title: ADP-ribosylation of STAT1α by PARP-1  is Required for IFNγ-stimulated Transcriptional Responses in  Macrophages [iBMDM_Stat1_mutant_RNAseq]

city: Dallas

first: W. Lee

last: Kraus

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

summary: A key determinant of the pro-inflammatory responses in macrophages is the Signal Transducers and Activators of Transcription (STAT) family member, STAT1α.  STAT1α activation by interferon-gamma (IFNγ) leads to induction of a transcriptional program that is coordinated in a large part by post-translational modifications such as phosphorylation.  Poly(ADP-ribose) Polymerases (PARPs), which include PARP-1, catalyze the addition of ADP-ribose moieties (ADP-ribosylation) to target proteins and modulate their function.  We found that PARP-1 mediates IFNγ-stimulated transcription by regulating genome-wide binding of STAT1α and its IFNγ-dependent phosphorylation.  We identified STAT1α as a target of PARP-1 and found sites of ADP-ribosylation on its DNA-binding (DBD) and Transcription Activation (TA) domains.  Surprisingly, ADP-ribosylation on the DBD and TA domains had distinct functional consequences on STAT1α transcriptional activity.  Moreover, loss of ADP-ribosylation on either site led to diminished pro-inflammatory responses.  These results suggest that PARP-1-driven ADP-ribosylation of STAT1α is a critical mediator of inflammation in macrophages.

overall_design:
RNA-seq was perfomed in immortalized bone marrow derived macrophages (iBMDM) expressing wildtype or ADP-ribosylation deficient mutants.
Please note that each processed data file was generated from both replicates and is linked to the corresponding rep1 sample records.

first: Gupte

last: Rebecca

first: Nandu

last: Tulip

first: Kraus

last: W Lee


title: Zur-dependent zinc starvation response in Vibrio cholerae N16961

status: Public on May 06 2021

city: Ithaca

first: Tobias

last: Doerr

state: NY

address: 525 N Campus Rd

department: Microbiology

country: USA

institute: Cornell University

type: Expression profiling by high throughput sequencing

summary: Zur is a transcription factor that represses zinc starvation response genes under zinc-rich conditions. Our goal was to identify candidate Zur-regulated genes by looking for transcripts significantly upregulated in the absence of Zur.

sample_organism: Vibrio cholerae O1 biovar El Tor str. N16961

overall_design: Differential gene expression in Δzur relative to wild-type N16961

first: Shannon

middle: G

last: Murphy


title: Gene expression in Aspergillus nidulans on multiple nitrogen sources

city: Headington

first: Damien

last: Downes

state: Oxfordshire

address: John Radcliffe Hospital

department: MRC Weatherall Institute of Medicine

country: United Kingdom

institute: The University of Oxford

summary: Stranded RNA-seq of wild type Aspergillus nidulans during growth on a range of nitrogn sources

overall_design: Stranded RNA-seq was carried out in triplicate from wild type Aspergillus nidulans (MH1; biA1) grown in liquid culture with glucose as the main carbon source and on of 10mM ammonium, glutamine or alanine as the nitrogen source.

middle: J

first: Richard

middle: B

last: Todd


title: Molecular Logic of Cellular Diversification in the Mouse Cerebral Cortex (scATACseq)

city: Cambridge

first: Paola

last: Arlotta

state: MA

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

institute: Harvard University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The mammalian cerebral cortex has an unparalleled diversity of cell types, which are generated during development through a series of temporally orchestrated events that are under tight evolutionary constraint and are critical for proper cortical assembly and function. However, the molecular logic that governs the establishment and organization of cortical cell types remains elusive, largely due to the large number of cell classes undergoing dynamic cell-state transitions over extended developmental timelines. Here, we have generated a comprehensive single-cell RNA-seq and single-cell ATAC-seq atlas of the developing mouse neocortex, sampled every day throughout embryonic corticogenesis and at early postnatal ages, complemented with a spatial transcriptomics time-course. We computationally reconstruct developmental trajectories across the diversity of cortical cell classes, and infer their spatial organization and the gene regulatory programs that accompany their lineage bifurcation decisions and differentiation trajectories. Finally, we demonstrate how this developmental map pinpoints the origin of lineage-specific developmental abnormalities linked to aberrant corticogenesis in mutant animals. The data provides a global picture of the regulatory mechanisms governing cellular diversification in the neocortex.

overall_design: Single-cell chromatin accessibility using the assay for transposase-accessible chromatin using sequencing (scATAC-seq) at three timepoints: E13.5, E15.5 and E18.5

first: Daniela

last: Di Bella

first: Ehsan

last: Habibi

first: Aviv

last: Regev


title: Total mRNA-seq to determine how the gene expression is altered in both parental and BRCA2-depleted CCNC- and MED12-KO cells.

city: Houston

first: Guangsheng

last: Pei

state: Texas

address: 7000 Fanin

institute: UTHealth

summary:
Background: Loss of RNA Pol II transcription Mediator components like CCNC, MED12 led to improved survival of PARPi-treated and untreated BRCA2-depleted cells. Mediator is best known for its function with RNA Pol II in regulating gene transcription, we performed total mRNA-Seq with control and BRCA2-depleted CCNC- and MED12-KO cells. The aim of the present prospective study was to reveal how the gene expression is altered in both parental and BRCA2-depleted CCNC- and MED12-KO cells which might contribute to the PARPi resistance in BRCA2 depleted cells.
Methods: HEK293A BRCA2 CKI mAID-EGFP WT, CCNC-KO, and MED12-KO with or without BRCA2 depletion cells (each with two biological replicates) were collected and total RNA was extracted and subjected to RNA-seq at HiSeq3000 (Illumina).
Results: Based on the transcriptomic data, we examined differentially expressed genes and performed KEGG pathway enrichment analysis.The results suggested that in both control and BRCA2-depleted CCNC- and MED12-knockout cells,  several signaling pathways like the transforming growth factor (TGF)-beta signaling pathway and extracellular matrix (ECM)-receptor interaction pathway et al were activated which probably facilitate cell proliferation upon BRCA2 loss.
Conclusions: Our results imply that TGF-beta signaling and other signaling pathways such as the ECM-receptor interaction pathway which play roles in the regulation of cellular functions such as proliferation, adhesion, apoptosis, differentiation and migration,  may together contribute to the involvement of CCNC and MED12 in drug resistance.

overall_design: RNA-seq data of 2 HEK293A WT, 2 HEK293A CCNC KO, 2 HEK293A MED12 KO, 2 HEK293A BRCA2 iKO, 2 HEK293A CCNC KO BRCA2 iKO,2 HEK293A MED12 KO BRCA2 iKO cells were generated by deep sequencing.


title: NANOS2-binding regulates mRNA half-life and key spermatogonial stem cell self-renewal pathways

city: London

first: Kamil

middle: R

last: Kranc

address: Charterhouse Square

institute: Queen Mary University of London

summary: We have identified NANOS2 bound targets transcriptome wide by employing CRAC and RNA-seq in mouse SSCs. We have determined the average mRNA half-life in SSCs by SLAM-seq. By comparing CRAC and SLAM-seq datasets, we have demonstrated that NANOS2 binding reduces mRNA stability in SSCs.

overall_design: After engineering a Nanos2TAG mouse allele, we derived mouse spermatogonial stem cells (SSCs) from P7 testes. SSCs were expanded in vitro and used to generate libraries for all the sequecing methods described here. First, we have identified NANOS2 RNA occupancy by CRAC, which was normalized by RNA-seq. We then examined global mRNA stability by SLAM-seq and compared this with the relative stability of NANOS2 targets, previously defined by CRAC.

first: Azzurra

last: Codino

first: Tomasz

last: Turowski

first: Louie

middle: N

last: van de Lagemaat

first: Donal

last: O’Carroll


title: Analysis of gene network branching during optic cup morphogenesis in zebrafish

city: Sevilla

first: Lorena

last: Buono

state: Sevilla

address: Carretera de Utrera km 1

country: Spain

institute: CABD

summary: We captured chromatin accessibility branching using ATAC-seq in isolated NR and RPE populations in zebrafish. We identify differentially active cis-regulatory modules and classify them as activating or repressing elements.

overall_design: ATAC-seq profile of sorted zebrafish cell populations of NR and RPE at 23 hpf


title: Molecular Logic of Cellular Diversification in the Mouse Cerebral Cortex (scRNAseq)

overall_design: Single cell RNA-seq (scRNA-Seq) profiles from the full thickness of the developing somatosensory cortex from mouse embryos over the entire period of corticogenesis: E10.5, E11.5 (transition from amplifying to neurogenic progenitors); E12.5 and E13.5 (birthdate of layer 6 and 5 excitatory neurons); E14.5, E15.5 and E16.5 (birthdate of layer 2 to 4 excitatory neurons); and E18.5 and P1 and P4 (transition from neurogenesis to gliogenesis).  Overall,  78,503 cells with 4,000 to 10,000 cells per time point were profiled.


title: Highly metastatic claudin-low mammary cancers can originate from luminal epithelial cells

status: Public on May 05 2021

city: Detroit

first: Kay-Uwe

last: Wagner

state: MI

address: 421 East Canfield, EL01TM

department: Department of Oncology

institute: Barbara Ann Karmanos Cancer Institute  Wayne State University School of Medicine

summary: Claudin-low breast cancer represents an aggressive molecular subtype that is comprised of mostly triple-negative mammary tumor cells that possess stem cell-like and mesenchymal features. Little is known about the cellular origin and oncogenic drivers that promote claudin-low breast cancer. In this study, we show that persistent oncogenic RAS signaling causes highly metastatic triple-negative mammary tumors in mice. More importantly, the activation of endogenous mutant KRAS and expression of exogenous KRAS specifically in luminal epithelial cells in a continuous and differentiation stage-independent manner induces preneoplastic lesions that evolve into basal-like and claudin-low mammary cancers. Further investigations demonstrate that the continuous signaling of oncogenic RAS as well as regulators of EMT play a crucial role in the cellular plasticity and maintenance of the mesenchymal and stem cell characteristics of claudin-low mammary cancer cells.

overall_design: The RNA of 6 mammary tumor cell lines was sequenced. 3 off_dox cell lines that were left untreated and their 3 isogenic cell lines that were treated with Doxycycline. The 3 cell lines represent biological replicates and are derived from distinct mammary tumors. Additionally, the RNA of 10 primary mammary tumors [from the MMTV-Flp FSF-Kras(G12D) p53(R172H)] was sequenced. The tumors all originate from distinct animals and were not treated. The tumors all represent biological replicates.

first: Patrick

middle: D

last: Rädler


title: RNA Sequencing of unc-30(ok613) and  wild type (WT) N2 C elegans

first: Benson

last: Otarigho

address: 6767 Bertner Avenue

department: Department of Genetics

institute: The University of Texas MD Anderson Cancer Center

summary:
Purpose: To uncover immune and longevity genes and pathways that are modulated by the homeodomain PITX1/UNC-30, which plays a vital role in the GABAergic signaling  in C elegans
Methods: RNA was extracted from synchronized L4 stage unc-30(ok613) and WT animals grown at 20 C using Qiagen extraction kits and following standard methods
Results: RNA seq analyses shows enriched and signficant upregulated immune, neuropeptide, ageing and metabolism genes and pathways that are dependent of GABAergic signaling
Conclusions: Our study uncovered GABAgergic signaling to be modulator of the innate immunity in C elegans

overall_design: RNA seq  profiles of L4-stage unc-30(ok613) and wild type (WT) C elegans animals were generated by deep sequencing, in triplicate, using Illumina NovaSeq 6000 platform.

