomas due to germline AIP mutations (AIPmut+) have an early onset and are aggressive and resistant to treatment with somatostatin analogs (SSAs), including octreotide. The molecular underpinnings of these clinical features remain unclear.  We investigate the role of miRNA dysregulation in AIPmut+ versus AIPmut- PA samples by array analysis. miR-34a and miR-145 were found highly expressed in AIPmut+ vs AIPmut-somatotropinomas. Ectopic expression of AIPmut (p.R271W) in Aip-/- mouse embryonic fibroblasts upregulated miR-34a and miR-145, establishing a causal link between AIPmut and miRNA expression. In PA cells (GH3), miR-34a overexpression promoted proliferation, clonogenicity, migration and suppressed apoptosis, whereas miR-145 moderately affected proliferation and apoptosis. Moreover, high miR-34a expression increased intracellular cAMP, a critical mitogenic factor in PAs. Crucially, high miR-34a expression significantly blunted octreotide-mediated GH inhibition and anti-proliferative effects. miR-34a directly targets Gnai2 encoding Gαi2, a G protein subunit inhibiting cAMP production. Accordingly, Gαi2 levels were significantly lower in AIPmut+ versus AIPmut- PA.  Taken together, somatotropinomas with AIP mutations overexpress miR-34a, which in turn   downregulates Gαi2 expression, increases cAMP concentration and ultimately promotes cell growth. Upregulation of miR-34a also impairs the hormonal and antiproliferative response of PA cells to octreotide. Thus, miR-34a is a downstream target of mutant AIP that promotes a cellular phenotype mirroring the aggressive clinical features of AIPmut+ acromegaly.

overall_design: We compared human somatotropinoma and prolactinoma with wild-type AIP to tumors with mutant AIP

first: Eva-Maria

last: Bogner

first: Adrian

middle: F

last: Daly

first: Auli

last: Karhu

first: Martin

last: Irmler

first: Albert

first: Natalia

last: Pellegata


title: ZAK activation on colliding ribosomes triggers SAPK signaling pathways to regulate cell fate

city: Frederick

first: Colin

last: Wu

state: MD

department: RNA Biology Laboratory

institute: NCI

summary: Problems arising during translation of mRNAs lead to ribosome stalling and collisions with trailing ribosomes. These collisions are known to trigger a series of events including degradation of the stalled nascent polypeptide, decay of the problematic mRNAs, and ribosome rescue. However, the systemic cellular response of ribosome collision has not been explored. Here, we uncover a novel function for ribosome collisions in signal transduction. Using multiple translation elongation inhibitors and cellular stress conditions, we show that ribosome collisions activate both the SAPK (Stress Activated Protein Kinase) and GCN2-mediated cellular stress response pathways that lead to apoptosis and the integrated stress response (ISR), respectively. We further show that the MAPKKK ZAK functions as the sentinel for ribosome collisions, and ZAK is required for activation of both SAPKs p38/JNK and GCN2 signaling pathways. Selective ribosome profiling and biochemistry demonstrate that ZAK preferentially associates with the minimal unit of colliding ribosomes, the disome, inducing ZAK phosphorylation. While ZAK associates with elongating ribosomes under non-stressed conditions, activation of ZAK is specifically trigger by colliding ribosomes. Together, these results provide new insights into how perturbation of translational homeostasis, as read-out by colliding ribosomes, regulates cell fate.

overall_design:
4 samples for selective ribosome profiling experiments using ZAK OE HeLa cells.
4 samples for ribosome profiling experiments using HeLa cells.

first: Rachel

last: Green


title: Long-term epigenomic modifications underlying trait canalization to high CO2 in the biogeochemically-important marine cyanobacterium Trichodesmium

city: Los Angeles

first: Eric

middle: Alva

last: Webb

address: 3616 Trousdale Parkway

institute: University of Southern California

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Long-term epigenomic modifications underlying trait canalization to high CO2 in the biogeochemically-important marine cyanobacterium Trichodesmium [WGBS]

summary: Our paper presents the results of a study in which we used whole genome bisulfite sequencing (WGBS) and RNA-Seq (i.e. transcriptomics) to examine the long-term epigenomic dynamics of an experimenta evolution study under high CO2 in the marine cyanobacterium Trichodesmium. We identify m5C methylated sites that rapidly change in response to short-term high CO2 exposure, which are then maintained for 4.5 years even after adaptation (i.e. trait canalization). After 7 years of CO2 selection, high-CO2 triggered methylation levels return to ancestral, low-CO2 levels, consistent with genetic assimilation theory and observations in eukaryotic model systems. These data suggest a potential role for m5C methylation in prokaryotic trait canalization and identify genetic assimilation as an evolutionary mechanism of potential biogeochemical importance under global change factors.

overall_design: Experimental design can be found at Walworth, N. G., Lee, M. D., Fu, F.-X., Hutchins, D. A., & Webb, E. A. (2016). Molecular and physiological evidence of genetic assimilation to high CO2 in the marine nitrogen fixer Trichodesmium. Proceedings of the National Academy of Sciences of the United States of America, 201605202–8. http://doi.org/10.1073/pnas.1605202113. For whole-genome bisulfite samples (WGBS), we sampled the founding ancestral population (T0). We then sampled WGBS biological replicates 4.5 years later (another time point near the time of Walworth et al. PNAS 2016) from the 380-selected cell lines (adapted to low-CO2), the 380s-to-750 cell lines (380-selected cell lines transferred to 750 µatm CO2 to 2 weeks), the 750-selected cell lines (adapted to high CO2), and the 750s-to-380 cell lines (750-selected cell lines transferred to 380 µatm CO2 for 2 weeks). The WGBS metadata is below. We also sequenced two biological replicate samples for RNA-Seq for all treatments at this time point (n=4 treatments) whose metadata is described in the other spreadsheet associated with this accession number. Then, we sampled for WGBS again 2.5 years later for both the 380-selected cell lines (adapted to low-CO2) and 750-selected cell lines (adapted to high CO2).

first: Nathan

middle: G

last: Walworth


title: Comparative Transcriptomics of heads and tails between Steinernema carpocapsae and Caenorhabditis elegans

city: Irvine

first: Ali

last: Mortazavi

address: 2300 Biological Sciences 3

department: Developmental and cell biology

institute: University of California, Irvine

summary: we used short-reads to perform a comparative analysis S. carpocapsae ALL strain IJs and young adults and C.elegans dauer strain N2 and young adult strain him-8.

sample_organism:
Caenorhabditis elegans
Steinernema carpocapsae

overall_design: we used short-reads from the illumina sequencing of cDNA of males and females/hermaphrodites and IJ/dauers to perform a comparative transcriptomic analysis between S. carpocapsae and C. elegans.

