title: Bacterial Fitness Landscapes Stratify Based on Proteome Allocation Associated with Discrete Aero-types

city: La Jolla

first: Ke

state: California

address: Bioengineering Department, 9500 Gilman Dr.

department: Bioengineering

institute: UCSD

summary: The fitness landscape is a concept commonly used to describe evolution towards optimal phenotypes. It can be reduced to mechanistic detail using genome-scale models (GEMs) from systems biology. We use recently developed GEMs of Metabolism and protein Expression (ME-models) to study the distribution of Escherichia coli phenotypes on the rate-yield plane. We found that the measured phenotypes distribute non-uniformly to form a highly stratified fitness landscape. Systems analysis of ME-model simulations suggest that this stratification results from discrete ATP generation strategies. Accordingly, we define "aero-types", a phenotypic trait that characterizes how a balanced proteome can achieve a given growth rate by modulating 1) the relative utilization of oxidative phosphorylation, glycolysis, and fermentation pathways; and 2) the differential employment of electron-transport-chain enzymes. This global, quantitative, and mechanistic systems biology interpretation of fitness landscape formed upon proteome allocation offers a fundamental understanding of bacterial physiology and evolution dynamics.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: Expression profiling data for eight ETC-gene-knockout strains were generated by RNA-seq, in duplicate.

first: Amitesh

last: Anand

first: Connor

last: Olson

first: Ye

last: Gao

first: Bernhard

middle: O

last: Palsson


title: CRISPR Screening for CALM-AF10 interactome and transcriptional targets

status: Public on Jan 05 2021

city: San Diego

first: Aniruddha

last: Deshpande

address: 10901 N Torrey Pines Road

country: USA

institute: Sanford Burnham Prebys Medical Discovery Institute

summary: We performed pooled CRISPR screens to determine the whether the CALM-AF10 target genes and protein interactors identified by RNA-Seq and proteomics methods are functional dependencies for CALM-AF10-driven AML. We constructed a pooled CRISPR library of CALM-AF10 mouse target genes and interactors, and used it to transduce CALM-AF10 mouse AMLs. The cells were sampled at "Day 0" and kept in culture to determine in vitro dependencies at day 12. For in vivo screens, the input cell pool from day 0 was injected in mice and mice where sacrificed upon signs of AML disease, and the AML cells were harvested.

overall_design: Examination of sgRNA abundance in library of cultured cells and mouse AML tumors.

first: Karina

last: Barbosa

first: Bo-Rui

last: Chen

first: Anagha

middle: J


title: Genome-wide H3K27acetylation ChIP-seq in  CALM-AF10 On and Off AML cells

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We report calling of super-enhancers in CALM-AF10 mouse AML cells where the fusion is either on (DMSO) or turned off (using Doxycycline).

overall_design: H3K27ac antibody Abcam, ab4729


title: Transriptome profiling of breast cancer cells T47D overexpressing ZNF528-AS1

city: Jinan

first: Qifeng

last: Yang

state: Shandong

address: Wenhua West Road No.44

department: Department of Breast Surgery

country: China

institute: Qilu Hospital

type: Expression profiling by high throughput sequencing

summary: Effect of ZNF528-AS1 overexpression in T47D breast cancer cells

overall_design: Comparisons of genes regulated by ZNF528-AS1 in T47D breast cancer cells


title: SNParray data for banking lines in Korea National Stem Cell Bank

city: Cheongju-si

first: Kim

last: Jung-Hyun

address: 202, Osongsaengmyeong 2-ro, Osong-eup, Heungdeok-gu

department: Division of Intractable Diseases

country: South Korea

institute: Korea National Institute of Health

summary: Copy number variantions (CNVs) were calculated using SNP array data for banking lines in Korea National Stem Cell Bank.

overall_design: Affymetrix CytoScan HD arrays were performed according to the manufacturer's directions on DNA extracted from cell pellet of hPSCs.

first: Hye-Yeong

last: Jo

first: Jung-Hyun

last: Kim


title: Network-based systems pharmacology identifies heterogeneity in LCK and BCL2 signaling and differential vulnerability of T-cell acute lymphoblastic leukemia to targeted therapy

city: Memphis

first: Jiyang

last: Yu

state: TN

address: 262 Danny Thomas Pl

department: Dept. of computational biology

institute: stjude children's research hospital

summary: T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematological malignancy, and novel therapeutics are much needed. Profiling patient leukemia’ drug sensitivities ex vivo, we discovered that 44.4% of childhood and 16.7% of adult T-ALL cases exquisitely respond to dasatinib. Applying network-based systems pharmacology analyses to examine signal circuitry, we identified preTCR-LCK activation as the driver of dasatinib sensitivity, and T-ALL-specific LCK dependency was confirmed in genome-wide CRISPR-Cas9 screens. Dasatinib-sensitive T-ALLs exhibited high BCL-XL and low BCL2 activity and venetoclax resistance. Discordant sensitivity of T-ALL to dasatinib and venetoclax is strongly correlated with T-cell differentiation, particularly with the dynamic shift in LCK vs. BCL2 activation. Finally, single-cell analysis identified leukemia heterogeneity in LCK and BCL2 signaling and T-cell maturation stage, consistent with dasatinib response. In conclusion, our results indicate that developmental arrest in T-ALL drives differential activation of preTCR-LCK and BCL2 signaling in this leukemia, providing unique opportunities for targeted therapy.

overall_design: 10xGenomics scRNA-seq profiles of T-ALL PDX with or without Dasatinib treatment

first: Jun

first: Jingjing

last: Liu

first: Jianzhong

last: Hu


title: Plasticity of epididymal adipose tissue in response diet-induced obesity at single-nucleus resolution.

city: Odense M

first: Susanne

last: Mandrup

state: Fyn

address: Campusvej 55

department: Department of Biochemistry and Molecular Biologi

country: Denmark

institute: University of Southern Denmark

summary: Adipose tissues display a remarkable ability to adapt to the dietary status. Here, we have applied single-nucleus RNA-seq to map the plasticity of mouse epididymal white adipose tissue at single cell resolution in response to high-fat diet-induced obesity. The single-nucleus approach allowed us to recover all major cell types and to reveal distinct transcriptional stages along the entire adipogenic trajectory from preadipocyte commitment to mature adipocytes. We demonstrate the existence of different adipocyte subpopulations and show that obesity leads to disappearance of the lipogenic subpopulation and increased abundance of the stressed lipid scavenging subpopulation. Moreover, obesity is associated with major changes in the abundance and gene expression of other cell populations, including a dramatic increase in lipid handling genes in macrophages at the expense of macrophage-specific genes. The data provide a powerful resource for future hypothesis-driven investigations of the mechanisms of adipocyte differentiation and adipose tissue plasticity.

overall_design: We applied single-nucleus RNA-seq (10X Genomics) to epididymal white adipose tissue from lean and obese mice to characterize the tissue composition and plasticity during obesity.

first: Anitta

middle: K

last: Sárvári

first: Elvira

middle: L

last: Van Hauwaert

first: Lasse

last: Markussen

first: Ellen

last: Gammelmark

first: Ann-Britt

last: Marcher

first: Morten

middle: F

last: Ebbesen

first: Ronni

last: Nielsen

first: Jonathan

middle: R

last: Brewer

first: Jesper

middle: G

last: Madsen


title: RNA_seq Analysis of Murine Leukemias for Identifying Potential Leukemia Fusion Targets and JAK1 regulated genes

first: Aniruddha

last: Deshpande

summary:
Purpose: The goals of this study are to compare transcriptomes after shutting off the CALM-AF10, MLL-AF10 and MLL-AF9 fusion proteins in mouse AML cells. Furthermore, we also perform transcriptomic experiments to assess the changes in transcripts upon JAK1 deletion in mouse CALM-AF10 AML.
Methods: Mouse AMLs cells grown in Mouse leukemia medium (see below) were treated with DMSO (Tet-On) or 4ug/ul Doxycycline (Tet-Off) and RNA was isolated to perform RNA-seq. RNA for CALM-AF10, MLL-AF10 was poly-A selected and MLL-AF9, total RNA was used to make RNAseq libraries using the NEB RNAseq lbrary prep kit. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays
Results: Using an optimized data analysis workflow, we mapped about 20 million sequence reads per sample to the mouse genome (build mm9) and 60 million reads for MLL-AF9 data. Data analysis with BWA and TopHat workflows revealed genes that are significantly changed after shutting off the fusions or after deleting Jak1 in CALM-AF10 Jak1 floxed cells using the Cre recombinase.
Conclusions:

overall_design: RNA-seq analysis of inducible RNA-seq

first: Anagha


title: Influence of a Ctsk-/-/Mct8-/y/Mct10-/- triple knockout on the tanscriptome of thyroid tissue in male mice

status: Public on Jan 04 2021

city: Greifswald

first: Janine

last: Golchert

address: Felix-Hausdorff-Str. 8

department: Department of Functional Genomics

country: Germany

institute: University Medicine Greifswald

summary: To investigate the influence of cathepsin k and the monocarboxylate transporters 8 and 10 on the gene expression profile in thyroid tissue, we used a Ctsk-/-/Mct8-/y/Mct10-/- triple knockout mouse model and performed microarray analyses.

overall_design: We used male wild type C57Bl/6J and Ctsk-/-/Mct8-/y/Mct10-/- triple knockout mice at 5-8 months of age. Snap-frozen thyroid tissue from four animals per genotype was used for RNA extraction. Transcriptome analyses were performed using individual RNA samples.

first: Georg

last: Homuth

first: Vaishnavi

last: Venugopalan

first: Klaudia

last: Brix


title: Analysis of gene expression in co-culture of PBMCs with Hepatocellular carcinoma by High-Throughput Sequencing

city: Bangkok

first: Natthaya

last: Chuaypen

address: 1873 Rama 4 road, Pathumwan

country: Thailand

institute: Chulalongkorn University

summary:
Objectives: To characterize the transcripts profile of PBMCs when co-cultured with HCC cell lines using High-Throughput Sequencing and To validate the differentially expressed genes via quantitative reverse transcription polymerase chain reaction (qRT-PCR) in PBMCs of HCC pateints.
Methods: Transcription profiles of PBMC (control) and PBMC co-cultured with liver cancer cell lines (treatment) were generated by deep sequencing, in triplicate, using Illumina Illumina HiSeq 4000.
Results and conclusion: Transcriptome analysis of PBMCs has revealed the presence of biological process alterations when co-cultured with HCC cell lines and qRT-PCR validation have indicated that four genes were up-reglurated in HCC patients when compared with healthy donors including IL1b, INHBA, PLOD2, PRG4.

overall_design: Transcription profiles of PBMC (control) and PBMC co-cultured with cancer (treatment) were generated by deep sequencing, using Illumina HiSeq 4000.