first: Alejandro

last: Aballay


title: Regulation of alpha-like globin gene expression in murine primitive erythropoiesis (NG CaptureC)

first: Damien

last: Downes

summary: Haemoglobin, the oxygen-carrying molecule of red blood cells, at all stages of development comprises a tetramer of two α-like and two β-like globin chains.  In humans and mice the highly conserved α- and β-globin loci contain genes encoding globin chains specifically expressed only during the first trimester of gestation (termed embryonic globins) in addition to the genes encoding globin chains expressed throughout adult life. In humans the β-globin locus also encodes a β-like chain that is expressed throughout the second and third trimesters of development; this is termed γ-globin and complexes with α-globin to form fetal haemoglobin (HbF).  The sequential activation and repression of the genes at each of these loci throughout development to maturity is termed haemoglobin switching and is a poorly understood process. α-thalassemia, which results from insufficient production of α-globin, is a major global health problem with several hundred thousand sufferers world-wide. The embryonically expressed ζ-globin, encoded by the gene HBZ (Hba-x in mice), can functionally substitute for α-globin in adult erythroid cells. Reactivation of this gene is consequently likely to ameliorate the symptoms of α-thalassemia in individuals with a severe phenotype. Little is currently known about the regulation of ζ-globin expression in terms of both the trans- and cis-acting regulatory elements responsible for high-levels of expression of this gene during embryonic erythropoiesis and its maintenance in a transcriptionally inactive state throughout adult life. Using ATACseq and NG Capture C and mutant mouse lines this work aims to identify and define the cis-acting regulatory network underlying zeta-globin expression,  and define the contribution of each regulatory element.

overall_design: NG Capture-C combines 3C library preparation with oligonucleotide capture for the desired viewpoint restriction fragments. The method was applied to biological triplicates of embryonic stem cells (ESC), primitive erythroid cells (E10.5), and definitive erythroid cells (Fetal Liver: FL) capturing either promoter or enhancer elements.

first: Chris

last: Babbs

first: Andrew

last: King

first: Bee

last: Danutida


title: RNA-seq analysis of HNSCC cells after JQ1 treatment

city: Richmond

first: Jiong

last: Li

state: Virginia

address: 800 E Leigh Street, suite 212

institute: VCU

summary: We performed RNA sequencing (RNA-seq) of HNSCC cells to examine genome-wide gene expression pattern following JQ1 treatment. BET inhibition by JQ1 significantly inhibits a cohort of key oncogenes associate with tumorigenesis and metastasis. Suggesting BET inhibition is effective strategy to suppress the tumorigenesis and metastasis of head and neck squamous cell carcinoma.

overall_design: Examination of RNA-seq of  HNSCC cells treated with JQ1.


title: ChIP-seq analysis of BRD4, MED1 and P65 in SCC1 cells after JQ1 treatment

summary: To explore genome-wide alteration of BRD4, MED1, p65 and H3K27Ac during BET inhibition, we performed chromatin immunoprecipitation sequencing (ChIP-seq) of SCC1 cells to examine genome-wide recruitment of the MED1, BRD4, p65 and H3K27ac following JQ1 treatment. BET inhibition by JQ1 led to dramatically loss of the recruitment of MED1, BRD4 and p65 at a cohort of key oncogenes associate with tumorigenesis and metastasis. Suggesting BET inhibition is effective strategy to suppress the tumorigenesis and metastasis of head and neck squamous cell carcinoma.

overall_design: Examination of ChIP-seq of  HNSCC cells treated with JQ1.


title: The transcriptome of paired major and minor salivary gland tissue in patients with primary Sjögren's syndrome

city: West Windsor

first: Yanhua

last: Hu

state: NJ

address: 3551 Lawrenceville Princeton Rd

institute: Bristol Myers Squibb

summary: While all salivary glands (SGs) can be involved in primary Sjögren’s syndrome (pSS), their respective role in pathogenesis remains unclear. To assess immunopathway activation in paired parotid and labial gland tissue from biopsy-positive and biopsy-negative pSS and non-SS sicca patients, paraffin-embedded, paired parotid and labial salivary gland tissue and peripheral blood mononuclear cells were obtained from 39 pSS and 20 non-SS sicca patients. The patients were subdivided based on fulfillment of ACR-EULAR criteria and histopathology and the samples were analyzed for differentially expressed genes (DEGs).  The principal component analysis of SG gene expression could only separate biopsy-positive pSS from non-SS sicca patients. However, when comparing the transcriptome of biopsy-positive pSS and biopsy-negative non-SS sicca patients, 1235 and 624 DEGs (FDR<-1 or >1) were identified for parotid and labial glands, respectively. The number of DEGs between biopsy negative pSS and non-SS sicca patients was scarce. The overall, transcript expression levels correlated strongly between parotid and labial glands (R2=0.86, p‐value<0.0001). Gene signatures present in both glands of biopsy‐positive pSS patients included IFN‐α signaling, IL-12/IL-18 signaling, CD3/CD28 T-cell activation, CD40 signaling in B-cells, DN2 B-cells, and FcRL4+ B-cells. Signature scores varied considerably amongst pSS patients. In conclusion, the transcriptomes of paired major and minor SGs in pSS were overall comparable, although significant inter-individual heterogeneity in immunopathway activation existed. The SG transcriptome of biopsy-negative pSS was indistinguishable from non-SS sicca patients. The different patterns of SG immunopathway activation in pSS argue for personalized treatment approaches.

overall_design: Differential expression analysis of a cohort of 39 patients with primary Sjogren's syndrome and 20 non-SS sicca patients.

first: Gwenny

middle: M

last: Verstappen

first: Lu

last: Gao

first: Sarah

last: Pringle

first: Erlin

middle: A

last: Haacke

first: Bert

last: van der Vegt

first: Silvia

middle: C

last: Liefers

first: Vishal

last: Patel

first: Sumanta

last: Mukherjee

first: Julie

last: Carman

first: Laurence

last: Menard

first: Frederik

middle: K

last: Spijkervet

first: Arjan

last: Vissink

first: Hendrika

last: Bootsma

first: Frans

last: Kroese


title: Analysis of gene network branching during optic cup morphogenesis in zebrafish (RNA-Seq)

first: Lorena

last: Buono

summary: We characterize transcriptomic landscape using RNA-seq in isolated NR and RPE populations in zebrafish.

overall_design: RNA-seq profile of sorted zebrafish cell populations of retinal progenitors, NR at 18 hpf, NR at 23 hpf, RPE at 18 hpf and RPE at 23 hpf


title: Regulation of alpha-like globin gene expression in murine primitive erythropoiesis (ATAC-seq)

first: Damien

last: Downes

overall_design: ATAC-seq of Primitive and Definitive Erythrocytes (3 replicates each)

first: Chris

last: Babbs

first: Andrew

last: King

first: Bee

last: Danutida

first: Maria

last: Suciu


title: Regulation of alpha-like globin gene expression in murine primitive erythropoiesis

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

overall_design: Refer to individual Series


title: SCD2-mediated monounsaturated fatty acid metabolism regulates cGAS-STING-dependent type I IFN in mouse CD4+ T cells

status: Public on May 04 2021

city: Kisarazu

first: Toshio

last: Kanno

state: Chiba

address: 2-6-7 Kazusa-kamatari

country: Japan

institute: KAZUSA DNA Research Institute

summary: ACC1 is known to rate limitng enzyme of fatty acid biosynthesis. We report that modulation of fatty acid biosynthesis pathway increased tonic expression of anti-viral genes. RNA sequence was conducted to compare global gene expression between control, ACC1 inhibitor (TOFA)-treated, ACC1 KO and IFNb-treated Th1 cells. We found that inhibition or deletion of ACC1 resulted in the enhancement of anti-viral genes expression as comparable level to IFNb-treated Th1 cells. This study provides a framework for the relationship between fatty acid biosynthesis pathway and anti-viral responses in CD4 T cells.

overall_design: RNA-seq was performed to investigate the role of fatty acid syntehsis pathway for gene expression  In primay CD4+ T cells.

first: Takahiro

last: Nakajima

first: Satoru

last: Yokoyama

first: Hikari

last: Asou

first: Shigemi

last: Sasamoto

first: Yasuhiro

last: Kamii

first: Koji

last: Hayashizaki

first: Yasuo

last: Ouchi

first: Taishi

last: Onodera

first: Yoshimasa

last: Takahashi

first: Kazutaka

last: Ikeda

first: Yoshinori

last: Hasegawa

first: Yuki

last: Kinjo

first: Osamu

last: Ohara

first: Toshinori

last: Nakayama

first: Yusuke

last: Endo


title: ChIP-seq data of prefoldin subunit PFDN5 in HCT116 human colon carcinoma cells

first: Jose

middle: C.

last: Reyes

address: Av. Américo Vespucio

department: Genome biology

institute: CABIMER

summary: Prefoldin is a heterohexameric complex conserved from archaea to humans that plays a cochaperone role during the co-translational folding of actin and tubulin monomers. Additional functions of prefoldin in the cell nucleus have been described, including a positive contribution to transcription elongation and chromatin dynamics in yeast. Here we show that prefoldin perturbations provoked transcriptional alterations across the genome of human cells. We detected genome-wide prefoldin binding to transcribed genes and found that this binding negatively correlate with the impact of prefoldin depletion on gene expression. Moreover, lack of prefoldin caused significant global decrease in the levels of Ser2 and Ser5 phosphorylation of the RNA polymerase II carboxy-terminal domain (CTD). Altogether the reported results indicate that human prefoldin is able to act locally on the genome to modulate gene expression by influencing phosphorylation of elongating RNA polymerase II, and thereby regulating co-transcriptional splicing.

overall_design: ChIP-seq using anti-Flag antibody was carried out in HCT116 Flag-PFDN5 or HCT116-containing Flag cell lines.

first: Laura

last: Payán-Bravo

first: Sara

last: Fontalva

first: Xenia

last: Peñate

first: Ildefonso

last: Cases

last: Guerrero-Martínez

first: Yerma

last: Pareja-Sánchez

first: Yosu

last: Odriozola-Gil

first: Esther

last: Lara

first: Silvia

last: Jimeno-González

first: Carles

last: Suñé

first: Sebastián

last: Chávez


title: Transcriptome sequencing of human neutrophil

city: HangZhou

first: Qian

last: Ou

state: Zhejiang

address: Medical College of Zijingang Campus of Zhejiang University

department: Medical College

country: China

institute: Zhejiang University

summary: TcpC is a multifunctional virulence factor of uropathogenic E. coli (UPEC). Neutrophil extracellular trap formation (NETosis) is a crucial anti-infection mechanism of neutrophils. Here we show the influence of TcpC on NETosis and related mechanisms. In situ NETosis of kidneys from pyelonephritis mouse model induced by TcpC-secreting wild-type CFT073 (CFT073wt) and LPS-induced in vitro NETosis in CFT073wt- or recombinant TcpC (rTcpC)-treated neutrophils are inhibited. rTcpC enters neutrophils through caveolin-mediated endocytosis and inhibits LPS-induced production of ROS, proinflammatory cytokines and protein but not mRNA levels of peptidylarginine deiminase 4 (PAD4). rTcpC treatment enhances PAD4 ubiquitination and accumulation in proteasomes. Moreover, in vitro ubiquitination kit analyses suggest that TcpC is a PAD4-targetd E3 ubiquitin-ligase. These data suggest that TcpC inhibits NETosis primarily by serving as an E3 ligase that promotes degradation of PAD4. Our findings provide a novel mechanism underlying TcpC-mediated innate immune evasion.

