title: CRISPR-Cas9 mutagenesis of A549 cells for variants resistant to the ExoU toxin from Pseudomonas aeruginosa

status: Public on Dec 01 2020

city: Grenoble

first: Vincent

last: Deruelle

address: 17 avenue des Martyrs

institute: CEA Grenoble

summary: Pseudomonas aeruginosa is a leading cause of nosocomial infection and is responsible for severe acute and chronic infections such as pneumonia, urinary tract infections and lung infections in cystic fibrosis patients. The bacterium possesses a type 3 secretion system whose expression is linked with poor outcomes in both animal models and human patients. In particular, this syringe-like apparatus injects ExoU, the most toxic T3SS effector. However, the mechanism of ExoU in P. aeruginosa’s virulence remains elusive compare to the other T3SS toxins. It was previously suggested that the toxin uses a host trafficking system to reach the plasma membrane and to induce cell necrosis. In this work, we demonstrated that once injected into the cell cytoplasm, ExoU binds to DNAJC5+ vesicles to rapidly reach the plasma membrane.

overall_design: PA14 is a P. aeruginosa strain expressing ExoU, as well ExoT and ExoY T3SS effectors. The virulence of this strain has been associated with ExoU injection, as ExoU induces rapid cell death in different cell types (epithelial or endothelial cells and macrophages). A549 cells are adenocarcinomic human alveolar basal epithelial cells and were selected for this study, as they possess characteristics from pneumocytic cells, which are in contact with P. aeruginosa in lung infection. PA14 causes A549 cell death in an ExoU-dependent manner. A549 cells were transduced with a lentiviral library expressing guide-RNAs with the endonuclease Cas9 in the same plasmid. This one-component library contains 71,090 total gRNAs targeting 18,053 genes (4 gRNAs per gene). The gRNA library-expressing A549 cells (or A549-CRISPR cells) were infected for 90 min with PA14 at MOI of 10. Remaining cells (20-30%) were expanded with antibiotics to approximately 70% confluence and were subjected to a second and third round of infection. The gRNA sequences from surviving cells were identified via next-generation sequencing (NGS) and candidate genes ranked based on the number of unique gRNAs versus NGS reads according to MAGeCK method. DNAJC5 was the only gene to stand out with the most significant gRNAs compared to uninfected cells. DNAJC5 is an ubiquitous cytoplasmic protein, mostly located at the surface of late endosomes. It functions as a co-chaperone with Hsc70/Hsp70 proteins in protein homeostasis and is involved in an unconventional protein secretion pathway named MAPS (Misfoded-Associated Protein Secretion) allowing the transportation of misfolded proteins from the perinuclear region to the plasma membrane.

first: Philippe

last: Huber


title: A cell competition-based drug screen identifies a novel compound that targets c-Myc addiction of leukemia cells

status: Public on Dec 07 2020

city: Oslo

first: Jorrit

last: Enserink

address: Ullernchausseen 70

department: Molecular Cell Biology

country: Norway

institute: The Norwegian Radium Hospital

type: Expression profiling by high throughput sequencing

summary:
Purpose: BCR-ABL-positive acute lymphoid leukemia (ALL) has a dire prognosis. Despite improved disease-free survival due to implementation of TKIs in front-line therapy, patient survival remains unsatisfactory and there exists a need for new treatments. Therefore, we performed a drug screen based on competition between untransformed cells and BCR-Abl-transformed cells, and identified several compounds that selectively reduce the competitive fitness of BCR-Abl-transformed cells. Using a systems approach we discovered that one of these compounds, DJ34,  induces potent activation of p53 and rapid degradation of c-Myc, which is frequently deregulated in leukemia. DJ34 treatment induced apoptosis, cell cycle arrest and cell differentiation and inhibited survival of primary AML cells, both ex vivo and in a zebrafish PDX model. The goals of this study is to check the effect of DJ34 on transcriptome profile of BCR-Abl expressing BaF3 cells.
Methods: mRNA profiles of BaF3 cells expressing BCR-Abl treated with DMSO or 20µM DJ34 for 6hrs were generated by Illumina Hiseq 4000 SE50, in triplicate. Then, clean reads (as provided by BGI) were mapped to the GRCm38.85 genome assembly using Tophat2 (v. 2.1.1) [1] using default options BAM files were indexed using SAMtools [2]. Differential expression data was produced using cuffquant and cuffdiff with default options, from the cufflinks suite (v 2.2.1 / SVN rev 4237) [3]. Reference genome for the primary assembly and gene annotations used are revision 85 of GRCm38, from ensembl.org. The .Bam and .tdf files were used for quantification and visualization in IGV respectively.  [1] Kim, Daehwan, et al. "TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions." Genome biology 14.4 (2013): R36.  [2] Li, Heng, et al. "The sequence alignment/map format and SAMtools." Bioinformatics 25.16 (2009): 2078-2079.  [3] Trapnell, Cole, et al. "Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks." Nature protocols 7.3 (2012): 562.
Results: Using data analysis workflow described above, we identified differentially expressed genes in the control and DJ34 treated BaF3 cells expressing BCR-Abl cells.
Conclusions: Competition based drug screening has  identified DJ34 that selectively erradicates BCR-Abl expressing BaF3 cells. Our RNa-seq basaed transcriptome analysis  shows that DJ34 induces potent activation of p53 and rapid degradation of c-Myc, which is frequently deregulated in leukemia.

overall_design: Total mRNA profiles of BaF3 cells expressing BCR-Abl treated with DMSO or 20µM DJ34 were generated by Illumina Hiseq 4000 SE50, in triplicate.

first: Dagim

middle: S

last: Tadele

first: Joseph

last: Robertson

first: Richard

last: Crispin

first: Maria

middle: C

last: Herrera

first: Marketa

last: Chlubnova

first: Laure

last: Piechaczyk

first: Pilar

last: Ayuda-Durán

first: Sachin

last: Kumar Singh

first: Tobias

last: Gedde-Dahl

first: Yngvar

last: Floisand

first: Jørn

last: Skavland

first: Jørgen

last: Wesche

first: Bjørn-Tore

last: Gjertsen

middle: M


title: Use of NanoLuc-Based Reporters that Monitor Nonsense Suppression and Inhibition of Nonsense-Mediated mRNA Decay to Identify Potent New Agents That Partially Reverse the Effects of Nonsense Mutations

city: Baltimore

first: Rachel

last: Green

state: MD

address: 725 N Wolfe St

department: Molecular Biology and Genetics

country: USA

institute: Johns Hopkins University School of Medicine

summary: Premature termination codons (PTCs) lead to loss of protein function by 1) ending mRNA translation before a full-length protein is made, and 2) by triggering nonsense-mediated mRNA decay (NMD), a pathway that targets a PTC-containing mRNA for degradation. Nonsense suppression therapy aims to restore protein function by suppressing termination at PTCs (called readthrough, or RT). However, the efficiency of current readthrough agents is generally quite low. We reasoned that by stimulating both readthrough and increasing mRNA levels, greater protein function can be restored than with readthrough alone. In this study, we developed a series of novel NanoLuc reporters designed to identify and differentiate compounds that induce readthrough, enhance mRNA abundance (by NMD inhibition or other mechanisms), or target both mechanisms simultaneously (referred to as dual RT/NMD reporters). We show that treatments that promote readthrough and NMD inhibition led to synergistic increases in NanoLuc activity of the RT/NMD reporter over either condition alone. We then used a dual RT/NMD reporter to carry out a high throughput screen of a library of 771,345 compounds. We identified 180 compounds with the ability to increase NanoLuc activity in our dual RT/NMD reporter assay. To confirm that such synergy can also amplify protein function in a disease model, we treated cells expressing a CFTR-Y122X mini-intron construct with one hit from this screen, SRI-37240. We found that this compound produced a much larger increase in CFTR activity compared to either the RT compound G418 +/- the NMD inhibitor amlexanox, and the activity obtained could be further enhanced with CFTR modulators. These results confirm the utility of these new reporters to identify many potent new molecules that counteract the effects of nonsense mutations.

overall_design: 9 ribosome profiling samples are included from HEK293T cells

first: Jamie

last: Wangen


title: Transcriptomic Signaling Pathways involved in a naturalistic model  of Inflammation-related Major Depressive Disorder and its remission

city: Bordeaux

first: Aline

last: FOURY

address: 146 rue Léo Saignat

country: France

institute: INRAE

summary: This study aimed at identifying molecular biomarkers specific to inflammation-related subtype of MDD in order to improve diagnosis and treatment. For this, we performed whole-genome expression profiling from peripheral blood in a naturalistic model of inflammation-associated MDD represented by comorbid depression in obese patients.

overall_design: Depressed patients were diagnosed with the Mini-International Neuropsychiatric Interview and the 10-item, clinician administered, Montgomery-Asberg Depression Rating Scale. From a cohort of 100 massively obese patients we selected 33 of them for transcriptomic analysis with 24 patients that were again analyzed 4-12 months after bariatric surgery.

first: Marie-Pierre

last: Moisan

last: Foury

first: Sandra

last: Dexpert

first: Lison

last: Huet

first: Steve

middle: W

last: Cole

first: Cédric

last: Beau

first: Damien

last: Forestier

first: Patrick

last: Ledaguenel

first: Eric

last: Magne

first: Lucile

last: Capuron


title: Liver regeneration patterns in hiPSCs-derived HLCs matured on-chip

city: Tokyo

first: Stéphane

last: Poulain

address: Fw-203, 4-6-1, Komaba, Meguro-ku

department: Institute of Industrial Science

country: Japan

institute: The University of Tokyo

summary: We investigated the transcriptome of human induced pluripotent stem cells (hiPSCs) differentiated into hepatocyte-like cells (HLCs) in a biochip culture environment vs. standard Petri dishes cultures using nanoCAGE, a method for promoters, transcription factors, and transcriptome analysis.

overall_design: Analysis of the transcriptome profiles of human induced pluripotent stem cells (hiPSCs) differentiated into hepatocyte-like cells (HLCs) in a biochip culture environment vs. standard Petri dishes cultures.

first: Mathieu

last: Danoy

first: Yannick

last: Tauran

first: Rachid

last: Jellali

first: Johanna

last: Bruce

first: Marjorie

last: Leduc

first: Morgane

last: Le Gall

first: Francoise

last: Gilard

first: Taketomo

last: Kido

first: Hiroshi

last: Arakawa

first: Karin

last: Araya

first: Daiki

last: Mori

first: Yukio

last: Kato

first: Hiroyuki

last: Kusuhara

first: Charles

last: Plessy

first: Atsushi

last: Miyajima

first: Yasuyuki

last: Sakai

first: Éric

last: Leclerc


title: The role of CD11C positive and negative microglia populations in Neuromyelitis optica

city: La Jolla,

first: Inge

last: Holtman

state: California

address: 9500 Gilman Drive

department: CMM

institute: UCSD

summary: Background: Tissue macrophages contribute to development and protection, both requiring appropriately timed and located source(s) of factors controlling growth, cell differentiation and migration. Goal: To understand the role of microglia (tissue macrophages of the central nervous system), in promoting neurodevelopment and controlling neuroinflammation. Summary of findings: We show that microglia fulfill both these roles. In contrast to adult cells, neonatal microglia show a unique neurogenic phenotype with stem cell-like potential. Neonatal microglia are protective against neuroinflammation, and their transplantation ameliorates experimental autoimmune encephalomyelitis. A CD11c+ microglial subset predominates in primary myelinating areas of the developing brain and expresses genes for neuronal and glial survival, migration and differentiation. CD11c+ microglia are also found in clusters of repopulating microglia after experimental ablation and in neuroinflammation in adult mice, but despite some similarities, they do not recapitulate neurogenic neonatal microglia characteristics. Conclusions: We therefore identify a unique phenotype of neonatal microglia that deliver signals necessary for neurogenesis and myelination and suppress neuroinflammation.