first: Isaryhia

last: Rodriguez

first: Lorrayne

middle: S

last: Clague

first: Cassandra

last: McGill

first: Bryan


title: Comparative de novo mRNA transcriptome analysis of Oryza sativa cv. IR-64 under control and fluoride stress

city: Kolkata

first: Aditya

last: Banerjee

state: West Bengal

address: 30, Mother Teresa Sarani

department: Biotechnology

country: India

institute: St. Xavier's College

summary:
Purpose: The goal of this study was to identify the differentially expressed genes (DEGs) in the fluoride susceptible indica rice cultivar IR-64 in response to prolonged fluoride stress. The genes exhibiting high significance of relative expression were further analyzed by RT-PCR.
Results: De novo transcriptome assembly by Trinity v2.8.3 led to the identification of 158411 transcripts. The Percent GC was 49.67, contig N50 was 1327, Median contig length was 422, average contig was 768.66 and total assembled bases were 121764099. After refinement and open reading frame detection with TransDecoder 70578 transcripts were retained. Among them, 68009 transcripts had at least one hit from Uniref100, Uniprot or Pfam. Differential expression analysis identified 1303 genes to be overexpressed and 93 genes to be down regulated in response to fluoride stress. After filtering, the transcripts with absolute log2 fold change 2 or more and p-value < 0.05 were considered as significantly differentially expressed. A total of 1396 transcripts with differential expression (majority overexpressed and some down regulated) were considered for further analysis. Next, PCR analysis with gene-specific primers was performed with some of the significant DEGs associated with transport, cytoskeletal organization and signaling to identify the genes/transcripts that are involved in stress

overall_design: Comparative mRNA transcriptome profile of total seedlings of Oryza sativa cv. IR-64 under control conditions and under 25 day long fluoride stress.

first: Aryadeep

last: Roychoudhury


title: BrphyB is critical for rapid recovery to darkness in mature Brassica rapa leaves

first: Jennifer

last: Nemhauser

address: department of biology, university of washington, box 351800

department: Biology

summary: Here, we examine the transcriptomic response of adult wild-type and BrphyB leaves to darkening and recovery in light. Three days of dark was sufficient to elicit a response in wild type leaves suggesting a shift from carbon fixation and nutrient acquisition to active redistribution of cellular resources. Upon a return to light, wild-type leaves appeared to transcriptionally return to a pre-darkness state restoring a focus on nutrient acquisition. BrphyB mutant plants have a similar response with key differences in genes involved in photosynthesis and light response which deviate from the wild type transcriptional dynamics. Genes targeted to the chloroplast are especially affected. Adult plants had fewer, larger chloroplasts suggesting a link between phytochromes, chloroplast development, photosynthetic deficiencies and resource allocation.

overall_design: Two developmentally matched leaves from each wild-type and BrphyB-3 plant were tagged that corresponded to the first and second true leaves. Samples were collected at 5 ZT using a standard whole punch (28 mm2 of leaf tissue) with symmetrical harvest for chlorophyll assay, chloroplast measurements and transcriptome analysis. Tissue from 3 plants was combined to make one biological replicate. At 3 weeks of age the “Pre” sample was collected from the first leaf while the second one was covered with tinfoil. 24 hours later the “24hr” sample were harvested from the uncovered leaf, the same leaf that provided the “Pre” sample. Then, 48 hours later the tinfoil was removed from the covered leaf and the “dark” samples were similarly collected. Finally, 24 hours later the “recovery” samples were collected from this same leaf. RNA-seq data from 4 biological replicates of wild-type (WT_3 to WT_6), and 3 of BrphyB-3 (phyB_3 to phyB_5) plants were used in this study.

first: Andrej

middle: A

last: Arsovski

first: Nathalie

last: Nesi

first: Joseph

last: Zemke

first: Morgan

last: Hamm

first: Lauren

last: Houston

first: Andrés

last: Romanowski

first: Karen

last: Halliday

middle: L


title: Channelopathy pathogenesis in a human neural cell model of Angelman Syndrome

city: Singapore

first: Giuseppe

middle: Alessandro

last: D'Agostino

state: Singapore

address: 11 Mandalay Road

country: Singapore

institute: Lee Kong Chian School of Medicine - NTU

summary: Angelman syndrome (AS) is a neurogenetic developmental disorder that results from the loss of E3 ubiquitin ligase UBE3A due to mutations in or deletions of the maternally inherited UBE3A allele. While mouse models of AS have implicated abnormal synaptic signaling and plasticity underlying behavioral dysfunction, how the loss of UBE3A contributes to hyperactivity of neuronal networks seen in AS patients remains unclear.  Here, by utilizing human induced neurons and 3D cortical organoids derived from AS patient iPSCs and CRISPR-Cas9 mediated UBE3A KO hESCs, we uncovered a novel role of UBE3A in suppressing neuronal hyperexcitability via ubiquitin-mediated degradation of BK channels. More importantly, augmented BK channel activity in neurons manifested as increased intrinsic excitability of neurons and network level bursting and synchronization, which can be pharmacologically normalized by BK antagonists. Our study has illustrated the utility of modeling neurological diseases with human neural cells, and our results have provided new insights into underlying pathophysiological mechanisms and potential therapeutic strategy in Angelman syndrome.

overall_design: 3 control vs 3 KO NGN2-induced neurons from H1 and H9 human embryonic stem cell lines

first: Alfred

middle: X

last: Sun

first: Qiang

last: Yuan

first: Masahiro

last: Fukuda

first: Weonjin

last: Yu

first: Danlei

last: Wang

first: Hoang-Dai

last: Tran

first: Hidayat

last: Lokman

first: Stephanie

middle: W

last: Lim

first: Stuart

last: Cook

first: Owen

last: Rackham

first: Eng

last: Tan

first: Huck

last: Ng

first: Chwee

middle: T

first: Kah

first: Yong-Hui

last: Jiang

first: H

last: Je


title: Novel roles for GZMA and RASGRP1 in suppressing dissemination of both Theileria annulata-transformed macrophages and human B-lymphoma cells

city: Thuwal

first: AMIT

middle: KUMAR

last: SUBUDHI

state: Thuwal

address: Level4, Builiding, 2, KAUST

department: BESE

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

summary: Theileria annulata is a tick-transmitted apicomplexan parasite that infects and transforms bovine leukocytes into disseminating tumors that cause a disease called tropical theileriosis. Using comparative transcriptomics we identified genes transcriptionally perturbed during Theileria-induced transformation and highlighted a small set of genes associated with leukocyte dissemination. CRISPR/Cas9-mediated knock-down of GZMA and RASGRP1 in macrophages attenuated for dissemination led to a regain in their dissemination in Rag2/gC mice confirming their suppressor roles in vivo. Comparing the transcriptomes of 934 human cancer cell lines to that of Theileria-transformed bovine B cells again highlighted GZMA and RASGRP1 and CRISPR-mediated overexpression of GZMA and RASGRP1 dampened the dissemination potential of human B-lymphomas. The ensemble provide evidence for a novel suppressor function in the dissemination of both T. annulata-transformed bovine leukocytes and human B-lymphomas.