overall_design: TcpC inhibits neutrophil extracellular trap formation by enhancing ubiquitination mediated degradation of peptidylarginine deiminase 4

first: Jia-qi

last: Fang

first: Jian-ping

last: Pan


title: Heteromeric HSFA2/HSFA3 complexes drive transcriptional memory after heat stress in Arabidopsis

city: Potsdam

first: Isabel

last: Bäurle

address: Karl-Liebknecht-Str. 24-25

department: Institut für Biochemie und Biologie

country: Germany

institute: Universität Potsdam

summary: Adaptive plasticity in stress responses is a key element of plant survival strategies. For instance, moderate heat stress (HS) primes a plant to acquire thermotolerance, which allows subsequent survival of more severe HS conditions. Acquired thermotolerance is actively maintained over several days (HS memory) and involves the sustained induction of memory-related genes. We find FORGETTER3/ HEAT SHOCK TRANSCRIPTION FACTOR A3 (FGT3/HSFA3) to be specifically required for physiological HS memory and maintaining high memory-gene expression during the days following a HS exposure. HSFA3 mediates HS memory by direct transcriptional activation of memory-related genes after return to normal growth temperatures. HSFA3 binds HSFA2, and in vivo both proteins form heteromeric complexes with additional HSFs. Our results indicate that only complexes containing both HSFA2 and HSFA3 efficiently promote transcriptional memory by promoting histone H3 lysine 4 (H3K4) hyper-methylation. In summary, our work defines the major HSF complex controlling transcriptional memory and elucidates the in vivo dynamics of HSF complexes during somatic stress memory.

overall_design: Gene expression in wild type, hsfa2 and hsfa3 single mutants and hsfa2 hsfa3 double mutants for non treated controls and for plants 4, 28 and 52 hours after acclimatation. Three biological replicates for each combination.

first: Thomas

last: Friedrich

first: Vicky

last: Oberkofler

first: Christian

last: Kappel


title: VISTA is an activating receptor that binds the proteoglycan Syndecan-2 on monocytes.

city: Redwood City

first: Xu

last: Shi

state: CA

address: 1500 Seaport Blvd

institute: AbbVie Inc.

summary: As indicated by its name, V-domain Ig suppressor of T cell activation (VISTA) is thought to primarily serve as an inhibitory protein that limits immune responses. VISTA-antibodies can dampen the effects of several concomitantly elicited activation signals including T cell receptor (TCR) and Toll-like receptor (TLR) activation, but it is currently unclear if VISTA agonism could singly affect immune cell biology.  In this study, we discovered two novel agonistic VISTA antibodies and characterized their effects on human peripheral blood mononuclear cells (PBMC) by scRNA/CITE-seq.  Both antibodies agonize VISTA in an Fc-functional manner to elicit transcriptional and functional changes in monocytes consistent with activation.  We also used pentameric VISTA to identify Syndecan-2 (Sdc2) and several heparan sulfate proteoglycan (HSPG) synthesis genes as novel regulators of VISTA binding to monocytic cells adding further evidence of bidirectional signaling.  Together, our study highlights several novel aspects of VISTA biology that have yet to be uncovered in myeloid cells and serves as a foundation for future research.

overall_design: Examination of immune response to anti-VISTA treatment. There are four treatments included in the study: two anti-VISTA treatments (1B1-G1 and 5B1-G3) and two control (095 and msl109).

first: Bryan

last: Rogers

first: Laura

last: Smith

first: Zoltan

last: Dezso

first: Enrico

last: DiGiammarino

first: Denny

last: Nguyen

first: Pingping

last: Zhang

first: Donghee

last: Choi

first: Dong

first: Andrew

first: Kathleen

last: McGuire

first: Wei

last: Liu

first: Namjin

last: Chung

first: Debra

middle: T

last: Chao

first: Shiming

last: Ye

first: Gabriel

last: Starbeck-Miller


title: Dissecting regulatory pathways for transcription recovery following DNA damage reveals a non-canonical function of the histone chaperone HIRA

city: Ann Arbor

first: Mats

last: Ljungman

state: Michigan

address: NCRC, B520 Room 1346 2800 Plymouth Rd.

institute: University of Michigan

summary: Transcription restart after a genotoxic challenge is a fundamental yet poorly understood process.  Here, we dissect the interplay between transcription and chromatin restoration after DNA damage by focusing on the human histone chaperone complex HIRA, which is required for transcription recovery post UV. We demonstrate that HIRA is recruited to UV-damaged chromatin via the ubiquitin-dependent segregase VCP to deposit new H3.3 histones. However, this local activity of HIRA is dispensable for transcription recovery. Instead, we reveal a genome-wide function of HIRA in transcription restart that is independent of new H3.3 and not restricted to UV-damaged loci. HIRA coordinates with ASF1B to control transcription restart by two independent pathways: by stabilizing the associated subunit UBN2 and by reducing the expression of the transcription repressor ATF3. Thus, HIRA primes UV-damaged chromatin for transcription restart at least in part by relieving transcription inhibition rather than by depositing new H3.3 as an activating bookmark

overall_design: Three independent Bru-seq experiments were run on siRNA-treated HeLa cells: siHIRA#1 vs. siLUC (control), siHIRA#2 vs. siLUC, siERCC6 vs. siLUC. Nascent RNA labeling with bromouridine was performed 0 h, 2 h, 6 h and 24 h after 10 J/m2 UVC irradiation. Non-irradiated cells (noUV) were used as negative controls.

first: Déborah

last: Bouvier

first: Juliette

last: Ferrand

first: Odile

last: Chevallier

first: Michelle

last: Paulsen

first: Sophie

middle: E

last: Polo


title: Circulating non-coding RNAs in Huntington disease

status: Public on May 03 2021

city: Rome

first: Silvia

last: Romano

address: Via di Grottarossa 1035

department: NESMOS

country: Italy

institute: University of Rome La Sapienza

summary:
We performed a  study of whole non-coding RNA expression profiles, by microarray, in plasma from 9 patients with Huntington disease (CH) in early stage and 13 controls: 8 healthy subjects (HD) and 5 patients with schizophrenia (SC). The CH patients were under antipsychotic drugs, the most effective treatment option also in SC patient (we included in the study SC control group to minimize the impact of neuroleptic drugson the expression of non-coding RNAs and to identify a HD-specific set of non-coding RNAs).
Blood samples were obtained by venous punctures in EDTA-tubes for plasma preparation. Cell- and platelet-free plasma was prepared following a step centrifugation protocol: samples were centrifuged at 1.500 g for 15′ at 4 °C and supernatant will be stored at −80 °C. RNA was extracted using Plasma/Serum Circulating RNA purification Kit (NORGEN) following the manufacturer’s instructions. Labeled RNA from each sample was analyzed by GeneChipmiRNA 2.0 Array (Affymetrix) according to the manufacturer’s instructions. Raw data were analyzed using Partek Genomic Suite software. Looking for differently expressed non-coding RNAs, we found a candidate HC-specific set compared to both control groups (HD and SC) (p<0.05 and │foldchanges│>1.5): hsa-miR-98 has proved to be down-regulated, while hsa-miR-323b-3p was up-regulated; 2 novel snoRNAs were up-regulated.

overall_design: We performed a  study of whole non-coding RNA expression profiles, by GeneChipmiRNA 2.0 Array (Affymetrix - according to the manufacturer’s instructions), in plasma from 9 patients with Huntington disease (CH) in early stage and 13 controls: 8 healthy subjects (HD) and 5 patients with schizophrenia (SC). The CH patients were under antipsychotic drugs, the most effective treatment option also in SC patient (we included in the study SC control group to minimize the impact of neuroleptic drugson the expression of non-coding RNAs and to identify a HD-specific set of non-coding RNAs)

first: Giovanni

last: Ristori

first: Viviana

last: Annibali


title: A transcriptomic analysis of dorsal root ganglia (DRG) with tumor cell injection (TCI, Walker 256 mammary gland carcinoma cell)

city: shenzhen

first: Mingzhu

last: Zhai

state: guangdong

address: shenzhen nanshan

institute: Southern university of science and technology

summary: The present study is aimed to analyze the transcriptomic changes across the generation and development of cancer induced bone pain (CIBP) in primary afferent neuron, which would provide a comprehensive understanding of the molecular mechanisms of CIBP. The transcriptomic profiles of primary afferent neuron in DRG from different time points were examined by RNAseq technique, including gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis.  Our study provide the first detailed analysis of DRG transcriptomes during the generation and development of CIBP.

overall_design: In total 16 samples were ananlyzed from four groups including TCI D1, TCI D7, TCI D14 and sham as control.  Each group has four replicates.


title: RNA-seq analysis of NDP and F4L5.13 treated bEnd.3 endothelial cell line

city: Toronto

first: Graham

last: MacLeod

state: ON

address: 144 College Street

department: Pharmaceutical Sciences

country: Canada

institute: University of Toronto

summary: bEnd.3 cells were treated with NDP (Norrin) or F4L5.13 (FZD4-LRP5 agonist) for 8 or 24 hours

overall_design: 3 biological replicates each for untreated, NDP-8hours, NDP-24hours, F4L5.13-8hours, F4L5.13-24hours

first: Rony

last: Chidiac

first: Andy

last: Yang

first: Stephane

last: Angers


title: RIP-seq using ILF3 antibodies to reveal RNAs that binds to ILF3 protein

city: Shiyan

first: Qin

last: Shanshan

address: Renmin Road 30, Maojian District

institute: Institute of Basic Medical Sciences, School of Basic Medical Sciences, Hubei University of Medicine

summary: RNA pulldown assay showed that lncRNA UBE2CP3 could bind to ILF3 protein. In order to further verify the interaction between ILF3 and UBE2CP3, RNA Immunoprecipitation (RIP) assay was performed to identify the RNAs that binds to ILF3 protein. RIP-seq data verifies the interaction between ILF3 and UBE2CP3. Interestingly, UBE2CP3 could also binds to 3'UTR of IGFBP7 mRNA. Mechanismly, lncRNA UBE2CP3 and 3' UTR of IGFBP7 could forms an double-stranded RNA. Then, the RNA duplex could interact with the Double-Stranded RNA-Binding Protein ILF3.

overall_design: The potent RNA was immunoprecipitated by ILF3 antibodies using RIP assay. Then, all the potent ILF3-binding target RNAs were identified by deep sequencing, using Illumina HiSeq 4000.

first: Shanshan

last: Qin

first: Dandan

last: Li


title: Identification of differentially expressed miRNAs after overexpression of UBE2CP3 in gastric cancer

type: Non-coding RNA profiling by high throughput sequencing

summary: In this study, we used miRNA sequencing to analyze and identify possible miRNAs that can be regulated by and UBE2CP3 in gastric cancer. The results showed that lncRNA UBE2CP3 overexpression decreased the expression of miR-138-5p. Due to miR-138-5p was able to target ITGA2 expression, and UBE2CP3 knockdown significantly downregulates ITGA2 expression, we speculated UBE2CP3 may positively regulate ITGA2 expression through sponging miR-138-5p in GC.

overall_design: To reveal the possible target miRNAs of UBE2CP3 in gastric cancer, we overexpressed the expression of UBE2CP3 in SGC7901 cells. The potent differential expressed microRNAs after overexpressing UBE2CP3 were identified by microRNA sequencing.