overall_design:
The overall design was to compare transcriptomes of subsets of microglia isolated adult mice with a neuroinflammatory disease (Neuromyelitis optica)
NMO = neuromyelitis optica


title: Microglial responses to CSF1 overexpression do not promote expansion of other glial lineages

city: Madison

first: Ziyue

last: Wang

state: WI

address: 425 Henry Mall

institute: UW Madison

summary: CSF1 expression in the central nervous system (CNS) increases in response to a variety of stimuli, and CSF1 is overexpressed in many CNS diseases. In young adult mice we previously showed that CSF1 overexpression in the CNS caused proliferation of IBA1+ microglia without promoting expression of M2 polarization markers. Here we further examine the impacts of increased CSF1 levels in the brain. As CSF1 over-expressing mice age, IBA1+ cell numbers are constrained by a decline in proliferation rate. Compared to controls, there were no differences in expression of the M2 markers ARG1 and MRC1 (CD206) in CSF1 overexpressing mice of any age, indicating that even prolonged exposure to increased CSF1 is not sufficient to promote M2 polarization in vivo. Moreover, RNA-sequencing (RNA-seq) confirmed the lack of increased expression of markers of M2 polarization in microglia exposed to CSF1 over-expression, but did reveal changes in expression of other immune related genes. Although treatment with inhibitors of the CSF1 receptor, CSF1R, has been shown to impact other glia, no increased expression of astrocyte or oligodendrocyte lineage markers was observed in CSF1 OE mice. Our data indicate that CSF1 overexpression as an isolated stimulus has limited impacts in the CNS, and that microglia ultimately adapt to the presence of the CSF1 mitogenic signal.

overall_design: Compared mRNA profiles of 4 samples from CSF1 over-expression mice with 4 control mice samples.

first: Lara

last: Collier


title: RNA sequencing of human primary myotubes from lean and obese subjects

status: Public on Nov 28 2020

city: Salt Lake City

first: Katsuhiko

last: Funai

state: UT

department: Molecular Medicine

institute: University of Utah

summary: Fasting muscle biopsy samples from the vastus lateralis were collected from lean (LN: BMI < 25 kg/m2) and obese (OB: BMI > 40 kg/m2) subjects. Primary myoblasts were isolated from the biopsy samples, maintained in vitro, and differentiated to myotubes.

overall_design: Total RNA from three samples per group was isolated by Qiagen RNeasy kit and quality was assessed on a bioanalyzer (RIN>8 for each sample). Poly-A selected cDNA libraries were constructed and sequenced on an Illumina HiSeq2000 by Otogenetics Corp (Norcross, GA) producing at least 20 million 2X101 paired end reads per sample. Reads were aligned to the NCBI GRCh37 USCS hg 19 reference genome with TopHat. RefSeq annotations were used as the gene model and differential expression was assessed with Cufflinks, correcting for multiple comparisons. Gene enrichment and pathway analysis were conducted with the Database for Annotation, Visualization and Integrated Discovery (DAVID).


title: DNA Methylation in the PFC in response to peripheral neuropathic pain and therapeutic treatment with s-adenosylmethionine

status: Public on Nov 24 2020

city: Minneapolis

first: Laura

last: Stone

address: 420 Delaware Street SEMMC 294

institute: University of Minnesota

type: Methylation profiling by high throughput sequencing

summary: Chronic pain is associated with persistent but reversible structural and functional changes in prefrontal cortex (PFC). This stable yet malleable plasticity implicates epigenetic mechanisms, including DNA methylation, as a potential mediator of chronic pain-induced changes. We have previously demonstrated that chronic oral administration of the methyl donor S-adenosyl methionine (SAM) is capable of attenuating long-term peripheral neuropathic pain and affecting global PFC DNA methylation. However, there was no evidence as of yet that alterations in DNA methylation underlie SAM-mediated pain attenuation. To elucidate these mechanisms, we performed epigenome-wide analysis of mouse PFC after 4 months of SAM treatment initiated 3 months following induction of peripheral nerve injury. Over injury triggered chronic pain was associated with 4000 differentially methylated genomic regions which were enriched in intracellular signaling, cell locomotion and migration, cytoskeletal structure, and cell adhesion pathways. A third of the regions that were differentially methylated in chronic pain mice (1415 regions representing 1030 genes) were reversed by SAM treatment. 100 genes with known pain-related function were differentially methylated following nerve injury; several of which were reversed by SAM treatment. These results demonstrate that DNA methylation alterations in the PFC caused by chronic pain and reversed by SAM treatment providing at least partially a mechanism of action.  These data point to the possibility of epigenetic modulators such as SAM as novel approach to treat chronic pain.

overall_design: Comparison of DNA Methylation between Sham-Vehicle, Sham-SAM Treated, Injury-vehicle, and injury-SAM treated animals

first: Lucas

last: Topham

first: Moshe

last: Szyf

first: Stephanie

last: Gregoire


title: Transcriptional Changes in Rat Dorsal Root Ganglia Neurons During Stretch-Mediated Axon Growth

status: Public on Nov 30 2020

city: Newark

first: Joseph

middle: R.

last: Loverde

state: NJ

address: 111 Lock Street

department: Department of Biomedical Engineering

institute: New Jersey Institute of Technology

summary: The development of meter-long axons within the nervous system is a remarkable, yet unresolved biological process.  The most widely studied aspects of neuronal growth focus on the extension and chemotropism of growth cones.  However, over the course of organismal development, short axons elongate up to one meter in length with the systemic expansion of mitotic tissues.  The preeminent regulatory mechanism for such synchronized growth between the nervous system and the tissues it spans, is the biomechanical stretch of axons, a known stimulus of axon growth.  Here, we reveal the transcriptional profile of stretch-mediated axon growth as found using embryonic rat dorsal root ganglia neurons stretch-grown in vitro.

overall_design: Computer-controlled bioreactors were used to maintain a persistent state of 25 % axon strain for one week to maximize mechanotransduced signaling changes in vitro.  Genome-wide DNA microarray analysis was performed on the corresponding somata of contiguous high density axons that spanned 1.7 cm in length.  Non-stretch grown sham cultures were established from the same biological samples as stretch-grown cultures, which were used to calculate fold-changes relative to stretch-grown cultures.

middle: R

first: Patricia

last: Soteropoulos

first: Bryan

middle: J

last: Pfister


title: The pan-cancer lncRNA PLANE regulates an alternative splicing program and promotes cancer pathogenesis

status: Public on Nov 27 2020

city: Zhengzhou

first: liu

last: Teng

address: No 7,Weiwu Road,Jinshui  District

department: Translational Research Institute

country: China

institute: Henan Provincial People’s Hospital and People’s Hospital of Zhengzhou University

summary: Genomic amplification of the distal portion of chromosome 3q that encodes a number of oncogenic proteins is one of the most prevalent chromosomal deformities. Here we functionally characterise a non-protein product of this region, the long noncoding RNA (lncRNA) PLANE, which is upregulated in diverse cancer types through copy number gain as well as transcriptional activation by E2F1. PLANE forms an RNA-RNA duplex with the nuclear receptor co-repressor 2 (NCOR2) pre-mRNA at intron 45, binds to heterogeneous ribonucleoprotein M (hnRNPM) and facilitates the association of hnRNPM with the intron, leading to repression of the alternative splicing (AS) event generating NCOR2-202, a major protein-coding NCOR2 AS variant. As such, PLANE promotes cancer cell proliferation and tumorigenicity and its upregulation is associated with poor outcome of patients. These results uncover the function and regulation of PLANE and suggest that PLANE may constitute a therapeutic target in the pan-cancer context.

overall_design: For RNA-seq analysis of PLANE siRNA versus control siRNA, the A549 cells were transfected with siRNAs for 48 hours before harvesting.

first: Liu

first: YuChen

last: Feng

first: Su

middle: T

last: Guo

first: Pei

middle: L


title: Influence of histone lysine demethylase JMJD2-specific inhibition on the senescence-associated secretory phenotype developed in human stromal cells upon DNA damage

city: Shanghai

first: Yu

last: Sun

address: 320 Yueyang Rd, Life Sciences Building A #1508

department: Shanghai Institute of Nutrition and Health

institute: Chinese Academy of Sciences

summary: Recent advances in next generation sequencing (NGS) has revolutionized system-based analysis of genome-wide expression, cellular pathways and responses. We performed this epigenetic study to streamline the transcriptome profiling (RNA-seq) of human stromal cells developing a typical senescence-associated secretory phenotype (SASP) upon stress induced by DNA damage or DNA damage together with pharmacological targeting of JMJD2, a trimethylation-specific demethylase of histone H3K9 and H3K36.

overall_design: Overall transcript profiles of human primary prostate stromal cells (PSC27) were generated by deep sequencing in triplicate, using Illumina NovaSeq 6000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays

first: Boyi

last: Zhang


title: Effect of UBLCP1 knockdown on gene expression in HeLa S3 cells

city: Toyama

first: Yutaka

last: Hirose

state: Toyama

address: 2630 Sugitani

department: Graduate School of Medicine and Pharmaceutical Sciences

institute: University of Toyama

summary:
Human UBLCP1 is a unique nuclear phosphatase which has both ubiquitin-like domain and CTD phosphatase-like domain. UBLCP1 interacts with proteasome subunit Rpn1 and suppresses the activity of proteasome, but its role in gene expression is unknown.
To identify genes whose expression levels are affected by UBLCP1 knockdown in human cultured cells, we performed gene expression profiling by microarray analysis.

overall_design: HeLa S3 cells were seeded on 6-well plates at 1.0 × 10^5 cell/well and cultured at 37°C 24 h before transfection. Cells were transfected with either negative control siRNA or siRNA specific to human UBLCP1 gene using Lipofectamine RNAi MAX (ThermoFisher) and further cultured for 72 h at 37°C.

first: Hiroyasu

last: Ishiguro

first: Miyuki

last: Kano

first: Yoshiaki

last: Tabuchi


title: An epigenetic program established by gene - environment interactions initiates pancreatic carcinogenesis

city: New York

first: Yu-Jui

last: Ho

state: New York

address: 417 E 68th St

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Protein mimetic amyloid inhibitor potently abrogates cancer-associated mutant p53 aggregation and restores tumor suppressor function

status: Public on Nov 23 2020

city: Abu Dhabi

first: Mohamed

last: Al-Sayegh

address: Saadiyaat Island - 1st floor ERB, Room 136, P.O. Box 129188

department: Biology

country: United Arab Emirates

institute: New York University Abu Dhabi

summary: Transcriptome analysis of protein mimetic amyloid inhibitor that potently abrogates cancer-associated mutant p53 aggregation and restores tumor suppressor function

overall_design: RNA isolates of Mia PaCa-2 cells extracted at different conditions. Conditions include growth media (DMEM + 10%FBS) with or without ADH-6 inhibitor.