overall_design: Bovine BL3, TBL3, BL20, TBL20  B lymphocytes, and Ode macrophages were cultured in RPMI 1640 medium supplemented with 2 mM of L-glutamine (Lonza, catalogue number 12-702F) and 10 mM Hepes (Lonza, catalogue number 17-737E), 10 % heat-inactivated FBS (Gibco, catalogue number 10082147), 100 units/ml of Penicillin and 100 μg/ml of streptomycin (Lonza, catalogue number 17-602E) and 10mM beta-mercaptoethanol (Sigma-Aldrich, catalogue number M6250) for BL3/TBL3 and BL20/TBL20. The virulent (Vir) hyper-disseminating Ode cell line was used at low passage (53-71), while its attenuated (Att) poorly disseminating vaccine counterpart corresponded to passages 309-317. The OCI-LY19 cell line (DSMZ, ACC 528) was cultured in Minimum Essential Medium Eagle - Alpha Modification (Gibco, catalog number 12000063) supplemented with 2.2g/L of sodium bicarbonate (Thermofisher Scientific, catalog number 25080094), 20% FBS, 10 mM Hepes and 100 units/ml of Penicillin and 100 μg/ml of streptomycin. The RI-1 cell line (DSMZ, ACC 585) was cultured in RPMI1640 and supplemented with 10% FBS, 100 units/ml of Penicillin and 100 μg/ml of streptomycin and 10 mM Hepes. All cell lines were incubated at 37°C with 5% CO2 and were regularly tested for mycoplasma contamination.  Cells were seeded in 3 biological replicates at a density of 2.5x105 cell/ml. RNA extraction was performed using the PureLink RNA Mini Kit (Life technologies, catalogue number 12183018A) following the manufacturer’s instructions. Strand-specific RNA-sequencing (ssRNA-seq) libraries were prepared using the Illumina Truseq Stranded mRNA Sample Preparation Kit (Illumina, catalogue number RS-122-2101) following the manufacturer’s instructions. Transcriptome data was analyzed further.

first: Zineb

last: Rchiad

first: Malak

last: Haidar

first: Hifzur

middle: R

last: Ansari

first: Shahin

last: Tajeri

first: Sara

last: Mfarrej

first: Fathia

middle: B

last: Rached

first: Abhinav

last: Kaushik

first: Gordon

last: Langsley

first: Arnab

last: Pain


title: Enhancer-dependence of gene expression increases with developmental age

city: Boston

first: Jialiang

last: Huang

state: MA

address: 450 Brookline Avenue

institute: Dana-Farber Cancer Institute

summary: How overall principles of gene regulation (the "logic") may change during ontogeny is largely unexplored. We compared transcriptomic, epigenomic and topological profiles in embryonic (EryP) and adult (EryD) erythroblasts. Despite reduced chromatin accessibility compared to EryP, distal chromatin of EryD is enriched in H3K27ac, Gata1 and Myb occupancy. In contrast to EryP-specific genes, which exhibit promoter-centric regulation through Gata1, EryD-specific genes employ distal enhancers for long-range regulation through enhancer-promoter looping, confirmed by Gata1 HiChIP. Genome editing demonstrated distal enhancers are required for gene expression in EryD but not in EryP. Applying a metric for enhancer-dependence of transcription, we observed a progressive reliance on enhancer control with increasing age of ontogeny among diverse primary cells and tissues of mouse and human origin. Our findings highlight fundamental and conserved differences in regulatory logic at distinct developmental stages, characterized by simpler promoter-centric regulation in embryonic cells and combinatorial enhancer-driven control in adult cells.

overall_design: In order to profile chromatin structure and organization during the ontogeny of primitive and definitive erythroblasts, we used two cell surface-markers CD71 and Ter119, which were used in previous studies to define and distinguish erythroblasts, to FACS isolate CD71+/Ter119+ primitive (EryP) and definitive erythroblasts (EryD) from E10.5 embryonic peripheral blood and E13.5 fetal liver, respectively. FACS sorted cells were subsequently used for profiling of chromatin accessibility, histone modifications, master TFs occupancy and chromatin interactions profiles. The genome-wide transcriptome profilings were determined by RNA-seq, and were used throughout the whole study as reference to evaluate the association between chromatin features and transcription.

first: Wenqing

last: Cai

first: Qian

last: Zhu


title: Subpopulations second heart field ATAC-seq

city: MARSEILLE

first: Sonia

last: Stefanovic

address: 27 BD JEAN MOULIN

country: France

institute: INSERM U1251

summary: Profiling of open chromatin on second heart field subpopulations FACS sorted

overall_design: Microdissection of the second heart field region in E9.5 embryos, digestion and cell sorting

first: Jean-Pierre

last: Devignes

first: Stéphane

last: Zaffran


title: Metabolic adaptations underlie epigenetic vulnerabilities in chemoresistant breast cancer

city: Montreal

first: Genevieve

last: Deblois

state: Quebec

address: 2950, chemin de Polytechnique

country: Canada

institute: Université de Montréal


title: Metabolic adaptations underlie epigenetic vulnerabilities in chemoresistant breast cancer. [RNA-Seq1]

city: Toronto

first: Alexander

middle: James

last: Murison

state: Ontario

address: 101 College Street, TMDT room 11-706

institute: University Health Network

summary:
Purpose:Assess the difference in gene expression of taxol-resistant TNBC cells relative to parental cells (MDA-MB-436 and HS 578T) upon treatment with UNC1999 3uM
Conclusions: Our study identified genes significantly enriched or repressed in taxol-resistant cells relative to parental cells in both TNBC models (MDA_MB-436 and HS 578T)

overall_design: Methods: RNA-seq was performed on paclitaxel-treated MDA-MB-436 cells that are resistant to Paclitaxel (R20A, R20B, R20C) and in control-treated (DMSO) parental MDA-MB-436 cells that are sensitive to Paclitaxel (DMSO)

first: Mathieu

last: Lupien


title: Metabolic adaptations underlie epigenetic vulnerabilities in chemoresistant breast cancer. [RNA-Seq2]

summary:
Purpose:Assess the difference in gene expression of taxol-resistant TNBC cells relative to parental cells (MDA-MB-436 and HS 578t)
Methods: RNA-seq was performed on paclitaxel-treated MDA-MB-436 cells that are resistant to Paclitaxel (R20A, R20B, R20C) and in control-treated (DMSO) parental MDA-MB-436 cells that are sensitive to Paclitaxel (DMSO)
Results: We mapped about 20 million sequence reads per sample to the human genome (hg19) and identified identified differentially expressed genes
Conclusions: Our study identified genes significantly enriched or repressed in taxol-resistant cells relative to parental cells in both TNBC models (MDA_MB-436 and HS 578T)


title: Metabolic adaptations underlie epigenetic vulnerabilities in chemoresistant breast cancer [Methylation profiling]

first: Paul

last: Guilhamon

state: ON

address: 686 Bay Street

institute: SickKids

summary: Purpose: Assess the difference in DNA methylation of taxol-resistant TNBC cells relative to parental cells (MDA-MB-436)

overall_design: Bisulphite converted DNA from each sample was hybridised to the Illumina Infinium 850k Human Methylation BeadChip.