title: Next Generation Sequencing Facilitates Quantitative Analysis of IL4/IL13 treated wild-type BMDMs

city: Martinsried

first: Assa

last: Yeroslaviz

state: Bavaria

address: Am Klopferspitz 18

department: computational Biology

institute: Max-Planck-Institute for biochemistry

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived IL4/IL13 treated BMDMs transcriptome profiling (RNA-seq) to quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods.
Methods: BMDMs mRNA profiles of 8 weeks old wild-type (WT) mice were generated, stimulated with IL4/IL13, IL4/IL13+ TNF or TNF, deep sequenced, in triplicate, using Illumina NovaSeq 6000 platform.
Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the mouse genome (build mm9).
Conclusions: Our study represents the first detailed analysis of IL4/IL13 or IL4/IL13+TNF stimulated BMDMs, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

overall_design: mRNA profiles of wild-type BMDMs stimulated with IL4/IL13, IL4/IL13 + TNF or TNF for 6 or 24 hours

first: Stefanie

last: Dichtl


title: Knockdown of pseudogene lncRNA UBE2CP3 in gastric cancer cells

summary: Our data showed that UBE2CP3 was aberrantly upregulated in gastric cancer (GC), but its biofunction in GC is largely unknown to date. To explore the function of lncRNA UBE2CP3 in gastric cancer, loss-of-function and RNA sequencing studies were performed in SGC7901 cell line. The results showed that depletion of UBE2CP3 significantly decreased the expression of ITGA2. Interestingly, ITGA2 was also a target gene of miR-138. Our data showed that UBE2CP3 promotes GC progression through regulating miR-138/ITGA2 axis. Additionally, lncRNA UBE2CP3 could be stabilized by IGFBP7 mRNA. IGFBP7 depletion also significantly decreased ITGA2 expression.

overall_design: To reveal the possible target genes of UBE2CP3 and miR-138 in gastric cancer, we transfected UBE2CP3-targeted siRNAs and miR-138-5p mimics in the SGC7901 and AGS cell lines. The potent UBE2CP3 and miR-138 target genes were identified by deep sequencing, using Illumina HiSeq 4000.


title: Transcriptomic profiling of collagenous colitis identifies hallmarks of non-destructive inflammatory bowel disease [Microdissected IEC]

city: Kiel

first: Celia

last: Escudero-Hernández

state: Schleswig-Holstein

address: Institute of Clinical Molecular Biology (IKMB), Am Bota

department: Dep. Cell Biology

institute: University Hospital Schleswig-Holstein

summary:
Background and Aims:  The pathophysiology of the diarrhoea-predominant inflammatory bowel disease collagenous colitis (CC) is poorly described. Our aim was to use RNA sequencing of colonic biopsies from patients with active CC, CC in remission, refractory CC, ulcerative colitis (UC), and controls to gain insight into CC pathophysiology, identify additional genetic signatures linked to CC, and uncover targets for future therapeutic agents.
Methods: We performed whole transcriptome sequencing of CC colonic samples from patients before and during treatment with the corticosteroid drug budesonide, steroid-refractory patients, UC and healthy controls (n=9-13). Bulk mucosa and laser-captured microdissected intestinal epithelial cell gene expression was functionally analyzed by gene-set enrichment and gene-set variation analyses to identify statistically significant pathways and cells, respectively, that change in CC. Leading genes and cells were validated using reverse transcription quantitative PCR and/or immunohistochemistry. Finally, we compared CC transcriptome with that from UC samples.
Results: We identified an activation of the adaptive immune response to bacteria in active CC compared to that in remission that could be mediated by dendritic cells. However, a unique signature of genes related to the immune response and DNA transcription remain dysregulated after achieving remission. Budesonide-refractory CC patients fail to restore normal gene expression, which results in a transcriptomic profile close to UC. Intestinal epithelial CC cells displayed an impaired cell proliferation and increased antigen presentation.
Conclusion: Our study confirmed previous findings from GWAS and immunological studies related to CC pathogenesis and describes novel genes, pathways and cells that might contribute to the pathophysiology of CC, ongoing epithelial damage, and complications associated with CC.

overall_design:
Intestinal epithelial cell (IEC) mRNA profiles of collagenous colitis (CC), including paired active/untreated CC (auCC) and inactive/budesonide-treated CC (itCC) samples, active/refractory (budesonide non-responding) CC (aRCC), and healthy controls (Hc)

>>> Please note that raw data is not provided as Norwegian law does not allow public access to human sequences raw data. <<<


title: Transcriptomic profiling of collagenous colitis identifies hallmarks of non-destructive inflammatory bowel disease


title: Transcriptome analysis of peripheral blood from Lyn-deficient mouse SLE model lacking Ifnar1 or Irf5

status: Public on May 02 2021

city: Yokohama

first: Tomohiko

last: Tamura

address: 3-9 Fukuura, Kanazawa-ku

department: Department of Immunology

institute: Yokohama City University

summary: To clarify the role of interferon regulatory factor 5 (IRF5) other than inducing type I interferons (IFNs) in the pathogenesis of systemic lupus erythematosus (SLE), we performed transcriptome analysis of peripheral blood from Lyn-deficient mice with concomitant Ifnar1 or Irf5 deficiency. The results of gene set enrichment analysis (GSEA) suggest that IRF5 is involved in the induction of not only IFN-inducible genes (ISGs) but also oxidative phosphorylation (OXPHOS)-related genes in the SLE pathogenesis.

overall_design: Peripheral blood RNA from WT, Lyn-/-, Lyn-/-Ifnar1-/-, Lyn-/-Irf5+/-, and Lyn-/-Irf5-/- mice at 22-23 weeks of age was subjected to RNA-seq (n = 4 for each genotype, 20 samples in total).

first: Tatsuma

last: Ban

first: Masako

last: Kikuchi

first: Akira

last: Nishiyama


title: Transcriptomic profiling of collagenous colitis identifies hallmarks of non-destructive inflammatory bowel disease [Whole mucosa]

overall_design:
Whole colonic mucosa mRNA profiles of collagenous colitis (CC), including paired active/untreated CC (auCC) and inactive/budesonide-treated CC (itCC) samples, active/refractory (budesonide non-responding) CC (aRCC), healthy controls (Hc), and ulcerative colitis (UC) samples.

>>> Please note that raw data is not provided as Norwegian law does not allow public access to human sequences raw data. <<<


title: RNA-seq data of prefoldin subunits PFDN2 and PFDN5 knockdowns in HCT116 human colon carcinoma cells

first: Sebas

last: Chavez

address: Av. Manuel Siurot s/n

department: Instituto de Biomedicina de Sevilla

institute: Universidad de Sevilla

summary: We report gene expression data from total RNA-seq of HCT116 human colon carcinoma cells treated with siRNA against PFDN2 and PFDN5 (both part of a complex known as prefoldin). Cells were independently treated with one of the previously mentioned siRNAs or with an exogenous control siRNA (luciferase GL2). All cells were treated with the different siRNAs for 24 hours, then serum-starved them for 48 hours, and finally stimulated by adding serum for 90 minutes. Samples were taken before and after serum stimulation. Prefoldin depletion provoked transcriptional alterations across the genome of human cells. Severe pre-mRNA splicing defects were also detected, particularly under serum stimulation conditions. We found a significant impairment of co-transcriptional splicing during transcription elongation.

overall_design: RNA-seq of cells treated with siRNA against PFDN2, PFDN5 or Control for 24 hours, serum starved for 48 hours, and samples taken before serum stilmulation and 90 minutes after serum stimulation.

first: Laura

last: Payán Bravo

first: Xenia

last: Peñate

first: Ildefonso

last: Cases

first: Yerma

last: Pareja-Sánchez

first: Sara

last: Fontalva

first: Yosu

last: Odriozola

first: Esther

last: Lara

first: Silvia

last: Jimeno-González

first: Carles

last: Suñé

first: José

last: Reyes

first: Sebastián

last: Chávez


title: MicroRNA-138 Suppresses Glioblastoma Proliferation through Downregulation of CD44

status: Public on May 01 2021

city: Houston

first: Zhongming

last: Zhao

address: 7000 fannine St

institute: University of Texas Health Science Center at Houston

overall_design: RNA-seq of control brain and GBM snap-frozen samples.


title: Delineating the heterogeneity of matrix-directed differentiation towards soft and stiff tissue lineages via single-cell profiling.

city: Jerusalem

first: Amnon

last: Buxboim

state: Jerusalem

address: The Edmond J. Safra Campus - Givat Ram, Jerusalem 9190401,Israel

department: The Department of Cell and Developmental Biology

country: Israel

institute: The Hebrew University of Jerusalem

summary: Mesenchymal stromal/stem cells (MSCs) are a heterogeneous population of multipotent progenitors that contribute to tissue regeneration and homeostasis. MSCs assess extracellular elasticity by probing resistance to applied forces via adhesion, cytoskeletal, and nuclear mechanotransducers, that direct differentiation toward soft or stiff tissue lineages. Even under controlled conditions, MSC differentiation exhibits substantial cell-to-cell variation that remains poorly characterized. By single-cell transcriptional profiling of naïve, matrix-conditioned, and early differentiation state cells, we identified distinct MSC subpopulations with distinct mechanosensitivities, differentiation capacities, and cell cycling. We showed that soft matrices support adipogenesis of multipotent cells and endochondral ossification of non-adipogenic cells, whereas intramembranous ossification and pre-osteoblast proliferation are enhanced by stiff matrices. Using diffusion pseudotime mapping, we delineated hierarchical matrix-directed differentiation and identified mechanoresponsive genes. We found that tropomyosin-1 (TPM1) is highly sensitive to stiffness cues both at RNA and protein levels and that changes in expression of TPM1 determine adipogenic or osteogenic fates. Thus, cell-to-cell variation in tropomyosin-mediated matrix-sensing contributes to impaired differentiation with implications to the biomedical potential of MSCs.

overall_design: Here, we exposed naïve bone-marrow derived MSCs, which had been harvested for bone-marrow transplantation treatments, to matrices with controlled elasticities and to a bipotential induction cocktail that permits differentiation towards fat or bone.

first: Shlomi

last: Brielle

first: Danny

last: Bavli

first: Alex

last: Motzik

first: Yoav

last: Kan-Tor

first: Xue

last: Sun

first: Chen

last: Kozulin

first: Batia

last: Avni

first: Oren

last: Ram


title: Expression data from Rat neuronal Schwann cells (SCs) that under different extracellular matrix (ECM) conditions

city: Cincinnati

first: zhenyuan

last: xu

state: OH

address: 2378 Montana Ave, AptE

department: Chemical Engineering

institute: University of Cincinnati

summary:
Post peripheral injuries, Schwann cells express certain regenerative genes to promote nerve regeneration. The expression of regenerative genes can be regulated by ECM cues such as stiffness and cell shape.
We used microarray to illustrate the interplays between SC regenerative gene expression and different ECM conditions.

overall_design: The ECM stiffness was modulated by seeding SCs on PDMS (Polydimethylsiloxane) substrates with different mixing ratios. SC morphology was controlled by micropatterning technique.

first: Zhenyuan

last: Xu

first: Shawn

last: Smith


title: A short report on optimization of nucleic acid probes by DNA microarray synthesis and next generation sequencing

city: Uppsala

first: Rachel Yuan

last: Nong Mikkelsen

address: Biomedical Center (BMC)

department: Department of Immunology, Genetics and Pathology

country: Sweden

institute: Uppsala University

summary: Initial single 2fold probe was designed at the Landegren lab in Uppsala University, and the following experiments were performed at the Broad Institute at the Mikkelsen lab.

overall_design: 12000 2fold probes were synthesized by a B3 Custom Array DNA synthesizer in their reverse complementary oligonuleotide-order. After stripped off from microarrays, synthesized products were pooled, emulsion-PCR amplified, lambda exonuclease and restriction enzymes treated and resulted in single stranded 2fold probes – briefly, the 9 nucleotides positions next to an nicking enzyme binding site at the stem structure within a probe were computationally designed to be variable thus a set of 4000 probe sequences, namely MlyI-Nb.BtsI in parallel with two matched control-sets: MlyI-Nb.BbvCI and MlyI-NoNick. A solid phase (magnetic beads) assay protocol was utilized and end-result products were subsequently analyzed in a HiSeq2000 sequencer whereas variable sequences were read and served as tags to generate a count file.