first: Laura

last: Karpauskaite

first: Ibrahim

last: Chehade

first: Mazin

last: Magzoub


title: Next Generation Sequencing  Quantitative Analysis of altered expression of genes in lncRNA ELNAT1 knockdown bladder cancer cells

status: Public on Nov 20 2020

city: Guangzhou

first: Yuming

last: Luo

state: Guangdong

address: 107 Yanjiang West Avenue,Yuexiu district

department: General Surgery

institute: Sun yat-sen Memorial Hospital

summary: Bladder cancer (BCa) is one of the most common genitourinary malignancies worldwide, with a high recurrence and mortality rate. Previous study revealed that EV-packaged ELNAT1 played an important role in the occurrence and development of human cancer. However, the specific mechanism of EV-packaged ELNAT1 in inducing the lymphangiogenesis and lymphatic metastasis of BCa is still unclear. Our study aims to detect the target genes of ELNAT1 and the underlying mechanism in the lymphatic metastasis of BCa.

overall_design: To explore the molecular mechanism of ELNAT1 in the lymphatic metastasis of bladder cancer, the UM-UC-3, T24 and 5637 bladder cancer cell lines with ELNAT1 stably overexpress were constructed. The total RNA of the transfected cells was extracted and the next generation sequencing was used to identify the expressing profile difference between NC and overexpression group.

first: Changhao

last: Chen

first: Tianxin

last: Lin


title: CIT functions as an oncogene in ESCC

first: Wenfeng

last: Lu

address: 180 Fenglin Street

institute: Zhongshan Hospital and Laboratory of Neurology, Institute of Integrative Medicine, Fudan University

summary:
High expression of citron kinase contributes to the development of esophageal squamous cell carcinoma
This study aimed to investigate the role and potential regulatory mechanism of citron kinase (CIT) in esophageal squamous cell carcinoma (ESCC).

overall_design: Culture conditions of ecA-109 cells DMEM+10%FBS were used to infect 3V3 cell samples with the effective target virus KD and control NC, respectively. PCR and microarray detection were performed on the samples collected 72 hours after infection

first: Lu

last: Wenfeng


title: Time-course transcriptomic profiling of C57BL/6 mouse neurons from the dorsal root ganglion before and after a carrageenan injection into the left hind paw

status: Public on Nov 19 2020

city: Marseille Cedex 9

first: Michaël

last: Pierrelée

address: Case 907 - Parc Scientifique de Luminy

institute: Aix-Marseille University, CNRS, IBDM

summary: Carrageenan injection induces tissue inflammation and high mechanosensitivity. Dorsal root ganglions contain the cellular body of the sensory neurons which project their axon to the periphery, monitoring this inflammation and transmitting the mechanical stimuli to the spinal cord. To explore whether the sensory neurons underwent transcriptional changes and how long these changes lasted, we injected carrageenan into the left hind paw of mice and sequenced the dorsal root ganglions related to this area 1, 3 and 30 days after the injection.

overall_design: For each biological sample, 2 to 3 mice were sacrificed and the dorsal root ganglions related to their left hind paw (L3 to L5) were pooled together before RNA extraction and sequencing. The experiment consisted of injecting 20µL carrageenan 1% into the left hind paw of 8 weeks old C57BL/6J mice and sacrificing them 1, 3 and 30 days after the injection. Baseline material (D0) was obtained from naïve untreated mice. Each time-point had two biological replicates.

first: Ana

last: Reynders

first: Aziz

last: Moqrich

first: Bianca

middle: H

last: Habermann


title: RNA-seq profiling of fibroblasts isolated from two distinct lung metastases stages and from normal lungs

city: Tel Aviv Yaffo

first: Neta

last: Erez

address: Haim Levanon

department: Pathology

country: Israel

institute: Tel Aviv University

summary: We found that fibroblasts derived from lung metastases display specific gene signatures related to distinct functional enrichments, including stress, ECM remodelling, and inflammation.

overall_design: Fibroblasts were isolated from lungs of MMTV-PyMT;Col1a1-YFP mice at defined metastatic stages (micro-metastases, macro-metastases), and from age-matched normal control mice (FVB/n;Col1a1-YFP mice). RNA was isolated and RNA-seq was performed.

first: O

last: Shani

first: N


title: Gene expression profiling in the pathogenesis of Visna-Maedi viral disease

city: Leioa

first: Begoña

last: Jugo

state: Basque Country

address: Sarriena auzoa s/n

department: Genetics, Physical Anthropology and Animal Physiology

country: Spain

institute: University of the Basque Country (UPV/EHU)

summary: The major goal of this research is to find out the host cellular factors that are associated with VMV infection and lesions, using a gene expression microarray technology.

overall_design: For gene expression microarray analysis, a total of 15 Rasa sheep were included, belonging to a herd located in Zaragoza (Spain). 11 of the animals were infected with VMV, 6 had lung lesions and 5 were seropositive for VMV but asymptomatic. The remaining 4 animals were seronegative for VMV

first: Naiara

last: Abendaño

first: Aitor

last: Esparza-Baquer

first: Irantzu

last: Bernales

first: Ramses

last: Reina

first: Damián

last: de Andrés


title: Effect of empagliflocin on basal and IL1-ß-mediated gene expression in human proximal tubular cells

status: Public on Nov 18 2020

city: Innsbruck

first: Johannes

last: Leierer

address: Anichstr. 35

department: Internal Medicine IV - Nephrology

country: Austria

institute: Medical University Innsbruck

summary: We aim at elucidating pathways involved in SGLT2i-mediated nephro-protection by using a systematic molecular approach in 2 independent human proximal tubular cell lines.

overall_design: Human proximal tubular cells (HK-2 and RPTEC/TERT1) were serum- and supplement-starved for 24 h and then - after an additional medium change - stimulated for 24 h with 10 ng/ml IL-1ß or 500 nM empagliflocin or left unstimulated for another 24h (control).

first: Markus

last: Pirklbauer

first: Gert

last: Mayer

first: Petra

last: Staudinger


title: Microarray profiling analysis of circular RNAs expression in bladder cancer [lncRNA profiling]

city: Shenyang

first: Yunhong

last: Zhan

address: No. 36 Sanhao Street

institute: Shengjing Hospital of China Medical University

summary: Background: Growing evidence has shown the association of long noncoding RNA/microRNA/mRNA is implicated in tumor initiation, development, and progression. Long noncoding RNA (lncRNA) HAND2-AS1 exhibits anti-cancer effects in diverse cancers. However, the knowledge of HAND-AS1 in bladder cancer remains largely unknown. The present study aims to investigate the effects and mechanisms of HAND-AS1 in bladder cancer progression.  Methods: The expression of lncRNA was analyzed by RT2 lncRNA PCR Arrays. The differential expressed lncRNAs were further verified by qRT-PCR. The relationship between lncRNA expression and clinical features was evaluated with Spearman correlation test. Cell proliferation was measured by MTT assay. Cell apoptosis percentage was detected by ANNEXIN V-PI analysis. The promoter activity was illustrated by Luciferase assay, and the change of microRNA and protein was detected by qRT-PCR and western blot, separately.  Results: The expression of HAND2-AS1 declined in bladder cancer and correlated with depth of invasion and grades negatively. Restoration of HAND2-AS1 hampered cell growth by provoking cell apoptosis. Furthermore, one of the HAND2-AS1 sponge, miR-146, was found overexpression in bladder cancer tissue and cell lines. Expression of miR-146 related to HAND2-AS1 expression negatively. One of the targeted genes of miR-146, retinoic acid receptor beta (RARB) was downregulated in bladder cancer. In addition, the expression of RARB related to miR-146 negatively. Lost-of-function and gain-of-function experiments were used to identify the mechanisms underlying association of lncRNA HAND2-AS1: miR-146: RARB. miR-146 targeted RARB directly and hindered RARB-mediate apoptosis. However, the hindrance was impaired by HAND2-AS1 notably.  Conclusion: HAND2-AS1 diminished miR-146 expression, thereby releasing the suppression of miR-146 on RARB-mediated apoptosis, promoting bladder cancer regression.

overall_design: Three primary patients primary bladder cancer were recruited in the present study. Microarray based LncRNA expression profiles were obtained with Qiagen custom RT2 PCR Arrays.


title: Microarray profiling analysis of circular RNAs expression in bladder cancer


title: RNA sequencing comparing mouse lung cancer cell lines derived from Kras G12D Trp53 -/- and Kras G12D Trp53 -/- sgMga tumors

status: Public on Nov 17 2020

city: Seattle

first: Haritha

last: Mathsyaraja

state: WA

address: 1100 Fairview Ave N

department: Basic Sciences

institute: Fred Hutch

summary: The goal of this study was to compare expression profiles of mouse Kras G12D Trp53 -/- lung cancer cells that have inactivated MGA compared to controls

overall_design: Each condition (Empty vs. sgMga) is represented in 3 independent sgMga lines in biological triplicates and 2 control Empty lines in biological triplicate (n=9 sgMga n=6 Empty)

first: Robert

middle: N

last: Eisenman


title: Microarray profiling analysis of circular RNAs expression in bladder cancer [miRNA profiling]

overall_design: Three primary patients primary bladder cancer were recruited in the present study. Microarray based miRNA expression profiles were obtained with Qiagen custom miScript miRNA PCR Arrays.


title: RNA sequencing comparing mouse Kras G12D lung tumors that have WT or inactivated Mga via CRISPR

summary: The goal of this study was to compare expression profiles of mouse Kras G12D lung tumors that have inactivated MGA compared to controls

overall_design: 8 Kras G12D Empty vector control tumors and 6 sgMga Kras G12D tumors were used for expression profiling


title: RNA sequencing comparing human colon organoids transduced with Empty control vs. sgMGA (guide RNA targeting MGA)

status: Public on Nov 16 2020

summary: The goal of this study was to compare expression profiles of normal colon organoids that have inactivated MGA compared to control organoids

overall_design: Each condition (Empty vs. sgMGA) is represented in quadruplicate (4 biological replicates each harvested 14D post transduction with control or sgMGA lentivirus)


title: CUT&RUN studies comparing occupancy of MAX, MGA, MYC and L3MBTL2 occupancy in Empty vector and sgMGA transduced A549 lung adenocarcinoma cells

summary: The goal of this study was to examine the genomic occupancy of  MAX, MGA, MYC and L3MBTL2 in MGA depleted vs. control cells

overall_design: Two independent sets of control Empty and one set of sgMGA A549 cells


title: Genomic occupancy of MYC and members of the PRC1.6 complex (MGA, E2F6, MAX, L3MBTL2) in MGA WT (Empty) and MGA depleted (sgMga) KrasG12D Trp53 -/- mouse lung cancer lines

summary: Conventional crosslinked ChIP was performed on cell lines derived from control (Empty) and sgMga transduced tumors. We wanted to assess PRC1.6 member and MYC binding in the presence and absence of MGA.

overall_design: Conventional X-ChIP was performed on Empty and sgMga KP mouse lung cancer lines. Antibodies used: IgG control rabbit, IgG control mouse, anti-MAX, anti-MYC, anti-MGA, anti-L3MBTL2, anti-E2F6)


title: Engineered Tr1 cells designed for clinical use can eliminate primary pediatric AML blasts

status: Public on Nov 10 2020

city: Stanford

first: Molly

last: Uyeda

state: CA

address: 265 Campus Drive

institute: Stanford University

summary:
Purpose: To investigate the transcriptome of primary pediatric acute myeloid leukemia to identify molecular signatures  correlated with sensitivity to LV-10 mediated killing
Method: RNA sequencing of polyA enriched pediatric acute myeloid leukemia bone marrow aspirates
Results: pAML killing sensitivity is associated with the expression of a myeloid maturation signature, while resistant pAMLs expressed a more stem cell-like signature
Conclusions: Pediatric acute myeloid leukemia samples have different sensitivities to killing by LV-10 in vitro and the transcriptomes of killing-sensitive and killing-resistant lines differ

overall_design: 14 primary pediatric acute myeloid leukemia bone marrow aspirates were incubated for 2h in complete X-VIVO15 supplemented with IL-3 (20 ng/mL, Peprotech) and G-CSF (20 ng/ml, Peprotech) at 10^6 cells/ml and then lysed for RNA sequencing

first: Cieniewicz

last: Brandon

first: Uyeda

last: Molly

first: Cepika

last: Alma-Martina

first: Roncarolo

last: Maria-Grazia


title: Oxidative stress dependent regulon of AosR

status: Public on Nov 11 2020

city: Delhi

first: Vinay

middle: K.