title: Differentially expressed miRNAs identified in various influenza virus infection

status: Public on Aug 17 2020

city: Nanjing

first: Yanna

last: Guo

address: No.6 Tongwei Road

department: Institute of Immunology

institute: Nanjing Agriculture university

summary: To further identified miRNAs  of BALB/c mouse lungs infected with A/Anhui/1/2013 (H7N9) (hereafter referred to as H7N9/AH1-PB2-627K(WT)) and mutant variants with PB2 amino acid substitutions (avian-like H7N9/AH1-PB2-627E and mammalian-adapted H7N9/AH1-PB2-627E/701N) , miRNA microarray was carried out.

overall_design: Balb/c mice were inoculated with 5x105 EID50 influenza A virus, and lungs were collected on day 3 and 5 post-infection. Then total RNA was extracted  and RNA integrity were then assessed for miRNA microarray  experiment.

first: Jihui

last: Ping


title: Metabolic adaptations underlie epigenetic vulnerabilities in chemoresistant breast cancer. [ChIP-Seq]

summary:
Purpose:Assess the reprogramming of H3K4me1, H3K4me3, H3K27ac and H3K27me3 in paclitaxel-resistant triple-negative breast cancer cells relative to paclitaxel-sensitive cells
Methods: ChIP-seq was performed on paclitaxel-treated MDA-MB-436 cells that are resistant to Paclitaxel (R20A, R20B, R20C) and in control-treated (DMSO) parental MDA-MB-436 cells that are sensitive to Paclitaxel (DMSO)
Results: Using we mapped about 20 million sequence reads per sample to the human genome (hg19) and identified significant peaks in each cell lines using MACS.2.0 tool.
Conclusions: Our study identified major reprogramming of H3K27me3 in the taxol-resistant TNBC cells relative to parental (TNBC cells), with loss of discrete H3K27me3 peaks in the resistant cells concomittent to acquisition of clusters of H3K27me3.


title: Mitochondrial fatty acid synthesis coordinates mitochondrial oxidative metabolism

city: Salt Lake City

first: Jeff

last: Morgan

state: UT

address: 15 N Medical Drive East

department: Biochemistry

institute: University of Utah

summary: Cells harbor two systems for the synthesis of fatty acids, one in the cytoplasm (FASN or fatty acid synthase) and one in the mitochondria (mtFAS). In contrast to FASN, mtFAS is poorly characterized, with the major product(s), metabolic roles, and cellular function(s) essentially unknown. Here we show that hypomorphic mtFAS mutants display a profound loss of electron transport chain (ETC) complexes and exhibit compensatory reductive carboxylation. This effect on ETC complexes is independent of the synthesis of lipoic acid, the best characterized function of mtFAS, as mutants lacking lipoic acid synthesis have an intact ETC. Finally, mtFAS impairment blocks the differentiation of skeletal myoblasts in vitro. These data suggest that ETC activity in mammals is profoundly controlled by mtFAS function, thereby connecting anabolic fatty acid synthesis with the oxidation of carbon fuels.

overall_design: 44 total samples from C2C12 immortalized mouse skeletal myoblasts (ATCC CRL-1772). Samples include GFP (control), Mcat, Oxsm, and Mecr mutant cell lines grown and harvested at days −1, 0, and 1 of a muscle differentiation time course. Three or four biological replicates of each line at each day are included.

first: Sara

middle: M

last: Nowinski

first: Jeffrey

first: Jared

last: Rutter


title: EED-mediated histone methylation is critical for CNS myelination and remyelination by inhibiting WNT, BMP and senescence pathways

city: Cincinnati

first: Richard

last: Lu

state: OH

address: 3333 Burnet Ave

department: CBDI

institute: Cincinnati Children's Hospital Medical Center

summary: PRC2 catalyzes tri-methylation of histone H3 lysine residue K27 (H3K27me3), and then H3K27me3 recruits downstream regulatory factors to create a transcriptionally repressive chromatin environment. PRC2 is involved in diverse biological processes, including cell growth, cell differentiation and the maintenance of cell identity. Here, to study the role of PRC2 on oligodendrocyte myelination and remyelination, we performed  RNA-seq and ATAC-seq analysis of isolated control and Eed cKO mouse OPCs.

overall_design: RNA-seq: 2 Control vs 2 Eed cKO; ATAC-seq: 2 Control vs 2 Eed cKO

first: Jiajia

last: Wang

first: Qing


title: Single Cell RNA Profiling Reveals Adipocyte to Macrophage Signaling Sufficient to Enhance Thermogenesis

city: Worcester

first: Michael

last: Czech

state: Massachusetts

address: 373 Plantation Street

department: Program in Molecular Medicine

institute: University of Massachusetts Medical School

summary: Adipocytes deficient in fatty acid synthase (iAdFASNKO) emit signals that mimic cold exposure to enhance the appearance of thermogenic beige adipocytes in mouse inguinal white adipose tissues (iWAT). Both cold- and iAdFASNKO-induced iWAT “browning” pathways upregulate the sympathetic nerve fiber (SNF) modulator Nrg4 and activate SNFs adjacent to beige adipocytes. Adipocyte cAMP/protein kinase A signaling is necessary for beige adipocyte appearance, as we show here it is blocked in Gsa deficient cold exposed or iAdFASNKO mice. Surprisingly however, denervation of iWAT failed to block adipocyte browning in iAdFASNKO mice, as it does in cold-exposed mice. Similarly, Nrg4 deficiency markedly reduced iWAT UCP1 in the cold, but not in double FASN/Nrg4 KO mice. Single-cell transcriptomic analysis of iWAT stromal cells revealed increased macrophages displaying gene expression signatures of the alternately activated type in iAdFASNKO mice, and their depletion abrogated iWAT beiging. Altogether, these findings reveal divergent cellular pathways are sufficient to cause adipocyte browning. Importantly, adipocyte signaling to enhance alternatively activated macrophages in iAdFASNKO mice is associated with enhanced adipose thermogenesis independent of the sympathetic neuron involvement this process requires in the cold.