first: Rachel

middle: Y

first: Tarjei

last: Mikkelsen

first: Xiaolan

last: Zhang


title: Transcriptomic analysis of Caenorhabditis elegans treated with mitochondrial Na+/Ca2+ exchanger inhibitor CGP37157 vs untreated control.

city: Valladolid.

first: Javier

last: Alvarez

address: Calle Sanz y Forés, 3

institute: IBGM, CSIC / Univerity of Valladolid

summary: We report that CGP37157 improved the evolution with age of the sarcomeric regular structure, delaying development of sarcopenia in C. elegans body wall muscle. Similarly, CGP37157 favoured the maintenance of a regular mitochondrial structure during aging. CGP37157 induced a four-fold increase in the expression of ncx-6, one of the C. elegans mitochondrial Na+/Ca2+ exchangers.

overall_design: Examination of 3 replicates of CGP37157 treated C.elegans and 3 replicates of control C.elegans.

first: Paloma

last: García-Casas

first: Pilar

last: Alvarez-Illera

first: Eva

last: Gomez-Orte

first: Juan

last: Cabello

first: Rosalba

middle: I

last: Fonteriz

first: Mayte

last: Montero


title: Differentially expressed profile of LncRNA in PBMCs (peripheral blood mononuclear cells) of asthma patients

city: Shanghai

first: Xiang

last: Wang

address: 399 Wanyuan Road, Minhang District, Shanghai

department: Children’s Hospital and Institute of Biomedical Sciences

institute: Fudan University

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

summary: To determine LncRNA  transcribed in PBMCs, we have employed whole genome microarray expression profiling as a discovery platform to identify LncRNA expression in PBMCs donated by patients of asthma and healthy volunteers.

overall_design: The changed LncRNA expression in human PBMCs normal or asthma patients, respectively. Four persons  in each group.

first: Li

last: Xia

first: Yufeng

last: Zhou


title: B cells and their progenitors reside in homeostatic meninges

city: Muenster

first: I-Na

last: Lu

state: NRW

address: Domagkstraße 20

department: Department of Pediatric Hematology and Oncology

institute: University Children's Hospital Münster

summary: The central nervous system (CNS) is ensheathed by the meninges and cerebrospinal fluid.  Recent findings suggest complex immunological functions of these CNS-associated border  tissues. Unlike myeloid lineage cells, lymphocytes in border compartments have been largely  disregarded in previous studies.  Based on single cell transcriptomics, we here identified a highly location-specific composition  and expression profile of tissue-resident leukocytes in every border compartment. Only the  dura layer of the meninges contained a large population of B cells under homeostatic  conditions in multiple species. Murine dura B cells exhibited slow turnover, long-term tissue  residency and matured in experimental neuroinflammation. The dura also contained B  lineage progenitors at the pro-B cell stage unexpected outside of bone marrow, without direct  influx from the periphery or the skull bone marrow.  This identifies the dura as an unexpected site of B cell residence and potentially  development in homeostasis and neuroinflammation.

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: Single-cell RNA sequencing of CNS-associated border compartments in rats and mice (naive and EAE)

first: David

last: Schafflick

first: Jolien

last: Wolbert

first: Michael

last: Heming

first: Gerd

last: zu Hörste


title: Effects of OCT4/NRF1 knockdown in castration-resistant prostate cancer cells

city: Itabashi-ku

first: Ken-ichi

last: Takayama

address: Sakaecho

institute: Tokyo Metropolitan Institute of Gerontology

summary:
Prostate cancer is the most common cancer in men and AR downstream signalings promote prostate cancer cell proliferation. Although initially hormone-deprovation therapy is effective to inhibit cancer progression, most of cancers relapse as castration-resistant prostate cancer (CRPC). In this study, we examined the effect of OCT4 or NRF1 knockdown in CRPC cells.
In order to investigate the OCT4 and NRF1 function in CRPC cells, we performed gene expression in AR-positive CRPC cell line, 22Rv1, AR-negative CRPC cell lines, PC3-CR (Cabazitaxel resistant), DU145, and DU145-CR, after siOCT4 (10 nM) or siNRF1 (10 nM) treatment. We also treated cells with vehicle, ribavirin (riba), or dihydrotestosterone (DHT) to analyzed the effects of thiese drug treatments.

overall_design: Observation of gene expression changes in CRPC after treatmet with siRNAs targeting OCT4/NRF1 or drugs using microarray.


title: Glucose deprivation induced gene expression

city: shanghai

first: Yongfeng

last: Liu

address: 320 Yueyang Road, Shanghai, 200025 P.R. China

institute: The Institute of Health Sciences, SIBS, CAS / SJTUSM

summary: Glucose is the main substrates of cancer cell metabolism. Relying on glucose for rapid proliferation and maintaining intracellular redox homeostasis is one of the hallmarkers of cancer cells. During physiology or cancer treatment, cancer cells will face a limited supply of glucose. In these case, cancer cells will undergo cell death . The plasticity of cancer cells is the main factor that allows cancer cells to survive this difficult situation. So in order to better understand the cplasticity of cancer cells, we use glucose-free medium to treat the colorectal cancer cell line HCT116, and perform RNA-Seq analysis on the treated samples.

overall_design: Genome-wide expression profiling of HCT116 which are treated with or without 0mM glucose medium.


title: Carbonic anhydrase inhibition improves right ventricular metabolic dysregulation and function in experimental pulmonary arterial hypertension

city: Boston

first: Brian

last: Kalish

state: MA

address: 220 Longwood Ave

department: Neurobiology

institute: Boston Children's Hospital

summary: In the Sugen 5416/hypoxia (SuHx) rat model of severe PAH, RV transcriptomic analysis was performed by RNA-seq

overall_design: RNA-seq of rat right ventriular heart tissue


title: Fluid flow-induced left-right asymmetric decay of Dand5 mRNA in the mouse embryo requires a Bicc1-Ccr4 RNA degradation complex

city: Kyoto

first: Kaoru

last: Komatsu

address: 53 Kawahara-cho, Shogoin Sakyo-ku

institute: Kyoto University

summary: Molecular left-right (L-R) asymmetry is established at the node of the mouse embryo as a result of the sensing of a leftward fluid flow by immotile cilia of perinodal crown cells and the consequent degradation of Dand5 mRNA on the left side. We here examined how the fluid flow induces Dand5 mRNA decay. We found that the first 200 nucleotides in the 3' untranslated region (3'-UTR) of Dand5 mRNA are necessary and sufficient for the left-sided decay and to mediate the response of a 3’-UTR reporter transgene to Ca2+, the cation channel Pkd2, the RNA-binding protein Bicc1 and their regulation by the flow direction. We show that Bicc1 preferentially recognizes GACR and YGAC sequences, which can explain the specific binding to a conserved GACGUGAC motif located in the proximal Dand5 3'-UTR. The Cnot3 component of the Ccr4-Not deadenylase complex interacts with Bicc1 and is also required for Dand5 mRNA decay at the node. These results suggest that Ca2+ currents induced by leftward fluid flow  stimulate Bicc1 and Ccr4-Not to mediate Dand5 mRNA degradation specifically on the left side of the node.

overall_design: Determination of Bicc1 binding motifs with the use of a random RNA sequence library.

first: Hirohide

last: Saito


title: An ER stress inducer decreases the H3k27 trimethylation (H3k27me3) modification of Crytochrome 1 in mouse embryo fibroblasts

first: Xu

address: No. 639, Zhizaoju Road

institute: Shanghai Jiao Tong university, School of Medicine

summary: The perturbations of ER homeostasis lead to the development of a condition referred to as ER stress. However, the repressive trimethylation on histone H3 lysine 27 (H3k27me3) under ER stress remains largely elusive. Here, we identify a critical role for H3k27me3 to impact the expression of Crytochrome 1 (Cry1). To examine the effect of ER stress on histone modification, MEFs were treated with vehicle 2μg/ml tunicamycin for 6 h. The cell lysate were collected and ChIP-seq assays were performed with the primary H3k27me3 or H3k4me3 antibody. When compared to the Vehicle group, the tunicamycin treatment reduced the 23,008 H3k27me3 peaks. In line with the roles of H3k27me3 in the regulation of gene transcriptions, annotation of the peak in genomic positions to the cloest genes indicated that many peaks were positioned after the transcription start site. Cry1 is one of the most regulated genes. However, the tunicamycin treatment slightly reduced H3k4me3 modification in MEFs. There are only 3109 peaks were decreased by the tunicamycin treatment. These data suggest ER stress selectively regulated H3k27me3 modification in the hisone 3 and reactivate Cry1 gene expression in MEFs.

overall_design: Examination of 2 different histone modifications in mouse embryo fibroblasts.

first: Yan

last: Wei


title: Inducible hepatic expression of CREBH mitigates diet-induced obesity, insulin resistance and hepatice steatosis in mice.

status: Public on Apr 30 2021

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

summary: Cyclic AMP-responsive element-binding protein H (CREBH, encoded by Creb3l3) is a transcription factor that regulates the expression of genes that control lipid and glucose metabolism, as well as inflammation. CREBH is upregulated in the liver under conditions of overnutrition, and mice globally lacking the gene (CREBH-/-) are highly susceptible to diet-induced obesity, insulin resistance (IR) and hepatic steatosis. The net protective effects of CREBH have been attributed in large part to the activities of Fibroblast growth factor (Fgf)-21 (Fgf21), a target gene that promotes weight loss, improves glucose homeostasis and reduces hepatic lipid accumulation. To explore the possibility that activation of the CREBH-Fgf21 axis could ameliorate established effects of high fat feeding, we generated an inducible transgenic hepatocyte-specific CREBH overexpression mouse model (Tg-rtTA). Acute overexpression of CREBH in livers of Tg-rtTA mice effectively reversed diet-induced obesity, IR and hepatic steatosis. These changes were associated with increased activities of thermogenic brown and beige adipose tissues in Tg-rtTA mice, leading to reductions in fat mass, along with enhanced insulin sensitivity and glucose tolerance. Genetically silencing of Fgf21 in Tg-rtTA mice abrogated the CREBH-mediated reductions in body weight loss, but only partially reversed the observed improvements in glucose metabolism. These findings reveal that the protective effects of CREBH activation may be leveraged to mitigate diet-induced obesity and associated metabolic abnormalities in both Fgf21-dependent and -independent pathways.

overall_design: Hepatocytes were transduced with adenoviruses encoding green fluorescent protein (Ad-GFP; Control) or nuclear CREBH (Ad-nuclear CREBH), and 24 hrs later gene expression was profiled.

first: Christopher

middle: S

last: Krumm

last: Xu

first: Curtis

last: Bare

first: Corey

last: Holman

first: Sander

last: Kersten

first: Lukas

last: Dow

first: Ann-Hwee

last: Lee

last: Cohen


title: Mechanistic Targets of Diallyl Trisulfide (DATS) in Human Breast Cancer Cells Identified by RNA-seq Analysis

city: Pittsburgh

first: Shivendra

middle: V

last: Singh

state: PA

address: 5117 Centre Avenue UPMC HCC Research Pavilion Suite 2.32A

department: Pharmacology and Chemical Biology

institute: University of Pittsburgh

summary: We report differential gene expression changes by DATS in breast cancer cells

overall_design: Examination of DATS-regulated transcriptome in two human breast cancer cells with different subtypes including MCF-7 (luminal type) and MDA-MB-231 (basal type).