last: Nadnicoori

state: DELHI

address: National Institute of Immunology, Near JNU EAST GATE, ARUNA ASAF ALI MARG, NEW DELHI-110067

country: India

institute: National Institute of Immunology

summary: Analyzing differences in transcriptome profile of Rv and RvDaosR under normal and oxidized conditions

overall_design: Wild type H37R v (Rv) and mutant of Rv1332/ AosR (RvDAosR) were inoculated at 0.05 OD. At 0.2 OD, cultures were either left untreated or treated with 50 micromolar of CHP. Post 24 hours total RNA was isolated and RNA seq was performed

last: Kumar Nandicoori

first: Mehak

last: Zahoor Khan


title: Chromatin accessibility profiling in Neurospora crassa reveals features associated with accessible and inaccessible chromatin

status: Public on Nov 12 2020

city: Athens

first: Zachary

middle: A

last: Lewis

state: GA

address: 1000 Cedar St. Biosciences Bldg

department: Microbiology

institute: University of Georgia

summary: Background: Regulation of chromatin accessibility and transcription are tightly coordinated processes. Studies in yeast and higher eukaryotes has described accessible chromatin regions, but little work has been done in filamentous fungi. Results: Here we present a genome-scale characterization of accessible chromatin regions in Neurospora crassa, which revealed characteristic molecular features of accessible and inaccessible chromatin. We present experimental evidence of inaccessibility within heterochromatin regions in Neurospora, and we examine features of both accessible and inaccessible chromatin, including the presence of histone modifications, types of transcription, transcription factor binding, and relative nucleosome turnover rates. Chromatin accessibility is not strictly correlated with expression level. Accessible chromatin regions in the model filamentous fungus Neurospora are characterized the presence of H3K27 acetylation and commonly associated with pervasive non-coding transcription. Conversely, methylation of H3 lysine-36 catalyzed by ASH1 is correlated with inaccessible chromatin within promoter regions. Conclusions: In N. crassa, H3K27 acetylation is the most predictive histone modification for open chromatin. Conversely, our data show that H3K36 methylation is a key marker of inaccessible chromatin in gene-rich regions of the genome. Our data are consistent with an expanded role for H3K36 methylation in intergenic regions of filamentous fungi compared to the model yeasts, S. cerevisiae and S. pombe, which lack homologs of the ASH1 methyltransferase.  of accessible chromatin in Neurospora

overall_design: Mycelial cultures collected at 18 hours. Cells lysed and subjected to ATAC-seq or chromatin immunoprecipitation. 18 total samples, replicates vary by sample.

first: Aileen

last: Ferraro

first: Zefu

last: Lu

first: Abigail

last: Courtney

first: Masayuki

last: Kamei

last: Schmitz


title: Long-Term Soy Protein Isolate Intake Reduces Liver Steatosis through Changes in Global Gene Expression in Obese Zucker Rats

city: Fayetteville

first: Byung-whi

last: Kong

state: AR

address: 1260 W. Maple, POSC, L-426

department: Poultry Science

institute: University of Arkansas

summary: To understand how soy protein isolate (SPI) reduced liver steatosis in male obese Zucker rats, we conducted global gene expression (RNAseq) analysis on liver samples of male rats fed either the SPI or a control casein (CAS)-based diet (n=8 per group) for 16 wks.   Bioinformatics was conducted using Ingenuity Pathway Analysis (IPA) software (Qiagen, CA) with P < 0.05 and 1.3 fold differential expression cutoff values.

overall_design: Liver transcriptomics was analyzed using an Ilumina HiSeq system with 50 base pair single end read method.

first: B

first: W

last: Bottje

first: R

last: Hakkak


title: Transcriptome profiling of m6A mRNA modification in inflammation of bovine mammary epithelial cells infected by Staphylococcus aureus and Escherichia coli

status: Public on Nov 09 2020

city: Wuhan

first: Changmin

last: Hu

state: Hubei

address: No.1 Shizishan Street

institute: Huazhong Agricultural University

summary: Mastitis is a common disease in dairy cows and brings massive losses to the dairy industry.  m6A is a type of modification strongly associated with many diseases. However, the role of m6A in  mastitis caused by Staphylococcus aureus and Escherichia coli has not been investigated.We used MeRIP-seq technology to sequence the bovine mammary epithelial cells (MAC-T)  infected with inactivated S. aureus/E. coli for 24 h.

overall_design: meRIP-seq, RNA-seq for bovine mammary epithelial cells (MAC-T) infected by inactivated  S. aureus and E. coli for 24h

first: Ting

last: Li


title: T-5224, a selective inhibitor of c-Fos/AP-1, suppresses IgE-mediated mast cell activation†

status: Public on Nov 13 2020

city: Shenzhen

first: Hui

last: Wang

address: Taoyuanjiedao

institute: Shenzhen University

summary:
Purpose:The goal of this study is to asses the gene expression changes  in  non-stimulated  mast  cell and  anti-IgE-stimulated mast cell
Methods:RBL-2H3 mRNA profiles of non-stimulated  mast  cell and  anti-IgE-stimulated mast cell were generated by deep sequencing, in triplicate. Differential expression analysis was performed using the DESeq2(v1.4.5) with Q value ≦0.05, following the heatmap was drawn by pheatmap(v1.0.8) .
Results:Compared with non-stimulated mast cell, anti-IgE-stimulated mast cell induced a robust  transcriptional response, with 191 differentially expressed genes following anti-IgE treatment (116 upregulated and 75 downregulated). Among the up-regulated genes.
Conclusions:Our study represents the first detailed analysis of RBL-2H3 transcriptomes, with biologic replicates, generated by RNA-seq technology.

first: Jiajie

last: Chen

first: Kunmei

last: Ji


title: DOT1L-interacting protein AF10 (MLLT10) is a barrier to somatic cell reprogramming

city: Istanbul

first: Kenan

last: Sevinç

address: Rumelifeneri Yolu, Sariyer

department: School of Medicine

country: Turkey

institute: Koç University

summary: Epigenetic regulators have important roles during embryonic development as well as somatic cell reprogramming. We previously showed that inhibition of DOT1L, the histone H3 lysine 79 methyltransferase, increases the efficiency of reprogramming via regulation of lineage specific genes. However, the role of DOT1L-interacting proteins in reprogramming remains unknown. In this study, DOT1L interactors were identified using the BioID method in which a promiscuous BirA ligase (BirA*) was employed to biotinylate DOT1L-proximal proteins. The resulting interaction candidates were investigated for their effects on reprogramming. Candidate genes were knocked-down in human fibroblasts via shRNAs followed by reprogramming. Our results indicated that knock-down of AF10 (MLLT10), significantly increased the iPSC generation efficiency, suggesting that it acts as a barrier to reprogramming similar to DOT1L. This finding was verified by CRISPR/Cas9 mediated knockout of AF10.  Overexpression of AF10 reversed the effect of AF10 knockout and decreased reprogramming efficiency. To determine how AF10 silencing changes the gene expression, RNA-sequencing was performed on human fibroblasts undergoing reprogramming. AF10 suppression resulted in downregulation of fibroblast-specific genes and accelerated the activation of pluripotency-related genes. Our analysis also demonstrated that silencing of AF10 results in gene expression changes similar to DOT1L inhibition during reprogramming. Taken together, this study uncovered AF10 as a novel barrier to reprogramming and contributed to our understanding of epigenetic mechanisms that maintain cell identity.

overall_design: Examination of CRISPR-Cas9 mediated AF10 knockout effect on gene expression profile of dH1f cells 6 days after OSKM transduction. 3 biological replicates from each of reprogramming fibroblasts that express control sgRNA or sgRNA targeting AF10 were prepared.

first: Deniz

last: Uğurlu-Çimen

first: Tamer

last: Önder


title: Antagonistic role of Hnf4a and FoxO1 metabolic networks through enhancer interactions in beta-cell function [RNA-seq]

status: Public on Nov 07 2020

first: Taiyi

middle: Diana

last: Kuo

state: NY

address: 1150 St Nicholas Ave., Ste. 237

department: Medicine

institute: Columbia University

summary: To investigate the relationship between key beta-cell transcription factors Hnf4a and Foxo1.

overall_design: We performed RNAseq in FAC-sorted primary mouse beta cells from male mice. There are total of 4 genotypes: wild type (WT), Foxo1 knockout (IKO), Hnf4a knockout (HKO), and Foxo1 and Hnf4a double knockout (DKO).

middle: D


title: Antagonistic role of Hnf4a and FoxO1 metabolic networks through enhancer interactions in beta-cell function [ChIP-seq]

summary: To identify transcription factors in Foxo1's network with H3K27ac ChIPseq performed in WT and beta cell-specific Foxo1 knockout beta cells.

overall_design: We performed H3K27ac ChIPseq in FAC-sorted beta cells from female mice. There are a total of 6 conditions: 3-month-old nulliparous WT and beta cell-specific FoxO1 knockout (IKO) mice, 12-month-old nulliparous WT and IKO mice, and 12-month-old multiparous WT (labeled as NGT) and IKO (labeled as DM) mice.


title: Antagonistic role of Hnf4a and FoxO1 metabolic networks through enhancer interactions in beta-cell function

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

overall_design: Refer to individual Series


title: AHR IS A MASTER REGULATOR OF HIPPOCAMPAL-DEPENDENT MEMORY BY CONTROLLING NEUROGENESIS, DENDRITE GRANULE CELL MORPHOLOGY AND SYNAPTIC MATURATION

city: MADRID

first: JUAN

last: DE LA PARRA

address: AV. COMPLUTENSE

institute: COMPLUTENSE UNIVERSITY

summary: Identification of genes differentially expressed between hippocampus derived from wild type (WT) and Ahr-KO mice

overall_design: Hippocampi were dissected from hemibrains from wild type and Ahr-KO mice. For each experimental condition, three microarray experiments corresponding to three independent RNA replicates were carried out

first: Juan

last: de la Parra

first: Miguel

last: Vega

first: Maribel

last: Cuartero

first: Maria

last: Angeles Moro


title: The increase of miR-378a-3p in keratinocyte associated with pathogenesis of psoriasis

status: Public on Nov 06 2020

city: Bangkok

first: Pattarin

last: TANGTANATAKUL

state: กรุงเทพมหานคร

address: Thoethai Road

country: Thailand

institute: Chulalongkorn University

summary: We report the high-throughput profiling of human primary keratinocytes transfected with either miR-378 mimic or miR-378 inhibitor at 24 or 48 hours. Our study focused on the dysregulation of microRNAs that might partially be a fundamental mechanism leading to psoriasis development.  We knock-in and knock-out a specific miR-378 and see the cellular responses.  As expected, overexpression of miR-378a inhibited the proliferation, enhanced the apoptosis and disturbed the cell cycle. Regarding to the confirm experiment, our results suggested that the expression of miR-378a associated with the psoriasis pathogenesis enhancing the severity of psoriatic lesion, and might useful for further development of therapeutic strategy for psoriasis.