first: P

last: Kunadirek

first: N

last: Tangkijvanich


title: A defined glycosylation regulatory network modulates total glycome dynamics during pluripotency state transition

city: Hachioji

first: Shoko

last: Nishihara

state: Tokyo

address: 1-236 Tangi-machi

department: Bioinformatics

country: Japan

institute: Soka University, Graduate School of Engineering

summary: PRC2 coordinates glycome dynamics during ESC (naive) to EpiLC (primed) transition

overall_design: RNA-seq to compare the expression of glycosyltransferases and glycosylation related genes during ESC to EpiLC transition and in ESCs untreated/treated with PRC2 inhibitor

first: Federico

last: Pecori

first: Ikuko

last: Yokota

first: Hisatoshi

last: Hanamatsu

first: Taichi

last: Miura

first: Chika

last: Ogura

first: Hayato

last: Ota

first: Jun-ichi

last: Furukawa

first: Shinya

last: Oki

first: Kazuo

last: Yamamoto

first: Osamu

last: Yoshie


title: Neural stem cells alter nucleocytoplasmic partitioning and accumulate nuclear polyadenylated transcripts during quiescence

city: London

first: Rita

last: Sousa-Nunes

address: New Hunt's House, Newcomen Street

department: Centre for Developmental Neurobiology

country: United Kingdom

institute: King's College London

summary: Quiescence is a cellular state characterized by reversible cell-cycle arrest and diminished biosynthetic activity that protects against environmental insults, replicative exhaustion and proliferation-induced mutations. Entry into and exit from this state controls development, maintenance and repair of tissues, plus in the adult central nervous system, generation of new neurons and thus cognition and mood. Cancer stem cells too can undergo quiescence, which confers them resistance to current therapies. Despite clinical relevance, quiescence lacks understanding and is defined functionally given lack of molecular markers. Inhibition of the Target of Rapamycin pathway is a common denominator of quiescence across species and cell types. This pathway integrates diverse signals towards control of metabolism and cytoskeleton, and lowered pathway activity in quiescence ensures decrease of the most resource-¬intensive cellular process of protein synthesis. Here, we combine Drosophila genetics and a mammalian model to show that altered nucleocytoplasmic partitioning and nuclear bias of a fraction of polyadenylated RNAs are novel evolutionarily conserved mechanisms of quiescence regulation. Altogether, these mechanisms contribute a new regulatory layer to inhibition of protein translation in quiescent cells, whilst likely priming them for quick reactivation in response to appropriate cues.

overall_design: In vitro derived primary cultures of mouse hippocampal neural stem cells were either kept in proliferative conditions (0-days in BMP4 or active state: A) or induced into quiescence by exposure to BMP4 for 3 days (Q_3-day) or 10 days (Q 10-days). Nuclear/Cytoplasmic fractionation was performed and total RNA was extracted from each fraction. Four replicates per condition were acquired.

first: Alice

last: Rossi

first: Antoine

last: Coum

first: Manon

last: Madelenat

first: Harris

last: Lachlan

first: Alina

last: Miedzik

first: Stephanie

last: Strohbuecker

first: Andrea

last: Chai

first: Hania

last: Fiaz

last: Chaouni

first: Peter

last: Faull

first: William

last: Grey

first: Dominique

last: Bonnet

first: Evgeniy

last: Makeyev

first: Ambrosius

middle: P

last: Snijders

first: Gavin

last: Kelly

first: Francois

last: Guillemot


title: Thymic stromal lymphopoietin limits primary and recall CD8+ T cell anti-viral responses

city: Bethesda

first: Peng

last: Li

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

summary: Thymic stromal lymphopoietin (TSLP) is a cytokine that acts directly on CD4+ T cells and dendritic cells to promote progression of asthma, atopic dermatitis, and allergic inflammation. However, a direct role for TSLP in CD8+ T-cell primary responses remains controversial and its role in memory CD8+ T-cell responses to secondary viral infection is unknown.  Here, we investigate the role of TSLP in both primary and recall responses using two different viral systems. Interestingly, TSLP limited the primary CD8+ T cell response to influenza but did not affect T cell function nor significantly alter the number of memory CD8+ T cells generated after influenza infection. However, TSLP inhibited memory CD8+ T cell responses to secondary viral infection with influenza or acute systemic LCMV infection. These data reveal a previously unappreciated role for TSLP on recall CD8+ T cell responses in response to viral infection, findings with potential translational implications.

overall_design: RNA-Seq analysis on sorted naïve and memory CD8+ T cells after 4 or 24 hours incubation with medium or TSLP with or without TCR stimulation. RNA-Seq analysis on recall responses of wild-type and Tslpr-/- CD8+ T cells at day 8 after secondary infection.

first: Risa

last: Ebina-Shibuya

first: Erin

middle: E

last: West

first: Rosanne

last: Spolski

first: Jangsuk

last: Oh

first: Majid

last: Kazemian

first: Daniel

last: Gromer

first: Phillip

middle: A

last: Swanson II

first: Ning

last: Du

first: Dorian

middle: B

last: McGavern

first: Warren

last: Leonard


title: Deletion of the helicase RTEL1 in RNA:DNA hybrids throughout the genome and how this may be affected by overexpression of the protein WT RNaseH1GFP in MEFs

first: Simon

last: Boulton

address: 1 Midland Rd

institute: The Francis Crick Institute

summary: The goal of this study is to assess the effect of the deletion of the helicase RTEL1 in RNA:DNA hybrids throughout the genome and how this may be affected by overexpression of the protein WT RNaseH1GFP in mouse embryonic fibroblasts.

overall_design: We used RTEL1F/F mouse embryonic fibroblasts that upon infection with Cre adenoparticles delete Rtel1 and upon addition of doxycycline overexpress WT RNaseH1GFP (Rtel1F/F;WT RNH1-GFP MEFs). Rtel1F/F;WT RNH1-GFP MEFs were infected with GFP or Cre-GFP adenovirus, after 48 h doxycycline (2 μg/ml) was added and cells were collected after 48 h. RNA:DNA hybrids were pulled down using the DRIP protocol and DNA was isolated and send for sequencing.

first: Pol

last: Margalef

first: Panagiotis

last: Kotsantis

first: Sandra

last: Segura-Bayona

first: Anna

last: Poetsch

first: Harshil

last: Patel

first: Phil

last: Ruis

first: Paulina

last: Marzec

first: Roberto

last: Bellelli

first: Graeme

last: Hewitt

first: Tyler

middle: H

last: Stanage

first: Robert

last: Goldstone


title: RTEL1 regulates G4/R-loops to avert replication-transcription collisions

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

overall_design: Refer to individual Series


title: HuR knockdown in humanized and wildtype mice liver samples

first: Haiming

last: Cao

summary: HuR shRNA adenoviruses were delivered into WT or humanized mice intravenously at 2 × 109 pfu/mouse for both control virus and HuR shRNA virus . After seven days, liver tissue samples were harvested after a four hours fasting and stored immediately in liquid nitrogen till further analysis.The frozen liver tissue samples were homogenized in Trizol reagent (Invitrogen) using TissueLyser LT system (Qiagen). The isolated RNA was purified by MagMAX RNA Extraction Kit (ThermoFisher) and the construction of strand specific sequencing libraries using TruSeq Stranded Total RNA Prep kit (Illumina) and the sequencing was performed at NHLBI DNA Sequencing and Genomics Core using Illumina HiSeq 3000 paired-end sequencing platform.

overall_design: RNA sequencing profiles were generated for HuR konckdown in humanized  and wild type mice.  The humanized livers are generated by engrafting human hepatocytes in immunodeficient mice livers.

first: Chengfei

last: Jiang

first: Ping

last: Li

first: Xiangbo

last: Ruan

first: Yonghe

last: Ma


title: Single Cell Transcriptomic Analysis of Lung and Hematopoietic Megakaryocytes from Embryonic and Adult Mice.

city: Boston

first: Carlos

last: Villacorta-Martin

state: MA

address: 670 Albany St

institute: Center for Regenerative Medicine at Boston University

summary: To create a transcriptomic library that spans multiple stages and sites of megakaryocyte development, scRNA-Seq was performed on cells isolated from embryonic day 13 fetal liver and lung, as well as week 10 adult bone marrow and lung. Enrichment of megakaryocytes in all tissues was accomplished using flow cytometry to sort for live-CD41+ cells. Only the top 1% of CD41+ events were captured in order to further enhance enrichment of megakaryocyte-lineage cells.

overall_design: Single cell transcriptomic analysis of live-CD41+ megakaryocytes isolated from the murine fetal lung and fetal liver, as well as the murine adult lung and bone marrow.

first: Anthony

last: Yeung

first: George

last: Murphy


title: Next Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes of BMDCs treated without or with exosomes from tumor cells or normal cells

city: Beijing

first: Wenfeng

last: Zeng

address: 15 Datun Road

institute: Institute of Biophysics, Chinese Academy of Sciences

summary: The goals of this study are to compare the transcriptome profiling (RNA-seq) of tumor cell-derived exosome treated BMDCs to normal cell-derived exosome treaed BMDCs or untreated BMDCs to explore the differential regulated signaling pathways or cellular processes.

overall_design: Transcriptome profiles of untreated BMDCs, normal cell-derived exosome treated BMDCs and tumor cell-derived exosome treated BMDCs

first: Xiaozhe

last: Yin


title: Tissue specific transcription patterns support the kinship theory of intragenomic conflict in honey bees (Apis mellifera)

city: University Park

first: David

middle: Asher

last: Galbraith

state: Pennsylvania

address: 19a Chemical Ecology Lab

institute: Penn State University

summary: Kin selection may act differently on genes inherited from the two parents (matrigenes and patrigenes), resulting in intragenomic conflict. This conflict can be observed as differential expression of matrigenes and patrigenes, or parent specific gene expression (PSGE).  In honey bees (Apis mellifera), intragenomic conflict is hypothesized to occur in multiple social contexts.  Previously, we found patrigene expression in reproductive tissues was associated with increased reproductive potential in worker honey bees, consistent with the prediction that patrigenes are selected to promote selfish behavior in this context.  Here, we examined brain expression patterns to determine if PSGE is also found in other tissues.  As before, the number of transcripts showing patrigene expression bias was significantly greater in the brains of reproductive versus sterile workers, while the number of matrigene-biased transcripts was not significantly different. Twelve transcripts out of the 374 showing PSGE in either tissue showed PSGE in both brain and reproductive tissues; this overlap was significantly greater than expected by chance.  However, the majority of transcripts showed PSGE only in one tissue, suggesting the epigenetic mechanisms mediating PSGE show plasticity between tissues.  There was no significant overlap between transcripts that showed PSGE and transcripts that were significantly differentially expressed.  Weighted gene correlation network analysis identified modules which were significantly enriched in both types of transcripts, suggesting that these genes may influence each other through gene networks.  Our results provide further support for the kin selection theory of intragenomic conflict, and provide valuable insights into the mechanisms which may mediate this process.

overall_design: Examination of allele specific expression in the brains of reproductive and sterile honey bees. The samples were run across two lanes using paired end sequencing.

first: Rong

first: Christina

middle: M

last: Grozinger


title: Hyperosmotic stress induces downstream-of-gene transcription and alters the RNA Polymerase II interactome despite widespread transcriptional repression

city: New Haven

first: Nicolle

middle: A.

last: Rosa-Mercado

state: CT

address: 295 Congress Avenue

department: Molecular Biophysics and Biochemistry

institute: Yale University

summary:
Stress-induced readthrough transcription results in the synthesis of thousands of downstream-of-gene (DoG) containing transcripts. The mechanisms underlying DoG formation during cellular stress remain unknown. Nascent transcription profiles during DoG induction in human cell lines using TT-TimeLapse-seq revealed that hyperosmotic stress induces widespread transcriptional repression. Yet, DoGs are produced regardless of the transcriptional level of their upstream genes. ChIP-seq confirmed that the stress-induced redistribution of RNA Polymerase (Pol) II correlates with the transcriptional output of genes. Stress-induced alterations in the Pol II interactome are observed by mass spectrometry. While subunits of the cleavage and polyadenylation machinery remained Pol II-associated, Integrator complex subunits dissociated from Pol II under stress conditions. Depleting the catalytic subunit of the Integrator complex, Int11, using siRNAs induces hundreds of readthrough transcripts, whose parental genes partially overlap those of stress-induced DoGs. Our results provide insights into the mechanisms underlying DoG production and how Integrator activity influences DoG transcription.