overall_design: We pooled SVF cells from iWAT from 7 control (C57BL/6) and 8 iAdFASNKO mice. The cells were separate into immune and non-immune cells via magnetic cell sorting. Single cell library preparation was performed using the 10X Genomics Single Cell 3’ v3 according to the manufacturer’s instructions.

first: Felipe

last: Henriques

middle: H

last: Bedard

first: Lawrence

last: Lifshitz

middle: P


title: Gene expression signatures for lung adenocarcinoma

city: Jinan

first: Jinghui

last: Liang

address: Wenhuaxi street

institute: Shandong University

summary: We used whole genome microarray expression profiling as a discovery platform to identify genes through 7 pairs lung adenocarcinoma tissues and normal tissues

overall_design: We chose 7 pairs lung adenocarcinoma tissues and normal tissues

first: Jin

last: Jiang

first: Jingyi

last: Han


title: Total RNA sequencing of cultured splenic PKM2WT and PKM2KO NK cells

first: Jessica

last: Walls

address: Bulding 560, Rm 31-45

institute: National Cancer Institute

summary: PKM2 has recently been characterised in macrophages and T cells to play a crucial signalling role, impacting the transcription of downstream metabolic enzymes and effector molecules. We sought to test whether it plays a role in NK cells through whole RNA sequesncing of cells with or without PKM2.

overall_design: PKM2 WT and PKM2 KO NK cells were expanded for 6 days with IL-15 and then treated with IL-2/12 or IL-2/12 + vehicle or TEPP-46 (50uM) (PBS) for 18 hours. Total RNA was extracted from 3 biological replicates for each group and was subject to total RNA sequencing.

first: Daniel

last: McVicar


title: Acquisition of optimal human follicular helper CD4 T cell function is defined by specific molecular, positional and TCR dynamic signature

city: Cleveland

first: Rafick

last: Pierre-Sekaly

address: 2103 Cornell Avenue

department: Pathology

institute: Case Western Reserve University

summary: The purpose of this study was to study TFH cells and their transitionaing Status and its association with positioning in the Germinal Center. We observed significant transcriptomic signatures associated with CD57hi TFH status.

overall_design: To use sorted tonsillar CD4 subsets for analysis of transcriptome signatures and investigate whether these signatures are associated with other biological factors of these CD4 T cell subsets. Cells were collected and lysed for RNA extraction. Reverse transcription reactions were performed to obtain cDNAs which were hybridized to the Illumina Human HT-12 version 4 Expression BeadChip according to the manufacturer’s instruction, and quantified using an Illumina iScan System. The data were collected with Illumina GenomeStudio software.

first: Kartika

last: Padhan

first: Eirini

last: Moysi

first: Alessandra

last: Noto

first: Alexander

last: Chassiakos

first: Khader

last: Ghneim

first: Vasilis

last: Papaioannou

first: Giulia

last: Fabozzi

first: David

last: Ambrozak

first: Antogoni

last: Poultsidi

first: Maria

last: Ioannou

first: Craig

last: Fenwik

first: Rafick-Pierre

last: Sekaly

first: Giuseppe

last: Pantaleo

last: Koup

first: Constantinos

last: Petrovas


title: Bronchial Epithelial cells gene expression profiles in response to Mycobacterium abscessus

status: Public on Aug 16 2020

city: Miami

first: Anthony

last: Griswold

state: FL

address: 1501 NW 10th Ave, BRB 318

institute: University of Miami

summary: Bronchial Epithelial cells were exposed to microparticles generated from mycobacterium abscessus MAB cell wall per an in-house protocol. Control group was exposed to saline. Differentially expressed genes related to MAB cell wall particles were determined.

overall_design: Lung on membrane model was developed using human bronchial epithelial cells and lung small vessels  endothelial cells. Air liquid interface (ALI) challenged with MAB microparticles (5 samples). Controls challenged with saline (5 samples). Samples were collected after 48 hours. RNA extracted and RNASeq was performed.

middle: J

first: Mehdi

last: Mirsaeidi


title: Mice lung gene expression profiles in response to Mycobacterium abscessus

summary: Mice were challneged with Mycobacterium abscessus cell wall particles intra- tracheally or saline. Lung was harvested after 3 weeks. RNA extracted from lungs and RNASeq was performed to identify differentially expressed genes.

overall_design: Mice challenged with MAB cell wall microparticles up to 4 times. 3weeks later mice killed and lung harvested. Control group was challenged with saline under same procedure. Treated group is 4 animals compared to 3 controls.


title: Adverse effect of folic acid supplementation on cilia

status: Public on Aug 15 2020

city: Boulder

last: Engelhardt

state: CO

address: 347 UCB

department: MCDB

institute: CU Boulder

summary: We report that fortified levels of folic acid adversely affect cilia strucure and function. This data set agrees with previous experiements which have demonstrated that elevated folic acid levels can increase transcription variability on a genome-wide level. Furthermore, we demonstrate that among these dysregulated genes, genes contained within SYSgold cilia database are proportionally over-represented. This over-representation of cilia genes among dysregulated genes may play a key role in ciliopathys' sensitivity to elevated folic acid levels.

overall_design: Examination of mice fed two levels of folic acid (moderate[8 samples] and enriched[8samples]) that are either WT(4 samples per diet) or homozygous IFT88-null (4 samples per diet)

first: Lee

last: Niswander

first: Kenneth

last: Jones

first: Juliette

last: Petersen


title: The Polycomb-Associated Factor Phf19 Controls Hematopoietic Stem Cell Status and Differentiation

city: Barcelona

first: Enrique

last: Blanco

address: Dr. Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

country: Spain

institute: Center for Genomic Regulation (CRG)

summary: Adult hematopoietic stem cells (HSCs) are rare, multipotent cells in bone marrow that are responsible for generating all blood cell types. HSCs are a heterogeneous group of cells with high plasticity, in part conferred by epigenetic mechanisms. PHF19, a subunit of the Polycomb repressive complex 2 (PRC2), is preferentially expressed in mouse hematopoietic precursors. Here, we show that genetic deletion of Phf19 increases HSC specific status. While proliferation of HSCs is normally triggered by forced mobilization, defects in differentiation impede long-term correct blood production, eventually leading to aberrant hematopoiesis. At the molecular level, PHF19 controls deposition of the histone repressive mark H3K27me3, which accumulates in blood lineage-specific genes. Our results identify PHF19 as having a key role in regulating the epigenetic landscape of HSCs, thus permitting proper blood production.