title: RNA-sequencing gene expression data from FACS-purified Ventricular-Subventricular Zone (V-SVZ) and cortical cells from hGFAP::GFP mice.

city: Ann Arbor

first: Dogukan

last: Mizrak

address: NCRC Building 26, 263S

department: Cardiac Surgery

institute: University of Michigan

summary: Quiescent neural stem cells (NSCs) in the adult ventricular-subventricular zone (V-SVZ) undergo activation and divide to generate neurons and glia. Here we show that Platelet-derived Growth Factor Receptor beta (PDGFRβ) is expressed by quiescent and early activated adult V-SVZ NSCs, and maintains their quiescence. We further showed that selective deletion of PDGFRβ in adult V-SVZ NSCs leads to activation of quiescent NSCs. We performed RNA-seq on FACS-sorted V-SVZ quiescent, early activated and late activated NSCs, as well as cortical cells from adult 2-4 month old mice.

overall_design: RNA was isolated from FACS-purified cell types from hGFAP::GFP animals with three replicates for each cell population. cDNA was amplified using oligo(dT) primers and the resulting products were sequenced to reveal the gene expression profiles.

first: Fiona

last: Doetsch


title: Pumilio2 and Staufen2 selectively balance the synaptic proteome

city: Planegg-Martinsried

first: Michael

middle: A.

last: Kiebler

address: Großhaderner Straße 9

department: Department for Cell Biology & Anatomy

institute: Biomedical Center (BMC)

summary: Cells, in particular neurons, have the capacity to adapt to environmental stimuli, a phenomenon termed cellular plasticity. The underlying processes are controlled by a network of RNA-binding proteins (RBPs). Their impact on cellular plasticity, however, is largely unknown. To address this important question, we chose Pumilio2 (Pum2) and Staufen2 (Stau2) that both regulate synaptic transmission. Surprisingly, even though both RBPs dynamically interact with each other in neurons, their respective impact on the transcriptome and proteome is highly selective. While Pum2 deficiency leads to reduced translation and protein expression, Stau2 depletion preferentially impacts RNA levels and increases protein abundance. Furthermore, we show that Pum2 activates expression of key GABAergic synaptic components, e.g. the GABAA receptor scaffold protein Gephyrin. Consequently, Pum2 depletion selectively reduced the amplitude of miniature inhibitory postsynaptic currents. Together, our data clearly demonstrate that RBPs are needed to maintain proteostasis in order to control distinct signaling pathways which critically balance synaptic transmission.

overall_design: 3 replicates of shControl, 3 replicates of shPum2 and 3 replicates of shStau2 transduced cultured cortical neurons (10+4DIV)

first: Rico

last: Schieweck

first: Sophia

last: Derdak

first: Martin

last: Bilban


title: Virus-Host interaction of E. coli DksA-deficient cells infected by phage P1vir

city: Gdansk

first: Grzegorz

middle: M.

last: Cech

state: Pomorskie

address: Wita Stwosza 59 pok. A242

department: Department of Bacterial Molecular Genetics

country: Poland

institute: Uniwersytet Gdański, Wydział Biolog

summary:
Bacteriophage P1 along with λ and T4 phages are among the best described bacterial viruses in molecular biology. For years, P1 features as well as its life cycle have been studied and its complete genome was published. Undeciphered phenomenon of improved P1vir lytic development in the absence of DksA protein in cell engaged us to more holistic experimental approach. Bacterial wild type and dksA strains were cultured to OD600 = 0.2. Next, P1vir was added, samples were withdrawn at 0, 10 and 30 minutes after P1vir infection. Total RNA was isolated and checked for quality using the Bioanalyzer 2100. The sequencing run was conducted on the Illumina NovaSeq6000 platform. 30 million pair-end reads per samples were assessed with 101 pb read length. Reference P1 phage genome sequence and annotations were downloaded from GenBank. We have discovered many changes in virus transcriptome. For instance: downregulation of phage genes encoding the main repressor of lysogeny C1 or proteins triggering cell lysis (e.g., lysozyme, holin) and upregulation of genes encoding antiholins in dksA mutant. This results support our gentle lysis hypothesis – less efficient lysis, combined with minor improvements of phage development which  may lead to higher phage yield in DksA-devoid cells. We have observed upregulated expression of phage genes responsible for virion-parts production in the dksA mutant. Interestingly, expression of lysogeny-related c8 gene is upregulated in the dksA mutant. We speculate that P1vir developing in the dksA host is at the brink of lysogeny but is unable to established it and eventually enters the lytic pathway. We also found some interesting events in host cells upon infection. P1vir is taking control of the cellular protein, sugar and lipid metabolism in both, the wild type and dksA mutant hosts. However, in dksA mutant several genes involved in sulfur metabolism were uniquely upregulated. It remains unclear if this associates with obtaining new energy sources or with global reprograming via H2S signaling functions. Generally, the hosts are reacting by activating SOS response or upregulating the heat shock proteins. But we also found downregulation of proteolysis which was unique for the dksA strain. We believe that this extensive and comprehensive study not only finds reasonable explanations for the improved P1vir development in dksA strain, but also makes a great contribution to the field of P1 phage biology.
Funding: This research was funded by the National Science Center, Poland (grant PRELUDIUM 2013/09/N/NZ2/01899 to G.M.C.)

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

overall_design: To obtain a widespread and holistic overview of the virus–host interactions, we analyzed the transcriptome of both, the P1vir phage and the dksA and wild type hosts during the infection. Total RNA sequencing was performed to assess the changes in gene expression pattern at 0, 10 and 30 min of P1vir infection

first: Agnieszka

last: Szalewska-Pałasz


title: Comprehensive single cell RNA-seq datasets of mice trachea epithelial progenitors in 6 time points from E12.5 to E18.5 and mature epithelial cells in 2-month mice

city: Kobe

first: Hirofumi

last: Kiyokawa

state: Hyogo

address: 2-2-3 Minatojima-minamimachi, Chuo-ku

department: Center for Biosystems Dynamics Research

institute: Riken

summary: We delineate the comprehensive developmental trajectories of trachea epithelial progenitors in mice using scRNA-seq datasets. After obtaining the scRNA-seq data in 6 time points from E12.5 to E18.5, we merged all the datasets to describe the establishment process of basal cell population during development, which works as airway facultative stem cells. We found that Krt17 is a novel intermediate marker for basal cell progenitors and Id genes are key transcriptional factors for balancing the proliferation and differentiation programs by promoting their cell cycle.

overall_design: Transcriptomic analyses at single cell resolution of tracheal epithelial cells in 7 time points (E12.5, E13.5, E14.5, E15.5, E16.5, E18.5, and 2 months)

first: Mitsuru

last: Morimoto


title: Unique evolutionary trajectories of breast cancers with distinct genomic and spatial heterogeneity

city: Scottsdale

first: michael

middle: thomas

last: barrett

state: Arizona

address: 13400 east shea boulevard

institute: mayo clinic arizona

summary: To define the sources and the extent of heterogeneity, we performed an in-depth analysis of the genomic architecture of three chemoradiation-naïve breast cancers with well-defined clinical features including variable ER, PR, Her2 receptor expression and distinct pathogenic BRCA2mut genotypes. The latter included a germ line carrier and a patient with a somatic variant. In each case we combined DNA content-based flow cytometry with whole exome sequencing and genome wide copy number variant (CNV) analysis of distinct populations sorted from multiple (4-18) mapped biopsies within the tumors and involved lymph nodes. Interrogating flow-sorted tumor populations from each biopsy provided an objective method to distinguish fixed and variable genomic lesions in each tumor. Notably we show that tumors exploit CNVs to enrich fixed mutations and deletions that are shared throughout each tumor. The identification of fixed genomic lesions in distinct populations, that are shared or unique within each tumor, has broad implications for the study of tumor heterogeneity including the presence of tumor markers and therapeutic targets, and of candidate neoepitopes in breast and other solid tumors that can advance more effective treatment and clinical management of patients with disease.

overall_design:
We applied DNA content based flow sorting to isolate the nuclei of clonal populations from multiple (4-18) biopsies from resected tumors from each of three breast cancer patients. We coupled this strategy with oligonucleotide array CGH (aCGH) and next generation sequencing, thereby obtaining high definition genomic profiles of clonal populations from each tumor. We identified fixed genomic lesions in each distinct population, including those that are shared or unique within each tumor. We then identified shared neoepitopes notably those arising from fixed shared variants in each tumor.

>>>Submitter states that raw data files for many samples are not available due to file loss.<<<

first: Tanya

last: Phung

first: Timothy

last: Webster

first: Elizabeth

last: Lenkiewicz

first: Smriti

last: Malasi

first: Mariacarla

last: Andreozzi

first: Ann

last: McCullough

first: Karen

last: Anderson

first: Barbara

last: Pockaj

first: Melissa

last: Wilson

last: Barrett


title: Matrisome gene expression in treatment-naïve and chemotherapy-treated primary tumor and metastatic tissues of high-grade serous ovarian carcinoma

city: Helsinki

first: Elina

last: Pietilä

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

summary:
The extracellular matrix (ECM) of tumors differ significantly from that in normal tissues. Biochemical cues from the tumor ECM critically affect intratumoral signaling contributing to tumor malignancy, growth and response to treatment.
In this study, we characterized the expression of 1,027 genes encoding core extracellular matrix and associated proteins defined as the matrisome (Naba et al., 2016) in treatment-naïve and chemotherapy-treated high-grade serous ovarian carcinoma (HGSC) using longitudinal patient cohort consisting of 165 samples.
The expression profiling was conducted by using 45 primary tumor samples, 93 metastatic omental-peritoneal-mesenteric tissue samples and 27 ascites-derived cancer cell samples from HGSC patients. By comparing the matrisome gene expression between the primary tumor and metastatic tissues pre- and post-chemotherapy, we identified the cancer cell surrounding fibro-inflammatory tumor-microenvironment to be markedly different in primary tumors compared to metastatic tissues and to change in response to chemotherapy, in terms of both the extent and type of the extracellular matrix proteins. Further study on these specific genes may aid finding potential therapeutic ECM gene targets to enhance HGSC patient outcome.

overall_design:
Transcriptome profiling analyses of tumor matrisome were performed on 165 high-grade serous ovarian carcinoma patient samples including both treatment-naïve and post-chemotherapy tissue and ascites-derived cancer cells.
The raw RNA sequencing data that these effective counts are based on have been deposited in the European Genome-phenome Archive under the accession code (EGAD00001006456, under the study EGAS00001004714).

first: Sanaz

last: Jamalzadeh

first: Kaiyang

last: Zhang

first: Rainer

last: Lehtonen

first: Sampsa

last: Hautaniemi

first: Kaisa

last: Lehti


title: Physiology of Pseudomonas aeruginosa cells without major RND-type multidrug efflux pumps

city: Norman

first: Justyna

middle: Weronika

last: Adamiak

state: OK

address: 101 Stephenson Parkway

department: Chemistry and Biochemistry

institute: University of Oklahoma

summary:
Purpose: In this study, we analyzed how P. aeruginosa physiology is adapted to the lack of RND-mediated efflux activities.
Methods: In this study, we use PΔ6 cells to analyze how P. aeruginosa changes its physiology in response to the lack of efflux pumps and increased permeability of the cell envelope. We compared the transcriptomes of the exponentially growing and stationary PΔ6 and its parent PAO1 cells and identified the cellular functions stressed by the lack of active efflux. High quality total RNA was further processed by removing 23S and 16S rRNAs using the Illumina Ribo-Zero Plus rRNA Depletion kit. Samples were analyzed in duplicate using Illumina MiSeq. Raw data for each sample was analyzed using CLC Genomics Workbench version 12.0.1 software (QIAGEN Aarhus, Denmark).
Results: P. aeruginosa PΔ6 strain lacking six best characterized RND pumps activates a specific adaptation response that involves significant changes in expression of specific subset of genes encoding e.g. several transport systems, quorum sensing or iron acquisition.
Conclusion: Our results suggest that all changes we observe serve to protect the cell envelope of efflux-deficient P. aeruginosa.