overall_design: We investigated microRNA expression in psoriatic skin. Experiment found miR-378 was dsyregulated in the skin biopsy from patients.  To investigate the entire effects of miR-378, overall design was eventually come out with RNA-sequencing on 4 groups at 2 timepoints (24 and 48 hours). These are including miR-378 mimic transfection, control mimic transfection, miR-378 inhibitor transfection, and control inhibitor transfection.

last: Soonthonchai


title: A homeodomain-containing transcriptional factor PoHtf1 regulated the development and cellulases expression in P. oxalicum

city: Jinan

first: Mei

state: Shandong

address: No.3501,Daxue Road

department: Qilu University of Technology

institute: Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences

summary: RNA-seq was used to analyze the effects of absence of PoHtf1.

overall_design: A total of 6 samples were analzyed.  The wild-type strain  114-2 was considered as a reference.

first: Zhonghai


title: Transcriptome profiling of Mesoplasma florum strain L1 using RNA sequencing (RNA-Seq) and genome-wide 5'-rapid amplification of cDNA ends (5'-RACE)

status: Public on Nov 02 2020

city: Sherbrooke

first: Sebastien

last: Rodrigue

state: QC

address: 2500 boul. de l'Université

department: Biologie

country: Canada

institute: Université de Sherbrooke

summary: Mesoplasma florum is a near-minimal bacterium belonging to the Mollicutes class particularly characterized by its small genome, fast growth rate, and lack of pathogenic potential. Here, we report the first genome-wide transcriptomic analysis of this microorganism using directional RNA sequencing (RNA-Seq) and 5'-rapid amplification of cDNA ends (5'-RACE). 5'-RACE sequencing reads were used to identify 605 putative transcription start sites (TSSs), of which more than 400 could be associated to a conserved promoter sequence. Along with terminator predictions, these TSSs allowed the reconstruction of M. florum transcription units, covering more than 90% of annotated genes. We evaluated the expression level of all M. florum protein coding genes using paired-end RNA-Seq reads according to the number of fragments per kilobase per million of mapped reads (FPKM). FPKM values were converted to absolute transcript abundances using biomass quantification data. These efforts aim at reaching a deep understanding of global cellular mechanisms in M. florum and will guide future genome engineering projects in this simple organism.

overall_design: One 5'-RACE replicate and a total of six RNA-Seq replicates (three biological replicates, each processed in technical duplicate) performed on log-phase M. florum cultures growing in ATCC 1161 medium.

first: Dominick

last: Matteau

first: Frédéric

last: Grenier

first: Pierre-Étienne

last: Jacques

first: Sébastien


title: The primary immune response to Vaccinia virus vaccination includes cells with a distinct cytotoxic effector CD4 T cell phenotype

status: Public on Nov 08 2020

city: Sydney

first: C. Mee Ling

last: Munier

state: NSW

address: Level 5, Wallace Wurth Building, UNSW Sydney

department: Immunovirology and Pathogenesis Program

country: Australia

institute: The Kirby Institute, UNSW Sydney

summary: Background: Smallpox was eradicated by a global program of inoculation with Vaccinia virus (VV). Robust VV-specific CD4 T-cell responses during primary infection are likely essential to controlling VV replication. Although there is increasing interest in cytolytic CD4 T-cells across many viral infections, the importance of these cells during acute VV infection is unclear. Methods: We undertook a detailed functional and genetic characterization of CD4 T-cells during acute VV-infection of humans. VV-specific T-cells were identified by up-regulation of activation markers directly ex vivo and through cytokine and co-timulatory molecule expression. At day-13-post primary inoculation with VV, CD38highCD45RO+ CD4 T-cells were purified by cell sorting, RNA isolated and analysed by microarray. Differential expression of up-regulated genes in activated CD4 T-cells was confirmed at the mRNA and protein levels. We compared analyses of VV-specific CD4 T-cells to studies on 12 subjects with primary HIV infection (PHI). VV-specific T-cells lines were established from PBMCs collected post vaccination and checked for cytotoxicity potential. Results: A median 11.9% CD4 T-cells were CD38highCD45RO+ at day-13 post-VV inoculation, compared to 3.0% prior and 10.4% during PHI. Activated CD4 T-cells had an up-regulation of genes related to cytolytic function, including granzymes K and A, perforin, granulysin, TIA-1, and Rab27a. No difference was seen between CD4 T-cell expression of perforin or TIA-1 to VV and PHI, however granzyme k was more dominant in the VV response. At 25:1 effector to target ratio, two VV-specific T-cell lines exhibited 62% and 30% cytotoxicity respectively and CD107a degranulation. Conclusions: We show for the first time that CD4 CTL are prominent in the early response to VV. Understanding the role of CD4 CTL in the generation of an effective anti-viral memory may help develop more effective vaccines for diseases such as HIV.

overall_design: The study was performed in 2005. PBMCs were isolated from 2 healthy volunteers 13 days following vaccination with Vaccinia virus. Freshly isolated PBMCs were then stained with CD4, CD8, CD45RA and CD38 for cell sorting on a Becton Dickinson FACSAria. Lymphocytes were identified from an initial forward scatter-area vs side scatter-area plot, then single cells from side scatter-width vs side scatter-height and forward scatter-width vs forward scatter-height, a CD4 vs CD8 plot used to identify CD4 T cells and CD8 T cells. A CD38 vs CD45RA plot was drawn from both the CD4 and CD8 T cell populations. CD4 T cells were sorted into naïve (CD45RA+CD38dim), activated effector (CD45RA-negCD38+++) and resting memory (CD45RA-negCD38-neg). Activated CD8 T cells were sorted as CD38+++CD45RA+/neg. The sorted cell populations from the 2 vaccinated volunteers (S2 and S3) were assigned the following nomenclature S2P6 (activated effector CD4+), S2P7 (resting memory CD4+), S2P8 (naïve CD4+) and S2P9 (activated effector CD8+) for the first vaccinated volunteer and S3P7, S3P7, S3P8 and S3P9 for the second vaccinated volunteer.

first: C

last: MUNIER

first: John

last: ZAUNDERS


title: TET1 KO affects Sox9 function

status: Public on Nov 05 2020

first: Nidhi

last: Bhutani

state: California

address: 300 Pasteur Drive, R164 Edwards Bldg

department: Orthopaedic Surgery


title: Macrophage expression and prognostic significance of the long pentraxin PTX3 in COVID-19

status: Public on Oct 29 2020

city: Pieve Emanuele

first: sarah

middle: natalia

last: mapelli

state: Milan

address: Via Rita Levi Montalcini 4

department: Experimental Immunopathology

country: Italy

institute: Humanitas research

summary: PTX3 is an essential component of humoral innate immunity, involved in resistance to selected pathogens and in the regulation of inflammation1-3. The present study was designed to assess the presence and significance of PTX3 in COVID-194-7. RNA-seq analysis of peripheral blood mononuclear cells, single-cell bioinformatics analysis and immunohistochemistry of lung autopsy samples revealed that myelomonocytic cells and endothelial cells express high levels of PTX3 in COVID-19 patients. Increased plasma concentrations of PTX3 were detected in 96 COVID-19 patients. PTX3 emerged as a strong independent predictor of 28-day mortality in multivariable analysis, better than conventional markers of inflammation, in hospitalized COVID-19 patients. The prognostic significance of PTX3 abundance for mortality was confirmed in a second independent cohort (54 patients). Thus, circulating and lung myelomonocytic cells and endothelial cells are a major source of PTX3, and PTX3 plasma concentration can serve as an independent strong prognostic indicator of short-term mortality in COVID-19.

overall_design: Monocytes were isolated from peripheral blood samples of three healthy donors and six COVID-19 patients and RNA expression was measured with total RNA-Seq.

first: Alberto

last: Mantovani

first: Cecilia

last: Garlanda

first: Barbara

last: Bottazzi

first: Sarah

last: Mapelli


title: Basal expression of nine pancreatic cancer cell lines

status: Public on Oct 30 2020

city: Heidelberg

first: Matthias

last: Neulinger Munoz

address: INF 133

country: Germany

institute: Universitätsklinikum Heidelberg

summary: RNAseq-based comparison of basal expression profiles of nine different pancreatic cancer cell lines

overall_design: mRNA profile of nine pancreatic cancer cell lines (ASAN, AsPC1, BxPC3, Capan1, Colo357, MiaPaca2, Panc1, SU8686, T3M4)

first: Gabriel

last: Salg

first: Eric

last: Poisel

last: Neulinger-Munoz

first: Nathalia

last: Giese


title: Transcriptomic RNA sequence analysis of bone marrow mesenchymal stem cells derived neural progenitor-like cells under the influence of different growth factor combinations

city: Sharjah

first: Amir

middle: Ali

last: Khan

address: Emirates of Sharjah

department: Department of Applied Biology

institute: University of Sharjah

summary:
Purpose: The goal of this study is to unravel the differential gene expression profiles (RNA-Seq) during the early differentiation of bone marrow mesenchymal stem cells (BMSCs) into neural progenitor-like stem cells (NPCs) under the influence of different growth factor combinations using high-throughput RNA sequencing method; Group A: EGF and bFGF, Group B: EGF + bFGF and IGF-1, and Control: untreated BMSCs.

Methodology: mRNA profiles of BMSCs (Control) and BMSCs-derived NPCs under the influence of growth factor combinations (Group A and Group B)  were generated by deep sequencing, in triplicate, using Illumina NextSeq500. Raw reads were evaluated for quality checks in terms of sequencing quality and contamination. Reads were trimmed and filtered using BBDuk. Reads were then aligned to the latest reference genome (rn6) with GTF from Ensembl (v99) using STAR aligner. Aligned reads were transformed into read counts per gene using the RSEM tool. Pairwise differential expression analysis was performed using the DESeq2 R package. qRT–PCR validation was performed using the RT² Profiler PCR Array Rat Custom array (Array ID: CAPR13765E).

Results: Using an optimized data analysis workflow, we mapped about 50 million sequence reads per sample to the Rattus norvegicus genome (Rnor_6.0 Assembly) and identified an average of 27,146 transcripts in Group A, 25,850 transcripts in Group B, and 21,683 transcripts in the control group. All transcripts have a fragment count estimation of at least 10 counts per gene. Differential analysis was performed as pairwise grouping. Comparison of Group A
vs MSC identified 3,252 differentially expressed genes. Thirteen significantly expressed genes with the potential roles during neural differentiation were randomly selected for validation with qRT–PCR. RNA-seq data had a linear relationship with qRT–PCR. Hierarchical clustering of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to neural differentiation of mesenchymal stem cells. Data from the present study analysis revealed a significant overlap yet provided complementary insights in transcriptome profiling of mesenchymal stem cells derived neural progenitor-like cells.