overall_design: ChIP-seq for H3K27me3 (4 samples),  RNA-seq (4 samples), MARS-Seq (4 samples) and ATAC-seq (2 samples) of HSCs. FF means Floxed-condition (Control) and KO means PHF19 KO mice.

first: Pedro

last: Vizan

first: Arantxa

last: Gutierrez


title: CTCF orchestrated enhancer hijacking accelerated tumorigenesis through remodeling 3D chromosomal architecture in NTS locus

city: Shanghai

first: Peiwei

last: Chai

state: Shanghai

address: No.833 Zhizaoju Road

department: Opthalmology

institute: Shanghai Ninth people's hospital

summary: We identified aberrant CTCF binding lead to a 3D chromosomal interactional driver in NTS locus that accelerates tumorigenesis of uveal melanoma. Both enhancer deletion and abolishing CTCF binding lead to the loss of chromosomal looping and triggered therapeutic efficacy in inhibiting tumorigenesis. Our study shed light on a functional chromosomal architecture induced enhancer hijacking, thereby provide novel concept of 3D-chromosomal conformation exploration.

overall_design: We performed microarray in 2 types of ocular melanoma cells with or without decoyed CTCF

first: Xianqun

last: Fan


title: Transcription profiling of wild-type and epic2 mutant plants

city: Beaucouzé

first: Etienne

last: Bucher

address: 42 rue Georges Morel

institute: IRHS

summary: Chromatin and its covalent modifications play important roles during development. However, how different types of chromatin regulators individually control gene expression in different cell types has so far not been investigated in detail. To explore their role in these processes we performed forward and reverse genetic experiments using an epigenetically silenced reporter gene in Arabidopsis. We found three chromatin regulators, each involved in different epigenetic pathways, to control reporter gene expression in distinct tissues and cell-types. Here we report on the roles of the RNA polymerase Pol V, the histone deacetylase HDA6 and the SWI/SNF class chromatin remodeler SPLAYED (SYD) in silencing expression of the reporter in different cell-types. Furthermore, we demonstrate that a highly conserved domain in HDA6 is involved in its target specificity. And we present data showing that SYD controls transcription of epigenetically silenced genes. The results presented here provide evidence supporting the notion that tissue specificity of gene expression and its fine-tuning can be influenced by the activity of different chromatin regulators.

overall_design: 2 samples, 3 biological replicates each

first: Kateryna

last: Fal

first: Emilija

last: Histova


title: Essential gene profiles for human pluripotent stem cells identify uncharacterized genes and substrate dependencies

first: Jason

last: Moffat

address: 686 Bay Street, Room 13.9705

department: Molecular Genetics

institute: University of Toronto

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: The microRNA, miR-133b, functions to slow Duchenne muscular dystrophy pathogenesis

city: Blacksburg

first: Robert

last: Settlage

address: 1 Washington St

department: Advanced Research Computing

institute: Virginia Tech

summary: Duchenne muscular dystrophy (DMD) is characterized by progressive skeletal muscle degeneration. No treatments are currently available to prevent the disease. While the muscle enriched microRNA, miR-133b, has been implicated in muscle biogenesis, its role in DMD remains unknown. To assess miR-133b function in DMD-affected skeletal muscles, we genetically ablated miR-133b in the mdx mouse model of DMD. In the absence of miR-133b, the tibialis anterior muscle of juvenile and adult mdx mice is populated by small muscle fibers and exhibits increased fibrosis, characterized by thickened interstitial space. Additional analysis revealed that loss of miR-133b exacerbates DMD-pathogenesis partly by altering satellite cell numbers and through widespread transcriptomic changes. These include known miR-133b targets as well as genes involved in cell proliferation and fibrosis. Altogether, our data demonstrate that skeletal muscles utilize miR-133b to mitigate the deleterious effects of DMD.

overall_design: Number of replicates for each sample: Control, 4; miR-133b-/-, 4; mdx, 4; mdx/miR-133b-/-, 4

first: Thomas

last: Taetzsch

first: Dillon

last: Shapiro

first: Randa

last: Eldosougi

first: Tracey

last: Myers

first: Gregorio

last: Valdez


title: Identification of specific lncRNA signatures in breast cancer (BC)

status: Public on Aug 14 2020

first: Zhanghan

last: Chen

address: 180 Fenglin Road, Xuhui District

institute: Fudan University

summary: In order to develop novel biomarkers in breast cancer, we applied a competing endogenous RNA (ceRNA) microarray to identify differentially expressed lncRNAs in BC tissue.

overall_design: Six pairs of breast cancer and paracancerous tissues were used for the microarray assay to investigate the differentially expressed lncRNAs between the tumor tissues and paracancerous tissues

first: Ying

last: Jiang

first: Zehuan

last: Li


title: Exploring differentially expressed genes in the hypothalamic-pituitary-gonadal axis of estrous and anestrous primiparous sows using RNA-Seq technique

city: Zhengzhou

first: Jiaqing

last: Zhang

address: No. 116 Huayuan Road

department: Institute of Animal Husbandry and Veterinary Science

institute: Henan Academy of Agricultural Sciences

summary: To investigate the effects of HPG axis on reproductive function and the underlying mechanisms involved, six libraries, including hypothalamic, pituitary and ovarian samples (termed A, B and C) from the sows in normal estrus and the corresponding samples (termed A1, B1 and C1) from the sows in which anestrus was caused by inactive ovaries, were constructed and sequenced to analyze the differentially expressed genes (DEGs) between different HPG axises. A total of 710 (392 up and 318 down), 707 (283 up and 424 down), and 956 (635 up and 321 down) DEGs were identiﬁed in A vs. A1, B vs. B1 and C vs. C1, respectively. Gene ontology (GO) and KEGG pathway analyses showed that the DEGs were most enrichment in neuropeptide hormone activity, ovarian steroidogenesis, FoxO signaling pathway and GnRH signaling pathway etc.

overall_design: Hypothalamic, pituitary and ovarian mRNA profiles of estrous primiparous sows and anestrous primiparous sows were generated by deep sequencing using Illumina HiSeqTM 2500

first: Baosong

last: Xing


title: Next-generation sequencing facilitates quantitative analysis of control and Lhx6-/- molar transcriptomes

city: Los Angeles

first: Shuo

state: California

address: 2250 Alcazar Street, Clinical Science Annex, Room 103, CLINICAL SCIENCE ANNEX ROOM 103

institute: Center for Craniofacial Molecular Biology, University of Southern California

summary: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived molar transcriptome profiling (RNA-seq) between control and Lhx6-/- mice to identify the potential target of Lhx6.

overall_design: Methods: Molar mRNA profiles from 4.5-day-old control and Lhx6-/- mice were generated by deep sequencing, in triplicate, using Illumina NextSeq500.