This SuperSeries is composed of the SubSeries listed below.


title: Whole transcriptome sequencing of kidney tissues in lupus nephritis

city: Zhengzhou

first: Zhaohui

last: Zheng

address: 1 Eastern Jianshe Road

institute: The First Affiliated Hospital of Zhengzhou University

type: Non-coding RNA profiling by high throughput sequencing

summary: Lupus nephritis (LN) is a well-known complication of SLE, which is the leading cause of morbidity and mortality. mRNA and non-coding RNAs, including long non-coding RNA (lncRNA), circular RNA (circRNA) and microRNA(miRNA), could play important roles in LN onset and development. In this study, we identified differential lncRNA/miRNA/circRNA and mRNA expression profiles of renal tissues from LN patients compared with the healthy renal tissues by whole transcriptome sequencing. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to investigate the potential functions of these DE mRNAs and ncRNAs. Besides, the competing endogenous RNA (ceRNA) networks (circRNA-miRNA-mRNA network) were also constructed to understand the internal regulating relationships of these mRNAs and circRNAs. And key ceRNA relationships were verified by dual-luciferase reporter experiments. Moreover, gene function enrichment analysis showed that dysregulated RNAs were mostly related to innate and adaptive immune response, especially against virus infection. The analysis for these DE mRNAs and ncRNAs in LN patients provided a new perspective for the pathophysiology, diagnosis, and treatment of LN.

overall_design: Six samples, 3 renal tissues from LN patients and 3 healthy renal tissues from cancer patients. The standard of healthy tissues was the distance from the tumors, at least 5 cm, confirmed by microscopic examination.

first: Congcong

last: Gao

first: Siwan

last: Cui

first: Chunyi

last: Zhang

first: Menghui

last: Yao


title: A Specific Neuroligin3-αNeurexin1Signaling Regulates GABAergic Synaptic Function in Mouse Hippocampus

city: Hershey

first: Yuka

last: Imamura Kawasawa

state: PA

address: 500 University Dr.

department: College of Medicine, Pharmacology

summary: Synapses are fundamental organizers of precise signal propagation between neurons. Maintaining synapse assemblies require interactions between pre- and post- synaptic proteins, notably cell adhesion molecules (CAMs). It has been proposed that the function of Neuroligins (Nlgn1 - 4), postsynaptic CAMs, relies on the formation of trans-synaptic complexes with Neurexins (Nrxs), presynaptic CAMs. Nlgn3 is a unique Nlgn isoform that localizes at both excitatory and inhibitory synapses. However, Nlgn3 function mediated through Nrx interaction is mostly unknown. Here, we find for the first time that Nlgn3 localizes at postsynaptic sites apposing vesicular glutamate transporter 3 (VGT3)-expressing inhibitory terminals. Overexpression and knockdown approaches indicate that Nlgn3 regulates VGT3-positive inhibitory interneuron-mediated synaptic transmission. Fluorescent in situ hybridization and single-cell RNA sequencing studies revealed that αNrxn1 and βNrxn3 are VGT3 interneuron-specific Nrxn isoforms and the expression levels of Nrxn splice isoforms are highly diverse in VGT3 interneurons, respectively. Most importantly, postsynaptic Nlgn3 requires presynaptic αNrx1+AS4 expressed in VGT3-positive interneurons to regulate inhibitory synaptic transmission. Our results strongly suggest that specific Nlgn-Nrx interaction generate distinct functional properties at synapses.

overall_design: The cytosol of single cell VGT3-, Pv- and Sst-positive inhibitory interneuron was harvested using the whole cell patch-clamp technique

first: Motokazu

last: Uchigashima

first: Kotaro

last: Konno

first: Emily

last: Demchak

first: Amy

last: Cheung

first: Takuya

last: Watanabe

last: Keener

first: Manabu

last: Abe

first: Timmy

last: Le

first: Kenji

last: Sakimura

first: Toshikuni

last: Sasaoka

first: Masahiko

middle: I

last: Kawasawa

first: Kensuke

last: Futai


title: The consequences of RPB1-CTD truncation for human transcriptome dynamics

city: Goettingen

first: Anna

last: Sawicka

address: Am Fassberg 11

department: Dep. of Molecular Biology

institute: Max Planck Institure for Biophysical Chemistry

summary: The carboxy-terminal domain of RPB1 subunit of RNA Polymerase II (CTD) plays an essential function in the regulation of gene expression and the coordination of co-transcriptional processes. CTD consists of hepta-amino acid repeats varying in number from 52 in humans to 26 in yeast and its length is crucial for spatial organization of transcriptional machinery in the nucleus. We found that the proximal half of the CTD is sufficient to support RNA metabolism and co-transcriptional processing in steady state conditions in human cells. Signal induced transcription, however, is severely impaired upon CTD shortening. Our data suggest that CTD length increased in evolution to allow for spatio-temporal control of gene expression patterns at least in part by facilitating enhancer function.

overall_design: Effects of RPB1-CTD shortening (from 52 to 25 heptad repeats) on transcription in human cells without treatment and in cells tratead with 12-O-Tetradecanoylphorbol-13-acetate (TPA) or DMSO (solvent) for 15 min or 30 min.

first: Patrick

last: Cramer


title: Cell autonomous requirement of Neurofibrimin (Nf1) for postnatal muscle hypertrophic growth and metabolic homeostasis

city: Berlin

first: Xiaoyan

last: Wei

address: Thielallee 63

institute: Free University of Berlin

summary: Our results demonstrate a cell-autonomous role for Nf1 in myogenic cells during postnatal muscle growth required for metabolic and proteostatic homeostasis.

overall_design: We sequenced total RNAs that were isolated from two Nf1 deleted (Nf1flox/flox/Myf5+)  and two Het (Nf1flox/+/Myf5+) p21 mouse TA muscle.

first: Sigmar

last: Stricker


title: Comparative genome-wide transcriptional profile after RTEL1 depletion and G4 stabilisation.

first: Simon

last: Boulton

summary: The goal of this study is to compare the transcription profile of mouse embryonic fibroblasts upon deletion of the helicase RTEL1 and stabilisation of G-quadruplexes (G4) with the G4 stabilisation drug TMPyP4.

overall_design: RNA-seq analysis of Rtel1f/f Mouse Embryonic Fibroblasts cells, infected with Ad-GFP or Ad-Cre adenovirus. RNA was collected 96 hours after the infection. In the indicated cases, cells were treated with TMPyP4 for 48 hours prior to the RNA collection. Three conditions were compared: cells infected with Ad-GFP, cells infected with Ad-Cre, and cells infected with Ad-GFP and treated with TMPyP4.

first: Pol

last: Margalef

first: Panagiotis

last: Kotsantis

first: Sandra

last: Segura-Bayona

last: Poetsch

first: Harshil

last: Patel

first: Phil

last: Ruis

first: Paulina

last: Marzec

first: Roberto

last: Bellelli

first: Graeme

last: Hewitt

first: Tyler

last: Stanage

first: Robert

last: Goldstone


title: Distinctive cellular and metabolic reprogramming in porcine lung myeloid cells infected with type I PRRSV strains

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

country: France

institute: IBENS

summary: The Porcine Reproductive and Respiratory Syndrome (PRRS) has an extensive impact on pig production. The causative virus (PRRSV) is divided in two species, PRRSV-1 (European origin) and PRRSV-2 (North American origin). Within PRRSV-1, PRRSV-1.3 strains such as Lena are more pathogenic than PRRSV-1.1 strains such as Flanders 13 (FL13). To date, the molecular interactions of PRRSV with primary lung mononuclear phagocytes (MNP) subtypes including conventional dendritic cells type 1 (cDC1) and type 2 (cDC2), monocyte-derived DCs (moDC) and parenchymal macrophages (PIM) have not been thoroughly investigated. Here, we analysed the transcriptome profiles of in vivo FL13-infected parenchymal MNP subpopulations and of in vitro FL13- and Lena-infected parenchymal MNP. The cell specific expression profiles of in vivo sorted cells correlated with their murine counterparts (AM, cDC1, cDC2, moDC) with the exception of PIM. Both in vivo and in vitro, FL13 infection altered the expression of a low number of host genes while in vitro infection with Lena confirmed the higher ability of this strain to modulate host response. Machine learning (ML) and GSEA analyses unraveled additional relevant genes and pathways modulated by FL13 infection that were not identified by conventional analyses. GSEA increased the cellular pathways enriched in FL13 dataset, but ML allowed a more complete comprehension of functional profiles during FL13 in vitro infection. Data indicated that cellular reprogramming differed upon Lena and FL13 infection, and that the latter keeps antiviral and inflammatory macrophages/DC functions silent, suggesting a different mechanism of pathogenesis during early infection.

overall_design: transcriptome profiles of in vivo FL13-infected parenchymal MNP subpopulations and in vitro FL13- and Lena-infected parenchymal MNP obtained using RNAseq

first: Elisa

last: Crisci

first: Marco

last: Moroldo

first: Thien-Phong

last: Vu Manh

first: Ammara

last: Mohammad

first: Laurent

last: Jourdren

first: Celine

last: Urien

first: Edwige

last: Bouguyon

first: Elise

last: Bordet

first: Claudia

last: Bevilacqua

first: Mickael

last: Bourge

first: Jérémy

last: Pezant

first: Alexis

last: Pléau

first: Olivier

last: Boulesteix

first: Isabelle

last: Schwartz

first: Nicolas

last: Bertho

first: Elisabetta

last: Giuffra


title: p53 transcription factor mediates nuclear speckle association of target genes

city: Philadelphia

first: Katherine

last: Alexander

address: Smilow Center for Translational Research

institute: University of Pennsylvania

summary: Nuclear speckles are prominent nuclear bodies that contain a myriad of factors involved in gene expression. The role of nuclear speckles as activating transcriptional compartments is emerging. However, the extent that the association between speckles and DNA is regulatable, and the mechanisms that govern regulated speckle association are currently unclear. Using DNA- and RNA-FISH, we show that speckle association can be mediated by the p53 transcription factor, finding that p53 activation drives speckle association of specific p53 transcriptional targets. Analysis of a key p53 target, p21, revealed an increase in nascent transcripts at speckle-adjacent transcription sites, supporting a role for speckles in amplifying transcriptional output. Importantly, p53-regulated speckle association of p21 did not depend on transcriptional activation, demonstrating that speckle association is not merely a consequence of gene expression. In contrast, speckle association of p21 did require DNA binding functions of p53, providing a mechanism for the specificity by which speckle association is regulated. Beyond p21, a substantial subset of p53 targets have p53-regulated speckle association, while other p53 targets do not, and we find that genomic context is highly deterministic of which target genes have regulated speckle association. These findings reveal a novel means by which transcription factors may control gene expression and provide a mechanism for the specificity of regulated speckle association.

overall_design: IMR90 cells were treated with 5uM Nutlin3a or the equivalent volume of DMSO for 6 hours. DMSO- or Nutlin-treated cells were then harvested along for TSA-seq using an antibody against SON (SON TSA-seq). Untreated IMR90 cells were used for a no primary control. Each of the three conditions (DMSO SON TSA-seq, Nutlin SON TSA-seq, and No Primary TSA-seq) were perfomed in duplicate, and sequenced with their respective Input (chromatin before pulldown) controls.

first: Shelley

last: Berger


title: Cardiac endothelial cells maintain open chromatin and expression of cardiomyocyte myofibrillar genes

city: PHILADELPHIA

first: Arndt

last: Siekmann

address: 421 Curie Boulevard, 1114 Biomedical Research Building II/III

department: Perelman School of Medicine

institute: UNIVERSITY OF PENNSYLVANIA

summary: Endothelial cells (ECs) are widely heterogenous depending on tissue and vascular localization. Jambusaria et al. recently demonstrated that ECs in various tissues surprisingly possess mRNA signatures of their underlying parenchyma. The mechanism underlying this observation remains unexplained, and could include mRNA contamination during cell isolation, in vivo mRNA paracrine transfer from parenchymal cells to ECs, or cell-autonomous expression of these mRNAs in ECs. Here, we use a combination of bulk RNASeq, single-cell RNASeq datasets, in situ mRNA hybridization, and most importantly ATAC-Seq of FACS-isolated nuclei, to show that cardiac ECs actively express cardiomyocyte myofibril (CMF) genes and have open chromatin at CMF gene promoters. These open chromatin sites are enriched for sites targeted by cardiac transcription factors, and closed upon expansion of ECs in culture. Together, these data demonstrate unambiguously that the expression of CMF genes in ECs is cell-autonomous, and not simply a result of technical contamination or paracrine transfers of mRNAs, and indicate that local cues in the heart in vivo unexpectedly maintain fully open chromatin in ECs at genes previously thought limited to cardiomyocytes.

overall_design:
NuTRAP/Cdh5-Cre (NuTRAP from Roh, 2017, Cell Reports) animals were generated to GFP tag endothelial cell nuclei. Total nuclei were isolated from whole hearts of 8-12week old male animals. Endothelial cell nuclei (GFP+) were isolated by flow cytometry in addition to non-endothelial nuclei (GFP-).
100-50,000 purified  GFP+ ("Pos") and GFP- ("Neg") nuclei were processed for ATACSeq, using the protocol outlined in Buenrostro, et al 2013, using 2.5uL of Tn5 per 50,000 nuclei.