overall_design: RNAseq analysis of the exponential and stationary PAO1 and its efflux knockout cells (parent: PAO1, knockout mutant PΔ6: PAO1 ΔmexAB-oprM ΔmexCD-oprJ ΔmexEF-oprN ΔmexJKL ΔmexXY ΔtriABC); 4 samples in duplicate

middle: W

first: Helen

last: Zgurskaya


title: cIAP1/2 antagonism eliminates MHC class I negative tumors through T cell-dependent reprogramming of mononuclear phagocytes

first: Stephanie

last: Dougan

address: 1 Jimmy Fund Way

department: Cancer Immunology & Virology

institute: Dana-Farber Cancer Institute

summary: Induction of non-canonical NF-kB signaling with IAP antagonists mimics costimulatory signaling, augmenting anti-tumor immunity. We now show that induction of non-canonical NF-kB signaling induces T-cell dependent immune responses even in B2M-null tumors, demonstrating that direct CD8 T cell recognition of tumor cell expressed MHC class I is not required. Instead, T cell-produced cytokines reprogram macrophages to be tumoricidal. In wildtype mice IAP antagonism reduces tumor burden by increasing phagocytosis of tumor cells. We characterized by RNA-Seq the transcriptional profile of intratumoral phagocytes with and without treatment with the IAP antagonist LCL161.

overall_design: CD45+ CD11b+ cells were sorted by FACS from orthotopic 6694c2 pancreatic tumors implanted in C57BL/6 mice treated with vehicle or the IAP antagonist LCL161 for 12 days.

first: Kevin

last: Roehle

first: Li

last: Qiang

first: Katherine

last: Ventre

first: Daniel

last: Heid

first: Lestat

middle: R

last: Ali

first: Patrick

last: Lenehan

first: Max

last: Heckler

middle: J

last: Crowley

first: Courtney

last: Stump

first: Anze

last: Godicelj

first: M

last: Bhuiyan

first: Annan

last: Yang

first: Maria

middle: Q

last: del Rey

first: Tamara

last: Biary

first: Adrienne

last: Luomo

last: Bruck

first: Jana

middle: F

last: Tegethoff

first: Svenja

middle: L

last: Nopper

first: Jinyang

last: Li

first: Katelyn

last: Byrne

first: Marc

last: Pelletier

first: Kai

last: Wucherpfennig

first: Ben

middle: Z

last: Stanger

first: James

last: Akin

first: Joseph

middle: D

last: Mancias

first: Judith

last: Agudo

first: Michael


title: m6A-RIP-seq of heat shock-exposed HeLa cells upon HSATIII knockdown

city: 吹田市山田丘１－３

first: KENSUKE

last: NINOMIYA

state: 大阪府

department: Graduate school of Frontier Biosciences

institute: Osaka university

summary: To investigate the effect of HSATIII lncRNA on m6A modification, we performed m6A-RIP(RNA immuno precipitation) RNA-seq from heat shock-exposed HeLa cells upon HSATIII knockdown.

overall_design: We performed m6A RIP from non-stress and heat shock-exposed HeLa cells  with or without recovery upon HSATIII knockdown.

first: Tetsuro

last: Hirose

first: Kensuke

last: Ninomiya


title: Kdm6 inhibitor as leptin sensitizer in the hypothalamus of high fat diet induced obesity mice

first: Xu

last: Wang

summary: To further identify the mostly influenced signal pathways under Kdm6 inhibitor treatment, the microarray analysis was performed to screen the gene expression profile in the hypothalamus of DIO mice. The DIO mice were administrated with vehicle or 30 mg/kg GSK-J4 i.p. for 4 days. Totally, 205 genes were up regulated over 2 fold and 845 genes were down regulated over 2 fold.

overall_design: GSK-J4 induced gene expression in mouse hypothalamus was measured at 4 d after exposure to doses of 0 and 30mg/kg.  Three independent experiments were performed using different mouse for each experiment.

first: Yan

last: Wei


first: Stephanie

last: Dougan

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

overall_design: Refer to individual Series


title: Time-course transcriptomic profiling of cell-cycle entry in MCF10A cells

status: Public on Apr 29 2021

city: Stanford

first: Tobias

last: Meyer

address: 318 Campus Dr

institute: Stanford University

summary: To identify potential novel regulators of G1/S transition and S-phase progression, we performed an RNA sequencing (RNA-Seq) time-course analysis of non-transformed human breast epithelial cells (MCF10A) released into the cell cycle from serum starvation, in the presence of DMSO or a specific CDK4/6 inhibitor palbociclib.

overall_design: Conditions include: 0hr, 3hr DMSO, 6hr DMSO, 9hr DMSO, 9hr palbociclib, 12hr DMSO, 12hr palbociclib, 15hr DMSO, 15hr palbociclib, 24hr DMSO, 24hr palbociclib. A total of 31 samples containing triplicates (except 24-hour time point, which was performed in duplicates) were analyzed.

first: Yilin

last: Fan

first: Marielle

last: Köberlin

first: Chad

last: Liu


title: RNA-seq data (STAG2 WT and mutated Ewing sarcoma cell lines)

city: Paris

first: Olivier

last: Delattre

address: 26 rue d'ulm

country: France

institute: Institut Curie

summary: STAG2 is a member of cohesin complex and its gene is one of the most recurrently mutated in human cancer including in Ewing sarcoma. Here, we investigated STAG2 function in the context of Ewing sarcoma and performed transcriptome profiling of a panel of 15 WT and 15 mutated STAG2 established Ewing sarcoma cell lines.

overall_design: Transcriptome profiling of a panel of 15 WT and 15 mutated STAG2 established Ewing sarcoma cell lines was performed using RNA-sequencing.

first: Didier

last: Surdez

first: Sakina

last: Zaidi

first: Sandrine

last: Grossetête

first: Karine

last: Laud-Duval

first: Virginie

last: Raynal

first: Sylvain

last: Baulande

first: Véronique

last: Hill


title: Genome-wide RNAi Screening Identifies pseudouridine synthase DKC1 promotes CRC proliferation through regulating ribosomal proteins expression

city: Guangzhou

first: guangyan

last: kan

address: 651 Dongfeng East Road

institute: Sun Yat-sen University Cancer Center

summary: Colorectal cancer (CRC) with high rate of mortality is one of the most commonly diagnosed cancers in worldwide. Advanced colorectal cancer is often accompanied by malignant proliferation of tumor cells. Further researches on colorectal cancer proliferation to find new targets and develop new therapeutic regimen are an important direction for colorectal cancer treatment. In this study, genome-wide RNAi screening was used to discover the essential genes associated with colorectal cancer cell proliferation. We found DKC1 (dyskerin pseudouridine synthase 1) promoted CRC proliferation through binding and modifying ribosomal proteins (RPL10A, RPL22L1, RPL34, RPS3) mRNA to increase the mRNAs stability and eventually increasing their expression. Besides, DKC1 is highly expressed in colorectal cancer and its aberrantly high expression is associated with poor prognosis of colorectal cancer patients. These results suggest that DKC1 could be a new therapeutic target for colorectal cancer.

overall_design: Examination of DKC1 binding RNA in DKC1 knockdown colorectal cancer cells and control cells.

first: Guangyan

last: Kan

first: Shuai

last: Chen


title: Bone invigorates metastatic seeding

city: HOUSTON

first: Igor

middle: L.

last: Bado

state: Texas

address: One Baylor Plaza, Alkek Building N1130

department: Breast Center

institute: Baylor College of Medicine

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


first: Stephanie

last: Dougan

summary: Induction of non-canonical NF-kB signaling with IAP antagonists mimics costimulatory signaling, augmenting anti-tumor immunity. We show that induction of non-canonical NF-kB signaling induces T-cell dependent immune responses even in B2M-null tumors, demonstrating that direct CD8 T cell recognition of tumor cell expressed MHC class I is not required. Instead, T cell-produced cytokines reprogram macrophages to be tumoricidal. In wildtype mice, IAP antagonism reduces tumor burden by increasing phagocytosis of tumor cells. We characterized by RNA-Seq the transcriptional response of macrophages to T-cell produced lymphotoxin (LT) in the presence or absence of the IAP antagonist LCL161.

overall_design: Bone Marrow Derived Macrophages (BMDMs) were incubated for 24 hours with LCL161 plus LTα1β2 (n = 2) or LTα1β2 alone (n = 2) or Vehicle (n = 2).

first: Kevin

last: Roehle

first: Li

last: Qiang

first: Katherine

last: Ventre

first: Daniel

last: Heid

first: Lestat

last: Ali

first: Patrick

last: Lenehan

first: Max

last: Heckler

last: Crowley

first: Courtney

middle: T

last: Stump

first: Anze

last: Godicelj

first: M

middle: A

last: Bhuiyan

first: Annan

last: Yang

first: Maria

last: del Rey

first: Tamara

last: Biary

first: Adrienne

middle: M

last: Luomo

last: Bruck

first: Jana

last: Tegethoff

first: Svenja

last: Nopper

first: Jinyang

last: Li

first: Katelyn

last: Byrne

first: Marc

last: Pelletier

first: Kai

last: Wucherpfennig

first: Ben

last: Stanger

first: James

last: Akin

first: Joseph

last: Mancias

first: Judith

last: Agudo

first: Michael

middle: K


title: The HIF target MAFF promotes tumor invasion and metastasis through IL11 and STAT3 signaling

city: Headington

first: Eui Jung

last: Moon

address: Old Road Campus Research Building, Roosevelt Drive

department: Department of Oncology

institute: University of Oxford

summary: Using RNA-sequencing and ChIP-sequencing, we identified direct target genes of the transcription factor MAFF in MDA-MB-231 under normoxia and hypoxia.

overall_design: MDA-MB-231, a human breast cancer cell line, was treated either under normoxia or hypoxia. After ChIP or RNA extraction, sequencing was performed. After knocking down endogenous MAFF in MDA-MB-231, we overexpressed V5-tagged MAFF with mutations on shRNA target sites. Then nuclei was extracted and we proceeded to ChIP procedures using V5 antibody to further determine direct targets of MAFF.

first: Eui

first: Stephano

last: Mello

first: Jake

last: Kirkland

first: Amato

last: Giaccia


title: CgEfg1 and CgTec1 transcription factors controlling biofilm formation in Candida glabrata

city: Lisbon

first: Miguel

middle: Cacho

last: Teixeira

address: Av. Robisco Pais

country: Portugal

institute: Institute for Bioengineering and Biosciences, Instituto Superior Técnico

summary: This work reports the transcriptome-wide changes of C. glabrata cells (RNA-seq) upon 24h of biofilm formation on polystyerene surface, comparatively to planktonic conditions. The role of CgEfg1 and CgTec1 transcription factors is explored through the comparison of the transcriptome profiles of WT and CgEfg1 mutant cells, as well as the comparison between the profile of WT and CgTec1 mutant cells, in planktonic and 24h of biofilm conditions. mRNA profiles of WT and deletion mutant cells were generated by deep sequencing, in duplicate, using Illumina HiSeq. The sequence reads  that passed quality filters were analyzed with TopHat followed by HTSeq. RNA-seq data allowed to identify genes whose expression is altered upon 24h of biofilm comparatively to planktonic conditions (1567 upregulated and 1505 downregulated). RNA-seq data allowed to identify genes regulated by the CgEfg1 (650 positively regulated and 514 negatively regulated)  and CgTec1 (487 positively regulated and 595 negatively regulated) transcription factors in biofilm conditions. In all cases a log2fold change ≥1 and p value <0.01 was considered. The transcriptomics data was then used to guide further work to detail the function of each transcription factor in regulating biofilm formation.