first: Jinzhi

last: He

first: Yang

last: Chai


title: The orphan actin-related protein EhARPv2 belongs to the nucleolar snoRNPs molecular complexes of Entamoeba histolytica

city: Ciudad de México

first: Pedro

middle: Antonio

last: Avila

state: CDMX

address: Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco

department: Molecular Biomedicine

country: Mexico

institute: CINVESTAV

summary:
In eukaryotes, ribosomal RNA biogenesis consists of ribosomal DNA transcription to pre-rRNA, which must be modified and processed in the nucleus resulting in the 18S, 5.8S, and 28S ribosomal units. Molecular components involved in this process comprise the catalytic ribonucleoproteins complexes (snoRNPs) formed by non-coding RNAs classified as box C/D and box H/ACA snoRNA that associates to at least four proteins highly conserved through evolution and combined to multiple transient proteins.
Taking advantage of computational and multidisciplinary experimental approaches, we determine that the orphan EhARPv2, a member of the Actin-related family from Entamoeba histolytica, interacts with nucleolar proteins. EhARPv2 and its partners here identified colocalize in the nuclear periphery, considered the nucleolus, and interact with both box C/D and H/ACA snoRNAs.
Moreover, we find the reassortment of some components of snoRNPs from C/D- or H/ACA complexes mixed in vitro and in entire cells indicating that in E. histolytica snoRNP of C/D or H/ACA machineries alternate using common elements and that EhARPv2 is a part of this peculiar snoRNP. Our findings substantiate a role for EhARPv2 in the biogenesis of ribosomal RNA.

overall_design: CLIP-seq assay with α-EhARPv2, α-EhNop58, α-EhABP-12035 and α-EhFibrillarin in Entamoeba histolytica HM1: IMSS.

first: Miguel

last: Vargas

first: Eva

last: Luna-Rivera

first: Ma

last: de Jesús Almaraz-Barrera

first: Araceli

last: Hernández-Flores

first: Arturo

last: González-Robles

first: Ana

last: Gutiérrez-Escolano

last: Ávila-López

first: Jesús

last: Valdés-Flores

first: Christian

last: Weber

first: Rosaura

last: Hernández-Rivas

first: Nancy

last: Guillén


title: Multivalent proteins rapidly and reversibly phase-separate upon osmotic cell volume change [RNA-seq]

city: Ann Arbor

first: Pushpinder

middle: Singh

last: Bawa

state: Michigan

address: 1500 East Medical Center Drive

institute: University of Michigan

summary: Processing bodies (PBs) and stress granules (SGs) are prominent examples of subcellular,  membrane-less compartments that are observed under physiological and  stress conditions, respectively. We observe that the trimeric PB protein DCP1A rapidly  (within ~10 s) phase-separates in mammalian cells during hyperosmotic stress and  dissolves upon isosmotic rescue (over ~100 s) with minimal impact on cell viability  even after multiple cycles of osmotic perturbation. Strikingly, this rapid intracellular  hyperosmotic phase separation (HOPS) correlates with the degree of cell volume  compression, distinct from SG assembly, and is exhibited broadly by homo-multimeric  (valency ≥ 2) proteins across several cell types. Notably, HOPS sequesters pre-mRNA  cleavage factor components from actively transcribing genomic loci, providing a  mechanism for hyperosmolarity-induced global impairment of transcription termination.  Together, our data suggest that the multimeric proteome rapidly responds to changes  in hydration and molecular crowding, revealing an unexpected mode of globally  programmed phase separation and sequestration that adapts the cell to volume  change.

overall_design: RNAseq of U2OS cells stably overexpressing GFP-DCP1a were perfromed under isotonic (150 mM Na+) conditions, hypertonic (300 mM Na+) conditions or rescued with isotonic media after hypertonic treatment to assess transcriptional changes. Treatment, 4 h; Rescue, 4h.

first: Ameya

last: Jalihal

first: Sethuramasundaram

last: Pitchiaya

first: Lanbo

last: Xiao

first: Xia

last: Jiang

first: Karan

last: Bedi

first: Abhijit

last: Parolia

first: Marcin

last: Cieslik

first: Mats

last: Ljungman

first: Arul

last: Chinnaiyan

first: Nils

middle: G

last: Walter


title: Multivalent proteins rapidly and reversibly phase-separate upon osmotic cell volume change [ChIP-seq]

overall_design: ChIPseq of U2OS cells stably overexpressing GFP-DCP1a were perfromed under isotonic (150 mM Na+) conditions or hypertonic (300 mM Na+) conditions to assess chromatin occupancy of factors involved in RNA metabolism. Treatment, 30 min.


title: Multivalent proteins rapidly and reversibly phase-separate upon osmotic cell volume change


title: Novel, Selective Inhibitors of USP7 Uncover Multiple Mechanisms of Antitumor Activity in Vitro and in Vivo

city: South San Francisco

first: Gene

last: Cutler

state: CA

address: 561 Eccles Ave

institute: RAPT Therapeutics

summary:
The human lung tumor cell line, NCI-H526, was treated with DMSO vehicle control or 0.5 µM of the novel small molecule USP7 inhibitor, USP7-797.  At 24 and 48 hour time points, cells were harvested and used for RNA-Seq analysis.  In order to identify pathways impacted by USP7 (Ubiquitin Specific Peptidase 7) inhibition, we used RNASeq to profile transcriptomic changes in human lung cancer NCI-H526 cells following treatment with the novel, selective USP7 inhibitor, USP7-797, or control DMSO for 24 or 48 hours.  USP7 inhibitor treatment resulted in upregulation of a large number of genes normally silenced by the polycomb repressive complex 2 (PRC2).  PRC2, whose components include the proteins EZH2, SUZ12 and EED, trimethylates histone H3 at lysine 27 (H3K27me3).  Gene set enrichment analysis showed that the top 10 significantly enriched gene sets are all regulated by this pathway.
RNA was extracted from approximately 1 million cells using the Allprep DNA/RNA Mini Kit (Qiagen).  Whole transcriptome non-stranded libraries were prepared using the TruSeq RNA Library Prep Kit v2 (Illumina).  Sequencing was performed on Illumina NovaSeq using paired-end mode, 200 cycles, targeting 40 million reads per sample.

overall_design: USP7-797- or DMSO vehicle-treated H526 cell lines at 24 hours or 48 hours.