Please note that *narrowPeak data was generated from both replicates and is linked to the corresponding *1_ATACSeq sample records.

first: Nora

middle: D

last: Yucel

first: Zoltan

last: Arany


title: Subtype-associated epigenomic landscape and 3D genome structure in bladder cancer

city: Chicago

first: Feng

last: Yue

state: IL

address: 303 E. Superior Simpson Querrey 7-518

department: Biochemistry and Molecular Genetics

institute: Northwestern University

summary:
Muscle-invasive bladder cancers are characterized by their distinct expression of luminal and basal genes, which could be used to predict key clinical features such as disease progression and overall survival. Transcriptionally, FOXA1, GATA3, and PPARg are shown to be essential for luminal subtype-specific gene regulation and subtype switching, while TP63, STAT3 and TFAP2 family members are critical for regulation of basal subtype-specific genes. Despite these advances, the underlying epigenetic mechanisms and 3D chromatin architecture responsible for subtype-specific regulation in bladder cancer remains unknown.

Result: We determine the genome-wide transcriptome, enhancer landscape and transcription factor binding profiles of FOXA1 and GATA3 in luminal and basal subtypes of bladder cancer.   Furthermore, we report the first-ever mapping of genome-wide chromatin interactions by Hi-C in both bladder cancer cell lines and primary patient tumors. We show that subtype-specific transcription is accompanied by specific open chromatin and epigenomic marks, at least partially driven by distinct transcription factor binding at distal-enhancers of luminal and basal bladder cancers. Finally, we identify a novel clinically relevant transcription factor, Neuronal PAS Domain Protein 2 (NPAS2), in luminal bladder cancers that regulates other subtype-specific genes and influences cancer cell proliferation and migration.

Conclusion: In summary, our work identifies unique epigenomic signatures and 3D genome structures in luminal and basal urinary bladder cancers and suggests a novel link between the circadian transcription factor NPAS2 and a clinical bladder cancer subtype.

overall_design:
We performed epigenomic analysis including RNA-Seq, H3K27ac ChIP-Seq, GATA3 ChIP-Seq, ATAC-Seq and Hi-C on molecular subtypes of bladder cancer cell lines and 5 patient tumors.

Raw data for tumor samples not provided due to patient privacy concerns.

first: Tejaswi

last: Iyyanki

first: Qixuan

last: Wang


title: Cellular and molecular aspects of the interaction of Trichophyton rubrum in the human macrophage cell line THP-1 that simulates a deep infection

city: Ribeirão Preto

first: Ana

middle: Lucia

last: Fachin

state: SP

address: Av. Costabile Romano, 2201

department: Biotechonology  Unit

country: Brazil

institute: Unaerp

summary: Evaluate the cellular and molecular response of co culture inactive conidia of T. rubrum and THP-1 cell line, by interleucine, EROS, LDH quantification and the transcriptional profile of miRNA-seq involved in deep infection.

sample_organism:
Trichophyton rubrum
Homo sapiens

platform_organism:
Trichophyton rubrum
Homo sapiens

overall_design: The control (THP-1) and co-culture were carry out in triplicate

first: Gabriela

last: Segura

first: Bruna

last: Cantelli

first: Kamila

last: Peronni

first: Pablo

last: Sanches

first: Tatiana

middle: T

last: Komoto

first: Elen

last: Rizzi

first: Rene

middle: O

last: Beleboni

first: Wilson

last: da Silva Junior

first: Nilce

last: Martinez-Rossi

first: Mozart

last: Marins


title: The hepatic transcriptome of liver-specific insulin receptor knockout (LIRKO) mouse offspring

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

summary: At 2 months of age, liver-specific insulin receptor knockout (LIRKO) mice present hyperglycemia and hyperinsulinemia. Furthermore, LIRKO mice have increased levels of hepatic cholesterol. Indeed, many changes seen in cholesterol metabolism in LIRKO mice are also observed in humans with metabolic syndrome. For example, both show decreased levels of HDL and increased secretion of apoB and VLDL. These findings make the LIRKO mouse a unique non-dietary model of insulin resistant, hyperglycemia, dyslipidemia and atherosclerosis that resembles several clinical features of the human metabolic syndrome. By hepatic transcriptomic analysis of the wild-type (WT) offspring of LIRKO mice, we identify that members of the TGF-β family are differentially expressed in the offspring, including the NREP and GDF15.

overall_design: LIRKO (insulin receptor-IRlox/lox; Albumin-Cre+/-) mice were generated as previously described. The control offspring group consisted of the F1 offspring from a control male and female (insulin receptor-IRlox/lox; Albumin-Cre-/-). Control parents were crossed for 4 generations for minimizing any epigenetic memory from the presence of Cre. Father LIRKO offspring (FL) resulted from the crossing of a male LIRKO with a control female. Mother LIRKO offspring (ML) resulted from the breeding of a control male with a LIRKO female. Liver total RNA  was extracted using standard Trizol reagent (Invitrogen)  and cleaned up using RNeasy mini kit columns (Qiagen). Polyadenylated RNAs were isolated using NEBNext Magnetic Oligo d(T)25 Beads and first-strand cDNA synthesis was performed using NEBNext RNA first-strand synthesis module (New England BioLabs). Directional second strand synthesis was performed using NEBNExt Ultra Directional second strand synthesis kit. The NEBNext DNA Library Prep Master Mix Set for Illumina was then used to prepare individually bar-coded next-generation sequencing expression libraries. Paired-end sequencing was performed on an Illumina HiSeq2500 sequencer.

first: Dario

last: De Jesus

first: Rohit

middle: N

last: Kulkarni


title: Oxygen Level Modulates Mitochondria Mass and Pluripotent Marker Expression in Induced Pluripotent Stem Cells Through Sirtuin 1

city: Silver Spring

first: Ian

last: Bellayr

state: Maryland

address: 10903 New Hampshire Ave

institute: FDA

summary: Gene Expression microarrays were used to evaluate gene expression differences between induced pluripotent stem cells (iPSCs) cultured under hypoxia and normoxia conditions

overall_design: Four cell lines were grown in hypoxia and normoxia cell culture conditions

first: Cindy

last: Osborn

first: Deborah

last: Hursh


title: The hepatic methylome of liver-specific insulin receptor knockout (LIRKO) mouse offspring

type: Methylation profiling by high throughput sequencing

summary: Liver-specific insulin receptor knockout (LIRKO) mouse is a unique non-dietary model of insulin resistant, hyperglycemia, dyslipidemia and atherosclerosis that resembles several clinical features of the human metabolic syndrome. By enhanced reduced representation bisulfite sequencing (ERRBS) analysis of the livers of wild-type (WT) offspring of LIRKO mice, we identified that genes with differential DNA methylation were enriched for cholesterol synthesis, MAPK, AKT, insulin and TGF-β signaling,  including the NREP and GDF15.

overall_design: LIRKO (insulin receptor-IRlox/lox; Albumin-Cre+/-) mice were generated as previously described. The control offspring group consisted of the F1 offspring from a control male and female (insulin receptor-IRlox/lox; Albumin-Cre-/-). Control parents were crossed for 4 generations for minimizing any epigenetic memory from the presence of Cre. Father LIRKO offspring (FL) resulted from the crossing of a male LIRKO with a control female. Mother LIRKO offspring (ML) resulted from the breeding of a control male with a LIRKO female. High molecular weight DNA was isolated from control, FL and ML offspring livers using the Gentra puregene tissue kit (Qiagen). ERRBS library preparation, sequencing, and post-processing of the raw data were performed at the Epigenomics Core at Weill Cornell Medicine. Briefly, 75 ng of DNA (>20kb in size) were digested with MspI. After phenol extraction and ethanol precipitation MspI ends were end-repaired, A-tailed and ligated to methylated TruSeq adapters (Illumina Inc. San Diego, CA). Samples were size selected in a 1.5% agarose gel and two size fragment lengths of 150–250 bp and 250–400 bp were gel isolated. These two fractions were subjected to overnight bisulfite conversion (55 cycles of 95 °C for 30 sec, 50 °C for 15 min) using EZ DNA methylation kit (Zymo Research, Irvine CA). Purified bisulfite converted DNA was PCR amplified using TruSeq primers (Illumina Inc. San Diego, CA) for 18 cycles of denaturing, annealing and extension/elongation steps: 94 °C for 20 secs, 65 °C for 30 secs, 72 °C for 1 min, followed by 72 °C for 3 min. The resulting libraries were normalized to 2 nM and pooled at the same molar ratio. The final samples were pooled according to the desired plexity, clustered at 6.5 pM on the single-read flow cell and sequenced for 50 cycles on an Illumina HiSeq 2500. The primary processing of sequencing images was done using Illumina’s Real Time Analysis software (RTA). Illumina’s BCL2FASTQ version 2.17 software was then used to de-multiplex samples and generate raw reads and respective quality scores. For analysis of bisulfite-treated sequence reads (with an average bisulfite conversion rate of >99% for all samples), reads were filtered for adapter sequences using the FLEXBAR software. The adapter sequence present in the 3’ end of the reads was removed if it aligned with the adapter sequence at least 6 bps and had at most a 0.2 mismatch error rate. Reads were aligned to the whole genome using the Bismark alignment software with a maximum of two mismatches in a directional manner and only uniquely aligning reads were retained. In order to call a methylation score for a base position, read bases aligning to that position had at least a 20 phred quality score and that base position had at least 10x coverage. The percentage of bisulfite converted cytosines (representing unmethylated cytosines) and non-converted cytosines (representing methylated cytosines) were recorded for each cytosine position in CpG, CHG, and CHH contexts (with H corresponding to A, C, or T nucleotides).

middle: F


title: Aberrant gene expression leakage from linage-specific heterochromatic loci during senescence

first: Shamith

last: Samarajiwa

address: ICTEM Building, Hammersmith Campus, Du Cane Road,

department: Genetics and Genomics Section  Department of Metabolism, Digestion and Reproduction

institute: Imperial College London

summary: To understand induction of cornification genes on lineage appropriate (keratinocyte differentiation) and inappropriate (fibroblast senescence) conditions , we generated histone modification and gene expression dataset. Then we compared these keratinocyte's dataset with our previous fibroblast senescence dataset in the study.

overall_design: Histone modification and mRNA profiles of proliferating and differentiated keratinocytes were generated.