Conclusion: Our study represents the first detailed analysis of mesenchymal stem cells derived neural progenitor-like cell transcriptomes, generated by RNA-seq technology. Our data has explored crucial and novel genes involved during the early differentiation of mesenchymal stem cells into neural progenitor-like cells under the influence of different growth factor combinations.

overall_design: RNA profile of BMSCs-derived NPCs under the influence of different growth factor combinations (Group A, Group B and control) were deep-sequenced on Nextseq500 instrument using High Output sequencing kit in triplicate. Group A was treated with combination of EGF and bFGF, Group B was treated with combination of EGF, bFGF and IGF-1, whereas untreated mesenchymal stem cell served as control group.

first: Tee

last: Huat

first: Abdullah

middle: F

last: Al-Mutery

first: Ahmed

last: El-Serafi

first: Jafri

last: Abdullah

first: Hasnan

last: Jaafar


title: TET1 KO affects Sox9 function [growth plate tissue]

last: Bhutani

summary: We report that TET1 mediated 5hmC deposition is necessary for Sox9 function in embryonic cartilage development

overall_design: We examine the transcriptional changes after TET1 KO in E17.5 mouse chondrocytes

first: Fiorella

last: Grandi

first: Piera

last: Smeriglio


title: Survival and Proliferation of T-cell Acute Lymphoblastic Leukaemia Depends on mTOR-regulated Glutamine Uptake and EAAT1 Activity

status: Public on Nov 01 2020

city: Birmingham

first: Maarten

last: Hoogenkamp

state: West Midlands

address: Vincent Drive

department: Institute of Cancer and Genomic Sciences

country: United Kingdom

institute: University of Birmingham

summary: With the aim to identify new therapeutic targets for T-ALL treatment, we integrated transcriptomics and metabolomics data, including live-cell NMR-spectroscopy, of cell lines and patient samples. We found that T-ALL cells have limited energy availability, resulting in down-regulated mTOR-signalling and reduced autophagy. Despite this, mTOR kinase activity is essential for the glutamine-uptake and rapid proliferation. T-ALL cells use glutamine as a source for all nitrogen atoms in purines  and for all but one carbon in pyrimidines. We show that EAAT1, the glutamate-aspartate transporter normally only expressed in the CNS, is a crucial facilitator of the glutamine conversion to nucleotides. T-ALL cell proliferation depends on EAAT1 function, identifying it as a target for T-ALL treatment.

overall_design: RNAseq (paired end) of ARR, DU.528, HSB2 and CCRF-CEM cell lines in duplicate.

first: Vesna

middle: S

last: Stanulovic


title: Retrotransposons and the global shutdown of homeostatic innate immunity in the tumor cells by oncolytic parvovirus H-1PV

summary: RNAseq-based comparison of H-1PV infected vs. non-infected cells revealed global suppression of antiviral innate immunity in the PDAC cells (AsPC1, MiaPaca2 and T3M4 taken at 48hpi) and global stimulation – in the healthy donor PBMCs (taken at 24hpi).

overall_design: total RNA profile +/- infection with H-1PV of 3 pancreatic cancer cell lines (48h) and healthy donor PBMCs (24h)


title: Single cell analysis of endothelial cells in mouse LLC tumors by STING activation

status: Public on Oct 28 2020

city: Daejeon

first: Myung Jin

last: Yang

country: South Korea

institute: Institute for Basic Science

summary: To investigate the trancriptomic changes of endothelial cells (ECs) in response to STING activation, Lewis Lung Carcinoma (LLC) tumor ECs either treated by PBS or cGAMP were sorted by FACS and single-cell RNA seq was performed.

overall_design: Tumor endothelial cells treated with PBS or cGAMP were sorted and single-cell RNA libraries were made.

first: Gou

middle: Y

last: Koh

first: Seung-hwan

last: Jeong

first: Myung


title: Transcriptomic analysis of ATP6V1A knock-down and amyloid beta-treated neurons

city: New York

first: Bin

last: Zhang

address: 1470 Madison Avenue

department: Genetics and Genomic Sciences

country: USA

institute: Icahn School of Medicine at Mount Sinai

summary: ATP6V1A plays a unique role in synapse function in neurons and we found decreased neuronal activity in ATP6V1A-deficient neurons. To characterize the molecular pathways regulated by ATP6V1A under both normal and stressed conditions, we generated hiPSC-derived NGN2-neurons with reduced ATP6V1A expression by CRISPRi knock-down (KD) and performed RNA-seq analysis on the wild-type and KD neurons which were subject to amyloid-beta or vehicle treatment. A number of gene ontology (GO)/pathways were identified in KD neurons without amyloid-beta treatment (proton transporting V-ATPase complex, phagosome acidification and trivalent inorganic cation transport were down-regulated, and mitochondrial protein complex up-regulated), while KD in amyloid-beta treated cells specifically resulted in down-regulation of cell adhesion, synapse assembly and structure/activity and up-regulation of UPR and ER stress response.

overall_design: RNA from four groups of hiPSC-derived NGN2-neurons (designated WT-V and WT-Aβ for vehicle-treated and amylod beta (Ab)-treated ATP6V1A wild-type (WT) neurons, respectively, and KD-V and KD-Aβ for vehicle-treated and Aβ-treated ATP6V1A KD neurons, respectively) were collected and loaded to RNA-sequencing analysis. There are five independent neuronal differentiation experiments in each group.

first: Aiqun

last: Li

first: Minghui

last: Wang

first: Alex

last: Yu

first: Liwei

last: Lyu

first: Kristen

last: Brennand


title: The transcriptional signal of laser capture microdissection fibroblkastic foci from idiopathic pulmonary fibrosis (IPF) patients

city: Stevenage

first: Adam

last: Taylor

address: Medicine Research Center

institute: GalxoSmithKline

summary: Contractile and highly synthetic myofibroblasts are the key effector cells involved in excessive extracellular matrix (ECM) deposition in multiple fibrotic conditions, including idiopathic pulmonary fibrosis (IPF). In order to define the key drivers of the fibrotic response, we used laser capture microdissection to isolate RNA from myofibroblasts within fibroblastic foci and performed microarray analysis in combination with a novel eigengene approach to identify functional clusters of genes which associate with collagen gene expression.

overall_design: Using laser capture microdissection (LCM) the myofibroblast core was isolated from multiple fibroblastic foci in each of 13 patient samples taken either as lung biopsies (3 samples) or at the time of lung transplant (10 samples). Care was taken to avoid capturing the overlying epithelium and parallel staining of sections for α-smooth muscle actin (αSMA) indicated the captured cells represented an almost pure population of myofibroblasts. Each sample was independently processed and hybridised on microarrays before computational pooling of all detected genes in patients where gene expression was noted in at least two of the foci captured.

first: Delphine

last: Guillotin

first: Andy

last: Blanchard

first: Lindsay

middle: M

last: Edwards

first: Paul

last: Mercer

first: Ross

last: Haggart

first: Gino

last: Miele


title: Determine the differential miRNA levels in plasma of heroin addicts

city: 宁波

first: Haixiong

last: Liu

state: Zhejiang

address: 浙江省宁波市江北区

department: Ningbo Institute of Medical Science

institute: Ningbo University

summary: To determine the differential miRNA levels in heroin addicts, we comparatively profiled plasma miRNA expression of heroin abusers and healthy controls using Agilent Human miRNA Array.

overall_design: plasma miRNA expression of 4 heroin abusers and 5 healthy controls


title: Expression data from untreated and irradiated Nipa WT and Nipa KO hematopoietic stem cells (HSCs)

status: Public on Oct 21 2020

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg

summary:
The F-Box-Protein NIPA might define a novel regulator of aging and critical stress response in hematopoietic stem cells
To investigate the underlying mechanisms and activated pathways of NIPA-mediated HSC function in steady state and under stress conditions, we performed Affimetrix-based global gene expression analysis on untreated and irradiated, aged Nipa WT and Nipa KO LSK (Lineage-, SCA1+, cKIT+) cells and identified different expression profiles depending on NIPA

overall_design: LSKs out of 3 aged Nipa WT or Nipa KO mice were merged to one sample, cultured in BM media, either not treated or 4 Gray irradiated and harvested 3 hours later for RNA extraction and Affimetrix-based global gene expression analysis.

first: Lena

last: Illert

first: Stefanie

last: Kreutmair

first: Melanie

last: Boerries


title: Transcriptome changes of endothelial cells in mouse breast tumors by STING activation II

first: Myung Jin

last: Yang

summary: In order to identify transciptomic changes of endothelial cells (Ecs) in response to STING activation, endothelial cells were soted using FACS and RNA-seq was performed.  We compared ECs from 3 models; normal mammary fat pad, MMTV-PyMT spontaneous breast tumor, implanted breast tumor.  Tumor cells derived from MMTV-PyMT spontaneous breast tumor were expanded on culture and implanted in mammary fat pad of female FVB mice to establish implanted breast tumor model.

overall_design: PBS or cGAMP (STING agonsit) was directly injected to mammary fat pad or tumors. Samples were harvested 3 hr later.

first: Seung-hwan

last: Jeong

first: JungMo

last: Kim

first: Gou

last: Koh


title: Epigenetic landscape of HEK cells upon epithelial-to-mesenchymal transition

status: Public on Oct 20 2020

city: Paris

first: Violaine

last: Saint-Andre

address: 26 rue d'Ulm

country: France

institute: Institut Curie

summary: Epithelial-to-mesenchymal transition (EMT) allows progressive loss of epithelial traits and acquisition of mesenchymal identity promoting cell migratory and invasive properties. It is expressed by changes in gene expression program induced by changes of chromatin state and organization. To identify epigenetic landscape associated with EMT  we performed chromatin immunoprecipitation (ChIP) experiments allowing nucleosome profiling (H3), distribution of histone modifications linked to  actively transcribed  (H3K4me3, H3K36me3 and H3K27ac) and repressed (H3K27me3) regions in epithelial (Epi) and mesenchymal (Mes) cells. These cell lines were generated by immortalization of primary HEK cells before and after naturally occured EMT.

overall_design: For the two Epi and Mes cell lines, crosslinked chromatin was purified from two independent biological duplicate cell cultures. For each replicate, an aliquot was kept as Input while the rest was used for Chromatin Immunoprecipitation using antibodies against H3, H3K36me3, H3K27me3, H3K27ac and H3K4me3.

first: Marina

last: Pinskaya

first: Julien

last: Jarroux

last: Saint-André

first: Antonin

last: Morillon


title: CNS-Native Myeloid Cells Drive Immune Suppression in the Brain Metastatic Niche through Cxcl10

city: Dallas

first: Siyuan

last: Zhang

address: 6001 Forest Park Rd

department: Department of Pathology

institute: UT Southwestern Medical Center

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

overall_design: Refer to individual Series


title: Differential production of small RNAs in Mycobacterium tuberculosis infected primary human monocyte-derived macrophages

status: Public on Oct 15 2020

city: Baltimore

first: Monika

last: Looney

state: MD

address: 1503 E Jefferson Street

institute: Johns Hopkins University

type: Non-coding RNA profiling by high throughput sequencing

summary: Primary human monocytes were isolated from four healthy donors. Monocytes were differentiated into macrophages, infected with virulent Mycobacterium tuberculosis (Mtb), strain H37Rv, for 24 or 48 hours, at a multiplicity of infection of 5 or 10. Following infection, infected cells and time-matched uninfected controls were harvested, total RNA including small RNAs was isolated and used for next-generation small RNA sequencing. Small RNA sequencing data was processed using miRge2.0, including a novel miRge2.0-based tRF detection tool. Processed data was used to determine differential expression of microRNAs and differential production of tRNA-derived fragments (tRFs) during infection with Mtb.

overall_design: miRNA-seq of Primary monocyte-derived macrophages infected with Mycobacterium tuberculosis (Mtb), strain H37Rv, for 24 or 48 hours, at a multiplicity of infection of 5 or 10.