first: Yamini

last: Ohol

first: Michael

last: Sun

first: Paul

last: Leger

first: Dennis

last: Hu

first: Berenger

last: Biannic

first: Payal

last: Rana

first: Cynthia

last: Cho

first: Scott

last: Jacobson

first: Steve

last: Wong

first: Jerick

last: Sanchez

first: Niket

last: Shah

first: Deepa

last: Pookot

first: Betty

last: Abraham

first: Kyle

last: Young

first: Silpa

last: Suthram

first: Lisa

last: Marshall

first: Delia

last: Bradford

first: Nathan

last: Kozon

first: Xinping

last: Han

first: Akinori

last: Okano

first: Jack

last: Maung

first: Christophe

last: Colas

first: Jacob

last: Schwarz

first: David

last: Wustrow

first: Dirk

last: Brockstedt

middle: D

last: Kassner


title: Transcriptome analysis of desmoplastic small round cell tumors identifies actionable therapeutic targets: a report from the Children's Oncology Group

city: bethesda

last: Shern

state: MD

address: 10 Center drive

institute: NCI

summary: The oncoprotein encoded by EWS-WT1, the hallmark diagnostic alteration in DSRCT, binds to FGFR4 and IGF2.

overall_design: JN-DSRCT-1 cells were subjected to chromatin immunoprecipitation using antibodies against RNA polymerase-II (positive cotnrol), the c-terminus of WT1 (to precipitate the EWS-WT1 fusion protein), or IgG (negative control)

first: Pooja

last: Hingorani

first: Troy

middle: A

last: McEachron


title: Sacharomyces cerevisiae Transcript Isoform mapping (rrp6)

city: Heidelberg

first: Wu

last: Wei

address: EMBL Heidelberg,Meyerhofstraße 1

department: Genome Biology Unit

institute: EMBL Heidelberg

summary: Application of TIF-Seq to mutants of the molecular components involved in transcription process.

overall_design: Application of TIF-Seq (Transcript IsoForm Sequencing) to S.cerevisiae. The method was applied to simultaneously identify the 5’ capped mRNA transcription start site and the 3’polyadenylation site in delta rrp6 mutant strain grown in glucose media [rrp6, 2 biological replicates (bio) and 2 independent library preparations, technical replicates(lib)].

first: Vicent

last: Pelechano

first: Lars

last: Steinmetz


title: Whole transcriptome shotgun sequencing of type 1 IFN key proteins knock out clones

city: Rehovot

first: Gilgi

last: Friedlander

address: Hertzel st

country: Israel

institute: Weizmann Institute of Science

summary: Purpose: Describe the contribution of the receptor parts IFNAR1 and IFNAR2 as well as STAT1 and STAT2 proteins to type 1 IFN signaling pathway.

overall_design: Examination of the four knock out clones post 16h of 2nM IFNβ treatment compared to the HeLa WT cells

first: Gideon

last: Schreiber

first: Maya

last: Shemesh

first: Victoria

last: Urin


title: Neuroglobin (Ngb) Knockdown effect on glioblastoma cell line G422.

city: Wuhan

first: Liu

last: Feng

state: Hubei

address: 13 Hangkong Road, Hankou

department: School of Basic Medicine

institute: Huazhong University of Science and Technology

summary: The aim was to identify genes that were influenced by Ngb Knockdown in glioblastoma cell lines.

overall_design: Glioblastoma cell line G422 was stably transfected with Ngb or its vector control via lentivirus infection. Three independent Tumor tissues of G422/shNgb or G422/shVec were analyzed.

first: Xiaoqian

last: Chen

first: Feng

last: Liu


title: Passive Transfer of Vaccine-Elicited Antibodies Protects Against SIV in Rhesus Macaques

first: Rafick

last: Pierre-Sekaly

address: 2103 Cornell Avenue

institute: Case Western Reserve University

summary: In this study, we show that passive transfer of purified antibodies from vaccinated macaques can protect naïve animals against SIVmac251 challenges. The protective signature included multiple antibody functions and correlated with upregulation of interferon pathways in the vaccinated animals.  Adoptive transfer of purified IgG from the vaccinated animals with the most robust protective signatures provided partial protection against SIVmac251 challenges in naïve recipient rhesus macaques.  These data demonstrate the protective efficacy of purified vaccine-elicited antiviral antibodies, even in the absence of virus neutralization.

overall_design: We vaccinated 30 rhesus macaques with Ad26-SIV Env/Gag/Pol and SIV Env gp140 protein vaccines and assessed the induction of antibody responses that conformed to a putative protective signature. Animals were primed with 3x1010 viral particles (vp) Ad26-SIVsmE543 Env/Gag/Pol vectors at weeks 0 and 12 and boosted the animals with 3x1010 vp Ad26 vectors combined with 0.25 mg purified SIVmac32H Env gp140 protein with alum adjuvant at weeks 24 and 50. We ranked antibody profiles in all the vaccinated animals based on the protective signature. To define the pathways responsible for the induction of this protective signature, we utilized transcriptomic profiling by RNA-Seq to assess the association between innate immune responses at baseline and following the first protein boost and the subsequent development of the protective signature

first: Ghneim

last: Khader

last: Sekaly

first: Barouch

last: Dan

first: Alter

last: Galit


title: Functional genomics of Non-NF2 meningioma development and progression [RNA-seq]

city: Leuven

first: Peihua

last: Zhao

address: Herestraat 49

country: Belgium

institute: KU Leuven

summary: Meningiomas are the most common primary brain tumors, where complete surgical resection is often challenging giving rise to recurrence. Mutations of the E3 ubiquitin ligase TRAF7 are found in one-fourth of meningioma patients and typically co-occur with mutations in either KLF4, AKT1, or PI3KCA. By creating an in vitro meningioma model derived from primary meningeal cells, we elucidated the cooperative interactions that conspire meningioma development. A multi-omics framework on meningeal cells revealed TRAF7-mediated rewiring of the proteome with the majority of protein expression being post‐transcriptionally‐regulated. Integrating TRAF7-driven ubiquitinome and proteome alterations and TRAF7 interactome highlight the role of TRAF7 in posttranslational regulation of the cytoskeleton organization. TRAF7 controls actin dynamics by acting as a proteostatic regulator of the RAS-related small GTPases. TRAF7 loss-of-function diminishes ubiquitination of RAS and CDC42, leading to the activation of the PAK and MAPK signaling pathways. Up-regulation of CDC42 signaling promotes anchorage-independent growth of meningeal cells. On the other hand, the RAS/MAPK pathway triggers the tumor suppressive activity of KLF4 that inhibits meningeal cell growth due to the activation of the Semaphorin pathway. Simultaneous loss of KLF4 and TRAF7 function enhances tumorigenic transformation of meningeal cells, functionally confirming their roles in meningioma development.

overall_design:
RNA sequencing was performed to identify differentially regulated genes upon expression of different constructs in normal human meningeal cells (HMCs) and mengioma HBL-52 cells
Cells were infected with viral vectors expressing genes of interest and kept in culture

first: Anna

last: Sablina

first: Paul

last: Najm