first: Kosuke

last: Tomimatsu

first: Dóra

last: Bihary

first: Masashi

last: Narita


title: Inflammatory versus non-inflammatory breast cancers

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

summary: Inflammatory Breast Cancer (IBC) is the most aggressive form of breast carcinoma characterized by the rapid onset of inflammatory signs. The molecular fingerprint for this rare, severe and unique clinical entity is still not elucidated. The goal of the present work was to detect both gene expression levels and alternate RNA splice variants specific to IBC.   Experimental Design: In order to identify differentially expressed genes and splicing events, we performed splice-sensitive array profiling using Affymetrix Exon Array and quantitative RT-PCR analyses in a large series of 177 IBC compared to 183 non-IBC. We also assessed the prognostic value of the identified candidate genes and splice variants.  Results: A 5-splice signature (HSPA8, RPL10, RPL4, DIDO1 and EVL) was able to distinguish IBC from non-IBC tumors (p<10-7). This splice signature was associated with poor metastasis-free survival (MFS) in hormone receptor-negative non-IBC (p=0.02), whereas it had no prognostic value in IBC patients. A PAM analysis of deregulated genes in IBC compared to non-IBC identified a 10-gene signature highly predictive of IBC phenotype and conferring a poor prognosis in non-IBC. The most up-regulated genes in IBC were 3 hemoglobin genes able to highly discriminate IBC from non IBC (p<10-4). In epithelial breast tumor cells, Hb protein expression was confirmed by immunohistochemistry.  Conclusions:  IBC has a specific spliced transcript profile that deserves further functional studies. Above all, IBC is characterized by hemoglobin genes overexpression, a fact that may lead to increased tumor progression. If confirmed, hemoglobins may serve as therapeutic targets.

overall_design: Training set of 33 IBC and 28 non IBC

first: F

last: Lerebours

first: D

last: Vacher

first: J

last: Guinebretiere

first: M

last: Le Cann

first: S

last: Rondeau

last: Caly

last: Gentien

last: Van Laere

last: Bertucci

first: P

first: I

last: Bieche

first: C

last: Callens


title: RNA-seq identifies a distinct response in macrophages infected with Mycobacterium tuberculosis for a serial time points.

city: Chongqing

first: Fake

last: Li

state: Chongqing

address: Changjiangzhilu 10 Yuzhong District

department: Clinical Laboratory Medicine

institute: Daping Hospital

summary:
Purpose: The goals of this study are to obtain the NGS-derived transcriptome profiling (RNA-seq) for THP-1 macrophages response to Mycobacterium tuberculosis (H37Rv and H37Ra)
Methods: mRNA and long noncoding RNA profiles of THP-1 macrophages infected with H37Rv and H37Ra for 1, 4, 12, 24, 48 hours were generated by deep sequencing, using Illumina Hiseq3000. The sequence reads that passed quality filters were first mapped to the latest UCSC transcript set using Bowtie2 (version 2.1.0). Then the gene expression level was estimated using RSEM (RNA-Seq by Expectation Maximization, v1.2.15), for lncRNA analysis, reads were mapped to lncRNA transcript set from LNCipedia.org. The sequence reads were normalized with TMM (trimmed mean of M-values) to identify differentially expressed genes (DEGs) using the edgeR package edgeR. qRT–PCR validation was performed using SYBR Green assays.
Results: Using an optimized data analysis workflow, we mapped about 20 million sequence reads per sample to the human genome (GRCh38/hg38) and identified 25,343 mRNA and 47877 long non-coding RNA transcripts.
Conclusions: Our study represents the detailed analysis of transcriptomes for THP-1 macrophages response to H37Rv and H37Ra, generated by RNA-seq technology.

overall_design: NGS-derived transcriptome profiling (RNA-seq) for THP-1 macrophages response to Mycobacterium tuberculosis H37Rv and H37Ra.

first: Jie

last: Luo

first: Huan

last: Xu

first: Ming

last: Chen


title: Long noncoding RNA expression in rituximab-sensitive and -resistant diffuse large B-cell lymphoma cell lines

status: Public on Jan 03 2021

city: Copenhagen SV

first: Shizuka

last: Uchida

email: heart.lncrna@gmail.com, suc@dcm.aau.dk

address: Frederikskaj 10B, 2. (building C)

department: Department of Clinical Medicine

institute: Aalborg University

summary: Diffuse large B-cell lymphoma is an aggressive tumor, killing approximately 200,000 people each year. Rituximab, a recombinant monoclonal CD20 antibody, added to the treatment scheme in 1997 improved both progression-free survival and general survival rate. Despite the existing treatment and relatively high cure rate, 30-40% of the patients develop a relapse or are originally resistant. Long noncoding RNAs (lncRNAs) have been implicated as regulators of numerous important cancer-related processes, including establishment and maintenance of anti-cancer drug resistance. However, their role in DLBCL resistance to the treatment is poorly understood. In this study, we analyzed gene expression in DLBCL cell lines, either sensitive or resistant to rituximab.

overall_design: We analyzed the transcription profiles of six DLBCL cell lines, which are either sensitive (n=3) or resistant (n=3) to rituximab, by RNA-seq .

first: Sakari

last: Kauppinen


title: H3K4me3/H3K27me3 bivalent chromatin function to fine-tune gene expression level

first: Alexander

last: Ruthenburg

state: Illinois

address: 920 E 58th St

department: Molecular Genetics and Cell Biology

institute: The University of Chicago

summary: Bivalency, the paradoxical juxtaposition of transcriptionally activating trimethylation of histone H3 lysine 4 (H3K4me3) and the repressive trimethylation of histone H3 lysine 27 (H3K27me3), has been proposed to decorate developmental genes poised for gene expression regulation. Here, we report development of sequential internally calibrated chromatin immunoprecipitation (Re-ICeChIP-seq), capable of measuring absolute quantities of nucleosomal patterns of histone marks in a genome-wide fashion, combined with in situ control of antibody specificity. Re-ICeChIP-seq of H3K4me3/H3K27me3 in mESC reveals that bivalent genes can be delineated into two classes, distinguished by the nucleosomal ratio of H3K4me3 to H3K27me3. Consistent with the canonical role of bivalency, H3K27me3-rich bivalent nucleosomes demarcate promoters of poorly expressed developmental genes that may be poised for activation or repression.  Yet our measurements reveal surprisingly widespread presence of bivalency at promoters of highly-expressed housekeeping genes, characterized by H3K4me3-rich bivalent nucleosomes. Moreover, the ratio of H3K4me3 to H3K27me3 at transcription start sites better correlates with gene expression than H3K4me3 or H3K27me3 alone, suggesting cooperation between opposing marks to fine-tune gene expression. Finally, we report that major H3K4 methyltransferases exhibit wide acceptance of various H3K27me3 substrates.

overall_design: Examination of H3K4me3/H3K27me3 bivalency in mouse Embryonic Stem Cells using Sequential ICeChIP-seq.

first: Adrian

last: Grzybowski

first: Zhonglei

first: Carolin

middle: C

last: Lechner

first: Takamitsu

last: Hattorie

first: Beat

last: Fierz

first: Shohei

last: Koide

middle: J


title: The transcriptomic changes induced by NREP downregulation in HepG2 cells

city: Boston

first: Hui

last: Pan

summary: To evaluate the global transcriptomic changes induced by Neuronal Regeneration Related Protein (NREP) downregulation,  we employed RNA-sequencing in HepG2 cells lacking NREP. Enriched pathway analyses of upregulated genes revealed pathways involved in cholesterol synthesis, fatty acid metabolism, NAFLD and PI3K-250 AKT signaling. In contrast, enriched downregulated genes included those for membrane trafficking, non-sense mediated decay, glucagon signaling, and cell-cycle. Differentially expressed genes included HMGCR (cholesterol synthesis) and TGFBR1 (TGF-β signaling and fibrosis).

overall_design: HepG2 cells were obtained from ATCC and were cultured in DMEM supplemented with 10% (v/v) fetal bovine serum and non-essential amino acids.  Cells were trypsinized at 70% of confluency and reverse transfection was performed using 30 nM of genome smart-pool non-target siRNA (scramble), or siNREP targeting 4 different sequences (Dpharmacon). At 72 hours post-transfection, total RNA  was extracted using standard Trizol reagent (Invitrogen)  and cleaned up using RNeasy mini kit columns (Qiagen). Polyadenylated RNAs were isolated using NEBNext Magnetic Oligo d(T)25 Beads and first-strand cDNA synthesis was performed using NEBNext RNA first-strand synthesis module (New England BioLabs). Directional second strand synthesis was performed using NEBNExt Ultra Directional second strand synthesis kit. The NEBNext DNA Library Prep Master Mix Set for Illumina was then used to prepare individually bar-coded next-generation sequencing expression libraries. Paired-end sequencing was performed on an Illumina HiSeq2500 sequencer.

first: Dario

last: De Jesus

first: Rohit

last: Kulkarni


title: Expression data for Npac depleted E14 mES cells

city: singapore

first: SU E

last: YU

state: SINGAPORE

address: NUS, MD7, level 4

department: Biochemistry

country: Singapore

institute: NUS

summary: Though chromatin modification makes great contribution to pluripotency maintenance in embryonic stem cell (ESC), it remains obscure for the mechanisms. Here, we show that one “reader” of histone H3 trimethyl lysine 36 (H3K36me3), Npac, is essential to maintain mouse ESC pluripotency. On one hand, depletion of Npac causes mESC differentiation by repressing genes associated with pluripotency while activating developmental related genes. On the other hand, depletion of Npac inhibits reprogramming efficiency. Further, ChIP-seq reveals that Npac co-localizes with H3K36me3 in the gene bodies of active genes in mouse ES cells. In addition, we find Npac interacts with P-TEFb, RNA Pol II Ser2 and Ser5, depletion of Npac results in the transcriptional elongation defect at pluripotency genes Nanog and Rif1. Thus, we propose that Npac activates pluripotency-associated gene expression by recruiting of P-TEFb and interacting with RNA Pol II Ser2 and Ser5, further promotes productive transcriptional elongation.

overall_design: Npac depleted (RNAi) E14 mES cells were used for RNA extraction and hybridization on Affymetrix microarrays. We compared these microarray samples with the corresponding wild type (control RNAi cells).

first: Su-e

last: Yu

first: Jia

first: Wu

last: Qiang

first: Herry

last: Yang


title: Npac_ChIPSeq

summary: Though chromatin modification makes great contribution to pluripotency maintenance in embryonic stem cell (ESC), it remains obscure for the mechanisms. Here, we show that one "reader" of histone H3 trimethyl lysine 36 (H3K36me3), Npac, is essential to maintain mouse ESC pluripotency. On one hand, depletion of Npac causes mESC differentiation by repressing genes associated with pluripotency while activating developmental-related genes. On the other hand, depletion of Npac inhibits reprogramming efficiency. Further, ChIP-seq reveals that Npac co-localizes with H3K36me3 in the gene bodies of active genes in mouse ES cells. In addition, we find Npac interacts with P-TEFb, RNA Pol II Ser2 and Ser5, depletion of Npac results in the transcriptional elongation defect at pluripotency genes Nanog and Rif1. Thus, we propose that Npac activates pluripotency-associated gene expression by recruiting of P-TEFb and interacting with RNA Pol II Ser2 and Ser5, further promotes productive transcriptional elongation.

overall_design: Examination of Npac-binding sites in mouse embryonic stem cells.


title: MTA1 interacts with primary RNAs to regulate expression and AS by protein dependent manner [ChIP]

city: wuhan

first: dong

last: chen

state: Hubei

address: GaoXin 2nd Road

institute: ablife

summary: MTA1 is known as its metastatic and invasive function in cancers and the core member of NuRD complex. But the mechanism of regulating gene expression by MTA1 is limited. Besides the interaction with chromosome, MTA1 may play important role at the transcriptional level. We performed co- immunoprecipitation (co-IP) on HCT116 cells and found numerous RNA binding proteins (RBPs), which functions as spliceosome and RNA transport. We then validated that MTA1 interacts with RBPs by RNA dependent manner. By performing the CLIP-seq of MTA1, ten thousands of peaks and thousands of genes were emerged. More detailed analysis and high level of intronic peaks reveal MTA1 prefers to bind pre-mRNAs and regulate the alternative splicing progression by binding the splice site. High overlapping between MTA1 binding and MTA1 regulated genes highlights the direct regulation of RNAs by MTA1 coupling with RBPs. LTK is one of the obvious examples regulated by MTA1. Together, these findings uncover a novel mechanism of MTA1 regulation in transcriptional level as RBPs, and suggest MTA1 regulates pre-mRNA splicing with other RBPs.