first: Marc

middle: K

last: Halushka

first: Petros

middle: C

last: Karakousis


title: Detection of novel fusion transcriptVTI1A-CFAP46 in HHC by RNA-seq

status: Public on Oct 17 2020

city: Sendai

first: Shunichi

last: Tsuge

state: Miyagi

department: Molecular biology

country: Japan

institute: Tohoku University School of Medicine

summary: HCC is now the second-highest cause of cancer death worldwide. Recent studies have discovered a wide range of somatic mutations in HCC. These mutations involve various vital signaling pathways, such as: Wnt/β-Catenin, p53, telomerase reverse transcriptase (TERT), chromatin remodeling, RAS/MAPK signaling, and oxidative stress. However, fusion transcripts have not been explored in HCC. To identify novel fusion transcript in HCC, in the first phase of our study, we performed targeted RNA sequencing on 6 patients with the diagnosis of HCC who underwent liver transplant (from HCC and paired non-HCC tissues). As a result of these studies, we discovered the novel fusion transcript, VTI1A-CFAP46. In the second phase of the study, we measured the expression of wild-type VTI1A in total of 21 HCC specimens (additional 13 patients) showing that 10 of 21 had up-regulation of wild-type VTI1A. VTI1A (Vesicle Transport via Interaction with t-SNARE homolog 1A) is a member of the Soluble N-ethylmaleimide-Sensitive Factor (NSF) attachment protein receptor (SNARE), which is essential for membrane trafficking and function in endocytosis, autophagy, and Golgi transport. Notably, it is known that autophagy is involved in HCC. The link between this alteration and autophagy as a potential therapeutic target in HCC patients deserves further investigation. Moreover, this study shows that fusion transcripts are worthy of additional exploration in HCC.

overall_design: To identify novel fusion transcript in HCC, we performed targeted RNA sequencing on 6 paired patients with diagnosis of HCC who underwent liver transplant.(from HCC and paired non-HCC tissues)

first: Behnam

last: Saberi


title: The transcription factor ETS1 is a master regulator of human NK cell differentiation [RNA-seq]

city: Ghent

first: Wouter

last: Van Loocke

state: East Flanders

address: C. Heymanslaan 10

department: Biomolecular Medicine

country: Belgium

institute: Ghent University

summary: Natural killer (NK) cells are innate lymphoid cells that play a critical role in the direct immune defense against tumor cells and pathogens, and additionally have important immune regulatory functions by cytokine secretion. Whereas NK cell biology has been extensively studied in mouse models, transcriptional control of human NK cell differentiation is poorly understood. In this study, we generated ETS1-deficient human embryonic stem cell (hESC) clones using the CRISPR/Cas9 technology. In a complementary approach, we generated ETS1 loss-of-function cord blood hematopoietic stem cells (HSCs) by retroviral transduction of the dominant-negative ETS1 p27 isoform. We show that the transcription factor ETS1 is required for human NK cell differentiation. Transcriptome and ChIP analysis reveal that ETS1 directly regulates expression of several NK cell-linked transcription factors. Also, expression of genes involved in cytokine secretion and cytotoxic activity is ETS1-dependent, whereby these effector functions are decreased in residual NK cells developing from ETS1 loss-of-function cord blood hematopoietic stem cells. Our data show that ETS1 is a critical regulator of human NK cell development and function, and provide important insights in the underlying molecular mechanisms.

overall_design: Day 21 in vitro cultered NK cells (4 control (ctrl) samples: NK cells derived from control transduced CD34+ cord blood stem cells and 4 p27 samples: NK cells derived from Ets-1 p27 transduced CD34+ cells)  were sorted to perform transcriptome analysis using an Illumina sequencing library preparation (QuantSeq 3' mRNA-Seq Library Prep Kits) followed by library quantification by qPCR.

first: Sylvie

last: Taveirne

first: Laurentijn

last: Tilleman

first: Filip

last: Van Nieuwerburgh

first: Georges

last: Leclercq


title: Expression data from circulating and lung tissue resident memory CD4 T cell responding towards infuenza A virus infection

status: Public on Oct 18 2020

city: Orlando

first: Tara

middle: M.

last: Strutt

state: FL

address: 6900 Lake Nona Blvd.

department: Burnett School of Biomedical Sciences

institute: University of Central Florida

summary:
How tissue resident memory CD4 T cell differ from circulating memory CD4 T cells and how such differences impact functional recall responses to pathogens is unknown.
We used microarrays to detail the global programme of gene expression underlying differences between sort purified circulating memory CD4 T cells from the lung and spleen, which are labelled with flourescent antibody following intravenous administration, and lung tissue resident memory CD4 T cells, which are not labelled with flourescent antibody following intravenous administration, on day 28 post influenza infection.

overall_design: Congenic memory TCR trangenic CD4 T cells were sort purifed from the spleens and lungs of infected mice on day 28 post influenza infection for RNA extraction and hybridization on Affymetrix microarrays. We sought to determine differences in CD4 T cell populations that were either circulating (labeled with intravenously administered florescently labelled antibody) or tissue resident (shielded from intravenoulsy administered florescently labelled antibody).

first: Karl

last: McKinstry

first: Susan

last: Swain


title: The transcription factor ETS1 is a master regulator of human NK cell differentiation


title: Microtus fortis liver RNA-Seq during Schistosoma japonicum infection

city: Shanghai

first: hong

last: li

address: 320 Yueyang Road

country: China

institute: SIBS

summary: The gogal of this study is to use RNA-Seq to systematically investigate the dynamics of the liver transcriptome over Schistosoma japonicum infection.

overall_design: Time-series RNA-Seq (0d, 7d, 10d, 14d, 21d, 28d)

first: Hong

last: Li


title: Mice liver RNA-Seq during Schistosoma japonicum infection

overall_design: Time-series RNA-Seq (0d, 7d, 10d, 14d, 28d, 42d)


title: Chromatin remodeler SPLAYED maintains the balance of miR156 dependent developmental pathways in Arabidopsis

status: Public on Oct 12 2020

city: Beaucouzé

first: Etienne

last: Bucher

address: 42 rue Georges Morel

institute: IRHS

summary: In plants, micro RNAs and chromatin remodeling are both known to regulate plant development and reproduction, however evidences for molecular links between these pathways have remained sparse. The antagonistic activities of miR156 and its target mRNAs, encoding several SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factors, control the juvenile-to-adult and vegetative-to-reproductive developmental phase transitions. In recent years a number of proteins were shown to act in the transcriptional control of MIR156 genes, demonstrating the complexity of the regulatory network involved in this process. Spatiotemporal control of gene expression involves interactions between transcription factors and changes in the chromatin structure. SPLAYED (SYD) is a well-characterized SWI2/SNF2 chromatin remodeling ATPase, which has been shown to be an important regulator of flowering time, flower organ identity and homeotic gene expression. In this study, we investigated the interaction between the miR156 and SYD pathways and provide evidence that SYD directly influences the transcription of several MIR156 and SPL genes in Arabidopsis. We propose that SYD maintains the balance between the miR156-dependent and miR156-independent developmental pathways. More generally, we then show that SYD may also play a very broad role in the control of gene expression by associating to most genes in Arabidopsis. We show that binding to these genes is dependent on the meristem identity factor LEAFY and the PRC2 component SWINGER. These results uncover a much more general role for SYD in regulating and balancing key developmental processes in Arabidopsis than previously assumed.

overall_design: chromatin immunoprecipitation of the SYD chromatin remodeler using a native antibody in Arabidopsis flowers

first: Kateryna

last: Fal

first: David

last: Windels

first: Christel

last: Carles


title: RNA-seq analysis of control and DIS3, RRP6, CSL4, ENP1, and SRM1 gene mutants in budding yeast.

status: Public on Oct 07 2020

city: Davis

first: Ben

last: Montpetit

state: CA

address: One Shields Ave

department: Viticulture and Enology

institute: University of California, Davis

summary: We report RNA-seq data for S. cerevisiae strains following temperature shift using oligo dT purified, ribo-depleted, or 3'-TAG sequencing libraries.

overall_design: Gene expression analysis in control and mutant strains following growth at 37 degrees celcius for 90 minutes.

first: Biplab

last: Paul

first: Lisbeth-Carolina

last: Aguilar

first: Taylor

last: Reiter

first: Sebastian

last: Pechmann

first: Marlene

last: Oeffinger


title: Differential expression of miRNA in Tax1BP1 knock-out mice [miRNA]

status: Public on Oct 06 2020

city: Frankfurt

first: Claudia

last: Döring

address: Theodor Stern Kai 7

department: Medical School, Institite of Pathology

institute: Johann Wolfgang-Goethe University Frankfurt a.M.

summary:
To further characterize differential expression of miRNA and mRNA levels in livers of 12 weeks old male Tax1BP1 wildtype and knock-out mice, the untreated mice were sacrificed and miRNA and mRNA levels were determined
miRNA was labeled with the Affymetrix FlashTag Biotin HSR RNA Labeling Kit

overall_design: miRNA from total liver of 3 Tax1BP1 wild type and 3 Tax1BP1 knock-out mice (age: 12 weeks, all male) was extracted and miRNA expression was determined

first: Oliver

last: Waidmann


title: Differential expression of mRNA in Tax1BP1 knock-out mice [mRNA]

summary: To further characterize differential expression of miRNA and mRNA levels in livers of 12 weeks old male Tax1BP1 wildtype and knock-out mice, the untreated mice were sacrificed and miRNA and mRNA levels were determined

overall_design: mRNA from total liver of 4 Tax1BP1 wild type and 4 Tax1BP1 knock-out mice (age: 12 weeks, all male) was extracted an mRNA expression was determined


title: Next Generation Sequencing Facilitates Quantitative Analysis of overexpression of KLF14 in mouse primary hepatocytes and control cells

status: Public on Oct 16 2020

city: Hefei

first: Huabing

last: Zhang

address: Mieshan Road

department: Ibochemistry

institute: Anhui medical University

summary: Purpose: KLF14 gene is closely linked to the development of Type 2 diabetes. The goals of this study are to compare KLF14-derived retinal transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis

overall_design: Methods:total RNA from the mouse primary hepatocytes, infected with the adenovirus carrying KLF14 expression vector or the empty vector was utilized for RNAseq to assess the global gene expression Retinal mRNA profiles  were generated by deep sequencing, in triplicate. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays


title: Selective inhibition of JAK1 with filgotinib reverses pathogenic processes in the DSS preclinical model for IBD

status: Public on Oct 19 2020

city: Mechelen

first: Maté

last: Ongenaert

address: Generaal De Wittelaan L11A3

institute: Galapagos

summary: The pathogenesis of inflammatory bowel diseases (IBD) is associated with a dysregulated mucosal immune response. The signaling of several cytokines regulating this immune response is mediated by kinases of the JAK family, i.e. JAK1, JAK2, JAK3 and TYK2. Filgotinib is a JAK1-selective inhibitor with demonstrated efficacy in phase 2 trials in patients with rheumatoid arthritis (RA) and Crohn’s disease (CD). Here, we investigated the effects of filgotinib on the DSS (dextran sulfate sodium) mouse model

overall_design: Balb/cJ female mice were purchased from Janvier Labs (France) and housed in Galapagos animal facilities. All procedures were reviewed and approved by the Galapagos Ethical Committee for the Animal Care and Use . Chronic colitis was induced in eight weeks old mice by cyclical administration of 4% DSS via drinking water, involving 3 cycles of DSS for 4 days interrupted by washout periods of 3 days under regular drinking water. The mice (n=5 per group) were assigned in 3 groups:  1/ Drinking water,  2/ DSS in water and filgotinib vehicle 3/ DSS in water and filgotinib. Filgotinib was given at 30 mg/kg, once a day by oral gavage.