overall_design: Yeast mRNA profiles after WT, ∆cgefg1 and ∆cgtec1 cells at planktonic and 24h biofilm conditions were generated by RNA-Seq, in duplicate (each duplicate made of triplicate samples pooled together) using Illumina HiSeq

first: Mafalda

last: Cavalheiro

first: Diana

last: Pereira

first: Carolina

last: Leitão

first: Pedro

last: Pais

first: Cécile

last: Formosa-Dague

first: Easter

last: Ndlovu

first: Andreia

middle: I

last: Pimenta

first: Rui

last: Santos

first: Azusa

last: Takahashi-Nakaguchi

first: Michiyo

last: Okamoto

first: Michaela

last: Ola

first: Hiroji

last: Chibana

first: Arsénio

last: Fialho

first: Geraldine

last: Butler

first: Etienne

last: Dague

middle: C


title: Bone invigorates metastatic seeding [RNA-seq]

first: Igor

last: Bado

summary: We herein examine the transciptioal alteration of a single cell derived MDA-MB-231 subline,SCP21. By retrieving tumor cells inoculated in different sites, we generated multiple mammary fat pad tumor, lung metastases or bone metastasis derived SCP21 sublines. RNA-sequencing uncovered the decreased expression of EZH2 target genes in bone metastases derived cells compared other organ entrained and parental SCP21 cells , suggesting enhanced EZH2 activity. Moreover, such phenotype is reversible upon in vitro culture. As a positive control, bone derived cells were also treated with EZH2 inhibitor, EPZ011989, to confirm the decreased level of EZH2 target genes upon EZH2 inhibition.

overall_design: !0E4 SCP21 cells were implanted to mammary fat pad, lung or right hindlimb of 6 weeks old female nude mice. 4 weeks later, the tissues with tumors were dissected and subjected to tumor dissociation kit. RFP+ tumor cells were sorted by flow cytometry and culture on dishes to collect enough cells for subsequent analysis. The total RNA of SCP21 cells retrieved from different sites , and cultured in vitro for different passages, or treated with EZH2 inhibitor were sequenced, in pair-end way, using Illumina NovaSeq platform.

first: Weijie

last: Zhang

first: Xiang

middle: H


title: ChIP-seq data in A673 Ewing cell line (siCT & siSA2)

first: Olivier

last: Delattre

summary: STAG2, a member of cohesin, is one of the most recurrently mutated genes in human cancer. Here, we investigated STAG2 function in the context of Ewing sarcoma, an aggressive bone tumor driven by EWS-FLI1 oncogene chimeric transcription factor. We transfected A673 cell line with siCT or 2 differents siSTAG2 (siSA2#6 or siSA2#8)  during 72h. The cells were profiled by ChIP-seq for EWS-FLI1, CTCF, cohesin members and H3K27ac marks and highlighted a global conservation of binding for these marks upon STAG2 knock-down

overall_design: ChIP-seq were performed in A673 Ewing sarcoma cell line. Cells were transfected during 72h with either siCT, siSA2#6 or siSA6#8. For each siRNA, we performed ChIP-seq for CTCF, cohesin members (RAD21, SMC1A, STAG1 and STAG2), EWS-FLI1 and H3K27ac. Input of A673 WT was used as normalization controls.

first: Didier

last: Surdez

first: Sakina

last: Zaidi

first: Sandrine

last: Grossetête

first: Virginie

last: Raynal

first: Sylvain

last: Baulande

first: Véronique

last: Hill


title: RNA m6A methylation of 3ʹ splice site prevents binding of U2AF35 to inhibit splicing

city: Gneveva

first: Ramesh

last: Pillai

address: 30, Quai Ernest-Ansermet

department: Department of Molecular Biology

country: Switzerland

institute: University of Geneva

summary: OThe N6-methyladenosine (m6A) RNA modification is widely used to alter the fate of mRNAs. Here we demonstrate that the C. elegans writer METT-10 (orthologue of mouse METTL16) deposits an m6A mark on the 3′ splice site (AG) of the SAM synthetase pre-mRNA which inhibits its proper splicing and protein production. The mechanism is triggered by a rich diet, and acts as an m6A-mediated switch to stop SAM production and regulate its homeostasis. Although the mammalian SAM synthetase pre-mRNA is not regulated via this mechanism, we show that splicing inhibition by 3′ splice site m6A is conserved in mammals. The modification functions by physically preventing the essential splicing factor U2AF35 from recognizing the 3′ splice site. We propose that use of splice site m6A is an ancient mechanism for splicing regulation.

sample_organism:
Caenorhabditis elegans
Bombyx mori
Mus musculus

overall_design: Abundance and distribution of m6A modification was compared between transcriptomes of the mouse and the worm by m6A-IP RNA-Seq on mixed equimolar amounts of corresponding RNAs.    The effect of METT-10 on m6A distribution was analyzed by performing  m6A-IP RNA-Seq on RNA isolated from wild-type and mutant METT10 worms grown either on NA22 or OP50 plates. Biological triplicates were used throuhout the study.

first: Mateusz

last: Mendel

first: Kamila

last: Delaney

first: Radha

last: Raman Pandey

first: Kuan-Ming

last: Chen

first: Joanna

last: Wenda

first: Cathrine

last: Broberg Vågbø

first: Florian

last: Steiner

first: David

last: Homolka

middle: S


title: Bone invigorates metstatic seeding [evolving barcode]

first: Igor

last: Bado

summary: Following the removal of implanted mammary tumors,  nude mice develop multiple-organ metastases at late stage. The metastases may originate from the primary tumors before the resection surgery, or alternatively, from some established metastases. By multiple approaches, we have proved that bone environment could invigorate cancer cells for further dissemination. this study aims to examine if metastatic dissemination from bone to other sites occurs in natural setting of metastatic spread. We herein apply the rapidly evolving barcode system using homing guide RNA/Cas9 to trace the metastases formation in mouse. hgRNA/Cas9 is a self-targeting Crispr system which allows the mutation occurs in the DNA sequence of guide RNA. Tumor cells wer labelled with doxycycline inducible evolving barcoding system. Upon doxycycline treatment the DNA sequence of hgRNA accumulate mutations with time. The diversity of barcodes in each lesion can infer the timeing of seeding while the mutation patterns of barcodes suggest the phylogenetic correlation of metastases. Several findings were made on this study. First, at the terminal stage, multi-organ metastases are not genetically grouped according to sites of metastases. Nonnegative Matrix Factorization (NMF) analysis of mutant barcodes suggested the early disseminated metastases, which have highest level of Shannon entropy, were featured with a common cluster of mutant barcodes irrespective of their locations. Second, most metastases are potentially multiclonal as indicated by multiple clusters of independent mutant barcodes. Third, when we use Shannon entropy as an index of metastasis age , putative parent-child relationship between metastases with unique mutant barcodes clearly exemplified secondary metastatic seeding from bone to other organs. Finally, we did not observe a clear correlation between tumor burden and Shannon entropy across different metastases, suggesting that putative parental metastases might remain small after seeding further metastases.

overall_design: Nude mice or C57BL/6 mice were implanted with barcoded MDA-MB-231 or AT-3 cells, respectively. the mammary tumors were removed when the tumor size reached 1.2cm, and a dose of doxycycline were administated to the mice weekly via intra-peritoneal injection for 5 weeks in nude mice or 4 weeks in C57-BL/6 mice. the metastatic lesions were then dissected with assistance of ex vivo BLI imaging and the DNA of each metastases were isolated. The barcodes from DNA samples were then targeted sequenced using Illumina NextSeq 500/550. Mutation events were categorized from the sequence of barcodes and subjected to the following bioinformatic analysis.

first: Weijie

last: Zhang

first: Jingyuan

last: Hu


title: CTCF HiChIP data in A673 Ewing sarcoma cell lines (siCT & siSA2)

first: Olivier

last: Delattre

summary: STAG2, a member of cohesin, is one of the most recurrently mutated genes in human cancer. Here, we investigated STAG2 function in the context of Ewing sarcoma, an aggressive bone tumor driven by EWS-FLI1 oncogene chimeric transcription factor. A673 Ewing sarcoma cell line was trasfected with siCT or 2 different siRNA targetting STAG2 during 72h and CTCF HiChIP experiments were preformed for each conditions. Analyses of HiChIP data show that STAG2 knowck-down alters  CTCF-anchored loop extrusion.

overall_design: A673 Ewing sarcoma cell line was trasfected with siCT or 2 different siRNAs targeting STAG2 (siSA2#6 or siSA2#8) during 72h. CTCF HiChIP experiments were preformed for each conditions.

first: Didier

last: Surdez

first: Sakina

last: Zaidi


title: Deconvoluting global cytokine signaling networks in natural killer cells [RNA-Seq]

city: Ithaca

first: Colleen

last: Lau

state: New York

address: 930 Campus Road

department: Microbiology & Immunology

institute: Cornell University

summary: Cytokine signaling via signal transducer and activator of transcription (STAT) proteins is crucial for optimal antiviral responses of natural killer (NK) cells. However, the pleiotropic effects of both cytokine and STAT signaling preclude the ability to precisely attribute molecular changes to either source. In this study, we employ a multi-“omics” approach to deconstruct and rebuild the complex interaction of three major STAT signaling pathways in NK cells. We uncover a global STAT4-STAT5 cooperative axis that is distinct and sometimes antagonistic to the STAT1 axis. We generate a network of STAT targets that highlights an integrated negative feedback loop, and demonstrate distinct STAT modes of epigenetic regulation. Finally, we identify shared signatures between mouse in vitro profiles and profiles from viral infection and humans, highlighting clinically translatable targets. Overall, we begin to unravel the intricate crosstalk between cytokine signaling pathways, and offer a valuable resource for improving cellular immunotherapy.

overall_design: RNA-seq was performed on ex-vivo NK cells stimulated with various cytokine combinations.

first: Joseph

last: Sun


title: TBX2 regulated genes in cultured human myometrial cells

city: Amsterdam

first: Remco

last: Keijser

address: Meibergdreef 9

department: Reproductive Biology Laboratory

institute: Amsterdam UMC

summary: Preterm birth, defined as delivery before the 37th week of gestation, is the most common cause of neonatal mortality and the second leading cause of death in children under five years of age. Preterm birth is associated with immediate and long term morbidity as well as growth and developmental delay. The lack of access to human myometrial samples during ongoing uncomplicated pregnancy seriously hampers proper understanding of the sequence of events leading to parturition initiation. In our previous work we used mouse as a model and profiled gene expression in mouse uterus from early E6.5 to late gestation E17.5. We identified Tbx2 as one of the putative upstream regulators during mid-gestation (E10.5, E12.5, E15.5). The role of TBX2 in human myometrium has not been investigated. In this study we identify the gene targets of TBX2 by overexpressing TBX2 in cultured telomerase immortalised myometrial cells followed by gene expression profiling using microarrays.

overall_design: pLenti-CMV-BLAST-DEST vectors harbouring TBX2 or EGFP (control) were transduced into telomerase immortalised human myometrial cells. Total RNA from three independent experiments were isolated 3 days post transduction and used for generating gene expression profiles by microarray hybridisation. Differential gene expression was calculated between TBX2 overexpressing cells and EGFP expressing controls.

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