overall_design: ChIP-seq experiments performed on MTA1 protein. Input was performed with the same steps as control.Each was with two replicates.

first: Yi

last: Zhang

first: Haili

last: Qian


title: A longitudinal study defines circulating microRNAs as reliable biomarkers for disease prognosis and progression in ALS human patients

city: Rome

first: Julie

last: Martone

address: P.le Aldo Moro 5

country: Italy

institute: "Sapienza" University

summary: Background   Amyotrophic Lateral Sclerosis (ALS) is a fatal neurodegenerative disease associated with motor neuron degeneration, muscle atrophy and paralysis. To date, multiple panels of biomarkers have been described in ALS patients and murine models. Nevertheless, none of them has sufficient specificity and thus the molecular signature for ALS prognosis and progression remains to be fully elucidated. Circulating microRNAs (miRNAs) are highly stable molecules that are recently used as promising biomarkers for many types of human cancer and muscle disorders. Here we overcome this limitation through a longitudinal study, analyzing serum levels of circulating miRNAs in ALS patients during the progression of the pathology.  Method  We performed next-generation sequencing (NGS) analysis and absolute RT quantification of serum samples of 27 ALS patients and 11 healthy control; among them 13 ALS patients were studied every three months till the end of the disease.  Results  We demonstrated that miR-151a-3p, miR-206 and miR-199a-3p are significantly expressed at the mild, moderate and severe stages of ALS pathology, whereas the expression levels of miR-133a and miR-199a-5p remained low during the whole study and retain diagnostic significance in the moderate and severe stages (miR-133a) and in mild and terminal stages (miR-199a-5p) of the disease. Moreover, we analysed the miRNAs serum levels during the progression of the disease in each patient and we demonstrated that high levels of miR-206, miR-133a, miR-151a-5p, miR-151a-3p can predict a slower clinical decline of patient functionality suggesting that these miRNAs represent good potential prognostic markers for ALS disease.  Conclusion  This study is the first to perform a longitudinal absolute quantification of circulating miRNAs during ALS disease. We highlighted putative biomarkers for diagnosis, prognosis and disease stage identification of ALS patients providing cut-off threshold for most of the miRNAs analyzed. In addition, our results define a molecular signature of ALS phenotypes that could help to define appropriate enrollments of patients in clinical trials.

overall_design: We performed small RNA-Seq analysis of serum samples from 13 ALS patients and 6 healthy control

first: Gabriella

last: Dobrowolny

first: Elisa

last: Spelta

first: Irene

last: Casola

first: Antonio

last: Petrucci

first: Maurizio

last: Inghilleri

first: Stefano

last: Modigliani

first: Alessio

last: Colantoni

first: Mariangela

last: Morlando

first: Giulia

last: Bisogni

first: Mario

last: Sabatelli

first: Adriano

last: Chiò

first: Andrea

last: Calvo

first: Giuseppe

last: Fuda

last: Bozzoni

last: Musarò


title: Microarray expression data for iron and zinc stresses in maize

city: new delhi

first: M G

last: MALLIKARJUNA

address: Indian Council of Agricultural Research

department: Division of Genetics

country: India

institute: ICAR-Indian Agricultural Research Institute

summary:
Elucidation of molecular basis of Iron and zinc homeostasis is crucial to breed  iron and zinc use efficient and iron -zinc biofortified maize cultivars. The present investigation was framed to decipher the global expression snapshot maize seedlings in response to iron and zinc starvtion. Genome-wide transcriptome assay was performed with  ~18,000 transcripts distributed across the maize genome,  in maize seedlings after exposing the seedlings to three Fe and Zn stress treatments (+Fe–Zn, –Fe+Zn, –Fe–Zn) along with control (+Fe+Zn).
Microarrays were used to study the global gene expression pattern iron and zinc starvation responsive genes in maize.

overall_design: Experiment was designed as a two-factor experiment with the four possible treatments among iron and zinc combination viz., 1) +Fe+Zn, 2) +Fe–Zn, 3) –Fe+Zn and 4) –Fe–Zn.  Three biological replications were included in each treatment.

first: Mallikarjuna

last: Mallana Gowdra

first: Nepolean

last: Thirunavukkarasu

first: H

middle: S

last: Gupta


title: Gene expression profile of bladder cancer cell lines treated with Mitomycin C

status: Public on Jan 02 2021

city: Rozzano (MI)

first: Daniele

last: Braga

address: Via Manzoni 56

institute: Humanitas Clinical and Research Center

summary: Mitomycin C (MMC) is the gold standard treatment for non-muscle invasive bladder cancer (NMIBC). We aimed to evaluate in bladder cancer cell lines (T24, 5637, TCC-SUP and CLS-439) the transcriptomic response to MMC treatment. We used Gene Set Enrichment Analysis (GSEA) to identify biological processes and pathways modulated by MMC treatment.

overall_design: mRNA profiles of T24, 5637, TCC-SUP and CLS-439 bladder cancer cell lines treated or not with Mitomicyn C (3 biological replicates for each condition)

first: Bianca

last: Oresta

first: Maria

last: Rescigno


title: Effects of NGF and BDNF on chondrocytes

first: Marta

last: Barba

address: L.go F. Vito 1

institute: Università Cattolica del Sacro Cuore

summary: the objective of this study was to analyze the role of NGF and BDNF in the inflammatory process of OA and their effects on chondrogenesis, chondrocyte differentiation, cartilage degeneration and pain

overall_design: 3 condrocyte cell culture were treated with NGF or BDNF, alternatively


title: Def6 suppresses osteoblastic differentiation and bone formation through endogenous type I interferon-mediated feedback inhibition

city: NEW YORK

first: Kazuki

last: Inoue

state: New York

address: 535 E70TH STREET, S building 8th floor

institute: HOSPITAL FOR SPECIAL SURGERY

summary: Def6 suppresses osteoblast differentiation and mineralization both in vitro and in vivo. Def6 knockout (KO) mice exhibit osteoporotic phenotype with enhanced osteoclast formation. Osteoblast differentiation and bone formation are elevated as well in Def6 KO mice, indicating a high bone turnover rate that leads to bone loss in Def6 KO mice. Thus, lack of Def6 leads towards unbalanced activities between osteoclastic resorption and osteoblast mediated bone formation and disrupts normal bone remodeling. Def6 suppresses osteoblast differentiation via endogenous type I IFN-mediated feedback inhibition. These findings reveal that Def6 is a novel bone remodeling regulator that controls both osteoclast and osteoblast differentiation to maintain bone remodeling.

overall_design: Osteoblastic cells were isolated from the calvarial bone of newborn (0-3d) mice. mRNA profiles of calvarila osteoblsts(day0 and day12) from wild type (WT) and Def6-/- mice were generated by deep sequencing using Illumina Hiseq4000.

first: Baohong

last: Zhao


title: Effects of Sphingosine 1-Phosphate on Gene Expression in C3H10T1/2 Cells via RNA-seq

first: David

last: Manning

address: 3620 Hamilton Walk

institute: University of Pennsylvania

summary: RNA sequencing was used to evaluate genes regulated in C3H10T1/2 cells by the G protein-coupled receptor agonist sphingosine 1-phosphate.

overall_design: Cells were treated with an optimized concentration (5 micromolar) of sphingosine 1-phosphate for 24 hours, at which time RNA was isolated and sequenced.

first: Andrey

last: Parshin

middle: R


title: Comparative transcriptomic analyses of high and low oleic acid content sunflower (Helianthus annuus L.) seed development

status: Public on Jan 01 2021

city: Harbin

first: Jian

last: Wang

address: 600 Changjiang Road

institute: Northeast Agricultural University

summary: RNA sequencing in sunflower for detect mRNA expression of developmental seeds. The two cultivars (86-1, L-1-OL-1) with significant difference in oleic acid content in two different seed developmental stages (oleic acid accumulated rapidly at 17 DAF, and kept relatively stable at 27 DAF) for transcriptome sequencing

overall_design: Transcriptome sequencing of the seeds at 17 DAF and 27 DAF in high and low oleic acid content sunflower were performed, and the gene expression profiles were compared.

first: Fei

last: Zhou

first: Yan

last: Liu

first: Xutang

last: Huang


title: RNAseq Comparison of WT and CD40LΔ5 mice

city: Belle Mead

first: Bitha

last: Narayanan

state: New Jersey

address: 241 Berkley Ave

institute: Rutgers

summary: CD40L expression on T helper cells is quintessential for initiation and development of germinal centers resulting in the subsequent generation of high affinity class switched antibodies. Post transcriptional regulation of CD40L has been implicated in orchestrating the activation dependent expression of this protein. Our lab has previously shown that the deletion of a PTBP1 binding stability region in the 3’ UTR of the CD40L mRNA, results in the in vitro decrease in half-life of the CD40L transcript and subsequently the surface expression.   Here we describe a mouse model generated with a 196 bp deletion of the stability sequence that shows decreased humoral response in response to immunogen challenge in vivo. We further strived to evaluate the differences in the immunophenotypic distribution and organization in the germinal centers of wild type and CD40LΔ5 mice. Based on our results we conclude that activation mediated post transcriptional stabilization of the CD40L mRNA and the consequent regulation of surface expression ensures the timely availability of CD40L on Tfh cells to signal activated B cells effectively producing a robust humoral response.

overall_design: Total B cells were extracted from WT and  CD40LΔ5 mice mouse spleens and RNA was extracted and sequenced

first: Diego

last: Prado de Maio

first: Lori

last: Covey


title: CRISPR induced exon skipping of beta-catenin reveals unexpected tumorigenic mutants driving distinct subtypes of liver cancer

city: Cold Spring Harbor

first: Semir

last: Beyaz

state: NY

address: 1 Bungtown road

institute: Cold Spring Harbor Laboratory

summary: we induce exon skipping and generate a gain-of-function of an oncogene, β-catenin, using CRISPR/Cas9 in mouse liver cells. Specifically, a single guide RNA (sgRNA) targeting exon 3 of β-catenin induces exon skipping and gain-of-function of β-catenin in mouse hepatocytes. In synergy with YAPS127A, exon skipped hepatocytes gain tumorigenic ability and are thus enriched via tumor formation. Surprisingly, characterization of the exon-skipped tumors reveals two distinct subtypes with different histological features. Remarkably, ectopic expression of two representative exon-skipped β-catenin transcripts together with YAPS127A phenocopies the two histologically distinct subtypes of liver cancer. Finally, the transcriptome sequencing analysis reveal two subtypes of liver cancer and most importantly, one subtype of the exon-skipped tumor shows features of hepatoblastoma, while the other does not. This exon skipping model reveals CRISPR/Cas9 can lead to exon-skipped transcripts with in frame coding and gain-of-functions.

overall_design: Transcriptome and histology to dinstinguish two subtypes of liver cancer driven by exon-skipped isoform of beta-catenin

first: Haiwei

last: Mou

first: Deniz

last: Ozata

first: Ying

last: Jin


title: RNA sequencing of SUNE1 cells transfected with WIPI-1 shRNA

city: Guangzhou

first: Yin

state: Guangdong

address: 651 Dongfeng Road East

department: State Key Laboratory of Oncology in South China

institute: Sun Yat-sen University Cancer Center

summary: To investigate the downstream genes of WIPI-1 comprehensively, we conducted RNA sequencing after knocking down WIPI-1 in SUNE1 cells.

overall_design: High-throughput RNA sequencing analysis was performed in the human nasopharyngeal carcinoma cell line SUNE1 after transfection with control shRNA or WIPI-1 shRNA.