title: A Chinese hamster transcription start site atlas that enables targeted editing of CHO cells

city: La Jolla

first: Nathan

middle: E

last: Lewis

address: 9500 Gilman Dr

department: Pediatrics

institute: UCSD

summary: Gene expression is a key determinant of phenotypes that made Chinese Hamster Ovary (CHO) cells, with their human-like glycosylation profile and high protein titers, one of the most widely used cells for the production of therapeutic proteins and biopharmaceuticals. Engineering CHO gene expression thus holds a key to improve drug quality and cost effective production. However, the success of engineering gene expression or ectopic activation of silent genes to optimize desired pathways requires accurate annotation of the underlying regulatory elements and the transcription start site (TSS). Unfortunately, to date, most TSSs of CHO-expressed genes and the ~50% of hamster genes that are silent in CHO were computationally predicted and are frequently inaccurate. To oust this hurdle, we report revised TSSs annotations for 15,308 Chinese Hamster genes and 4,145 non-coding RNAs based on experimental data from CHO K1 cells and 10 hamster tissues. In the example of the glycosyltransferase gene Mgat3, we further demonstrate how accurate annotations readily facilitate activating silent genes by CRISPRa. Together, we envision that our annotation and data from the Chinese Hamster will provide a rich resource for the CHO community, improve genome engineering efforts and additionally aid comparative and evolutionary studies.

overall_design: Examination of transcription start sites in the Chinese Hamster in various tissues and cell-lines using csRNA-seq and 5'GRO-seq . Total-RNA and ATAC-seq and backgrounds sRNA and GRO-seq were additionally performed.

first: Sascha

last: Duttke

first: Isaac

last: Shamie


title: DNA methylation profile of a hepatosplenic gamma/delta T-cell lymphoma patient associated with response to interferon-α therapy

status: Public on Oct 05 2020

city: Kiel

first: Jaydeep

last: Bhat

address: Arnold-Heller-Str.

institute: Institute of Immunology

type: Methylation profiling by genome tiling array

summary: We report changes in the DNA methylome in a patient with γδ hepatosplenic T-cell lymphoma (HSTCL) who responded to treatment with interferon-α2c. We studied the methylome by 450k methylation array in 5 blood samples taken within a time period of 20 months. During this time period, the WBC counts dropped from 22,300 to 7,200/μl blood, yet the proportion of γδ T cell lymphoma blasts remained around 90%. We observed time-dependent changes in overall DNA methylation and performed an in-depth bioinformatic analysis of the modulated CpG sites associated with disease progression. We identified a CpG site differentially regulating methylation, possibly related to the interferon response during the course of treatment in this particular case. Therefore, the present case report will help to understand the substantial changes in DNA methylation of lymphoma resulting in a survival benefit of this γδ HSTCL patient.

overall_design: Bisulphite converted DNA from the 5 samples were hybridised to the Illumina HumanMethylation450 Beadchip.

first: Ole

last: Ammerpohl

first: Dieter

last: Kabelitz


title: Wnt inhibition confers hESCs a unique transcriptional state compatible with differentiation, but not with derivation

status: Public on Oct 13 2020

city: Gent

first: Laurentijn

last: Tilleman

address: Ottergemsesteenweg 460

summary: Human embryonic stem cells (hESCs) hold great value for future clinical applications. However, standard culture conditions maintain hESCs in a primed state, which bears heterogeneity and a tendency for spontaneous differentiation. To counter these drawbacks, hESCs have been converted to a naive state, but this has in turn restricted the efficiency of existing directed differentiation protocols. We show that adaptation of hESCs to Wnt-inhibiting condition (Wnt-i) conferred a unique transcriptional signature with high levels of pluripotency markers and reduced levels of differentiation markers. Moreover, neuronal and cardiac differentiation of Wnt-i hESCs progressed similarly to primed hESCs, unlike their naïve counterparts. Remarkably, in contrast to mouse, Wnt-i conditions failed to support direct derivation of hESCs, suggesting that active Wnt signaling is required for the transition from inner cell mass to hESCs. Wnt-i hESCs retained advantages of both primed and naive counterparts and may therefore be a better starting point for differentiation towards clinically desired cell types.

overall_design: Biological triplicates of UGent11-2 and UGent11-60 hESC lines cultured in primed, Wnt-i and naive conditions were sequenced.

first: Jasin

last: Taelman

first: Mina

last: Popovic

first: Monika

last: Bialecka

first: Sharat

last: Warrier

first: Margot

last: Van der Jeught

first: Bjorn

last: Menten

last: Deforce

first: Petra

last: De Sutter

first: Filip

last: Van Nieuwerburgh

first: Kuniya

last: Abe

last: Heindryckx

first: Susana

last: Chuva de Sousa Lopes


title: Specific ectodermal enhancers control the expression of Hoxc genes in developing mammalian teguments

city: Lausanne

first: Lucille

last: Lopez-Delisle

address: Station 19

country: Switzerland

institute: EPFL


title: Differential expression of miRNA and mRNA in Tax1BP1 knock-out mice

first: Claudia

last: Döring

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

platform_organism:
Mus musculus
synthetic construct


title: Digoxin treatment is associated with thyroid cancer differentiation and radioactive iodide treatment response

status: Public on Oct 01 2020

city: Nijmegen

first: Theo

last: Plantinga

address: Geert Grooteplein Zuid 10

country: Netherlands

institute: Radboud University Medical Center

summary: Non-medullary thyroid cancer (NMTC) is the most frequent endocrine tumor with in most cases a good prognosis. Unfortunately, 30-40% of patients with metastatic NMTC are unresponsive to 131-I radioactive iodide (RAI) treatment as a result of tumor dedifferentiation. Autophagy has emerged as an important mechanism involved in NMTC dedifferentiation. Furthermore, activation of autophagy by cardiac glycosides such as digoxin has been demonstrated to induce effective in vitro redifferentiation of poorly differentiated and anaplastic thyroid cancer cell lines, thereby restoring sensitivity to RAI treatment. However, the in vivo effects of digoxin treatment on tumor differentiation in NMTC patients remains unclear. In the present retrospective clinical study, archived tumor material obtained from NMTC patients that received digoxin as treatment of heart disease before and after NMTC diagnosis was investigated. By a national PALGA-PHARMO database search, 11 digoxin-treated NMTC patients were included encompassing all major histological NMTC subtypes. In addition, 11 control NMTC patients never treated with digoxin were included that were matched for age, gender, histological tumor type, TNM staging and genetic profile. From the collected tumor material, autophagy activity has been determined by LC3 immunofluorescent staining and RNA expression profiles have been generated by RNA sequencing to assess differential expression of thyroid-specific genes. Interestingly, the results indicate that tumor material from digoxin-treated NMTC patients exhibit significantly higher autophagy activity as compared to tumor material of matched control NMTC patients. Moreover, in all 11 tumor tissues obtained from digoxin-treated NTMC patients the differentiation status was profoundly higher as compared to the matched control NMTC patients, of which the effect size was however dependent on histological NMTC subtypes and genetic profile of the tumor. In conclusion, treatment of NMTC with digoxin before and after NMTC diagnosis is associated with a higher tumor differentiation grade as compared to tumor tissue from closely matched NMTC patients not treated with digoxin. These in vivo data confirm our previous in vitro findings and provide accumulating evidence that digoxin could represent a beneficial adjunctive treatment modality to improve RAI sensitivity in patients with RAI-refractory thyroid carcinoma.

overall_design: Archived, paraffin-embedded, formalin-fixed primary tumor material obtained from 25 patients with non-medullary thyroid cancer. RNA was isolated and prepared for RNA sequencing by the NuGEN SoLo kit and Illumina NextSeq500.

first: Marika

last: Tesselaar

first: Thomas

last: Crezee


title: tsRibo-Seq: An Approach to Zoom In into Translation of Single Transcripts

status: Public on Oct 03 2020

city: Hamburg

first: Zoya

last: Ignatova

address: Martin -Luther-King-Platz 6

institute: Universitaet Hamburg

summary: Ribo-Seq (ribosome profiling) enables global assessment of translation efficiency, yields and fidelity. However, low-abundance transcripts receive little coverage and fall outside of the Ribo-Seq detection limit. We developed a new twist of the Ribo-Seq approach, termed transcript specific Ribo-Seq (tsRibo-Seq) to specifically detect lowly abundant messenger RNAs (mRNAs). This approach yields unprecedented depth in the coverage of individual low-abundance transcripts allowing identification of slow and fast translating regions with nucleotide resolution.

overall_design: Ribosome Profiling of CFBE cells 48h after transfection with wild-type CFTR

first: Robert

last: Rauscher


title: Epigenetic and metabolic remodeling during the acquisition of extended pluripotency

status: Public on Oct 02 2020

city: Wuhan

first: Wei

last: Jiang

address: Donghu Road 116, District Wuchang

department: Medical Research Institute

institute: Wuhan University

summary: Totipotent cells with bidirectional chimeric ability attracts more attention from developmental biology and regenerative medicine. Human extended pluripotent stem cells can be obtained and maintained by converting conventional embryonic stem cells using the combo of chemicals, however, the transition and culture system is based on feeder and the mechanism during the acquisition of extended pluripotency is largely unknown. Here we first showed an adapted Matrigel-based feeder-free conversion and maintenance system to generate extended pluripotent stem cells from human embryonic stem cells. We demonstrated the extended pluripotency by molecular markers, chimeric ability and transcriptome. Our data provided an epigenetic and metabolic insight into the maintenance and transition of extended pluripotency.

overall_design:
mRNA profiles of ESC (embryonic stem cell)  HUES8 and converted EPSC (extended pluripotent stem cell) were generated by deep sequencing, using Illumina Hiseq X ten.

ffEPSC-single-cell library were generated by Smart-seq2 protocal, and the paired-end single-cell sequencing data were generated by Illumina HiSeq 2000.

first: Ting

last: Geng

first: Ran

last: Zheng


title: Investigating the effect of inflammatory conditions on acetaminophen-induced liver injury using 3D human multicellular microtissues

status: Public on Oct 04 2020

city: Maastricht

first: Jian

address: Maastricht University

department: Toxicogenomics

institute: Maastricht University

summary: To investigate the molecular mechanisms of the inflammation-mediated exacerbation of increased acetaminophen (APAP) toxicity.

overall_design: 3D-co-cultured microtissues (MTs), consisting of primary human hepatocytes (PHH) and Kupffer cells (KCs), were exposed to 0, 0.5, 5 and 10 mM acetaminophen for 24h with/without lipopolysaccharide (LPS).

first: Jens

last: Kelm

first: Marcel

last: van Herwijnen

first: Danyel

middle: G

last: Jennen

first: Jos

last: Kleinjans

last: de Kok


title: RNA-Sequencing used to identify the targets of NHR-49, a transcription factor that acts in distinct tissues to promote longevity versus immunity

status: Public on Sep 30 2020

city: Pittsburgh

first: Francis Amrit Raj

last: Gandhi

address: 4401 Penn Ave

institute: University of Pittsburgh

summary: Previously, we identified NHR-49, functional homolog of the key vertebrate lipid metabolism regulator HNF4/PPARa, as essential for the longevity of Germiline Strem Cell (GSC)-less animals. Since longevity and stress resistance have been reported to be strongly linked, we examined the role of NHR-49 in resistance against the human opportunistic pathogen Pseudomonas aeruginosa, strain PA14. As a part of this effort we employed RNA-Sequencing to determine the downstream targets of NHR-49 in GSC-less animals.

overall_design: Comparison of adult day 2 whole worm NGS-derived transcriptomic profiles of nhr-49;glp-1 and glp-1 animals

first: Francis

middle: R

last: Amrit

first: Arjumand

last: Ghazi