first: Jun

last: Ma


title: Expression data from mouse Treg

city: La Jolla

first: Jeeho

last: Lee

state: CA

address: 9420 Athena Circle

institute: La Jolla Institute for Immunology

summary:
Foxp3+ regulatory T cells play a role in suppressing excessive inflammatory
We used microarrays to investigate the global gene expression regulated by CYLD in Foxp3+ Treg cells.

overall_design: Foxp3-restricted CYLD knockout mice were generated by crossing floxed CYLD mice with Foxp3-YFP-cre mice. YFP+ Treg cells were facs-sorted from lymph nodes (linguinal, axillary, brancial) and spleen.

first: J

first: Y

first: M

last: Croft


title: MTA1 interacts with primary RNAs to regulate expression and AS by protein dependent manner [RNA]

first: dong

last: chen

overall_design: RNA-seq experiments performed on siMTA1 and WT samples from HCT116 cells. Each was performed with three replicates.

first: Yi

last: Zhang

first: Haili

last: Qian


title: Gene expression data from C57BL/6 mouse hepatocyte spheroids on days 1, 7 and 14 post spheroid formation.

city: Chapel Hill

first: Merrie

last: Mosedale

state: North Carolina

address: 301 Pharmacy Lane, Kerr Hall CB#7569

department: Division of Pharmacotherapy and Experimental Therapeutics

institute: UNC Eshelman School of Pharmacy

summary:
Hepatocytes were isolated from C57BL6/J mice and cryopreserved. Spheroids were generated from cryopreserved hepatocytes by spontaneous self-aggregation in ultra-low attachment 96-well plates.
Microarray profiling of the entire transcriptome was performed on spheroids cultured for 1, 7, and 14 days post spheroid formation from N=2 spheriod preparations from each sex.
Only 287 of 13,081 total mRNAs detected (2.2%) were differentially expressed in spheroids over time.

overall_design: 12 spheroid samples were analyzed representing N=2 per sex per culture day (sex_donor#_type_day as indicated in the sample titles)


title: RNA sequencing of MSCs from R-treated group and matched control

city: Tianjin

first: Quan

last: Gu

address: 288 Nanjing Road

institute: State Key Laboratory of Experimental Hematology, Institute of Hematology & Blood Diseases Hospital

summary: We performed RNA-seq of MSCs  from  R-treated group and matched control

overall_design: Examination of gene expression profiles aGVHD_R and aGVHD_vehicle sample

first: Yan

last: Lin

first: Hui

last: Cheng

first: Tao


title: Epidermal Growth Factor Receptor Maintains Cardiac Contractility Via Modulation of Protein Phosphatase 2A B' Regulatory Subunit PR72 Expression

city: Philadelphia

first: yinfei

last: tan

address: 333 cottman ave

department: Genomic Core

institute: Fox Chase Cancer Center

summary: To determine the differences of gene expression pattern in 7 and 9 weeks old cardiac EGFR KO mice versus control

first: Douglas

last: Tilley


title: Genomic analysis of 5-FU treatment on colon cancer cells

city: New Haven

last: Lu

address: 10 Amistad St.

department: Yale Stem Cell Center

institute: Yale University

summary: This dataset contains RNAseq experiments of in vitro cultured MC38 colon cancer cell line treated with PBS or 5-FU

overall_design: MC38 cells were treated with PBS or 5-FU (1mM) or 24 hours.

first: Jingru

last: Tian


title: Transcriptomic analysis of young roots of spruce tianshan treated with 1mMDHAP (3,4 dihydroxyacetophenone)

city: Ningbo

first: Xie

last: Xiaoting

state: Zhejiang

address: 1 Qianhu South Road

department: Biotechnology and chemical Engineering

institute: NingboTech University

summary: In past studies the hypothesis of "self-toxicity of natural regeneration barriers of Spruce tianshan" were proposed, and verified that 3, 4-dihydroxyacetophenone (DHAP) contained in litter of Spruce Tianshan was the direct cause of population regeneration barriers.The molecular basis of DHAP-induced autotoxicity was explored through transcriptomic analysis of young roots of spruce tianshan treated with DHAP (3,4 dihydroxyacetophenone).

overall_design: The overall experiment included the construction of four libraries: 19E15R-79, 19E15R-80, 19E15R-81, 19E15R-82;12 samples and biological replicates were analyzed: (1) Water treated roots: W_root-1, W_root-2, W_root-3;(2) Suppressed seedling roots were grown with high concentrations of DHAP: HD_Iroot-1, HD_Iroot-2, HD_Iroot -3 (3) Roots of high seedlings treated with high concentrations of DHAP: HD_Hroot-1 HD_Hroot-2 HD_Hroot-3 (4) Roots of dwarf seedlings treated with high concentration DHAP: HD_Sroot-1 HD_Sroot-2 HD_Sroot-3

first: Xiao

last: Ruan

first: Li

last: Yang

first: Qiang

last: Wang

first: Yingxian

last: Zhao

first: Feng

last: Wei


title: Identification of LINC00152 target genes in comparison in A172 and U87 glioblastoma cells

city: Leipzig

first: Stefanie

last: Binder

address: Perlickstr. 1

department: Diagnostics

institute: Fraunhofer Institute for Cell Therapy and Immunology

summary: The long noncoding RNA LINC00152 shows ubiquitous expression and is often upregulated in tumor entities compared to healthy tissues. LINC00152 promotes malignant progression in the glioblastoma cell line U87. Here, LINC00152 knockdown leads to a reduction of migration and invasion of tumor cells. However, LINC00152 seems to have an opposite effect in another glioblastoma cell line A172. For this reason, the transcriptional patterns after LINC00152 knockdown in both cell lines (U87 and A172) were compared to identify the differences.

overall_design: Gene expression profiles (all protein-coding- and several important non-coding transcripts) after LINC00152 knockdown in the human glioblastoma cell lines A172 and U87 were measured 40 hours after transfection with either a negative control siRNA and an siRNA to LINC00152 (exon1). Three independent biological experiments for A172 and four independent biological experiments for U87 were performed for each siRNA approach, yielding 14 approaches in total.

first: Ivonne

last: Zipfel

first: Kristin

last: Reiche

first: Karolin

last: Wiedemann

first: Friedemann

last: Horn

first: Maik

last: Friedrich


title: Liver-specific loss of the three TTP family proteins results in the development of hepatocellular carcinoma

city: Baton Rouge

first: Sonika

last: Patial

address: Baton Rouge, LA 70803

institute: Louisiana State University

summary: The objective of this project is to identify the differential gene expression changes between WT and liver-specific knockout of the three TTP family proteins post HCC development

overall_design: 8 samples


title: XIST modulates mammary stem cell homeostasis and tumor fate [RNA-seq]

city: Paris

first: Laia

last: Richart

address: 13 Rue Pierre et Marie Curie

department: Developmental Biology

institute: Institut Curie

summary: Disruption of XIST expression in mammary epithelial cells leads to chromatin changes on the inactive X chromosome, transcriptional reactivation of X-linked genes, and defective luminal differentiation.

overall_design:
Cells from both luminal (ML) and mammary stem cell (MaSC) compartments were isolated from wild-type (WT) and XIST-KO HMLE (Human Mammary Epithelial cells) by FACS sorting based on their positivity for the cell surface antigen ESA (Epithelial Specific Antigen) (ML: ESA+; MaSC: ESA-). Two replicates were generated per compartment and genotype. Total RNA was isolated and sequenced to perform gene expression and allele-specific analyses.
Cancer Stem Cells (CSCs) from WT and XIST-KO HMLER were isolated by FACS according to their positivity for CD44 and CD24. Total RNA was isolated and sequenced to perform allele-specific gene expression analyses.

first: L

first: M

middle: L

last: Picod

first: E

last: Charafe-Jauffret

last: Heard

first: R

last: Margueron

first: C

last: Ginestier


title: Epigenomes of clonal palms with different fruit phenotypes.

city: Bandar Baru Bangi

first: Norashikin

last: Sarpan

state: Selangor

address: 6 Persiaran Institusi

department: Advanced Biotechnology and Breeding Centre

country: Malaysia

institute: Malaysian Palm Oil Board

summary: Leaf tissue was sampled from normal and mantled clonal palms producing normal and mantled fruits respectively. ChIP-Seq libraries for histone modifications H3K4me3 and H3K27me3 were generated and sequenced on Illumina platform. Genomic regions associated with specific histone marks were identified.

overall_design: Leaf tissue used in this study was sampled from clonal palms derived from a single ortet (mother palm). These 10 clonal palms comprised 5 normal and 5 mantled phenotype palms. Leaf tissues of frond 0 were sampled and used for isolation of chromatin. Chromatin was sheared and a portion of sheared chromatin was set aside for ChIP assay. Sheared chromatin was then immunoprecipitated with H3K4me3- and H3K27me3-mouse monoclonal antibodies (ChIP grade). ChIP-Seq libraries were prepared using DNA from non-immunoprecipitated and ChIP assay. Paired-end sequencing was conducted. Sequencing reads were analysed to identify regions in oil palm genome associated with H3K4me3 and H3K27me3 histone marks.

first: Tatiana

middle: V

last: Tatarinova

first: Eng-Ti

last: Low

first: Meilina

last: Ong-Abdullah

first: Sapian

last: Suhayu

first: Siew-Eng

last: Ooi


title: CHK1 Inhibitor Blocks Phosphorylation of FAM122A and Promotes Replication Stress

city: Boston

first: Huy

last: Nguyen

state: Massachusetts

address: 450 Brookline Ave

department: Radiation Oncology

institute: Dana-Farber Cancer Institute

summary: While effective anti-cancer drugs targeting the CHK1 kinase are advancing in the clinic, drug resistance is rapidly emerging.  Here, we demonstrate that CRISPR-mediated knockout of the little-known gene FAM122A confers cellular resistance to CHK1 inhibitors and cross-resistance to ATR inhibitors.  Knockout of FAM122A results in activation of PP2A-B55α, a phosphatase which dephosphorylates the WEE1 protein and rescues WEE1 from Ubiquitin-mediated degradation.  The resulting increase in WEE1 protein expression reduces replication stress, activates the G2/M checkpoint, and confers cellular resistance to CHK1 inhibitors.  Interestingly, in tumor cells with oncogene-driven replication stress, CHK1 can directly phosphorylate FAM122A, leading to activation of the PP2A-B55α phosphatase and increased WEE1 expression.  A combination of a CHK1 inhibitor plus a WEE1 inhibitor can overcome CHK1 inhibitor resistance of these tumor cells, thereby enhancing anti-cancer activity.  The FAM122A expression level in a tumor cell can serve as a useful biomarker for predicting CHK1 inhibitor sensitivity or resistance.

overall_design: Prexasertib-resistant cells were generated by first culturing with graded concentrations of prexasertib for one week and surviving cells in the drug concentrations of IC90 or IC80 were harvested. These cells were then cultured in the IC50 drug concentrations for 1-2 weeks and were gradually adapted to higher doses of drug for almost 2-3 months. The resistant cells were then maintained in a medium without the drug. The experiment was performed in duplicates. Total RNAs were extracted and sequenced on an Illumina NovaSeq 6000. RNA-sequence data were analyzed using the VIPER snakemake pipeline. Differential gene expression analysis was performed by DESeq2 and limma, comparing the mRNA expression levels of prexasertib-resistant cells to those of the parent cells.

first: Feng

last: Li

first: David

last: Kozono

first: Peter

last: Deraska

first: Timothy

last: Branigan

first: Connor

last: Dunn

first: Xiao-Feng

last: Zheng

first: Kalindi

last: Parmar

first: James

last: DeCaprio

first: Geoffrey

last: Shapiro

first: Dipanjan

last: Chowdhury

first: Alan

last: D’Andrea


title: XIST modulates mammary stem cell homeostasis and tumor fate [WGS]

first: Laia

last: Richart

overall_design: Genomic DNA was isolated from HMLE cells and sequenced to identify heterozygous SNPs on the X chromosome in order to evaluate the transcriptional and epigenetic status of the X chromosome upon XIST deletion.

first: L

first: M

last: Picod

first: E

last: Charafe-Jauffret

last: Heard

first: R

last: Margueron

first: C

last: Ginestier


title: XIST modulates mammary stem cell homeostasis and tumor fate

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

overall_design: Refer to individual Series


title: The cannabinoid agonist WIN55,212-2 (WIN) suppresses the inflammation-associated transcriptional response of astrocytes to interleukin 1 beta

first: Hai-Ri

last: Li

address: 9500 Gilman Dr.

department: Medicine

institute: University of California, San Diego

summary: Accumulating evidence suggest that the endocannabinoid system is an attractive target to attenuate inflammatory responses that are implicated in neurodegeneration. Alterations in astrocytic functions play a crucial role in neuroinflammation as a consequence of the loss of their neuroprotective role or the gain of their toxic inflammatory properties. In this study, we explore the possible immunosuppressive action of the cannabinoid receptor agonist WIN55,212-2 using an in vitro model of primary human astrocytes that are activated by the pro-inflammatory cytokine interleukin 1 beta (IL1B). Genome-wide transcriptomic analysis using RNA-seq revealed that the pretreatment of astrocytic cultures with WIN55, 212-2 prevents the transcriptional activation of pro-inflammatory genes induced by IL1B. We report the immunosuppressive function of WIN55,212-2 in replicates RNA samples that were extracted from human astrocyte cultures established from one donor.

overall_design: primary astrocytes cultures were collected from two biological replicates and RNA samples were analyzed by RNA-seq for each of 4 conditions (Vehicle, IL1B 6hr, WIN 24hr, WIN 24hr + IL1B 6hr)

first: Francesca

last: Telese


title: Alteration of keratinocyte gene expression as a result of Flg deficiency

city: Heidelberg

first: Axel

last: Roers

address: Im Neuenheimer Feld 305

department: Institute of Immunology

institute: Heidelberg University Hospital

summary: Defects of filaggrin (FLG) compromise epidermal barrier function and represent an important known genetic risk factor for atopic dermatitis (AD), but also for systemic atopy, including allergic sensitization and asthma. A loss of epidermal barrier integrity can provide a significant stress for the keratinocytes in the skin, either due to the increased moisture evaporation from the skin or increased penetration of the antigens and microflora into the lower epidermal layers. To understand the effect of this loss of barrier integrity on keratinocyte function our aim is to analyze the alterations in the transcriptional profile of keratinocytes from Flg-deficient mice.

overall_design: CD45- CD49f+ cells were were isolated from skin cell suspensions by FACS. Total RNA was isolated using the RNeasy Micro Kit+ (Qiagen). mRNA libraries were prepared using a SMART protocol and subjected to deep sequencing on an Illumina Nextseq 500.

first: Lina

last: Muhandes


title: Cholesterol-lowering Decreased mTOR Complex 2 Signaling and Enhanced Antitumor Immunity

city: LA

first: Sungyong

last: You

address: Beverly Blvd 8400

department: Surgery

institute: Cedars-Sinai Medical Center

summary: In an exploratory human study, RNAseq was performed to quantify immune cells present in prostate cancer. Two patients were examined, and both showed increased CD8+ lymphocytes and M1 macrophages scores following cholesterol-lowering intervention with the combination of ezetimibe and simvastatin.

overall_design: Two patients were examined and matched pre-treatment prostate biopsy and post-treatment prostatectomy tissue showed that cholesterol-lowering therapy increased immune infiltration in the tumor

first: Hyung

last: Kim


title: RNA sequencing of cell populations isolated from one GW14.5 human fetal cortex

city: Shanghai

first: Minyi

last: Ou

address: 393 Middle Huaxia Road, Pudong, Shanghai, 201210

institute: ShanghaiTech University

summary: To understand prenatal cortex on transcriptional level, we profiled the transcriptomes of ventricular radial glial cells (vRGs), outer RGs (oRGs), intermediate progenitors (IPs) and neurons sorted from one GW14.5 prefrontal cortex.

overall_design: Prefrontal cortex tissues were processed by mechanical cutting and trypsin digestion to obtain single-cell suspention. Cells were fixed and incubated with primary antibodies: anti-CRYAB (Abcam, ab13496), anti-TBR2 (R&D systems, AF6166) , anti-HOPX (Sigma, HPA030180), and anti-SATB2 (Abcam, ab69995), followed by incubation of secondary antibodies conjugated with Alexa-488 or Alexa-555. Neural cells sorting used acknowledged marker: CRYAB+TBR2- cells as vRGs; HOPX+CRYAB- cells as oRGs; TBR2+ cells as IPs; SATB2+TBR2- cells as neurons. Total RNA of each cell population was extracted by miRNeasy FFPE Kit (Qiagen) following the manufacture’s protocol.  Fusion transcripts were recognized by SOAPfuse software. Differentially expressed genes among each cell type were identified using the R package Ballgown

first: Min-Yi

first: Xiang-Chun

last: Ju

first: Qi

last: Xiao


title: CMV-CTLs scVDJ-RNAseq

city: Saitama

first: Hideki

last: Nakasone

address: 1-847, Amanuma-cho, Omiya-ku

department: Hematology

institute: Jichi Medical University Saitama Medical Center

summary: We conducted immune- and RNA-sequencing of HLA-A24-restricted CMVpp65-specific CTLs to better understand the immune reconstitution of CMV-CTLs after allo-HCT. To the best of our knowledge, this is the first report on the features of TCRβ-CDR3, diversity, and GEP of HLA-A24 CMV-CTLs according to the CMV-reactivation pattern among recipients after allo-HCT. In addition, we further sought to demonstrate homogeneity or heterogeneity according to individual CTL clones using single-cell RNA-sequencing technology.

overall_design: Compare GEP in CMV-CTLs according to CMV-CTL clones within each recipient.


title: XIST modulates mammary stem cell homeostasis and tumor fate [Cut&Run]

first: Laia

overall_design: Cells from both luminal (ML) and mammary stem cell (MaSC) compartments were isolated from wild-type and XIST-KO HMLE (Human Mammary Epithelial cells) by FACS sorting based on their positivity for the cell surface antigen EpCAM (ESA) (ML: ESA+; MaSC: ESA-). Two replicates were generated per compartment and genotype. Cells were processed for Cut&Run to map the genome-wide distribution of a panel of histone modifications.


title: Prognostic biomarkers of antipsychotic-induced weight gain

first: Olivia

last: Osborn

address: 9500 Gilman Drive

institute: UCSD

summary: Antipsychotic drugs (APs) are used to treat psychiatric disorders but also have the prominent side effect  of weight gain resulting in a higher incidence of metabolic disease in this patient group.   While the majority of patients gain significant weight in response to APs some patients are relatively resistant to these effects.  APs such as clozapine and olanzapine are deemed to be highly efficacious at treating psychiatric conditions yet they have some of the highest weight gain liabilities.  Therefore, there is a need to determine which patients are less susceptible to the metabolic side effects of APs and would be good candidates for drugs such as olanzapine, and conversely, identifying patients that should be prescribed alternative APs with less weight gain liabilities.

overall_design: The C57BL/6 female mice (stock #000664) were purchased from Jackson Laboratory at 9 weeks of age. Blood was collected, RNA was extracted, and stored at -80°C.  The mice were fed normal chow diet until 10 weeks of age, when the mice were transitioned to a high fat diet (HFD) (45% kcal from fat) for  3 days to acclimatize to the caloric density.  Mice were then fed a formulation of 45% HFD with olanzapine incorporated into HFD (Research Diets, Inc., D09092903). All mice were singly housed throughout the study, and food intake was measured daily, and body weight was measured every other day for 14 days. At the end of the study, mice were anesthetized and sacrificed. Blood was collected and processed for RNA collection.

first: Rizaldy

last: Zapata

first: Besma

last: Chaudry


title: microRNA-101a enhances trabecular bone accrual in male mice

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

summary: High-throughput microRNA sequencing was used to identify microRNAs (miRs) that regulate osteoblast differentiation. We establish that miR-101a, which targets the epigenetic enzyme Ezh2, is up-regulated in differentiated MC3T3 cells and robustly expressed in mouse calvaria. Our previous studies showed that loss of Ezh2 function enhances osteogenesis and bone formation. Thus, we tested the attractive mechanistic model that increased miR-101s expression may suppress Ezh2 to stimulate the osteogenic process. Transient miR-101a over-expression suppresses Ezh2 levels and reduces tri-methylation on lysine 27 of histone 3 (H3K27me3), a heterochromatic mark catalyzed by Ezh2. Importantly, over-expression of miR-101a stimulates osteogenic differentiation of MC3T3 cells as quantified by alizarin red staining. Therefore, we examined skeletal phenotypes of mice transgenic for miR-101a under the control of Col1a1promoer and doxycycline administration. Experimental controls and mir-101 over-expressing mice were exposed to doxycycline during pregnancy and postnatal stages (phenotyping at 8 weeks) to maximize penetrance of skeletal phenotypes. Our analyses revealed that miR-101a over-expressing male mice are bigger as measured by total body weight and exhibit an increase in long bone length. These mice exhibit significant increases in trabecular bone volume fraction, trabecular number, trabecular thickness, as well as a reduction in trabecular spacing based on microCT analysis. Histomorphometric examination established a significant reduction in osteoid volume to bone volume and osteoid surface to bone surface. These findings suggest that the enhancement in trabecular bone may be due to accelerated bone mineralization in miR-101a over-expressing male mice. Remarkably, while female mice exhibit a significant increase in bone length, no significant changes were noted by microCT (trabecular bone parameters) and histomorphometry (osteoid parameters). We conclude that miR-101a upregulation during osteoblast maturation enhances trabecular bone parameters in male mice. Thus, miR-101 and Ezh2 may form part of an intricate epigenetic feed-forward mechanisms to regulate bone formation.

overall_design: MC3T3 E1 sc4 murine calvarial osteoblasts were purchased from American Type Culture Collection and maintained in α-minimal essential medium without ascorbic acid (Gibco) containing 10% fetal bovine serum (Atlanta Biologicals), 100 units/ml penicillin (Gibco), and 100 μg/ml streptomycin (Gibco) in cell culture incubators (37oC and 5% CO2). Cells were plated at 10,000 cells/cm2 in maintenance medium. Osteogenic differentiation was induced the next day by the addition of 50μg/ml ascorbic acid (Sigma) and 4mM β-glycerol phosphate (Sigma). Osteogenic medium was replaced every two to three days. RNA was harvested in QIAzol and stored at -80oC until further processing. Parietal and frontal bones (calvaria) were harvested from 2-3 days old C57/B6 Prrx1-Cre+ female mice, washed in cold phosphate buffered saline (PBS), incubated in collagenase digestion medium (αMEM, 2mg/ml Collagenase type II, and 0.005% trypsin) for 20 minutes at 37oC, washed in PBS, snap-frozen in liquid nitrogen, and stored at -80oC until further processing. Before isolation, calvaria (2 to 3 day old mice) were homogenized for 30 seconds in ice-cold QIAzol using the Ultra Turrax T25 tissue homogenizer (IKA). Total RNA from MC3T3 cells and calvaria was isolated using the Direct-zol™ RNA kit (Zymo Research). RNA was quantified using the NanoDrop 2000 spectrophotometer (Thermo Fischer Scientific). For MC3T3 samples, three biological samples were pooled (equal amounts of RNA) for each time point assessed (days 0, 6, 10, 17, and 24).

first: Amel

last: Dudakovic

first: Andre

last: van Wijnen